A thermostable endonuclease III homolog from the archaeon Pyrobaculum aerophilum

Pyrimidine adducts in cellular DNA arise from modification of the pyrimidine 5,6-double bond by oxidation, reduction or hydration. The biological outcome includes increased mutation rate and potential lethality. A major DNA N-glycosylase responsible for the excision of modified pyrimidine bases is the base excision repair (BER) glycosylase endonuclease III, for which functional homologs have been identified and characterized in Escherichia coli, yeast and humans. So far, little is known about how hyperthermophilic Archaea cope with such pyrimidine damage. Here we report characterization of an endonuclease III homolog, PaNth, from the hyperthermophilic archaeon Pyrobaculum aerophilum, whose optimal growth temperature is 100°C. The predicted product of 223 amino acids shares significant sequence homology with several [4Fe-4S]-containing DNA N-glycosylases including E.coli endonuclease III (EcNth). The histidine-tagged recombinant protein was expressed in E.coli and purified. Under optimal conditions of 80–160 mM NaCl and 70°C, PaNth displays DNA glycosylase/β-lyase activity with the modified pyrimidine base 5,6-dihydrothymine (DHT). This activity is enhanced when DHT is paired with G. Our data, showing the structural and functional similarity between PaNth and EcNth, suggests that BER of modified pyrimidines may be a conserved repair mechanism in Archaea. Conserved amino acid residues are identified for five subfamilies of endonuclease III/UV endonuclease homologs clustered by phylogenetic analysis.

Initiation of clement surface conditions on the earliest Earth

In the beginning the surface of the Earth was extremely hot, because the Earth as we know it is the product of a collision between two planets, a collision that also created the Moon. Most of the heat within the very young Earth was lost quickly to space while the surface was still quite hot. As it cooled, the Earth's surface passed monotonically through every temperature regime between silicate vapor to liquid water and perhaps even to ice, eventually reaching an equilibrium with sunlight. Inevitably the surface passed through a time when the temperature was around 100°C at which modern thermophile organisms live. How long this warm epoch lasted depends on how long a thick greenhouse atmosphere can be maintained by heat flow from the Earth's interior, either directly as a supplement to insolation, or indirectly through its influence on the nascent carbonate cycle. In both cases, the duration of the warm epoch would have been controlled by processes within the Earth's interior where buffering by surface conditions played little part. A potentially evolutionarily significant warm period of between 105 and 107 years seems likely, which nonetheless was brief compared to the vast expanse of geological time.

Paper-like electronic displays: Large-area rubber-stamped plastic sheets of electronics and microencapsulated electrophoretic inks

Electronic systems that use rugged lightweight plastics potentially offer attractive characteristics (low-cost processing, mechanical flexibility, large area coverage, etc.) that are not easily achieved with established silicon technologies. This paper summarizes work that demonstrates many of these characteristics in a realistic system: organic active matrix backplane circuits (256 transistors) for large (≈5 × 5-inch) mechanically flexible sheets of electronic paper, an emerging type of display. The success of this effort relies on new or improved processing techniques and materials for plastic electronics, including methods for (i) rubber stamping (microcontact printing) high-resolution (≈1 μm) circuits with low levels of defects and good registration over large areas, (ii) achieving low leakage with thin dielectrics deposited onto surfaces with relief, (iii) constructing high-performance organic transistors with bottom contact geometries, (iv) encapsulating these transistors, (v) depositing, in a repeatable way, organic semiconductors with uniform electrical characteristics over large areas, and (vi) low-temperature (≈100°C) annealing to increase the on/off ratios of the transistors and to improve the uniformity of their characteristics. The sophistication and flexibility of the patterning procedures, high level of integration on plastic substrates, large area coverage, and good performance of the transistors are all important features of this work. We successfully integrate these circuits with microencapsulated electrophoretic “inks” to form sheets of electronic paper.

Filmes de óxido de zinco e nitreto de zinco depositados por magnetron sputtering com diferentes pressões de argônio, oxigênio e nitrogênio.

O óxido de zinco é um material semicondutor que apresenta alta transparência óptica no espectro visível, alta energia de ligação de éxcitons e piezoeletricidade. Por suas propriedades, ele é utilizado na área de sensores, eletrodos transparentes e dispositivos optoeletrônicos. No entanto, sua utilização ainda é limitada pela dificuldade de obtenção de condutividade tipo p, cujo principal dopante é o nitrogênio, devido à assimetria de dopagem ocasionada por defeitos intrínsecos do material, dopagem em valências diferentes das esperadas e formação de níveis de aceitadores profundos na banda proibida. A aplicação em dispositivos piezoelétricos também exige alta resistividade e ótimas propriedades cristalinas. Muitos processos de deposição estabelecidos hoje ainda utilizam altas temperaturas, o que impede sua deposição sobre superfícies ou substratos sensíveis a altas temperaturas. O objetivo deste trabalho é desenvolver técnicas de deposição de filmes de ZnO, principalmente em baixas temperaturas ( 100°C), pelo método de magnetron sputtering de rádio frequência, para avaliar a influência dos gases de processo nas características estruturais, estequiométricas, elétricas e ópticas dos filmes. Para isso, foram obtidos filmes utilizando pressão total de argônio, e pressões parciais de argônio e oxigênio e argônio e nitrogênio, utilizando alvo cerâmico de óxido de zinco ou alvo metálico de zinco. Para alvo de ZnO, filmes com condutividade tipo n foram obtidos em ambiente de argônio, em condições que geraram deficiências de oxigênio. Filmes altamente resistivos foram obtidos com a utilização de pressão parcial de oxigênio no gás de processo, em condições que resultaram em filmes estequiométricos, inclusive com condutividade tipo p. Condutividade tipo p mais alta foi observada, apenas por ponta quente, para uma amostra obtida em argônio logo após a utilização de nitrogênio na câmara de processo, que provavelmente sofreu influência da dopagem não intencional do cobre, que foi identificado como um contaminante do processo devido à estrutura da câmara. Para alvo de Zn, observou-se a formação de nitreto de zinco, que demonstrou alta capacidade de oxidação em ambiente atmosférico, e portanto, transforma-se naturalmente ao longo do tempo ou por processos de oxidação térmica em ZnO dopado com nitrogênio. Filmes de ZnO produzidos a partir de nitreto de zinco foram os únicos dos testados que apresentaram fotoluminescência característica do ZnO, mesmo para processos onde não houve aquecimento intencional.

Estudio de la influencia de la temperatura en las propiedades físicas y mecánicas de la calcarenita de San Julián

En este trabajo se muestran los resultados de una serie de ensayos de laboratorio realizados para estudiar el efecto de las altas temperaturas en las propiedades físicas y mecánicas de una calcarenita muy usada como material de construcción en edificios y monumentos históricos de la ciudad de Alicante. El objetivo es evaluar el daño térmico producido en el material al exponerlo a diferentes temperaturas y la influencia de los diferentes procesos de enfriamiento (al aire y por inmersión en agua), así como la viabilidad del diagnóstico del daño mediante métodos no destructivos (ultrasonidos). Se han utilizado probetas cilíndricas extraídas de bloques de roca sobre las que se han realizado ensayos de caracterización del material intacto obteniendo la porosidad, velocidades de propagación de las ondas P y S, módulos dinámicos y estáticos y resistencia a compresión uniaxial. El calentamiento se ha efectuado en horno eléctrico a temperaturas de entre 105 y 600ºC, en intervalos de 100ºC. Para cada temperatura (excepto 105 ºC) se han calentado diez probetas, enfriándolas posteriormente mediante dos procesos diferentes, obteniendo datos de un total de 55 probetas sometidas a diferentes condiciones de temperatura y método de enfriamiento. Finalmente, se han determinado de nuevo las propiedades de las probetas tras su calentamiento, comparando y correlacionando las diferentes variables. Las conclusiones principales destacan un acusado descenso de los valores de las propiedades medidas con la temperatura (excepto la porosidad que aumenta). Este descenso se acelera notablemente con enfriamiento por agua. Los ensayos no destructivos detectan el deterioro producido en el proceso de igual forma que los destructivos.

Reformulation of a thermostable broadly protective recombinant vaccine against human papilloma virus

The causal relationship between Human Papilloma Virus (HPV) infection and cervical cancer has motivated the development, and further improvement, of prophylactic vaccines against this virus. 70% of cervical cancers, 80% of which in low-resources countries, are associated to HPV16 and HPV18 infection, with 13 additional HPV types, classified as high-risk, responsible for the remaining 30% of tumors. Current vaccines, Cervarix® (GlaxoSmithKline) and Gardasil®(Merk), are based on virus-like particles (VLP) obtained by self-assembly of the major capsid protein L1. Despite their undisputable immunogenicity and safety, the fact that protection afforded by these vaccines is largely limited to the cognate serotypes included in the vaccine (HPV 16 and 18, plus five additional viral types incorporated into a newly licensed nonavalent vaccine) along with high production costs and reduced thermal stability, are pushing the development of 2nd generation HPV vaccines based on minor capsid protein L2. The increase in protection broadness afforded by the use of L2 cross-neutralizing epitopes, plus a marked reduction of production costs due to bacterial expression of the antigens and a considerable increase in thermal stability could strongly enhance vaccine distribution and usage in low-resource countries. Previous studies from our group identified three tandem repeats of the L2 aa. 20-38 peptide as a strongly immunogenic epitope if exposed on the scaffold protein thioredoxin (Trx). The aim of this thesis work is the improvement of the Trx-L2 vaccine formulation with regard to cross-protection and thermostability, in order to identify an antigen suitable for a phase I clinical trial. By testing Trx from different microorganisms, we selected P. furiosus thioredoxin (PfTrx) as the optimal scaffold because of its sustained peptide epitope constraining capacity and striking thermal stability (24 hours at 100°C). Alternative production systems, such as secretory Trx-L2 expression in the yeast P. pastoris, have also been set-up and evaluated as possible means to further increase production yields, with a concomitant reduction of production costs. Limitations in immune-responsiveness caused by MHC class II polymorphisms –as observed, for example, in different mouse strains- have been overcome by introducing promiscuous T-helper (Th) epitopes, e.g., PADRE (Pan DR Epitope), at both ends of PfTrx. This allowed us to obtain fairly strong immune responses even in mice (C57BL/6) normally unresponsive to the basic Trx-L2 vaccine. Cross-protection was not increased, however. I thus designed, produced and tested a novel multi-epitope formulation consisting of 8 and 11 L2(20-38) epitopes derived from different HPV types, tandemly joined into a single thioredoxin molecule (“concatemers”). To try to further increase immunogenicity, I also fused our 8X and 11X PfTrx-L2 concatemers to the N-terminus of an engineered complement-binding protein (C4bp), capable to spontaneously assemble into ordered hepatmeric structures, previously validated as a molecular adjuvant. Fusion to C4bp indeed improved antigen presentation, with a fairly significant increase in both immunogenicity and cross-protection. Another important issue I addressed, is the reduction of vaccine doses/treatment, which can be achieved by increasing immunogenicity, while also allowing for a delayed release of the antigen. I obtained preliminary, yet quite encouraging results in this direction with the use of a novel, solid-phase vaccine formulation, consisting of the basic PfTrx-L2 vaccine and its C4bp fusion derivative adsorbed to mesoporus silica-rods (MSR).

The Single drop drying of heat-sensitive materials

The literature relating to the principles and practice of drying of materials, particularly those susceptible to thermal degradation or undesirable loss of volatile components, has been reviewed. Single droplets of heat-sensitive materials were dried whilst suspended in a horizontal wind tunnel from a specially-designed, rotating thermocouple which enabled direct observation of drying behaviour and continuous measurement of droplet temperature as drying progressed. The effects of drying air temperature and initial solids concentration on the potency of various antibiotics, viz. ampicillin, chloramphenicol, oxytetracycline, streptomycin and tetracycline, were assessed using a modified Drug Sensitivity Testing technique. Only ampicillin was heat-sensitive at temperatures above 100°C, e.g. at an air temperature of 115°C its zone diameter was reduced from 100% to 45%. Selected enzymes, viz. dextran sucrase and invertase, were also dried and their residual activities determined by High Performance Liquid Chromatography. The residual activity of dextran sucrase was rapidly reduced at temperatures above 65°C, and the residual activity of invertase reduced rapidly at temperatures above 65°C; but drying with short residence times will retain most of its activity. The performance of various skin-forming encapsulants, viz. rice and wheat starch, dextrin, coffee, skim milk, fructose, gelatine 60 and 150 Bloom, and gum arabic, was evaluated to determine their capabilities for retention of ethanol as a model volatile, under different operating conditions. The effects of initial solids concentration, air velocity and temperature were monitored for each material tested. Ethanol content was analysed by Gas Liquid Chromatography and in some cases dried crusts were removed for examination. Volatiles retention was concluded to depend in all cases upon the rate and nature of the skin formation and selective diffusion phenomena. The results provided further insight into the inter-relationship between temperature, residence time and thermal degradation of heat-sensitive materials. They should also assist in selection of the preferred dryer for such materials, and of the operating parameter to enable maximum retention of the required physico-chemical characteristics in the dried materials.

Some studies relating to the design of shallow, fluidized bed boilers

The concept of shallow fluidized bed boilers is defined and a preliminary working design for a gas-fired package boiler has been produced. Those areas of the design requiring further study have been specified. Experimental investigations concerning these areas have been carried out. A two-dimensional, conducting paper analog has been developed for the specific purpose of evaluating sheet fins. The analog has been generalised and is presented as a simple means of simulating the general, two-dimensional Helmholtz equation. By recording the transient response of spherical, calorimetric probes when plunged into heated air-fluidized beds, heat transfer coefficients have been measured at bed temperatures up to 1 100°C. A correlation fitting all the data to within ±10% has been obtained. A model of heat transfer to surfaces immersed in high temperature beds has been proposed. The model solutions are, however, only in qualitative agreement with the experimental data. A simple experimental investigation has revealed that the effective, radial, thermal conductivities of shallow fluidized beds are an order of magnitude lower than the axial conductivities. These must, consequently, be taken into account when considering heat transfer to surfaces immersed within fluidized beds. Preliminary work on pre-mixed gas combustion and some further qualitative experiments have been used as the basis for discussing the feasibility of combusting heavy fuel oils within shallow beds. The use of binary beds, within which the fuel could be both gasified and subsequently burnt, is proposed. Finally, the consequences of the experimental studies on the initial design are considered, and suggestions for further work are made.

The fatigue properties of pressure diecast zinc-aluminium based alloys

The fatigue behaviour of the cold chamber pressure-die-cast alloys: Mazak3, ZA8, ZA27, M3K, ZA8K, ZA27K, K1, K2 and K3 was investigated at temperature of 20°C. The alloys M3K, ZA8K and ZA27K were also examined at temperatures of 50 and 100°C. The ratio between fatigue strength and tensile strength was established at 20°C at 107 cycles. The fatigue life prediction of the alloys M3K, ZA8K and ZA27K was formulated at 20, 50 and 100°C. The prediction formulae were found to be reasonably accurate. All of the experimental alloys were heterogeneous and contained large but varying amounts of pores. These pores were a major contribution and dominated the alloys fatigue failure. Their effect, however, on tensile failure was negligible. The ZA27K possessed the highest tensile strength but the lowest fatigue strength. The relationship between the fracture topography and the microstructure was also determined by the use of a mixed signal of a secondary electron and a back-scattered electron on the SEM. The tensile strength of the experimental alloys was directly proportional to the aluminium content within the alloys. The effect of copper content was also investigated within the alloys K1, K2, ZA8K and K3 which contained 0%, 0.5%, 1.0% and 2.0% respectively. It was determined that the fatigue and tensile strengths improved with higher copper contents. Upon ageing the alloys Mazak3, ZA8 and ZA27 at an ambient temperature for 5 years, copper was also found to influence and maintain the metastable Zn-Al (αm) phase. The copper free Mazak3 upon ageing lost this metastable phase. The 1.0% copper ZA8 alloy had lost almost 50% of its metastable phase. Finally the 2.0% copper ZA27 had merely lost 10% of its metastable phase. The cph zinc contained a limited number of slip systems, therefore twinning deformation was unavoidable in both fatigue and tensile testing.

Behaviour of concrete frame structures under localised fire scenarios

This thesis encompasses an investigation of the behaviour of concrete frame structure under localised fire scenarios by implementing a constitutive model using finite-element computer program. The investigation phase included properties of material at elevated temperature, description of computer program, thermal and structural analyses. Transient thermal properties of material have been employed in this study to achieve reasonable results. The finite-element computer package of ANSYS is utilized in the present analyses to examine the effect of fire on the concrete frame under five various fire scenarios. In addition, a report of full-scale BRE Cardington concrete building designed to Eurocode2 and BS8110 subjected to realistic compartment fire is also presented. The transient analyses of present model included additional specific heat to the base value of dry concrete at temperature 100°C and 200°C. The combined convective-radiation heat transfer coefficient and transient thermal expansion have also been considered in the analyses. For the analyses with the transient strains included, the constitutive model based on empirical formula in a full thermal strain-stress model proposed by Li and Purkiss (2005) is employed. Comparisons between the models with and without transient strains included are also discussed. Results of present study indicate that the behaviour of complete structure is significantly different from the behaviour of individual isolated members based on current design methods. Although the current tabulated design procedures are conservative when the entire building performance is considered, it should be noted that the beneficial and detrimental effects of thermal expansion in complete structures should be taken into account. Therefore, developing new fire engineering methods from the study of complete structures rather than from individual isolated member behaviour is essential.

Mechanisms of drying of particulate slurries

The literature on the evaporation of pure liquid drops and the drying of drops of solutions and slurries has been reviewed with particular reference to spray drying. A 0.1-0.2 mm glass filament-thermocouple was constructed and used to study simultaneously, heat and mass transfer from a single suspended drop placed in a humidity and temperature controlled, 28 mm OD vertical wind tunnel. Heat conduction through the filament was minimised eg at 100¦C it accounted for only 9.3% of the total heat transferred to a drop. Evaporation of single water drops was also studied in a 101 mm OD vertical wind tunnel. The Nusselt number was found to be a function of the Reynolds, Prandtl and Transfer number over an air temperature range of 17¦C to 107¦C. The proposed correlation is: Nu = 2+(-12.96B+0.76)Re¦-5Pr0-33 Experimental drying studies were carried out on single suspended 1 to 2.5 mm diameter drops of aqueous sodium sulphate decahydrate, sodium chloride, potassium sulphate, copper sulphate and sodium acetate solutions and slurries at temperatures of 20¦C to 124¦C. Dried crusts were examined by Scanning Electron Microscopy. The drying history of any material depended upon the nature of the crust formed. Sodium acetate formed a non-rigid skin prior to the formation of a rigid crust. A modified receding evaporation interface model was proposed for the drying of solutions and slurries. This covered both the constant rate period prior to crust formation and the subsequent falling rate period. The model was solved numerically for the variation in core temperature, drop weight and crust thickness. Good agreement was obtained between model predictions and experimental results for materials forming rigid crusts i.e. sodium sulphate decahydrate, sodium chloride, potassium sulphate and copper sulphate. However, the drying histories of drops of 10-20% weight initial concentration sodium acetate were unpredictable since formation of a non-rigid skin deviated from the model assumption of a rigid outer surface. At higher initial concentrations (40% weight) where a rigid crust was formed for sodium acetate, good agreement was obtained between experimental results and model predictions. Single suspended drop studies are concluded to provide a valuable insight into the drying mechanisms of specific solutions and slurries.

Synthesis, characterisation and applications of diamond materials

This thesis presented a detailed research work on diamond materials. Chapter 1 is an overall introduction of the thesis. In the Chapter 2, the literature review on the physical, chemical, optical, mechanical, as well as other properties of diamond materials are summarised. Followed by this chapter, several advanced diamond growth and characterisation techniques used in experimental work are also introduced. Then, the successful installation and applications of chemical vapour deposition system was demonstrated in Chapter 4. Diamond growth on a variety of different substrates has been investigated such as on silicon, diamond-like carbon or silica fibres. In Chapter 5, the single crystalline diamond substrate was used as the substrate to perform femtosecond laser inscription. The results proved the potentially feasibility of this technique, which could be utilised in fabricating future biochemistry microfluidic channels on diamond substrates. In Chapter 6, the hydrogen-terminated nanodiamond powder was studied using impedance spectroscopy. Its intrinsic electrical properties and its thermal stability were presented and analysed in details. As the first PhD student within Nanoscience Research Group at Aston, my initial research work was focused on the installation and testing of the microwave plasma enhanced chemical vapour deposition system (MPECVD), which will be beneficial to all the future researchers in the group. The fundamental of the on MPECVD system will be introduced in details. After optimisation of the growth parameters, the uniform diamond deposition has been achieved with a good surface coverage and uniformity. Furthermore, one of the most significant contributions of this work is the successful pattern inscription on diamond substrates by femtosecond laser system. Previous research of femtosecond laser inscription on diamond was simple lines or dots, with little characterisation techniques were used. In my research work, the femtosecond laser has been successfully used to inscribe patterns on diamond substrate and fully characterisation techniques, e.g. by SEM, Raman, XPS, as well as AFM, have been carried out. After the femtosecond laser inscription, the depth of microfluidic channels on diamond film has been found to be 300~400 nm, with a graphitic layer thickness of 165~190 nm. Another important outcome of this work is the first time to characterise the electrical properties of hydrogenterminated nanodiamond with impedance spectroscopy. Based on the experimental evaluation and mathematic fitting, the resistance of hydrogen-terminated nanodiamond reduced to 0.25 MO, which were four orders of magnitude lower than untreated nanodiamond. Meanwhile, a theoretical equivalent circuit has been proposed to fit the results. Furthermore, the hydrogenterminated nanodiamond samples were annealed at different temperature to study its thermal stability. The XPS and FTIR results indicate that hydrogen-terminated nanodiamond will start to oxidize over 100ºC and the C-H bonds can survive up to 400ºC. This research work reports the fundamental electrical properties of hydrogen-terminated nanodiamond, which can be used in future applications in physical or chemical area.

Annealing and temperature coefficient study of type IA fibre Bragg gratings inscribed under strain and no strain - Implications to optical fibre component reliability

The annealing properties of Type IA Bragg gratings are investigated and compared with Type I and Type IIA Bragg gratings. The transmission properties (mean and modulated wavelength components) of gratings held at predetermined temperatures are recorded from which decay characteristics are inferred. Our data show critical results concerning the high temperature stability of Type IA gratings, as they undergo a drastic initial decay at 100°C, with a consequent mean index change that is severely reduced at this temperature However, the modulated index change of IA gratings remains stable at lower annealing temperatures of 80°C, and the mean index change decays at a comparable rate to Type I gratings at 80°C. Extending this work to include the thermal decay of Type IA gratings inscribed under strain shows that the application of strain quite dramatically transforms the temperature characteristics of the Type IA grating, modifying the temperature coefficient and annealing curves, with the grating showing a remarkable improvement in high temperature stability, leading to a robust grating that can survive temperatures exceeding 180°C. Under conditions of inscription under strain it is found that the temperature coefficient increases, but is maintained at a value considerably different to the Type I grating. Therefore, the combination of Type I and IA (strained) gratings make it possible to decouple temperature and strain over larger temperature excursions.

Super-high temperature sensitivity of long-period gratings in B/Ge co-doped fiber

Long period fiber grating (LPFG) can be used as active gain controlling device in EDFA. However, LPFGs fabricated in the standard telecom fiber only have a typical temperature sensitivity of 3-10nm/100°C, which may not be sufficient for implementing tuneable filters capable of wide tuning range and high tuning efficiency. In this paper, we report a theoretical and experimental investigation of thermal properties of LPFGs fabricated in B/Ge co-doped optical fiber. We have found that the temperature sensitivity of the LPFGs in the B/Ge fiber is considerably increased compared with those produced in the standard fiber. The LPFGs written in the B/Ge fiber have achieved, on average, one order of magnitude higher sensitivity than that of the LPFGs produced in the standard telecom fiber. We have also identified that the thermal response of LPFG is strongly dependent on the order of the coupled resonant cladding mode. The maximum sensitivity of 1.75nm/°C achieved by the 10th cladding mode of the 240μm LPFG is nearly 24 times that of the minimum value (0.075nm/C) exhibited by the 30th mode of the 34μm LPFG. Such devices may lead to high-efficiency and low-cost thermal/electrical tunable loss filters or sensors with extremely high temperature resolution.