Viruses are the most abundant biological agents in the global marine environment. Through cellular lysis viruses influence many biogeochemical and ecological processes, including energy and nutrient cycling, host distribution and abundance, algal bloom control and genetic transfer. Nano- and picophytoplankton are ubiquitous in the world’s oceans and are responsible for a high proportion of the annual global carbon fixation. However, relatively few viruses have been isolated and described that infect these key primary producers and little is known of their diversity, dynamics or propagation strategies. The aims of this study were to detect, isolate and characterise novel marine viruses that infect these important members of the phytoplankton assemblage. Screening of seawater samples for viruses that infect a broad representation of nano and picophytoplankton species was undertaken here. To enable this, a large culture collection of 106 phytoplankton species was established and used to screen seawater samples for viruses on a weekly basis over a two year period. A total of 12 novel viruses infecting the prasinophyte species’ Ostreococcus tauri and Micromonas pusilla were isolated from seawater sampled in coastal waters of the Western English Channel. Viruses were purified by plaque purification or liquid serial dilution techniques. Characterisation of novel virus isolates included growth kinetics, visualisation using transmission electron microscopy, host range analysis and estimates of viral genome sizes using pulsed field gel electrophoresis. Phylogenetic analysis of these viruses was conducted based on the sequence of the conserved DNA polymerase gene. Genome sequencing of two of the viruses infecting O. tauri was completed and revealed many exciting features, including a suite of genes hitherto unreported, or with rare occurrence, in viruses. Evidence is presented for horizontal gene transfer between viruses isolated in this study and their hosts, as well as between other eukaryotic and bacterial sources. Functional characterisation of the viral genomes sequenced and described in this study will provide clearer insights into viral dynamics and evolutionary history.

Integrated approaches to the reconstruction of Lower Devonian vegetation and environments are presented, combining palaeobotanical, palynological and sedimentological evidence from Old Red Sandstone strata of the Anglo-Welsh Basin. A new lower Lochkovian plant assemblage from central-south Wales is similar in diversity to contemporaneous assemblages along the southern margins of Laurussia. Coalified megafossils of rhyniophytes and rhyniophytoids e.g. Cooksonia hemisphaerica, represent basal embryophytes. Geometric morphometric analysis of sporangial morphology revealed a strong taphonomic control on shape. Newly discovered highly-branched mesofossils are synonymous with published charcoalified specimens from lower Prídolí and middle Lochkovian localities, and represent stem-group embryophytes with bryophytic characters. The non-embryophytes, with the largest biomass, include the fungal-like Prototaxites and associated mycelia, Pachytheca, and evidence for microbial biofilms. Several new dispersed palynomorph taxa are described, assemblages dominated by cryptospores. With additional published palynomorph and sedimentological data, broad palynofacies are constructed to reveal some information regarding lower Lochkovian habitats. Using core data from this locality, lower strata are correlated to the Raglan Mudstone Formation, and a two-stage, ephemeral, mud-dominated, dryland river system is envisaged. The appearance of sandier, meandering channel deposits in upper strata are correlated to the St. Maughans Formation, which suggests either a change in fluvial morphology or the switching-on of trunk channels, the causes for which are discussed. By combining palaeobotanical and sedimentological data, several plant taphofacies are recognised and a taphofacies model envisaged, the most significant taphonomic constraint on palaeoecological studies being the stratinomic partitioning of vegetation prior to burial by fluvial hydraulic sorting. Plant material is restricted to channel elements with low preservational potential, therefore the extent of phytoterrestrialisation and soil productivity may have previously been underestimated. Indirect evidence for significant soil productivity, which may have increased chemical weathering, potentially altering atmospheric CO2 levels, is calculated from the stable carbon isotopic values of pedogenic carbonate nodules.

Ponds are diverse habitats that make major contributions to regional biodiversity, yet have received relatively little attention compared to other freshwater environments. This study investigated the physico-chemical characteristics and ecology of a nationally important concentration of temporary upland ponds in Radnorshire, Wales in both spatial and temporal dimensions (up to 80 ponds over 18 months). Plant and macroinvertebrate communities were typical of oligotrophic, acidic ponds and appeared to vary along gradients of pH and hydroperiod, whilst including several nationally rare/threatened taxa. A national classification based on the biological community of temporary ponds grouped Radnorshire ponds with a few others in western Britain. Ponds were generally small, shallow and acidic with low concentrations of nutrients and dissolved minerals. Water chemistry was associated with concentration by evaporation and dilution by rainwater, whilst the overall hydrology of ponds was successfully modelled using local meteorological data. Over the course of the study, large increases in macroinvertebrate abundance were observed, but assemblage composition and richness were broadly constant. Seasonality in the abundance of individual macroinvertebrate taxa was evident and suggested that autumn was the optimum time for invertebrate sampling in terms of abundance and diversity. Nearly 40% of the variation among ponds in macroinvertebrate and plant communities was explained by a combination of a species-area effect and differences in pH: no effect of pond isolation was detected within the context of the study region. A cumulative species-area analysis found that a group of small ponds support higher biodiversity than a single large pond of the same area, highlighting the importance of considering beta diversity. Taken together, the findings of this PhD project justify the designation of Radnorshire as an Important Area for Ponds: the ponds form a distinct ‘pondscape’ of >80 waterbodies, with a highly dynamic environment and biota, and which provide a major habitat resource for rare species in the UK.

Flavonoids and polyphenolic compounds are widely distributed in commonly consumed foods, beverages and herbs. Their consumption has been associated with improving the health and reducing the risk of several chronic diseases. In Saudi Arabia, recent interest in the health-promoting properties of traditional herbs has been increased. To-date researchers have focused on testing these therapeutic properties. However, information about their chemical profile is largely unexplored. Thus, the beginning of this project aimed to use HPLC–PDA–MS2 to identify polyphenolic compounds in a medicinal herbal tea made from seeds of Anastatica hirerochuntica. Twenty compounds comprising a series of flavone C- and O-linked glycosides, phenolic acids, chlorogenic acids and flavonols were identified or partially identified on the basis of co chromatography with reference compounds and MS2 and MS3 fragmentation patterns. The flavones were the principal components, occurring as luteolin, apigenin and diosmetin conjugates. The antioxidant potential of individual compounds in Anastatica was assessed using HPLC with an on-line ABTS•+ detection system. Under the experimental conditions, 14 compounds exhibited antioxidant activity. The highest contribution to the antioxidant capacity of the tea, 56%, came from 3,4-dihydroxybenzoic acid and caffeoyl- and dicaffeoylquinic acids while 6-C-glucosides of luteolin and apigenin contributed 41%. These findings together with tests in the FRAP antioxidant assay and the Folin–Ciocalteu total phenolics assay revealed that aqueous infusion of A. hirerochuntica seed is rich in polyphenolic compounds. Another perspective of investigating these polyphenolic compounds is not just knowing their chemical constituents but also studying their bioavailability upon ingestion. Therefore, blackberries and strawberries were chosen for intervention studies with human subjects to examine the bioavailability of anthocyanins, a group of flavonoids, due to their importance as natural antioxidants that have been linked with beneficial effects on health to humans. In the first in vivo study, plasma and urine were collected from eight healthy subjects after ingestion of 180 g of blackberries and analysed by HPLC-PDA-MS2. Cyanidin-3-O-glucoside was metabolised principally to peonidin-O-glucuronide. Cyanidin-3-O-glucoside and its metabolites appeared rapidly in the plasma in low concentrations ranging from 5 to 20 nmol/L with low urinary excretion of ~0.08% of the total intake. In the second in vivo study, both blackberry and strawberry were used to examine the small intestinal absorption and metabolism of both cyanidin-3-O-glucoside and pelargonidin-3-O-glucoside by feeding five ileostomy volunteers with 180 g of berries. Samples of urine and ileal fluid were collected over a 0-24 h period after ingestion and analysed by HPLC-PDA-MS2 Unmetabolized anthocyanins of blackberries and strawberries were recovered in ileal fluids at a level of 5.1% and 13.6%. This indicates either low level of absorption or lack of stability at the non-acid pH in the small intestine. The overall urinary excretion of anthocyanins was 0.06% and 0.87% of intake of blackberries and strawberries respectively. The urine data shows that both cyanidin and pelargonidin glucosides were metabolised primarily to peonidin-O-glucuronide and pelargonidin-O-glucuronide respectively. Although low recoveries of the two compounds are reported in this investigation in both ileal fluid and urine, pelargonidin-3-O-glucoside showed a slightly higher recovery compared to cyanidin-3-O-glucoside. The data from both in vivo studies reflect the influence of the aglycone structure on the bioavailability of these anthocyanins. The stability of anthocyanins in the gastrointestinal tract was also assessed using in vitro models (Chapter 5). The results indicated that at neutral pH the salivary enzymes and oral microbiota had no impact on cyanidin-3-O-glucoside but degraded pelargonidin-3-O-glucoside by ~20%. With simulated and human gastric juice, both anthocyanins were unstable and the breakdown continued dramatically under pancreatic digestion where a 5.1% recovery was obtained. Their low recovery levels were comparable to those obtained in vivo with ileal fluid. These findings imply that the chemical structure of both anthocyanins influence their stability similarly. However, the data provide no explanation about the higher bioavailability of pelargonidin-3-O-glucoside compared to cyanidin-3-O-glucoside in vivo. This presumably is a consequence of the more ready access of pelargonidin-3-O-glucoside to the enterocytes of the small intestine. In conclusion, the work here has shown the diversity of compounds with potential health benefits that are present in a natural product from Saudi Arabia. Experiments were carried out, using local products from the UK, to investigate factors that would affect their potential to provide health benefits. The in vivo and in vitro experiments show the complexity of investigations of potential bioactive compounds in human nutritional research. Polyphenols which differ by only a single hydroxyl group show very different absorption, metabolism and stability properties.

Homologous recombination is an integral part of meiosis and is essential for generating crossovers that ensure balanced segregation of homologous chromosomes and establish genetic variation within offspring. It is therefore exceedingly important that meiotic cells employ stringent control mechanisms to safeguard crossover formation. Work in yeast has indicated that the meiotic axis, a proteinaceous structure that tethers meiotic chromosomes into looped arrays, plays a crucial role in many aspects of homologous recombination, from double strand break formation to crossover interference. It has also been suggested that increased crossover interference helps to establish meiotic stability by inhibiting multivalent formation during autopolyploid meiosis. Using immunocytochemistry coupled with super-resolution microscopy, we have further investigated the role played by the meiotic axis protein ASY1 in stabilising meiosis in the established autotetraploid Arabidopsis arenosa. We have also used Arabidopsis arenosa as a model for studying how meiotic interference might operate within an autopolyploid context. Alongside this, experiments using transgenic lines of the model plant Arabidopsis thaliana have helped to shed light on how crossover formation and synapsis are affected by reduced expression of ASY1 and ASY3 and to determine what effect limiting meiotic crossover numbers might have on neopolyploid meiotic stabilisation.

Lathyrus species are well placed to meet the increasing global demand for food and feed, at the time of climate change, provided that the problem of the neurotoxins is solved. Conservation and sustainable use of the genetic resources of Lathyrus is of significant importance to allow the regain of interest in Lathyrus species in world. A comprehensive global database of Lathyrus species originating from the Mediterranean Basin, Caucasus, Central and West Asia is developed using accessions in major genebanks and information from eight herbaria in Europe. This information allowed to determine gaps in ex situ collections, mainly for wild relatives of cultivated species, and to identify appropriate sites for in situ conservation, mainly in the Fertile Crescent region. Core subsets were identified and the Focused Identification of Germplasm Strategy (FIGS) was used to derive a subset for heat and drought tolerance. This study used morphological characters and AFLP markers to better understand the taxonomic classification of different Lathyrus sections and species and to gain insights on the phylogenetic relationships among them. A Field Guide for Lathyrus L. species of the Mediterranean Basin and Caucasus, Central and West Asia is produced, to ease their identification by non-professional taxonomists.

QTL mapping with segregating populations results in poor map resolution which limits the applicability of mapped QTL in further research such as gene cloning. The current research project aimed mainly at developing STepped Aligned Recombinant Inbred Strains (STAIRS) covering the top region of chromosome 3 and demonstrating the feasibility of using STAIRS in high resolution mapping of QTL in Arabidopsis. The top region of chromosome 3 of Arabidopsis had been reported to house QTL related to flowering time. This region was first saturated with 24 polymorphic microsatellite markers and 23 narrow STAIRS were produced within the region via a marker-assisted backcross breeding programme using whole chromosome substitution lines. The analysis of QTL with the narrow STAIRS revealed a major pleiotropic QTL within 2-3 cM affecting flowering time, leaf number at day 20 and rosette and cauline leaf numbers at flowering. A second QTL with less but opposite effect on the same traits were located within 15-20 cM. The search for candidate genes within 2-3 cM of chromosome 3, to locate possible candidate genes revealed COL-2, CONSTANS-Like gene which affects flowering time. Microarray gene expression profiling was performed using the two genotypically closest lines which differ for flowering time to compare the two lines at the same chronological and physiological ages in two experiments respectively. The lists of differentially expressed genes were obtained from the two experiments. Differential expression was observed for the possible candidate gene in the latter experiment. The results emphasized the power of STAIRS in fine mapping of QTL and the possibility of using them in transcriptional profiling to study the expression of genes.

The non-native predatory phytoseiid mite \(Neoseiulus\) \(californicus\) has been found in recent years in UK apple orchards. The aims of this study were to determine whether this mite could establish in the UK and its potential as a biocontrol agent for \(Panonychus\) \(ulmi\). By reviewing the literature and examining specimens of \(N. californicus.\) it was concluded that taxonomic synonymies with \(Amblyseius\) \( californicus.\) \( Amblyseius\) \(chilenensis\) and \(Typhlodromus\) \( mungeri\) could be supported, but those with \(Typhlodromus\) \( marinus\) and \(Neoseiulus\) \(fallacis\) could not. \(Neoseiulus\) \(californicus\) was found in strawberry, hop, blackcurrant and apple plantations in the main fruit growing regions of the UK. Field and laboratory studies showed that \(N.californicus\) possesses the ability to diapause, is a chill tolerant species and can survive winter field conditions in the UK. \(Neoseiulus\) \(californicus\) was found to readily consume both \( Panonychus\) \(ulmi\) and \(Tetranychus\) \(urticae\) and consumed greater numbers of prey than the native phytoseiid \(Typhlodromus\) \(pyri\). Deutonymphs consumed an average of 1.8 and 1.6 immature \(P. ulmi\) stages per day respectively and an average of 2.6 and 1.4 \(T. urticae\) respectively. The total mean development time for \(N. californicus\) was 7.47 days and for \(T. pyri\) was 12.45, feeding on \(P.ulmi\). \(Neoseiulus\) \(californicus\) from USA, Spain and UK displayed differences in measurements of a selection of morphological characteristics, diapause ability (16, 0 and 960/0 diapause respectively), development times (shortest for USA and longest for UK), fecundity (0.82-0.97 eggs per day) and esterase banding patterns, indicating the existence of different detectable strains. In conclusion, \(N. californicus\) was found to be a component of fruit plantation fauna in the UK, has the potential to survive winter field conditions and readily consumes \(P. ulmi\) and \(T.urticae\).

Self-incompatibility (SI) is the major mechanism used by flowering plants to prevent self-pollination and thus avoid inbreeding. It is a genetically controlled mechanism that encodes a highly specific recognition system that inhibits the growth of incompatible pollen, whereas compatible pollen from an unrelated plant of the same species is able to grow and effect fertilization. In Papaver rhoeas, inhibition of incompatible pollen is mediated by a signal transduction pathway that activates a complex network of intracellular events including Ca\(^{2+}\)-dependent phosphorylation of p26, an inorganic pyrophosphatase required for pollen tube growth, depolymerisation of the pollen actin cytoskeleton and ultimately programmed cell-death (PCD). To further understand the mechanisms involved in Papaver rhoeas SI it is important to identify and characterize components of the signalling network that mediate the SI response. Recent studies have revealed that p56, a mitogen-activated protein kinase (MAPK), is involved in activation of PCD during SI. MAPKs have been shown to be important signalling components in a range of cellular responses in eukaryotes. In Arabidopsis thaliana there are 20 MAPKs with roles including cell division, abiotic stress response, wounding response and hormone signalling. Preliminary studies suggested an MPK3-like gene might encode p56, as an anti-AtMPK3 antibody cross-reacts with a protein corresponding to p56. Experiments carried out here suggest this is not the case. Using a combination of bioinformatics and proteomics data it has been possible to identify and clone a candidate p56 gene from Papaver rhoeas pollen. The putative p56 gene has homology to AtMPK9 and is a member of the T-D-Y class of MAPKs. It has been designated PrMPK9-1. An antibody raised against recombinant PrMAPK9-1 protein is being used to confirm that this gene/protein does indeed correspond to p56.

The aim of this project was to combine species distribution modelling (SDM) with the results of a molecular genetic diversity study to make suggestions for sites on which to locate genetic reserves. This work was complemented by a molecular genetic diversity and a forest management policy study, to examine the potential for in situ conservation of the crop wild relative species, Prunus avium. In order to identify the species distribution, the most widely available occurrence data were in the form of historical records, gathered from online repositories and herbaria. A selection of environmental variables were incorporated with occurrence records in the SDM software, MaxEnt, to estimate the existing and possible future distribution of this species. Different sampling methods and combinations of accessions were used to evaluate model performance. This work was supplemented by the use of microsatellite marker analysis, to identify genetic distance among samples collected, covering the species‘ range. Clear separation was found between the individuals from the south-eastern edge of the range, and all other European samples. The effect of management practices on the persistence of wild cherry in managed forests and the impact of conservation policy was also considered, using case studies from the UK and Belgium, interviews and grey literature. Results showed that the difficulties of obtaining reliable, unbiased data can be overcome, as long as these factors are considered in conservation planning. Suggestions are made for several potential reserve sites across Europe, in a variety of forested environments, with differing management priorities.