Tropical peatlands play an important role in the global carbon cycle, but little is known about the factors which regulate carbon dioxide (CO2) and methane (CH4) fluxes from these ecosystems. To improve our understanding of the potential impact of future changes in climate and/or land-use, this study aimed to quantify current fluxes of these gases from a large domed peatland, San San Pond Sak, in Panama and assess the influence of environmental factors. Three sites with differing dominant vegetation species (Raphia taedigera, Campnosperma panamensis and Cyperus species) and nutrient status were investigated between February 2007 – September 2009 using a combination of in situ closed chamber gas sampling and ex situ headspace gas sampling to quantify current and potential gas fluxes from the peat surface and at depths of 2 m from the surface. Physical and chemical properties of the peat were determined concurrently. Laboratory experiments were carried out to investigate patterns of litter decomposition and microbial activity. Gas fluxes differed significantly between sites. CO2 fluxes were greatest at the C. panamensis site (100–400 mg m-2 h-1), followed by the R. taedigera (74–352 mg m-2 h-1) and Cyperus sp. (59–294 mg m-2 h-1). The seasonal patterns associated with rainfall were similar for all sites, with the release of CO2 being greatest during the dry season. CH4 fluxes also varied between sites, but no seasonal variation was evident. CO2 flux varied diurnally at the C. panamensis and Cyperus sp. sites, perhaps due a circadian rhythm in vegetation processes. CO2 and CH4 production occurred throughout the upper 2 m of the profile, both in situ and ex situ, with potential CO2 fluxes of up to 1,000 mg m-2 h-1 being found in the surface layer. The peat became increasingly recalcitrant and P-limited with increasing depth. Measurements of litter decomposition and microbial activity indicated that the availability of labile substrates and nutrients differed between sites. In conclusion, CO2 and CH4 fluxes differed between sites experiencing similar environmental conditions, and were influenced by variation in environmental factors. Fluxes varied on both short- and long- timescales, but not at all sites. The magnitude of the gas fluxes was influenced by different environmental factors at each site, indicating that fluxes and the most important driving variables vary dependent on surface vegetation even within a single peatland system. With regard to climate and/or land-use change, it was concluded that San San Pond Sak peatland would be sensitive to water table drawdown, with the likely outcome of increased CO2 releases and the potential for CH4 uptake, rather than release.

This thesis discusses the development of a novel scanning capacitance microscope (SCM) that enables the investigation of the local capacitance and conductivity of surfaces and near-surface nanostructures at cryogenic temperatures and high magnetic fields. Simultaneous atomic force microscopy (AFM) and SCM measurements can be made at a temperature of 1.5K and a magnetic field of 12T. The AFM/SCM sensor is based on a quartz-tuning fork with an etched metal tip. SCM measurements are made using an RF tuned filter design which allows changes in capacitance to be measured with sub-attofarad resolution and a bandwidth of 200Hz. Test measurements were made over an evaporated gold film. The capacitance distance curve was recovered from the measured quantities using a deconvolution scheme normally used for force-distance curves. Measurements have been made of a two-dimensional electron gas in the quantum Hall effect (QHE) regime. Highly conductive stripes form near the edge of the sample at integer Landau level filling factors in agreement with theoretical predictions. These measurements are the first direct imaging of the compressible stripes at the physical edge of a Hall bar device. Measurements were also made by point spectroscopy in a region that was locally depleted. Around this region a ring-shaped stripe of considerably larger width than at the sample edge is observed. The increased width was explained in terms of a shallower potential gradient compared to the physical edge of the sample. Preliminary measurements have demonstrated that the microscope is capable of imaging edge states whilst passing current through the device.

Low-carbon energy production is potentially a major method of reducing greenhouse gas emissions and anthropogenic climate change. In the UK, tall perennial grass crops show potential as “biomass crops”, providing renewable energy sources with a low net carbon cost. However, conversion of large areas of farmland to biomass production would constitute a major land-use change with possible negative effects on native biodiversity, particularly as some biomass crop types are not native to the UK. The aim of this thesis was to assess biological diversity within mature (>3 years old) crops of non-native Miscanthus x giganteus and native Phalaris arundinacea. Biomass crop structural characteristics and management regimes were recorded, and their biodiversity was surveyed with particular reference to birds and small mammals in comparison with adjacent land uses. Food resources in terms of non-crop vegetation and invertebrates were also recorded. Live-trapping revealed eight species of small mammal in the study crops, including a conservation priority species, the harvest mouse Micromys minutus, which was most abundant in Phalaris crops. Phalaris also contained the highest small mammal diversity, but the field headlands held the greatest small mammal abundance. Trapping and direct observations revealed a higher abundance and diversity of birds in the Miscanthus crops in comparison with Phalaris. Most of the bird species found in biomass crops were associated with woodland or reedbed rather than farmland habitat. Phalaris crops had a higher percentage of ground cover of the crop itself and non-crop vegetation, whereas Miscanthus fields had greater cover of crop litter. Miscanthus crops contained fewer invertebrates than Phalaris or the field headlands. Management specific to biomass grass crops involves harvest in spring, thus providing winter habitat of importance to birds and small mammals. The crop fields also provide a refuge for invertebrates and non-crop vegetation and overall, supported high levels of biodiversity.

Ecological and host adapted races provide evidence that evolutionary divergence and sympatric speciation can occur through divergent natural selection in the face of continued gene flow. Likewise, hybridisation and introgression (interspecific gene flow) are commonly identified in natural populations, between what are described as distinct taxa. These processes have implications for how we define species and the processes necessary for the persistence and initiation of species and speciation, above and below the species level. The main focus of the present study was elucidation of the nature and extent of differentiation, and processes involved in shaping diversity within and between, species of the Aphrodes leafhopper genus, Curtis 1833, particularly from UK saltmarshes. A multidisciplinary approach was taken, combining the use of morphological, behavioural (vibrational mating signals), mitochondrial DNA (cytochrome oxidase subunit I gene sequencing) and multiple genome-wide nuclear marker (amplified fragment length polymorphism) analyses to test hypotheses relating to taxonomy, ecological speciation and hybridisation among Aphrodes leafhoppers. Of primary interest were: 1) identification of Aphrodes inhabiting saltmarshes, and first confirmation that two species (A. makarovi and A. aestuarina) exist there; 2) comparison of divergent ecological lineages of inland and estuarine A. makarovi, showing possible incipient speciation and evidence of convergent morphological evolution of estuarine A. makarovi and A. aestuarina; 3) exploration of the evolutionary significance of an introgressed hybrid population of A. aestuarina, found only in the Medway estuary, showing complete mitochondrial capture and some nuclear introgression.

This thesis investigates ionotropic and metabotropic signalling mechanisms in developing neurons from human embryonic stem cell and primary sources. Focus is placed on the measurement of functional activity using primarily whole-cell patchclamp and Ca2+ imaging techniques These signalling mechanisms were investigated in undifferentiated human embryonic stem cells, hESC-derived neurons, fetal primary human neurons and neonatal primary mouse neurons. The results of this research are separated into three chapters. Preliminary work carried out on iPSC-derived neurons is also included as an indication of future direction Chapter 3: P2 Receptors in hESCs Purinergic signalling was shown to be active in undifferentiated hESC populations. Specifically, the activity of P2Y1 receptors was confirmed pharmacologically. This is a novel observation and indicates a mechanism for physiologically relevant signalling molecules to modify [Ca2+]i Chapter 4: Functional Characterisation of hESC-Derived and Primary Neurons Functional characteristics associated with neuronal development were measured in human embryonic stem cells during terminal neuronal differentiation in a chemically-defined medium. The presence and activity of voltage-gated Na+, K+ and Ca2+ channels were recorded, alongside data on neuronal excitability (Vm, iAP induction and threshold and spontaneous electrical activity). These data were also recorded in fetal hWGE- and neonatal mWGE-derived neurons for comparison. hESC-derived neurons were shown to be functionally more similar to fetal hWGEneurons suggesting an immature neuronal phenotype Chapter 5: GABAergic Signalling in hESC-Derived and Primary Neurons GABAergic signalling in hESC-, mWGE- and hWGE-derived neuronal populations was investigated. Focus was placed on hWGE-derived neurons and the developmental state of GABAergic responses. In fetal hWGE-derived neurons, a percentage of cells displayed an ‘inhibitory’ response to GABAAR activation. This is a novel observation with implications in human neuronal development. In vitro modulation of GABAergic signalling was also shown, providing potential tools for future research into this phenomenon Chapter 6: Future Developments and General Discussion iPSC-derived neuronal populations were shown to display basic neuronal functional properties. This work will form the basis of future studies on these cells

Eight Wolbachia variants were identified in the wasp community. Identical Wolbachia variants were identified in inquiline and parasitoid wasp species suggesting that horizontal transmission of Wolbachia occurs in this community

This thesis examines the tolerance and effects of unnatural amino acid (Uaa) incorporation into proteins in Escherichia coli using an expanded genetic code. Uaa incorporation was used to alter or install new properties in the target proteins, superfolder Green Fluorescent Protein (sfGFP) and cytochrome b562. Chapter 3 deals with the technical aspects of Uaa incorporation including orthogonality of the machinery and yield. Substitution of residues in sfGFP for unnatural analogues of tyrosine was shown to be a valuable way of altering the properties of the protein. Variants were generated with red-shifted fluorescence and altered excitation spectra. The majority of this work focused on the Uaa, p-azido-L-phenylalanine (azPhe) as it has a number of properties that would be desirable for use in proteins such as photoreactivity and selective reactivity with alkynes. By incorporating azPhe into key residues of sfGFP, variants were created that could be controlled using light (Chapter 4). Light-dependant fluorescence activation, deactivation and switching were demonstrated in vitro and in live cells. The molecular basis for these changes was investigated by a combination of spectroscopy and X-ray crystallography in Chapter 5. The photoreactivity of azPhe was exploited for a different purpose in Chapter 6. Proteins were used as an alternative to synthetic cages for studying low temperature phenyl azide photochemistry. Here, two radicals (anilino and triplet phenyl nitrene) were successfully caged and detected on photolysis, with the radical observed dependant on the protein environment. Finally, in Chapter 7 the selective reactivity of azPhe was used to create proteins capable of site-specific modification (via Click chemistry). The position of azPhe on the protein surface was shown to have a significant effect on reaction yield and kinetics. Modification was used to install proteins with novel properties such as red-shifted fluorescence emission and the ability to bind to non-biological materials like graphene.

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This thesis deals with the structure and innervation of 3 different types of attachments - the fibrous enthesis of the medial collateral ligament, the muscular attachment of the tibialis anterior onto the tibia, and the fibrocartilaginous enthesis organ of the Achilles tendon.&nbsp;Particular attention was paid to the latter and it was shown that in rats at all ages (neonate, 4 week, 4 month, and 2 month) only the retromalleolar fat pad of the enthesis organ was innervated.&nbsp;In the light of these findings, the fat was studied in further detail and an <italic>in vitro</italic> investigation determined whether nerve fibres are specifically attracted to the adipose tissue.&nbsp;In man, it was confirmed that the equivalent fat pad (Kager's fat pad) was also innervated and a number of anatomical and histopathological observations associated with this tissue in elderly dissecting room cadavers were described.&nbsp; The relationship between weight, height and foot length with fat pad structure in human cadaveric tissue was investigated, and the effect of the appetite-inducing hormone, ghrelin on the size of the fat pad in the rat was also explored. As entheses are the primary target organs in the seronegative spondyloarthropathies (autoinflammatory rheumatic conditions), the presence of resident and inflammatory macrophages and neutrophils in the rat Achilles tendon enthesis organ was investigated at a variety of ages.&nbsp;Overall, it was concluded that adipose tissue associated with entheses may play a role in proprioception and be a source of pain in enthesopathies.