The complex environment of a living cell contains many molecules interacting in a variety of ways. Examples include the physical interaction between two proteins, or the biochemical interaction between an enzyme and its substrate. A challenge of systems biology is to understand the network of interactions between biological molecules, derived experimentally or computationally. Sophisticated dynamic modelling approaches provide detailed knowledge about single processes or individual pathways. However such methods are far less tractable for holistic cellular models, which are instead represented at the level of network topology. Current network analysis packages tend to be standalone desktop tools which rely on local resources and whose operations are not easily integrated with other software and databases. A key contribution of this thesis is an extensible toolkit of biological network construction and analysis operations, developed as web services. Web services are a distributed technology that enable machine-to-machine interaction over a network, and promote interoperability by allowing tools deployed on heterogeneous systems to interface. A conceptual framework has been created, which is realised practically through the proposal of a common graph format to standardise network data, and the investigation of open-source deployment technologies. Workflows are a graph of web services, allowing analyses to be carried out as part of a bigger software pipeline. They may be constructed using web services within the toolkit together with those from other providers, and can be saved, shared and reused, allowing biologists to construct their own complex queries over various tools and datasets, or execute pre-constructed workflows designed by expert bioinformaticians. Biologically relevant results have been produced as a result of this approach. One very interesting hypothesis has been generated regarding the regulation of yeast glycolysis by a protein found to interact with seven glycolytic enzymes. This has implied a potentially novel regulatory mechanism whereby the protein in question binds these enzymes to form an 'energy production unit'. Also of interest are workflows which identify termini (system inputs and outputs), and cycles, which are crucial for acquiring a physiological perspective on network behaviour.

Given the ever increasing quantity of sequence data, functional annotation of new gene sequences persists as being a significant challenge for bioinformatics. This is a particular problem for transcriptomics studies in crop plants where large genomes and evolutionarily distant model organisms, means that identifying the function of a given gene used on a microarray, is often a non-trivial task. Information pertinent to gene annotations is spread across technically and semantically heterogeneous biological databases. Combining and exploiting these data in a consistent way has the potential to improve our ability to assign functions to new or uncharacterised genes. Methods: The Ondex data integration framework was further developed to integrate databases pertinent to plant gene annotation, and provide data inference tools. The CoPSA annotation pipeline was created to provide automated annotation of novel plant genes using this knowledgebase. CoPSA was used to derive annotations for Affymetrix GeneChips available for plant species. A conjoint approach was used to align GeneChip sequences to orthologous proteins, and identify protein domain regions. These proteins and domains were used together with multiple evidences to predict functional annotations for sequences on the GeneChip. Quality was assessed with reference to other annotation pipelines. These improved gene annotations were used in the analysis of a time-series transcriptomics study of the differential responses of durum wheat varieties to water stress. Results and Conclusions: The integration of plant databases using the Ondex showed that it was possible to increase the overall quantity and quality of information available, and thereby improve the resulting annotation. Direct data aggregation benefits were observed, as well as new information derived from inference across databases. The CoPSA pipeline was shown to improve coverage of the wheat microarray compared to the NetAffx and BLAST2GO pipelines. Leverage of these annotations during the analysis of data from a transcriptomics study of the durum wheat water stress responses, yielded new biological insights into water stress and highlighted potential candidate genes that could be used by breeders to improve drought response.

Understanding how function relates to multiple layers of inactions between biological entities is one of the key goals of bioinformatics research, in particular in such areas as systems biology. However, the realisation of this objective is hampered by the sheer volume and multi-level heterogeneity of potentially relevant information. This work addressed this issue by developing a set of integration pipelines and analysis methods as part of an Ondex data integration framework. The integration process incorporated both relevant data from a set of publically available databases and information derived from predicted approaches, which were also implemented as part of this work. These methods were used to assemble integrated datasets that were of relevance to the study of the model plant species Arabidopsis thaliana and applicable for the network-driven analysis. A particular attention was paid to the evaluation and comparison of the different sources of these data. Approaches were implemented for the identification and characterisation of functional modules in integrated networks and used to study and compare networks constructed from different types of data. The benefits of data integration were also demonstrated in three different bioinformatics research scenarios. The analysis of the constructed datasets has also resulted in a better understanding of the functional role of genes identified in a study of a nitrogen uptake mutant and allowed to select candidate genes for further exploration.

In this thesis, a series of mathematical models suitable for describing biological tissue growth are developed. The motivation for this work is a bioreactor system which provides perfusion and compressive mechanical stimulation to a cell-seeded scaffold; however, the formulation is sufficiently general to be applied to a vast range of tissue engineering applications. Our models are used to investigate the influence of (i) cell-cell and cell-scaffold interactions, and (ii) the mechanical environment, on tissue growth. In the first part of the thesis, we extend a model due to Franks (2002) (in which the cell and culture medium phases are represented by viscous fluids) by including perfusion and coupling the cells' response to their environment. Specifically, we consider the effect of the cell density and pressure on tissue growth. We analyse the model using analytic and numerical techniques; numerical simulations suggest that comparison of construct morphology in the presence and absence of perfusion provides a means to identify the dominant regulatory growth stimulus. The solid characteristics of the construct and interactions between the cells and scaffold are necessarily neglected in the two phase model. Guided by this, we develop more complex three phase models. Using numerical simulations, the influence of cell-cell and cell-scaffold interactions is investigated and less porous scaffolds are shown to improve control over cell behaviour. We use the model to compare the cells' response to different regulatory stimuli, including flow-induced shear stress. Our results suggest that uniform initial cell seeding and stimulating cell movement are crucial in maintaining the mechanical integrity of tissue constructs. We also study the effect of scaffold compression on the mechanical environment of the cells contained within, developing both a classical Biot formulation and a multiphase model. We demonstrate that the bioreactor geometry introduces significant spatial variation in the mechanical stimuli relevant to tissue growth and that such considerations will play a key role in comprehensive models of mechanotransduction-affected growth.

Tropical peatlands play an important role in the global carbon cycle, but little is known about the factors which regulate carbon dioxide (CO2) and methane (CH4) fluxes from these ecosystems. To improve our understanding of the potential impact of future changes in climate and/or land-use, this study aimed to quantify current fluxes of these gases from a large domed peatland, San San Pond Sak, in Panama and assess the influence of environmental factors. Three sites with differing dominant vegetation species (Raphia taedigera, Campnosperma panamensis and Cyperus species) and nutrient status were investigated between February 2007 – September 2009 using a combination of in situ closed chamber gas sampling and ex situ headspace gas sampling to quantify current and potential gas fluxes from the peat surface and at depths of 2 m from the surface. Physical and chemical properties of the peat were determined concurrently. Laboratory experiments were carried out to investigate patterns of litter decomposition and microbial activity. Gas fluxes differed significantly between sites. CO2 fluxes were greatest at the C. panamensis site (100–400 mg m-2 h-1), followed by the R. taedigera (74–352 mg m-2 h-1) and Cyperus sp. (59–294 mg m-2 h-1). The seasonal patterns associated with rainfall were similar for all sites, with the release of CO2 being greatest during the dry season. CH4 fluxes also varied between sites, but no seasonal variation was evident. CO2 flux varied diurnally at the C. panamensis and Cyperus sp. sites, perhaps due a circadian rhythm in vegetation processes. CO2 and CH4 production occurred throughout the upper 2 m of the profile, both in situ and ex situ, with potential CO2 fluxes of up to 1,000 mg m-2 h-1 being found in the surface layer. The peat became increasingly recalcitrant and P-limited with increasing depth. Measurements of litter decomposition and microbial activity indicated that the availability of labile substrates and nutrients differed between sites. In conclusion, CO2 and CH4 fluxes differed between sites experiencing similar environmental conditions, and were influenced by variation in environmental factors. Fluxes varied on both short- and long- timescales, but not at all sites. The magnitude of the gas fluxes was influenced by different environmental factors at each site, indicating that fluxes and the most important driving variables vary dependent on surface vegetation even within a single peatland system. With regard to climate and/or land-use change, it was concluded that San San Pond Sak peatland would be sensitive to water table drawdown, with the likely outcome of increased CO2 releases and the potential for CH4 uptake, rather than release.

This thesis discusses the development of a novel scanning capacitance microscope (SCM) that enables the investigation of the local capacitance and conductivity of surfaces and near-surface nanostructures at cryogenic temperatures and high magnetic fields. Simultaneous atomic force microscopy (AFM) and SCM measurements can be made at a temperature of 1.5K and a magnetic field of 12T. The AFM/SCM sensor is based on a quartz-tuning fork with an etched metal tip. SCM measurements are made using an RF tuned filter design which allows changes in capacitance to be measured with sub-attofarad resolution and a bandwidth of 200Hz. Test measurements were made over an evaporated gold film. The capacitance distance curve was recovered from the measured quantities using a deconvolution scheme normally used for force-distance curves. Measurements have been made of a two-dimensional electron gas in the quantum Hall effect (QHE) regime. Highly conductive stripes form near the edge of the sample at integer Landau level filling factors in agreement with theoretical predictions. These measurements are the first direct imaging of the compressible stripes at the physical edge of a Hall bar device. Measurements were also made by point spectroscopy in a region that was locally depleted. Around this region a ring-shaped stripe of considerably larger width than at the sample edge is observed. The increased width was explained in terms of a shallower potential gradient compared to the physical edge of the sample. Preliminary measurements have demonstrated that the microscope is capable of imaging edge states whilst passing current through the device.

Advances in phage display technology revolutionised our understanding of molecular interactions. The aim of using phage display is to screen a peptide library for the identification of rare ligand-bound variants with enhanced specific interaction. One of the most common challenges in dealing with an exhaustive peptide library is the selection of target-unrelated peptides. Here we improved methodical approaches that reduce phage binding to the substrate surrounding the target protein. With this we were able to improve the quality of peptide interactions selected from phage libraries. The main purpose of this study is investigate the range of applications of phage-displayed peptide libraries in the context of identifying peptides that interact with virus proteins and antibodies. Using our refined methods, we were able to select inhibitory peptides to Hepatitis C Virus (HCV) that blockade its entry into the host, along with mapping antigenic determinants of several monoclonal antibodies such as anti non-primate hepacivirus (NPHV) antibodies and human HC33.4 anti-HCV antibody. Epitope mapping proved easier than discovering potent viral therapeutics. However, lead sequences were identified that neutralise HCV entry in in vitro models. The presence of thousands of HCV quasispecies leads to another difficulty of discovering pangenotypic inhibitors. Robust alignment and significant binding were demonstrated with peptides selected with both NPHV and HC33.4 human antibodies, while the selection failed with other target proteins. There might be no hot spot residues presented in the libraries used against these proteins. Future investigations should focus on developing the suggested HCV-selected peptides to enhance their affinity. All in all, phage display technology has been successfully developed to improve the performance of peptide libraries in a way that can avoid undesirable sequences during library sorting and enhancing the chance to find favourable ligands.

A palaeolimnological study of three lakes on Disko Island, West Greenland was conducted across a hydrogeomorphic landscape gradient, to reconstruct principally changes in algal pigments, lipid biomarkers and carbon isotopes (δ13C) to investigate carbon cycling at multiple scales and resolutions. All three records reconstructed recent change on Disko, with records from lake Disko 2 additionally spanning since ~7640 cal. yr BP and lake Disko 4 since ~1260 cal. yr BP. Changes in sedimentary proxies were broadly consistent with the spatially and temporally heterogeneous environmental change known to have occurred across the Arctic over these periods, including recent warming (RW), the Little Ice Age (LIA) and the Medieval Climate Anomaly (MCA). However, the individual lake responses to these changes were highly landscape specific. Changes in algal pigments were linked to variations in the inputs of nutrients and DOC from soil microbial activity, variations in permafrost melt regime and glacier melt. Evidence of disturbance from catchment freeze-thaw processes, glacier inputs and the effects of permafrost melt on algal communities varied between lakes. At the highest position in the landscape gradient, lake Disko 2 had poorly developed soils and lower glacier coverage, with simple algal communities, but pigment and δ13CTOC changes since ~7640 cal. yr BP reflected individualistic responses to overarching drivers, consistent with the current understanding of heterogeneous pan-Arctic environmental change. Replicate cores with proximity to talus and debris flow had differing signatures, highlighting the role of geomorphology. In lake Disko 2 there was some similarity between Greenland Ice Sheet surface area and pigment biomarkers of cryptophytes (alloxanthin), which suggests if locally similar, catchment ice variation may regulate nutrient and DOC release from catchments, stimulating algae. At a mid-elevation position in the catchment, lake Disko 1 meltwater inputs from an upstream retreating glacier (since the end of the LIA) may be stimulating algae through increased nutrients and DOC supply, although soil nutrient cycling and permafrost release present in the catchment U-shaped valley may also be contributing to these increases. At the lowest position in the landscape, lake Disko 4 has a complex and variable pigment response likely influenced by multiple glacier inputs, thicker permafrost, greater vegetation and more developed wetland areas, together regulating the cycling of nutrients and DOC. Higher maximum pigment concentration during the MCA, compared with the LIA reflect the spatially and temporally heterogeneous expression of these events across the Arctic. Despite individuality in catchment filtering, all three lakes on Disko Island were found to have recent increases in algal production, which when combined with recent increases in carbon burial suggests these lakes are becoming increased carbon sinks. Although this increased carbon burial reflects a minor store in lakes compared with release to downstream waterbodies, if upscaled across the Arctic this change could be globally significant and should be integrated in future models. With future warming, catchment processes are likely to play a pronounced role in mediating algal community structure in lakes across the Arctic.

This thesis considers two modelling frameworks for interaction networks in biology. The first models the interacting species qualitatively as discrete variables, with the regulatory graphs expressing their mutual influence. Circuits in the regulatory structure are known to be indicative of some asymptotic behaviours. We investigate the relationship between local negative circuits and sustained oscillations, presenting new examples of Boolean networks without local negative circuits and admitting a cyclic attractor. We then show how regulatory properties of Boolean networks can be investigated via satisfiability problems, and use the technique to examine the role of local negative circuits in networks of small dimension. To enable the application of Boolean techniques to the study of multivalued networks, a mapping of discrete networks to Boolean can be considered. The Boolean version, however, is defined only on a subset of the Boolean states. We propose a method for extending the Boolean version that preserves both the attractors and the regulatory structure of the network. Chemical reaction network theory models the dynamics of species concentrations via systems of ordinary differential equations, establishing connections between the network structure and the dynamics. Some results assume mass action kinetics, whereas biochemical models often adopt other rate forms. We propose algorithms for elimination of intermediate species, that can be used to find whether a mass action network simplifies to a given chemical system. We then consider the problem of identification of generalised mass action networks that give rise to a given mass action dynamics, while displaying useful structural properties, such as weak reversibility. In particular, we investigate systems obtained by preserving the reaction vectors of the mass action network, and outline a new algorithmic approach.

Lowland tropical peatlands can act as sinks and sources of carbon, interchanging greenhouse gases (GHG) with the atmosphere. Despite the importance of lowland tropical peatlands in the past, present and future global carbon cycle, uncertainties exists about the controls regulating the processes of carbon turnover. Therefore, this study examined different controls of carbon turnover, including abiotic, biotic and anthropogenic. For this purpose, six peatlands with different dominant vegetation were selected in the north western region of the Republic of Panama (9° 4' 16.06" N; 82° 6' 28.98" W). Two phasic communities were used as experimental models; Raphia taedigera palm swamps and mixed forest swamps with Campnosperma panamensis. A combination of in situ and ex situ experiments were performed between March 2010 and November 2012: i) ex situ respirometric assays were used to quantify differences in carbon turnover through the peat profile under different redox regimes, ii) litter bags experiments were used to investigate the effect of plant materials with distinct botanical origins on peat accumulation, iii) the effect of vegetation on greenhouse gases emissions was assessed with in situ and ex situ experiments and iv) land use change (LUC) was monitored to evaluate its consequences on the short term carbon turnover processes. Ex situ respirometric assays suggested that organic matter composition of peat plays a major role in controlling the potential CO2 and CH4 production. Under anaerobic conditions, the potential CO2 and CH4 production decreased with depth. The potential CO2 and CH4 productions in the surface peat layers of the anaerobic assays were 7 and 120 fold higher than those in deeper layers of the peat profile respectively. The change in redox regime affected the carbon turnover; the CO2 potential production in the surface layers (< 50 cm depth) increased 20 fold when exposed to aerobic conditions, whilst the deeper layers (> 50 cm depth) increased 47 fold. In contrast, CH4 production was reduced two orders of magnitude under aerobic conditions. Tissue types of R. taedigera and C. panamensis showed different in situ decomposition rates. Decomposition was significantly slower belowground than at the surface, reflecting the importance of the redox regime on the litter decomposition. Roots presented the lowest in situ decomposition rates among tissues both at the surface (R. taedigera: 0.59 ± 0.04 y-1; C. panamensis: 0.45 ± 0.01 y-1) and belowground (R. taedigera: 0.13 ± 0.01 y-1; C. panamensis: 0.17 ± 0.005 y-1). Macromolecular analyses revealed that roots and stems have similar composition to the peat material accumulated in deeper layers. Vegetation exerted a direct control on GHG fluxes from lowland tropical peatlands. In both ex situ and in situ measurements, fluxes of CO2 and CH4 varied with vegetation activity. In terms of CO2eq (Addition of mass flow of GHG, converted with the global warming potential of each gas), the agricultural LUC increased CO2eq emissions from the R. taedigera swamp at Cricamola by ca. 20 t CO2eq ha-1 y-1. At the pristine site, CO2, CH4 and N2O contributed with ca. 90, 9 and 1 % of the TCO2eq respectively. In contrast, in the anthropogenically impacted plot, CO2, CH4 and N2O contributed with ca. 29, 69 and 2 % of the TCO2eq respectively. Water table strongly influenced the carbon turnover. Under flooded conditions (water table at or above the surface; 0 to 0.15 m), the CH4 emissions were ca. 4 times higher in comparison with those where the water table was below the surface (−0.01 to −0.4 m). In contrast, CO2 emissions were ca. 1.5 times higher when the water table was below the surface. It was concluded that the interdependence of hydrology, peat composition and vegetation activity are the main factors controlling carbon turnover in the lowland peatlands of the north western region of Panama. This thesis has shown that fine scale alterations of these three factors can have large scale consequences, demonstrating sensitivity to perturbations and ease shift of lowland tropical peatlands from carbon sinks to carbon sources.