DNA topology is dependent on axis proteins during eukaryotic cellular processes. Chromosome axis organization is complex during meiosis, when DNA repair needs to be coordinated with homology searching and synapsis. Although roles for the axis component Topoisomerase II (TOPII) and the post-translational modification (PTM) of ASY1 homologues during meiosis have previously been reported, few studies have been performed in plants. The aim of this thesis is to investigate the effects of these proteins on meiotic DNA topology and axis morphology, and their implications for homologous recombination (HR) in Arabidopsis thaliana. Using a combination of cytogenetic and molecular techniques, we show the role of PTM of ASY1 differs from that of its budding yeast orthologue. Phosphorylation of a plant specific set of residues in ASY1 affected chiasmata distribution. Analysis of the first TOPII mutants described in plants also revealed a link with HR. Chromosome replication, condensation and segregation phenotypes were consistent with previous studies of TOPII in other organisms. For the first time, we report that TOPII and chromosome movement collaborate in interlock resolution during meiosis, confirming predictions from decades ago. Overall, these investigations have revealed new roles for the axis in plant meiosis, which could have potential for crop breeding.

Over the past century there have been substantial declines in farmland biodiversity as a result of the intensification of agricultural practice. Concerns over these declines have led to the development of agri-environment schemes designed to mitigate the effects of intensive agriculture and to benefit biodiversity. Prior to commencing this thesis it was not clear if flower-rich, pollinator-focused agri-environment schemes had a population level impact on wild bees on farmland. Whilst previous work has shown that the creation of flower-rich habitat can provide suitable foraging resources for bumblebees, little was known about the impact of this management on bumblebee population sizes and even less on whether these resources were used by and benefited solitary bees. This thesis compares bee populations between farms with and without flower-rich, pollinator focused agri-environment schemes in Hampshire and West Sussex, UK. Using genetic techniques to estimate colony density, and hence population size, farms implementing targeted schemes had a significantly higher density of bumblebee nests for the four species studied (212 nests/km2 against 112 nests/km2). However, there was no difference in the species richness of bees between these different farm types. When assessing pollen use by solitary bees, flowering plants sown as part of pollinator-focused agri-environment schemes were not widely used, representing 27% of pollen foraging observations and 23% of pollen collected by volume. Only 35% of solitary bee species were found to use sown plants for pollen to a meaningful extent, with most pollen collected from plants persisting in the wider environment. The creation of flower-rich habitat significantly increased resource availability, but did not increase resource diversity. These results indicate that if diverse bee populations are to be maintained on farmland then agri-environment schemes must be developed that effectively increase the number of flowering plant species present at the farm scale.

In commercial barley cultivars meiotic crossover (CO) distribution is skewed to the distal regions of the paired chromosomes. This restricts recombination to these regions thereby reducing the potential genetic variation that can be exploited in plant breeding programs. The aim of this project was to develop experimental strategies that will enable the frequency and distribution of meiotic crossovers to be modified in order to generate progeny with novel gene combinations. Treatment with the histone deacetylase inhibitor trichostatin A, led to significant modifications in crossover frequency in a concentration-dependent manner with lower concentrations not greatly impacting fertility, allowing for the extraction of fertile seeds. The genetic screening of a treated marker population at The James Hutton Institute (JHI), demonstrated subtle but significant shifts in the distribution of meiotic recombination, indicating that modifying recombination through chemicals applied via the transpiration stream is indeed feasible in barley and hence, possibly in other cereals. The cytological study of a barley desynpatic mutant \(des8\) in collaboration with JHI revealed that synapsis is normal despite reduced chiasma frequency. Genetic mapping studies are in progress to identify the mutant gene responsible for this phenotype which will help us to improve our current knowledge of meiosis in barley.

The aim of this thesis is to investigate the factors controlling the spread and distribution of bracken (Pteridium aquilinum) in Scotland. Bracken has long been an agricultural problem and, more recently, fears have been raised about the plant's carcinogenic properties. Despite the seriousness of the problem, there has been little quantitative research into factors controlling the plant's vigour, although there are many anecdotal references on the subject. It is the aim of this thesis to; study the climatic, edaphic and biotic characteristics of the bracken zone; establish the statistical relationship between these factors and bracken vigour and to apply the findings to explain how these factors affect bracken in Scotland. The climatic, soil, vegetation and biotic characteristics of four sites in the bracken zone (west, south-west, north-east and south-east) are reviewed first. By comparisons of inter-site factors and bracken vigour at the sites, it is possible to formulate hypotheses on the factors that control bracken vigour. Correlation and regression analyses of individual factors with frond height, density and litter depth are than carried out, followed by a Stepwise Regression Analysis. Finally the findings of the two sections are summarised and the results applied to explain bracken distribution and spread in Scotland. The major conclusions of this thesis can be summarised as follows: Early season temperature strongly affects bracken vigour and largely accounts for the east-west difference in bracken vigour. Vigorous bracken in the west can withstand a greater degree of frosting than the less vigorous bracken in the east. Soil moisture stress, heavy frost and relatively intensive agriculture in the east results in a higher bracken zone (and therefore suboptimal soils and temperatures) in the east than in the west.

Flower initiation and development to anthesis in Dutch iris were investigated using three cultivars, 'Wedgwood', 'Ideal' and 'Professor Blaauw'. In particular, environmental effects on flower initiation and on flower abortion were studied. With the aid of a thermal-time model, the rate of initiation (the reciprocal of time to initiation) was shown to be linearly related to the temperature used to store dry bulbs, provided that this was constant. When bulbs were transferred from one temperature to another, however, the rates of initiation differed from those expected. It was concluded that the sequence of temperatures was important and a possible mechanism for flower induction was discussed. Following the start of flower initiation per se, a different optimum temperature for flower-organ differentiation was observed. The effect of both pre-planting and post-planting temperatures on the growth and development of the flower were investigated. The proportion of bulbs with successful flower development to anthesis increased with mean flower and stem dry weight. The heaviest flower and stems were produced by those bulbs with the greatest leaf weight. This was attributed to the increased availability of current photosynthates in plants with the largest foliage frames. Flower development was affected by an interaction between time of planting, bulb size and glasshouse temperature for a given light integral. With later bulb plantings, between January and March, higher light integrals were required for the same flower development at moderately high temperatures (16-18°C). This higher light requirement was detected with the largest bulbs first and not until the last planting date with smaller bulbs. At higher temperatures (20°C) flower development was poor regardless of the light integral. At lower temperatures (14°C) the same flower development achieved regardless of the light integral within the range tested. Further investigation in controlled environments enabled the detection of a photoperiodic effect at the moderately high temperatures. Daughter-bulb growth was promoted by long photoperiods and high temperatures increasing sink strength there for assimilates with a corresponding decrease in flower development. The partitioning of assimilates under high and low light was examined by determining the distribution of 14C-labelled assimilates during growth in the glasshouse. Daughter bulbs under low light had a higher relative specific activity than those under high light, at the time when the flower was most prone to abortion. Application of cytokinin to the flower bud resulted in a reduced daughter bulb weight, but heavier flower buds. It was concluded that flower development was affected by the total current assimilate available and the partitioning of these assimilates between daughter bulbs and flower bud.

Linum usitatissimum (flax), Brassica napus var. oleifera (oilseed rape), Miscanthus x giganteus (miscanthus) and Urtica dioica (nettle) were investigated to assess their potential as phytoremediation crops. Germination experiments using flax and oilseed rape established that seedling germination was not inhibited by exposure to metals in solution except at the highest concentrations considered. Germination was, however, not a reliable indicator of plant metal tolerance as metal toxicity to emerged seedlings was evident in contaminated soil treatments exhibiting good germination rates. Four plant species were grown in soils containing six metals at both highly and marginally spiked levels, to reproduce genuine contaminated soils whilst allowing the study of each metal in isolation. A sewage sludge treated soil with a high metal and organic matter content was also included in the study. Miscanthus was the species most tolerant of the highly contaminated soils. The highest tissue concentrations recorded in plants exposed to the highly contaminated soils were (969 mg Zn/kg) in stems of miscanthus and (919 mg Cd/kg) in stems of nettle, but plant growth in these soils was generally poor. The plant species survived well in the sewage sludge soil, although metal uptake from this matrix was low. Oilseed rape and nettle accumulated the highest tissue metal concentrations in the study of marginally contaminated soils. Indeed the highest tissue concentration recorded for plants grown in all of the soils was found in nettle grown in the marginally contaminated Zn soils (1937 mg/g). Miscanthus, was able to remove a greater weight of metal from the soil owing to its higher biomass, despite having a lower tissue metal concentration than the other species. Flax, miscanthus, nettle and oilseed rape have been shown to have potential to act as part of a phytoremediation programme, however, more work with these crops is required before film advice can be given on commercial application of the crops in contaminated land remediation.

The overall aim of this research is to develop a new root-image based approach to modelling water uptake by plants. The approach developed employs a digitized image of the root zone to determine an ‘effective root density ratio’ that is subsequently used to yield a spatially variable sink term. The moisture flow model chosen is based on Richards’ Equation added a sink term to facilitate inclusion of a water uptake model (i.e. 1D, 2D and 2D axisymmetric format). A numerical solution was achieved via the finite element method for spatial discretisation along with a finite difference time-marching scheme. The numerical evaluation of the root density ratio was coded in Matlab. The resulting values were then used to define the spatial variation of the sink term within the finite element code. Initial applications of the new model operating in a one-dimensional mode provided some confidence with respect to the implementation of the new image-based root density approach to simulate moisture migration patterns beneath a uniform cover of vegetation. A new two-dimensional axi-symmetric form of the model was then developed and applied to simulate moisture migration near established trees. The model was validated by direct comparison to the field measurements recorded. The study provided an assessment of the significance of water content (and therefore suction) changes on the stability of unsaturated soil slopes. Two typical root architectures were considered to investigate the influence of root architecture on slope stability. In particular, effects of root architecture were emphasized. In conclusion, a new root-image based approach to modelling water uptake by plants has been developed. In general, it is hoped that the current research has provided a useful further contribution on modelling water-uptake process and on the overall assessment of slope stability.

Ogi is a fermented food made from maize, sorghum or millet which serves as complementary food for infants and breakfast for adults in Nigeria, West Africa. This study characterized the microbial diversity of maize and sorghum grains and ogi produced by their natural fermentation in an attempt to understand the roles of the key microbial species and the impact of the population dynamics and selected species on changes in nutritional composition and aroma notes of ogi during fermentation. A combined approach of culture dependent and culture independent methods of analysis was applied to investigate the microbial community of grains and ogi from two different sources. Microbial diversity and viable populations varied with the source of the grain. Bacterial and fungal genera identified with the partial 16S rRNA and 26S rRNA sequence analysis respectively in maize and sorghum were Bacillus, Enterobacter, Micrococcus, Kytococcus, Pantoea, Staphylococcus, Amycolatopsis, Methanoculleus, Aspergillus, Penicillium, Eupenicillium, Acremonium, Schizosaccharomyces, Meyerozyma, Hyphopichia, and Pichia in maize grains; Enterococcus, Enterobacter, Pantoea, Bifidobacterium, Aspergillus, Cladosporum, and Penicillium in maize ogi; Enterococcus, Enterobacter, Pantoea, Aeribacillus, Cyanobacterium, Acinetobacter, Fusarium and Trametes in sorghum grains; and Pediococcus, Lactobacillus, Enterococcus, Bacillus, Cladosporum and Penicillium in sorghum ogi. Similar species were observed in both sources of maize while those of sorghum differed slightly. Predominant microbes included species of Enterobacteriaceae and moulds. Acetic acid bacteria were not identified as part of the diverse community. Following the predominance of moulds during the natural fermentation, preliminary screening was performed by PCR using specific biosynthetic gene primers to test whether they are the mycotoxin producing species. None of the genes tested were detected by PCR thus they may not be the toxin producing species. Starch, non-starch polysaccharide (NSP), phytate and phenolic compounds were determined in the grains and respective ogi to ascertain the levels of these nutritionally important components in the naturally fermented ogi and the impact of the varying microbial populations on the fate of these compounds during fermentation. In the grains, the average starch and NSP contents in each case were 80.35 g/100g and 9.40g/100g in maize and 93.12 g/100g and 8.14 g/100g in sorghum. Out of the total in grain the average percentage recovery of starch and NSP respectively in the ogi showed 63% and 42% in maize and 58% and 27% in sorghum. Maize showed good starch and fibre (NSP) retention than sorghum after fermentation. To further understand the types and levels of polymers in NSP hydrolysis in ogi fermentation, HPLC analysis of the hydrolysed extract was performed. Glucose was entirely present in maize and sorghum ogi which represents the beta-D-glucans while arabinose and xylose (in maize only), mostly lost with the pomace, signify the arabinoxylans. Overall variations in the microbial populations of sorghum seemed causal to the difference in starch and NSP recoveries. Phytate was assessed based on release of total phosphorus in the samples by enzymatic and chemical methods. Recovery of phytate in the naturally fermented ogi ranged from 18-25% in maize and 40-48% in sorghum suggesting greater phytase activity and more nutrient bioavailability in maize ogi than in the sorghum. Greater activity in maize reflects the presence of phytate hydrolysing species such as Aspergillus in the grain. Total phenolic content (TPC) was assessed by Folin-Ciocalteu colorimetric method after direct extraction of samples by saponification. TPC in the original grains ranged from 410–437 mg GAE/100g in maize and 221–247 mg GAE/100g in sorghum. Due to the nutritional significance, the amount of phenolics that are either freely soluble or are covalently bound to the food matrix were assessed. Soluble phenolics in ogi ranged from 16-38% in maize and 32-49% in sorghum based on the total soluble fraction in the original grain. In all cases loss of soluble phenolics with the waste waters accounted for 12-25% and 31-39% with the pomace. Only the LAB population seemed to correlate with the release of phenolics in the natural fermentation. Given the higher value of soluble phenolics, naturally fermented sorghum ogi appeared to have higher antioxidant potential than the maize ogi. Furthermore an attempt was made to ascertain whether the use of selected microbes would improve the antioxidant properties and aroma of ogi while minimizing the incidence of pathogens due to chance inoculation. Thus the impact of selected LAB (Pediococcus pentosaceus) and fungi (T. hirsuta and A. zeae previously shown to have phytase activity) on changes in phytate, phenolics and aroma of ogi was assessed following a parallel experiment to the previous study but using autoclaved grains. Five fermentation treatments of the pure and co-cultures were investigated. Cell populations in all culture fermentations varied and reached the average maximum of log 6-9 cfu/ml. Changes in the distribution of bound and soluble phenolics were observed showing esterase activity. Leaching of phenolics was evident in all cases but was higher in the sorghum fermentations. Higher levels of soluble phenolics were recovered in pure culture fermented ogi using T. hirsuta or P. pentosaceus than in the natural fermentation having 76% and 45% of the original soluble fraction in maize and sorghum respectively. This suggests greater antioxidant potentials than the naturally fermented ogi. Pure culture fermentations using T. hirsuta and co-culture of P. pentosaceus with A. zeae reduced phytate by 97% and 96% in maize and sorghum ogi respectively showing greater phytase activity and more nutrient bioavailabilty in the ogi than in the natural fermentation. The aroma profile of ogi was analysed by solid-phase microextraction and gas chromatography-mass spectrophotometry (SPME GC-MS). Ethyl acetate, butyl acetate and ethyl hexanoate were observed as the key active aroma components in ogi. The ester, methyl thiobutanoate was found to be unique to the naturally fermented ogi suggesting that it may have been generated by species other than the selected starter organisms. Overall in both natural and starter culture fermentations, maize ogi showed high relative abundance of volatile components suggesting good substrate compatibility and utilization during fermentation. Thus compounds with high threshold values may be significant in the aroma notes of maize ogi. P. pentosaceus and T. hirsuta in pure and in co-culture fermentations produced ogi with aroma notes mostly related to the naturally fermented product. In conclusion the diversity and levels of the initial microflora and the structural composition of grain could be major factors contributing to the nutritional compositional changes in ogi fermentation.

No description available.

Natural products have been the source of numerous leads for several drugs. As these natural products are often isolated in small quantities, it is necessary to produce them synthetically to allow testing for biological activity. Furthermore, synthesis allows the preparation of unnatural analogues for SAR studies. Cyclic peptides represent an important family of biologically active natural products. The hepta- and octacyclopeptides sanguinamide A and sanguinamide B were recently isolated in submicromolar amounts by the Molinski group. The lack of material prevented biological evaluation of the natural products. For this reason and to confirm the structural elucidation we have targeted the total synthesis of sanguinamides. In addition to two proline residues, sanguinamides A and B include heterocycles and natural L-amino acid residues. We have completed the total syntheses of sanguinamides A and B; however the synthetic rotamers differed in both cases from the natural rotamers. We have investigated the influence of macrocyclisation on cis/trans conformational preference of the proline residues for the synthesis of sanguinamide A. We attempted several isomerisations and calculated the relative energies of the different sanguinamide conformers. [D-Ile]-Sanguinamide A, Cys(tBu) analogue of sanguinamide A and the synthetic sanguinamide B displayed antibacterial activity while the synthetic trans, trans-sanguinamide A displayed mild tyrosine kinase inhibitory activity. While extracted stylissamide A showed inhibition of translation during the elongation step, even though being structurally identical to the natural product, the synthetic compound prepared by macrocyclisation from a linear precursor was found to be totally inactive. Histones undergo different types of covalent modifications on the N-terminal tails such as acetylation, phosphorylation and methylation. Histone modification is a major mechanism of regulation in gene expression, replication and repair. Deregulation of histone modifications leads to cancer progression and therefore, inhibitors of enzymes which are able to catalyse the addition and removal of these epigenetic marks have therapeutic potential for treating cancer. An enzyme of particular interest is the family of zinc-dependent histone deacetylases (HDACs) that remove acetyl groups from acetylated lysine residues. Depsipeptides were prepared as HDAC inhibitors. We will ii present our total synthesis of largazole along with a range of analogues and discuss the SAR obtained from HDAC and cell proliferation assays. We elucidated the stereochemistry of burkholdac B by total synthesis of three diastereomers. The diastereomers made along with the natural product were tested as HDAC inhibitors. We are interested in inhibitors of lysine-specific demethylase 1 (LSD1) which is a different kind of epigenetic enzyme involved in demethylation of histone proteins in chromatin. Tranylcypromine is known to be an LSD1 inhibitor. Analogues of PCPA have been synthesised in order to explore the structure-activity relationships of this inhibitor. Analogues were also prepared and tested as LSD1 inhibitors.