Investigation of micro-devices for neurobiological applications

The aim of this project is to integrate neuronal cell culture with commercial or in-house built micro-electrode arrays and MEMS devices. The resulting device is intended to support neuronal cell culture on its surface, expose specific portions of a neuronal population to different environments using microfluidic gradients and stimulate/record neuronal electrical activity using micro-electrode arrays. Additionally, through integration of chemical surface patterning, such device can be used to build neuronal cell networks of specific size, conformation and composition. The design of this device takes inspiration from the nervous system because its development and regeneration are heavily influenced by surface chemistry and fluidic gradients. Hence, this device is intended to be a step forward in neuroscience research because it utilizes similar concepts to those found in nature. The large part of this research revolved around solving technical issues associated with integration of biology, surface chemistry, electrophysiology and microfluidics. Commercially available microelectrode arrays (MEAs) are mechanically and chemically brittle making them unsuitable for certain surface modification and micro-fluidic integration techniques described in the literature. In order to successfully integrate all the aspects into one device, some techniques were heavily modified to ensure that their effects on MEA were minimal. In terms of experimental work, this thesis consists of 3 parts. The first part dealt with characterization and optimization of surface patterning and micro-fluidic perfusion. Through extensive image analysis, the optimal conditions required for micro-contact printing and micro-fluidic perfusion were determined. The second part used a number of optimized techniques and successfully applied these to culturing patterned neural cells on a range of substrates including: Pyrex, cyclo-olefin and SiN coated Pyrex. The second part also described culturing neurons on MEAs and recording electrophysiological activity. The third part of the thesis described integration of MEAs with patterned neuronal culture and microfluidic devices. Although integration of all methodologies proved difficult, a large amount of data relating to biocompatibility, neuronal patterning, electrophysiology and integration was collected. Original solutions were successfully applied to solve a number of issues relating to consistency of micro printing and microfluidic integration leading to successful integration of techniques and device components.

Matching search in fractal video compression and its parallel implementation in distributed computing environments

Fractal video compression is a relatively new video compression method. Its attraction is due to the high compression ratio and the simple decompression algorithm. But its computational complexity is high and as a result parallel algorithms on high performance machines become one way out. In this study we partition the matching search, which occupies the majority of the work in a fractal video compression process, into small tasks and implement them in two distributed computing environments, one using DCOM and the other using .NET Remoting technology, based on a local area network consists of loosely coupled PCs. Experimental results show that the parallel algorithm is able to achieve a high speedup in these distributed environments.

A preliminary investigation of the in vitro bioactivity of white Portland cement

Freshly-mixed and partially-cured ordinary Portland cement (OPC) pastes have been shown to exhibit good biological compatibility with a range of cells and tissue-types; particularly those associated with bone formation. Formulations based on OPC have been used as dental restoratives and are now being investigated for their potential use in orthopaedic repair. Despite the current clinical interest in OPCs, very little is known about their chemistry in the physiological environment. In this respect, research to investigate aspects of the interactions between a white Portland cement (WPC) paste and simulated body fluid (SBF) has been carried out in vitro. Exposure to SBF has been found to promote the precipitation of a layer of 'bone-like' hydroxyapatite on the surface of WPC paste which underpins its ability to integrate with living tissue. The dissolution of portlandite and formation of calcite were also observed on contact with SBF.

Realizing an Applied Gaming Ecosystem: Towards Supporting Service-based Innovation Knowledge Management and Transfer

The EU-based industry for non-leisure games is an emerging business. As such it is still fragmented and needs to achieve critical mass to compete globally. Nevertheless its growth potential is widely recognized. To become competitive the relevant applied gaming communities and SMEs require support by fostering the generation of innovation potential. The European project Realizing an Applied Gaming Ecosystem (RAGE) is aiming at supporting this challenge. RAGE will help by making available an interoperable set of advanced technology assets, tuned to applied gaming, as well as proven practices of using asset-based applied games in various real-world contexts, and finally a centralized access to a wide range of applied gaming software modules, services and related document, media, and educational resources within an online community portal called the RAGE Ecosystem. It is based on an integrational, user-centered approach of Knowledge Management and Innovation Processes in the shape of a service-based implementation.

Production and characterization of a trehalolipid biosurfactant produced by the novel marine bacteriumRhodococcussp., strain PML026

AIMS: The aim of this study was to evaluate biosurfactant production by a novel marine Rhodococcus sp., strain PML026 and characterize the chemical nature and properties of the biosurfactant. METHODS AND RESULTS: A novel marine bacterium (Rhodococcus species; strain PML026) was shown to produce biosurfactant in the presence of hydrophobic substrate (sunflower oil). Biosurfactant production (identified as a trehalolipid) was monitored in whole-batch cultures (oil layer and aqueous phase), aqueous phase (no oil layer) and filtered (0·2mum) aqueous phase (no oil or cells; extracellular) and was shown to be closely associated with growth/biomass production. Extracellular trehalolipid levels increased postonset of stationary growth phase. Purified trehalolipid was able to reduce the surface tension of water to 29mN m(-1) at Critical Micellar Concentration (CMC) of c. 250mgl(-1) and produced emulsions that were stable to a wide range of conditions (pH 2-10, temperatures of 20-100°C and NaCl concentrations of 5-25% w/v). Separate chemical analyses of the intact trehalolipid and its constituents demonstrated the compound was in fact a mixture of homologues (>1180MW) consisting of a trehalose moiety esterified to a series of straight chain and hydroxylated fatty acids. CONCLUSIONS: The trehalolipid biosurfactant produced by the novel marine strain Rhodococcus sp. PML026 was characterized and exhibited high surfactant activity under a wide range of conditions. SIGNIFICANCE AND IMPACT OF STUDY: Strain PML026 of Rhodococcus sp. is a potential candidate for bioremediation or biosurfactant production for various applications.

Optimal foraging strategies: Lévy walks balance searching and patch exploitation under a very broad range of conditions

While evidence for optimal random search patterns, known as Lévy walks, in empirical movement data is mounting for a growing list of taxa spanning motile cells to humans, there is still much debate concerning the theoretical generality of Lévy walk optimisation. Here, using a new and robust simulation environment, we investigate in the most detailed study to date (24×10(6) simulations) the foraging and search efficiencies of 2-D Lévy walks with a range of exponents, target resource distributions and several competing models. We find strong and comprehensive support for the predictions of the Lévy flight foraging hypothesis and in particular for the optimality of inverse square distributions of move step-lengths across a much broader range of resource densities and distributions than previously realised. Further support for the evolutionary advantage of Lévy walk movement patterns is provided by an investigation into the 'feast and famine' effect, with Lévy foragers in heterogeneous environments experiencing fewer long 'famines' than other types of searchers. Therefore overall, optimal Lévy foraging results in more predictable resources in unpredictable environments.

XoxF encoding an alternative methanol dehydrogenase is widespread in coastal marine environments

The xoxF gene, encoding a pyrroloquinoline quinone-dependent methanol dehydrogenase, is found in all known proteobacterial methylotrophs. In several newly discovered methylotrophs, XoxF is the active methanol dehydrogenase, catalysing the oxidation of methanol to formaldehyde. Apart from that, its potential role in methylotrophy and carbon cycling is unknown. So far, the diversity of xoxF in the environment has received little attention. We designed PCR primer sets targeting clades of the xoxF gene, and used 454 pyrosequencing of PCR amplicons obtained from DNA of four coastal marine environments for a unique assessment of the diversity of xoxF in these habitats. Phylogenetic analysis of the data obtained revealed a high diversity of xoxF genes from two of the investigated clades, and substantial differences in sequence composition between environments. Sequences were classified as being related to a wide range of both methylotrophs and non-methylotrophs from Alpha-, Beta- and Gammaproteobacteria. The most prominent sequences detected were related to the family Rhodobacteraceae, the genus Methylotenera and the OM43 clade of Methylophilales, and are thus related to organisms that employ XoxF for methanol oxidation. Furthermore, our analyses revealed a high degree of so far undescribed sequences, suggesting a high number of unknown species in these habitats.

Xanthoria parietina as a biomonitor of airborne heavy metal pollution in forest sites in the North East of Morocco

Xanthoria parietina, common foliose lichen, growing in its natural habitat, was analysed for the concentration of five heavy metals (Fe, Cr, Zn, Pb and Cu) from different forest sites of North East of Morocco (Kenitra, Sidi Boughaba, Mkhinza, Ceinture Verte near Temara city, Skhirate, Bouznika and Mohammedia). The quantification was carried out by inductively coupled plasma - atomic emission spectrometry (ICP-AES). Results were highly significant p<0,001. The concentration of metals is correlated with the vehicular activity and urbanization. The total metal concentration is highest at the Kenitra area, followed by Ceinture Verte site near Temara city, which experience heavy traffic throughout the year. Scanning electron microscopy (SEM) of particulate matter on lichen of Xanthoria parietina was assessed as a complementary technique to wet chemical analysis for source apportionment of airborne contaminant. Analysis revealed high level of Cu, Cr, Zn and Pb in samples near roads.  

Upregulation of osteopontin and alpha B crystallin in the normal-appearing white matter of multiple sclerosis: an immunohistochemical study utilizing tissue microarrays

Tissue microarrays assembled from control and multiple sclerosis (MS) brain tissue have been used to assess the expression patterns and cellular distribution of two antigens, the proinflammatory cytokine osteopontin and the inducible heat shock protein alpha B -crystallin, which have previously been implicated in MS pathogenesis. Tissue cores were taken from paraffin-embedded donor blocks containing chronic active or chronic inactive plaques and normal-appearing white matter (NAWM) in seven MS cases, and white matter (WM) in five control cases. Expression patterns of both proteins were assessed against myelin density and microglial activation in the different tissue categories. Both proteins showed increased expression in all categories of MS tissue compared with control WM. The results indicate progressive up-regulation of expression of osteopontin with increased plaque activity, while elevation of alpha B-crystallin expression in MS tissue was independent of demyelination. In MS NAWM a significant correlation was observed between high levels of expression of osteopontin and alpha B -crystallin. Osteopontin expression was predominantly confined to astrocytes throughout MS tissues. alpha B -crystallin was expressed on astrocytes, oligodendrocytes and occasionally on demyelinated axons. Taken together, these data indicate a wider distribution of osteopontin and alpha B -crystallin in MS tissues than previously described and support their proposed role in MS pathogenesis.

Three-dimensional macroporous silicon photonic crystal with large photonic band gap

Three-dimensional photonic crystals based on macroporous silicon are fabricated by photoelectrochemical etching and subsequent focused-ion-beam drilling. Reflection measurements show a high reflection in the range of the stopgap and indicate the spectral position of the complete photonic band gap. The onset of diffraction which might influence the measurement is discussed.

Variation in offspring size towards the high elevational range edge of a montane annual

Understanding the ecological determinants of species’ distribution is a fundamental goal of ecology, and is increasingly important with changing limits to species’ range. Species often reach distributional limits on gradients of resource availability, but the extent to which offspring provisioning varies towards range limits is poorly understood. Selection is generally expected to favour higher provisioning of individual offspring in environments with short growing seasons and limited moisture, nutrients, or hosts for parasitism. However, individual provisioning may decline if parent size is limited by resources. This thesis focuses on three major questions: 1) does seed size vary over an elevational gradient? 2) does this variation respond adaptively towards the range limit? and 3) is potential elevational variation environmentally or genetically controlled? I tested variation in seed investment towards the upper elevational limit of the hemiparasitic annual herb Rhinanthus minor, sampled across an elevational range of 1,000m in the Rocky Mountains of Alberta, Canada. I also used a reciprocal transplant experiment to address the heritability of seed mass. Seed mass increased marginally towards higher elevations, while seed number and plant size declined. There was a strong elevational increase in seed mass scaled by overall plant size. Therefore, investment in individual seeds was higher towards the upper range edge, indicating potential adaptation of the reproductive strategy to allow for establishment in marginal environments. Genetic, environmental, and genotype-by-environment interactions were observed in transplanted populations, but the relative proportions of these effects on seed size were unclear.

Phenotypic diversity amongst strains of Pleurotus sajor-caju: implications for cultivation in and environments

In arid regions, biodiversity and biomass are limited by water availability, and this problem has been compounded by desertification associated with global climate change. The saprotrophic macrofungi that are indigenous to hot subtropical and tropical regions, such as Pleurotus spp., can play key roles in water sequestration, nutrient cycling, human nutrition, and bioremediation of waste materials. We studied 15 strains of Pleurotus sajor-caju, a widespread and phenotypically-diverse species, to establish variability in growth response and primordium development over a range of stress parameters: osmotic potential (-0.5 to -5 MPa), temperature (5-40 degrees C) and pH (2-12). The initiation of primordia precedes basidiome production and therefore represents a key stage in bioremediation strategies and fungi-driven nutrient cycles. Primordia were produced at low pH (4-6), at suboptimal growth temperatures (<or =25 degrees C), and under moderate water stress (-0.5 to -3.5 MPa). Although the growth windows for different strains were similar, their maximum growth rates and the optimum conditions for growth varied. We discuss the phenotypic diversity of Pleurotus strains and discuss their potential for cultivation, bioremediation and ecological regeneration.