A disintegrin and metalloproteinase with thrombospondin motifs (ADAMTS) are a family of proteins that are closely related to the matrix metalloproteinases (MMPs). It has been suggested that the proteins have a critical role in the breakdown of articular cartilage during osteoarthritis (OA). More recently it has been suggested that their actions could potentially regulate atherosclerotic plaque stability. Atherosclerosis is a chronic, inflammatory disorder characterised by lipid and cholesterol accumulation and the development of fibrotic plaques within the walls of large and medium arteries. The stability of the plaques is very important because clinical symptoms are only presented after rupture of the unstable plaques, leading to thrombosis and ischemia. During the current study, immunohistochemical analysis confirmed that ADAMTS-­1, -­4 and -­5 were being expressed within human carotid atherosclerotic lesions; macrophages were identified as major contributors to their expressions. Following on from this THP-­1 macrophages were stimulated with transforming growth factor-­β (TGF-­β), interferon-­γ (IFN-­γ), TNF-­like protein 1A (TL1A), interleukin (IL)-­17A and IL-­33. The regulation of ADAMTS-­1, -­4 and -­5 expressions were analysed using quantitative polymerase chain reactions (QPCR) and western blots. It was shown that TGF-­β increased the expressions of ADAMTS-­1 and -­5 and decreased the expression of ADAMTS-­4. IL-­33 decreased the expressions of ADAMTS-­1, -­4 and -­5 and IFN-­γ also decreased the expression of ADAMTS-­1. TL1A and IL-­17A stimulation of macrophages had no regulatory actions over ADAMTS-­1, -­4 or -­5 expressions. Looking at evidence from previous studies, TL1A and IL-­17A were identified as agents that could potentially act in synergy to amplify pro­inflammatory cytokine responses. To investigate this further, THP-­1 macrophages were stimulated with TL1A and IL-­17A, TL1A and IFN-­γ and also IL-­17A combined with IFN-­γ. TL1A and IL-­17A were shown to act in synergy to increase the expressions of ADAMTS-­1, -­4 and -­5 in macrophages. The regulation of ADAMTS-­1, -­4 and -­5 expressions in macrophages by IL-­33 was studied further. The mechanism of signal transduction was studied using RNA interference (RNAi) targeting extracellular signal-­‐regulated kinases (ERK)-­1, ERK-­2, p38, c-­Jun N-­terminal kinases(JNK)-­1/2, c-­Jun, phosphoinositide 3-­kinase(PI3K)-­γ, PI3K-­δ, p50, p65 and Janus kinase(JAK)-­1/2. It was determined that the attenuation of ADAMTS-­1, -­4 and -­5 expressions occurred through transcriptional regulation that was dependent on the ST2 receptor. ERK-­1, ERK-­2, JNK-­1/2, c-­Jun, PI3K-­γ and PI3K-­δ were also involved in the signal transduction of the response. The cellular roles of ADAMTS activity within atherosclerotic disease progression remain poorly understood. During the current study adenoviral vectors were created that delivered shRNA-­targeting ADAMTS-­1, -­4 and -­5. The adenoviral vectors were utilised in studies designed to investigate the roles of ADAMTS-­1, -­4 and -­5 during macrophage migration and foam cell formation. The studies showed that knockdown of ADAMTS-­1, -­4 and -­5 had no effect on macrophage migration or foam cell formation. More research is required into the cellular roles that ADAMTS proteases play during atherosclerotic disease progression. The field of research is now growing and could potentially provide some exciting opportunities for novel therapeutics of the future.

Oxbow lakes are of high ecological importance due to the number and the diversity of habitats they provide. They are created after the abandonment of meanders and subsequent sediment infilling leads to their progressive terrestrialisation, taking from a few months up to several centuries. Nonetheless, little is known about oxbow lake terrestrialisation processes, sediment composition, or why such a disparity exists in lakes’ longevity. To understand the controls on oxbow lakes alluviation, field observations, remotely sensed data and GIS analyses were combined. Sediment transfers in oxbow lakes were documented by topographic and sampling surveys of sites in France and Wales. Aerial photographs and maps were used to date cutoff events, analyse oxbow lakes geometry, and understand the controls on oxbow lake terrestrialisation for eight rivers of different characteristics. Findings from this study illustrate that the specific mechanism by which an oxbow lake is formed is critical to its persistence as a lake and to the sedimentary processes experienced. Chute cutoff oxbow lakes filled in 10 times faster than neck cutoffs and showed significantly different sediment deposits. Results also highlighted that oxbow lakes are not only fine-grained sediment stores, as often referred to, but can be significant bed material sinks since a site on the Ain River sequestered up to 34% of the bed material supply. However, the volume of sediment mobilised in the main channel during cutoff appeared to be larger than the bed-load stored in the former channel within the first decade after abandonment (40%). Sedimentary evidence showed that the terrestrialisation of oxbow lakes is driven by several processes: a flow separation zone at the entrance of the channel creating a sediment plug, sediment sorting by flow gradients and decantation in ponded areas. These results have important implications for the management of meandering rivers by providing a comprehensive analysis of depositional processes which also helps to predict oxbow lake longevity.

1. Rivers are highly structured ecosystems in which habitat complexity and heterogeneity are postulated to affect species diversity and abundance. However, the exact links between habitat structure and organisms such as macro-invertebrates remain poorly understood. 2. Field surveys at the patch and reach scale were combined with a field experiment in the Rivers Wye and Usk, Wales, to: i) quantify variations in habitat complexity and heterogeneity among habitats and river sections, ii) assess their influence on macro-invertebrates, iii) separate the ecological effects of confounding physical factors and iv) determine whether habitat type and heterogeneity promote nestedness of assemblages. 3. At the patch scale, surface complexity but not habitat heterogeneity increased macro-invertebrate diversity, richness and abundance independently of surface area, but only when habitat type was ignored. Surface complexity and heterogeneity were minor determinants of variations in macro-invertebrates among habitat types. 4. A field experiment involving baskets containing cobbles, pebbles, gravel or 50:50 mixtures revealed that flow type explained significant variations in macro-invertebrate richness, abundance and composition, and appeared to filter organisms based on their body size. Surface complexity and interstitial volume had no ecological effect, implying that differences in assemblages among mineral habitats may result from flow-related effects. 5. Macro-invertebrate assemblages occurring in some mineral habitats, typically with lower macro-invertebrate diversity, richness, abundance and trait diversity, appeared to be nested sub-sets of those occurring in some organic habitats. Nested assemblages had reduced trait diversity and altered trait representation. River sections containing fewer habitats supported assemblages of lower abundance, which appeared to be weakly nested sub-sets of those in heterogeneous sections. 6. Habitat complexity and heterogeneity are concluded to have consistently weak effects on macro-invertebrates at the scales studied. In contrast, habitat type and flow type affected macro-invertebrate assemblage composition, structure, and traits, with important implications for river management and conservation.

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This thesis offers an immanent critique and reconstruction of green moral and political theory. In chapter 1, the critical-reconstructive approach and spirit of the thesis is outlined in terms of contributing to the process of developing a green political theory that is different from 'ecologism' or ideological accounts of green politics. In chapter 2, deep ecology is critically interrogated in terms of its metaphysical (2.3) and psychological claims (2.4). Its view of the 'ecological crisis' as a 'crisis' of western culture is criticised as is its a priori defence of environmental preservation over the human productive use of nature. While its ecocentrism is rejected as the normative basis for green politics, its concern with virtue ethics is held to be an important contribution. In chapter 3, a self-reflexive version of anthropocentrism is developed as the most appropriate moral basis for green politics. Some naturalistic arguments are presented in order to support 'speciesism', and defend it from claims of arbitrariness and as being akin to sexism or racism. Arguments centring on demonstrating the tenuous character of the differences between humans and nonhumans are argued to neglect the fundamental moral significance of the difference between 'human' and 'nonhuman'. I argue that an ethic of use, understood as a reflexive mode of interaction with the nonhuman world, is a defensible form of anthropocentrism for green political purposes. The basis of this reflexive anthropocentrism turns on the claim that while human interests are a necessary condition for justifying a particular human use of nature, it is not a satisfactory one. Issues pertaining to the 'seriousness' of the human interest which is fulfilled are held to be important in distinguishing 'use' from 'abuse'.

Phytoplankton aggregations come in a wide range of space and time scales and, as such, simulating such behavior is computationally restrictive. I present a Large-eddy simulation of the upper mixed layer, resolving scales of o(1m). I then show how aggregations are promoted by nutrient upwellings (something which macroscale models struggle to emulate), facilitated primarily by Langmuir circulations. I then demonstrate how certain levels of turbulent mixing encourage planktonic thin layering, a phenomenon which is widely observed.

This thesis aims to improve our understanding of the macroevolutionary implications of antipredator defences, particularly with regard to how defence impacts biodiversity (including both species and trait diversity). To do this I took a phylogenetic comparative approach and used multiple study systems in an attempt to ensure the generality of my work. I begin by investigating how chemical defence and protective coloration influence ecology by testing for life history and ecological correlates of these defences (Chapter 1). Upon finding evidence for an increased niche space in chemically-defended species, and to some degree in conspicuously-patterned species, I explore whether this leads to increased diversification by increasing speciation rates and/or lowering extinction rates (Chapter 2), as also predicted by escape-and-radiate theory (a major and highly influential framework for the macroevolution of natural enemy interactions). Both conspicuous coloration and chemical defence increased speciation rates, but extinction rates were also raised in chemically-defended lineages, leading to a reduction in net diversification. Macroevolutionary extinction rates may or may not be related to contemporary extinction risk, but if they are then there may be conservation implications by allowing prediction of threat status of species with limited direct information. Consequently, in Chapter 3 I asked whether chemically-defended species are more threatened than those lacking such a defence. In accordance with the macroevolutionary results from Chapter 2, I found that chemical defence is indeed associated with a higher extinction risk even amongst contemporary species. In addition to factors that promote diversity, in this thesis I also investigated convergent evolution as a means of constraining diversity of phenotypic traits, using mimicry as a case study for antipredator defences. Many antipredator defences are convergent to some degree, with examples in the repeated evolution of chemical defences and warning coloration as well as independently derived similarity in protective mimicry. However, methods of quantifying the strength of convergent evolution are lacking, not to mention a conceptual framework to define 'strength' in this context, I began by developing a new method to do this which I called the Wheatsheaf index (Chapter 4). Subsequently, I (in collaboration with a colleague, Amanda Minter) also designed software in the form of an R package (called 'windex') to enable user-friendly implementation of the Wheatsheaf index in a familiar statistical environment to many biologists (Chapter 5). In the final data chapter of this thesis, I apply this method in a case study to explore the patterns of phenotypic convergence that result from the evolution of Batesian and Müllerian mimicry complexes. I find that these two types of protective mimicry are generally characterised by convergence in different broad types of traits, but that the specific traits which converge in a given mimicry complex are less predictable (Chapter 6). Overall, this thesis provides novel insights into the evolutionary patterns and consequences of antipredator defences, develops a framework and methods for the analysis of convergent evolution, and suggests further avenues of research for future studies.

There is increasing concern about the adverse effects of the road network on wildlife. The impacts of roads in the ecological landscape include habitat loss, habitat fragmentation and habitat degradation. These interrupt and modify natural processes, altering community structures and population dynamics. The large number of animal fatalities from road traffic accidents is also of concern. Only limited work has been carried out to investigate the intensity of these effects in the UK landscape. This study investigates the effects of roads on both small and large mammals and reviews mitigation measures that have been installed to ameliorate some of these effects. Roads of all sizes present a significant barrier to animal movement and they affect it in specific ways. Movement of small mammals is inhibited by lack of cover and the hostile road surface, whilst fragmentation of the road-verge by highway-related structures, impedes dispersal and compromises the benefits of connectivity often ascribed to such areas. Large animals, which use roads to travel through their territory, are more likely to be struck by traffic and are therefore, more directly affected by traffic-intensity. There is room for further mitigation to reduce the worst of the road-related impacts.

The Middle Ordovician to Late Silurian represents an interval of approximately 50 million years, which has been recognised as the initial, cryptic, period in the evolutionary history of chondrichthyan fish. The fossil remains attributed to early chondrichthyans are dominated by isolated dermal scales that predate the appearance of undisputed chondrichthyan teeth and articulated skeletons in the Lower Devonian. Investigation of the inter-relationships of these scale taxa and their systematic position relative to high- ranked chondrichthyan clades has been hampered by the lack of developed scale-based classification schemes for jawed gnathostomes, coupled with the limited use of scale characters in phylogenetic studies of Palaeozoic Chondrichthyes. Here, all previously documented scale types of alleged Lower Palaeozoic chondrichthyans were examined using a combination of X-ray microtomography, SEM and Nomarski DIC optics. These were found to exhibit a set of characteristics (symmetrical trunk scales, areal crown growth and lack of hard-tissue resorption, cancellous bone and enamel) recognised as specific to the dermal skeleton of chondrichthyans among derived gnathostomes. The collected data permitted the establishment of a hierarchy of scale characters for separate taxonomic ranks, leading to the recognition of three Orders (Mongolepidida, Elegestolepida ordo nov. and Altholepida ordo nov.) of early chondrichthyans, differentiated by distinct types of scale-crown morphogenesis. A scale-based cladistic analysis of jawed gnathostomes corroborated these results by recovering a chondrichthyan clade that incorporates all examined taxa and ‘acanthodians’ with non-superpositional crown growth patterns. It is thus proposed that chondrichthyan dermoskeletal characters carry a phylogenetic signal, allowing to interpret the documented diverse types of scale morphogenesis as evidence for a major radiation of chondrichthyan lineages in the Lower Palaeozoic.