As antimicrobial resistance persistently disrupts the treatment of microbial infection, identifying novel drugs with novel modes of action is critical to getting ahead of resistance. The primary goal of this project is to extract and identify novel chemical products produced by Arthrobacter sp. TAJX1902, particularly antimicrobial metabolites. Although underexplored, Arthrobacter sps. have been shown to produce bioactive compounds of great versatility; one such is a depsipeptide with quorum-sensing inhibitory activity.1 In this research, Arthrobacter sp. TAJX1902 isolated from a soil sample showed inhibitory activity against a filamentous indicator-type bacterium and a violacein-producing Janthinobacterium sp. A. sp. TAJX1902 was cultured using rich medium broth and agar and extracted with solvents of varying polarity. Characterization of purified bioactive compounds from A. sp. TAJX1902 was done via spectroscopic techniques, including 1D and 2D-NMR spectroscopy, FTIR, and GCMS analysis. The A. sp. TAJX1902 was found to produce pyrrolo[1,2-a]pyrazine-1,4-dione,hexahydro-3-(2-methylpropyl), and five other bioactive cyclic dipeptides (CDP).

TetratricoPeptide Repeats or TPRs are a class of repeat proteins made up of - helices. Each repeat contains 34 amino acids that form a helix-turn-helix motif and is stabilised by short range interactions creating a non-globular fold. Tandem arrays of these repeats form stable superhelical structures. The modular nature of the TPR fold has allowed a series of consensus TPRs (CTPRs) to be designed where the number of repeat units has been varied. We have exploited the modular nature of CTPR proteins in order to create fibres via a bottom-up approach. Using Native Chemical Ligation (NCL) we have been able to trigger specific assembly of monomeric CTPR units to form extended fibrous structures up to microns in length (as viewed by TEM). This reaction proceeds at room temperature and neutral pH, with filaments observed within 12 hours. The equilibrium unfolding of CTPRs is prone to the population of partially folded states. Through studying the stability of a series of deletion mutants and using a Heteropolymer Ising model to analyse the unfolding data we have been able to design a CTPR with a conformational ‘switch’. This new CTPR was designed to populate a stable intermediate, with an exposed dimerisation interface, under certain conditions. When this new construct was analysed using 2D NMR and CD spectroscopy, it was found to selectively unfold its C-terminal -helix at a specific concentration of GuHCl. Our aim is to develop a system in which a ‘switching’ CTPR is used as a sensor that, when triggered by environmental conditions, partially unfolds and oligomerises.

The field of nanomedicine has witnessed an incredible expansion, from a total market value in 2003 of $500 million expected to rise to $160 billion by 2015 (Global Industry Analysts, Inc.). The nanomedicine industry is forecasted to grow and have a significant impact on the economy, with sectors such as biomaterials, diagnostics and drug delivery expected to play a major role. This thesis gives a detailed account of the synthesis and characterisation of molecularly imprinted nanogels for drug delivery. Their toxicity and potential use as a targeted carrier to cancerous cells is evaluated. Initially an overview of nanomaterials and their uses in many areas such as agriculture, energy storage and technology are discussed. The impact of nanomaterials on the life sciences is examined; in particular their application in drug delivery is focussed upon. Chapters 2, 3 and 4 make up the results and discussion of this work. Chapter 2 focuses on developing the synthesis of the acrylamide based nanogels and, vitally, incorporating a suitable fluorescent tag in order to track the nanogels in vitro and in vivo. Fundamentally toxicity studies carried out on the nanogels, both in vitro and in vivo in Danio rerio (zebrafish) are reported in Chapter 3 to ensure the nanogels are biocompatible. Chapter 4 introduces an innovative approach, molecular imprinting, to incorporating a drug into the nanogels. The upload and release of Tamoxifen (a drug used to treat breast cancer) at reduced pH, was also analysed. Finally future development of the carrier is discussed and key issues that need to be addressed.

Coastal saltmarshes are vital ecosystems because (a) they physically buffer the land against storms and flooding from the sea and (b) ecologically they are high-productivity systems in estuaries and marine coastlines that shelter and support fish and bird populations. Saltmarshes are highly sensitive to sea level change. Any saltmarshes are now threatened by rising sea level, but how they will respond and at what rate is unclear. Managing saltmarshes is therefore necessary, but requires a good understanding of their development in order to predict how they might respond to sea level change. Current management practice in the UK is mainly managed realignment landward and future scenarios are predicted with computer models. Both use the hypothesis of facilitation succession, whereby saltmarsh progrades seawards. An alternative hypothesis is saltmarsh development by transgression landward due to rising sea level. This thesis critically examines how saltmarshes have developed under different sea-level change regimes in order to gain an insight into how they are likely to be affected by future sea level rise. Using established micropalaeontological techniques, Foraminifera tests and Ostracoda shells were extracted from sediment cores taken from saltmarshes representing a range of sea level change histories during the Holocene. Sampling of modern environments allowed saltmarsh vegetation zones to be characterised by foraminiferal and ostracod assemblages which were then used to reconstruct the development of saltmarshes over time as preserved in the cores. Sediment layers in the cores were dated using three techniques: Optically Stimulated Luminescence (OSL), radio carbon (14C) and 137Cs / 210Pb. The latter hypothesis is supported in southern England where marine transgression caused saltmarshes to migrate landwards, in contradiction to the facilitation succession hypothesis. In Scotland saltmarshes advanced seawards but due to a marine regression. Future studies should explore the applicability of these findings to saltmarshes outside the British Isles.

Photosystem II (PSII) is the primary generator of electrons required for photosynthesis. The reaction center protein of PSII (RCII) is the most susceptible component of the photosynthetic machinery to damage. Photodamage can lead to long-term downregulation of photosynthesis. This occurs because plants are exposed to rapid light fluctuations and high light conditions, leading to the over accumulation of excess energy around PSII. Plants have developed a mechanism to dissipate this excess energy called nonphotochemical quenching (NPQ). In order to quantify the protectiveness of NPQ (pNPQ), a novel methodology was developed and employed. During methodology development, development, it is shown that a variable PSI fluorescence should be taken into account, and how it can be calculated. Application of the procedure assessed the contribution of xanthophylls lutein, violaxanthin, zeaxanthin, and the PsbS protein to pNPQ. Results show that the most important factors governing photoprotection are the PsbS protein and the correct xanthophyll composition in their natural binding sites. The more xanthophyll variation, the greater the photodamage at the end of the pNPQ assessment procedure. PsbS is essential to achieve the maximum pNPQ. PsbS increases the aggregation of LHCII. Arabidopsis with excess PsbS has three-times more aggregated LHCII than wild type levels of PsbS. The phototolerance and pNPQ required for Arabidopsis grown under different conditions and for leaves of different ages was also calculated. Plants grown under low light conditions accumulate disconnect antenna (LHCII), which is inefficient at protecting RCII, despite the high NPQ levels. Investigating plants of different ages, it was found that eight-week old Arabidopsis are the optimum age for pNPQ effectiveness. Younger and older leaves suffer photodamage at lower light intensities and form less pNPQ. This thesis demonstrates the novelty and adaptability of the pNPQ assessment procedure, and offers a sound case for its use in acclimation and photoinhibition experiments.

Neuropeptides are neuronal signaling molecules that regulate many physiological and behavioural processes in vertebrates and invertebrates. Investigation of neuropeptide signaling in echinoderms (e.g. starfish) can provide insights into the evolution of neuropeptide systems because as deuterostomian invertebrates they occupy an "intermediate" phylogenetic position between vertebrates and protostomian invertebrates. Recent analysis of neural transcriptome data from the starfish Asterias rubens has identified 40 transcripts encoding neuropeptide precursors. Here the expression and function of neuropeptides derived from four of these precursors was investigated: relaxin-like gonad-stimulating peptide precursor (AruRGPP), relaxin-like peptide precursor 2 (AruRLPP2), pedal peptide-like neuropeptide precursors 1 and 2 (ArPPLNP1 and ArPPLNP2). AruRGP induces spawning of ovarian fragments from A. rubens. Analysis of the expression of AruRGPP in A. rubens using mRNA in situ hybridization revealed expression by cells in the radial nerve cords, circumoral nerve ring and tube feet. Furthermore, a band of AruRGPP-expressing cells was also identified in the body wall epithelium lining the cavity that surrounds the sensory terminal tentacle and optic cushion at the tips of the arms. Discovery of these cells is important because they are candidate physiological mediators for hormonal control of starfish spawning in response to environmental cues. Interestingly, AruRLPP2 is also expressed in the same region of the arm tip as AruRGPP but the physiological role(s) of AruRLP2 is not yet known. Analysis of the expression of ArPPLNP1 and ArPPLNP2 using mRNA in situ hybridization revealed a widespread pattern of expression in A. rubens. Furthermore, immunohistochemical localization of peptides derived from these precursors revealed immunostaining in neuronal processes innervating muscles. Consistent with this pattern of expression, peptides derived from ArPPLNP1 and ArPPLNP2 act as muscle relaxants in starfish. Interestingly, this contrasts with previous findings from protostomian invertebrates, where pedal peptide/orcokinin-type neuropeptides act as muscle contractants.

The persistence of woody plant populations faces numerous environmental challenges, including climate change, hybridisation and population fragmentation. Here I explore the genomic signatures and relative importance of these pressures in Dwarf Birch (Betula nana), which has declined significantly over the last century across the Scottish Highlands. Firstly, I find that future climate is likely to result in a significant range reduction and that relict populations are likely to display reduced fitness. Secondly, I show that combining multiple mutation rate markers yields more accurate estimates of demographic history and the impact of fragmentation. I develop a novel method to derive high mutation rate markers from short sequencing reads, to facilitate more widespread application. Thirdly, I assess the degree of local adaptation, and explore potential for composite provenancing for the restoration of B. nana populations. Surprisingly, the data yields little evidence of adaptive introgression from the related tree B. pubescens, suggesting that this may not be an alternative route to climate tolerance. Finally, I review published literature on the population structure and genetic diversity of genus Betula in Europe and consider options for the conservation and management of B. nana, including assisted gene flow and prioritization of in situ genetic diversity.

Genome size (GS) is a fundamental trait influencing cellular, developmental and ecological parameters, and varies c. 2400- fold in angiosperms. This astonishing range has the potential to influence a plant's nutrient demands, since nucleic acids are amongst the most phosphate and nitrogen demanding cellular biomolecules, and hence its ability to grow and compete in environments where macronutrients are limited. Angiosperm GS are strongly skewed towards small genomes, despite the prevalence of polyploidy in the ancestry of most if not all angiosperm lineages. This thesis examines the hypothesis that large genome sizes are costly to build and maintain and that angiosperm species with large GS are constrained by nitrogen and phosphate limitation. It untangles the interactions between GS, polyploidy and competition in plant communities, and examines how herbivory and GS play a role in plant productivity, measured as above-ground biomass. The hypothesis that large GS are costly was approached by analysing: 1) plant communities growing under different macronutrient conditions at the Park Grass Experiment (Rothamsted, UK); 2) plant communities under different conditions of macronutrient limitation and insect, mollusc, and rabbit herbivory at Nash's Field in Silwood Park (UK); and, 3) Ellenberg's indicator values which represent the realised niche of a species in terms light, water, and soil fertility. Support for the hypothesis was found in all experiments. The range of analyses show that angiosperm plants with large genomes (e.g. 1C-value > 5 pg) are indeed under greater macronutrient limitation in comparison to plants with small genomes, and that it is polyploid plants with large GS which are the most competitive when macronutrient resources are plentiful. In terms of herbivory, the key finding is a highly significant negative association between GS and rabbit herbivory. A species' realised niche for soil fertility was found to show a positive association with its GS. Overall the thesis shows that angiosperm GS plays a central role in plant community composition and responses to macronutrient conditions, and potentially on higher ecosystem processes through associations at different trophic levels.

European ash trees (Fraxinus excelsior ) are under threat from the fungal pathogen Hy- menoscyphus fraxineus causing ash dieback disease (ADB). Previous research has shown heritable variation in ADB susceptibility in natural ash populations. Prior to this project, very little genetic data were available for ash, thus hampering efforts to identify markers associated with susceptibility. In this thesis, I have presented nuclear and organellar assemblies of the 880 Mbp F. excelsior genome, with a combined N50 scaffold size of over 100 kbp. Using Ks distributions for six plant species, I found evidence for two whole genome duplication (WGD) events in the history of the ash lineage, one potentially shared with olive (Ks 0.4), and one potentially with other members of the Lamiales order (Ks 0.7). Using a further 38 genome sequences from trees originating throughout Europe, I found little evidence of any population structure throughout the European range of F.excelsior, but nd a substantial decrease in effective population size, both in the distant (from 10 mya) and recent past. Linkage disequilibrium is low at small distances between loci, with an r2 of 0.15 at a few hundred bp, but decays slowly from this point. From whole genome DNA methylation data of twenty F. excelsior and F. mandshurica trees, I identi ed 665 Differ- entially Methylated Regions (DMRs) between those with high and low ADB susceptibility. Of genes putatively duplicated in historical WGD events, an average of 25.9% were differen- tially methylated in at least one cytosine context, possibly indicative of unequal silencing. Finally, I found some variability in methylation patterns among clonal replicates (Pearson's correlation coefficient 0.960), but this was less than the variability found between different genotypes ( 0.955). The results from this project and the genome sequence especially, will be valuable to researchers aiming to breed or select ash trees with low susceptibility to ADB.

Learning and memory offer animals the ability to modify their behavior in response to changes in the environment. A main target of neuroscience is to understand mechanisms underlying learning, memory formation and memory maintenance. Honeybees and bumblebees exhibit remarkable learning and memory abilities with a small brain, which makes them popular models for studying the neurobiological basis of learning and memory. However, almost all of previous molecular level research on bees' learning and memory has focused on the olfactory domain. Our understanding of the neurobiological basis underlying bee visual learning and memory is limited. In this thesis, I explore how synaptic organization and gene expression change in the context of visual learning. In Chapter 2, I investigate the effects of color learning and experience on synaptic connectivity and find that color learning result in an increase of the density of synaptic complexes (microglomeruli; MG), while exposure to color information may play a large role in experience-dependent changes in microglomerular density increase. In addition, microglomerular surface area increases as a result of long-term memory formation. In Chapter 3, I investigate the correlations between synaptic organizations and individual performance and the results show that bees with a higher density of microglomeruli in visual association areas of the brain are predisposed to faster learning and better long-term memory during a visual discrimination task. In Chapter 4, I explore the genes involved in visual learning and memory by transcriptome sequencing and I show the unique gene expression patterns at different times after visual learning. In summary, my findings shed light on the relationship between synaptic connections and visual learning and memory in bees at the group and individual level and show new candidate genes involved in visual learning, which provide new avenue for future study.