Fish farming in the UK and around the world faces serious economical threats from viruses and bacteria causing outbreaks and loss of valuable livestock. Vaccines and immunostimulants are often administered to fish to prevent these outbreaks. Continuous research is required to verify whether new products are effective. In order to do so, research worldwide is routinely carried out whereby large groups of animals are experimentally infected with a pathogen. The level of mortalities in groups of fish treated with such substances are then compared with a group of untreated fish. Other researchers have focused on understanding how the fish immune system works and how it combats invasion by bacteria and viruses. For this, experiments are undertaken whereby a group of fish is experimentally infected with viral or bacterial pathogens, then at regular intervals, at least 5 fish are killed and analysed. Both methods are very costly in terms of the number of animals used, and we propose to reduce this from the work carried out during this 2 year project. Instead of killing fish at regular intervals, we propose to take small volumes of blood repeatedly during the course of the infection without harming the fish. The number of animals required for this experiment design represents only 20 % of the number of fish required using traditional sampling methods. In addition, following the same fish during the course of the infection will allow a better understanding of the immune response elicited by the fish, and the outcome of this response i.e. death or survival. Part of the project will be dedicated to improving the analysis method. Because only a small volume of blood is repeatedly sampled over the course of the infection, novel methods are required to measure and describe the immune response. Some of the tools to be includes are antibodies, specifically recognise individual immune molecules, information on fish immune genes and the existence of immortal fish cells that can be cultivated in vitro. These methods will be adapted for use with the small volumes of blood collected and will be used to understand which blood cells, and serum molecules are important in combating the pathogen. The relation between the cell types, the molecules involved, the type of pathogen and the final outcome of the infection will be very important in predicting the severity of infection, determining the appropriate immunostimulant to be used and improving existing fish vaccines.

This proposal is for a new EPSRC Centre for Doctoral Training in Wind and Marine Energy Systems and Structures (CDT-WAMSS) which joins together two successful EPSRC CDTs, their industrial partners and strong track records of training more than 130 researchers to date in offshore renewable energy (ORE). The new CDT will create a comprehensive, world-leading centre covering all aspects of wind and marine renewable energy, both above and below the water. It will produce highly skilled industry-ready engineers with multidisciplinary expertise, deep specialist knowledge and a broad understanding of pertinent whole-energy systems. Our graduates will be future leaders in industry and academia world-wide, driving development of the ORE sector, helping to deliver the Government's carbon reduction targets for 2050 and ensuring that the UK remains at the forefront of this vitally important sector. In order to prepare students for the sector in which they will work, CDT-WAMSS will look to the future and focus on areas that will be relevant from 2023 onwards, which are not necessarily the issues of the past and present. For this reason, the scope of CDT-WAMSS will, in addition to in-stilling a solid understanding of wind and marine energy technologies and engineering, have a particular emphasis on: safety and safe systems, emerging advanced power and control technologies, floating substructures, novel foundation and anchoring systems, materials and structural integrity, remote monitoring and inspection including autonomous intervention, all within a cost competitive and environmentally sensitive context. The proposed new EPSRC CDT in Wind and Marine Energy Systems and Structures will provide an unrivalled Offshore Renewable Energy training environment supporting 70 students over five cohorts on a four-year doctorate, with a critical mass of over 100 academic supervisors of internationally recognised research excellence in ORE. The distinct and flexible cohort approach to training, with professional engineering peer-to-peer learning both within and across cohorts, will provide students with opportunities to benefit from such support throughout their doctorate, not just in the first year. An exceptionally strong industrial participation through funding a large number of studentships and provision of advice and contributions to the training programme will ensure that the training and research is relevant and will have a direct impact on the delivery of the UK's carbon reduction targets, allowing the country to retain its world-leading position in this enormously exciting and important sector.

See lead proposal

The National Centre for Statistical Ecology (NCSE) has established itself as an international centre of excellence, with a reputation for producing ground-breaking research. It was founded in October 2005, supported by a five-year multi-disciplinary grant from EPSRC, with nodes at the Universities of Cambridge, Kent and St Andrews. We now seek to build on this success by bringing together those active in developing statistical ecology methodology in the UK, to form a world-leading coordinated team. In this way, we can bring the best expertise to bear to solve key problems facing ecologists and wildlife resource managers, and maintain the UK's record of internationally-leading research in the field. We will build on the experience gained within NCSE for working effectively on joint projects within a geographically distributed Centre. This will involve regular meetings supplemented by video- and tele-conferences as well as video-seminars. Annual workshops will bring all members of the Centre together for research and learning. The planned research will span six broad themes, covering biodiversity monitoring, spatial and spatio-temporal models for ecological communities, stochastic models for population dynamics, movement models, and overarching new statistical methods and diagnostics. Current perspectives regarding loss of biodiversity are largely driven by results from the monitoring of specific sites, which typically are not representative. Further, it is usually assumed that individuals of all species are equally detectable, which is far from the case in most surveys. The research of one of the themes will develop indices for use in quantifying regional trends. In another theme, methods will be developed to describe the non-linear dynamics that are a feature of forest insects and zooplankton populations. Only recently have statistical methods been devised which take account of features such as animal movement and the interactions between different species; this is important for instance in determining the development of coral reefs. New methods developed by the grant investigators are allowing for greater complexity in stochastic models, which properly account for randomness. This is especially important when populations reduce in size. Common to the themes of the proposal is increasing realism in modelling, combined with the ability to match these developments with appropriate analytical, computational and inferential tools.The Centre will be run by an Executive Committee, chaired by the Director, which will meet regularly (usually by videoconference). The committee will select the Director annually from its members. An International Advisory Panel will provide the wider perspective. The new Centre will have post-doctoral research assistants at the Universities of Bath, Kent, Sheffield and St Andrews. In addition there will be annual appointments of cohorts of research students throughout the Centre, through which we will seek to maintain research activity in all six research themes. The Centre will link 8 university departments and 5 external agencies. We will endeavour to recruit and train the next generation of researchers in statistical ecology, foster the development of user-friendly computer software to ensure that the methods developed are readily available to the community, train scientists from the user community through a wide range of workshops, and provide a forum for our researchers to interact with the international community through the series of International Statistical Ecology Conferences, instigated in 2008 and organised by NCSE. The research of the Centre is timely and vitally important. It will ensure that national and international decisions regarding pressing contemporary issues, such as the effects of anthropogenic changes on the environment, as well as those of climate change and alternative energy generation, are made using the best possible science.

Phytoplankton form the base of the marine food web. Through their primary production they are crucial to carbon cycling. Some species that form "harmful algal blooms (HABs) are harmful to human health and/or finfish and shellfish aquaculture operations. There are many thousands of species of phytoplankton. The diversity in responses of these to changing environmental conditions means that long term time series are required to understand the role of environment/climate in driving the productivity and biodiversity of our oceans. Phytoplankton increases (blooms) can occur over short timescales (days). Should blooming species be harmful, rapid early warning is required for the aquaculture industry and its regulators to protect human health (from HAB generated toxins that are vectored to humans by shellfish) and minimise mortalities, as a consequence of other HAB genera, of farmed fish. At present, the time and cost to analyse phytoplankton samples by microscopy or molecular methods prevents the high resolution monitoring required to a) understand climate effects and b) provide rapid early warning to the aquaculture industry and its regulators of HAB events. A solution to this problem is the Imaging FlowCytobot (IFCB) https://mclanelabs.com/imaging-flowcytobot/ This is an in-situ automated submersible imaging flow cytometer that also generates images of phytoplankton in-flow. The IFCB allow real time (every 20 minutes) monitoring of phytoplankton including HAB events. Once the instrument is "trained", images can be automatically classified to genus or even species level with accuracy comparable to that of human experts. Data are therefore comparable in quality with traditional microscope counts but are obtained at a much higher temporal resolution. Data collection is achieved through a novel combination of flow cytometric and video technology to capture high resolution images of suspended particles. Laser induced fluorescence and light scattering from individual particles are measured and used to trigger targeted image acquisition; the optical and image data are then transmitted to shore in real time. Images collected during this continuous monitoring are processed with automated image classification software. The IFCB can be deployed from a raft or pier to track the progression of annual phytoplankton cycles or HAB events. It can also be configured to sample from shipboard underway seawater systems, allowing phytoplankton communities to be monitored continuously along cruise routes. IFCBs have been used to collect data in a range of environments ranging from Florida to the Arctic with, e.g., the first harmful bloom so the shellfish biotoxin producing dinoflagellate Dinophysis being revealed by use of an IFCB (Campbell et al. 2010 J Phycol 46:60-75). IFCBs are now also being utilised for harmful algal bloom detection in Scandinavia and New Zealand. At present, there is no IFCB or similar capability in the UK. This instrument will therefore provide a step change in the capability of UK environmental science to monitor phytoplankton and provide early warning of the HABs that impact aquaculture. In this project we propose to purchase, train and deploy at IFCB in UK coastal waters allowing, for the first time, the production of the long term, temporally resolved data sets we require to understand the environmental control of phytoplankton and HABs in UK waters. The instrument will ordinarily be located at the Marine Scotland Coastal Observatory in Shetland close (a major site of aquaculture). IFCB data will be made freely available in real time via our web portal (www.HABreports.org) in a similar manner to an instrument in the Gulf of Mexico http://toast.tamu.edu/IFCB111. Our own expert data interpretation will enhance its benefit for aquaculture practitioners. The IFCB will therefore provide a long term data resource for scientists, policy makers the aquaculture industry and its regulators.