Microscale mesoarrays created by dip-pen nanolithography for screening of protein-protein interactions

Using microarrays to probe protein-protein interactions is becoming increasingly attractive due to their compatibility with highly sensitive detection techniques, selectivity of interaction, robustness and capacity for examining multiple proteins simultaneously. The major drawback to using this approach is the relatively large volumes and high concentrations necessary. Reducing the protein array spot size should allow for smaller volumes and lower concentrations to be used as well as opening the way for combination with more sensitive detection technologies. Dip-Pen Nanolithography (DPN) is a recently developed technique for structure creation on the nano to microscale with the capacity to create biological architectures. Here we describe the creation of miniaturised microarrays, 'mesoarrays', using DPN with protein spots 400× smaller by area compared to conventional microarrays. The mesoarrays were then used to probe the ERK2-KSR binding event of the Ras/Raf/MEK/ERK signalling pathway at a physical scale below that previously reported. Whilst the overall assay efficiency was determined to be low, the mesoarrays could detect KSR binding to ERK2 repeatedly and with low non-specific binding. This study serves as a first step towards an approach that can be used for analysis of proteins at a concentration level comparable to that found in the cellular environment.

Cellular interactions with hydrogels

An efficient means of evaluating potential biomaterials is to use the in vitro fibroblast cell culture model. However, the chemistry which influences cell adhesion on polymer substrates is poorly understood. The work in this thesis aims to rationalise several theories of current opinion and introduce new chemical techniques that may predict cellular behaviour. The keratoprosthesis is a typical example of the need to be able to manipulate cell adhesion of materials since both adhesive and non adhesive sections are needed for proper integration and optical function. Calcein AM/ethidium homodimer-1 and DAPI assays were carried out using 3T3 and EKl.BR cells. Poly(HEMA) was found to be the most cell adhesive hydrogel tested. The reactivity of monomers and the resulting sequence distribution were found to affect surface properties and this may explain the poor levels of cell adhesion seen on NVP/MMA copolymers. Surface free energy is shown to be dependent on the polar and non polar groups present along the backbone chain of the polymers. Dehydrated and hydrated contact angle measurements show the effect of rotation of surface groups around the backbone chain. This effect is most apparent on hydrogels containing methacrylic acid. Dynamic contact angle measurements confirm sequence distribution irregularities and demonstrate the mobility of surface groups. Incorporation of NVI or DEAEMA into the hydrogels does not affect the mobility of the surface groups despite their bulkiness. Foetal calf serum was used for the first time as a test solution in an attempt to mimic a biological environment during surface experiments. A Vroman effect may be present, and may involve different surface proteins for each material tested. This interdisciplinary study combines surface characterisation and biological testing to further the knowledge of the biomaterial/host interface. Surface chemistry techniques appear to be insufficiently sensitive to predict cellular behaviour. The degree of ionisation of hydrogels containing ionic groups depends on the nature of the functional groups as well as the concentration and this is an important parameter to consider when comparing charged materials.

Setting parameters in MRP for the effective management of bought-out inventory in a JIT assembly environment

In recent years, UK industry has seen an explosive growth in the number of `Computer Aided Production Management' (CAPM) system installations. Of the many CAPM systems, materials requirement planning/manufacturing resource planning (MRP/MRPII) is the most widely implemented. Despite the huge investments in MRP systems, over 80 percent are said to have failed within 3 to 5 years of installation. Many people now assume that Just-In-Time (JIT) is the best manufacturing technique. However, those who have implemented JIT have found that it also has many problems. The author argues that the success of a manufacturing company will not be due to a system which complies with a single technique; but due to the integration of many techniques and the ability to make them complement each other in a specific manufacturing environment. This dissertation examines the potential for integrating MRP with JIT and Two-Bin systems to reduce operational costs involved in managing bought-out inventory. Within this framework it shows that controlling MRP is essential to facilitate the integrating process. The behaviour of MRP systems is dependent on the complex interactions between the numerous control parameters used. Methodologies/models are developed to set these parameters. The models are based on the Pareto principle. The idea is to use business targets to set a coherent set of parameters, which not only enables those business targets to be realised, but also facilitates JIT implementation. It illustrates this approach in the context of an actual manufacturing plant - IBM Havant. (IBM Havant is a high volume electronics assembly plant with the majority of the materials bought-out). The parameter setting models are applicable to control bought-out items in a wide range of industries and are not dependent on specific MRP software. The models have produced successful results in several companies and are now being developed as commercial products.

The influence of environment on foliose lichen growth and its ecological significance

This chapter considers various aspects of the influence of the environment on the growth of foliose lichens and its significance in determining the ecology of individual species. Radial growth (RaG) and growth in mass of foliose lichens is influenced by climate and microclimate and also by substratum factors such as rock and bark texture, substrate chemistry, and nutrient enrichment. Seasonal fluctuations in growth, as measured by radial growth rate (RaGR) per month, often correlate best with average or total rainfall, the number of rain days, or rainfall in a specific season. Temperature has also been identified to be an important climatic factor influencing growth in some studies. Interactions between microclimatic factors and especially light intensity, temperature, and moisture status are important in determining differences in growth in relation to aspect and slope of the substratum. The physical and chemical nature of the substratum has a profound influence on the growth of foliose lichens. Hence, the effects of texture, porosity, rate of drying, and the physical changes of the substratum on growth are likely to influence lichen distributions. Bird droppings may influence growth and survival by smothering the thalli, altering the pH, or adding inhibitory and stimulatory compounds. Nitrogen and phosphate availability may also influence growth. Chemical factors also have an important influence on lichens of maritime rocks, the effect of salinity and calcium ions being of particular importance. Effects of environmental factors on growth influence the competitive ability of a lichen and ultimately its ecology and distribution.

The influence of environment on foliose lichen growth and its biological significance

Radial growth and growth in mass of lichens is influenced by climatic and microclimatic factors and also by substratum factors such as rock and bark texture, chemistry, and nutrient enrichment. Seasonal fluctuations in growth, as measured by radial growth rate (RaGR) per month, often correlate best with average or total rainfall, the number of rain days, or rainfall in a specific season. Temperature is also considered to be an important climatic factor in some studies. Interactions between microclimatic factors and especially light intensity, temperature, and moisture are the most important in determining local annual growth rates. The physical and chemical nature of the substratum has a profound influence on the growth of foliose lichens. Hence, the effects of texture, porosity, rate of drying, and the physical changes of the substratum on growth are likely to influence lichen distributions. Bird droppings may influence growth and survival by smothering the thalli, altering the pH, or adding inhibitory and stimulatory compounds. Nitrogen and phosphate availability may also influence growth. Chemical factors may also have an important influence on lichens of maritime rocks, the effect of salinity and calcium ions being of particular importance. Zinc, copper, and mercury may also be important in lichen growth as they have been shown to affect the chlorophyll content of lichen algae. Effects of environmental factors on growth influence the competitive ability of lichens thus influencing their ecology and distribution.

Biomaterial interactions with compromised tissue surfaces

This thesis is concerned with the nature of biomaterial interactions with compromised host tissue sites. Both ocular and dermal tissues can be wounded, following injury, disease or surgery, and consequently require the use of a biomaterial. Clear analogies exist between the cornea/tear film/contact lens and the dermal wound bed/wound fluid/skin adhesive wound dressing. The work described in this thesis builds upon established biochemistry to examine specific aspects of the interaction of biomaterials with compromised ocular and dermal tissue sites, with a particular focus on the role of vitronectin. Vitronectin is a prominent cell adhesion glycoprotein present in both tear fluid and wound fluid, and has a role in the regulation and upregulation of plasmin. The interaction of contact lenses with the cornea was assessed by a novel on-lens cell-based vitronectin assay technique. Vitronectin mapping showed that vitronectin-mediated cell adhesion to contact lens surfaces was due to the contact lens-corneal mechanical interaction rather than deposition out of the tear film. This deposition is associated predominantly with the peripheral region of the posterior contact lens surface. The locus of vitronectin deposition on the contact lens surface, which is affected by material modulus, is potentially an important factor in the generation of plasmin in the posterior tear film. Use of the vitronectin mapping technique on ex vivo bandage contact lenses revealed greater vitronectin-mediated cell adhesion to the contact lens surfaces in comparison to lenses worn in the healthy eye. The results suggest that vitronectin is more readily deposited from the impaired corneal tissue bed than the intact healthy tissue bed. Significantly, subjects with a deficient tear film were found to deposit high vitronectin-mediated cell adhesion levels to the BCL surface, thus highlighting the influence of the contact lens-tissue interaction upon deposition. Biomimetic principles imply that adhesive materials for wound applications, including hydrogels and hydrocolloids, should closely match the surface energy parameters of skin. The surface properties of hydrocolloid adhesives were found to be easily modified by contact with siliconised plastic release liners. In contrast, paper release liners did not significantly affect the adhesive surface properties. In order to characterise such materials in the actual wound environment, which is an extremely challenging task, preliminary considerations for the design of an artificial wound fluid model from an animal serum base were addressed.

Universal duality in a Luttinger liquid coupled to a generic environment

We study a Luttinger liquid (LL) coupled to a generic environment consisting of bosonic modes with arbitrary density-density and current-current interactions. The LL can be either in the conducting phase and perturbed by a weak scatterer or in the insulating phase and perturbed by a weak link. The environment modes can also be scattered by the imperfection in the system with arbitrary transmission and reflection amplitudes. We present a general method of calculating correlation functions under the presence of the environment and prove the duality of exponents describing the scaling of the weak scatterer and of the weak link. This duality holds true for a broad class of models and is sensitive to neither interaction nor environmental modes details, thus it shows up as the universal property. It ensures that the environment cannot generate new stable fixed points of the renormalization group flow. Thus, the LL always flows toward either conducting or insulating phase. Phases are separated by a sharp boundary which is shifted by the influence of the environment. Our results are relevant, for example, for low-energy transport in (i) an interacting quantum wire or a carbon nanotube where the electrons are coupled to the acoustic phonons scattered by the lattice defect; (ii) a mixture of interacting fermionic and bosonic cold atoms where the bosonic modes are scattered due to an abrupt local change of the interaction; (iii) mesoscopic electric circuits.

Ocular biotribology and the contact lens:Surface interactions and ocular response

Biotribology is essentially the study of friction, lubrication and wear in biological systems. The area has been widely studied in relation to the behaviour of synovial joints and the design and behaviour of hip joint prostheses, but only in the last decade have serious studies been extended to the eye. In the ocular environment - as distinct from articular joints - wear is not a major factor. Both lubrication and friction are extremely important, however; this is particularly the case in the presence of the contact lens, which is a medical device important not only in vision correction but also as a therapeutic bandage for the compromised cornea. This chapter describes the difficulty in replicating experimental conditions that accurately reflect the complex nature of the ocular environment together with the factors such as load and rate of travel of the eyelid, which is the principal moving surface in the eye. Results obtained across a range of laboratories are compared.

Glue ear, hearing loss and IQ:an association moderated by the child's home environment

BACKGROUND: Glue ear or otitis media with effusion (OME) is common in children and may be associated with hearing loss (HL). For most children it has no long lasting effects on cognitive development but it is unclear whether there are subgroups at higher risk of sequelae. OBJECTIVES: To examine the association between a score comprising the number of times a child had OME and HL (OME/HL score) in the first four/five years of life and IQ at age 4 and 8. To examine whether any association between OME/HL and IQ is moderated by socioeconomic, child or family factors. METHODS: Prospective, longitudinal cohort study: the Avon Longitudinal Study of Parents and Children (ALSPAC). 1155 children tested using tympanometry on up to nine occasions and hearing for speech (word recognition) on up to three occasions between age 8 months and 5 years. An OME/HL score was created and associations with IQ at ages 4 and 8 were examined. Potential moderators included a measure of the child's cognitive stimulation at home (HOME score). RESULTS: For the whole sample at age 4 the group with the highest 10% OME/HL scores had performance IQ 5 points lower [95% CI -9, -1] and verbal IQ 6 points lower [95% CI -10, -3] than the unaffected group. By age 8 the evidence for group differences was weak. There were significant interactions between OME/HL and the HOME score: those with high OME/HL scores and low 18 month HOME scores had lower IQ at age 4 and 8 than those with high OME/HL scores and high HOME scores. Adjusted mean differences ranged from 5 to 8 IQ points at age 4 and 8. CONCLUSIONS: The cognitive development of children from homes with lower levels of cognitive stimulation is susceptible to the effects of glue ear and hearing loss.