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Kennelly, Steven James. "The Empirical Study of Marine Biological Resources". University of Sydney, Marine Studies Centre, 1999. http://hdl.handle.net/2123/390.
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The papers presented in this thesis represent my contributions to the empirical study of marine biological resources. This research has adopted the same experimental approach to: (i) develop scientifically validated techniques to solve specific problems; (ii) use these techniques to detect patterns and form conceptual models about the processes that may have caused them; (iii) do manipulative field experiments to support or refute hypotheses derived from these models; (iv) use these results to develop new models and hypotheses and to test them in new experiments; and (v) recommend, where appropriate, changes to the management of the resources examined. A rigorous, empirical approach is the common feature throughout my research (in its overall direction and subject-to-subject execution) and represents one of the few attempts to adopt such an approach across the three fields in which I have worked: (1) the ecology of underwater kelp systems; (2) the biology of and fishery for a commercially exploited crab; and (3) solving by-catch problems in commercial trawl fisheries.
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Evans, Louise A. "Electroanalytical chemistry for biological and environmental applications". Thesis, University of Hull, 2008. http://hydra.hull.ac.uk/resources/hull:1616.
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Electroanalytical chemistry provides an elegant technique by which to explore, amongst others, various biological and environmental applications. To this end, four areas of electroanalytical chemistry are investigated in order to develop biologically- and environmentally-relevant sensors, together with exploring the electro-generation of a biologically important molecule and the diffusional factors that may affect this generation.The first study involves the dynamics of the bond cleavage involved in the electro-generation of nitric oxide from a range of N-nitrosoamines. Adsorption phenomena is found to be of pivotal significance in the release of nitric oxide from two of the compounds explored, namely cupferron and N-itrosodiphenylamine, whilst bis(nitroso)phenylenediamine released, as hoped, two moles of nitric oxide in a single step. The challenge is to isolate the product, and to determine which form of nitric oxide was generated, i.e. the cation, NO+ or nitric oxide, NO. Isolation remains a challenge, however analysis of the reaction mechanism does allow a prediction of the product, be it NO+ or NO. NO+ is a highly oxidising species and hence is difficult to isolate, therefore it is far more preferable to electro-generate NO, which cupferron was the only compound investigated that achieved this.The second study involved the investigation of axiosymmetric anisotropic diffusion to disc shaped microelectrodes, with theoretical expressions examined with experimental data in order to examine the factors. A ferrocene/PEG in acetonitrile system was examined in order to test this theory and to determine the effect of viscosity on the diffusion coefficients, and also if it was possible to investigate the anisotropy by effectively "blocking" either Dr or Dz. Excellent symmetry between theory and experiment was found, hence the focus turned to a ferricyanide in caesium pentadecafluorooctanoate/D2O system where once again the calculated value of root(Dr.Dz) affords a theoretical waveshape with reasonable agreement between theory and experiment. Potential step chronoamperometry then determined separate values for Dr and Dz, with the resulting values affording an anisotropic ratio of 1.7, suggesting radial diffusion dominance over planar diffusion.Third, the modification of electrodes is explored in order to develop biologically and environmentally relevant sensors. In a first strand, two liquid crystal ferrocene compounds are examined, immobilised on the surface of a glassy carbon electrode simply via solvent evaporation. Both compounds demonstrated typical ion transfer processes across the liquid | liquid interface, with both anion insertion and cation expulsion processes demonstrated. The differing voltammetry observed in the presence of different anions formed the basis of the anion sensor.In a second avenue in this modified electrode work a cation sensor is developed, working on the basis of a biofilm, i.e. developing a modification of the electrode surface to mimic the action of a biofilm in chelating with cations. With this in mind, a basal plane graphite electrode was modified with a diazonium salt and polyphenol, and through the introduction of alginic acid into the polyphenol layer a degree of selectivity between the Group 2 cations was demonstrated, although quantitative properties eluded the work.Last, an environmental sensor for cyanide was developed using an electrochemical probe, tetramethylphenylenediamine (TMPD). The reaction between the electro-generated TMPD.+ and cyanide is successfully followed colorimetrically, before product characterisation studies help to determine the reaction mechanism. Voltammetric studies form the basis of a sensor, with square wave voltammetry achieving a detection limit of 4.4 microM. The reaction between TMPD and cyanide allowed remediation studies to be undertaken, with river freshwater samples from North Yorkshire (54deg 15' 19.19" N, 1deg 46' 13.49" W) and the Rodalquilar mine, Spain, (36deg 50' 52.9" N, 2deg 02' 36.87" W) demonstrating the removal of cyanide by an impressive three orders of magnitude.
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Bogdanyuk, O. "Increase of accounting role in biological resources preservation". Thesis, Видавництво СумДУ, 2008. http://essuir.sumdu.edu.ua/handle/123456789/11597.
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Ita, Sajida. "Synthesis of porphyrins and metalloporphyrins for biological applications". Thesis, University of Hull, 2005. http://hydra.hull.ac.uk/resources/hull:16866.
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Porphyrins are ideal candidates for PDT (Photodynamic therapy). Their ability to localise preferentially in diseased tissue allows specific targeting of cancerous tissue in certain areas. In recent years, linking photosensitisers to sugar moieties has attracted great interest. Glycosylated porphyrins have increased solubility which enhances their uptake into cells, and also selectivity of the porphyrins. Cationic porphyrins have also been studied due their increased solubility and selective accumulation into mitochondria. In this project, we have successfully combined these two properties of water- soluble derivatives of porphyrins to enhance their efficacy as potential PDT agents. Thioglycosylated cationic porphyrins have been synthesised, characterised and their photocytotoxicity assays against human colorectal adenicarcinoma cells (HT-29) assessed. Metalloporphyrins on the other hand were synthesised with the intention of using them as molecular oxygen sensors. Oxygen-dependant changes in phosphorescence lifetime can be used to measure oxygen concentration in biological systems. A versatile method was developed which allowed palladium metal insertion into porphyrin macrocycles. The metalloporphyrins were synthesised, purified and analysed using TLC, MS, 'H NMR and UV spectroscopy. Further functionalisation of the metalloporphyrins was achieved by the selective substitution of the para-fluoro substituent of the pentafluorophenyl group with thiols. In this way, a range of palladium(II) porphyrins were synthesised. Failure of cells to internalise these porphyrins using conventional methods has prompted further considerations of encapsulating them in nanoparticles.
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Lonsdale, Jemma-Anne. "Developing an estuarine planning support system : a case study for the Humber Estuary, UK". Thesis, University of Hull, 2018. http://hydra.hull.ac.uk/resources/hull:16549.
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Estuaries are often challenging to manage, as management must strike a balance between the needs of the users and the ecological and economic values within the context of multiple legislative drivers. To help facilitate integrated management, a novel Estuarine Planning Support System (EPSS) framework, using the Humber Estuary in Eastern England as a case study, has been developed. This integrated EPSS framework goes beyond previous approaches as it brings together the legislative drivers, management tools and other mechanisms for controlling plans (formal/legal management, action or work plans (e.g. shoreline management plans) and projects (a new structure or activity such as extending a port). It thereby enables managers and users to assess and address both the current environmental state, and the way in which the new project could impact an estuary in an accessible and understandable tool. This study has been primarily completed by desk based research using peer reviewed literature, technical and research reports, marine licence applications and legislation, with correspondence to several sources to determine the baseline information and existing knowledge gaps. Further to the framework, an EPSS tool was developed to provide a practical application of these requirements. The GIS-based tool ensures that the information is accessible for regulators, managers, the scientific community, developers and the public. Whilst the tool is adaptable for regions within and outside the United Kingdom (UK), the research presented in this thesis focussed on the Humber Estuary. The successful application of the tool for a complex socio-economic and environmental system such as the Humber Estuary shows that the tool can efficiently guide users through the complex administrative requirements needed to implement a management plan, and therefore support sustainable development. In addition, the tool can be used as a scoping mechanism to identify potential stressors which are to be addressed in an environmental impact assessment (EIA). The tool was validated against four case studies and was also tested by a number of stakeholders to determine the utility and accuracy of the tool. The tool was subsequently updated to reflect feedback from the stakeholders. This project should be viewed as a ‘proof of concept’ in that its primary purpose is to demonstrate the potential for developing and operationalizing an approach in the field. The method has the potential to integrate highly technical knowledge from scientists, and the views of non-scientists, to make better-informed management and planning decisions and to provide reasonable assurance to justify those decisions. The tool can be used to prevent conflicts among stakeholders and/or between uses and users and the environment, and makes it possible to integrate all the existing background data in thematic maps and identifies the human activities that use the areas, resources and services. The EPSS tool can save time and resources, aid in the decision-making process and make the decision process more transparent and consistent. It has the potential to make the governance of the marine area more logical, simple, fast and therefore more cost effective. The tool has been developed to be flexible in its approach, this means that it can be easily adapted to be used internationally and to allow for it to be adaptable to future changes. It combines the many aspects required for a holistic approach to marine management, from the inclusion of governance and stakeholder views, to the need for, and use of, monitoring information. In marine management, there will always be a need for robust and scientifically and legally defendable science to inform management. The increasingly large spatial scales that are addressed by policy makers, and the reduction in funding, means that new methods are needed to provide the evidence base which this tool helps to provide, and can be applied worldwide. The developed toolbox is an important step towards such an integrated, holistic ecosystem based approach for marine management, demonstrating that a single tool can bring together the legislative, environmental and economic considerations. The tool is a method to undertake the assessments that are currently being carried out by separate organisations, to combine in a single process that is consistent and transparent and on a quicker timescale helping to reduce costs.
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Ethaeb, Ali Mahdi. "Elucidation of the signalling mechanisms involved in TF-mediated apoptosis in endothelial cells". Thesis, University of Hull, 2018. http://hydra.hull.ac.uk/resources/hull:16586.
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Tissue factor (TF) is the main initiator of blood coagulation. In addition to its procoagulant property, TF has the ability to regulate various functions within cells including proliferation, angiogenesis and apoptosis. These outcomes appear to depend on the amount of TF with which the cell comes into contact with. In this study, human dermal blood endothelial cells (HDBEC) were transfected to express wild-type TF which is released following the activation of PAR2 in a normal physiological response. In addition, a model for the accumulation of TF in vascular disease and cancer was used by expressing a mutant form of TF (TFAla253-tGFP) which although expressed is not released by the cells and therefore it accumulates intracellularly. Initially, the phosphorylation of Src1 and Rac1 were monitored in order to determine any difference in phosphorylation patterns following PAR2 activation of cells. Phosphorylation of Src1, but not Rac1 was prolonged on expression of TF and was further enhanced on intracellular accumulation of TF. Therefore, the role of Src1 as a mediator of TF-induced apoptosis was examined next. Either inhibition of Src using pp60c-srcpeptide, or suppression of Src1 expression using siRNA prevented the TF-induced p38 MAPK activation and subsequent cellular apoptosis. Following confirmation of the role of Src1 in this process, an attempt was then made to delineate upstream intermediaries involved in this pathway. By using an inhibitory antibody (AIIB2), β1-integrin was shown to participate in TF-induced Src1 activation. In contrast, prevention of Src1-FAK complex formation using FAK inhibitor-14 did not interfere with the TF-mediated Src1 activation, despite a clear reduction in Src1 phosphorylation. Furthermore, TF-induced apoptosis did not appear to require Src1-FAK binding. In conclusion, this study has established further steps in the pathway by which TF can induce cellular apoptosis, and suggests a mechanism by which the increased amount of TF during inflammation can have detrimental outcome on the vascular system.
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Richardson, Andrew James. "Patterns of mussel bed infaunal community structure and function at local, regional and biogeographic scales". Thesis, University of Hull, 2015. http://hydra.hull.ac.uk/resources/hull:13238.
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Jones, Ashley. "Trace metal dynamics in mine-impacted, circum-neutral streams". Thesis, University of Hull, 2014. http://hydra.hull.ac.uk/resources/hull:11405.
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Atkinson, Robert. "Probing cardiac metabolism in uraemic cardiomyopathy". Thesis, University of Hull, 2017. http://hydra.hull.ac.uk/resources/hull:16521.
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Cardiovascular complications are the leading cause of death in patients with chronic kidney disease (CKD). Uraemic cardiomyopathy (UCM) is characterised by structural and cellular remodelling including left ventricular hypertrophy (LVH), metabolic remodelling and mitochondrial dysfunction. Although ex vivo studies have highlighted evidence of enhanced glucose utilisation in the hypertrophied heart, cardiac glucose metabolism in uraemia has yet to be established in vivo. In addition, little is known about mitochondrial morphology or the impact of iron therapy on cardiac mitochondrial function in CKD. The aims of this study were to (I) investigate cardiac glucose metabolism in vivo using 18F-flurodeoxyglucose positron emission tomography (18F-FDG PET) during the development of UCM and (II) characterise mitochondrial morphology and the impact of iron therapy on cardiac mitochondrial function in uraemia. Experimental uraemia was induced surgically in male Sprague-Dawley rats via a subtotal nephrectomy. Dynamic PET/CT scans were acquired at 5, 9 and 13 weeks post-surgery using 18F-FDG PET. The rate and distribution of 18F-FDG uptake were determined using Patlak and polar map analysis. In a separate series of experiments the iron complex, ferumoxytol, was administered 6 weeks post-surgery and mitochondrial respiratory rates and enzyme activities determined following sacrifice 6 weeks later. Cardiac mitochondrial morphology was characterised by probing the expression of key mitochondrial fusion and fission proteins and evaluating mitochondrial size and structure in left ventricular tissue and isolated mitochondria. Renal dysfunction was prominent in uraemic animals by 12 weeks as evidenced by elevated serum creatinine, urea and the presence of anaemia. LVH was associated with moderately increased 18F-FDG uptake in the uraemic heart at 5, 9 and 13 weeks. This was paralleled at the cellular level by altered mitochondrial morphology, characterised by a more sparsely packed cristae, and increased mitochondrial state 4 respiration, indicative of reduced efficiency. However, ferumoxytol treatment did not impact on cardiac mitochondrial function at this stage of uraemia. Collectively these data suggest there is evidence of enhanced glucose utilisation in the uraemic heart in vivo and these changes are associated with altered mitochondrial structure and bioenergetics.
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Billington, Sam. "Factors affecting Atlantic salmon (Salmo salar L.) in the Mersey catchment, North West England, and the potential for a recolonisation". Thesis, University of Hull, 2015. http://hydra.hull.ac.uk/resources/hull:13739.
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Salmon became locally extinct from the River Mersey, northwest England, during the 1950s – 1970s due to deterioration in water quality and man-made barriers. Stray salmon began entering the River Mersey in the 1990s but a self sustaining population has yet to become established. The aim of the study was to review and investigate the recent history of the Mersey catchment, the current status of and factors effecting the salmon population and the potential for a natural recolonisation of River Mersey. The requirements of adult and juvenile salmon and homing and staying in salmon were reviewed. The physiochemical requirements of salmon are highly specific with connectivity of fundamental importance to upstream migration. In reviewing the status of the Mersey catchment flow manipulation, obstructions to migration, poor water quality and river modifications were common in all rivers. Adult and juvenile salmon have been captured in the Mersey catchment since 2000 but have consistently been caught in low numbers and smolts have not been captured. Genetic analysis was used to assign salmon entering the Mersey to their region of origin. The Mersey is dependent on stray salmon with the majority from rivers in the Solway and Northwest England areas. A tracking study was used to determine salmon behaviour and route choice in the Mersey catchment and salmon were found to be prevented from moving freely within or upstream of the lower Mersey catchment. Habitat surveys undertaken throughout the catchment revealed a general trend of key habitats existing upstream of barriers and inaccessible to adult salmon. Salmon are unable to recolonise the Mersey catchment in its current state. There are a range of management and restoration options available to restore salmon to the Mersey catchment but a coordinated and concerted effort is required to be successful.
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Marsham, Sara. "The application of a functional group approach to algal-grazer interactions". Thesis, University of Hull, 2007. http://hydra.hull.ac.uk/resources/hull:16058.
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Algal morphology is considered to be influenced by physiological and environmental factors such as stress and disturbance; one key disturbance exerted on algae is grazing pressure from herbivores. The factors upon which herbivores base their food preferences include algal attractiveness and edibility. Steneck and Watling's (1982) functional group model advocates the combination of algal species into seven groups based upon morphology and ecological function; the basic premise being that algal attractiveness and edibility will decrease hierarchically from functional group one to functional group seven, and that species within a group will be similarly attractive and edible. Two grazers commonly found in the intertidal area are the gastropod Littorina littorea and the isopod !dotea granulosa. Attractiveness and edibility experiments were conducted in which both grazers were presented with algae representing functional groups two to seven in single- and two-way choice experiments, in order to determine whether their food preferences could be predicted using a functional group approach. Although L. littorea and I. granulosa exhibited preference for algae between functional groups with regards to attractiveness and edibility, preference for both functional group and algal species differed between grazers. When the effect of algal morphology was investigated by presenting grazers with algal homogenates in agar, both grazers displayed a preference for algal extracts in agar over whole plant material, and exhibited preference for algae both between- and within-functional groups. The fact that not all species within a functional group were consumed in similar amounts contradicts the functional group model. Further investigation of the effect of algal availability on the feeding preferences of L. Iittorea showed their food choices could not be predicted based upon the algal species dominant in their habitat of origin. Results from all experimental manipulations suggest that both the habitat and food requirements of a herbivore, along with algal characteristics such as morphological, structural and chemical defences, algal availability and nutritional composition all influence herbivore food choice. As such, the functional group model proposed by Steneck and Wading (1982) cannot be accurately used to predict the feeding preferences of L. littorea or I. granulosa. It is suggested that unless models are modified to meet the requirements of a specific question, current functional group approaches are not a useful tool for predicting algal-grazer interactions.
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Mitchell, Elaine. "Implications of the nature and quality of dredged material and its beneficial placement in the coastal environment". Thesis, University of Hull, 2007. http://hydra.hull.ac.uk/resources/hull:16066.
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Dredged sediment is increasingly being used in mudflat recharge schemes and in habitat restoration/recreation to counter the effect of erosion and sea-level rise. For this reason it is necessary to determine the response of indigenous mudflat fauna to anthropogenic sediment deposition and so in 2001 a manipulative experimental laboratory study was used to assess the biological response to the alternative beneficial use of uncontaminated maintenance dredged material. The experiment assessed the response of common temperate macro-benthic organisms to the addition of increasing amounts of simulated dredged material on to the surface of mudflat cores. Between 0 cm and 20 cm of defaunated sediment was added as both high and low frequency treatments and the vertical migration of species per 1 cm or 3 cm sediment increment was determined. The experiment showed that the bivalve Macoma balthica (Linnaeus) was able to vertically migrate into the surface layers of low or high depositions of sediment treatments but the Spionid polychaete Pygospio elegans (Claparede) and nematodes were less able to reach the surface layers with increased sediment deposition. The oligochaete Tubificoides benedii (Udekem) ability to vertically migrating into larger low frequency depositions of fine-grained sediment treatment placements was less when compared to coarser sand treatments. Hence the study showed that specific errant macro-zoobenthic species vertically migrated through increasing depths of sediment overburden. This concept was investigated further in the winter of 2001 as manipulative experimental field studies at the Skeffiing mudflats along the Humber Estuary and included an investigation to assess the biological response to increased depositions of simulated dredged material at the high-shore area. The main focus of these studies was to understand the relationship between the amounts of fine-grained simulated dredged material deposition and macro-faunal re-colonization through vertical and lateral migration. Defaunated sediment treatments were added as single low frequency amounts of 27 cm and 50 cm and the ability of macro-invertebrate species to migrate to a natural position within the vertical profile of the manipulated sediment was assessed. The re-colonization of defaunated fine-grained sediment via the below surface horizontal migration of macro-fauna occurred when 27 cm of sediment was deposited and the main colonizers were M balthica, juvenile Tellinacea and T. benedii. The macro-faunal re-colonization of a 50 cm deposition of defaunated fine-grained material occurred within 6 weeks via vertical migration. The main vertical migration colonizers were M balthica, juvenile Tellinacea and T. benedii. The deposition of a single large amount of fine-grained sediment had a detrimental affect on macro-faunal nematode recolonization. Further experimental investigations concerning the impact of burial following the high-frequency depositions of simulated fine-grained dredged material on a temperate intertidal mudflat community during the spring-summer period were carried out during 2002 and 2003. Additionally, the logistics of dredged material deposition at different tidal heights was investigated. This was achieved by examining the responses of key mudflat macro-fauna to burial by manipulated water content of fine-grained sediment treatments deposited at the upper-, high- and mid-shore areas of an estuarine intertidal mudflat and determining the macro-faunal re-colonization potential via settlement from the water column. Tubificoides benedii demonstrated a high ability to colonize an increased sediment water content treatment throughout the experiment when deposited at the high- and mid-shore areas but colonized the upper-shore sediment treatment from the middle to end period of the experiment. The polychaete Hediste diversicolor (O.F. Muller), in particular the juvenile stage demonstrated a good ability to colonize the upper-shore fine-grained sediment treatment. The high-shore early treatment colonizers included T. benedii and nematodes, other species colonized the treatment microcosms from July onwards; T. benedii, H. diversicolor, the Spionid polychaete Streblospio shrubsolii (Buchanan) and the gastropod Hydrobia ulvae (pennant) and M balthica throughout the experiment. At the mid-shore the early colonizers included T. benedii, M balthica, P. elegans and S. shrubsolii. The colonization ability of M balthica, juvenile Tellinacea and H. ulvae were negatively correlated to an increase in sediment water content especially when deposited at the high-shore. Tubificoides benendii was the only species to show a sediment-associated pattern at the high-shore and was positively correlated to the sediment water content of the treatments. When simulated fine-grained dredged material was deposited as small multiple amounts over time, the mudflat height was slowly recharged and allowed to build up, this allowed the gradual macro-faunal re-colonization of the recharge material over time. In general, the deposition of manipulated water content fine-grained sediment treatments did not inhibit macro-faunal recovery. This information may be used during the decision making process upon the feasibility of the alternative beneficial uses of dredged material such as when determining the type of dredged material used during a sediment recharge scheme or during simulated dredged material deposition studies.
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Chan, Kuan Yoow. "The characterisation of family-13 kinesins in Trypanosoma brucei". Thesis, University of Hull, 2008. http://hydra.hull.ac.uk/resources/hull:1361.
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Kinesins are motor proteins involved in the movement of organelles and sub-organelles along microtubule tracks within the cell. Phylogenetic analysis of the 46 kinesin genes coded by the Trypanosoma brucei genome resulted in the grouping of seven kinesin sequences into the Kinesin-13 family. Members of this family have been characterised in a number of model organisms and, unlike most kinesins, do not exhibit microtubule processivity and are capable of depolymerising microtubules. They play important roles in bipolar spindle assembly and chromosome segregation. Of the six T. brucei Kinesin-13 proteins that were characterised during this study, only one was found to have a nuclear localisation, while the rest were found localised to the mitochondrion, cell body or flagellum. Attempts to probe the function of these kinesins using RNAi resulted in a reduction of cell growth in three of the six kinesins studied, but no gross changes in cellular morphology were observed. The distinct localisation of five Kinesin-13 family members outside the nucleus suggests that the functional diversity of the Kinesin-13 family is larger than previously thought.
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Vince, Rebecca. "Identification of MRSA-specific peptides and expression of peptide containing recombinant proteins for targeted photodynamic therapy". Thesis, University of Hull, 2009. http://hydra.hull.ac.uk/resources/hull:2490.
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Staphylococcus aureus (S. aureus) is an opportunistic pathogen capable of causing infection at multiple sites and is one of the predominant organisms found in chronic wounds, such as venous ulcers. Furthermore, there is an ever-increasing prevalence of multi-drug resistant strains, such as methicillin-resistant S. aureus (MRSA) that can contribute to the non-healing and infection of wounds as well as other life-threatening complications. The increase in bacterial resistance necessitates the development of alternative modes of bacterial targeting and elimination whilst avoiding collateral damage to host cells and commensal bacteria. One such modality is photodynamic therapy (PDT), whereby the activation of a photosensitiser by light in the presence of oxygen produces reactive oxygen species to elicit bacterial cell death. PDT has previously been shown to be effective against a wide range of Gram-positive and Gramnegative bacteria and furthermore selective targeting of the photosensitiser directly to the pathogenic bacteria is likely to improve the efficacy of this treatment.The FliTrx (TM) bacterially-displayed random peptide library (Invitrogen), displaying 12-mer peptides in a conformationally constrained manner on the surface of E. coli was screened by panning against UV-inactivated MRSA. Panning was also performed against S. aureus and S. epidermidis in a similar manner. Clones (n = 20) were then randomly selected, DNA sequenced and peptide sequences analysed. No obvious consensus sequence or repeat sequences were observed. Two peptides selected from panning against MRSA were commercially synthesised (peptide19 and peptide12) as both cyclic and linear constructs with N-terminal biotin for characterisation of binding by flow cytometry. Furthermore, one peptide (peptide12) was synthesised as both a cyclic and linear construct replacing the biotin with C-terminal FITC for direct characterisation of peptide binding by flow cytometry. Binding of the cyclic construct was observed against 3 different strains of MRSA, with the greatest binding observed against the strain of MRSA originally panned against. No binding of the linear construct was observed. Low/no reactivity was observed with other Staphylococcal sp, Gramnegative bacteria and a mammalian cell line demonstrating apparent specificity for MRSA.Peptide sequences of interest were also cloned in-frame, situated within the full length thioredoxin sequence, so as to reflect the original display format, into an E. coli based expression vector. Recombinant protein expression was optimised and the protein extracted, purified and characterised by Western blotting. The porphyrin photosensitiser (5-(4-isothiocyanatophenyl)-10,15,20-tris-(4-N-methylpyridiniumyl) porphyrin trichloride) was conjugated to recombinant protein P12 at a molar ratio of 5:1 and the in vitro cytotoxic effect of the resulting bioconjugate was determined against MRSA, E. coli and keratinocytes. Pilot data demonstrated a 66% reduction in MRSA growth following incubation and irradiation with the bioconjugate in comparison to nonirradiated control cells. The conjugated porphyrin gave higher levels of cytotoxicity than equivalent concentrations of unconjugated capped porphyrin. No toxicity of the conjugate or the capped porphyrin against MRSA was observed when light of the correct wavelength was not given. Additionally no/little cytotoxic effect against E. coli or mammalian keratinocytes was observed.Additionally, binding of two other purified recombinant proteins (P5 and P19) to MRSA, E. coli and keratinocytes was assessed by flow cytometry. Both recombinant proteins were observed to bind MRSA in comparison to E. coli and keratinocytes.Furthermore, one sequence (P5) was expressed as an additional GFP fusion protein construct to allow direct characterisation of recombinant protein binding. A very small increase in binding was observed with an increasing concentration of recombinant protein against MRSA, E. coli and keratinocytes.In summary, this thesis has described a system to isolate and characterise novel peptides with binding specificity against MRSA. Furthermore, it has demonstrated the feasibility of expressing recombinant proteins and conjugation to a porphyrin photosensitiser for targeted PDT against pathogenic bacteria whilst limiting damage to the host, providing an alternative to antibody-based targeting in microbiology.
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Lippmeier, James Casey. "Fatty acid metabolism of marine microalgae". Thesis, University of Hull, 2007. http://hydra.hull.ac.uk/resources/hull:7014.
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Pathways for the biosynthesis of docosahexaenoic acid (DHA) and other polyunsaturated fatty acids (PUFA) were elucidated in two heterotrophic, marine microalgae; Schizochytrium sp. and Crypthecodinium cohnii. PUFA-requiring auxotrophs of both of these algae were created and used as tools for studying PUFA biosynthetic pathways. Additionally, equilibrium radio-labeling techniques were applied to algal cultures fed 14C-fatty acids. Both organisms were found to possess two distinct pathways for PUFA biosynthesis. One pathway, mediated by classical elongases and desaturases, was incomplete in both organisms and was not capable of complementing PUFA auxotrophic phenotypes or of producing PUFA de novo, but could produce DHA from simpler PUFA precursors. The second PUFA pathway in each organism was desaturase and elongase independent. In C. cohnii, this pathway was distinguished by a capacity to produce DHA from acetate, in a manner similar to that of Schizochytrium which was shown to employ a polyketide synthase (PKS) complex for primary DHA biosynthesis. Additionally, genes of the Schizochytrium PUFA-PKS were successfully expressed in transgenic yeast, which produced DHA. Candidates for genes encoding C. cohnii PUFA-PKS components and other genes of C. cohnii PUFA biosynthesis were identified and discussed.
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Petrovan, Silviu Octavian. "The landscape ecology of brown hares and European rabbits in pastures in the north east of England". Thesis, University of Hull, 2011. http://hydra.hull.ac.uk/resources/hull:5118.
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The declines of the brown hare (Lepus europaeus), a priority species for conservation in the UK, may have been caused by changes in agricultural management. This study aims to identify hare distribution, density, habitat selection and demography in grass lands in order to benefit their future conservation. In addition, this study aims to investigate the impact of current agricultural management on the populations of the European wild rabbit (Oryctolagus cuniculus), a major agricultural pest and potential competitor for hares. Hare and rabbit populations were surveyed in several large, pasture-dominated, sites in north -east England between 2007 and 2009. Estimated density of brown hares in the studied region was far higher than the published national average density for this species in pastures but with very large variation between superficially similar sites. We explored a new method to survey hares using night-time line transect distance sampling and compared this method with day time surveys. Night-time distance sampling produced improved precision estimates of hares with considerably less survey effort by maximising detectability during surveys. Hares and rabbits had different habitat requirements in grassland areas and areas dominated by intensive sheep grazing produced the lowest hare densities and in most cases were associated with high rabbit densities. Field size was an important determinant of the distribution of both hares and rabbits but with contrasting effects for the two species. Predator control appeared more important in increasing rabbit numbers than hares in the studied region. Our results indicate that recent changes in pasture management in the UK might favour high rabbit densities with potentially significant economic impacts for the agricultural sector. Hare productivity was high but female fertility and survival, in particular juvenile survival, were relatively low. Hares in the studied region were generally in good condition and reached sizes comparable with hares from arable areas. Population modelling suggested the hare population in the area was slowly increasing but was susceptible to decline even at relatively moderate levels of hunting. Radio-tracking indicated that habitat heterogeneity was important for hares at both between and within field levels. Hares preferentially used field margins during both active and inactive periods and selected woodland edges and unimproved grassland during diurnal periods, suggesting that they might benefit from measures designed to increase heterogeneity and re-establishment of non-farmed habitat features, particularly field margins. Equally, hares avoided sheep grazed fields with short swards for both foraging and resting indicating that reducing grazing intensity in pastural areas would also be beneficial for hare conservation. We suggest that grassland management could be adapted in order to minimize damage by high numbers of rabbits and increase the presence and abundance of the brown hare, a species of conservation concern in Europe and the UK.
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Churchill, Helen Ruth. "The role of macroalgal morphology and community structure on the accumulation of sediment and the subsequent effects on the dynamics of marine intertidal communities". Thesis, University of Hull, 2009. http://hydra.hull.ac.uk/resources/hull:5760.
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This study examines the influence of intertidal macroalgae on sediment accumulation, and the effect of sediment cover on intertidal community structure. Three shores on the North Yorkshire coast, England, were used to investigate differences in the quantity of sediment trapped by ten morphologically different algal species, and the relationship between morphology and the quantity of sediment trapped. The quantity of sediment accumulated in quadrats of four different macroalgal communities (canopy, turf, canopy/turf and bare rock) was also examined. Differences in sediment cover and community structure were investigated on the intertidal rocky shore at Holbeck, North Yorkshire. The distribution and position of both were described using transects across three sites, whilst relationships were examined using 54 fixed quadrats in the mid shore. Across three different shores the mass of dried sediment g⁻¹ macroalgal dry mass was found to differ between macroalgal species. All measured aspects of macroalgal morphology correlated with the quantity of sediment trapped. Macroalgae with different morphologies trapped different gram size compositions but no differences were found hi the quantity of sediment accumulated by turf, canopy, bare rock or unmanipulated algal communities. At three different sites at Holbeck, the site with the greatest sediment cover had lower macroalgal species diversity, richness and total abundance, patellid and littorinid abundance. Although differences were found in sediment cover between sites in the mid shore, no differences were found hi community structure. Sediment cover had negative correlations with macroalgal richness and diversity in algal quadrats, but positive correlations with macroalgal abundance and diversity in bare rock quadrats. Within individual macroalgae morphology was found to affect the quantity of sediment trapped, however at quadrat level macroalgal morphology had no effect. At both the level of the quadrat and the whole shore sediment cover influenced community structure, whilst within the mid shore alone sediment cover did not affect community structure. This work suggests that relationships/interactions between sedimentation and intertidal community structure are scale dependent.
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Bessat, Mohamed Said Nooh. "Functional characterisation of cohesin subunit SMC3 and separase and their roles in the segregation of large and minichromosomes in Trypanosoma brucei". Thesis, University of Hull, 2009. http://hydra.hull.ac.uk/resources/hull:2179.
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The genome of the African trypanosome, Trypanosoma brucei, presents an unusual karyotype in which two main classes of chromosomes, large and small minichromosomes, need to be faithfully replicated and segregated during the cell cycle. Although the large and minichromosomes are colocalised and segregated by association with the mitotic spindle, minichromosomes exhibit segregation patterns that differ from those observed for large chromosomes. To address whether this difference is reflected at a molecular level, two different proteins that have highly conserved functions in eukaryotic chromosomes segregation were characterised in this study. The first protein, SMC3, is a component of the chromosome cohesion apparatus that holds sister chromatids together after their replication until segregation at anaphase. The second protein, separase, is a cysteine protease that resolves sister chromatid cohesion at the onset of anaphase and has, in other organisms, additional functions during mitosis. The T. brucei cohesin subunit, TbSMC3, localised to the nucleus as a chromatin-bound protein from G1 phase until metaphase and dissociated from chromatin during anaphase until the completion of cell division. On the other hand, cytoplasmic localisation of separase with nuclear exclusion was prevalent until the onset of metaphase when the protein re-localised to the nucleus, thus providing a potential control mechanism to prevent premature cohesin cleavage. Interference with the normal expression of SMC3 and separase by RNA interference resulted in defects in growth rate, cell cycle progression and chromosomes segregation. TbSMC3 depletion produced a lethal phenotype and inhibition of cell cycle progression. Similarly, lethality with severe inhibition of cell cycle progression was the main feature of separase depletion. Using fluorescence in situ hybridisation (FISH), it was shown that SMC3 depletion had no visible effect on the symmetric segregation of the minichromosome population, but interferes with the faithful mitotic segregation of large chromosomes. In contrast, separase depletion blocks the segregation of both large and minichromosomes. In separase-depleted mitotic cells, cohesins remained bound to chromatin, which is in contrast to rapid dissociation of cohesins from chromatin in wild-type mitotic cells. The severity of segregation phenotypes after separase depletion was additionally explained by defects in the mitotic spindle assembly. In both SMC3 and separase depleted cells, cytokinesis in the absence of mitosis/karyokinesis was not inhibited in procyclic cells, resulting in the generation of anucleate 'zoid' cells. The lethality imposed on trypanosome cells after depletion of both SMC3 and separase proteins indicate that they can serve as potential drug targets for anti-parasite chemotherapy.
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Zidana, Hastings K. "Population genetics of the cichlid, Cynotilapia afra (Günther 1894), in its native and introduced ranges in Lake Malawi". Thesis, University of Hull, 2010. http://hydra.hull.ac.uk/resources/hull:2392.
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Species introductions can provide unplanned and occasionally replicated experiments that can be studied to understand fundamental ecological and evolutionary processes associated with range expansions in the natural world. The cichlid species flock of Lake Malawi consists of an estimated 451-800 species and is a textbook example of explosive speciation that has been studied as a model system of evolution in the past three decades. In addition, fish are of major socio-economic importance to Malawian people, and they form an important source (circa 70%) of animal protein in their diet. Furthermore, fisheries activity employs 3% of the country's population and contributes to 4% of the country's Gross Domestic Product (GDP). This thesis studies a well documented, human mediated introduction of a rocky-shore, plankton-feeding cichlid fish Cynotilapia afra into Lake Malawi National Park. This introduction has important evolutionary and ecological consequences on the native populations of Pseudotropheus zebra, and here I investigate its population genetic impacts using contemporary molecular genetic tools and analyses. Three hypotheses were tested: 1. Introduction events are usually associated with a small founder population size, and the resulting genetic bottleneck is expected to reduce genetic variation of C. afra in the introduced range. 2. The invasive scenario during the introduction followed a stepping stone pattern, or alternatively, it occurred as several independent introductions of C. afra in Lake Malawi National Park. 3. Introgressive hybridisation between C. afra and P. zebra may have facilitated the introduction of the invading C. afra population and restored its depleted genetic variation associated with the founder event. Furthermore, the gene pool of C. afra has more non-native genetic material as compared to P. zebra. Samples were collected from six native and four introduced populations of C. afra, as well as three native populations of P. zebra. The latter species is from a different genus, although laboratory experiments indicate that both species hybridise in laboratory conditions. Sequence variation in the mitochondrial DNA (mtDNA) control region was analysed using 15 individuals per sample population and 60 individuals per sample population were genotyped at six microsatellite loci. These data were analysed to test the three hypotheses and identify potential source populations, infer introduction patterns (stepping stone or independent), and deduct whether introgressive hybridisation may have facilitated the founder event and subsequent establishment of C. afra in the invasive range in Lake Malawi Natural Park. The three data chapters in this thesis discuss the findings of the mtDNA sequence study (Chapter 2) and the microsatellite study (Chapter 3). In Chapter 4, I analyse the microsatellite data in further detail and consider the role of introgression by using Bayesian analysis tools. The mtDNA study presented in Chapter 2 reveals that C. afra and P. zebra mtDNA sequences show high levels of lineage sorting (i.e. the DNA sequences of both species are remarkably distinct). This finding is in sharp contrast to previous studies on Lake Malawi rock-dwelling cichlids which have shown that cichlid species share the same or very similar mtDNA haplotypes. Furthermore, the introduced populations showed a higher sequence and haplotype diversity than their native counterparts. This analysis suggests that elevated gene diversity was largely due to C. afra populations being founded by individuals from several genetically distinct and geographically separate populations. In Chapter 4, I discuss the role of introgressive hybridisation with native P. zebra, and its impact on mtDNA variation in the introduced C. afra gene pool. In Chapter 3, I show that in contrast to the signal obtained from the mtDNA, the genetic variation at the microsatellite loci exhibited a significant reduction in the introduced range. Introduced C. afra populations have a lower mean effective number of alleles (ne) than C. afra populations in their native range. I use an approximate Bayesian analysis and show compelling evidence that at least two independent introductions have contributed to the introduced C. afra gene pool, a conclusion that is supported by high probability values. This conclusion differs from that of previous studies which suggested a stepping stone introduction pattern around Thumbi West Island. Surprisingly, a population of C. afra at Domwe Island was founded by a source population from Thumbi West Island, and this stepping stone introduction pattern is supported with a high probability (95%). Microsatellite analysis furthermore suggests that the founder event of C. afra in Lake Malawi National Park was associated with strong genetic drift associated with a genetic bottleneck. I was not able to detect this signal from the mtDNA genetic marker alone, which showed an increase in genetic variation at the mtDNA due to different source populations contributing to the founder event (see Chapter 2). These combined studies reported in Chapter 2 and 3 thus demonstrate that microsatellites may be well-suited to investigate questions related to conservation issues such as bottlenecks associated with founder events, while mtDNA is more suited to reveal the evolutionary processes and establish different source populations that have contributed to the introduction. In Chapter 4, I analyse the level of genetic differentiation at microsatellite loci, and show that the introduced C. afra and native P. zebra populations at Thumbi West Island are genetically more similar (G'ST=0.36+/-0.05) than the species-pair at Otter point (G'ST=0.94+/-0.18) and Domwe Island (G'ST=0.55+/-0.09). In addition, C. afra and P. zebra at Thumbi West Island showed a lower genetic distance than allopatric C. afra or P. zebra populations from Otter point and Domwe Island. Further analysis using a Bayesian assignment approach supports previous findings and demonstrates the likelihood of introgressive hybridisation between an introduced C. afra and a native P. zebra population at Thumbi West Island. No evidence of introgression is found at Otter point and Domwe Island, where the C. afra and P. zebra populations show distinct genetic structure. The occurrence of introgressive hybridisation at Thumbi West between species from distinct genera shows that translocations can have a dramatic impact even on the gene pools of heterospecific recipient populations. The results from this work have crucial implications in evolution of cichlid fishes and in invasion biology when predicting the evolution of invasiveness. In summary, the thesis shows that hybridisation, as well as the introduction of multiple genetically differentiated source populations has increased the genetic diversity of introduced C. afra populations, and this may have facilitated their establishment in Lake Malawi National Park. Translocation of cichlid species in Lake Malawi can have a dramatic impact even on heterospecific gene pools.
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McMullan, Mark. "Host-parasite co-evolution and genetic variation at the major histocompatibility complex in the Trinidadian guppy (Poecilia reticulata)". Thesis, University of Hull, 2010. http://hydra.hull.ac.uk/resources/hull:5820.
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The Major Histocompatibility Complex (MHC) is a region of the vertebrate genome believed to be responsible for an individual's ability to detect and recognise invading parasites. The MHC molecule has been shown to bind to short fragments of parasite and present these to the adaptive immune system. Theory developed to describe the maintenance of polymorphism within the MHC has focussed on the principle that different MHC alleles recognise different groups of parasites and that parasite diversity maintains diversity in the MHC (i.e. Red Queen dynamics). Nevertheless, after 50 years of research, the precise mechanism for the maintenance of extraordinary levels of polymorphism in the MHC remains yet to be resolved. In the present thesis, I use guppies (Poecilia reticulata) as a model to investigate the role of parasites in the maintenance of polymorphism in the MHC. In a study of spatial variation of both MHC and microsatellite variation, I find evidence to suggest that upstream populations of guppies have small population sizes and reduced gene flow into the population. However, these populations of guppies maintain similar levels of MHC polymorphism to that of larger populations of guppies further downstream. The maintenance of MHC in small upstream populations provides evidence for selection for the maintenance of MHC polymorphism despite the effect of random genetic drift. This finding is particularly interesting given that I show that this small upstream population has a significantly reduced parasite fauna. These data therefore provide evidence for other sources of selection on the MHC such as sexual selection or Associative Balancing Complex (ABC) evolution. Balancing selection maintains polymorphism above that expected under a neutral model of evolution. However, balancing selection is a general term that encompasses several distinct mechanisms, including negative frequency dependent selection (rare allele advantage), overdominance (heterozygote advantage) and selection that favours distinct alleles in different times and/or places (fluctuating selection). I use a temporal dataset of MHC and microsatellite variation to distinguish between these different models of balancing selection. In particular, I evaluate the ability of the different models of balancing selection to explain the empirical data of two guppy populations sampled in 2001 and 2007.1 conclude that the relatively low level of spatial genetic divergence of the MHC in 2001 is most consistent with the overdominance and negative frequency dependent selection models of balancing selection. By contrast, the data in 2007 suggest that MHC is subject to fluctuating selection, showing a higher level of spatial genetic differentiation than the microsatellites. Overtime, the MHC appears to change more rapidly than neutral microsatellite loci. Using a verbal model, I argue that this pattern of temporal genetic divergence and the rapid turnover of MHC alleles is consistent with all types of balancing selection. Balancing selection increases the effective migration rate, resulting in a rapid differentiation of the MHC gene pool over generations. Such allelic turnover can however only be realised in a metapopulation with a large gene pool of MHC alleles. Both these conditions (i.e. a source-sink metapopulation with circa 85 MHC alleles) have recently been demonstrated for guppy populations in the Caroni Drainage in Trinidad by different authors. Importantly, these findings demonstrate that in an open metapopulation, the impact of migration can differ dramatically between neutral genes and genes under balancing selection. Using a simulation model, I further explore whether the combination of balancing selection (in particular, overdominance) and gene flow in a metapopulation system can explain the large observed spatio-temporal differentiation of the MHC. Traditionally, authors have interpreted large temporal fluctuations in MHC allele frequencies as evidence for a coevolutionary arms race between host immune genes and parasite virulence genes (i.e. Red Queen dynamics). In this theoretical chapter, I explore whether such data can also be explained by simple overdominant selection in combination with migration from a source population with many distinct MHC alleles. I find that the commonly held assumption that balancing selection homogenises gene frequencies and reduces the level of genetic differentiation (G'sr) is not always correct, and it depends on the interaction between evolutionary forces and population demography. Furthermore, I demonstrate that balancing selection (overdominance) can explain the rapid turnover in MHC alleles, and that this observation should not be taken as evidence of Red Queen dynamics through host-parasite co-evolution. Altogether, this thesis highlights two main considerations that should be made in future studies of the MHC. Firstly, other sources of balancing selection should be considered in addition to parasite selection, particularly where no causal relationship between parasites and MHC alleles has been identified. Secondly, population demography can have a different impact on the population genetics of the MHC compared to that of neutral loci. The effect of a higher effective migration rate on MHC alleles is all too often interpreted as evidence for changes in the direction of parasite-mediated selection (i.e. Red Queen dynamics). However, theoretically, other forms of balancing selection, including overdominance, negative frequency dependent selection, fluctuating selection and ABC evolution, can also drive the temporal dynamics of the MHC.
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Simon, Andrea. "Genetic factors affecting establishment during invasions : the introduction of the topmouth gudgeon (Pseudorasbora parva) and the rainbow trout (Oncorhynchus mykiss) in Europe". Thesis, University of Hull, 2012. http://hydra.hull.ac.uk/resources/hull:6254.
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The study of biological invasions is a major research topic, both because of the ecological and economical damage caused by invasive species and also as a great natural experiment to study evolutionary responses of non-native populations to their new environment, and the factors influencing invasions. Introduced species often evolve rapidly, despite the assumed loss of genetic variation associated with bottlenecks during the invasion process. In order examine the processes and mechanisms affecting the outcome invasions I studied two non-native fish species, the topmouth gudgeon (Pseudorasbora parva) is an Asian cyprinid that is found in most European countries as a result of accidental introductions. Rainbow trout (Oncorhynchus mykiss) has been introduced from the United States for aquaculture and angling, however, despite numerous introductions, it has only been able to establish in few European waters. I used mitochondrial DNA and microsatellite markers to understand the invasion history of these species and the factors that influence their establishment success/failure. Part of the cytochrome b gene was analysed in European and native Asian P. parva populations and microsatellite markers were used to investigate the source populations of the species. The analyses elucidated the colonisation pattern of P. parva in Europe and supported the hypothesis that the species spread through long-distance and stepping-stone methods and originate from admixed source populations. In O. mykiss, part of the d-loop region of the mitochondrial genome was analysed to compare the phylogeographic structure of native US and introduced European populations to examine the spread of the species outside its native range, as well as to find out whether the resistant Hofer strain is the source population of the European rainbow trout populations. I found that European populations are likely to originate from various sources, mainly from California. The Hofer strain is likely to have contributed to some of the wild European populations. Assessing the role of these processes is fundamental in understanding invasive species and finding suitable management practices to control them. From an evolutionary point of view, I was able to detect some of the processes that are important during invasions, in these studies particularly the role of multiple introductions and introduction from genetically admixed source populations.
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Bolland, Jonathan David. "Factors affecting the dispersal of coarse fish". Thesis, University of Hull, 2008. http://hydra.hull.ac.uk/resources/hull:1366.
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Globally, freshwater fisheries are faced with numerous impacts that compromise fish populations. A knowledge and understanding of riverine fish movements are crucial for effective management and conservation of populations. However, there is a paucity of information about the spatial behaviour and ecology of wild and stocked cyprinids in floodplain rivers, especially under the influence of elevated flows. This study examined the factors affecting the lateral and longitudinal dispersal of juvenile and adult (wild and stocked) coarse fish in three lowland river catchments, namely the River Trent, the Yorkshire Ouse and the River Roding.A literature review was carried out to review the influence of floods on riverine ecosystem function and structure, and fish assemblage patterns. In unmodified lowland rivers, floods are characterized by lateral expansion onto floodplains resulting in high levels of habitat heterogeneity, essential for fish refuge, spawning, nursery and feeding. However, anthropogenic alterations to the flow regime and floodplain connectivity have had considerable detrimental impacts on fish populations. The main conclusion of the review was the need to restore and rehabilitate lowland rivers in an attempt to recover natural features or functionality. The effects of flood timing and magnitude were examined by sampling 0+ fish populations before, during and after floods in the Yorkshire Ouse, a constrained lowland river. Large numbers of eurytopic 0+ fishes were stranded on isolated floodplains when artificial levees ‘over-topped’ in summer (August). By contrast, backwaters provided refuge for high densities of 0+ eurytopic and rheophilic fishes. During floods, small fish were displaced or had lower survival. The results highlight the influence of flood timing on 0+ fish populations, the use of refuge areas and their importance of lowland river rehabilitation.In the River Trent, 0+ fish populations were sampled in the margins of the main river channel and in ten man-made floodplain waterbodies to evaluate the importance of variable connectivity between these habitats for rehabilitating the riverine-floodplain ecosystem. Fish assemblages compared favourably with studies on unmodified river reaches, i.e. succession of lotic-to-lentic habitat corresponded to a sequence of rheophilic-to-eurytopic-to-limnophilic fish species. Consequently it was concluded that the connection of man-made floodplain waterbodies to the river should incorporate variable, not just high, levels of hydrological connectivity into holistic riverine ecosystem management plans.Dual-Frequency Identification Sonar (DIDSON) was used to determine the influence of elevated flow on the lateral movements of adult fish between the Yorkshire Ouse and a marina (refuge habitat). Fish activity in the entrance was predominantly during daylight hours. Increased river flow resulted in significantly reduced fish movements, both towards and away from the marina, and fish presence in the entrance, except for larger fish (more than 30 cm) during the night. This study emphasised the importance of artificial floodplain waterbodies for adult cyprinid fish during winter months.The influence of environmental variation (flow and temperature) on movements of wild and stocked adult cyprinids is poorly understood, partially because of experimental difficulties. A laboratory study on PIT tagging individual juvenile cyprinids, identified that the method would be suitable for such investigations. In the River Roding, a combination of PIT and radio telemetry was used to compare habitat use, longitudinal movement (timing and direction), site fidelity and survival between wild populations and hatchery-reared fish. Wild cyprinids had high levels of ‘site fidelity’ but highly mobile individuals were present within the population, with movements positively correlated with temperature and flow. During elevated winter flows, wild fish occupied areas of reduced flow to reduce energy expenditure, but some fish performed exploratory movements. Movements of stocked fish were more frequent and longer than for wild fish, particularly just after release, possibly for exploratory purposes. Subsequently, movements of stocked fish were minimal, did not correlate with flow or temperature and the final distributions were more widely dispersed than found in wild fish. Importantly from a stocking perspective, stocked cyprinids had the behavioural and physiological ability to cope with elevated flows. However, differences in movements and habitat use between wild and stocked chub probably had consequences on survival.
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Welters, Ruth. "Spatial and temporal genetic variation in small and declining populations of Atlantic salmon". Thesis, University of Hull, 2008. http://hydra.hull.ac.uk/resources/hull:1689.
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Atlantic salmon is protected under national and European legislation but most populations are declining. The research investigated population size, habitat quality, population structure and stability over time using Atlantic salmon parr in the River Frome (a chalk stream in Dorset, England) surveyed at 15 sites, in summer and autumn over three consecutive years. The hypotheses were: * Abundance of juvenile Atlantic salmon in a chalk stream is related to habitat quality. * There is significant genetic differentiation between Atlantic salmon within one river, despite small geographic distance between sites and no barriers to migration. * Temporal stability of spatial population structure of Atlantic salmon occurs within a river. Habitat quality, assessed using HABSCORE, varied between sites and over time. Habitat quality was not a predictor of juvenile density but presence of adult brown trout reduced juvenile numbers. DNA for molecular analysis was extracted from fin-clips (removed non-lethally) and genetic variation and distribution of genetic variation was assessed using 5 microsatellites. Relatedness tests indicated that some 0+ parr within a site were closely related. It was inferred that 1+ parr had moved from their natal site, as they could not be assigned to a site of origin. Moderate heterozygosity was detected at each sample site. Low, but significant, genetic differentiation over all sites was detected in summer and autumn for three consecutive years. Isolation by distance was detected at two out of the six sample times, despite small distances between sites. This was strong evidence for structuring within the population. Using a new statistical test, no temporal stability of spatial population structure was detected in the River Frome, but significant temporal stability was detected using published data for Atlantic salmon in a Canadian river.
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Zhang, Dong. "Chemical communication and its ecological consequence in the Lysmata shrimp". Thesis, University of Hull, 2009. http://hydra.hull.ac.uk/resources/hull:2422.
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Male crustaceans must find and identify receptive females to mate successfully. Mate recognition depends mainly on sex pheromones, which are detected by antennae and antennules. Distance (soluble)pheromone mediates mating behaviour of some decapod crustaceans. Contact pheromone (an insoluble coating on the body surface) has been proposed but not confirmed to be used by male decapod crustaceans to detect females. Here we report for the first time the involvement of both distance and contact pheromones in the mating processes of Lysmata shrimp (a group of protandric simultaneous hermaphrodites), and we have partially identified the soluble and contact pheromones. Additionally, evolution of the sex pheromone system of Lysmata shrimp, and role of the sex pheromones in reproductive isolation of Lysmata shrimp were investigated.
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Smith, Katie. "The impact of erythropoietin on uraemic cardiomyopathy". Thesis, University of Hull, 2009. http://hydra.hull.ac.uk/resources/hull:2679.
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Cardiovascular complications are the leading cause of death in patients with chronic kidney disease (CKD). The uraemic heart is characterised by cellular and structural remodelling, including left ventricular hypertrophy LVH), which contribute to heart failure. Erythropoietin (EPO) has evolutionised the treatment of the anaemia associated with CKD. The discovery that the EPO receptor is also expressed on cardiomyocytes highlights a role of EPO beyond haematopoiesis. However, little is known on the cellular impact of EPO on the uraemic heart. The aim of this study was to determine the effect of EPO administration on uraemic cardiomyopathy.Uraemia was induced surgically in male Sprague-Dawley rats via a subtotal nephrectomy and animals retained for 3, 6, 9 or 12 weeks post-surgery. EPO was administered subcutaneously twice a week for 2 weeks prior to sacrifice at a dose of 30 μg/Kg. Cardiac function was assessed in vitro in the perfused heart and in vivo using an arterial pressure catheter. Cardiac metabolism was analysed using 13C NMR along with the activity and protein expression of key metabolic enzymes. In a separate set of experiments, mitochondrial function was determined in vitro using an oxygen electrode. To determine the extent of cardiac fibrosis, collagen was stained using picro-sirius red in frozen sections.Kidney dysfunction was observed from 3 weeks post-surgery as evident by significantly raised serum creatinine and urea, and development of anaemia. LVH was present at 6 and 12 weeks post-induction of uraemia, however in vitro and in vivo cardiac function was preserved,highlighting a compensatory phase. EPO did not impact on renal function, however, EPO significantly improved haematocrit and induced regression of LVH in uraemic animals at 12 weeks. In addition to preserved cardiac function, myocardial mitochondrial respiration was not modified by uraemia and unaffected by EPO administration. There was a decrease in palmitate utilisation in uraemic hearts compared to controls at 6 weeks post-surgery despite the unchanged activities of key metabolic enzymes including citrate synthase, medium chain acyl-CoA dehydrogenase and pyruvate dehydrogenase activity. Furthermore, the protein expression of CD36 and PPARα was the same in uraemic and control hearts. At 12 weeks post-surgery, uraemic animals exhibited significantly increased collagen within the heart compared to controls, highlighting cardiac fibrosis.In summary, by 12 weeks post-induction of uraemia, animals exhibited impaired kidney dysfunction, LVH, metabolic remodelling and cardiac fibrosis with preserved cardiac and mitochondrial function. Further work is required to determine whether the structural and metabolic remodelling which accompany uraemic cardiomyopathy would lead to a deterioration in cardiac function with prolonged uraemia.
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Swig, Bryan Allen. "The recreation of estuarine ecosystem : a case study at Paull Holme Strays, Humber Estuary, UK". Thesis, University of Hull, 2009. http://hydra.hull.ac.uk/resources/hull:2560.
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Habitat restoration can partially compensate for the extensive loss of coastal wetlands, which are transitional habitats that form the barriers between seas and oceans and the terrestrial environment. Coastal wetlands historically due to their location have either been altered by flooding or draining to suit human needs. Coastal wetlands when left unaltered function as water filters, flood buffers, nurseries for juvenile nekton and as wildlife habitat for birds and animals. Creation of costal wetland habitat with intact ecological functions remains a challenging task. Paull Holme Strays (PHS) is an example of a restored coastal wetland on the Humber Estuary, UK. This site was restored to natural coastal wetland in 2003, and is an effort in the restoration of both mud flat and salt marsh. To evaluate immediate restoration success of the restored wetland at PHS, the development of the abiotic [environmental] and biotic parameters (benthic invertebrate community development, shore bird assemblages and fish assemblages) at PHS were monitored. for the 3 years following restoration and compared to adjacent unaltered mudflats and salt marshes. In addition to the field surveys experimental studies on the colonization of halophytes within the salt mars were conducted. The study indicates that an abiotic factor such as sediment accretion is occurring at a rapid rate in the northwest of the restoration site. Grain size and organic content have remained constant and are at levels comparable to those in a natural reference habitat. The study also indicates that there has been an immediate biotic response to restoration, as both the biomass and species richness of invertebrates using the restoration site have increased since monitoring began, however levels are still lower than those of the natural reference habitat. Shorebird species diversity and densities were frequently as high in the restored habitat of PHS as in reference natural habitat between 2004 and 2005, although each species preferred specific sites. The examination of fish assemblages between 2004 and 2006 revealed that densities and species diversity were as high or higher in the restored habitat of PHS in comparison to reference unaltered habitats. The experimental studies of halophyte colonization, aimed to determine whether colonization could be expedited and showed that doing nothing to compacted farm soils prior to reinstatement of the flooding provided the best for initial colonization. These filed surveys that were conducted show that although restoration of PHS provided adequate habitat for some wetland species immediately, it takes decades for restoration sites to develop completely. Experimental manipulations allow evaluation of ecological functions and can supplement structural assessments of restoration success. This work indicates management measures, which will allow the development of new restoration sties to occur more rapidly, allowing for costal wetland function to start sooner.
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Rollins, Darren James. "The efficacy of back calculation methods for determining length at age data and the use of such data to determine growth standards, national growth patterns and recruitment dynamics of roach (Rutilus rutilus (L.)), dace (Leuciscus leuciscus (L.)) and chub (Leuciscus cephalus (L.)) in UK rivers". Thesis, University of Hull, 2009. http://hydra.hull.ac.uk/resources/hull:6740.
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The use of fish scales to age and back-calculate previous lengths at age and gain age and growth information has long been used as a management tool in fisheries. Calcified structures from fish, including otoliths, fin rays, and vertebrae have been used to gain length at age data. Scales however, are the most common structure used for aging freshwater fish (Borkholder and Edwards 2001). In order to gain accurate back-calculated length at age data gained from fisheries surveys, an appropriate method of back-calculation was sought. A number of back-calculation methods were found from the literature and applied to data from fish surveys. Back-calculated lengths at age from specific cohorts were compared to observed mean lengths at age from historic surveys, revealing the method proposed by Hile (1941) as being the most consistent method for providing accurate length at age data from fisheries surveys. Comparative assessments of population mean growth rates remain important aspects of stock assessment in river fisheries (Britton 2007). Standard growth curves were originally produced for roach, dace, chub and bream (Hickley and Dexter 1979) and later expanded to include pike (Hickley and Sutton 1984). Habitat rehabilitation (Quinn 1994) and water quality improvements (Environment Agency 2001; 2006) are among a number of factors that have changed in rivers since the inception of the standard growth curves. Comparison of standard growth curves produced in this study and those produced by Britton (2007) against the original growth standards affirm the suggestion that the observed growth of these species has changed. Standard growth curves were produced and proposed for use as an updated comparative data set and an update to these standard growth rates is made on a regular basis. Riverine fish communities are highly structured and follow non-random patterns along a longitudinal profile (Jackson et al. 2001). Plasticity in the growth of fish along the longitudinal gradient of rivers has been demonstrated (Cowx 1988; Zelt et al. 1999). This study affirms the longitudinal plasticity in the growth of roach, dace and chub along the longitudinal gradient and reveals areas where conditions are conducive to better growth in these species, namely the downstream areas for roach and the upstream areas for dace and chub. Many studies have demonstrated growth rates as being dependent on geographical variation (Pyron 1999), with evidence that some fish species attain larger sizes at lower latitudes (Modde and Scalet 1985) while other studies demonstrate increased growth at higher latitudes (Isley et al. 1987, Conover and Present 1990). Latitudinal variation of fish growth characteristics from rivers throughout England and Wales revealed the growth rate of dace as being strongly related to latitudinal position, with the growth of dace showing a preference toward the cooler temperatures in the higher latitudes. Roach were found to prefer the lower latitudes where temperatures were higher, while chub were found to prefer the high latitudes and easterly longitudes. The year class strength of fish is an important index in the management of freshwater fisheries (Cowx and Frear 2004) with early developmental stages representing a crucial period in cyprinid fishes where variations in mortality during this period are critical in determining year class strength (Cowx 2001). A number of specific periods, where elevated flows occurred, were found to be related to the year class strengths of roach, dace and chub and identified as being important in playing a role in determining year class strength. The Gulf Stream was demonstrated as having a relationship with the flow regimes of a number of rivers which in-turn related to variances observed in the year class strengths and mean lengths at the end of the first year of life, of the fish species analysed. Northerly shifts in the Gulf Stream were found to have a positive influence in the growth characteristics and consequently the year class strengths in a number of the populations tested. A lag phase in the influence of the Gulf Stream on year class strengths was also identified in roach, dace and chub from a number of rivers. In this instance it was postulated that northerly shifts in the Gulf Stream produced conditions conducive to the growth of the adult fish stock which may in turn relate to an increased fecundity and/or the production of higher quality gametes from an increased condition of the adult stock.
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Portocarrero, Aya Marcela. "Conservation of freshwater biodiversity in key areas of the Colombian Amazon". Thesis, University of Hull, 2011. http://hydra.hull.ac.uk/resources/hull:5386.
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Freshwater ecosystems maintain incredible ecological processes that support millions of species, including human beings. Important goods and services ranging from food and building materials to water cleansing, flood and erosion control, cycling of nutrients and flow of energy are provided. With expansion of the human population, the maintenance of economies based on extraction patterns and the dependence of people on natural resources (especially aquatic resources), the conservation of freshwater ecosystems is at serious risk. Due to this crisis it is a priority to implement effective conservation strategies that ensure the mitigation and prevention of threats and contribute to the proper use of freshwater biodiversity. Currently, the identification of key conservation areas has become one of the most accepted strategies among conservationists and local inhabitants. This strategy is essential in a country like Colombia where Amazonian rivers and lakes hold approximately 3000 species of algae and fish, provide at least 80% of the animal protein consumed by local communities, support daily transport, communication and recreation activities, and are the main supply of drinking water. This research constitutes the first attempt to systematically identify key conservation areas in the freshwater ecosystems of the South of the Colombian Amazonian Trapezium. This effort considered not only fine filter targets (species) as central elements of decision making, but coarse filter targets (habitats), ecosystem services, social benefits, and threats. Due to the complexity of the study area, a multi-criteria assessment constituted the best way to tackle the issues affecting a complex ecological, cultural, social, economic and political territory. The use of conservation surrogates (species and habitats) constitutes an accurate conservation strategy to identify the dynamics between humans and the environment, enabling the identification of human stressors to the ecosystem. Five of the ten sites assessed, the Tarapoto Lakes System (1), Caballo Cocha Lake (Peru) (2), Yahuarcaca Wetland System (3), Loreto River (4) and the Mocagua Island and surroundings (5), are considered critical areas for special protection. The remaining five sites, Patrullero Island and surroundings (6), Atacuari River (7), River Amazon – Naranjales area (8), River Amazon – San Jose area (9) and Yahuarcaca creek (10), although were not considered as important as the former ones, but their inclusion in all conservation initiatives is vital to ensure the continuity of all ecological processes and biodiversity maintenance in the area. Conservation initiatives and management actions are proposed not only aiming to ensure the conservation of habitats and species, but also to ensure the protection of ecosystem services and the improvement of the livelihoods of local communities. These actions are addressed through nine working lines: Fisheries Management, Agricultural practices improvement, Habitat restoration, Environmental Education, Local Communities Empowerment, Spatial Planning, Stakeholders Network Enforcement, Scientific Research, and Central and local Governments organization and primordial actions. These lines and actions are intended to strengthen self-management processes of the local hydro-biological resources respecting both aquatic and terrestrial realms as well as the socio-cultural patterns of the region. This research attempts to make an effective contribution to the conservation of the freshwater biodiversity and the quality of life of local inhabitants of the Colombian Trapezium as well as to contribute to the implementation of the objectives of the Convention on Biological Diversity (CBD), Ramsar Convention on Wetlands, the Convention on International Trade in Endangered Species (CITES), the Convention on the Conservation of Migratory Species of Wild Fauna and objectives proposed in the Colombian and Amazonian Environmental Policies.
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Turnbull, Shona. "Epigeal invertebrates of Yorkshire allotments : the influence of urban-rural gradient and management style". Thesis, University of Hull, 2012. http://hydra.hull.ac.uk/resources/hull:5765.
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There is a growing interest in urban ecology but it can be a difficult environment for wildlife due to a range of anthropogenic pressures. Allotments could be used to study this issue but they have been rather neglected in terms of academic research, particularly in relation to their biodiversity value. A questionnaire of plot-holders in east Yorkshire showed that whilst older men were still the principal plot-holders, there was reasonable interest from younger people. Respondents placed a high value on allotment wildlife, regardless of age or management style of their plots. Highly significant percentages were willing to allow sampling on their plot. From the questionnaire data seven allotment sites were selected to represent an urban-rural gradient. The gradient was verified using a range of environmental factors suggested in part by the literature for gardens due to the similarities in habitat use. Pitfall trapping for epigeal invertebrates on forty-two plots found a trend of increasing abundance from rural to urban plots, with beetles, woodlice and spiders constituting 79% of the catch. Diversity was highest on one suburban site, but lowest on another. When the plots were split by either traditional or wildlife-friendly management style, woodlice and molluscs were more abundant on the wildlife-friendly plots, beetles more abundant on the traditional ones, whilst spiders, opilione and myriapods showed no significant difference. Three allotment sites representing the urban-rural gradient were compared in relation to the individual spider, woodlice and beetle species present and management style. Whilst spider diversity did conform to the intermediate disturbance hypothesis, the beetles and woodlice did not. The majority of species found were generalists, thus conforming to the opportunistic species hypothesis. Most taxa could be categorised as either neutral or beneficial in terms of bio-control. Allotments offer great opportunities for further research regarding their biodiversity value.
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Katoh, Emi. "Sex, pheromone and aggression in Norway lobster (Nephrops norvegicus) : for a better future of scampi". Thesis, University of Hull, 2011. http://hydra.hull.ac.uk/resources/hull:6228.
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With a steadily increasing world population the demand for seafood has been growing rapidly over the past century. This has led to overfishing and decreasing catch rates in many seafood species. High fishing activity has endangered several aquatic species and pushed others to extinction. Signs of high fishing activity were also found in the Nephrops. In order to secure sustainability of important seafood species such as the Norway lobster (Nephrops norvegicus) it is important to intensify the research efforts on these species. Aggressive behaviour and injury are major constraints of communal holding of aquatic animals. A good knowledge of reproductive behaviour and larvae development is important for any hatching programs. Therefore, the aim of this thesis was to provide a research base that can improve sustainability of Nephrops and their well being in captivity, in order to culture them. Both male and female Nephrops show fighting behaviour. However, only in fights with males a clear dominance relationship was maintained. Males and females recognise the higher status of their male opponent. Blocking of urine release showed that chemical communication by urinary signals is important in maintaining dominance relationships between males. When comparing communal holding conditions to individual holding conditions over one months, no difference in death rate was found, indicating that a stable dominance hierarchy reduced aggression between animals that were kept in communal tanks. Although females lack the ability of recognising dominance in other females, they do recognise dominance in males. Male Nephrops have larger claws compared to the females showing additional sexual dimorphisms in the species. Moreover, Nephrops with larger claws tend to win the fights showing that claw size affects the outcome of fights. In lobsters, mating usually occurs after the female has moulted, and is in the soft shell condition. In Nephrops the highest number of matings occurred when the females were in the soft shell (postmoult) stage, but many males also tried to mate with a hard shelled (intermoult) female when the odour of a soft shell female was present. This indicates that soft shelled female odour has an important effect on male behaviour. Similar to European lobsters (Homarus gammarus) and American lobsters (Homarus americanus), some Nephrops males also mate with hard shelled females even if no chemical cues from soft females are present. Thus, intermoult mating indicates the presence of female sex pheromone beyond the post moult stage. This thesis provides applicable information to improve the Nephrops fishing industry and gives further details to enable Nephrops culturing in the future.
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Davies, Matthew John. "Chemical communication in the European otter, Lutra lutra". Thesis, University of Hull, 2008. http://hydra.hull.ac.uk/resources/hull:2574.
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European otter (Lutra lutra) scent marks (spraint and anal sac secretion material) from captive and wild animals were analysed using solvent extraction and solid phase micro extraction (SPME). An ageing study (using SPME) mapped spraint chemical composition changes following deposition and how low temperature storage and exposure to the environment affected these changes. Chemicals with opposite time dependence were found; providing a possible spraint ageing mechanism. Temperature and environmental conditions affected the rates of production and deterioration of these chemicals and therefore the accuracy of spraint age estimations. Identification of the fatty acid content of otter scent marking material from 4 otter species led to both intra-specific (L.lutra) and inter-specific (Canadian river, Lontra canadensis; Asian short claw, Aonyx cinerea; and Giant, Pteronura brasiliensis) comparisons. Low volatility fatty acids (C10-C24.1) were found in all scent mark types. Intra-specifically, differentiation was seen in spraint fatty acid profiles based on sexual identity. Differentiation was observed between L. lutra scent marking material types (Captive spraint; Wild spraint; Wild anal sac secretion). Inter-specific differences relied on a mixture of ‘digital’ and ‘analogue’ coding. SPME and gas chromatography – mass spectrometry (GCMS) were used to investigate intra- (L.lutra) and inter- specific (L. lutra, A. cinerea, L. canadensis, and badger, Meles meles) differences in the headspace chemicals of otter scent marks. Inter-sanctuary (possibly diet related) differences in spraint odour of L. lutra were seen. No overall male - female differences were found, although possible intra-sanctuary sexual differences were seen. Inter-specific differentiation in scent mark odour profiles due to a combination of both analogue and digital coding elements was observed.
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Ramli, Mohd Fadzil Shuhaimi bin. "Impacts of coastal land reclamation on the fisheries of Mukim Lekir, Malaysia". Thesis, University of Hull, 2005. http://hydra.hull.ac.uk/resources/hull:11158.
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In 1997, land reclamation works began in the coastal area of Mukim Lekir. Ultimately, an area of 8,094 ha was planned to be reclaimed along Lekir's coastline, but to date; only Phase 1 of the project has been completed. The Phase 1 project of 405 ha, created a man-made island for the location of a 2,100MW, coal-fired power plant; a first of its kind in Malaysia. Although the reclaimed land was only 5 % of the total intended area, its impacts on the livelihoods of the coastal communities, especially fishers, were serious and nearby mangroves were degraded. The effect of this intervention was observed to be long-term, contrary to the claims made by the project proponents. Fishers and other coastal inhabitants incurred monetary losses, which were neglected by the project proponents, who also failed over the issue of compensation. This study attempts to establish evidence that the project caused hardship to coastal population, especially fishers who depended on fishery resources that were found to decline after the commencement of the project. It began by assessing the status of fish stock, analysing its catch-rates trend and comparing them with resource status before the project. A socio-economic survey by face-to-face questionnaires interview was carried out on the population to obtain information on how the project had affected their livelihoods in terms of incomes, job opportunity, fishing activities, pollution, etc. The research design intended to prove that environmental degradation was caused by the project by comparing the status of resources before and after the intervention. On the issue of compensation, losses were valued in monetary terms, so that it was easily understood and appreciated. The purpose of valuing damages was to allow affected persons to claim compensation in monetary terms. This study emphasized losses through mangrove degradation and losses as result of fishery resources declining. In addition, losses incurred by cockle farmers and the government were also gauged. For mangrove degradation, a survey using the Contingent Valuation Method was carried out to estimate people's willingness to pay (WTP) on a hypothetical project aiming to protect the mangroves. The amount they were WTP was the benefit loss of not being able to use the mangroves. Other losses valuation was straightforward since it involved marketable or tangible goods. The standing of fishers and other affected communities claiming compensation in the court of laws was discussed. Fish stock assessment done in 2002 and 2003 in the Lekir waters indicated that the resource showed a declining trend since 1996. Commercial fish declined at a greater rate in sub-area A, which was closer to the impacted area, than in sub-area B; located further away. Subarea A was also found to loose its potential as breeding and nursery grounds, since fewer juveniles and fingerlings were caught compared with the 1996 survey. The decline in the fisheries indicative from the surveys was verified by fishers who complained of reduced catches and incomes. In the socio-economic survey, fishers were found not to benefit from the development since the project did not provide them with employment opportunity or generate other kinds of income-induced opportunity. The degradation ofthe mangroves and the fishery were proven to be caused by the present of the project since the control areas, in the absence of perturbation did not show similar characteristic as the impacted areas. The benefit loss of mangrove use was estimated at RM 81,959/year whereas other society losses were RM 118,333,321 in the six years since the perturbation. If fishers were to claim compensation, they have to prove that their losses were above and over the general public and preferably under the rule of Rylands V Fletcher. Other segments of the society may need government intervention since they were claiming pure economic loss, which is unrecoverable in the Common Laws. This study does not advocate monetary compensation to each affected individual but prefers long-term aid to regenerate rural livelihoods. Economic projects are proposed involving active participation of the community. Further researches are also suggested to improve data collection, developing comprehensive stock assessment and improving EIA procedures.
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Tessier, Wayne Danny. "The role of aldehyde dehydrogenases in Acetyl-CoA production by Saccharomyces cerevisiae". Thesis, University of Hull, 1998. http://hydra.hull.ac.uk/resources/hull:11284.
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Selim, Abdalla Eliwa Mohamed. "Sedimentation threats to Red Sea corals : an ecological study of reefs in the Hurghada Region, Egypt". Thesis, University of Hull, 2007. http://hydra.hull.ac.uk/resources/hull:2689.
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Hurghada coastal reefs have encountered a huge modification in the last three decades, associated with an increase in sediment input from coastal development. The aim of this study was to examine the impact of sediment on reef health at a number of sites along the coast of Hurghada encountering differing sedimentation loads. A range of physicochemical parameters were measured in the field and related to a variety of reef health indicators. This was supported by laboratory based experiments examining the direct impact of sediment on coral bleaching and mucus production. Annual and seasonal patterns of sedimentation were investigated along the Hurghada coastal area of the Red Sea using sediment traps. Suspended particulate matter (SPM) and the percentage of non-carbonate sediment in bottom sediment were sampled. Physicochemical parameters measured in the field included temperature, salinity, depth, pH, specific conductivity SPC, dissolved oxygen DO, total dissolved salts TDS, percentage of dissolved oxygen DO% and turbidity using a multprobe. Inorganic phosphates, silicate, ammonia, nitrite and nitrate concentrations were determined. Reefs were surveyed to determine a number of reef health indicators including coral cover, percentage of live and dead coral, new recruits, abundance, species richness, the percentage of r-strategist, Diversity Index, Deterioration Index (DI) and disturbance. Three species of Acropora were transplanted in this study and their survival was investigated. Six fish families were surveyed using belt transects to examine changes in community structure. Zooxanthellae density was measured in transplanted corals in field and laboratory conditions to determine the effect of sedimentation on coral bleaching. In addition, direct feeding experiments were performed using fluorescein-isothiocyanate sediment to assess coral ability to cope with higher sedimentation. Mucous secretion by corals was measured in field and laboratory to test variations under different sedimentation condition. Significant differences between sites in sedimentation rate, SPM and the percentage of non-carbonate sediment were observed. Sedimentation and SPM were also shown to reduce coral cover, species richness, diversity, mean colony size of branched corals and the abundance of algal feeding fish. Other parameters such as non-carbonate sediment, turbidity and percentage of mud in bottom sediment affected corals and fish to various degrees. Sedimentation did not appear to reduce the number of live or dead corals or new recruits. In addition, it did not affect the distribution of r-strategist as a pioneer group of corals. It did not affect transplant survival or macroborer distribution, although it did reduce zooxanthellae density and increase mucus secretion and sediment uptake by Lobophyllia hemprichii. Coral abundance, mean colony size of massive corals and coral feeder abundance were not reduced under the observed sedimentation conditions. The Deterioration Index did not provide a strong tool to gauge coral condition in this study. Although many indicators did not show significant correlations with sedimentation, SPM, turbidity or non carbonate sediment, it was found that sites with the highest readings of these parameters has the lowest biological quality. These finding support early studies that showed that low sedimentation levels do not have significant impact on coral health. Some sites showed continuous degradation and increased level of sedimentation from land sources and need urgent mitigation measures to be followed by coral restoration and transplantation.
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Pai, Namrata. "Development of novel methods for the detection of Vibrio parahaemolyticus in seafood". Thesis, University of Hull, 2003. http://hydra.hull.ac.uk/resources/hull:5591.
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Vibrio parahaemolyticus is marine bacterium found worldwide. It is most commonly associated with seafood related gastroenteritis, but can also be found naturally occurring in the estuarine environment. Infection is most common in the summer months, when the water temperature is suitable for the growth of bacteria. The infection is usually self limiting but morbidity can result in some cases. Currently very few methods are in use for rapid detection of this organism. In addition, these methods are not always specific and can give false positive reactions. This study describes the development of a novel method, based on phage antibody display, for the detection of V. parahaemolyticus in seafood. The initial part of the study focuses on the use of the Polymerase Chain Reaction (PCR) as a rapid method for the detection of V. parahaemolyticus. Four sets of primers were used for PCR, of which three were targeted to the toxin producing genes. The sensitivity and specificity of these primers in PCR was tested using pure cultures of V. parahaemolyticus and non parahaemolyticus spp. Homogenised oyster tissue was then seeded with these cultures and they were tested again by PCR. A semi-synthetic scFv bacteriophage antibody library was used to isolate bacteriophage antibodies against V. parahaemolyticus. After five rounds of panning, the clones were further tested by ELISA and flow cytometry. At least four of the clones showed a strong binding profile with strains of V. parahaemolyticus. These clones also did not cross-react with other Vibrio spp. Similar to the PCR reaction, the clones were tested by seeding oyster homogenate with bacterial cultures. It was found that the ELISA reaction was inhibited by the presence of oyster homogenate. Therefore, a3h pre-enrichment step was necessary before testing for the presence of bacterial cells. The phage antibody clones which showed strong binding in pure culture still retained their binding capacity, when tested in the presence of seafood (oyster homogenate). The sensitivity of the assay was further increased by using chemiluminescence detection of phage binding. The data also suggests that this method has the potential sensitivity to detect V. parahaemolyticus at or below the current action level.
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Al-Hafidh, Alawi Salim Ali. "Assessment and management of the abalone (haliotis mariae, Wood 1828) stock in the Omani waters". Thesis, University of Hull, 2006. http://hydra.hull.ac.uk/resources/hull:5661.
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This study investigates the status of Abalone fishery (Haflotis mariae) in the southern region of Oman. This fishery has been an important and valuable resource to both the population in this region as well as for the country. The fishery began around 1970 and produces annually between 29-56 t of fresh meat with the highest production during 2003 valued at 8.4 million US$, (but most of the landing during the last few years is below the minimum legal size of 90 mm shell length). This extraordinarily value has resulted in intensive fishing operations and the fishery today faces a serious decline in stock density and availability of large individuals. This study aims to assess the reasons for the decline, and provide information on the status of the fishery to develop a management plan. The study was carried out over two years including monthly sampling from three selected permanent stations: Mirbat, Hadbin and Sharbithat, following by an intensive survey along the whole coastline. It covers aspects of the ecology and dynamics of this fishery and presents information on the abalone distribution, abundance, morphometry and size composition structures, habitat, competitors, predators, commercial production and marketing, biochemical composition, environment parameters, preservation, genetics, biology including growth, reproduction, spawning season, sex distribution, maturity stages and size at first maturity. The fishery is restricted to the southern coastline, which is strongly influenced by the monsoon winds, which result in major changes in the environmental conditions and the upwelling of deep-cold nutrient-rich water. This could regulate the limited distribution of this fishery between Ras Mirbat and Suqrah. They occurred at more exposed shores at depths up to 20 m, but most of the populations are found between 5-10 m. Abalone habitats were mostly destroyed and showed signs of degradation in algal cover. Sea urchin is the main competitor present at 25 times the number of abalone. Sea star also abundant and shows sign of predation on abalone. Abalone population density was 0.07 individuals/m², which is inadequate to support a good reproductive level and maintain a sustainable fishery. The remaining stock was calculated at 707000 pieces (54.5 t of flesh wet weight). This fishery is regulated through a fishing season for two months a year combined with a MLS of 90 mm SL, but 50% of the divers catch is below this limit. Most of remain populations are of small and medium sizes. In addition, females are larger than males resulting in fishing selectivity; therefore, fewer females remain in the population, which has an impact on reproduction and recruitment. The species sexually matured at sizes over 60 mm SL. Spawning occurs from November to March/April at all the three sites. Growth is faster in the first year and decrease with age. Fishing mortality is high and egg production very low. Populations of Haliotis mariae found in all the three study areas of Oman were genetically linked. The H mariae stock is considered seriously compromised and the remaining population seems unsustainable under current fishing pressure combined by environment destruction and other biological failures. Reduction of exploitation rate by 50%, increasing the size at capture, relocating the fishing season, adequate monitoring, controlling and surveillance with strong enforcement of existing legislation are necessary to conserve and protect the fishery. The resource user groups need to be involved in management process of this fishery and education programmes and awareness campaign should be introduced to highlight the need for divers to change attitudes and practices to make the fishery more sustainable. Research and further studies on more aspects of this fishery are recommended.
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Addico, Gloria Naa Dzama. "Toxic cyanobacteria, cyanotoxins and drinking water production in Ghana: implications to human health". Thesis, University of Hull, 2008. http://hydra.hull.ac.uk/resources/hull:5872.
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The management and control of cyanobacteria and their toxins in drinking water reservoirs and water supplies have engaged the attention of many scientists worldwide due to their negative effects on population health. The cyanotoxin, microcystin, the main focus of this research has been responsible for much documented illness in humans and is the most wildly studied cyanotoxin. The World Health Organization has set a guideline limit of 1 µg/l in drinking water. A number of methodologies have been used in this research. These include the use of an inverted microscope for the identification and quantification of cyanobacteria species after sedimentation in counting chambers. The biomass of picocyanobacteria was determined by epifluorescence microscopy after staining with DAPI. Extraction, purification and concentration of dissolved microcystins were done using the Solid Phase Extraction method. Identification of microcystins was done through comparison with commercial standards and their characteristic UV- spectra, and quantified by extrapolations of HPLC peak areas at 238 nin to a linear calibration curve for microcystin-LR standard. Nutrients (N0₂-N, N0₃-N and P0₃-P) in reservoirs in Ghana were analysed using the American Public Health Association standard methods. The results which are the first of their kind from Ghana, and for most part in West Africa, highlight that the water treatment processing currently in place is not effective in removing cyanobacteria cells from the final drinking water. Positive correlations were obtained between cyanobacteria biomass and nutrients concentrations in the reservoirs. Fifteen new cyanobacteria species were identified for the first time in Ghana of which Cyanogranisferrugineais reported for the first time in tropical waters. Four known microcystin variants -1R, -RR, - LF and -YR in both dissolved and intracellular samples were identified in four drinking water reservoirs. The study concludes that, the presence and dominance of potentially toxic small sized cyanobacteria such as Aphanocapsa nubilum, Cyanogranis ferruginea, Geitlerinema unigranulatum and other toxic cyanobacteria species like Cylindrospermopsis raciborskii, Planktothrix agardhii and Microcystis spp in the Weija, Kpong, Barekese and the Owabi reservoirs all with basic conventional drinking water treatment facilities, shown to be ineffective in removing cyanobacteria and their toxins, present a potential risk to human health through exposure to cyanotoxins such as microcystins and cylindrospermopsin. Even though the concentrations of dissolved microcystins obtained in the reservoirs and drinking water supplies were lower than the WHO limit, there is potentially a risk to public health and ongoing monitoring would be a good idea.
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Du, Feu Timothy Avon. "Tropical reservoir fisheries : Lake Kainji, Nigeria: a case study". Thesis, University of Hull, 2003. http://hydra.hull.ac.uk/resources/hull:5505.
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Al-Hosni, Ahmed Harib. "Food safety policy and management : a case study of implementing the HACCP system in the fish industry in the Sultanate of Oman". Thesis, University of Hull, 2002. http://hydra.hull.ac.uk/resources/hull:8613.
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Oman is one of the most important countries engaged in fishing in the Middle East. Fishing and agriculture have been traditional Omani occupations and sources of food and employment for the people in Oman. Over the last 40 years, many major food-importing countries have established strict hygiene regulations and legislation, including definitive standards for fishery products. Many countries exporting fishery products, particularly developing ones, did not have the mechanisms in place to meet such requirements. This led to rejection of consignments and economic losses, a fate suffered by Oman in 1997. Since 1997 Oman, has adopted a preventive approach to food safety, inspired by Council Directive 91/493/EEC and Commission Decision 94/356/EC. The acronym HACCP (standing for Hazard Analysis Critical Control Point) denotes the management philosophy and family of techniques employed to implement the preventive approach. In the light of these factors, it was considered important in this study to examine, through case studies, the extent to which HACCP principles and associated practices were being applied within the fish industry. Thus the difficulties of their application in practice would be assessed, and their reception in the fish processing industry reviewed. To meet this gap in knowledge, a survey was designed and carried out in all Omani regions. Such a study would determine the problems, as seen by the industry, that obstruct the proper implementation of HACCP. The aim of this study is to explore the process of HACCP implementation in the Omani food sector, using the seafood processing sector as a case study. To carry out this study, a triangulation method was employed to collect and validate both qualitative and quantitative data. A questionnaire was employed as the main method of data collection supplemented by semi-structured interviews of key-informants together with the application of a checklist against existing practices in the plants. The analysis of the food safety policy and management in Oman, in relation to the food industry as a whole, reveals that most problems experienced are those related to: a poorly developed institutional and legal framework; weak technical regulations; ill-defined inspection and approval procedures; lack of skilled staff for inspection and laboratory testing; many sub-standard processing factories; and the absence of adequate infrastructure for fish marketing. At the level of individual businesses, fish processing strategies for HACCP system implementation were investigated. The findings of this study are that most Omani fish processors are focused primarily on the development of their HACCP plans. Although developing of the HACCP plan is a fundamental part of the HACCP process, it is not widely understood among managers that this is just the beginning. The implementation and sustaining of a HACCP system can be a difficult and time-consuming mission. The study attributes this weakness to three main elements: poor training of personnel; shortcomings in prerequisite programmes; and a lack of commitment to maintenance of HACCP.
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Turan, Cemal. "Population structure of Atlantic herring, Clupea harengus L., in the northeast Atlantic using phenotypic and molecular approaches". Thesis, University of Hull, 1997. http://hydra.hull.ac.uk/resources/hull:8070.
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Most genetic attempts to study the population structure of herring (Clupea harengus L.) have been limited by the low levels of genetic differentiation observed among discrete spawning aggregations over large geographic scales. Thus, the population genetic structure of Atlantic herring remains undefined. Three sets of phenotypic (meristics, morphometries, otolith shape) and molecular (allozymes, mitochondrial DNA RFLPs, micro satellites) markers were simultaneously used to investigate the morphological and genetic structure of herring populations in the Northeast Atlantic and also to assess the relative usefulness of phenotypic and genetic markers in population identification. Samples were collected from the Celtic Sea, North Sea and fjords, Baltic Sea, Norwegian Sea, Barents Sea, and Pacific Ocean (pacific herring, Clupea pallasi L.). The Truss morphometric method was very sensitive in detecting morphological differences, revealing significant differences among all discrete spawning aggregations. Otolith analysis showed a lower discriminatory ability than the morphometries, differentiation of more widely separated populations, revealing a clear discreteness in the Icelandic, Baltic and Trondheimsfjord herring populations. Meristic analysis was more effective for the identification of different species rather than conspecific populations, exhibiting a clear divergence of the Trondheimsfjord and Icelandic herring samples. With allozyme electrophoresis, twenty-eight putative enzyme-coding loci were examined, and the result was in accordance with previous allozyme studies, showing genetic homogeneity among widely separated populations and localised heterogeneity in the Norwegian fjords (Trondheimsfjord). Also, an allozymically unique Norwegian spring-spawning (NWl) population was detected off the northern Norwegian coast. The number of low-frequency alleles apparently was a major problem with allozymes, limiting the overall ability to detect weak differences in allele frequencies between populations. PCR-based RFLP analysis of ND 3/4 and ND 5/6 regions of mtDNA with six restriction enzymes revealed significant genetic discreteness of the Baltic, Icelandic and Norwegian spring-spawner (NWl) herring. The results also showed a high level of haplotype diversity at the ND genes which contrasts with low levels of genetic divergence. This is apparently due mainly to the high number of unique haplotypes, and low number of common haplotypes detected, which reduced the power of the statistical test. Microsatellites were the most effective molecular marker, revealing genetically distinct Icelandic, Trondheimsfjord, Balsfjord and Norwegian spring-spawner (NWl) herring populations. The detected a high number of alleles and heterozygosity at microsatellite loci provide a new perspective on past estimates of detectable low levels of genetic differentiation among Atlantic herring populations. In identification of Atlantic and Pacific herring, meristic characters is most effective among phenotypic markers, allozymes and mtDNA are good choices among molecular markers. The significance of these findings m terms of stock separation and management are discussed.
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Hadfield, Simon John. "Genetic structure and colonisation history of European and UK population of Gammarus pulex". Thesis, University of Hull, 2002. http://hydra.hull.ac.uk/resources/hull:5483.
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The structure of populations has been studied for many years and there have been three main factors that have been suggested as the cause for present-day distributions of species, those being environment, biology and history. With the use of molecular data and advanced phylogeographic approaches it is now possible to distinguish between the main causes of population structuring. The present study considers the extent of population structure in G. pulex on regional (UK) and large geographic (Europe) scales using studies of molecular genetic (allozymes, mtDNA sequencing and microsatellites) and morphological variation. Molecular analysis of Gammarus pulex in Europe revealed more diversity than previously thought. This was thought to be a consequence of two separate waves of colonisation after the formation of the major drainages in the Miocene. The UK appears to have been colonised once from either the Elbe, Mosel and Rhine drainages separately or cumulatively across the drainage basins late in the Pleistocene before a land bridge connection to mainland Europe was submerged. Limited molecular variation in the UK is thought to be a result of reduced genetic variation in the colonising individuals. This in turn was caused by repeated founder events during population expansion and contraction from European refugia. A detailed analysis of a transplantation experiment in 1950 in the Isle of Man revealed little genetic impoverishment of the introduced population when compared to the source. In contrast, morphological variation increased in the introduced population. Unlike in mainland Europe there was no historical explanation for the diversity recorded (as the introduced population was so young) and, in the absence of fragmentation, speciation and colonisation the contemporary forces of gene flow, selection and limited genetic drift are thought to be the determining factors in population structure.
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Arabeyyat, Zeinab H. "Molecular level biological effects of silver and titania nanoparticles on zebrafish embryos". Thesis, University of Hull, 2016. http://hydra.hull.ac.uk/resources/hull:15442.
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Nanotechnology raises issues concerning the toxic impact of nanoparticles (NPs) in organisms and the environment. Nanoparticles have been defined as materials with dimensions that are equal to or less than 100 nm. It is important to develop early warning tools of NP-induced biological effects to be able to monitor and manage for any possible impacts. In the current study, two types of NPs have been selected based on their wide use: silver-NPs (AgNPs) and titanium dioxide-NPs (TiO2NPs). Early zebrafish (Danio rerio) embryos exposed in vitro to 4-nm and 10-nm AgNPs, and to silver ions alone, and TiO2NPs have been used to measure the expression level of selected target genes. A global transcriptomic approach employing Suppression Subtractive Hybridization (SSH) was used in parallel to identify novel genes that may be involved in the fish embryo response as a result of exposure to NPs. TiO2NPs coated with different layers of anionic (PSS) and cationic (PAH) polyelectrolytes were also used to measure viability, morphology, and the expression level of selected target genes. The results indicate that pathways expressed in response to NP exposure differ among both AgNPs and TiO2NPs, either due to the size, concentration, exposure time, exposure conditions, surface chemistry and surface charge of coatings of the NPs. The responses indicate that D. rerio embryos respond to NPs with not only an oxidative stress response, but with transcripts associated with fertility and metabolic functions such as membrane transport and mitochondrial metabolism. This information may be used to inform early warning biomarker development for environmental monitoring applications in future.
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West, Hannah E. R. "The evolution of male parental care in mammals". Thesis, University of Hull, 2017. http://hydra.hull.ac.uk/resources/hull:16571.
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Males care for offspring across a diverse range of taxa. Why males give up mating opportunities and spend time and energy caring for offspring is unclear, especially when females already provide parental care. The evolutionary drivers for biparental care are currently uncertain, as are the evolutionary consequences of male care on female and offspring fitness. Using modern phylogenetic comparative methods, I test hypotheses on the evolution of biparental care in a sample of over 500 mammalian species while considering the diversity in parental care behaviours. Both male care and monogamy occur in species where levels of paternity are high, but only monogamy associates with reduced investment in sperm competition traits. Male care also has energetic benefits for females and offspring; females have higher fecundity and offspring faster growth in species with biparental care, in support of the ‘load-lightening’ hypothesis. I find strong support for the hypothesis that monogamy drives the evolution of male care but only for behaviours that provide fecundity benefits, while behaviours unrelated to female fecundity may either precede or follow monogamy. However, I find no support for the hypothesis that infanticide by males promotes the evolution of male care. Lastly, I investigate whether care by non-parental helpers exhibit similar associations with life history traits as male care and find that care by helpers associates with increased fecundity, but by influencing different times of the female reproductive cycle. Overall I identify a two-step process of evolution between male care and social monogamy, with care behaviours which do not confer fecundity benefits facilitating the evolution of social monogamy and higher paternity levels, which subsequently promote the evolution of further care behaviours with higher energetic benefits. Thus, this research demonstrates the importance of considering the care behaviour performed, the time of female reproduction at which it is performed, and the identity of the carer, in studies investigating the evolution of parental care.
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Cowing, Daniel Mark. "Optimising commerical practices and developing aquaculture techniques for the Norway lobster (Nephrops norvegicus) fishery". Thesis, University of Hull, 2017. http://hydra.hull.ac.uk/resources/hull:16589.
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The Nephrops norvegicus (referred to as Nephrops) fishery is regarded as one of the most important fisheries around the UK, yet data suggest that landings are declining. The role of hatcheries for other crustacean species has proved useful for stock enhancement and aquaculture. Nephrops larviculture has been relatively unsuccessful, with low survival to post larval stages. This thesis comprises four studies aimed at developing key stages that are important for optimising fishing related practices and the development of aquaculture for this species. In chapter 3, the social behaviour of adult Nephrops is examined in conjunction with physiological parameters. The findings indicate that the behavioural interactions have a physiological cost that is associated with the sex and size of the individual and the opponent. The findings are useful for developing fishing practices and broodstock holding and highlight the complexity of correlating physiological parameters with social stress. In chapter 4, a method for sedating and anaesthetising Norway lobster is investigated and successfully identified. Key behaviours are related to sedation stages as well as to several tested dosages. These techniques could be used to lower stress in Norway lobster during transport and handling. In chapter 5, several diets and feeding frequencies are examined for their potential in increasing larval survival and growth. The highest survival and growth were found in the enriched Artemia diets, with a continuous feeding frequency. Larvae fed on wild zooplankton had lower survival and delayed growth, especially for stage 1 larvae. The addition of probiotics yielded promising results in terms of better survival and less variation when compared to an enriched Artemia diet alone. Survival of larvae was increased to ~40% which is an improvement on previous findings and suggests further investigation for optimising larviculture techniques. In chapter 6, the behaviour of post larvae around an adult burrow and an alternative habitat is investigated. The post larvae showed a preference for entering the burrow when it was unoccupied, but would show vigilant behaviour when it was occupied. The post larvae would also find shelter in alternative habitats such as cobbles, which could be a promising application in future release protocols for this species. The results from the thesis demonstrate that Nephrops aquaculture for stock enhancement can currently take place, and that techniques for holding and transporting broodstock can be improved.
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Taylor, Marie Jane. "The influence of flow management and habitat improvement works on fish communities in Yorkshire rivers". Thesis, University of Hull, 2017. http://hydra.hull.ac.uk/resources/hull:15696.
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Many of the rivers in the UK are heavily modified by channelisation, impoundment (dams and weirs and off-river storages), land drainage and flood defence. These modifications have reduced the natural variability of flow and habitat diversity and in turn rivers are failing to meet Water Framework Directive (WFD: 2000/60/EEC) targets. Mitigation measures such as modifying reservoir flow releases and habitat improvement works are carried out to remediate the potential impacts of river development. This thesis examines the effectiveness of modified reservoir flow releases and habitat improvement works in Yorkshire rivers using brown trout (Salmo trutta L.) as the indicator of change. The importance of natural flow regimes and how reservoirs and flood defence works have had negative impacts on fish populations was reviewed. The current UK guidance around managing reservoir releases and reducing flood risk was reviewed with regards to what measures are in place to mitigate their impacts and what biological responses are expected. One of the main conclusion was that to meet WFD targets, monitoring is required to investigate the effectiveness of activities aimed at improving rivers to inform management decisions and ensure activities are efficient and cost effective. The long term effects of introducing seasonal compensation flows and a single freshet were examined by comparing differences in the hydrological regime and monitoring brown trout populations downstream of water storage reservoirs in Yorkshire. Hydrological parameters were not significantly different following the introduction of the revised reservoir release programme and brown trout populations were found to be variable throughout the years studied, and any changes in population characteristics could not be attributed to the new regime and further changes to the reservoir releases maybe required. Manual radio tracking was used to obtain a detailed knowledge of the movements and distribution of adult brown trout downstream of two water storage reservoirs in Yorkshire following the introduction of single freshet releases (November 2012) to stimulate upstream migration. Brown trout occupied small home ranges and a single freshet release did not result in long distance upstream migration possibly because the releases were not performed at the appropriate time of year or the magnitude was inadequate to promote migration. The number of releases was increased to one each in the months of October, November, and December 2013 but still did not result in long distance upstream migration. It was suggested that the freshet releases which lasted only 8 hr, provided brown trout with little opportunity to move a reasonable distance. Further changes to the reservoir releases may be made to meet the flow profile recommended by UKTAG for autumn and winter flow elevations to support spawning migrations. A monitoring programme was designed to detect changes in brown trout population following habitat improvement works. Baseline surveys carried out as part of this programme found brown trout to be present at low densities and exhibit slow growth rates, which was attributed to lack of suitable habitat, particularly spawning and juvenile riffle habitats, lack of deeper pooled areas for larger brown trout and lack of available cover. It was recommended any habitat improvement works should therefore improve flow, habitat and sediment issues. A further study compared brown trout population and habitat parameters at Malin Bridge on the River Don pre and post flood defence and subsequent habitat improvement works, the latter designed to mitigate adverse effects of flood defence works. The flood defence works provided very little habitat diversity and cover for larger brown trout, instream channel features were added to improve habitat. Following the improvement works brown trout populations returned to densities and composition found prior to flood defence works, indicating impacts associated with flood defence works can be reduced when incorporating habitat improvement works into flood risk management.
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Pierotti, Michele E. R. "Origin, maintenance and evolutionary consequences of male mating preference variation in East African cichlid fishes". Thesis, University of Hull, 2007. http://hydra.hull.ac.uk/resources/hull:11614.
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Davidson, Laura. "Ocean acidification and its effects upon fitness in nereidid polychaetes". Thesis, University of Hull, 2013. http://hydra.hull.ac.uk/resources/hull:8221.
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In recent years there has been increasing focus on predicting the potential effects of greenhouse gas driven global warming; this has proven to be a major challenge for science. In the last decade, there has been a major shift in research with growing scientific concern over the changing ocean carbonate chemistry as a result of ever increasing anthropogenic CO₂ emissions. Major changes to the basic chemistry of seawater, such as the water pH, are likely to have substantial implications for marine life in the future (Hardege et al., 2011). Research to date has focused largely upon those organisms that require calcium carbonate to build protective shells or skeletons (Orr et al., 2005). Using semelparous polychaetes, Platynereis dumerilii and Alitta succinea, it is shown that when exposed to pH levels forecasted to occur by 2100 (pH 7.8) survival, development, reproductive output and essential behaviours e.g. feeding and predator avoidance, are negatively impacted. A. succinea show severely reduced responses to natural chemical signals with subsequent low fertilisation and larval success. The ubiquity of chemical communication in the aqueous environment indicates that chemoreception disruption can potentially have dramatic consequences. Data show that if ocean acidification continues as predicted, marine chemoreception will have to adapt rapidly with potentially profound consequences for marine life and animal interactions. It is clear from this investigation that P. dumerilii and A. succinea are not capable of acclimatisation within one lifetime. Interestingly, P. dumerilii sampled and sequenced from a naturally occurring CO₂ vent in Ischia (Naples, Italy) are genetically different from other P. dumerilii populations within Europe. Individuals appear to show signs of adaptation in behavioural trials with few significant differences between pH treatments 8.2 and 7.8. Future studies are needed to ascertain how these organisms are adapted to life in low pH waters.
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Twine, Karen Gemma. "Conservation of barbel (Barbus barbus) in the River Great Ouse". Thesis, University of Hull, 2013. http://hydra.hull.ac.uk/resources/hull:8222.
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There have been growing fears relating to the distribution and a perceived lack in natural recruitment of barbel in European rivers. This project reviewed existing literature, examined the suitability of Environment Agency data to assess barbel populations and designed investigations to identify possible bottlenecks in recruitment focusing on all life history stages and environmental influences, with the intention of developing a practical management plan for the River Great Ouse fishery that can be applied to other rivers. This study examined seasonal movements of 20 wild barbel via radio telemetry in a nine kilometre river stretch on the upper Great Ouse, recording weekly movements over an 18 month period. The project aimed to ascertain the effects of environmental influences on movement and habitat use. Radio tracking over 100 consecutive days throughout the spring periods in 2010 and 2011 gave an understanding of their daily movements, identified barriers limiting longitudinal movements and located active spawning gravels. Health of spawning gravels was assessed by monitoring changes in diatom growth and hyporheic water quality during the embryonic development stage. Representative freeze core samples from spawning gravels were used to assess fine sediment infiltration. Larval drift measured the number of larvae leaving the spawning grounds, a range of methodologies were used to capture 0+ to 3+ barbel. Habitat and feeding preferences were then evaluated. It was found that temperature and flow impacted movement, individuals moved through the entire river stretch, despite the presence of a weir that was previously thought of as impassable. Variations in sediment loading were found between spawning habitats, but fine sediment and organic matter were improved with gravel jetting. Larval drift and electric fishing were found to be the most effective methods for catching young barbel, but the necessary habitats to support these young fish were not readily available within the study stretch.
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Simpson, Julia Louise. "Male gamete morphology in relation to swimming velocity and fertilisation microenvironment". Thesis, University of Hull, 2012. http://hydra.hull.ac.uk/resources/hull:6900.
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The heterogeneity of spermatozoa has been widely used to inform phylogenetic relationships among taxa, yet the reason such diversity has evolved, in relation to the sperms primary functional role in fertilisation and reproduction, is not well understood. Research into the evolutionary significance of sperm morphology is concomitant with the study of sexual selection and the evolution of the biological diversity of life. The formulation of sperm competition theory in the 1970s provided a new insight for the study of sexual selection and the development of the field of sperm biology. The idea that males not only competed for access to females but that, through direct competition, spermatozoa of individual males were also in competition to fertilise the maximum number of eggs was a revolutionary concept. An integral part of many sperm competition models is the assumption that there is a relationship between sperm morphology and swimming velocity in terms of fertilisation success. In addition to this it is further assumed that longer sperm swim faster than shorter sperm. During competitive mating, when the ejaculate from two or more males compete to fertilise a given set of eggs, longer and therefore faster, sperm should have a fertilisation advantage as they can reach and fertilise eggs first. However identifying the traits that make individual sperm more or less capable of successfully fertilising an egg remain largely unknown for most species. There has so far been little empirical support for a link between sperm morphology and swimming speed and mixed results regarding the importance of swimming speed when it comes to increasing fertilisation success. Here, three aspects of sperm biology were investigated in order to clarify functional links between sperm morphology and velocity. Firstly, the influence that female gametes have on the swimming behaviour of both fresh and cryopreserved bovine sperm was examined. Bovine samples were used because it is known that in the bovidae family, female gametes release chemoattractans which appear to play a role in sperm guidance towards the oocyte (egg). Additionally, a large literature base regarding damage caused by cryopreservation of bovine sperm exists. The second topic of research focuses on cichlid fish. Cichlids from Lake Malawi have been underrepresented in the published literature in sperm biology despite being extensively studied in relation to other aspects of their biology. A phylogenetically controlled study into links between sperm morphology and velocity across mouthbrooding cichlids from Lake Malawi was therefore undertaken. All endemic cichlids in Lake Malawi are maternal mouthbrooders in which the female broods both eggs and fry inside her buccal cavity (a cavity inside the mouth of the female between the jaw and cheek). The functional significance of the buccal cavity is also important as the point of fertilisation for some species. Variation in sperm length has been found in cichlid species in Lake Tanganyika where substrate fertilisers have significantly longer sperm than species fertilising inside the buccal cavity. However, links between morphology and velocity have found little support when using traditional methods that rely on the calculation of mean measurements of sperm morphology and velocity. Here an experimental approach focusing on measurements from individual sperm whilst accounting for within-male variation was employed to investigate the extent to which links between sperm morphology and velocity to be revealed across species. The third area expands on the idea that fertilisation point will have an influence on sperm form and function and compares sperm data from three internally and three externally fertilising species. Once again measurements from individual sperm were used and within-male variation was included in the analysis. The influence of chemoattractants on sperm swimming speed and direction are frequently omitted in the sperm competition literature, as are comparisons of the effects of sperm preservation methods such as cryopreservation. Such considerations are, in a large part left to articles on animal breeding and artificial insemination. It is however, widely acknowledged that chemoattractans do influence sperm motility in a range of taxa and that cryopreservation damages sperm. Whilst chemotaxis in bovine sperm was not detected in this study, variation in swimming characteristics of bovine sperm related to the method of preservation was observed. As cryopreservation appears to alter sperm behaviour it seems unlikely that observations of swimming velocity of fresh and cryopreserved sperm can be compared when considering relationships between sperm length and velocity. Information from both fresh and cryopreserved sperm is useful when considering links between sperm traits and fertilisation success but need to be considered independently. Using comparative methods to investigate sperm traits across closely related species of cichlid fish no phylogenetic correlation for sperm traits was found. Furthermore, sperm morphology did not show any correlation with velocity across species. However, when within-male variation was accounted for, a relationship between sperm morphology and velocity was revealed. Interestingly the relationship was frequently a negative one, a novel finding despite numerous studies into sperm morphology-speed relationships. When the results from data comparing internal and externally fertilising species was considered negative relationships tended to be more prevalent in internally fertilising species. If this is a general trend, that shorter sperm swim faster in internally fertilising species, we could extrapolate that the negative relationships between sperm length and velocity found in the cichlid data set exhibit sperm morphology adapted for internal fertilisation. A larger sample size would be required to conclusively support this suggestion that could confirm Lake Malawi cichlids share a common point of fertilisation, within the buccal cavity, despite high levels of diversity found in other aspects of the speciation of these cichlids. The findings of the work presented here highlight the negative influence cryopreservation has on sperm motility and that measurements of individual spermatozoa are vital if links between morphology and velocity are to be detected. The importance of sperm preservation method on the swimming behaviour, and by association the ability of the individual sperm to successfully complete fertilisation, requires further investigation to link the morphology and velocity of individual sperm to the method of preservation. This link would provide valuable insight into the structure of sperm subpopulations which are the most resistant to cryopreservation and therefore of most value for techniques such as artificial insemination. Using a new method for measuring individual sperm morphology and velocity whilst accounting for intra-male variation significant links between sperm morphology and velocity in a number of vertebrates and invertebrates were revealed. The data gathered here suggests that such links could be widespread across more species than current empirical work indicates. Furthermore, the direction of relationships between morphology and velocity appear to be revealing disparity between internally and externally fertilising species.
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Gao, Fei. "Mitochondrial ATP production and energy-buffering in the human pathogen Trypanosoma brucei". Thesis, University of Hull, 2013. http://hydra.hull.ac.uk/resources/hull:8492.
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The mitochondrion plays a vital role in the cellular energy (ATP) provision of the human pathogen Trypanosoma brucei. ATP is produced in the mitochondrial matrix from ADP and inorganic phosphate by substrate-level and oxidative phosphorylation. To maintain the cellular energy provision, ATP has to be exported from the mitochondrial matrix, and ADP and Pi imported from the cytosol. This exchange is in eukaryotes facilitated by specific mitochondrial carrier family (MCF) proteins, i.e. the ADP/ATP carrier and the phosphate carrier located in the mitochondrial inner membrane. The MCF protein inventory of T. brucei from our lab’s previous study showed two putative ADP/ATP carriers, i.e. TbMCP5 and TbMCP15, and two putative phosphate carriers, i.e. TbMCP8 and TbMCP11. In order to confirm the mitochondrial carrier family proteins and further study mitochondrial energy metabolism, proteomic analysis of mitochondria in both bloodstream form and procyclic form T. brucei were performed. The preliminary results showed that many enzymes required for TCA cycle, lipid metabolism, amino acid metabolism, nucleotide metabolism exist in both bloodstream form and procyclic form T.brucei. (Data were not shown in this thesis). Functional characterisation of TbMCP5 and TbMCP15 (Chapter II) revealed that only TbMCP5 functions as a mitochondrial ADP/ATP carrier, while the function of TbMCP15 remains unknown. TbMCP5 is able to functionally complement growth of ADP/ATP-carrier deficient Saccharomyces cerevisiae on a non-fermentable carbon source, and mitochondrial transport experiments (done by Ludovic Pelosi) revealed that TbMCP5 has similar biochemical ADP/ATP transport kinetics to the prototypical ADP/ATP carrier ScAnc2p from yeast. Silencing of TbMCP5 expression confirmed that this MCF protein is essential for the survival of the procyclic form T. brucei and represents the only ADP/ATP exchanger present in the procyclic form mitochondrion. Functional characterisation of the putative mitochondrial phosphate carriers TbMCP8 and TbMCP11 (Chapter III) revealed that only TbMCP11 is expressed in the bloodstream form and procyclic form of T. brucei. Silencing of TbMCP11 expression in the bloodstream form had no effect on growth, whereas in the procyclic form it resulted in a lethal growth phenotype. Heterologous expression of TbMCP11 in mitochondrial phosphate carrier-deficient S. cerevisiae restored its growth on a non-fermentable carbon source as well as the phosphate-dependent swelling of its mitochondria. ATP exported from the mitochondrion is either directly used by the rest of the cell or stored as an energy buffer, which can be used during periods of high energy demand. The phosphoarginine/arginine kinase energy (ATP) buffering system of T. brucei consists of three different arginine kinase isoforms, i.e. TbAK1-3 (Chapter IV). The TbAK1-3 isoforms are localised in different subcellular compartments, here respectively the flagellum, glycosome and cytosol, and are dependent on the presence of specific organellar targeting signals. Silencing of total TbAK expression in the procyclic form of T. brucei resulted in a significant growth defect, and was even lethal in the presence of the oxidative challenging agent hydrogen peroxide. These results suggest an important role of the T. brucei phosphoarginine/arginine kinase energy-buffering system in oxidative stress defence. Additional roles of the TbAK isoforms in the different subcellular compartments are proposed. In conclusion, the mitochondrial ADP/ATP carrier TbMCP5 and phosphate carrier TbMCP11, and the TbAK1-3-dependant energy buffering system play an essential role in the maintenance of the T.brucei energy metabolism.