Protecting valuable resources using optimal control theory and feedback strategies for plant disease management

Mathematical models of tree diseases often have little to say about how to manage established epidemics. Models often show that it is too late for successful disease eradication, but few study what management could still be beneficial. This study focusses on finding effective control strategies for managing sudden oak death, a tree disease caused by Phytophthora ramorum. Sudden oak death is a devastating disease spreading through forests in California and southwestern Oregon. The disease is well established and eradication is no longer possible. The ongoing spread of sudden oak death is threatening high value tree resources, including national parks, and culturally and ecologically important species like tanoak. In this thesis we show how the allocation of limited resources for controlling sudden oak death can be optimised to protect these valuable trees. We use simple, approximate models of sudden oak death dynamics, to which we apply the mathematical framework of optimal control theory. Applying the optimised controls from the approximate model to a complex, spatial simulation model, we demonstrate that the framework finds effective strategies for protecting tanoak, whilst also conserving biodiversity. When applied to the problem of protecting Redwood National Park, which is under threat from a nearby outbreak of sudden oak death, the framework finds spatial strategies that balance protective barriers with control at the epidemic wavefront. Because of the number of variables in the system, computational and numerical limitations restrict the control optimisation to relatively simple approximate models. We show how a lack of accuracy in the approximate model can be accounted for by using model predictive control, from control systems engineering: an approach coupling feedback with optimal control theory. Continued surveillance of the complex system, and re-optimisation of the control strategy, ensures that the result remains close to optimal, and leads to highly effective disease management. In this thesis we show how the machinery of optimal control theory can inform plant disease management, protecting valuable resources from sudden oak death. Incorporating feedback into the application of the resulting strategies ensures control remains effective over long timescales, and is robust to uncertainties and stochasticity in the system. Local management of sudden oak death is still possible, and our results show how this can be achieved

Survey of selected tufa forming sites in Staffordshire, UK

The report details a short survey of tufa forming sites in Staffordshire, commissioned by the Staffordshire Wildlife trust. Its principal aim was to determine which tufa sites could be classed as ‘H7220 Petrifying springs with tufa formation (Cratoneurion)’ under the Habitats Directive. Recommendations are also made for future site enhancements. Water chemistry data collected from these sites is compared to data from similar tufa forming springs across the UK

Novel methods for the assessment of chromium species bioavailability

Chromium (Cr) exists in the environment as two chemical species with very different physiological effects. The World Health Organization classifies hexavalent chromium (CrVI) as a carcinogen, whilst trivalent chromium (CrIII) is essential for the regulation of glucose and lipid metabolism. Assessing the risk to human health from CrVI is partly dependent on a greater understanding of the species interconversions at the soil-to-plant interface. Vital to this objective is the validation of techniques capable of accurately determining CrVI in solid matrices such as soil and plant tissues. This thesis aimed to develop, optimise and apply novel analytical methods to understand Cr species interconversions occurring at spatial and temporal scales relevant to plant uptake of Cr from soil. Initially, a modified speciated isotope dilution mass spectrometry (SIDMS) technique, incorporating microwave-assisted alkaline extraction and online species separation, was used to measure CrVI in agricultural soils exposed to elevated metal concentrations through dispersed mine tailings. The CrVI concentrations in all samples indicated a low exposure risk despite optimal conditions for preservation of Cr as the hexavalent species in the tailings material, highlighting the influence of soil characteristics on reduction of CrVI. The mechanisms of Cr species uptake into spinach plants, and the species interconversions occurring prior to uptake, were assessed on a solution basis using isotopic tracers. The impact of sulphate, reported to compete with CrVI for active uptake, was also investigated. The results showed that CrIII could be absorbed from solution into roots through active (symplastic) and passive (apoplastic) mechanisms, with reduction of CrVI observed both after uptake and in the tracer solutions. Sulphate promoted active uptake of CrVI, which was present in the symplast as CrIII. These findings suggested that plants can tolerate CrVI through reduction processes before and after uptake, with evidence of a synergistic effect in the presence of sulphur. The suitability of microdialysis for extracting CrVI from soil solution was appraised during the development of an online system, coupled to HPLC-ICP-QQQ. The setup was able to monitor changes in the concentration of labelled-53CrVI, added to soil through direct spiking and homogenised mixing, at 15-minute intervals, far surpassing the temporal resolution of previous passive sampling techniques. Analytical figures of merit show that the system was sufficiently sensitive (LOD ≤ 0.3 µg L 1) and produced repeatable measurements (RSD of standards < 2.5%), demonstrating that it is a powerful tool for providing further insight into the bioavailability of CrVI and its interactions with soil microbes and the rhizosphere. This thesis contributes to a better understanding of plant-Cr species dynamics, and demonstrates the importance of developing and validating accurate, high-resolution analytical techniques to investigate existing and emerging research questions surrounding soil-to-plant transfer of CrVI

Utilising electrodermal activity sensor signals to quantify nociceptive response during movement activities

ObjectiveWith an increasingly ageing population and osteoarthritis prevalence, the quantification of nociceptive signals responsible for painful movements and individual responses could lead to better treatment and monitoring solutions. Changes in electrodermal activity (EDA) can be detected via changes in skin conductance (SC) and measured using finger electrodes on a wearable sensor, providing objective information for increased physiological stress response.ResultsTo provide EDA response preliminary data, this was recorded with healthy volunteers on an array of activities while receiving a noxious stimulus. This provides a defined scenario that can be utilised as protocol feasibility testing. Raw signal extraction, processing and statistical analysis was performed using mean SC values on all participant data. Extra exploratory analysis on a case study was incorporated using various decomposition tools. The application of the stimuli resulted in a 35% average increase in mean SC with considerable gender differences in SC and self-reported pain scores. Though EDA parameters are a promising tool for nociceptive response indicators, limitations including motion artifact sensitivities and lack of previous movement-based EDA published data result in restricted analysis understanding. Refined processing pipelines with signal decomposition tools will be necessary to incorporate into a protocol that quantifies nociceptive response clinically meaningfully

Utilising electrodermal activity sensor signals to quantify nociceptive response during movement activities

ObjectiveWith an increasingly ageing population and osteoarthritis prevalence, the quantification of nociceptive signals responsible for painful movements and individual responses could lead to better treatment and monitoring solutions. Changes in electrodermal activity (EDA) can be detected via changes in skin conductance (SC) and measured using finger electrodes on a wearable sensor, providing objective information for increased physiological stress response.ResultsTo provide EDA response preliminary data, this was recorded with healthy volunteers on an array of activities while receiving a noxious stimulus. This provides a defined scenario that can be utilised as protocol feasibility testing. Raw signal extraction, processing and statistical analysis was performed using mean SC values on all participant data. Extra exploratory analysis on a case study was incorporated using various decomposition tools. The application of the stimuli resulted in a 35% average increase in mean SC with considerable gender differences in SC and self-reported pain scores. Though EDA parameters are a promising tool for nociceptive response indicators, limitations including motion artifact sensitivities and lack of previous movement-based EDA published data result in restricted analysis understanding. Refined processing pipelines with signal decomposition tools will be necessary to incorporate into a protocol that quantifies nociceptive response clinically meaningfully

Bioaccessibility performance data for fifty-seven elements in guidance material BGS 102

BGS 102, a guidance material for bioaccessible arsenic (As) and lead (Pb), was produced during validation of the in vitro Unified Bioaccessibility Method (UBM). This paper reports a compilation of reproducible bioaccessible guidance values for fifty-five additional elements in BGS 102, providing guidance for analysts to broaden the scope of UBM analyses for a wider range of elements based on data collected over an average of 60 separate analytical batches per element. Data are presented in categories for both gastric (STOM) and gastrointestinal (STOM + INT) extraction phases, where reproducibility, measured as relative standard deviation (RSD) was; ≤ 10% RSD for 27 elements (Mg, Al, Si, P, Ca, Cr, Mn, Co, Ni, As, Rb, Sr, Y, Ba, La, Ce, Pr, Nd, Sm, Eu, Tb, Gd, Dy, Ho, Er, Tm, Yb); between 10 and 20% RSD for 10 elements (Li, K, V, Fe, Cu, Zn, Cd, Lu, Pb, U); and ≥ 20% RSD for 19 elements in the gastric phase (Be, B, S, Ti, Ga, Se, Zr, Nb, Mo, Ag, Sn, Sb, Cs, Hf, Ta, W, Tl, Bi, Th). Two elements (Mg, Rb) met the ≤ 10% RSD criteria in the UBM gastrointestinal extraction phase due to the alkaline conditions of this phase precipitating out the majority of determinands. Certain elements, including Na, K, Zn and Se, were found to be a significant component of the extraction fluids with proportionally higher concentrations compared to the guidance material. Bioaccessible fractions (%BAF) were also calculated, but were found to be a less reproducible format for confirming the accuracy of measurements. The low concentration of some elements of interest in BGS 102, such as antimony (Sb), justifies the preparation of an alternative certified reference material (CRM). This paper presents an opportunity to broaden the scope of the UBM method to address food security issues (e.g. Fe and Zn micronutrient deficiencies) and contributions to dietary intake from extraneous dust or soil through evidence of the analytical possibilities and current limitations requiring further investigation

Limitations on the role of the hyporheic zone in chromium natural attenuation in a contaminated urban stream

The urban hyporheic zone may offer natural attenuation potential for contaminants. This potential is contaminant-specific and may be spatially and temporally variable. The aim of this study was the assessment of the natural attenuation potential of the hyporheic zone of an urban stream receiving hexavalent chromium (Cr)-rich effluents from the historical land disposal of chromite ore processing residue (COPR) in Glasgow, Scotland. The evidence based approach involved the use of a network of multilevel piezometers for best capturing potential anoxic field conditions and fine-scale spatial gradients in solute concentrations of surface water and porewater. In-situ porewater sampling was integrated with sediment sampling and reach-scale monitoring of stream water quality. The results show a sharp decrease of total dissolved (filtered <0.45 μm) Cr concentrations at the surface water – sediment boundary in all profiles, from Cr mean values of 1100 μg l−1 in surface water to 5 μg l−1 in porewater. Chromium speciation analysis indicates that no Cr(VI) was detectable in the neutral pH, moderately reducing porewater, while it was the dominant species in surface water. Evidence of historical COPR detrital grains contributed to the total Cr concentrations (size fraction <150 μm) up to 8800 mg kg−1 in the streambed sediment. The abundance in the porewater of Fe (mean value = 1700 μg l−1), mainly as Fe(II), a natural electron donor for Cr(VI) reduction to Cr(III), indicates a high natural attenuation potential of the hyporheic zone for downwelling dissolved Cr, through Cr(VI) reduction to Cr(III) and the formation of Cr(III) solids of low solubility. Authigenic Cr-rich rims on particles also documented active Cr precipitation from solution in the fine sediments. Large short-term changes of stream stage and stream water composition were not reflected in the hyporheic conservative (chloride) and reactive solute composition. This result indicates only limited surface water infiltration and suggests that small advective exchange might limit the effectiveness of the hyporheic zone for enhancing Cr surface water quality at the reach-scale. This is supported by further evidence from preliminary surface water quality synoptic sampling which shows only moderate to low downstream decrease in surface water Cr concentrations. The surface water investigation needs to be supported by combined water quality-flow monitoring and to be extended to a wider range of temporal and spatial scales to corroborate the reach-scale findings

Investigating the geochemical controls on Pb bioaccessibility in urban agricultural soils to inform sustainable site management

The solid-phase speciation of contaminants in soil plays a major role in regulating both the environmental mobility of contaminants and their bioavailability in biological receptors such as humans. With the increasing prevalence of urban agriculture, in tandem with growing evidence of the negative health impacts of even low levels of exposure to Pb, there is a pressing need to provide regulators with a relevant evidence base on which to build human health risk assessments and construct sustainable site management plans. We detail how the solid-phase fractionation of Pb from selected urban agricultural soil samples, using sequential extraction, can be utilised to interpret the bioaccessible fraction of Pb and ultimately inform sustainable site management plans. Our sequential extraction data shows that the Pb in our urban soils is primarily associated with Al oxide phases, with the second most important phase associated with either Fe oxyhydroxide or crystalline FeO, and only to a limited extent with Ca carbonates. We interpret the co-presence of a P component with the Al oxide cluster to indicate the soils contain Pb phosphate type minerals, such as plumbogummite (PbAl3(PO4)2(OH)5·H2O), as a consequence of natural “soil aging” processes. The presence of Pb phosphates, in conjunction with our biomonitoring data, which indicates the lack of elevated blood Pb levels in our gardeners compared to their non-gardening neighbours, suggests the (legacy) Pb in these soils has been rendered relatively immobile. This study has given confidence to the local authority regulators, and the gardeners, that these urban gardens can be safe to use, even where soil Pb levels are up to ten times above the UK’s recommended lead screening level. The advice to our urban gardeners, based on our findings, is to carry on gardening but follow recommended good land management and hygiene practices

Integrated multi-trophic aquaculture mitigates the effects of ocean acidification: Seaweeds raise system pH and improve growth of juvenile abalone

Integrated multi-trophic aquaculture (IMTA) has the potential to enhance growth, reduce nutrient loads, and mitigate environmental conditions compared to traditional single-species culture techniques. The goal of this project was to develop a land-based system for the integrated culture of seaweeds and shellfish, to test the efficacy of integrated versus non-integrated designs, and to assess the potential for IMTA to mitigate the effects of climate change from ocean acidification on shellfish growth and physiology. We utilized the red abalone (Haliotis rufescens) and the red seaweed dulse (Devaleraea mollis) as our study species and designed integrated tanks at three different recirculation rates (0%, 30%, and 65% recirculation per hour) to test how an integrated design would affect growth rates of the abalone and seaweeds, modify nutrient levels, and change water chemistry. We specifically hypothesized that IMTA designs would raise seawater pH to benefit calcifying species. Our results indicated that juvenile abalone grew significantly faster in weight (22% increase) and shell area (11% increase) in 6 months in tanks with the highest recirculation rates (65%). The 65% recirculation treatment also exhibited a significant increase in mean seawater pH (0.2 pH units higher) due to the biological activity of the seaweed in the connected tanks. We found a significant positive relationship between the mean pH of seawater in the tanks and juvenile abalone growth rates across all treatments. There were no significant differences in the growth of dulse among treatments, but dulse growth did vary seasonally. Seawater phosphate and nitrate concentrations were depleted in the highest recirculation rate treatment, but ammonium concentrations were elevated, likely due to the abalone effluent. Overall, our results indicate that there are benefits to IMTA culture of seaweeds and abalone in terms of improving growth in land-based systems, which will reduce the time to market and buffer commercial abalone operations against the effects of ocean acidification during vulnerable early life stages