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Following nutrient ingestion, glucagon-like peptide 1 (GLP-1) secreted from intestinal L-cells mediates anti-diabetic effects, most notably stimulating glucose-dependent insulin release from pancreatic β-cells but also inhibiting glucagon release, promoting satiety and weight reduction and potentially enhancing or preserving β-cell mass. These effects are through the GLP-1 receptor (GLP-1R) which is a therapeutic target in type 2 diabetes. The present study focused on desensitisation and re-sensitisation of GLP-1R-mediated signalling and interactions of orthosteric and allosteric ligands. Data demonstrate GLP-1R desensitisation and subsequent re-sensitisation following removal of extracellular ligand with ligand-specific features. Following GLP-1-mediated desensitisation, re-sensitisation is dependent on receptor internalisation, endosomal acidification and receptor recycling. Re-sensitisation is also dependent on endothelin converting enzyme-1 (ECE-1) activity, possibly through proteolysis of GLP-1 in endosomes, facilitating disassociation of receptor-β-arrestin complexes leading to GLP-1R recycling and re-sensitisation. ECE-1 activity also regulates GLP-1-induced activation of extracellular signal regulated kinase (ERK) and generation of cAMP possibly through a G protein independent/β-arrestin dependent mechanism. By contrast, following GLP-1R activation by the orthosteric agonist, exendin-4, or allosteric agonist, compound 2, re-sensitisation was slow and independent of ECE-1 activity. Thus, different ligands depend on different events during GLP-1R trafficking which could be important for re-sensitisation and signalling, particularly that mediated by scaffolding around β-arrestin. As the GLP-1R is targeted therapeutically at orthosteric and allosteric sites, this study examined activation of the GLP-1R by orthosteric and allosteric agonists and in particular interactions between ligands of these sites. Challenging the GLP-1R with the allosteric ligand, compound 2, along with GLP-1 9-36 amide, a low affinity, low efficacy metabolite of GLP-1 7-36 amide, results in synergistic receptor activation. This may be important for therapeutic approaches with allosteric ligands, as metabolites of GLP-1 may be present in vivo at concentrations higher than the classic endogenous ligand. Indeed this could present a novel therapeutic approach.

Sequential patterns mining is an important pattern discovery technique used to identify frequently observed sequential occurrence of items across ordered transactions over time. It has been intensively studied and there exists a great diversity of algorithms. However, there is a major problem associated with the conventional sequential patterns mining in that patterns derived are often large and not very easy to understand or use. In addition, more complex relations among events are often hidden behind sequences. A novel model for sequential patterns called Sequential Patterns Graph (SPG) is proposed. The construction algorithm of SPG is presented with experimental results to substantiate the concept. The thesis then sets out to define some new structural patterns such as concurrent branch patterns, exclusive patterns and iterative patterns which are generally hidden behind sequential patterns. Finally, an integrative framework, named Post Sequential Patterns Mining (PSPM), which is based on sequential patterns mining, is also proposed for the discovery and visualisation of structural patterns. This thesis is intended to prove that discrete sequential patterns derived from traditional sequential patterns mining can be modelled graphically using SPG. It is concluded from experiments and theoretical studies that SPG is not only a minimal representation of sequential patterns mining, but it also represents the interrelation among patterns and establishes further the foundation for mining structural knowledge (i.e. concurrent branch patterns, exclusive patterns and iterative patterns). from experiments conducted on both synthetic and real datasets, it is shown that Concurrent Branch Patterns (CBP) mining is an effective and efficient mining algorithm suitable for concurrent branch patterns.

Phytoplankton blooms have been regarded as a major threat to freshwater ecosystems. Macrophytes play a key role in maintaining a clear water state by competing with phytoplankton for nutrients and light, and/or releasing allelopathic chemicals to inhibit phytoplankton growth. However, macrophytes can become desiccated after severe water level drawdown, subsequently releasing substantial nutrients that stored in their biomass after rewetting. Previous studies have mainly focused on the nutrient uptake by macrophytes, with little attention paid to the potential negative implications of macrophyte loss during water level fluctuations (WLFs). This thesis compared the role of macrophytes as a nutrient sink versus a source during WLFs, and its implications for phytoplankton blooms during WLFs. The first data chapter of this thesis has examined the nutrient storage capacity of a floating-leaved macrophyte, Nymphoides indica in a subtropical reservoir. The nutrient stored in N. indica biomass in this reservoir was 30% of total nitrogen (TN) and 150% of total phosphorus (TP) stored in the water column. This species was subsequently used in glasshouse experiments to investigate the impact of different durations of water level drawdown, followed by rewetting on nutrient release from both macrophyte litter and their associated sediment. This study showed that macrophyte beds can shift from a nutrient sink to a source after desiccation, followed by rewetting. This occurred when minimum soil moisture content was reached after 10 weeks of desiccation. This shift also caused an increase in phytoplankton biomass, as nutrients were released. The effect of WLFs on two submerged macrophyte species, the invasive species Cabomba caroliniana (Cabomba) and the native species Hydrilla verticillata (Hydrilla) was also examined. Macrophytes were enriched with stable nitrogen isotope (15N), then used to examine the fate of released 15N from desiccated, and subsequently rewetted macrophytes. The study showed that 15N released from macrophytes was assimilated by phytoplankton faster than being transferred to other N pools, such as to living macrophytes and sediments. Desiccation of the associated sediment, followed by rewetting, resulted in a greater proportion of the macrophyte-derived 15N remaining in the water column and assimilated by phytoplankton, compared with the treatments without sediment desiccation (i.e. constantly wet conditions). Regrowth of macrophytes also changed the fate of nutrients released from macrophyte litter, following rewetting the desiccated sediment. Less 15N was transferred into the water column, sediments and phytoplankton when macrophytes regrew, compared to the treatment without macrophyte regrowth. As such, 28 d after rewetting, regrown Cabomba and Hydrilla assimilated 19–100% of released N and 6–42% of released P from macrophyte litter when the biomass ratio of macrophyte litter to regrown macrophytes was 9:1. In addition, regrown Hydrilla had significantly higher nutrient uptake rates than Cabomba. Despite this, Cabomba was more efficient at reducing water column N concentrations, and neither Cabomba or Hydrilla significantly reduced water column P concentrations. This indicates regrown Cabomba and Hydrilla differ in their use of water column versus sediment nutrients. This has important implications for the capacity of each species to reduce water column nutrients and control phytoplankton biomass. This study also showed that litter of the invasive species Cabomba decomposed faster and had a higher N and P content, compared with the same amount of Hydrilla litter. This resulted in higher water column nutrient and Chlorophyll a concentrations but lower dissolved oxygen concentrations in the Cabomba treatments. The Cabomba litter also had significantly higher N and P content compared with N. indica, indicating Cabomba could also have a greater impact on water column nutrients than N. indica during decomposition. Overall, both the submerged and floating-leaved macrophyte species in this study had a greater impact on water column P than N, after drying then rewetting. This changed the water column N:P ratio with potential flow-on effects to phytoplankton biomass and species assemblages. In summary, these findings of the thesis indicate that effective water level management is essential to protect macrophyte beds and reduce the risk of phytoplankton blooms, during drying then rewetting cycles. Management options could include reducing the frequency, amplitude, or duration of water level drawdown to minimize the loss of macrophytes and maximize their regrowth. Since invasive submerged macrophytes have greater potential to increase the phytoplankton biomass during WLFs, more attention should be paid to reservoirs or lakes dominated by invasive submerged macrophytes. Keywords: macrophytes; water level fluctuations; nutrient budgets; stable isotope; phytoplankton blooms; invasive species

Structure-based drug design (SBDD) is an essential component of many drug discovery programs. In SBDD, a large number of potential molecules are virtually screened against the known three-dimensional protein structure. Proper creation of ligand libraries and selection of target binding sites are critical for SBDD. This thesis focuses on knowledge-based approaches to improve SBDD in two aspects, the construction of the ligand libraries and analysis of the target binding sites used. First, this thesis presents ChemTreeMap, a visualization tool to explore structurally diverse molecules and mine for correlation between chemical structure and biological data. The visualization tool is applicable to a wide range of questions involving small molecule/drug binding and exploration and construction of ligand libraries. Experimental data and molecular properties can be interactively visualized with graph properties. With the help of this powerful tool, this thesis reports the findings on discriminating physicochemical properties between allosteric and orthosteric competitive molecules. It is observed that allosteric ligands are more hydrophobic, aromatic, and rigid. The result is useful to guide building new chemical libraries biased towards allosteric regulators. Thirdly, the selection of target binding sites of drug candidates needs to take account for possible interruption due to mutations which occur from non-synonymous single nucleotide polymorphisms (nsSNPs). Disease nsSNPs occur more frequently in a protein core or binding site, rather than the rest of the protein surface. The result can be used to imply the probability and consequence of nsSNP on new target binding sites.

This thesis presents new productivity and well testing formulae of horizontal wells. Taking a horizontal well as a uniform line source, this thesis finds velocity potential formula and the productivity formulae for a horizontal well in an ellipsoid of revolution drainage volume by solving analytically the involved three-dimensional partial differential equations. These formulae can account for the advantages of horizontal wells, and they are more accurate than other formulae which are based on two-dimensional hypotheses. This thesis also presents new well testing formulae of horizontal wells in a single porosity system and a double porosity system. Compared with the formulae published in the literature, our formulae, which do not use the sum of infinite series, are more reasonable and easy to be used in well testing analysis.