No description available.

Seed germination is a key process in world agriculture. For this reason, the capacity of a seed to germinate with minimum input from farmers is highly desirable, keeping the production costs as low as possible. The physiological mechanism of germination is well known, involving the rupture of the endosperm and testa envelope by the expanding embryo, but the molecular and biomechanical changes underlying this process are poorly understood. In order to answer the question of how the plant developmentally regulates changes in cell wall stiffness associated with germination, an innovative molecular biomechanics approach was developed. It combines biophysical, engineering and molecular biology approaches. A comparative approach was taken using the related species Arabidopsis thaliana and Lepidium sativum, the former due to the wealth of genomic resources, and the latter due to larger size and ease of use in biomechanics experiments. Environmental scanning electron microscopy imaging revealed that the endosperm structure is intact after protrusion of the radicle, confirming the fact that rupture occurs between individual cells. Germination is a process that requires targeted cell separation or/ and cell wall remodeling. For this reason, following the predictions of the gene network SeedNet, containing the endosperm-specific sub-network cluster 19 (Bassel et al., 2011), endosperm specific genes were studied. In order to localize their expression, promoter::GUS constructs were used for the genes DELTA-VPE, SCPL51 and DOF2.1, and different mutant alleles of four transcription factors from cluster 19 (athb23, bhlh-115, bee2 and dof2.1) were screened to identify changes in germination behaviour. DELTA-VPE and SCPL51 were proven to be endosperm specific and ABA insensitive. DELTA-VPE was GA insensitive and SCPL51 expression required GA. Also, DELTA-VPE expression could be observed after 15 minutes of imbibition in the whole endosperm, while SCPL51 showed a temporal expression requiring 18 hours of imbibition before being observed in all endosperm cells. The analysed T-DNA lines showed an epistatic relationship between ATHB23 and DOF 2.1 and a decreased sensitivity to stress factors like osmotic and salt stresses, than the wild type. Using nanoindentation, a differentiation between different regions of endosperm was attempted, but the methodology was not sensitive enough. However, different elastic modulus values for imbibed and dry Lepidium seeds were registered. To image the internal changes in seed structure during germination, micro-CT was used, estimating values for endosperm thickness from dry state to germinated one. This work enforces the knowledge of the molecular biology and biomechanical properties of the endosperm.

The research was undertaken at a sand dune system located along the South East coast of England, known as Sandwich Bay. Sandwich Bay has attracted a number of environmental designations, including Special Areas of Conservation and a Site of Special Scientific Interest due to the presence of rare habitats and flora found predominantly at this single site, such as Himantoglossum hircinum (lizard orchid) and Orobanche caryophyllacea (bedstraw broomrape). The research focus centred on concerns surrounding ecological change resulting in the loss of grey dunes, an Annex 1 priority feature. Sandwich Bay has been classed as a Special Site of Scientific Interest in unfavourable condition (Natural England, 2014), based primarily upon the loss of fixed grey dune habitats to neutral grasslands (SD8 to MG1/MG12 NVC classifications). The aim was to identify causative factors that might account for the observed historic and any current changes in vegetation. The research was conducted between October 2011 and September 2014, and focused upon hydro-chemical interactions in the environment. Analysis was undertaken by the installation of 103 dipwells across the 520 ha site, in order to obtain groundwater samples. The hydro-chemical and botanical analysis indicated that the vegetation composition was not affected significantly by the chemical constituents within the groundwater. However vegetation composition was significantly modified by variable surface elevation and the related height of the water table. An additional investigation focused upon the identification of management techniques that are thought to be beneficial to dune vegetation restoration. Three management trials were located at three different sites, investigating four different management treatments. Analysis showed that there was a significant difference between the various management treatments and species composition. Vegetation analysis indicated that both cut and remove, and burning, as management treatments encouraged a greater diversity of species, particularly in sheltered eutrophic areas.

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The cell cycle comprises the four phases of, G1, S-phase, G2 and mitosis. Two critical transitions are G1/S and G2/M; the latter is regulated by WEE1 kinase and CDC25 phosphatases. The scope of this thesis was to investigate the regulation of the G2/M transition of the cell cycle by WEE1 and CDC25, and how these genes interface with plant growth regulators in Arabidopsis thaliana. In Arabidopsis roots, the frequency of lateral roots was found to be increased by ectopic expression of Schizosaccharomyces pombe (Sp)cdc25e and reduced by Arath;WEE1 expression. I examined the effect of Arath;WEE1 and Spcdc25 on induction of shoots and roots in Arabidopsis hypocotyls in vitro. Hypocotyl explants from two over-expressing WEE1 lines , three T-DNA insertion lines and two expressing cdc25 (Spcdc25e) lines together with wild type (WT) were cultured on two-way gradients of kinetin (Kin) and naphthyl acetic acid (NAA). Below a threshold concentration of NAA (100 ng ml-1), WEE1 repressed morphogenesis in vitro, whereas at all NAA/Kin combinations Spcdc25 promoted morphogenesis (particularly root formation) over and above that in WT. Loss of function wee1-1 cultures were very similar to WT. Quantitative data indicated a significant increase in the frequency of root formation in Spcdc25e cultures compared with WT particularly at low Kin concentrations, and WEE1oe’s repressive effect was overcome by NAA but not Kin. In conclusion, WEE1 has a repressive effect on morphogenesis in vitro that can be overcome by auxin whereas Spcd25 by-passes a cytokinin requirement for the induction of morphogenesis in vitro. The role of CDC25 and WEE1 in DNA damage responses was also analysed. Two over-expressing Arath;CDC25 lines and T-DNA mutants showed no difference to WT either in standard conditions or zeocin-supplemented treatments. However, root length was longer in Arath;CDC25oe lines treated with hydroxyurea (HU) and lateral root number was increased compared to WT. This suggests a differential response of Arath;CDC25oe in the DNA replication (HU-induced) and DNA damage (zeocin-induced) checkpoints (Chapter 5). Finally the roles of WEE1 and CDC25 in cell cycle regulation were examined using tobacco TBY-2 cell cultures expressing Arath;WEE1, Nicotiana tabacum (Nicta)WEE1 or Arath;CDC25. Whilst Nicta;WEE1 lengthened G2 of the cell cycle, Arath;WEE1 had an unusual effect of shortening G2 phase and Arath;CDC25 had no observable effect (Chapter 6).

Niche-differentiation has been proposed to explain the coexistence of large numbers of tree species in tropical forests. Previous studies on established individuals have found little evidence for this. However, niche-differentiation may be apparent at the seed and seedling stages. This study investigated the effects of environmental variation in germination and seedling establishment for a range of Central Panamanian species. Firstly, topography has a large impact on soil water availability; slopes are wetter than nearby plateaux. The potential impact on seedling emergence and survival was studied by monitoring seedling emergence and survival over 15 months. This revealed that small-seeded species are unlikely to establish on plateaux, presumably because of the rider conditions. Secondly, the germination of four pioneer species in response to four environmental variables, related to canopy gap size, was investigated. Species exhibited consistent patterns of response suggesting adaptation for germination in particular gap sizes; Piper marginatum responded to nitrate, had a low base potential for germination and tolerated large temperature fluctuations, suggesting adaptation for germination in comparatively large gaps. Conversely, Pipe peltatum exhibited responses, which suggested adaptations for germination in small gaps. Finally, germination and seedling mortality for four pioneer species in two sizes of canopy gap was predicted using computer modelling. This indicated that large-seeded pioneers can germinate and establish in large gaps. Conversely, percentage germination and survival of small-seeded species was low in large gaps. However, small-seeded species produce greater quantities of seed than large-seeded species. Consequently they may "win by default" in large gaps, because of the absence of seeds of larger species. These results indicate that there are a number of axes of environmental variation along with nice-differentiation can occur. Furthermore, the response is variable between species. Thus niche-differentiation is important for fostering species coexistence, although density-dependent mortality and dispersal-limitation also contribute.

Auxin (Indole-3-acetic acid; IAA) can be considered one of the most important hormones in plant development as it coordinates plant development through transcriptional regulation. For years the principal auxin receptor was sought and only relatively recently was it identified as an F-box protein known as TIR1, with five homologues; the auxin F-Box proteins (AFB1–5). The elucidation of a crystallographic structure elegantly demonstrated IAA’s integral role in forming a ternary complex between auxin F-box proteins and Aux/IAA proteins, revealing the mechanism of auxin perception. An exact chemical description of an auxin has been pursued for decades and researchers have always faced the challenge of factoring in the complex nature of multiple auxin-receptor classes, transport and metabolism. My project aimed to develop a better understanding of auxin chemical specificity at the receptor level, focusing on TIR1 and one of its most distantly related homologues, AFB5. We employed a structure activity relationship study with a rational selection of compounds and have defined a pharmacophore for auxin activity for the TIR1 receptor. The thesis also describes a receptor-led, in silico rational drug design approach in which we replaced the carboxylic acid moiety with a tetrazole, giving a novel compound that demonstrated auxin-like activity both in vitro and in vivo. Furthermore this bioisosteric replacement serendipitously demonstrated a novel selectivity for TIR1, with no activity against AFB5. Preliminary in silico docking studies of the TIR1 binding site could not discern between active and in active compounds generating many false positive results, leading us to develop TomoDock; a novel in silico docking approach to study the entire TIR1 receptor binding pocket geometries. Results from TomoDock suggest that binding is a two phase process with active ligands firstly engaging with a niche, which orients them, allowing passage past and molecular filter region before interacting with the binding site. This process contributes to the mechanism of compound selection by the TIR1 pocket receptor. A range of multidisciplinary approaches utilised in this project have allowed us to investigate and report many new insights on the mechanism of auxin perception. Such rational approaches may also be used in other drug discovery programmes alike to help researchers discern compound perception and selectivity.

The potential factor of Mesolithic impact on the vegetation of south-west Scotland from c. 10 000 - 5000 b. p. was investigated by pollen and charcoal analysis of small peat-filled basins and blanket peat near to the sites of lithics and in the context of subsequent vegetational history (from c. 5000 b. p.). Attention focused on upland sites by Loch Doon and Loch Dee. Upland areas by Clatteringshaws Loch and a site at Palnure near the coast provided a late and relatively incomplete record respectively. Two cores were collected at each of Loch Doon and Loch Dee to enable comparison of microfossil stratigraphies. At Loch Doon several cores were analysed across the rise in Alnus. Preliminary counts were made from a core from Loch Doon itself. Radiocarbon dating gave additional confidence to the chronological framework. The availability of comparable pollen data enabled some distinction between local and more regional vegetational events. The charcoal profiles were more problematical to interpret, but the contrast between a very low level of charcoal prior to a rise in the early postglacial (Fl I) at both Loch Doon and Loch Dee may prove to be of regional significance. The strongest evidence for local Mesolithic disturbance came from Loch Dee. The results from the small-basin sites were contrasted with those previously recorded from larger mires and loch sediments.

The many advantages of light-emitting diode (LED) grow lamps in terms of programmability and energy efficiency make them an attractive replacement for old lighting systems. However, when replacing conventional broad-waveband ‘white’ lighting with narrow-waveband LED lighting it is important to ensure that the system is able to produce plants of an equal or higher quality and yield. In order to choose suitable light ‘recipes’, i.e. combinations of wavelengths for optimal plant growth, we must first understand how light quality affects plant growth and development. The following work explores the role of each part of the light spectrum, both in natural sunlight in canopy environments in the field and glasshouse, and in an artificial light environment in controlled environment growth rooms. It was determined that, blue, green, red and far-red wavebands are all instrumental in the provision of positional signals to the leaf which enable optimisation of plant physiology to light conditions, especially in the canopy environment. A new hypothesis for the role of the blue:green light ratio in whole-canopy water use efficiency is presented. Wavelength-specific effects were observed in hypocotyl elongation, leaf expansion, photosynthetic stoichiometry and absorption of different wavelengths, root architecture, photosynthetic capacity, whole-plant morphology (in terms of biomass partitioning between leaves, stems and roots) and fresh weight yield of stems and leaves. In the glasshouse, it was determined that monochromatic red LED lighting is a suitable alternative for conventional high-pressure sodium light, as it boosted leaf photosynthetic capacity as well as leaf area, fresh and dry weight yield, and was the most efficient light source in terms of ‘crop per watt’. Finally, further applications of the work such as those for commercial horticulture and farming in closed plant production systems are presented, and it is concluded that LED lighting is likely to have a crucial role in the future of global food security.

1. The invasion of Betula spp. (B.pendula and B.pubescens) triggers a phase transition between lowland heath and scrub vegetation states. Transition to scrub is currently the most serious threat to the conservation of UK lowland heath; it has been found to correlate with soil phosphorus sorption capacity (PSC) at the landscape scale. 2. It was hypothesised that Betula invasion of Lowland heath was limited by numerous factors that may be subdivided into safe-site and seed limitation and that phosphorus availability was a key axis in the determination of a Betula safe-site. 3. An implicit assumption of earlier research was that PSC affected the P available to invading plants. An approach combining observation, statistical modelling and experimentation found that PSC affected the retention and availability of phosphorus in heathland soils. Synthesis of these findings with the published literature suggests that the direct effect of PSC on P-availability is small compared to indirect effects on organic matter (SOM) accumulation and vegetation cycling. 4. These findings allowed the hypothesis that P-availability affects the likelihood of invasion to be tested within an experimental framework. P-availability, seed rain and disturbance were experimentally manipulated in a multifactorial field experiment on a wet heath ecosystem in a stable, uninvaded heath area. Betula seedling densities and numerous covariates were also measured. It was assumed throughout this research that Betula seedling densities were indicative of the likelihood of heath-scrub transition. 5. Analysis of deviance found that all three treatments had significant effects on Betula seedling densities with seed availability proving to be the single greatest limitation at the site. Conversion of the experimental treatment factors into a continuous form allowed for a more detailed description of the phase transitional area within the site. The most significant descriptors of seedling densities were seed-rain, various plant neighbour variables and P-availability. 6. Replication of this experiment with fewer treatment levels and replicates at two additional sites found that the identity of the factors controlling Betula seedling densities was broadly similar, (e.g. vegetation and seed availability factors played a role at all sites) but that their relative contributions to within-site heterogeneity varied widely. 7. A single statistical model was fitted to data collected from three experimental sites. The model, which explained 59.8% of the deviance in seedling densities, describes Betula colonisation as a function of biomass density, necromass density, vegetation height, seed bank density, phosphorus availability, and to a lesser extent, soil water content. The form of the fitted relationships was complex with numerous interaction and polynomial terms. If the model is applicable to a wider range of conditions then it may be concluded that it is heathlands close to seed sources and in the degenerate state, and possibly those subjected to severe bums, that are the most likely to shift to the Betula scrub state. At larger scales these conditions are probably most common in low management intensity, high phosphorus sorption capacity (PSC) regions. 8. Validification of the combined-site model was attempted using data that was equivalent to that used in the fitting of the model and which was collected over two 5ha grids of 130 sampling points and covering a wider range of heathland environments. Low predicted and actual seedling densities prevented formal testing of the models accuracy but predictions were qualitatively accurate, despite extrapolation. 9. Exploration of spatial heterogeneity in the determinant factors using the aforementioned spatial grid data, was achieved with geostatistics. This revealed that seed bank densities and edaphic factors displayed small-scale patchiness of around 50m while vegetation factors possessed longer ranging autocorrelation resulting in single across-site gradients. The proportion of spatially structured variance in the variables, within the studied range (17.6-150m), was low for many factors. The pattern of these factors is discussed with reference to the exclusion of Betula colonists and management recommendations are proposed. 10. It is concluded that the combined-site model provides a coarse but fairly accurate definition of the phase-transitional area between lowland heath and Betula scrub ecosystem states and that the determinant factors are at larger scales governed by landscape-scale processes (e.g. soil (PSC), climate and management regimes). These factors may explain regional differences in the scale and extent of scrub transition.