This collection contains the Doctoral and Masters by Research theses produced within the department.

Recent Submissions

  • The Social System, Behaviour and Communication of the Golden Monkey (Cercopithecus mitis kandti)

    Fletcher, Alison; Wiper, Susan M. (University of Chester, 2020-12)
    Forest guenons live in polygynous groups where males disperse on reaching sexual maturity and females remain within their natal group for life. During the mating season, the resident male regularly faces reproductive competition from extra-group males leading to extreme male-male competition for access to females. The golden monkey (Cercopithecus mitis kandti) is a little-understood, endangered guenon endemic to the Virunga Massif and Gishwati-Mukura National Park (Rwanda), known to live in large groups. The aim of this study was to provide the first behavioural account of this species and to describe and quantify its social system and communication. Behavioural and spatial data were collected five days a week over 15 months, using focal, instantaneous point samples and ad libitum sampling, from the habituated Kabatwa group in the Volcanoes National Park. A total of 31 adult males were individually identified within the home-range, and categorised as resident (n=11), transient (n=4), influx (n=10) or non-resident (n=6). Elo-ratings showeda consistently stable, tolerant, egalitarian hierarchy in resident males, who displayed low levels of non-contact aggression with more severe agonism directed towards extra-group males. Social network analysis revealed closer spatial relationships between resident males during the non-mating season in the forest and consistent agonistic networks. The mating season, defined through behavioural observations and estimating conception based on birth dates, extended over 5 months and females were observed copulating outside their conception window. Males followed females and both sexes mated with several partners over the season; the use of gestural displays were common in this reproductive context, as well as in agonistic contexts. The highly seasonal births coincided with bamboo shooting season when the group spent the majority of time in closed bamboo, with increased ground feeding; ground-feeding was frequent in this population (28% overall), and also reflected foraging for potatoes in agricultural land adjacent to the forest. The group spent about 50% of their time feeding; bamboo plant parts constituted 65.3% of their foraging effort throughout the year rising to 81.4% on bamboo shoots alone when they were available. Males exhibited a wide variety of sex-specific calls in different contexts; with some related to dominance rank. Vocalisations were examined through GLMMs and these were often different in form or context compared with other guenons, notably the single and double boom, nasal scream and male grunt. In summary, golden monkeys observed in this study had a multi-male, multi-female social organisation; both sexes were promiscuous during the mating season, and births were highly seasonal. Resident males were tolerant of each other, exhibited a stable egalitarian hierarchy with a broad communication repertoire including sex specific calls and gestures. Discussion focuses on comparison with other guenons, the unusually large group size and the unique, all-year-round, multi-male society observed in this golden monkey group. Further research is warranted on other groups, to explore female social structure and relationships, behavioural development, and to establish an understanding of life history strategies.
  • Application of genetic techniques to conservation of the Critically Endangered Grenada Dove Leptotila wellsi

    Geary, Matt; Peters, Catherine (University of Chester, 2022-09)
    The Grenada Dove Leptotila wellsi is a Critically Endangered species endemic to the island of Grenada. It exists in two geographically isolated populations across the island. As an endemic on a small island with a limited and decreasing population, this species is at risk from genetic deterioration. Particular risks include inbreeding depression and accelerated loss of genetic diversity resulting from ongoing habitat fragmentation and population isolation. The work reported in this thesis aimed to provide the first genetic data for the Grenada Dove, assess its genetic status and determine what conservation management recommendations can be made to help ensure its long-term survival. A systematic literature review revealed geographical bias in how genetic approaches have been applied to the conservation of island bird species, under-representation of threatened species and highlighted a gap between genetic research and active conservation management. A protocol for obtaining usable genetic material from moulted plumulaceous feather samples was developed and showed that samples collected non-invasively in the field, that were kept in non-optimal conditions for deoxyribonucleic acid (DNA) extraction, can be used effectively to sequence informative regions of mitochondrial DNA (mtDNA) for genetic analysis. The evolutionary and life history of the Grenada Dove were investigated by estimating its phylogenetic placement and using phylogenetic comparative methods for estimating unknown life history traits. The Grey-Chested Dove Leptotila cassinii was identified as the species with which the Grenada Dove shares the most recent common ancestor, with an estimated divergence of approximately 2.53 million years ago. Life history trait values were predicted for the Grenada Dove and suggest this species will be slow to recover after a major population decline. The mitochondrial genetic diversity of Grenada Dove populations was assessed for the two areas of occupancy. Two haplotypes were identified with one haplotype unique to the population in the West. Selective neutrality tests Fu’s Fs=0.78 and Tajima’s D=0.83 were positive and not significant, with an FST value = 0.71 suggesting a marked genetic divergence between the two populations. This study showed low mitochondrial genetic diversity, a non-expanding population and iii | iii clear evidence for genetically isolated populations. Population viability analysis (PVA) was used to evaluate extinction risk and the potential for conservation management for the two populations of the Grenada Dove. This PVA identified that loss of forest habitat to commercial development is likely to have the biggest impact on extant populations and that conservation management to increase productivity is likely be the most effective conservation strategy. This thesis contributes novel information regarding evolutionary history, life history, population genetics and future population trajectories to inform long-term conservation actions for the Critically Endangered Grenada Dove.
  • The status of cetaceans in Trinidad and Tobago

    Nelson, Howard P.; Oliver, Simon; Lawrence, Andrew; Naranjit, Alёsha R. (University of Chester, 2021-12-14)
    Marine ecosystems provide vital resources for humans and habitat for a vast number of other species. However, these ecosystems are being extensively degraded by human activities, and without effective management, will be unable to provide for humans or other species. In Trinidad and Tobago, as in other countries, one of the major obstacles to effective environmental management is a lack of appropriate information. This thesis aims to enhance the management of cetaceans in Trinidad and Tobago by providing much needed information on cetacean species within the country’s EEZ (Exclusive Economic Zone). Cetacean species diversity and distribution in Trinidad and Tobago is examined through the collation and verification of records from multiple data sources including systematic surveys, reports, skeletal remains, strandings and social media posts. This research provides the first comprehensive overview of the knowledge of cetacean species around Trinidad and Tobago through a verified cetacean species list, estimation of species diversity from local data and maps of species occurrence records. Species Distribution Models were developed for four species (Humpback Whales, Bottlenose Dolphins, Atlantic Spotted Dolphins and Rough-toothed Dolphins) which provide the first estimates of cetacean species distribution across the Trinidad and Tobago EEZ and identify possible cetacean species richness hotspots around the country. Fisher interviews were used to examine the threat posed by artisanal fisheries within the Trinidad and Tobago EEZ and provide the first comprehensive information on cetacean-fisheries interactions for the country. Hunting, depredation (a behaviour in which foraging cetaceans damage or remove catch or bait from fishing gear) and bycatch were all reported in the area. Bycatch was identified as the greatest threat posed by artisanal fisheries locally and analysis indicated that fishing with gillnets or fishing on the south coast of Trinidad with any gear increased the risk of bycatch. The findings of this study were used to recommend actions to improve cetacean management in Trinidad and Tobago, including the creation of a cetacean data management system, the development of a cetacean research programme to guide future research and mitigation of anthropogenic threats on the continental shelf, including cetacean bycatch in artisanal fisheries.
  • An Examination of the Social and Physiological Experience of Captive Livingstone’s Fruit Bats (Pteropus livingstonii)

    Stanley, Christina; Smith, Tessa; Hosie, Lottie; Edwards, Morgan J. (University of Chester, 2022-02-01)
    This thesis presents a series of empirical studies designed to quantify the complex social and physiological experiences of individuals within the captive population of a critically endangered bat species, the Livingstone’s fruit bat (Pteropus livingstonii). The ultimate goal of this work was to apply leading-edge methodologies and technology to gain novel, evidence-based insights into the behaviour and welfare of this species in captivity. This work has not only informed the captive management of P. livingstonii, but has also developed techniques that can be applied to maximise the captive welfare of a range of other species. A brief summary, explaining how each chapter is embedded within the overall thesis and summarising its major findings, precedes each chapter. Chapter One, the introductory chapter, will start by evaluating our current understanding of the natural history and behavioural ecology of P. livingstonii, with a focus on captive behaviour. The following sections of this chapter will then provide necessary background information to the methodologies applied in subsequent data chapters, including social network analysis, space use assessment, hormone analysis and radio-frequency identification technology. The introductory chapter is intended to provide the reader with sufficient scientific context to interpret the results of each data chapter. Chapter Two outlines the implementation of social network analysis to characterise individual social experiences in the largest captive population of P. livingstonii, housed at Jersey Zoo. Variation in network complexity and significant individual variable-based assortment is identified in this chapter. Chapter Three presents principal component analysis as a novel compliment to traditional enclosure use assessment methodologies, quantifying the individual spatial preferences of P. livingstonii. This chapter also quantifies the relationship between high-value resource location within the enclosure at Jersey Zoo and population-level space use. Chapter Four outlines the validation and application of an enzyme immunoassay to non-invasively measure faecal cortisol in the P. livingstonii population. This chapter examines the relationship between cortisol titres, individual social roles and behavioural frequencies performed by individuals in the captive population. We find that males, older individuals and lactating females have higher concentrations of cortisol than non-lactating females and younger individuals and that social roles related to conspecific affiliation were linked to decreased cortisol titres. Lastly, Chapter Five demonstrates the application of unique radio-frequency identification technology to autonomously collect individual locational data. The resulting dataset was then utilised to interrogate the foraging network displayed by P. livingstonii and Pteropus rodricensis (a cohabitating heterospecific) populations housed at Jersey Zoo, elucidating the relationship between individual bat characteristics and social foraging patterns. Finally, the discussion chapter evaluates the significance of the main findings of each chapter of this thesis, highlighting the wider applicability of results and methodologies to the assessment of captive animal welfare. This section also critically discusses recent challenges to hypothesis testing in the field of animal social network analysis, to evaluate the validity of methods utilised throughout this thesis. Finally, future research directives leading on from this work which may provide further benefit to the management of captive populations are proposed.
  • Open Carboniferous Limestone pavement grike microclimates in Great Britain and Ireland: understanding the present to inform the future

    Burek, Cynthia; Hosie, Lottie; Geary, Matt; York, Peter, J. (University of ChesterUniversity of Chester, 2020-04)
    Limestone pavements are a distinctive and irreplaceable geodiversity feature, in which are found crevices known as grikes. These grikes provide a distinct microclimate conferring a more stable temperature, higher relative humidity, lower light intensity and lower air speed than can be found in the regional climate. This stability of microclimate has resulted in an equally distinctive community of flora and fauna, adapted to a forest floor but found in an often otherwise barren landscape. This thesis documents the long-term study of the properties of the limestone pavement grike in order to identify the extent to which the microclimate may sustain its distinctive biodiversity, to provide recommendations for future research which may lead to more effective management. Over a five-year study, recordings of temperature, relative humidity, light intensity and samples of invertebrate biodiversity were collected from five limestone pavements situated in the Yorkshire Dales and Cumbria in Great Britain, and The Burren in the Republic of Ireland. An extensive description of the grike microclimate was undertaken using the data collected to understand the extent of the microclimate stability of the grike and the conditions for variation in the grike microclimate. Further insights into the grike microclimate were gained through simulation techniques more commonly used in engineering, to explore the effects of air flowing over a grike, the light from the sun entering the grike and regression analysis to simulate the temperature within the grike in the present and projected for the future. This study has indicated that although the whole of the grike confers a degree of microclimatic stability, it is made up of a less stable upper zone and a more stable lower zone. The instability of the upper zone is hypothesised to result from the extent to which the majority of light and external air can enter the grike, whereas the stability of the lower zone may be governed by the thermal stability of the limestone surrounding it. Based on this zonation and the projections for the grike temperature, it is hypothesised that climate change will have the most substantial effects in the upper grike zone where species obligated to this area could be most heavily impacted. This study recommends a range of areas in which research may be employed so that the limestone pavement habitat may be successfully managed in Great Britain and the Republic of Ireland.
  • The Functionality of “Ogi” – a fermented cereal gruel made in Nigeria, in the Management of Gastrointestinal Disease

    Pickles, Neil; Weili, Li; Olayanju, Adetokunbo T. (University of ChesterUniversity of Chester, 2019-04)
    Fermentation is an ancient food processing technique which has over the years had significant impact on food availability, production, economy and health. Fermented corn, ‘ogi’, is a popular meal in South and West African countries and is also traditionally administered to people, especially children, during the incidence of diarrhoea as it is believed to enhance gut health. Various authors have supported the advantageous health functions of fermented corn but have focussed on the possible health benefits that may be derived from the action of the fermentation organisms by investigating their probiotic potentials. Furthermore, in vivo studies have investigated effective functionality of fermented foods and where studies have suggested positive effect of the fermented food intervention, the component of the complex food matrix that may be responsible is often unknown. Though hypothesised, there has been little information on the possible effects of the end products of the fermentation on gut health. Therefore, this thesis aimed to explore the functionality potentials for ‘ogi’, to enhance gut health by investigating the mechanisms through which it may be able to confer the health benefits when consumed. An independent meta-analysis was undertaken to explore and review the analysis of the effectiveness of fermented foods to significantly reduce the duration of diarrhoea. The first experimental study was a comparison between spontaneously fermented vs controlled method of ‘ogi’ production with the aim to explore the possibility of achieving similar end products. The probiotic potential of fermentation organisms and antimicrobial effect of fermentation organisms against E. coli were also investigated. Colonic short chain fatty acids (SCFAs) are known to enhance immune function in the gut. The second experimental study explored the production of SCFAs in fermented corn with the theory that fermented corn may be a dietary source of SCFA and may produce a comparable effect in the gut as the colonic SCFA. It is established that one of the functions of endogenously synthesised nitric oxide (NO) in the body is to enhance immune functions. Therefore, the potential for ‘ogi’ to enhance immune response in the gut by being a dietary source of Nitric Oxide (NO) was explored in the third experimental study. The outcomes of this thesis suggest that it may not be possible to mimic the exact spontaneous fermentation process in a controlled setting. Weissella confuse, Pediococcus pentosaceus and Saccharomyces cerevisiae were the lactic acid bacteria (LAB) and yeast isolated from spontaneously fermented corn using 16S rRNA sequencing. The isolated organisms along with Lactobacillus plantarum were used as starter culture for controlled fermentation. There was a significant difference between the end products of both fermentations. All organisms except W. confuse showed probiotic potential. Acetate was produced during both fermentations but butyrate was produced during spontaneous fermentation only. There was however higher concentration of NO in controlled fermented corn than spontaneous fermentation with nitrate values of 30.54 µM and 23.21 µM and nitrite values of 17.50 µM and 10.11 µM respectively. These suggest that fermented corn may have probiotic potential and may be able to further enhance immune health in the gut by being a dietary source of SCFAs and NO.
  • An investigation of canine mesenchymal stem cells and their secretome in the context of spinal cord injury

    Johnson, Eustace; Wood, Chelsea R. (University of Chester, 2020-05-26)
    Spinal cord injury (SCI) is a condition that has devastating effects on both humans and animals alike. Damage inflicted causes loss of neural tissue and secondary inflammatory mechanisms produce an inhibitory environment that results in partial or complete loss of motor and sensory functions. Additionally, SCI can cause multisystem issues such as organ failures, infections, muscle atrophy and decrease in mental health. Coupled with emotional and financial burdens, these effects can reduce quality of life. Mesenchymal Stem Cells (MSC) are known to have immunomodulatory, angiogenic and paracrine activity, all of which are beneficial to wound healing following SCI. Pre-clinical studies have shown encouraging results of MSC therapy for SCI, however replication of results has been difficult to achieve in the clinic. Dogs also suffer from SCI and show the same heterogenous nature and pathophysiology of SCI as humans. This provides a good potential clinical model for MSC therapies for SCI, as well as providing benefit in the veterinary clinic. Therefore, the overall aim of this study was to assess if canine MSC (cMSC) and cMSC secretome (conditioned medium; CM) could potentially be used for treatment of SCI in veterinary clinics, simultaneously providing model data that could be translated into the human clinic. It was first required to confirm efficacy of cMSC when used to treat other conditions in dogs, such as arthritis, along with safety of autologous transplantation. Characterisation of both cMSC phenotype and paracrine (angiogenic and neurogenic) activity was confirmed using ISCT criteria and the established cell lines EA.hy926 and SH-SY5Y. Further examination showed that exposure to certain elements of the injured spinal cord, such as CSPG which are found within the inhibitory glial scar, exerted some effects on cMSC and cMSC angiogenic and neurogenic paracrine activity. To finish, the study aimed to assess the effect of cMSC CM on an ex vivo model of the spinal cord, a multicellular environment and it was found that cMSC CM increased astrocyte reactivity but reduced neuronal maturation and growth, suggesting that cMSC paracrine activity depends in part on the spinal cord microenvironment. Overall, this study has shown that cMSC, in particular cMSC CM, could be used as complete or partial treatment for SCI in dogs.
  • Changes in selective biomarkers after transurethral resection of the bladder tumour (TURBT), and their association with Non-muscle invasive bladder cancer (NMIBC) recurrence and progression

    Ella-Twongiis, Peter (University of ChesterUniversity of Chester, 2019-10-01)
    Introduction Bladder Cancer (BC) is the 10th most common cancer in the UK, with about 10,000 new cases annually. It affects more men than women (ratio 3:1). Major risk factors include tobacco, chemical carcinogens, schistosomiasis infection and age. About 75-85% of BC are non-muscle invasive (NMIBC), which is associated with high recurrence and progression rates (50-60% within 7-10 years). Currently, diagnosis, treatment and management of BC is via clinical procedures such as transurethral resection of the bladder tumour (TURBT) and endoscopy. Concerning laboratory investigations, there are no routine biomarkers currently available for identifying BC patients at increased risk of developing recurrence and progression. By monitoring changes in selective biomarkers post-TURBT, any sustained changes may be a predictor of cancer recurrence or progression. The main-focus of this research study was to evaluate changes in selective novel biomarkers and their association with recurrence and progression in BC. Materials & Methods In this research, 40 patients (n=40) scheduled for TURBT at the Wrexham Maelor Hospital, North Wales were recruited after written informed consent. Ethical approval for the project was granted via IRAS (REC4: 14/WA/0033). Venous blood samples were taken at baseline (pre-operative) and following TURBT surgery at 1, 3 and 6 months post-operatively. Bladder tumour samples were also taken during TURBT according to standard procedure. Selective biomarkers to assess inflammation, angiogenesis and tumour growth, were measured using commercially available ELISA and BioPlex multiplex assay kits. Tissue immunoreactivity of novel biomarkers were also assessed in BC tissues using immunohistochemistry, with clinical outcome measures being recorded for all patients. Results Significant increases in serum Cluster of differentiation 31 (CD31) (p=0.003) and Stem Cell Factor (SCF) (p=0.032) concentration, as well as trends of increasing concentration of serum basic Fibroblast Growth Factor (bFGF) (p=0.14), Vascular Endothelial Growth Factor Receptor-1 and 2 (VEGFR-1) (p=0.15), VEGFR-2 (p=0.15) and Follistatin (p=0.40) were observed in BC patients up to 6 months post-operative. There were also significant decreases in serum Macrophage Inflammatory Protein -2 (MIP-2) (p=0.001), Platelet Derived Growth Factor (PDGF) (p=0.012), Matrix Metalloproteinase-9 (MMP-9) (p=0.002) and Vascular Endothelial Growth Factor C (VEGF-C) (p=0.04) serum concentration. Trends of decreasing concentration in MMP-2 (p=0.79), MMP-3 (p=0.15), interleukin-6 (IL-6) (p=0.26), interleukin-8 (IL-8) (p=0.15) and tumour necrosis factor-α (TNF-α) (p=0.69) were observed in BC patients up to 6 months post-operative. There was significant immunoreactivity of CD31 (p< 0.001), CD34 (p< 0.001), Human epidermal growth factor receptor-2 (HER-2) (p=0.032), S100P (p< 0.001), Cyclooxygenase-2 (COX-2) (p< 0.001), VEGFR-3 (p< 0.001), SOX-2 (p< 0.001) and thrombomodulin (p=0.010) in bladder tumours. Although recurrence was significantly associated with cancer grade, there was no association with antibody immunoreactivity. Conclusion Findings from the present study may indicate an alternative approach in the monitoring and management of patients with BC. It is proposed that by allowing urological surgeons access to laboratory markers such as MIP-2, MMP-9, PDGF, SCF, HER-2, Thrombomodulin and CD31 (biomarker profile), potentially, in the future, these biomarkers may be used in addition to, or in combination with, currently used scoring systems to predict cancer recurrence and progression. However, verification and validation of these biomarkers are needed using larger cohorts.
  • A Geoconservation perspective on the trace fossil record associated with the end – Ordovician mass extinction and glaciation in the Welsh Basin

    Burek, Cynthia; Hosie, Lottie; Nicholls, Keith H. (University of Chester, 2019-03-24)
    In this thesis I have illustrated the value of our geological heritage and geodiversity by focussing on a particular detailed aspect of the geological and palaeontological record, i.e. the trace fossil record associated with the end Ordovician (Hirnantian) global glaciation and extinction episode. The major elements of this work that are new are: • a significantly improved understanding of the nature of the soft sediment deformation, and in particular the role of “debrites” as basal landslide decollements in the Lower Palaozic Llangrannog rock succession of West Wales, • a much more detailed description of the trace fossil ichnocoenose present in the Llangrannog succession than has previously been published • an improved understanding of the nature of the ecological perturbation associated with the Hirnantian (Late Ordovician) Glacial “ice-house”, and the apparent role of an opportunistic soft body fauna in filling ecological niches vacated as a consequence of the associated extinction. • Considerable thought has been given to the question of how to value abiotic nature, and it is argued that the methods of conservation valuation associated with “Geosystem services” and in particular “Natural Capital” hold considerable potential for the Geoconservation community to engage with the public and with policy makers. • As a direct result of this research, two formal proposals have been put forward for new RIGS sites, together with a new geological SSSI.
  • The Use of Qualitative Risk Analysis Methods to Facilitate Decision Making in the Management of Health and Welfare in Wildlife

    Hill, Sonya; Smith, Tessa; Hartley, Matt (University of Chester, 2018-10-08)
    This thesis is composed of a series of papers, all of which have been published in peer reviewed publications. The papers use the recognised process of qualitative risk assessment in a range of scenarios in the field of wildlife health and welfare in both in situ and ex situ environments. Chapter 1 discusses the challenges faced regarding availability of empirical data in field of wildlife and zoological health and welfare and justifies the exploration of techniques to assist with decision making. The development of risk analysis and its integration with risk management and risk communication to become risk assessment is described before being put into the specific context of wildlife and zoological disease. Chapters 2 and 3 consider two scenarios where disease risk assessment is well established as a tool, importation across national borders and in conservation interventions. Chapter 2 develops the standard import risk assessment approach to include multiple species and multiple diseases. Chapter 3 reviews developments made over the last 25 years and proposes best practice approaches to implement. Chapter 4 describes how the risk assessments formulated as described in Chapter 3 are used for licensing purposes emphasising the importance of risk management and communication. This theme is continued in Chapter 6 where the integration of risk assessment and evidence based decision making is considered in the broad context of a strategic approach to wildlife health bringing together the outcomes and processes described in Chapters 2, 3, 4 and 5. The papers in Chapters 2,5 and 8 are focused on how risk analysis aids in development of disease control approaches and policy. The evidence base is composed primarily of peer-reviewed literature supported by expert review of the finalised assessment. Chapter 7 uses risk assessment in an applied scenario, taking the recognised process and modifying it to structure an active disease investigation demonstrating the versatility of the technique. Chapter 9 takes this a step further by again adapting the methodology which, has historically been used primarily for infectious diseases, to consider reproduction and assess risks to welfare rather than purely health. The paper in Chapter 9 builds on the methodology by combining existing peer-reviewed literature with data collected specifically for the purpose of feeding into the assessment and utilising a stakeholder and expert opinion elicitation workshop to obtain data too. These process are proposed and described in Chapter 3. The final chapter critically reviews risk assessment, highlighting three key areas of potential weakness and proposing approaches to address these criticisms. The value of the approach in wildlife and zoological health and welfare as demonstrated by this series of papers is described
  • The genetics and evolution of the critically endangered Trinidad Piping Guan Pipile pipile, synonym Aburria pipile.

    McDowall, Ian; Hosie, Charlotte A.; Grass, Amelia (University of Chester, 2018-02)
    The Trinidad Piping Guan, Pipile pipile synonym Aburria pipile (Jaquin, 1784) is the only endemic Cracid on the island of Trinidad. The species is currently listed as Critically Endangered and is considered to be in ‘on-going decline’ by the IUCN, BirdLife International and Cracid Specialist Group. This study aims to examine aspects of genetic variation and the evolution of the mitochondrial genome in the Trinidad Piping Guan utilising, for the first time, samples collected from individuals in the wild and reference specimens of the genus Pipile sourced from museum collections. In this study the complete mitochondrial genome of the Trinidad Piping Guan was sequenced for the first time. Analysis of intra-specific variation of wild Trinidad Piping Guan individuals using single nucleotide polymorphisms demonstrates extremely limited variation within the genes of the mitochondrial genome and nuclear gene intron sequences. Limited variation within this population is consistent with both historical and contemporary contractions of populations within a restricted island system, which may have serious implications for the future of this species in terms of both genetic diversity and conservation management. Phylogenetic analysis of the complete mitochondrial genome of the Trinidad Piping Guan enabled placement of the genus Pipile within the Galliforme evolutionary tree for the first time, and subsequently places the genus within the broader context of the Aves class. Mito-genomic analysis confirms that the Cracids are one of the basal Galliforme clades, and sister taxa to the Megapodidae. Phylogenetic placement of the Pipile genus is basal to that of the Crax species within the Cracidae family, indicative of an earlier evolutionary origin of the Piping Guans. The inclusion of the Trinidad Piping Guan, in the avian evolutionary tree using the whole mitochondrial genomes expands the current genetic phylogeny of the Cracid family, yielding a better understanding of evolutionary relationships among the Galliforme order and the diversification of modern avian lineages. This study has established novel molecular techniques for the analysis of mitochondrial DNA in historical specimens of the genus Pipile from museum reference collections. The analysis of inter-specific relationships within the genus Pipile has clarified the evolutionary and biogeographic relationships between the Piping Guan species. Additionally, the Trinidad Piping Guan is genetically defined for the first time as an evolutionarily significant unit, which represents a unique evolutionary pathway within this important genus in a closed island system on the island of Trinidad.
  • Production of DNA aptamers with specificity for bacterial food pathogens

    Bonwick, Graham A.; Drasbek, Mette R.; Young, Niall; Smith, Christopher; McDowall, Ian; Kärkkäinen, Riikka M. (University of Chester, 2012-09)
    Aptamers are biomolecular ligands composed of nucleic acids. They can be selected to bind specifically to a range of target molecules and subsequently exploited in a fashion analogous to more traditional biomolecules such as antibodies. In this study a method for selecting new aptamers which specifically bind whole live bacterial cells is described. A non-pathogenic strain of Escherichia coli K12 was used to develop the method. A DNA library containing 100 bases long random nucleotide sequences was produced and the aptamer selection process was repeated nine times. An enzyme-linked technique was first used to detect bound aptamers thereafter fluorimetry and fluorescence microscopy methods were used for the detection. The aptamers were cloned and sequenced and the cloned aptamers produced with fluorescent labels. The E. coli K12-binding aptamers were used to demonstrate the detection of the bacterial cells in a complex food matrix, namely probiotic yogurt, by using fluorescence based detection method. The aptamer selection method with some modifications was also used to select aptamers with specificity for the food pathogens E. coli O157, Listeria monocytogenes, L. innocua, S. typhimurium and S. enteritidis. The aptamers against E. coli O157 and S. typhimurium were cloned and the sequences and the binding properties of these aptamers were analysed. The use of E. coli K12 as a target organism and the aptamer sequences presented in this study, have not previously been published in scientific literature. This is also the first report where the aptamers have been used in detection of live bacterial cells in yogurt.
  • The Role of Anaerobic Digestion in Achieving Soil Conservation and Sustainable Agriculture for Sustainable Development in the UK

    Burek, Cynthia V.; Bonwick, Graham A.; Alexander, Roy; Duruiheoma, Franklin I. (University of Chester, 2015-12)
    The subjection of soils to degradation directly and indirectly from rising world food demand and resultant intensified agricultural production, population growth, and climate change, demand that soils are better protected. The role of AD in addressing this challenge is examined using a pragmatic research paradigm and the questions: How can we raise awareness of AD in the UK? What factors motivate and hinder farmers towards adopting improved technology and sustainable agricultural practises? What is the perception of farmers about soils? To what extent does sustainable agriculture incorporate soil conservation in theory and practice? What role can legislation and policies play in AD adoption in the UK? The research was in two phases; qualitative and quantitative. The qualitative phase involved interviews with 21 AD stakeholder in the UK using electronic mail. The stakeholders who were divided into groups according to their expertise, were interviewed to explore their views on the areas of focus in the UK strategy and action plan regarding raising awareness of the technology, soil conservation, sustainable agriculture and sustainable development. Thematic analysis of interview data was carried out using MAXQDA 11 statistical software. The quantitative phase involved an online survey of 283 UK farmers aided by Yellow Pages directory for UK, Natural England directory, Twitter and electronic mail. Using SPSS 22.0 statistical software, the Chi square test was used to check for relationships between the variables measured at 95% confidence level (p<.05). Relationship strength was measured by means of Cramer’s V and Phi values. Answers to the 1st research question showed that: aligning AD with sustainable development goals, community AD and localism, small AD plants, provision of an available market for AD products, building UK skills and diversifying biogas use from AD are positive options for raising awareness of AD. Response to 2nd research question revealed: significant relationships between interests in agricultural technology and gender, level of education, and farm size; between knowledge of what AD is and gender, level of education and farm size; between interest in AD and age; between willingness to invest in AD if it improved soil properties and farm ownership; and between organic farming practice and age, farm type and farm size. Responding to the third research question, farmers’ describe soils in abstract, scientific, physical attribute and functional terms; awareness of soil benefits other than crop production was significantly related to age, and farm ownership; educational level was significantly related to familiarity with soil conservation, and opinion on whether soil should be protected like other natural resources. Findings regarding the 4th and 5th research questions showed: limited understanding of soil matters as a key challenge that has restricted the priority given to soil conservation, while level of education, knowledge of soil conservation and sustainable development and understanding of sustainable agriculture were also identified as influencing factors; digestate from AD is the main benefit viewed to contribute to soil conservation; finance, policy and legislation, low awareness and understanding, lack of feedstock and market, land use conflict and inefficiency of AD plants were identified as barriers to AD in the UK; promoting AD, providing finance, minimizing bureaucracy and simplification of AD systems are options for promoting AD adoption. This thesis also documents the implications of these findings for knowledge, policy and practice, and based on these recommendations are made, some of which are: better engagement of farmers in policy development for AD and soil management; use of small AD plants, demonstration, networking and training for AD adoption; promote soil conservation in theory and practice; and provision of enhanced support for owners, potential investors and farmers through incentives, simplified planning approval process, and available market for AD product.
  • Investigating Non-invasive Measures of Stress in Ornamental Fish

    Wolfenden, David C. C. (University of Chester, 2014)
    The transport of ornamental marine fish may cause stress, which to date has been the subject of limited research. The present study aimed to characterise the behavioural and physiological responses to simulated transport stress in the common clownfish Amphiprion ocellaris (Cuvier, 1830) with the additional goal of validating non-invasive measures of water cortisol in a marine teleost for the first time. Behaviour and physiology of the animals was measured at different stages of transport (from initial capture and handling up to 72 hours transport time) and water quality measurements were taken from the transport water at key sampling points. In a second experiment biological filtration materials (“Bioballs” with denitrifying bacteria) were added to the transport bag to determine if stress was reduced when water quality was improved. The results of the study suggest that capture, handling and transport are stressful for clownfish, and the stress response appears to peak between 24 and 48 hours after the onset of the stressor. Water-borne cortisol was found to be a valid alternative to invasive methods of sampling, although only an average of 53% cortisol was recovered from sea water. Although handling and confinement appeared to be highly significant factors in eliciting the stress response water quality measurements revealed that fish are temporarily subjected to relatively high concentrations of ammonia as transport time increased, which may contribute to long-term effects on the health of the animals. This was reflected in an increased latency to feed and reduced social behaviours in fish transported for 24 hours or longer. Improving water quality did reduce the concentration of ammonia present; however, fish still exhibited elevated cortisol excretion suggesting that water quality is not the primary stressor associated with transport. Thus, the duration of transport should be restricted to a maximum of 24 hours to reduce the stress associated with this practice. A separate study investigated the potential for beauty treatment ‘fish spas’ to elicit stress in the freshwater cyprinid fish Garra rufa (Heckel, 1843). Water cortisol was measured non-invasively to determine if stress was reduced through the provision of environmental enrichment / furnishings, and whether stocking density influenced stress. Water quality was monitored to determine the effects of stocking density on environmental parameters (pH, ammonia, nitrite and nitrate). Finally, the effect of ii human hands being placed into the aquarium was investigated, to determine whether this influenced stress. Three hundred G. rufa were used in total, with groups being allocated randomly to one of four treatment groups: OP/B (optimum stocking density / barren tank – i.e. no enrichment); OP/E (optimum stocking density / enriched tank); OS/B (overstocked / barren tank); and OS/E (overstocked / enriched tank). Human hands were placed in each tank, and water samples were collected before and after for measurement of cortisol by ELISA, and to determine water quality parameters. The results revealed that overstocking tanks with G. rufa produced relatively higher baseline cortisol levels, suggesting that stocking density may have a significant effect on stress levels. The addition of furnishings into the aquarium did not reduce baseline cortisol levels in the fish prior to the introduction of human hands. However, fish maintained under enriched conditions exhibited a greater cortisol response when compared to individuals in barren tanks. It is hypothesised that the provision of enrichment reduces the available space for fish following the introduction of human hands, thereby increasing stress. Further studies are required to attempt to determine the effect of enrichment based upon the results of the present study. Feeding on human hands resulted in an elevated cortisol response from three out of the four treatment groups (with the exception of OP/B), with the results suggesting that either 1) the lower (i.e. optimal) stocking density and lack of enrichment in holding tanks is preferable for G. rufa fish welfare, or 2) the elevated cortisol reflected a response to a rewarding stimulus and is linked to increased foraging. Overall, the results of these studies have shown that water cortisol measurements are a valid means of assessing physiological stress in two species of fish in different contexts. This negates the need for invasive sampling and is an important refinement to existing protocols where fish are killed for plasma or whole body samples. The results also highlight the welfare impacts of transport and overstocking of ornamental fish providing valuable evidence that may be relevant to improving the husbandry and guidelines with respect to the ornamental fish industry.
  • Investigating morphometrics, movement and oviposition in the Lissotriton and Triturus newts

    Johnson, Lisa (University of Chester, 2015-09)
    This thesis focuses on the UK pond newts, the smaller bodied species known as Lissotriton newts and the larger Triturus. The primary aims were to identify and address gaps in the current Tritus/Lissotriton literature; to provide a more complete understanding of this group as many assumptions about morphology and physiology exist untested, for example that larger/fatter females will lay more eggs. Specifically for Lissotriton helveticus, many assumptions are based on the similarly sized Lissotriton vulgaris, potentially missing any species specific differences. A further focus of the work was to provide a clearer view over the whole breeding season; using measures of condition over a season and egg-laying.
  • Physiological and behavioural measures of stress in domestic horses

    Young, Tamsin (University of Liverpool (Chester College of Higher Education), 2011-09)
    The welfare of domestic horses has been scrutinised by the scientific community in recent years. Traditional riding and stable management practices have been recognised to be at odds with the physical and behavioural adaptations of the horse. There is, therefore, a growing need to understand how modern horse management can impact on horse welfare. The first study in this thesis assessed the impact of common management practices on physiological stress in the horse. Faecal cortisol was higher in horses that were stabled and exercised, than turned out to grass with no exercise. The effect of exercise alone was also seen to increase levels of salivary cortisol. No change was seen in cortisol following short-term routine husbandry procedures such as exposure to the sound of electric coat clippers, but it was suggested that this required further investigation. The study confirmed exercise increased stress as reflected by cortisol concentration, and indicated that individual stabling may also contribute to elevated stress. The study recommended that horses may benefit from periods of rest and turn out to grass, to reduce stress levels and improve welfare. The measurement of stress for the purpose of welfare assessment is, however, best carried out using an integration of both physiological and behavioural measures. Behaviour scores offer non-invasive, quick and easy methods of assessing stress in domestic animals, but have typically been developed using only behavioural assessment of the stress response. In the second study a scale of behavioural indicators of stress was developed using behavioural and physiological measures for the purpose of assessing stress in stabled domestic horses. Principal component analysis of behavioural reactions and changes in salivary cortisol concentration in response to routine husbandry procedures, revealed three meaningful components that were used as the basis to the stress scale. Behavioural reactions to the husbandry procedures were further analysed by a panel of equestrian professionals using free choice profiling, and results were added to the appropriate components. The final scale comprised of four levels of stress (no stress, low, iii medium and high stress), and each category was further sub-divided into behaviour scores (BS). The scores represented accumulating levels of behavioural indicators of stress within each stress level, and provided indices of physiological stress. The scale offers an easy to use method of welfare assessment in horses, and reduces the need for additional physiological measures to be taken. The scale represented a novel approach to measuring stress, and was used in the final study to measure stress in horses stabled individually, group housed, and in horses moved from stabling to group housing. The effectiveness of the scale at measuring stress, was compared to the effectiveness of measures of heart rate variability (HRV) and faecal cortisol at measuring stress in the same horses. Lower levels of stress were recorded in group housed horses as measured by the BS, but measures of HRV and faecal cortisol showed no difference between those stabled or group housed. Stress levels were unaffected by the move to group housing, but BS declined significantly over the three weeks that the horses remained group housed. The physiological measures did not, however, reflect such a decrease in stress. Stress levels were also compared between horses housed in both environments whilst waiting to be fed. Group housed horses had lower stress levels as measured by the BS. Results provided by the BS were supported by relevant literature, and the scale appeared to be more sensitive than the physiological measures which did not yield significant results with the small sample sizes used in the study. The research confirmed short-term management practices horses are typically exposed to daily, can elevate their stress levels. Further research into which practices put horse welfare at a particular risk, and thus require modification or need to be avoided where possible, is necessary. The findings also suggest horse-owners may need to pay more attention to their horse’s stress levels, to avoid repeated or on-going stress that can jeopardise health and welfare. The scale of behavioural indicators of stress would provide a suitable method by which stress could be monitored and thus become a part of horse management.
  • Genetic analysis of the critically endangered Trinidad Piping guan (Pipile pipile): Implications for phylogenetic placement and conservation strategies

    McDowall, Ian; Hosie, Charlotte A.; Robinson, Louise A. (University of Chester, 2011-11)
    Classified as critically endangered since 1994, the Trinidad Piping guan (Pipile pipile) is an endemic species estimated to number less than 200 individuals. Known to locals of Trinidad as the ‘Pawi’ this bird has been the subject of substantial hunting pressures and much of the species habitat has been destroyed through deforestation. Although officially protected since 1958, occasional recreational hunting of this elusive species still occurs. Due to difficulties locating and capturing the species, no genetic research has previously been performed using samples obtained from Trinidad. All previous research studies have been conducted using biological materials obtained from captive birds outside Trinidad and island data has never been obtained or compared. The genetic diversity of the remaining population was therefore examined through the investigation of mitochondrial haplotypes, pairwise comparison and SNP analysis. With the intention of assisting the protection of this endangered species by the location of remaining areas of habitation, methods of genetic identification were established for the Trinidad Piping guan utilising non-invasive feather samples. Species specific primers were created in the regions of the ND2 and cyt b genes of the mitochondrial genome to identify Pipile pipile. Species detection was further verified with the use of PCR-RFLP of the same gene regions digested with BsaXI, EcoRV and BsrDI. This combined approach allowed the separation of closely related taxa based on single inter-species SNPs. Confirmation of species identification was subsequently performed through the use of forensically informative nucleotide sequencing. The established methodologies were used in the current study to correct the classification of a UK breeding population of Piping guans thought to be Pipile pipile and to identify Trinidad field samples. These detection methods have implications for ecological studies through the location of populations from trace evidence collected in the field. In addition this method could be used to assist Trinidadian police forces in the identification of bushmeats or simply act as a deterrent to hunters. The sequence data obtained in the present study were also used to re-assess the phylogeny of Piping guans. As genetic sequence from a true island bird was previously unstudied, differences between phylogenies created using non-island and island bird data sets were examined. Combined analysis was performed on 1884bp of the ND2 and cyt b genes and placement of Trinidad Piping guan was found to differ from that which has been previously published.
  • The sportization of swimming: A sociological examination of the development of swimming as a modern competitive sport, c.1595-1908

    Bloyce, Daniel; Cock, Steven (University of Chester, 2012-04)
    Modern competitive swimming is a highly structured, organized, codified and regulated sport. This has not always been the case. The aim of this thesis has been to examine the long-term development of competitive forms of swimming throughout the periods between the late sixteenth and early twentieth centuries. Despite some recent historical analyses, the emergence of swimming as a modern competitive sport is an under-researched topic. There are no sociological analyses relating to the development of competitive swimming and significant gaps within much historical research. This thesis has been conducted from a sociological perspective in order to test the relative adequacy of Norbert Elias’s concept of sportization. Figurational sociologists have often examined the concept of sportization in relation to the development of contact sports such as boxing and rugby. Some authors have sought to criticize figurational sociologists for over-emphasizing issues relating to the increasing control of violence when examining the development of such activities. In this manner, there is scope to contribute to existing empirical and theoretical knowledge by testing the relative adequacy of the concept of sportization in relation to the long-term development of the predominantly non-contact sport of competitive swimming. To this end, data have been examined from a range of documentary sources. Various swimming-based texts, treatises, periodicals and magazines were examined at the British Library and Colindale Newspaper Library in London. The original minute books of the Amateur Swimming Association and its predecessor bodies have also been analyzed. In addition, a range of digitized source material has been examined from several electronic databases. It has been argued that the development of modern competitive swimming was an unplanned and unintended outcome resulting from the complex interweaving of wider social processes in England throughout the periods between the Middle-Ages and the early twentieth century. The earliest reported swimming contests took place in the eighteenth and early nineteenth centuries in the form of a cash wager between two or more individuals. These events were less structured and regulated than modern forms of competitive swimming. Betting upon the outcome of such events was deemed to be an appropriate means to experience heightened levels of tension-excitement within the context of an emerging society in which people were increasingly expected to demonstrate greater self-control over their behaviour and emotions. More organized forms of competitive swimming gradually emerged during the nineteenth and early twentieth centuries. The emergence of an increasingly complex network of clubs, societies and associations at local, county, district and national levels facilitated such developments and contributed to the emergence of standardized rules and regulations within the emerging sport of swimming. Such developments have been explained in relation to ongoing processes of state-formation, pacification, lengthening chains of interdependence and a gradual lowering in the threshold of repugnance within England in the period between the Middle-Ages and the early twentieth century. In this manner, it has been argued that the concept of sportization is an appropriate theoretical framework for explaining the long-term development of the modern non-contact sport of competitive swimming.
  • A multidisciplinary approach to structuring in reduced triacylglycerol based systems

    Bonwick, Graham A.; Young, Niall; Wassell, Paul (University of Chester, 2013-05)
    This study (Wassell & Young 2007; Wassell et al., 2010a) shows that behenic (C22:0) fatty acid rich Monoacylglycerol (MAG), or its significant inclusion, has a pronounced effect on crystallisation (Wassell et al., 2010b; 2012; Young et al., 2008) and interfacial kinetics (3.0; 4.0). New interfacial measurements demonstrate an unusual surface-interactive relationship of long chain MAG compositions, with and without Polyglycerol Polyricinoleate (PGPR). A novel MAG synthesised from Moringa oleifera Triacylglycerol (TAG) influenced textural behaviour of water-in-oil (W/O) emulsions and anhydrous TAG systems (4.0: 5.0; 6.0). Emulsifier mixtures of PGPR and MAG rich in C18:1 / 18:2 and C16:0 / C18:0 do not decrease interfacial tension compared with PGPR alone. Only those containing MAG with significant proportion of C22:0 impacted interfacial behaviour. A mixture of C22:0 based MAG and PGPR results with decreasing tension from ~20°C and is initially dominated by PGPR, then through rearrangement, the surface is rapidly dominated by C22:0 fatty acids. A Moringa oleifera based MAG showed unusual decreased interfacial behaviour not dissimilar to PGPR. All other tested MAG (excluding a C22:0 based MAG), irrespective of fatty acid composition resulted with high interfacial tension values across the measured temperature spectrum (50°C to 5°C). A relative decrease of interfacial tension, with decreased temperature, was greater, the longer the chain length (Krog & Larsson 1992). Moreover, results from bulk and interfacial rheology showed that the presence of C22:0 based MAG has a pronounced effect on both elastic modulus (G’) and viscous modulus (G’’). Through a multidisciplinary approach, results were verified in relevant product applications. By means of ultrasonic velocity profiling with pressure difference (UVP-PD) technique, it was possible to examine the effect of a C22:0 based MAG in an anhydrous TAG system whilst in a dynamic non-isothermal condition (3.0). The non-invasive UVP-PD technique conclusively validated structural events. The application of a Moringa oleifera based MAG in low TAG (35% - 41%), W/O emulsions, results in high emulsion stability without a co-surfactant (PGPR). The bi-functional behaviour of Moringa oleifera based MAG is probably attributed to miscibility (Ueno et al., 1994) of its fatty acids, ranging ~30% of saturated fatty acids (SAFA), with ~70% of C18:1 (5.0). It is concluded that the surface-interactive behaviour of Moringa oleifera based MAG, is attributed to approximately 10% of its SAFA commencing from C20:0. When examined separately and compared, results showed that physical effect of a Moringa oleifera based MAG was not dissimilar to PGPR, influencing the crystallisation kinetics of the particular anhydrous TAG system. When either was combined with a C22:0 rich MAG, enhanced gelation onset and strong propensity to form dendrite structure occurred (5.0). Macrobeam and synchrotron radiation microbeam small angle x-ray diffraction (SR-μ-SAXD) was utilized (6.0) to assess behavior of C22:0 rich MAG, with and without PGPR (Wassell et al., 2012). The C22:0 based MAG combined with PGPR promoted TAG crystallisation as observed by differential scanning calorimetry (DSC). Polarised optical microscopy (POM) observations indicated that C22:0 based MAG eliminates formation of large crystal aggregates, resulting in the likely formation of tiny Pickering TAG / MAG crystals (6.0). It is concluded that the presence and interactive behaviour of Pickering surface-active MAG, is strongly linked to increased fatty acid chain length, which induce increased textural resilience owing to viscoelasticity (4.0; 5.0). A multidisciplinary approach was able to verify structuring behaviour (4.0; 5.0), using multiple analyses (Wassell et al., 2010b; 2012; Young et al., 2008). Novel structuring solutions in reduced TAG based systems have been provided (4.0; 5.0). This study both enhances current understanding of structuring in low TAG W/O emulsions and has led to novel MAG compositions, which address emulsification, structuring and texture in TAG based food systems (Wassell et al., 2010a; 2012a; 2012b; 2012c; 2012d; 2012e; Bech et al., 2013).
  • Delivery and engagement in public health nutrition: The use of ethnographic fiction to examine the socio-cultural experiences of food and health among mothers of young children in Skelmersdale, Lancashire

    Ellahi, Basma; Cox, Peter; Gregg, Rebecca A. (University of Liverpool (University of Chester), 2013-04)
    Encouraging good nutrition is particularly important in the early years of life for the development of appropriate food habits and healthy adults in later life. These are governed by many contending and conflicting influences. Objective: This research examines the food choice influences for mothers of young children in Skelmersdale, West Lancashire (UK). Participants were recruited from a large community food intervention (clients) and were compared with those not involved in the initiative (non-clients). This enabled the reflection of the broader socio-cultural experiences of food and the influence of “structure” and “agency” on food choices. The research adopted a phenomenological approach using ethnographic recording techniques (interview and observation). The research findings are presented as ethnographic fictions. These short fictional stories provide a “thick” description of the participant’s lifeworld. They locate these choices in the person and the place. A hierarchy of food choice influences emerged from the data, with three main findings. Most prominently, the influence of individual capacity on the food choices made. Secondly, the influence of place, town planning and the geography of an area on food choices. Thirdly, the influence of gender, relationships and social networks. Central to the thesis of this research is the use of ethnographic fiction to enable a better understanding of the complexity involved in food choice and community development approaches to nutritional change. The use of ethnographic fiction conveyed a better understanding of people and of the role and impact of an intervention upon the wider processes involved in food choice. Ethnographic fiction was used here for the first time in public health nutrition to explain the complex picture of food choice for mothers of young children in Skelmersdale, and to convey new insight on food choice and the complexity of food choice influence.

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