Solid State laser systems are now capable of generating temporal pulses of sub-10 fs duration and facilitate the study of ultrafast phenomena in chemical, biological and physical systems. The high field intensities inherent in these pulses, means that highly non-linear processes may be observed. Studies of solution phase transient absorption and femtosecond pulse laser ablation have been undertaken and in each case an experimental apparatus has been developed. Ultrafast pump-probe studies of room temperature solutions of 3-hydroxyflavone and a number of its derivatives have been undertaken. Measurement of transient absorption spectra attributable to the excited tautomer arising from ESIPT was observed throughout the visible wavelength range (400 - 700 nm). In cyclohexanea nd acetonitriles olutions, ESIPT was found to be so rapid that it was only possible to assign a time constant < 35 fs to the process. In ethanol, however, a time constant of 60 fs was determined. The slower ESIPT in this solvent is attributed to the greater strength of the solute-solvent interactions. The influence of substituents in the 4' position of the phenyl ring of 3-hydroxyflavone has also been investigated and we observe unusual behaviour for a cyano substituent in polar solvents and for dimethylamino and aza-Crown substituents. We attribute this behaviour to charge transfer followed by rapid solvent re-organisation. The possibility of the formation of TICT states is also discussed. Ultrafast laser ablation has been studied for a variety of dielectric, semiconducting and metallic substrates with emphasis on the development of the technique for rapid prototyping of micro-fluidic devices. Some fundamental observations of the ablation mechanisms and residual structures is presented along with results for prototyped devices for molecular diffusion and macro-filter applications.

The warm and cold water route ocean gateways are important oceanographic locations with respect to global climate. By the advection of salinity anomalies to the North Atlantic, changes at these ocean gateways are suggested to affect the strength and geometry of the Atlantic Meridional Overturning Circulation (AMOC). Adjustments of the AMOC can play a crucial role in the Earth‘s climate, and are suggested to be related to climate changes of the Late Pleistocene. However, little is known about the role of the warm and cold water route gateways on past glacial-interglacial and millennial time scales. This thesis documents a study which utilises Earth system modelling, combined with analyses of climate proxy data, to investigate the behaviour of these ocean gateways during changing climates of the past. The development of an adapted Earth System Model shows that it is possible to improve the simulation of climatological mean transport rates through the Indian-Atlantic Ocean Gateway (I-AOG, warm water route gateway) and Drake Passage (cold water route gateway). These ocean gateway transports are often overestimated in contemporary state-of-the-art climate models. The adapted model therefore provides a solid platform for the application of palaeo boundary conditions and the investigation of these ocean gateways during the past. Comparing pre-industrial and Last Glacial Maximum (LGM) climate simulations reveals that the I-AOG transport was only moderately weaker during the LGM, contrasting against the general hypothesis inferred from proxy data. A new hypothesis is developed which can consolidate these results. Supported by proxy data, the modelled Drake Passage throughflow is substantially weaker during the LGM. This might have potential implications for the geometry of the relatively shallow glacial AMOC. In response to freshwater perturbation - mimicking Heinrich events - an increase in Drake Passage throughflow is simulated, simultaneous with only weak changes of the I-AOG transport. The response at both locations is supported by proxy data, and suggests that the Drake Passage might be more important than previously considered with respect to the mechanisms involved in the abrupt resumption of the AMOC to interstadial conditions.

Cancer is a group of diseases that affects almost every organ of the human body. A normal cell transforms into a cancer cell as a consequence of cumulative failures that alter diverse cellular processes such as cell proliferation, adhesion, migration, and cell death. Focal Adhesion Kinase (FAK) is a ubiquitous protein that is involved in all these cellular processes. Therefore, it is not surprising that FAK plays important roles in cancer; in fact, it has been linked to tumour progression or regression depending on the cellular and genetic context. We used Drosophila melanogaster as a model organism to study FAK’s duality in cancer. In this thesis we describe two novel roles of Drosophila FAK (FAK56): as a tumour suppressor within receptor tyrosine kinases (RTKs)-driven contexts, and as a tumour promoter by inhibiting cell death in nervous tissues. We investigated how FAK56 regulates signalling resulting from the overexpression of RTKs RET and EGFR. Our data indicated that FAK is a suppressor of RTKs in fly epithelia. This was also observed in human cancer cell lines, suggesting an evolutionary conserved mechanism. On the other hand, we found FAK56 prevented caspase-dependent cell death and uncovered a novel link between FAK56 and Relish, the Drosophila homologue of human NF-κB: Relish mutants suppressed FAK56 loss-induced cell death in the larval central nervous system and eye imaginal discs. As supported by the results presented in this thesis, FAK may be a good therapeutic target in cancer biology; however, in some contexts it may also behave as a tumour suppressor. Therefore, we conclude it will be necessary to identify the context of FAK activity before designing therapeutic strategies against FAK-expressing tumours.

Protozoan parasites of the genus Plasmodium are the causative agent of malaria. The four human pathogenic species infect more than 500 million people each year, causing the death of at least 1 million people. The most severe form of human malaria is caused by P. falciparum, which is responsible for 90% of the malaria deaths. A major problem in the treatment of this disease is resistance of the parasites against most of the existing chemotherapies. Therefore, there is an urgent need to identify, validate and assess potential new drug targets. The prerequisite of a potential drug target is that it should not be of significance for the human host or it should be sufficiently different from the human counterpart, so that parasite-specific inhibition is feasible. Lipoic acid metabolism in Plasmodium differs from that of mammals in some ways and therefore it might be a promising target for the development of new antimalarials. This study investigated the importance of lipoic acid ligation in P. falciparum using reverse genetic approaches, to assess whether this pathway has potential for drug design. In addition, a spectrophotometric assay system was developed that allowed the biochemical characterisation of lipoic acid ligases and can be adapted to high-throughput screening approaches of inhibitors for these enzymes. Lipoic acid, also known as 6,8-thioctic acid, is an essential cofactor of alpha-keto acid dehydrogenase complexes (KADH) and the glycine cleavage system (GCV). The KADH include the pyruvate dehydrogenase (PDH), branched chain alpha-keto acid dehydrogenase (BCDH) and alpha-ketoglutarate dehydrogenase (KGDH), which are an integral part for any cell's metabolism. In Plasmodium spp. the lipoic acid dependent enzyme complexes are found in the apicoplast, a plastid related organelle, and in the mitochondrion and thus two organelle specific lipoylation pathways are present in these parasites. Biosynthesis of the cofactor occurs in the apicoplast. Octanoyl-[acyl carrier protein]: protein N-octanoyltransferase (LipB) catalyses the attachment of octanoyl-acyl carrier protein (octanoyl-ACP) to the PDH and lipoic acid synthase (LipA) then catalyses the insertion of two sulfurs into the octanoyl-chain to form lipoamide. In the mitochondrion, scavenged lipoic acid is ligated to the enzyme complexes by the action of lipoic acid protein ligase A (LplA1), in an ATP-dependent reaction. However, a second lipoate protein ligase A (LplA2) was identified in the genome of P. falciparum, but its subcellular localisation could not be predicted using the available prediction programs. To further analyse its localisation, parasites were generated expressing full length LplA2 in frame with green fluorescent protein (GFP). In addition, immunofluorescence analyses on wild-type parasites using LplA2 specific antibodies were performed. These studies showed that LplA2 is dually targeted to the apicoplast as well as to the mitochondrion, raising the question about potential redundancy between the ligases present in the parasites. To further analyse this possibility, knock-out studies of lplA1 and lplA2 were performed in the human and rodent malaria parasites P. falciparum and P. berghei, respectively. Knock-out studies showed that LplA1 and LplA2 are non-redundant and strongly suggested that LplA1 is crucial for intraerythrocytic development, whereas LplA2 is essential for sexual development in the mosquito. According to these results it appears that (1) a key regulator of lipoic acid metabolism in Plasmodium spp. is stage specific expression of the relevant proteins and (2) both ligases are potential drug targets as knock-out of lplA1 appeared impossible in the blood stages and knock-out of lplA2 resulted in the interruption of parasite sexual development in the mosquito, and thus transmission of the parasites would be blocked if LplA2 was inhibited. To further analyse the biochemical properties of P. falciparum LplA1 and LplA2, a spectrophotometric assay system was developed, which is also suitable for the development of a high-throughput assay system. The spectrophotometric assay monitors the first part of the LplA reaction - the activation of lipoic acid by ATP. The released pyrophosphate is converted to phosphate which is detected by acidic ammonium molybdate. Using the Escherichia coli LplA protein as a positive control, kinetic parameters for the bacterial protein were determined that are in reasonable agreement with the published data. The results validate the assay and suggest that it might be suitable for inhibitor screening in the future.

The research in this thesis investigates Case-Based Reasoning (CBR), a Knowledge-Based Reasoning technique that proved to be capable of providing good solutions in educational course timetabling problems. Following the basic idea behind CBR, experiences in solving previous similar timetabling problems are employed to find the solutions for new problems. A basic CBR system that is hierarchically organized with structured knowledge representations by attribute graphs is proposed in Chapter Four. The system is then further improved to solve a wider range of problems, which is described in Chapter Five. Evaluations on a large number of experiments indicate that this approach could provide a significant step forward in timetabling and scheduling research. This basic system works well on relatively small problems. To deal with this drawback a multiple-retrieval approach that partitions large timetabling problems into small solvable sub-problems is presented in Chapter Six. Good results are obtained from a wide range of experiments. In Chapter Seven, a new idea is introduced in CBR for solving timetabling problems by investigating the approach to select the most appropriate heuristic method rather than to employ it directly on the problem, in the attempt to raise the level of generality at which we can operate. All the evidence obtained from the first stage experiments indicates that there is a range of promising future directions. Finally in Chapter Eight the results of the work are evaluated and some directions for future work are present.

This PhD examines the role of individual and environmental characteristics in the intent to aggress, resulting in the development of a model to understand the intent to aggress in forensic settings. Study one focused on individual characteristics of aggressors in a prison sample of adult men (n=200). The study confirmed the importance of personality traits and beliefs in engagement in aggression in forensic settings. Aggressors reported low levels of agreeableness and high neuroticism and greater aggressive supportive beliefs, although the variance explained by personality traits and beliefs was low. Study two therefore aimed to examine other factors potentially of relevance, specifically environmental factors. Staff from two Young Offender sites (n=103), one closed and one open, participated. The results confirmed the influence of the physical and social aspects of the secure setting over attitudes and responses to aggression; the more secure physical environment was found to associate with negative attitudes towards prisoners and proaggressive attitudes. Attitudes were thus found to be important factors in the response to aggression. The final study aimed to combine both individual characteristics (e.g., beliefs, fear and personality) and environmental factors in a single study using prisoners (n=427) and staff (n=78) from one category B establishment housing adult men. Examination of emotion was lacking from study one and was therefore included in study three. The results confirmed the importance of beliefs via a moderating effect of fear. Greater perceptions of the threat in the forensic setting differentiated between aggressors and those not involved in aggression. The findings of the three studies were combined with existing theoretical frameworks and suggested two different pathways to increased aggression and one for the inhibition of aggression. These three pathways are presented via the Model of Intent to Aggress in Secure Settings (MIA-SS).

The majority of breast cancers express the oestrogen receptor and are potentially amenable to endocrine therapy, however the clinical effectiveness of these agents is limited by the phenomenon of acquired resistance which is associated with disease relapse and poor prognosis. It has been previously demonstrated that the CD44 receptor is overexpressed in acquired tamoxifen resistance where it associates with an enhanced migratory phenotype, however little is known regarding the effects of CD44 splice variants in this context. This thesis aimed to explore the role of CD44 variant isoforms in a model of ER+ breast cancer derived tamoxifen-resistance (Tam-R cells) and expand these explorations into an additional model of acquired fulvestrant-resistance (Fas-R cells). Multiple CD44 isoforms were found to be upregulated in resistance although a differential expression profile was observed between Tam-R and Fas-R cells. Inhibition of global CD44 expression in both endocrine resistant models led to a loss in their migratory, proliferative and invasive capacity and attenuated their responses to the CD44 ligand, hyaluronan. Overexpression of CD44v6 in endocrine sensitive MCF-7 cells induced EGFR pathway activation leading to enhanced cellular invasion, and attenuated response to fulvestrant. Accordingly, CD44v6 suppression in Tam-R cells resulted in a loss of EGFR pathway signalling and reduced invasion. Preliminary clinical analysis revealed that co-expression of CD44v6 and EGFR associated with a trend for worsened outcome in ER+ breast cancer patients treated with tamoxifen. These data suggest that upregulation of CD44v6 may contribute to an aggressive phenotype in tamoxifen resistant cells through a mechanism involving the EGFR. Future use of CD44v6 and EGFR as biomarkers may have potential therapeutic value to predict a cohort of ER+ breast cancer patients which relapse earlier on tamoxifen and may thus require more aggressive treatment strategies.

It is important for cells to respond to external signals. Central to these responses are the sensing and signalling pathways that communicate with the nucleus and facilitate necessary changes in gene expression. Of particular importance are the mitogen-activated protein kinase (MAPK) and the mammalian target of rapamycin (mTOR) pathways. Both of these pathways have been shown to be involved in cell growth, proliferation, motility and survival. They are under intensive investigation in connection with cancer with recent evidence suggests their role in mediating lipogenesis. Lipogenesis accompanies a variety of disease states, including the formation of brain tumours. Malignant brain tumours are rapidly growing and often invade surrounding healthy tissue, resulting in poor prognosis for the patient. The ability to limit tumour growth and reduce invasion through a better understanding of tumour associated lipid formation may offer targets for the development of new therapies. Yeast is frequently used as a paradimic organism for the study of human diseases. In this study a Nile red assay has been developed, optimised and validated to measure levels of both polar and neutral lipids within yeast cells. This method has been utilised in the yeast species, Saccharomyces cerevisiae and Schizosaccharomyces pombe, to study the role of the MAPK pathways in regulating lipid accumulation. Data in this thesis demonstrates that stress-activated protein kinase pathways (SAPK) play a key role in regulating lipid accumulation upon nitrogen limitation, as cells enter the stationary phase of growth. Evidence from S. cerevisiae proposes that the lipogenic switch occurs in two phases, with the central MAPK (Hog1) activated in both a MAPKK (Pbs2) independent and dependent manner. Analysis of Hog1 phosphorylation during various growth phases, suggests that there are previously uncharacterised sites on Hog1 which are potentially phosphorylated during phase one by the protein kinase Sch9, a target of the Tor1 complex. The second phase results in Hog1 being dually phosphorylated by the canonical pathway, via Pbs2p. It is proposed that Hog1 may have a number of downstream cytoplasmic and nuclear targets, including lipid related enzymes (Dga1) and transcription factors (Msn2/4). Data also suggests that lipid accumulation in S. pombe is also regulated in a similar manner. The oleaginous yeast Lipomyces starkeyi is able to accumulate high levels of lipid and has similarity to lipid enzymes found in mammalian cells. As such, it was proposed that L. starkeyi may be utilised as a model organism to further characterise the role of MAPK in lipid accumulation. Information from stress response studies and bioinformatics suggests the MAPK pathway in L. starkeyi is highly conserved. However, the application of yeast molecular tools to L. starkeyi was unsuccessful, demonstrating that further work is required to develop its use as a model organism. Data in this thesis has shown a novel role for the SAPK pathways in regulating lipid accumulation in yeast. It has also demonstrated cross talk between the MAPK and TOR pathways, resulting in an integrated cellular response. The high level of conservation of these pathways across species, suggests that directly targeting these pathways in cancer cells may reduce tumour associated lipogenesis, therefore inhibiting growth of glioma. With current treatments only delivering limited results, this could help extend patient survival.

Honey possesses therapeutic properties which are the result of a range of factors including high sugar content, low pH, hydrogen peroxide and bee-derived peptides. Honey also contains antimicrobial phytochemicals which represent a rich source of leads for the development of drugs for the treatment of microbial infections. Honey samples donated by UK beekeepers (217) and Manuka samples (3) were screened for the presence of novel antibacterial compounds by determining activity against methicillin resistant Staphylococcus aureus (MRSA) using optimised agar well diffusion and broth microdilution assays. The majority (92%) of the honeys showed inhibitory activity. Identification of unknown factors was performed by neutralising antibacterial honey components previously described in the literature. Of the samples screened four samples were found to contain potentially novel antibacterial compounds. The pollen present in honey represents a record of the plants which contributed to the making of the honey and may be the source of specific antibacterial factors. For this reason pollen was extracted from honey samples which demonstrated high levels of antimicrobial activity. Microscopic and DNA metabarcoding (454 and Illumina) analysis was performed. Plant species identified with DNA metabarcoding provided superior discrimination and greater repeatability. Key species identified in the antibacterial samples included woodruff (Galium odoratum), bluebell (Hyacinthoides non-scripta) and dandelion (Taraxacum officinale). Extracts from active honeys and characterised plants demonstrated antibacterial activity against MRSA, E. coli and P. aeruginosa using broth based methods and thin layer chromatography (TLC) bioautographic overlay methods. Activity-guided characterisation using a TLC/mass spectrometry (MS) interface and high performance liquid chromatography (HPLC) was performed. Compounds identified using these approaches included known pinobanksin derivatives and unknown compounds suggesting that the plants may be the original source of active compounds. The demonstration of antibacterial activity may provide new lead compounds that could serve as selective agents against MRSA and other antibiotic resistant bacteria.

Focal Adhesion Kinase (FAK) is an intracellular kinase known to mediate integrin signalling following cell adhesion to the extracellular matrix. It is now emerging as a promising therapeutic target in many tumour types due to its overexpression in tumour cells and is associated with various cellular processes involved in cancer progression. Given that existing literature demonstrating that FAK plays a key role in the transduction of HER2 signalling in HER2+ cells and that the levels of FAK expression strongly correlated with HER2 overexpression in clinical samples, we explored the potential for improvement of current therapies for HER2+ breast cancer by combination treatment strategies with the small molecule FAK inhibitor, PF878. FAK activity was assessed in a panel of cell lines reflecting HER2- (MCF7, T47D) and HER2+ (BT474, MDA-361, SKBr3) disease by Western blotting. FAK activity was relatively increased in HER2+ versus HER2- cell lines with HER2+ cells demonstrating greatest sensitivity to PF878 with respect to suppression of FAK phosphorylation at Y397. The effects of PF878 on cell proliferation as a monotherapy and in combination with Herceptin were assessed using MTT and direct coulter cell counting and by Ki67 immuno-staining. Whilst PF878 did not affect the proliferation as a monotherapy, treatment of HER2+ cells with PF878 and Herceptin combined resulted in synergistic inhibitory action on cell proliferation with an associated suppression in AKT pathway activity. This combination treatment strategy produced the greatest effects in MDA-361 cells which were intrinsically insensitive to Herceptin-monotherapy. Inhibition of FAK activity also suppressed HER2+ cell migration in response to the (1) exogenous ligand Heregulin and (2) conditioned-media derived from fibroblasts (FCM), as assessed in Boyden Chamber migration assays. In this latter context, our data suggests that FAK may act through a STAT3-dependent mechanism to regulate fibroblast-stimulated migratory and invasive responses. Collectively, these data support a role for FAK in HER2+ breast cancer where its targeting has the potential to improve Herceptin response as well as suppress stromal-induced signalling that can contribute to disease progression and spread.