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.

Exploiting the bioactive potential of marine sponge microbiota

Endospore-forming bacteria are often isolated from different marine sponges, but their abundance varies, and they are frequently missed by culture-independent studies. Within endospore-formers, Bacillus are renowned for the production of antimicrobials and other compounds of medical and industrial importance. Although this group has been well studied in many different environments, very little is known about the actual diversity and properties of sporeformers associated with marine sponges. Identification of the endospore-forming bacteria associated with the marine sponges; Haliclona simulans, Amphilectus fucorum and Cliona celata, has uncovered an abundant and diverse microbial population composed of Bacillus, Paenibacillus, Solibacillus, Halobacillus and Viridibacillus species. This diversity appears to be overlooked by other non-targeted approaches where spore-formers are masked by more dominant species within the ecosystem. In addition to the identification of two antibiotic resistant plasmids, this bank of sporeformers produce a range of bioactive compounds. New antimicrobial compounds are urgently needed to combat the spread of multidrug resistant pathogens, as few new options are entering the drug discovery pipelines for clinical trials. Based on the results of this project, endospore-formers associated with marine sponges may hold the answer. The power of coupling functional based assays with genomic approaches has enabled us to identify a novel class 1 lantibiotic, subtilomycin, which is active against several clinically relevant pathogens. Subtilomycin is encoded in the genomes of all the marine sponge B. subtilis isolates analysed. They cluster together phylogenetically and form a distinct group from other sequenced B. subtilis strains. Regardless of its potential clinical relevance, subtilomycin may be providing these strains with a specific competitive advantage(s) within the stringent confines of the marine sponge environment. This work has outlined the industrial and biotechnological potential of marine sponge endospore-formers which appear to produce a cocktail of bioactive compounds. Genome sequencing of specific marine sponge isolates highlighted the importance of mining extreme environments and habitats for new lead compounds with potential therapeutic applications.

From field to fermentation: characterisation and application of non-dairy cultures in dairy foods

This thesis investigates the phenotypic and genotypic diversity of non-dairy L. lactis strains and their application to dairy fermentations. A bank of non-dairy lactococci were isolated from grass, vegetables and the bovine rumen. Subsequent analysis of these L. lactis strains revealed seven strains to possess cremoris genotypes which did not correlate with their observed phenotypes. Multi-locus sequence typing (MLST) and average nucleotide identity (ANI) highlighted the genetic diversity of lactis and cremoris subspecies. The application of these non-dairy lactococci to cheese production was also assessed. In milk, non-dairy strains formed diverse volatile profiles and selected strains were used as adjuncts in a mini Gouda-type cheese system. Sensory analysis showed non-dairy strains to be strongly associated with the development of off-flavours and bitterness. However, microfluidisation appeared to reduce bitterness. A novel bacteriophage, ɸL47, was isolated using the grass isolate L. lactis ssp. cremoris DPC6860 as a host. The phage, a member of the Siphoviridae, possessed a long tail fiber, previously unseen in dairy lactococcal phages. Genome sequencing revealed ɸL47 to be the largest sequenced lactococcal phage to date and owing to the high % similarity with ɸ949, a second member of the 949 group. Finally, to identify and characterise specific genes which may be important in niche adaptation and for applications to dairy fermentations, comparative genome sequence analysis was performed on L. lactis from corn (DPC6853), the bovine rumen (DPC6853) and grass (DPC6860). This study highlights the contribution of niche specialisation to the intra-species diversity of L. lactis and the adaptation of this organism to different environments. In summary this thesis describes the genetic diversity of L. lactis strains from outside the dairy environment and their potential application in dairy fermentations.

The differences in the social competence of children who attend integrated junior infant classes and children who attend segregated learning environments

There are a number of reasons why this researcher has decided to undertake this study into the differences in the social competence of children who attend integrated Junior Infant classes and children who attend segregated learning environments. Theses reasons are both personal and professional. My personal reasons stem from having grown up in a family which included both an aunt who presented with Down Syndrome and an uncle who presented with hearing impairment. Both of these relatives' experiences in our education system are interesting. My aunt was considered ineducable while her brother - my uncle - was sent to Dublin (from Cork) at six years of age to be educated by a religious order. My professional reasons, on the other hand, stemmed from my teaching experience. Having taught in both special and integrated classrooms it became evident to me that there was somewhat 'suspicion' attached to integration. Parents of children without disabilities questioned whether this process would have a negative impact on their children's education. While parents of children with disabilities debated whether integrated settings met the specific needs of their children. On the other hand, I always questioned whether integration and inclusiveness meant the same thing. My research has enabled me to find many answers. Increasingly, children with special educational needs (SEN) are attending a variety of integrated and inclusive childcare and education settings. This contemporary practice of educating children who present with disabilities in mainstream classrooms has stimulated vast interest on the impact of such practices on children with identified disabilities. Indeed, children who present with disabilities "fare far better in mainstream education than in special schools" (Buckley, cited in Siggins, 2001,p.25). However, educators and practitioners in the field of early years education and care are concerned with meeting the needs of all children in their learning environments, while also upholding high academic standards (Putman, 1993). Fundamentally, therefore, integrated education must also produce questions about the impact of this practice on children without identified special educational needs. While these questions can be addressed from the various areas of child development (i.e. cognitive, physical, linguistic, emotional, moral, spiritual and creative), this research focused on the social domain. It investigates the development of social competence in junior infant class children without identified disabilities as they experience different educational settings.

Repairing wireless sensor network connectivity in damaged environments

A wireless sensor network can become partitioned due to node failure, requiring the deployment of additional relay nodes in order to restore network connectivity. This introduces an optimisation problem involving a tradeoff between the number of additional nodes that are required and the costs of moving through the sensor field for the purpose of node placement. This tradeoff is application-dependent, influenced for example by the relative urgency of network restoration. In addition, minimising the number of relay nodes might lead to long routing paths to the sink, which may cause problems of data latency. This data latency is extremely important in wireless sensor network applications such as battlefield surveillance, intrusion detection, disaster rescue, highway traffic coordination, etc. where they must not violate the real-time constraints. Therefore, we also consider the problem of deploying multiple sinks in order to improve the network performance. Previous research has only parts of this problem in isolation, and has not properly considered the problems of moving through a constrained environment or discovering changes to that environment during the repair or network quality after the restoration. In this thesis, we firstly consider a base problem in which we assume the exploration tasks have already been completed, and so our aim is to optimise our use of resources in the static fully observed problem. In the real world, we would not know the radio and physical environments after damage, and this creates a dynamic problem where damage must be discovered. Therefore, we extend to the dynamic problem in which the network repair problem considers both exploration and restoration. We then add a hop-count constraint for network quality in which the desired locations can talk to a sink within a hop count limit after the network is restored. For each new problem of the network repair, we have proposed different solutions (heuristics and/or complete algorithms) which prioritise different objectives. We evaluate our solutions based on simulation, assessing the quality of solutions (node cost, movement cost, computation time, and total restoration time) by varying the problem types and the capability of the agent that makes the repair. We show that the relative importance of the objectives influences the choice of algorithm, and different speeds of movement for the repairing agent have a significant impact on performance, and must be taken into account when selecting the algorithm. In particular, the node-based approaches are the best in the node cost, and the path-based approaches are the best in the mobility cost. For the total restoration time, the node-based approaches are the best with a fast moving agent while the path-based approaches are the best with a slow moving agent. For a medium speed moving agent, the total restoration time of the node-based approaches and that of the path-based approaches are almost balanced.

Subterfuge-safe trust management for delegation of permissions in open environments

Open environments involve distributed entities interacting with each other in an open manner. Many distributed entities are unknown to each other but need to collaborate and share resources in a secure fashion. Usually resource owners alone decide who is trusted to access their resources. Since resource owners in open environments do not have a complete picture of all trusted entities, trust management frameworks are used to ensure that only authorized entities will access requested resources. Every trust management system has limitations, and the limitations can be exploited by malicious entities. One vulnerability is due to the lack of globally unique interpretation for permission specifications. This limitation means that a malicious entity which receives a permission in one domain may misuse the permission in another domain via some deceptive but apparently authorized route; this malicious behaviour is called subterfuge. This thesis develops a secure approach, Subterfuge Safe Trust Management (SSTM), that prevents subterfuge by malicious entities. SSTM employs the Subterfuge Safe Authorization Language (SSAL) which uses the idea of a local permission with a globally unique interpretation (localPermission) to resolve the misinterpretation of permissions. We model and implement SSAL with an ontology-based approach, SSALO, which provides a generic representation for knowledge related to the SSAL-based security policy. SSALO enables integration of heterogeneous security policies which is useful for secure cooperation among principals in open environments where each principal may have a different security policy with different implementation. The other advantage of an ontology-based approach is the Open World Assumption, whereby reasoning over an existing security policy is easily extended to include further security policies that might be discovered in an open distributed environment. We add two extra SSAL rules to support dynamic coalition formation and secure cooperation among coalitions. Secure federation of cloud computing platforms and secure federation of XMPP servers are presented as case studies of SSTM. The results show that SSTM provides robust accountability for the use of permissions in federation. It is also shown that SSAL is a suitable policy language to express the subterfuge-safe policy statements due to its well-defined semantics, ease of use, and integrability.

Salutogenesis: a new paradigm for pervasive computing in healthcare environments?

Salutogenesis is now accepted as a part of the contemporary model of disease: an individual is not only affected by pathogenic factors in the environment, but those that promote well-being or salutogenesis. Given that "environment" extends to include the built environment, promotion of salutogenesis has become part of the architectural brief for contemporary healthcare facilities, drawing on an increasing evidence-base. Salutogenesis is inextricably linked with the notion of person-environment "fit". MyRoom is a proposal for an integrated architectural and pervasive computing model, which enhances psychosocial congruence by using real-time data indicative of the individual's physical status to enable the environment of his/her room (colour, light, temperature) to adapt on an on-going basis in response to bio-signals. This work is part of the PRTLI-IV funded programme NEMBES, investigating the use of embedded technologies in the built environment. Different care contexts require variations in the model, and iterative prototyping investigating use in different contexts will progressively lead to the development of a fully-integrated adaptive salutogenic single-room prototype.

Complexity as key to designing cognitive-friendly environments for older people

The lived environment is the arena where our cognitive skills, preferences, and attitudes come together to determine our ability to interact with the world. The mechanisms through which lived environments can benefit cognitive health in older age are yet to be fully understood. The existing literature suggests that environments which are perceived as stimulating, usable and aesthetically appealing can improve or facilitate cognitive performance both in young and older age. Importantly, optimal stimulation for cognition seems to depend on experiencing sufficiently stimulating environments while not too challenging. Environmental complexity is an important contributor to determining whether an environment provides such an optimal stimulation. The present paper reviews a selection of studies which have explored complexity in relation to perceptual load, environmental preference and perceived usability to propose a framework which explores direct and indirect environmental influences on cognition, and to understand these influences in relation to aging processes. We identify ways to define complexity at different environmental scales, going from micro low-level perceptual features of scenes, to design qualities of proximal environments (e.g., streets, neighborhoods), to broad geographical areas (i.e., natural vs. urban environments). We propose that studying complexity at these different scales will provide new insight into the design of cognitive-friendly environments.