The health of human, animal and plant populations is under constant threat due to infections by a large variety of pathogenic microorganisms, such as bacteria and viruses. The fact that pathogens are able to spread rapidly and harm human populations has also led to the development of a variety of biological weapons which threaten not only soldiers in the field of operations, but even civilian populations in benign public environments such as a tube stations or airports. Threats to civilians also include those from non malicious sources such as within healthcare (hospital acquired infections, e.g. the superbug MRSA) or from the food industry (contaminated foods with pathogenic E. coli). The ability to diagnose such infections rapidly would dramatically aid patient survival and outcome and prevent further spreading of the disease. In our proposal we describe a diagnostic solution based on 'single-molecule' fluorescence for the rapid identification of multiple pathogens. We have already established a basic test for the presence of DNA specific to a particular bacterial strain and aim to build on this to develop a range of 'intelligent' biosensors based on Boolean logic and signal amplification. Essentially, such sensors will be able to provide a yes/no answer on pathogen threat level given a combination of target inputs e.g. if (pathogen 1 AND pathogen 2) but (NOT pathogen 3). Our sensors aim to produce a time-to-result on the order of 10-15 min, compared with current technologies that vary between hours and days due to the requirement of sample amplification - either bacterial culturing or DNA amplification. In parallel, we propose to further develop a compact and affordable single-molecule fluorescence microscope to perform such tests. Currently single-molecule microscopes are prohibitive in terms of size and cost; we aim to produce a cut-down version with a footprint of approximately 30cmx50cmx20cm (suitable for benchtop operation) and a small fraction of the cost of the full-size microscopes.

This project will investigate high performance sensors for making high quality measurements of carbon dioxide (CO2) concentrations in both ocean waters and the atmosphere close to the ocean surface. This technology could equally be used in other applications including freshwater studies. The sensor technology is based on an indicator material that changes its optical properties in the presence of CO2. Specifically the indicator is fluorescent (i.e. when exposed to a high frequency light it emits lower frequency light). This fluorescence persists for a short time after the high frequency light is turned off. The length of time that the fluorescence persists (the fluorescence lifetime) changes with the concentration of CO2. Fluorescence techniques are particularly well suited to low level and high performance measurement. Currently such indicators have not been evaluated for use in the surface ocean, and can suffer from long-term drift. To combat this the proposed research will investigate novel techniques for the optical measurement used to measure fluorescence lifetime (that reduce bleaching of the indicator), will investigate novel methods of accounting for sensor drift even when operated remotely, and will comprehensively evaluate this new technology for this new application. This is the first step towards the creation of robust and low cost in situ CO2 sensing technology suitable for widespread use in this application. Carbon dioxide (CO2) is the main cause of global warming and also dissolves in seawater, increasing the acidity of the oceans which can have further negative consequence on marine life and the environment. The accurate determination of CO2 concentration in a number of locations and with short intervals between measurements, particularly in the surface ocean and lower oceanic atmosphere, is critical for assessing the response of the oceans to increasing atmospheric CO2 concentrations. Crucially data from immediately above and below the air-sea interface is of critical scientific interest particularly for predicting how much CO2 is absorbed or emitted by the oceans. Current measurement techniques using ship based systems or large complex submersible systems are too expensive and bulky to enable widespread repeated measurements. This requires accuracy of one part CO2 in ten million parts air (in air) and a similar performance for measurement of dissolved CO2 in water. We propose to evaluate the technology in conditions representative of common ocean going vehicles such as floats, profiling floats (i.e. periodically sinking to depth and then surfacing), and using opportunistic deployments on commercial ships (e.g. by analysing engine coolant water on ferries and cargo vessels). This includes measurements in the atmosphere where wash-over and spray are common, and in water whilst subject to vibration and large pressure changes. The potential commercial value of this research will be explored with Chelsea Technologies Group (a UK company).

Discussions between NOC, dstl(Ministry of Defence), the Royal Navy and Chelsea Technologies Group (CTG) have highlighted what can be gained from hull-mounted underway instruments and where a lack of appropriate formal communication is failing to exploit UK research and development. Advances in the scientific understanding of the marine environment through real-time underway monitoring are not yet being integrated with traditional operational training. And the operational tools needed to exploit these advances need research and development, the outputs of which will benefit both UK operators and UK business exports. It is vital that operational requirements are efficiently fed back to industry, with the knowledge based interaction of research organisations, such that complex measured parameters are provided in a simple visual user interface. The OBS programme seeks to address these problems through a number of formal routes for knowledge exchange. Royal Navy vessels including submarines carry a wide range of underway environmental monitoring instruments. Many vessels are equipped with underway instrument packages which, in addition to temperature and salinity, also measure chlorophyll fluorescence, a biological degradation product known as Gelbstoff or 'yellow substance', trace hydrocarbons and luminescence. Some training is provided for mariners and submariners in physical oceanography to maintain a level of understanding of the impact of the sound velocity characteristics of a water column on the ability to detect and be detected acoustically. However, both the RN and DSTL have a keen interest in establishing and exploiting the use of non-acoustic indicators that provide information on the operating environment for UK strategic advantage. The data from biogeochemical environmental sensors are currently poorly understood by operators. There are no mechanisms currently in place to provide the sustained knowledge transfer necessary for the routine interpretation of these data streams for operational environmental advantage. Currently the numbers and units provided by the fluorimeters (chlorophyll, gelbstoff and hydrocarbons) and the luminescence sensors mean nothing to the operator without the incorporation of suitable training in the mariner and sub-mariner curriculum. And, the multi-variable interpretation of these data streams is where the real added value for environmental advantage could arise. This requires the development of tactical environmental prediction firmware for the real-time guidance of operations. For example a coincident increase in gelbstoff fluorescence with decreasing chlorophyll(a) fluorescence would suggest a possible change towards a dinoflagellate dominated phytoplankton population and the likelihood of significant vessel wake-driven luminescence at perhaps the 40% risk level. If we further combine this with a knowledge of oceanographic characteristics then perhaps this risk might be reduced to 20% or increased to 70%. The overall OBS programme has three parts, for which this exchange project OBS(1) will form the foundation first part. OBS(1) is a collaborative fact-finding mission to catalogue the current state of operational ability, technical procurement, mature research knowledge and operational requirements. The most important overall objectives of OBS(1) are firstly to set the details for the incorporation of long term biogeochemical operational training in the mariner and sub-mariner syllabus, to be provided by front line researchers supported by the Royal Navy under OBS(2). Secondly OBS(1) will set out the framework for the research and development of operational environmental prediction tools under OBS(3); involving close interaction with research organisations and industry. This component will develop the operator interface of the future and will be supported by dstl.

Algae are present in nearly every body of water on the surface of the earth. These microscopic organisms produce roughly half of the oxygen on earth, and are vital to life on the planet. However, algae can also cause significant and expensive damage to their ecosystem, to human health, and to aquaculture stocks when the local environment changes and promotes the rapid growth of a large mass of algae, known as a bloom. Factors such as the concentration of nutrients, temperature, light conditions, and intentional or unintentional interventions by humans or other species all affect the dynamics of algae species and lead to the formation of harmful algal blooms (HABs). In the aquaculture context, HABs present a major health and economic hazard. Severe human health problems can arise from the consumption of shellfish which have been impacted by blooms of toxin-producing algae. These blooms also cause negative economic impacts on aquaculture through aquaculture stock mortality and through temporary site closures and bans on harvesting due to local algae prevalence. Large-scale mortalities of cultured fish due to algae blooms have been reported across the world and financial losses per large episode can range into the tens of millions of pounds. Monitoring of phytoplankton and of the toxins they produce has been undertaken in various forms in the UK for some decades but manual sampling and subsequent off-site analysis can be slow to identify areas with upcoming or rapidly-changing problems. Microscopy, the current standard for performing algae counts, requires trained personnel both in collection and particularly in analysis, and imposes a necessary delay as samples need to be preserved and transported to an analytical facility. The overall objective of this project is to develop new technology to decrease the economic losses and health risks caused by HABs by decreasing the costs of monitoring algae growth in real-time. This technology will complement and address shortcomings in existing monitoring techniques by providing low-cost, high resolution independent data. The PhytoMOPS technology is based on previous lab-based research demonstrating that algal cells could be sorted, counted, and classified using carefully-designed microfluidic channels combined with low-cost optical readouts. The sorting technique, known as "inertial microfluidics", relies on a carefully-designed channel geometry and flow rate to sort cells by shape and size. In this project, we will design a novel optical measurement section after the cell sorting region, in which the microalgal cells are counted and classfied according to their size, shape, and optical absorption properties. The technology will initially be built and evaluated in the lab where the results will be used to develop analytical methods for interpreting the data. In order to be able to make measurements directly in the water, we will adapt the National Oceanography Centre's (NOC's) water chemistry sensor platform which has already been used for long-term autonomous measurements in a wide range of harsh and inaccessible environments. We will combine the well-engineering NOC platform (including microfluidic chips, pumps, valves, and control/communication electronics) with the algae sorting technology to produce a deployable system capable of acting as a standalone, low-cost, low-power monitor of algal species dynamics for early warning of HABS formation. Lastly, this project involves initial field tests of the system. The deployments will be facilitated by two active HAB monitoring organisations who are also providing expert advice throughout the project: the Scottish Assocation for Marine Science and the Agri-Food Bioscience Institute (North Ireland). The system will will be compared directly against manual sampling and existing algal monitoring technology and will be be evaluated for its technical suitability, usability, and long-term potential.

Algae are present in nearly every body of water on the surface of the earth. These microscopic organisms produce roughly half of the oxygen on earth, and are vital to life on the planet. However, algae can also cause significant and expensive damage to their ecosystem, to human health, and to aquaculture stocks when the local environment changes and promotes the rapid growth of a large mass of algae, known as a bloom. Factors such as the concentration of nutrients, temperature, light conditions, and intentional or unintentional interventions by humans or other species all affect the dynamics of algae species and lead to the formation of harmful algal blooms (HABs). In the aquaculture context, HABs present a major health and economic hazard. Severe human health problems can arise from the consumption of shellfish which have been impacted by blooms of toxin-producing algae. These blooms also cause negative economic impacts on aquaculture through aquaculture stock mortality and through temporary site closures and bans on harvesting due to local algae prevalence. Large-scale mortalities of cultured fish due to algae blooms have been reported across the world and financial losses per large episode can range into the tens of millions of pounds. Monitoring of phytoplankton and of the toxins they produce has been undertaken in various forms in the UK for some decades but manual sampling and subsequent off-site analysis can be slow to identify areas with upcoming or rapidly-changing problems. Microscopy, the current standard for performing algae counts, requires trained personnel both in collection and particularly in analysis, and imposes a necessary delay as samples need to be preserved and transported to an analytical facility. The overall objective of this project is to develop new technology to decrease the economic losses and health risks caused by HABs by decreasing the costs of monitoring algae growth in real-time. This technology will complement and address shortcomings in existing monitoring techniques by providing low-cost, high resolution independent data. The PhytoMOPS technology is based on previous lab-based research demonstrating that algal cells could be sorted, counted, and classified using carefully-designed microfluidic channels combined with low-cost optical readouts. The sorting technique, known as "inertial microfluidics", relies on a carefully-designed channel geometry and flow rate to sort cells by shape and size. In this project, we will design a novel optical measurement section after the cell sorting region, in which the microalgal cells are counted and classfied according to their size, shape, and optical absorption properties. The technology will initially be built and evaluated in the lab where the results will be used to develop analytical methods for interpreting the data. In order to be able to make measurements directly in the water, we will adapt the National Oceanography Centre's (NOC's) water chemistry sensor platform which has already been used for long-term autonomous measurements in a wide range of harsh and inaccessible environments. We will combine the well-engineering NOC platform (including microfluidic chips, pumps, valves, and control/communication electronics) with the algae sorting technology to produce a deployable system capable of acting as a standalone, low-cost, low-power monitor of algal species dynamics for early warning of HABS formation. Lastly, this project involves initial field tests of the system. The deployments will be facilitated by two active HAB monitoring organisations who are also providing expert advice throughout the project: the Scottish Assocation for Marine Science and the Agri-Food Bioscience Institute (North Ireland). The system will will be compared directly against manual sampling and existing algal monitoring technology and will be be evaluated for its technical suitability, usability, and long-term potential.