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This thesis examines the queer and affective aspects of an online yaoi fan community. Yaoi is a genre of Japanese manga focussing on homoerotic/homosexual themes. A key point of interest about yaoi is that it is largely created by and for women. Set within the context of yaoi fan studies, this thesis utilises queer theory to investigate how a diverse group of fans comes together in a fan community on the internet in order to explore alternative identities and develop new relationships with like-minded others. According to David Halperin, queer is “whatever is at odds with the normal, the legitimate, the dominant” (cited in Sullivan 2003, p.43). I queer yaoi studies and suggest that its fandom is not a homogenous group of heterosexual female fans as has become customarily thought. Expanding on the work of other scholars, I combine original ethnographic research in AarinFantasy (http://www.aarinfantasy.com), a yaoi manga community to demonstrate how, for many fans, an online community is a place to explore and discuss queer alternatives to heteronormative gender and sexuality. I also discuss how members of AarinFantasy invest into the site through affective connections with other fans. By creating and maintaining valued friendships with others members create not only a queer space but also a space where they feel accepted as yaoi fans. Relationships in the community are formed and maintained through communication that is grounded in the fans’ experiences and the contextual state that yaoi manga has in their lives.

The cyclizer of an infinite permutation group G is the group generated by the cycles involved in elements of G, along with G itself. There is an ascending subgroup series beginning with G, where each term in the series is the cyclizer of the previous term. We call this series the cyclizer series for G. If this series terminates then we say the cyclizer length of G is the length of the respective cyclizer series. We study several innite permutation groups, and either determine their cyclizer series, or determine that the cyclizer series terminates and give the cyclizer length. In each of the innite permutation groups studied, the cyclizer length is at most 3. We also study the structure of a group that arises as the cyclizer of the innite cyclic group acting regularly on itself. Our study discovers an interesting innite simple group, and a family of associated innite characteristically simple groups.

In the face of increasingly dynamic market environments, firms are being urged to develop learning and innovation capabilities if they wish to secure competitive advantage and long-term growth. A bank of work written from numerous theoretical perspectives has converged on the view that knowledge underpins the formation of such capabilities. While much of this literature emphasises the importance of cognitive knowledge, a new approach grounded in techniques from social anthropology suggests that learning is a non-cognitive practice, drawing on embodied exploration, everyday sociality, and a communitarian infrastructure of human and non-human actants. This thesis aims to consolidate the current literature on 'possessed' knowledge by clarifying the relationship between cognition and learning, and to advance understanding of innovation practices within firms by examining the role of non-cognitive mechanisms in the development of organisational capabilities. Drawing on a nine-month period of ethnographic research, this thesis describes the on-the-ground processes of learning and innovation within the marketing department of a large UK organisation. This evidence is used to investigate critically the theoretical claims regarding the role of both cognitive and non-cognitive forms of knowledge. Based on the empirical findings, three interrelated arguments are proposed: the design and governance of strategic learning devices involve non-cognitive practices; informal mechanisms of learning underpin the formation of new capabilities; and communitarian theories of learning overemphasise the social construction of knowledge, while neglecting the agency of the materiality of context.

This study examines the sedimentology of salt marshes and lagoonal sediments from coastal wetland settings in south east Sicily. Palaeoenvironmentasl tudies have been carried out to assess the recent evolution of disturbed coastal wetlands, and to examine the sensitivity of these depositional settings in recording historical environmental change. The evolution of recent coastal wetland environments in the region can be related to anthrpogenic disturbance phases in drainage catchments due to changes in land-use. Archaeo-historical changes to the coastal topography are identified, in relation to the development of present-day coastal wetland areas in south east Sicily. The impact of 19th early 20th century salt workings is recognised as a major and continuing factor in the condition of present day wetlands. Measurement of 210Pb, 137Cs, pollen content, major and trace elements, loss on ignition and other sedimentological features generates valuable information on depositional processes that have occurred over the last 100-150 years. Sub-surfaces edimentological changes recognised in cores extracted from shallow sediment sequences (< 50 cm) can be related to coastal wetland land-use changes and hydrological flood events. A 30 cm depth sediment sequence analysed from the Mulinello estuary records the interaction between estuarine channel processes, following embankment construction and the variable influence of catchment generated flood episodes. A clearly identifiable change in accretion and core composition occurred during the mid-late 1940's and early 1950's which coincides with recorded peaks in monthly rainfall totals. The impact of marsh development, flooding and recovery is highlighted by the variable abundance of dominant pollen types. A marked increase of ruderal pollen types during periods of channel-dominated deposition is contrasted with an abundance of halophyte pollen during low-energy phases of organic marsh sedimentation. The two lagoonal cores from Pantano Piccolo record successive hydrological changes, due almost certainly to artificial enclosure in the late l8th to early 19th century. The apparent change in water levels dramatically affected marginal salt marsh communities. Artificial impoundment generated a lagoonal setting conducive to the accumulation of local and extralocal sources of pollen, reflecting the re- establishment of salt marsh vegetation. Although largely separated from catchment-overland flow patterns during the 20th century, large magnitude rainfall events were recorded in lagoonal accretion patterns. 21OPb-derived sediment accretion rates and estimated pollen accumulation rates have enabled the response and sensitivity, of coastal wetland and nearby plant communities to phases of disturbance and recovery, to be determined. Due to artificial impoundment of the lagoon, fringing-halophyte communities and organic accretion migrated outwards to occupy their present marginal position. To aid the interpretation of pollen encountered in estuarine and lagoonal settings, soil samples from nearby land surfaces around Pantano Piccolo were analysed for pollen content. Soil surfaces reflected the dominance of gravity fallout from surface vegetation and the accumulation of pollen from regional-atmospheric sources. The reliability of the multi-proxy approach and palaeoenvironmental analyses used, indicate that coastal wetlands in south east Sicily have evolved in a dynamic system of punctuated equilibria, due to climatic events and human activity over the last 100- 150 years. Their current status reflects the continued pressure on coastal systems by anthropogenic development and recent conservation measures.

The resource requirements and social behaviour of pigs housed in large groups were examined in a series of experiments. (i) The nipple drinker requirement was addressed by using four treatments (60 pigs, 3 drinkers; 20 pigs, 1 drinker; 60 pigs, 6 drinkers and 20 pigs, 2 drinkers). Drinker provision had no effect on water use, but in a larger group more water was used in less time (p<0.001). The diurnal pattern of drinking, overt aggression and lesion score indicated no difference between treatments. (ii) Pigs, housed on deep straw in groups of 20 or 80, were provided with a low (50 kg/m2) or high (32 kg/m2) floor space allowance. Large groups had a lower growth rate. Skin lesions were elevated and immune response was lowered by a low space allowance. (iii) Two feeder space allowances (32.5 and 42.5 mm/pig) for pigs housed in groups of 20 or 80 were investigated. Food intake was lower in the low feeder allowance treatments and pigs in large groups tended to have a reduced growth rate. (iv) Pigs from the same pen in an unfamiliar arena maintained a similar degree of proximity regardless of origin group size. (v) Pigs from groups of 80 demonstrated reduced aggressiveness (increased latency to fight, decreased rate of aggression) towards unacquainted pigs in an arena, but showed even less aggression towards pen mates. (vi) No evidence of spatial sub-division of the large group into smaller units capable of maintaining a dominance hierarchy was found. Resource provision and group size largely did not interact, but may independently compromise productivity and behaviour. A large group was associated with a reduction in performance. The dominance hierarchy was of less importance in large groups, despite recognition being intact, and sub-grouping behaviour did not provide an alternative strategy for group social organisation.

There is currently a poor understanding of the impact of chronic stress on the behaviour and physiology of beef cattle. In monogastrics, hormones released in response to stress can have deleterious effects on the balance of the microbiota present in the gut, which can last long after stress hormone levels have returned to normal. If comparable changes occur in the rumen microbiota, these could have important consequences for ruminal fermentation and digestibility, leading to suboptimal use of nutrients and increased methane emissions. However, there is little information regarding the effects of stress on the rumen microbiome. The overall aim of this thesis was to understand how commercially relevant stressors affect ruminal microbial populations, as well as concurrent effects on behaviour, feed efficiency and methane emissions in beef cattle. The first objective was to assess the direct contribution of glucocorticoids such as cortisol in mediating the effect of stress on the microflora and feed efficiency. Dexamethasone, a potent synthetic cortisol analogue, was used to evaluate the effect of an exogenous glucocorticoid on feed efficiency and the rumen microbial populations. This treatment was applied to 516 ± 50-day old Limousin cross steers selected based on extremes of feed efficiency, to contrast the effects on ruminal microbial communities of more efficient and less efficient animals. Animals in the treatment group (n=24) were injected with 0.05 mg/kg dexamethasone intramuscularly for 3 consecutive days, while matching extremes of feed efficiency controls (n=16) were treated with the equivalent volume of saline solution (Control group). The effect of dexamethasone was assessed on faecal cortisol metabolites, feeding behaviour, locomotor activity, as well as metagenomic information obtained from 16S rRNA gene sequencing of rumen fluid samples. Treatment with exogenous glucocorticoid dexamethasone induced transient changes in activity and faecal cortisol. Nonetheless, this glucocorticoid did not cause any significant changes in the rumen archaea population or microbial diversity, an indication that ruminal microbial populations might be resilient to the direct effects of exogenous glucocorticoids. The second objective was to quantify the behavioural and physiological responses to a putative composite chronic stressor treatment, by applying a series of commercially relevant stressors and assessing any changes in behaviour and HPA axis responsiveness. The commercially relevant stressors used were reduced space allowance, in addition to being subjected every week to regrouping, transport and a short period of isolation. Limousin (n=32) and Angus (n=32) crossbred beef steers, 400 ±13 days old at the beginning of the trial, were assigned in a balanced way to a composite stressor (S) or control (C) treatment, each treatment with four replicate groups. Blood samples and faecal samples were collected to measure cortisol levels. An ACTH challenge was performed using 0.5ug/kg of Synacthen Depot® with blood samples taken just before, 30 min post and 60 min post ACTH challenge to assess changes in HPA axis responsiveness on a subsample of animals (S=22; C=19). Behaviour was assessed from activity monitors, feed intake, an attention bias test, video observations of agonistic behaviour at the feeders and affiliative behaviour (rubbing and licking) in the home pen. Results showed differences between treatments in some parameters of activity and an attention bias test. However, there were no effects of treatment on agonistic or affiliative behaviour. Cortisol responses, although different between groups, could not be specifically attributed to the composite stressor treatment and the ACTH challenge employed did not detect any significant differences in adrenal sensitivity between treatments. Making use of metagenomic information obtained from 16S rRNA gene sequencing of rumen fluid samples taken during the composite stressor experiment, the last objective of this project assessed changes in the rumen microbiota in response to the applied stressors. Although there was a particular interest in the methanogenic populations, analyses also looked at effects on productivity and methane emissions. To this end a small cohort of 12 animals (six from each C and S treatments) was used to assess any effects of the composite stressor treatment on methane emissions. Although changes were detected in some microbial genera throughout the experiment, there were no major changes in the rumen archaea population or microbial diversity directly associated with the composite stressor treatment. Additionally, by the end of the experiment, there was no effect of stress on growth performance or methane emissions. In conclusion, circulating glucocorticoids do not appear to affect the rumen microbiota balance directly, although it is possible that they may affect microbial communities in other sites of the gastrointestinal tract. Some differences in behaviour but not cortisol were found in response to the composite stressor treatment, suggesting that beef cattle might be resilient to repeated but predictable stressors. The stressor regime applied did not cause substantial changes in rumen microbial diversity or methanogenic archaea populations. This thesis was a first step towards enhancing our understanding of the dynamics of the rumen microbiome in response to stress. Further research needs to examine more closely the links between biological changes in response to severe chronic stress and microbiota resilience in the rumen and other sites of the gastrointestinal tract.

Endeavours to advance understanding of KISS OF DEATH (KOD) gene function by established methods were taken forward. Particularly, by attempting to utilise the previously reported ability of ectopic KOD expression to induce Programmed Cell Death (PCD). To this end, KOD was expressed in Arabidopsis and tobacco. However the induction of a PCD phenotype by KOD could not be replicated in this work. As a consequence, efforts towards the aim of understanding how KOD induced PCD were inhibited. Some understanding of the biology of KOD function was gained by the investigation of KOD transcription. It was found that low level KOD expression could be induced by treatment with 500mM sodium chloride, in addition to the already characterised induction of KOD by H2O2, heat shock and Pseudomonas syringae AvrRPM1. This led to the hypothesis proposed here that KOD induction in response to stress treatments may be incidental to, rather than a contributory factor to, cell death. This is based on analysis of response to H2O2 and Pseudomonas syringae AvrRPM1 in kod mutants. Furthermore, a pKOD:GUS reported was developed and characterised. Taken together, evidence obtained here eroded support for perceiving KOD as a potent core component contributing to multiple PCD pathways. The design, construction, calibration and validation of a successful new conductivity meter system is presented. This was designed to update and improve the classic electrolyte leakage assay for cell death. The device is able to record measurements from a large number of individual samples simultaneously and continuously, without requiring further operator intervention. The device conforms to the principles of the open source hardware movement and the standards of the open-source Arduino micro-controller platform.

Our understanding of the importance of peptide hormone signalling in the growth and development of plants has improved in recent years with the identification of several protein families that regulate cell division and differentiation within a variety of meristematic tissues. One family in particular, known as CLAVATA3/ESR-RELATED (CLE) proteins, has been shown to be a diverse functioning family controlling differentiation of the xylem and phloem from the cambium and affecting root development. Previously CLE proteins were thought to contain a single CLE peptide at the C-terminal end however through bioinformatic investigation using a combination of BLAST and MEME FIMO we have identified numerous proteins spread across the plant kingdom that contain between two and twenty-four CLE peptides in a tandem array separated by a conserved spacer region. These Multi-CLE peptide proteins have been identified across a variety of agriculturally important crop species but are not present in species such as Arabidopsis thaliana. Due to the radial growth of the hypocotyl Arabidopsis thalaiana is an ideal model organism for investigating vascular development as its simple development allows for easy identification of developmental changes. Expression of the Gossypium raimondii Multi-CLE peptide protein in A. thaliana alters vascular tissue organisation in the hypocotyl, indicating that the protein is functional in vivo. Presumably protein cleavage occurs to release the individual CLE peptide(s) which are then recognised by native receptors and downstream effectors are activated or inhibited to alter cell division and differentiation. Western blot analysis suggests that peptides and subsequent spacers are cleaved off from the protein together, however further experimental analysis is required to elucidate this. The application of synthetic peptides indicates that the peptides are predominantly categorised as A-Type peptides as they are shown to be affecting root growth. In addition to this, we have identified that the spacer region appears to have no effect on root growth but also does not impede the activity of the peptide insinuating spacers at the N-terminal end of a peptide are cleaved off. However, we have yet to elucidate whether spacers at the C-terminal end affect peptide activity and whether they two are cleaved off through another proteolytic process.

Aggression between pigs is common in commercial farming as pigs fight to establish dominance relationships at regrouping. The behaviour has been studied extensively since the 1970s and several strategies to reduce aggression have been identified. However, the uptake of aggression research in commercial practice has been limited and the behaviour remains an important problem for animal welfare, farm productivity and profitability. This thesis is the first body of work to study the social and economic factors influencing farmers’ behaviour regarding the management of aggression, and adopted quantitative research methods in order to meet two primary aims. The first aim was to understand the behaviour of UK and Irish pig farmers with regard to aggression between pigs. This was important because understanding behaviour and the context in which is occurs can help to identify targets for initiating a change in practice. The second aim was to identify practical and cost effective solutions based on farmer demand. This is important because solutions based on industry input have the capacity to make real improvements to animal welfare in practice. At various stages of this project farmers perceptions of pig aggression and welfare were compared to other stakeholder groups in order to establish the impact of farmers’ role and experience. Comparison groups had experience of working with pigs but in a different context (specialised pig veterinarians); had knowledge of agriculture and livestock but no experience of working with pigs (agriculture students and animal science students); and were removed from animal production (citizens unrelated to agriculture). The first aim of this thesis was addressed in the first three studies. The results of the first study revealed widespread belief in pigs’ capacity to suffer amongst pig farmers (and non-farmers). Therefore, a lack of belief in pigs’ capacity to suffer does not appear to contribute to the non-financial reasons behind farmers’ reluctance to control pig aggression. In the second study, participants perceptions of aggression seen in video clips were compared to physiological measures of exhaustion (blood lactate) and injury (lesion score) taken from the animals. Results revealed that farmers’ (and non-farmers) recognised fights displayed in-action as a source of suffering for pigs. However, when they did not see the fight occurring but only saw the animals afterwards, participants underestimated pigs’ injuries. In the third study, an in-depth analysis of the range of factors likely to influence farmer behaviour revealed that farmers’ willingness to control aggression was influenced by: 1) whether they felt able to implement the change, 2) beliefs about the likely consequences, 3) perceptions of aggression as a problem on their farm, and 4) the opinion of relevant stakeholder groups, with the opinion of veterinarians being particularly significant. The second aim of this thesis was addressed in the final two studies. In the fourth study, an economic choice experiment revealed three independent groups of pig farmers, each with different willingness to pay (WTP) for aggression control strategies and motivation for making an investment. Specifically, farmers in Class 1 would not invest in an aggression control strategy as they were unlikely to regroup unfamiliar pigs. Farmers in Class 2 were willing to invest in an aggression control strategy, but were only interested in the extent to which the strategy improved growth rate. They were unwilling to pay for reductions in aggression specifically. Farmers in Class 3 were motivated by reducing aggression as well as improving growth rate, and were WTP £0.11 per pig place and £0.03 per pig produced for each 1% reduction in lesions as result of aggression. In the final study, cost-benefit analysis revealed that allowing litters to co-mingle prior to weaning is the most practical and economically viable aggression control strategy; meeting the demands of farmers in both Classes 2 and 3. Exposing pigs to synthetic maternal pheromones was unlikely to improve profitability, but did meet the WTP demands of farmers in Class 3. Changing current structures in order to house pigs in large social groups (100+ pigs) was associated with high economic costs which were not within the realms of farmers’ WTP. Overall, a major barrier preventing the uptake of aggression research in practice is that very few strategies can be practically and cost-effectively implemented and managed by farmers under commercial conditions. Based on the findings of this project, several evidence-based recommendations were made to encourage a real change in practice. For example, animal scientists working on the control of aggression should test new strategies for their practicality and cost-effectiveness. Furthermore, communication within the industry must take place through targeted campaigns which take care to consider the wide variety of factors which influence farmers’ behaviour. Applying the social sciences to stubborn and entrenched animal welfare issues has the capacity to bridge the gap between animal science research and practice, and have a huge impact on farm animal welfare. Therefore, the approach adopted in this project should be extended to other long-standing animal welfare issues where known solutions are poorly adopted.

In commercial systems, pigs are routinely regrouped with unfamiliar conspecifics which leads to physical aggression in order to establish new dominance relationships. Post-mixing aggression lasts approximately 24 hours before steeply declining, although chronic aggression amongst familiar individuals is also observed. These aggressive encounters result in skin injuries commonly referred to as lesions, the number and location of which have been shown to correlate with the type and duration of aggression an individual has engaged in. Correlations between anterior injury rates at 24 hours post-mixing (24hr-PM) and 3 weeks post-mixing (3wk-PM) are inversely related, indicating that reciprocal aggression can only be delayed and not avoided altogether. In order to meaningfully improve animal welfare, a solution that leads to a reduction in aggression at both time points needs to be identified. For this to be achieved, the variation in skin lesions needs to be studied further and better understood. Previous analyses have focussed on interactions only at the dyadic level and failed to explain a large proportion of the variation in lesion scores. As interactions do not occur in isolation but rather as a part of a larger interconnected dynamic, this thesis aims to apply social network analysis to post-mixing aggression in order to examine this behaviour within the wider social context. Social network analysis may reveal group level and indirect behaviours that play an important role in post-mixing aggression that may otherwise be undetectable. In Chapter 2 the relationship between pen level network properties and pen level injury rates were established. This revealed that networks containing large fully connected subgroups (cliques) tend to have fewer injuries 3wk-PM, whereas highly divided networks (betweenness centralisation) have considerably higher lesions. Chapter 3 follows on from Chapter 2 by examining the effect on lesions for individual pigs when occupying different positions within a social network. The first part of the chapter focuses on individual position within the network structures identified in Chapter 2. This chapter also quantifies a variety of commonly studied individual network positions to examine how these relate to individual lesions, and compares the model fit to dyadic traits. This chapter presents evidence that occupying centralised network positions can be beneficial for the central pig, but at the expense of pen-mates who are at risk of elevated rates of aggression and injury. In contrast, in pens with large cliques, no significant difference was found in injury rates between clique members (those who are part of a fully connected sub-group) and non members. This chapter concludes that while direct engagement in aggression at 24hr PM remains a strong predictor of injury at 3wk-PM, individual injury rates can be indirectly affected by the behaviours of pen mates that occurred at 24hr-PM. Chapter 4 builds upon Chapter 2 by quantifying different dominance metrics to establish whether pen level network properties relate to variations in hierarchical structure. This chapter revealed that pens with large cliques tend to have well-defined hierarchies (quantified by linearity and steepness), whereas the hierarchical structure in highly centralised pens tend to be poorly defined. This indicates that certain network structures are associated with poor hierarchy formation, which may partially explain the difficulties certain groups have with achieving and/or maintaining long-term social stability. Together the results indicate that SNA can complement conventional analyses of dyadic interactions to predict and understand the outcomes of aggressive interactions.

There has been growing interest in the use of plant biomass, particularly secondary cell walls, as a sustainable feedstock for second generation biofuels. However, the feasibility of converting cellulose and other cell wall carbohydrates into biofuels and other chemicals is hindered by the hydrophobic phenolic polymer, lignin, which makes the secondary cell wall inherently recalcitrant to breakdown and hampers enzymatic hydrolysis. Secondary cell walls with altered composition naturally occur in xylem fibres of 'Lord Lambourne' apple trees infected with Apple Rubbery Wood associated Virus (ARWaV). However, the development of symptoms has not been described in detail and the mechanism by which ARWaV modifies the secondary cell wall has never been studied. In this study, a detailed morphological and biochemical assessment of symptoms was performed during symptomatic wood development in branches infected with ARWaV. Symptomatic xylem was characterised by fibres with very thick secondary cell walls and overall, contained a third less lignin and a two-fold higher levels of soluble phenolics, whilst the total cellulose and hemicellulose content remained unchanged. These compositional modifications resulted in a two-fold increase in the glucose released from symptomatic xylem digested with cellulase. Using a systematic biological approach the molecular mechanism that determines secondary cell wall alterations during symptom development, specifically poor lignification was investigated. Proteomic and metabolomics analyses together demonstrated that the first committed stage of lignin biosynthesis, involving the conversion of phenylalanine to cinnamic acid via phenylalanine ammonia lyase, was disrupted in symptomatic xylem. RNA-sequencing analysis was also used to examine transcriptomic changes associated with symptom development. However, gene expression patterns were largely inconsistent with the biochemistry of symptomatic wood and other omics analyses indicating a potential tissue-sampling bias. Functional analysis experiments of apple MYB and NAC transcription factors in the Arabidopsis hypocotyl are also described, revealing potentially novel roles for MYB83 during secondary cell wall formation. Overall, the experiments performed in this study provide a comprehensive analysis of symptom development in the xylem of branches infected with ARWaV.

Secondary growth, the radial thickening of plant organs, is a major source of plant biomass and leads to a continual production of vascular tissues. The activity of the cambial meristem produces secondary xylem towards the inside and secondary phloem towards the outside of the plant body. A good understanding of the molecular mechanisms that drive cambial activity would aid attempts to increase biomass yield and to engineer plants that can better withstand extreme and unpredictable environments. The Arabidopsis hypocotyl is an ideal model organ for the study of secondary growth. The hypocotyl has two phases of secondary growth, separated at the onset of flowering. In the first phase, phloem and xylem are produced at equal rates, with the xylem tissue containing only parenchyma cells and water-conducting vessels. The second phase is known as 'xylem expansion' due to the increased rate of xylem production relative to phloem. It is also during this second phase that xylary fibres begin to differentiate, which provide structural support for the plant following flowering. The vascular tissue produced during the second phase is remarkably similar to the wood of trees. Here, xylem expansion expression datasets are used to identify novel regulators of hypocotyl vascular development. The phytohormone abscisic acid (ABA) is found to promote the onset of xylem fibre differentiation after flowering. Mutations in ABA-biosynthesis enzymes delays fibre production without affecting the relative rate of xylem production. Secondly, CLE17 is identified as a novel regulator of hypocotyl vascular development. Plants constitutively expressing CLE17 display various vascular defects in the hypocotyl and root but not the stem, including the loss of a clear cambial ring and delayed phloem differentiation. Experiments into other candidate regulators of xylem expansion are also described, including two Rapid Alkalinization Factors (RALFs). Although these two RALFs appear not to affect hypocotyl vascular development, the largest phylogenetic analysis of the RALF family undertaken to date is presented. It is found that a number of genes described in the literature as RALFs are actually highly diverged and could instead be referred to as RALF-related genes. Together, the work included in this thesis provides a novel insight into Arabidopsis vascular development.

The secondary cell wall of plants is a structure formed outside the cell during xylem development that comprises the largest amount of biomass available on earth. Currently the use of plant biomass has awakened large interest as a feedstock for the production of second generation biofuels. Nevertheless, there are still important aspects of the secondary cell wall synthesis and the xylem formation that need to be understood in order to make an efficient use of the available biomass. One of these aspects is the relationship between the plant cytoskeleton and the cell wall orientation. This study provided evidence about the involvement of ROP7 together with RIC2 and RIC4 interactors in the patterning of the cell wall during xylem development. Another aspect is the trafficking of the CESA proteins and the cell wall components from their places of synthesis to the plasma membrane. This study also suggests that RABA6A might be involved in the trafficking or recycling of some of these components required during cell wall assembly. Finally, it is necessary to properly deconstruct the tight linkage of lignin with the other components that confers recalcitrance to the biomass. In this study, it is suggested that members of the phytocyanin family might be involved in lignin assembly and that their manipulation could potentially change the characteristics of that linkage. The findings of this research could provide new insight into the process of secondary cell wall synthesis and xylem development.

The anatomy of bifurcations in trees requires further scientific investigation as the current anatomical model for them is logically flawed. The provision of a better model will assist in scientific studies of woody plants, the risk assessment of junctions in mature trees and provide bio-inspiration for Y-shaped joints in composite materials. In this study, the xylem formed in the central axis of a hazel (Corylus avellana L.) bifurcation is shown to provide a disproportionately greater amount of its tensile strength. CT scanning identified that this centrally-placed xylem was 28.1% denser, with 63% less vessels formed in this tissue, such vessels being 50.5% of the diameter and 32.5% of the length of those formed in adjacent stem tissues. The wood grain pattern at the bifurcation apices were 22 times more tortuous, forming interlocking patterns that acted to resist tensile forces by requiring the extraction or breaking of wood fibres along their length (the axial tensile strength of wood). Subsequent tests confirmed that this conferred more than 100% additional tensile strength to these specialised xylem tissues. These findings provided the basis of a novel anatomical model for bifurcations in woody plants. Further to this, the effects of several factors upon junction strength and biomechanical behaviour were assessed in bifurcations of hazel, identifying the weakening effect of bark inclusions and three types of artificial modification as well as differences in wind-induced movement between bifurcation types. This study concludes that further investigations of bifurcations in a wider range of woody plants and observations of the developmental stages of the interlocking wood grain patterns found at bifurcations would usefully add to existing knowledge.

Plant cell walls are dynamic and responsive structures rather than rigid cages. Disruption of cell wall integrity prevents cell expansion: for example, inhibition of cellulose biosynthesis with isoxaben rapidly reduces root elongation. This is not a passive consequence of mechanical failure but an active response regulated by cell wall integrity (CWI) sensing pathway. Interestingly, the plant response to pathogen-associated molecular patterns (PAMPs) like flagellin shares many similarities with the CWI pathway response; such as the production of reactive oxygen species (ROS) and lignin. While root elongation is also reduced by flagellin, microarrays show that the two treatments lead to a very different expression profile. Little is known about the mechanisms and components of the CWI pathway. Here we show that inhibiting the biosynthesis of 1-aminocyclopropane-1-carboxylic acid (ACC), the immediate precursor of the plant hormones ethylene, restores elongation in roots treated with isoxaben but exacerbates the extent of the cell wall damage. Unexpectedly, ethylene itself is not required for the process. Further experiments show that the response to flg22 in roots also requires this putative signalling pathway. Auxin appears to work downstream of ACC since inhibiting auxin activity prevents growth reduction in roots treated with ACC, isoxaben or flg22We have also identified a receptor-like kinase (SRK) which is required for growth repression in root cells that are experiencing cell wall damage. Expression of this gene is rapidly and transiently induced by isoxaben. SRK (S-locus RLK) is part of a highly expanded locus of RLKs related to self-incompatibility proteins in Brassica. However, while other genes of this family are induced by cell wall stress, only SRK mutants are insensitive to acute cell wall damage. Further characterisation of the SRK is under way to confirm its role in the CWI pathway.