Mathematical modelling of tumour growth and interaction with host tissue and the immune system

In this thesis, three mathematical models describing the growth of solid tumour incorporating the host tissue and the immune system response are developed and investigated. The initial model describes the dynamics of the growing tumour and immune response before being extended in the second model by introducing a time-varying dendritic cell-based treatment strategy. Finally, in the third model, we present a mathematical model of a growing tumour using a hybrid cellular automata. These models can provide information to pre-experimental work to assist in designing more effective and efficient laboratory experiments related to tumour growth and interactions with the immune system and immunotherapy.

Interaction of water with the fluorine-covered anatase TiO2(001) surface

The interaction of water with the fluorine-covered (001) surface of anatase titanium dioxide (TiO2) has been studied within the framework of density functional theory (DFT). Our results show that water dissociation is unfavorable due to repulsive interactions between surface fluorine and oxygen. We also found that the reaction of hydrofluoric acid with a surface hydroxyl group to form a surface Ti–F bond is exothermic, while the removal of fluorine from the surface needs additional energy of about half an eV. Therefore, water molecules are predicted to remain intact at the interface with the F-terminated anatase (001).

Nuclear instruments and methods in physics research section B : beam interactions with materials and atoms

The impact-induced deposition of Al13 clusters with icosahedral structure on Ni(0 0 1) surface was studied by molecular dynamics (MD) simulation using Finnis–Sinclair potentials. The incident kinetic energy (Ein) ranged from 0.01 to 30 eV per atom. The structural and dynamical properties of Al clusters on Ni surfaces were found to be strongly dependent on the impact energy. At much lower energy, the Al cluster deposited on the surface as a bulk molecule. However, the original icosahedral structure was transformed to the fcc-like one due to the interaction and the structure mismatch between the Al cluster and Ni surface. With increasing the impinging energy, the cluster was deformed severely when it contacted the substrate, and then broken up due to dense collision cascade. The cluster atoms spread on the surface at last. When the impact energy was higher than 11 eV, the defects, such as Al substitutions and Ni ejections, were observed. The simulation indicated that there exists an optimum energy range, which is suitable for Al epitaxial growth in layer by layer. In addition, at higher impinging energy, the atomic exchange between Al and Ni atoms will be favourable to surface alloying.

A case study of interactions between flood flow and buildings in an urban environment : Gardens Point during the 12-13 January 2011 flood of the Brisbane River (Australia)

Flood flows in inundated urban environment constitute a natural hazard. During the 12- 13 January 2011 flood of the Brisbane River, detailed water elevation, velocity and suspended sediment data were recorded in an inundated street at the peak of the flood. The field observations highlighted a number of unusual flow interactions with the urban surroundings. These included some slow fluctuations in water elevations and velocity with distinctive periods between 50 and 100 s caused by some local topographic effect (choking), superposed with some fast turbulent fluctuations. The suspended sediment data highlighted some significant suspended sediment loads in the inundated zone.

An in situ high pressure FT-IR study of CO2/H2 interactions with model ZnO/SiO2, Cu/SiO2 and Cu/ZnO/SiO2 methanol synthesis catalysts

In situ FT-IR spectroscopy allows the methanol synthesis reaction to be investigated under actual industrial conditions of 503 K and 10 MPa. On Cu/SiO2 catalyst formate species were initially formed which were subsequently hydrogenated to methanol. During the reaction a steady state concentration of formate species persisted on the copper. Additionally, a small quantity of gaseous methane was produced. In contrast, the reaction of CO2 and H2 on ZnO/SiO2 catalyst only resulted in the formation of zinc formate species: no methanol was detected. The interaction of CO2 and H2 with Cu/ZnO/SiO2 catalyst gave formate species on both copper and zinc oxide. Methanol was again formed by the hydrogenation of copper formate species. Steady-state concentrations of copper formate existed under actual industrial reaction conditions, and copper formate is the pivotal intermediate for methanol synthesis. Collation of these results with previous data on copper-based methanol synthesis catalysts allowed the formulation of a reaction mechanism

A combined temperature-programmed reaction spectroscopy and Fourier-transform infrared spectroscopy study of CO2/H2 and CO/CO2/H2 interactions with model ZnO/SiO2, Cu/SiO2 and Cu/ZnO/SiO2 methanol-synthesis catalysts

The reaction of CO2 and H2 with ZnO/SiO2 catalyst at 295 K gave predominantly hydrogencarbonate on zinc oxide and a small quantity of formate was evolved after heating at 393 K. Elevation of the reaction temperature to 503 K enhanced the rate of formation of zinc formate species. Significantly these formate species decomposed at 573 K almost entirely to CO2 and H2. Even after exposure of CO2-H2 or CO-CO2-H2 mixtures to highly defected ZnO/SiO2 catalyst, the formate species produced still decomposed to give CO2 and H2. It was concluded that carboxylate species which were formed at oxygen anion vacancies on polar Zn planes were not significantly hydrogenated to formate. Consequently it was proposed that the non-polar planes on zinc oxide contained sites which were specific for the synthesis of methanol. The interaction of CO2 and H2 with reduced Cu/ZnO/SiO2 catalyst at 393 K gave copper formate species in addition to substantial quantities of formate created at interfacial sites between copper and zinc oxide. It was deduced that interfacial formate species were produced from the hydrogenation of interfacial bidentate carbonate structures. The relevance of interfacial formate species in the methanol synthesis reaction is discussed. Experiments concerning the reaction of CO2-H2 with physical mixtures of Cu/SiO2 and ZnO/SiO2 gave results which were simply characteristic of the individual components. By careful consideration of previous data a detailed proposal regarding the role of spillover hydrogen is outlined. Admission of CO to a gaseous CO2-H2 feedstock resulted in a considerably diminished amount of formate species on copper. This was ascribed to a combination of over-reduction of the surface and site-blockage.

A fourier-transform infrared study of CO2 and CO2/H2 interactions with caesium-doped copper catalysts

FTIR spectra are reported of CO2 and COi/Hi on a silica-supported caesium-doped copper catalyst. Adsorption of COj on a "caesium"/silica surface resulted in the formation of COj and complexed CO species. Exposure of CO2 to' a caesium-doped reduced copper catalyst produced not only these species but also two forms of adsorbed carboxylate giving bands at 1550, 1510, 1365 and 1345 cm"1. Reaction of carboxylate species with hydrogen at 388 K gave formate species on copper and caesium oxide in addition to methoxy groups associated with caesium oxide. Methoxy species were not detected on undoped copper catalyst suggesting that caesium may be a promoter for the methanol synthesis reaction. Methanol decomposition on a caesium-doped copper catalyst produced a small number of formate species on copper and caesium oxide. Methoxy groups on caesium oxide decomposed to CO and U.2, and subsequent reaction between CO and adsorbed oxygen resulted in carboxylate formation. Methoxy species located at interfacial sites appeared to exhibit unusual adsorption properties.

Characterisation of two distinctly different processes associated with the electrocrystallization of microcrystals of phase I CuTCNQ (TCNQ= 7, 7, 8, 8-tetracyanoquinodimethane)

Semi-conducting phase I CuTCNQ (TCNQ = 7,7,8,8-tetracyanoquinodimethane), which is of considerable interest as a switching device for memory storage materials, can be electrocrystallized from CH3CN via two distinctly different pathways when TCNQ is reduced to TCNQ˙− in the presence of [Cu(MeCN)4]+. The first pathway, identified in earlier studies, occurs at potentials where TCNQ is reduced to TCNQ˙− and involves a nucleation–growth mechanism at preferred sites on the electrode to produce arrays of well separated large branched needle-shaped phase I CuTCNQ crystals. The second pathway, now identified at more negative potentials, generates much smaller needle-shaped phase I CuTCNQ crystals. These electrocrystallize on parts of the surface not occupied in the initial process and give rise to film-like characteristics. This process is attributed to the reduction of Cu+[(TCNQ˙−)(TCNQ)] or a stabilised film of TCNQ via a solid–solid conversion process, which also involves ingress of Cu+via a nucleation–growth mechanism. The CuTCNQ surface area coverage is extensive since it occurs at all areas of the electrode and not just at defect sites that dominate the crystal formation sites for the first pathway. Infrared spectra, X-ray diffraction, surface plasmon resonance, quartz crystal microbalance, scanning electron microscopy and optical image data all confirm that two distinctly different pathways are available to produce the kinetically-favoured and more highly conducting phase I CuTCNQ solid, rather than the phase II material.

Delineating breast cancer cell interactions with engineered bone microenvironments

The mechanisms leading to colonization of metastatic breast cancer cells (BCa) in the skeleton are still not fully understood. Here, we demonstrate that mineralized extracellular matrices secreted by primary human osteoblasts (hOBM) modulate cellular processes associated with BCa colonization of bone. A panel of four BCa cell lines of different bone-metastatic potential (T47D, SUM1315, MDA-MB-231, and the bone-seeking subline MDA-MB-231BO) was cultured on hOBM. After 3 days, the metastatic BCa cells had undergone morphological changes on hOBM and were aligned along the hOBM's collagen type I fibrils that were decorated with bone-specific proteins. In contrast, nonmetastatic BCa cells showed a random orientation on hOBM. Atomic force microscopy-based single-cell force spectroscopy revealed that the metastatic cell lines adhered more strongly to hOBM compared with nonmetastatic cells. Function-blocking experiments indicated that β1-integrins mediated cell adhesion to hOBM. In addition, metastatic BCa cells migrated directionally and invaded hOBM, which was accompanied by enhanced MMP-2 and -9 secretion. Furthermore, we observed gene expression changes associated with osteomimickry in BCa cultured on hOBM. As such, osteopontin mRNA levels were significantly increased in SUM1315 and MDA-MB-231BO cells in a β1-integrin-dependent manner after growing for 3 days on hOBM compared with tissue culture plastic. In conclusion, our results show that extracellular matrices derived from human osteoblasts represent a powerful experimental platform to dissect mechanisms underlying critical steps in the development of bone metastases.

Mathematical investigation of the interactions between the inflammatory response and mechanical aspects of dermal wound repair

Dermal wound repair involves complex interactions between cells, cytokines and mechanics to close injuries to the skin. In particular, we investigate the contribution of fibroblasts, myofibroblasts, TGFβ, collagen and local tissue mechanics to wound repair in the human dermis. We develop a morphoelastic model where a realistic representation of tissue mechanics is key, and a fibrocontractive model that involves a reasonable approximation to the true kinetics of the important bioactive species. We use each of these descriptions to elucidate the mechanisms that generate pathologies such as hypertrophic scars, contractures and keloids. We find that for hypertrophic scar and contracture development, factors regulating the myofibroblast phenotype are critical, with heightened myofibroblast activation, reduced myofibroblast apoptosis or prolonged inflammation all predicted as mediators for scar hypertrophy and contractures. Prevention of these pathologies is predicted when myofibroblast apoptosis is induced, myofibroblast activation is blocked or TGFβ is neutralised. To investigate keloid invasion, we develop a caricature representation of the fibrocontractive model and find that TGFβ spread is the driving factor behind keloid growth. Blocking activation of TGFβ is found to cause keloid regression. Thus, we recommend myofibroblasts and TGFβ as targets for clinicians when developing intervention strategies for prevention and cure of fibrotic scars.

Three-dimensional hydrogen-bonded structures in the hydrated proton-transfer salts of isonipecotamide with the dicarboxylic oxalic and adipic acid analogues

The structures of the 1:1 hydrated proton-transfer compounds of isonipecotamide (piperidine-4-carboxamide) with oxalic acid, 4-carbamoylpiperidinium hydrogen oxalate dihydrate, C6H13N2O+·C2HO4-·2H2O, (I), and with adipic acid, bis­(4-car­bam­oylpiperidinium) adipate dihydrate, 2C6H13N2O+·C6H8O42-·2H2O, (II), are three-dimensional hydrogen-bonded constructs involving several different types of enlarged water-bridged cyclic associations. In the structure of (I), the oxalate monoanions give head-to-tail carb­oxy­lic acid O-HOcarboxyl hydrogen-bonding inter­actions, forming C(5) chain substructures which extend along a. The isonipecotamide cations also give parallel chain substructures through amide N-HO hydrogen bonds, the chains being linked across b and down c by alternating water bridges involving both carboxyl and amide O-atom acceptors and amide and piperidinium N-HOcarboxyl hydrogen bonds, generating cyclic R43(10) and R32(11) motifs. In the structure of (II), the asymmetric unit comprises a piperidinium cation, half an adipate dianion, which lies across a crystallographic inversion centre, and a solvent water mol­ecule. In the crystal structure, the two inversion-related cations are inter­linked through the two water mol­ecules, which act as acceptors in dual amide N-HOwater hydrogen bonds, to give a cyclic R42(8) association which is conjoined with an R44(12) motif. Further N-HOwater, water O-HOamide and piperidinium N-HOcarbox­yl hydrogen bonds give the overall three-dimensional structure. The structures reported here further demonstrate the utility of the isonipecotamide cation as a synthon for the generation of stable hydrogen-bonded structures. The presence of solvent water mol­ecules in these structures is largely responsible for the non-occurrence of the common hydrogen-bonded amide-amide dimer, promoting instead various expanded cyclic hydrogen-bonding motifs.

Managed livestock grazing is compatible with the maintenance of plant diversity in semidesert grasslands

Even when no baseline data are available, the impacts of 150 years of livestock grazing on natural grasslands can be assessed using a combined approach of grazing manipulation and regional-scale assessment of the flora. Here, we demonstrate the efficacy of this method across 18 sites in the semidesert Mitchell grasslands of northeastern Australia. Fifteen-year-old exclosures (ungrazed and macropod grazed) revealed that the dominant perennial grasses in the genus Astrebla do not respond negatively to grazing disturbance typical of commercial pastoralism. Neutral, positive, intermediate, and negative responses to grazing disturbance were recorded amongst plant species with no single life-form group associated with any response type. Only one exotic species, Cenchrus ciliaris, was recorded at low frequency. The strongest negative response was from a native annual grass, Chionachne hubbardiana, an example of a species that is highly sensitive to grazing disturbance. Herbarium records revealed only scant evidence that species with a negative response to grazing have declined through the period of commercial pastoralism. A regional analysis identified 14 from a total of 433 plant species in the regional flora that may be rare and potentially threatened by grazing disturbance. However, a targeted survey precluded grazing as a cause of decline for seven of these based on low palatability and positive responses to grazing and other disturbance. Our findings suggest that livestock grazing of semidesert grasslands with a short evolutionary history of ungulate grazing has altered plant composition, but has not caused declines in the dominant perennial grasses or in species richness as predicted by the preceding literature. The biggest impact of commercial pastoralism is the spread of woody leguminous trees that can transform grassland to thorny shrubland. The conservation of plant biodiversity is largely compatible with commercial pastoralism provided these woody weeds are controlled, but reserves strategically positioned within water remote areas are necessary to protect grazing-sensitive species. This study demonstrates that a combination of experimental studies and regional surveys can be used to understand anthropogenic impacts on natural ecosystems where reference habitat is not available.

RAD51-associated Protein 1 (RAD51AP1) Interacts with the Meiotic Recombinase DMC1 through a Conserved Motif

Homologous recombination (HR) reactions mediated by the RAD51 recombinase are essential for DNA and replication fork repair, genome stability, and tumor suppression. RAD51-associated protein 1 (RAD51AP1) is an important HR factor that associates with and stimulates the recombinase activity of RAD51. We have recently shown that RAD51AP1 also partners with the meiotic recombinase DMC1, displaying isoform-specific interactions with DMC1. Here, we have characterized the DMC1 interaction site in RAD51AP1 by a series of truncations and point mutations to uncover a highly conserved WVPP motif critical for DMC1 interaction but dispensable for RAD51 association. This RAD51AP1 motif is reminiscent of the FVPP motif in the tumor suppressor protein BRCA2 that mediates DMC1 interaction. These results further implicate RAD51AP1 in meiotic HR via RAD51 and DMC1.

Raman and infrared spectroscopic characterization of the arsenate-bearing mineral tangdanite– and in comparison with the discredited mineral clinotyrolite

The minerals clinotyrolite and fuxiaotuite are discredited in terms of the mineral tangdanite. The mixed anion mineral tangdanite Ca2Cu9(AsO4)4(SO4)0.5(OH)9 9H2O has been studied using a combination of Raman and infrared spectroscopy. Characteristic bands associated with arsenate, sulphate and hydroxyl units are identified. Broad bands in the OH stretching region are observed and are resolved into component bands. These bands are assigned to water and hydroxyl stretching vibrations. Two intense Raman bands at 837 and approximately 734 cm−1 are assigned to the ν1 (AsO4)3− symmetric stretching and ν3 (AsO4)3− antisymmetric stretching modes. Infrared bands at 1023 cm−1 are assigned to the (SO4)2− ν1 symmetric stretching mode, and infrared bands at 1052, 1110 and 1132 cm−1 assigned to (SO4)2− ν3 antisymmetric stretching modes, confirming the presence of the sulphate anion in the tangdanite structure. Raman bands at 593 and 628 cm−1 are attributed to the (SO4)2− ν4 bending modes. Low-intensity Raman bands found at 457 and 472 cm−1 are assigned to the (AsO4)3− ν2 bending modes. A comparison is made with the previously obtained spectral data on the discredited mineral clinotyrolite.