Mapping quantitative trait loci in a wild population using linkage and linkage disequilibrium analyses

Historical information can be used, in addition to pedigree, traits and genotypes, to map quantitative trait locus (QTL) in general populations via maximum likelihood estimation of variance components. This analysis is known as linkage disequilibrium (LD) and linkage mapping, because it exploits both linkage in families and LD at the population level. The search for QTL in the wild population of Soay sheep on St. Kilda is a proof of principle. We analysed the data from a previous study and confirmed some of the QTLs reported. The most striking result was the confirmation of a QTL affecting birth weight that had been reported using association tests but not when using linkage-based analyses. Copyright © Cambridge University Press 2010.

Candidate gene analysis for quantitative traits using the transmission disequilibrium test : the example of the melanocortin 4-receptor in pigs

Population-wide associations between loci due to linkage disequilibrium can be used to map quantitative trait loci (QTL) with high resolution. However, spurious associations between markers and QTL can also arise as a consequence of population stratification. Statistical methods that cannot differentiate between loci associations due to linkage disequilibria from those caused in other ways can render false-positive results. The transmission-disequilibrium test (TDT) is a robust test for detecting QTL. The TDT exploits within-family associations that are not affected by population stratification. However, some TDTs are formulated in a rigid-form, with reduced potential applications. In this study we generalize TDT using mixed linear models to allow greater statistical flexibility. Allelic effects are estimated with two independent parameters: one exploiting the robust within-family information and the other the potentially biased between-family information. A significant difference between these two parameters can be used as evidence for spurious association. This methodology was then used to test the effects of the fourth melanocortin receptor (MC4R) on production traits in the pig. The new analyses supported the previously reported results; i.e., the studied polymorphism is either causal of in very strong linkage disequilibrium with the causal mutation, and provided no evidence for spurious association.

Cell death control : the interplay of apoptosis and autophagy in the pathogenicity of sclerotinia sclerotiorum

Programmed cell death is characterized by a cascade of tightly controlled events that culminate in the orchestrated death of the cell. In multicellular organisms autophagy and apoptosis are recognized as two principal means by which these genetically determined cell deaths occur. During plant-microbe interactions cell death programs can mediate both resistant and susceptible events. Via oxalic acid (OA), the necrotrophic phytopathogen Sclerotinia sclerotiorum hijacks host pathways and induces cell death in host plant tissue resulting in hallmark apoptotic features in a time and dose dependent manner. OA-deficient mutants are non-pathogenic and trigger a restricted cell death phenotype in the host that unexpectedly exhibits markers associated with the plant hypersensitive response including callose deposition and a pronounced oxidative burst, suggesting the plant can recognize and in this case respond, defensively. The details of this plant directed restrictive cell death associated with OA deficient mutants is the focus of this work. Using a combination of electron and fluorescence microscopy, chemical effectors and reverse genetics, we show that this restricted cell death is autophagic. Inhibition of autophagy rescued the non-pathogenic mutant phenotype. These findings indicate that autophagy is a defense response in this necrotrophic fungus/plant interaction and suggest a novel function associated with OA; namely, the suppression of autophagy. These data suggest that not all cell deaths are equivalent, and though programmed cell death occurs in both situations, the outcome is predicated on who is in control of the cell death machinery. Based on our data, we suggest that it is not cell death per se that dictates the outcome of certain plant-microbe interactions, but the manner by which cell death occurs that is crucial.

Qualitative methods in information systems research

Qualitative research methods are widely accepted in Information Systems and multiple approaches have been successfully used in IS qualitative studies over the years. These approaches include narrative analysis, discourse analysis, grounded theory, case study, ethnography and phenomenological analysis. Guided by critical, interpretive and positivist epistemologies (Myers 1997), qualitative methods are continuously growing in importance in our research community. In this special issue, we adopt Van Maanen's (1979: 520) definition of qualitative research as an umbrella term to cover an “array of interpretive techniques that can describe, decode, translate, and otherwise come to terms with the meaning, not the frequency, of certain more or less naturally occurring phenomena in the social world”. In the call for papers, we stated that the aim of the special issue was to provide a forum within which we can present and debate the significant number of issues, results and questions arising from the pluralistic approach to qualitative research in Information Systems. We recognise both the potential and the challenges that qualitative approaches offers for accessing the different layers and dimensions of a complex and constructed social reality (Orlikowski, 1993). The special issue is also a response to the need to showcase the current state of the art in IS qualitative research and highlight advances and issues encountered in the process of continuous learning that includes questions about its ontology, epistemological tenets, theoretical contributions and practical applications.

Australia's disabling income support system : tracing the history of the Australian disability income support system 1908 to 2007 : disablism, citizenship and the basic income proposal

The present study examined the historical basis of the Australian disability income support system from 1908 to 2007. Although designed as a safety net for people with a disability, the disability income support system within Australia has been highly targeted. The original eligibility criteria of "permanently incapacitated for work", medical criteria and later "partially capacitated for work" potentially contained ideological inferences that permeated across the time period. This represents an important area for study given the potential consequence for disability income support to marginalise people with a disability. Social policy and disability policy theorists, including Saunders (2007, Social Policy Research Centre [SPRC]) and Gibilisco (2003) have provided valuable insight into some of the effects of disability policy and poverty. Yet while these theorists argued for some form of income support they did not propose a specific form of income security for further exploration. Few studies have undertaken a comprehensive review of the history of disability income support within the Australian context. This thesis sought to redress these gaps by examining disability income support policy within Australia. The research design consisted of an in-depth critical historical-comparative policy analysis methodology. The use of critical historical-comparative policy analysis allowed the researcher to trace the construction of disability within the Australian disability income support policy across four major historical epochs. A framework was developed specifically to guide analysis of the data. The critical discourse analysis method helped to understand the underlying ideological dimensions that led to the predominance of one particular approach over another. Given this, the research purpose of the study centred on: i. Tracing the history of the Australian disability income support system. ii. Examining the historical patterns and ideological assumptions over time. iii. Exploring the historical patterns and ideological assumptions underpinning an alternative model (Basic Income) and the extent to which each model promotes the social citizenship of people with a disability. The research commitment to a social-relational ontology and the quest for social change centred on the idea that "there has to be a better way" in the provision of disability income support. This theme of searching for an alternative reality in disability income support policy resonated throughout the thesis. This thesis found that the Australian disability income support system is disabling in nature and generates categories of disability on the basis of ableness. From the study, ableness became a condition for citizenship. This study acknowledged that, in reality, income support provision reflects only one aspect of the disabling nature of society which requires redressing. Although there are inherent tensions in any redistributive strategy, the Basic Income model potentially provides an alternative to the Australian disability income support system, given its grounding in social citizenship. The thesis findings have implications for academics, policy-makers and practitioners in terms of developing better ways to understand disability constructs in disability income support policy. The thesis also makes a contribution in terms of promoting income support policies based on the rights of all people, not just a few.

Using Wikipedia to improve web service discovery

Building and maintaining software are not easy tasks. However, thanks to advances in web technologies, a new paradigm is emerging in software development. The Service Oriented Architecture (SOA) is a relatively new approach that helps bridge the gap between business and IT and also helps systems remain exible. However, there are still several challenges with SOA. As the number of available services grows, developers are faced with the problem of discovering the services they need. Public service repositories such as Programmable Web provide only limited search capabilities. Several mechanisms have been proposed to improve web service discovery by using semantics. However, most of these require manually tagging the services with concepts in an ontology. Adding semantic annotations is a non-trivial process that requires a certain skill-set from the annotator and also the availability of domain ontologies that include the concepts related to the topics of the service. These issues have prevented these mechanisms becoming widespread. This thesis focuses on two main problems. First, to avoid the overhead of manually adding semantics to web services, several automatic methods to include semantics in the discovery process are explored. Although experimentation with some of these strategies has been conducted in the past, the results reported in the literature are mixed. Second, Wikipedia is explored as a general-purpose ontology. The benefit of using it as an ontology is assessed by comparing these semantics-based methods to classic term-based information retrieval approaches. The contribution of this research is significant because, to the best of our knowledge, a comprehensive analysis of the impact of using Wikipedia as a source of semantics in web service discovery does not exist. The main output of this research is a web service discovery engine that implements these methods and a comprehensive analysis of the benefits and trade-offs of these semantics-based discovery approaches.

Exercise-recruited NK cells display exercise-associated eHSP-70

It is hypothesized that increased plasma or serum concentrations of extracellular heat shock proteins (eHSP) serve as a danger signal to the innate immune system. Cellular binding of eHSP leads to activation of NK cells and monocytes, as measured by their increased cytokine production, mitotic division and killing capacity. We examined whether eHSP binds to NK lymphocytes in vivo in athletes performing endurance exercise in the heat. Eighteen trained male runners ran at 70% VO2max at 35 degrees C and 40% relative humidity. Venous blood collected before, after and 1.5 h after exercise was analysed for leukocyte distribution, phenotype and eHSP70. NK cell-enriched samples were examined for co-localization of CD94 and eHSP70 expression. Plasma eHSP-70 concentration was measured by ELISA. Subjects ran for approximately 50 min, which elicited a reversible leukocytosis. NK cell count increased 83% (p < 0.01) immediately after exercise, then decreased to 66% of the resting level 1.5 h after exercise (p < 0.05). Plasma eHSP concentration increased 167% after exercise and remained elevated (by up to 71%) 1.5 h after exercise (p < 0.01). eHSP was expressed on both NK cells and monocytes at all times; the count of NK cells positive for eHSP doubled from 0.04 +/- 0.02 10(9)/L (mean +/- SD) to 0.08 +/- 0.06 10(9)/L after exercise. In summary, exercise in the heat increased free plasma eHSP concentration, and the eHSP co-localized with CD94 on NK cells. These data confirm the link between exercise and activation of the innate immune system.

Beyond knowledge : an insight into the practice of a learning support teacher

Increasingly, schools are being asked to meet the challenges of providing inclusive classrooms for all children. Inclusion is no longer about special education for a special group of students. It is about school improvement in order to bring about the changes that are needed to classroom practices to ensure the improvement of student learning outcomes. Inclusion is no longer a policy initiative. Rather it has been transformed to become a process that moves a school towards inclusive practices that will result in school improvement, heightened student learning outcomes and greater opportunities for all students to gain equal access to education. This study focuses on the challenge of diversity as it translates into implementing inclusive practices across two secondary school contexts. I have undertaken this research in my role as a Learning Support Teacher over a period of five years. Central to my research is a constructivist ontology and a practice epistemology that aligns with a practitioner research methodology of action research. Seven generalisable propositions have emerged from this research that inform the strategies I am using to more easily accommodate legislated inclusivitiy. These propositions include: 1. School communities need to share a common understanding of equity. 2. The school principal must provide overt leadership in moving towards an inclusive school culture. 3. A whole-school approach is needed to narrow the gap between inclusion rhetoric and classroom practice. 4. Pedagogical reform is the most effective strategy for catering for diverse student learning needs. 5. Differentiating curriculum is achieved when collaborative planning teams develop appropriate units of work. 6. School communities need to make a commitment to gather, share and manage relevant information concerning students. 7. The Learning Support Teacher needs to be repositioned within a curriculum planning team.

The interplay between chondrocyte redifferentiation pellet size and oxygen concentration

Chondrocytes dedifferentiate during ex vivo expansion on 2-dimensional surfaces. Aggregation of the expanded cells into 3-dimensional pellets, in the presence of induction factors, facilitates their redifferentiation and restoration of the chondrogenic phenotype. Typically 1×105–5×105 chondrocytes are aggregated, resulting in “macro” pellets having diameters ranging from 1–2 mm. These macropellets are commonly used to study redifferentiation, and recently macropellets of autologous chondrocytes have been implanted directly into articular cartilage defects to facilitate their repair. However, diffusion of metabolites over the 1–2 mm pellet length-scales is inefficient, resulting in radial tissue heterogeneity. Herein we demonstrate that the aggregation of 2×105 human chondrocytes into micropellets of 166 cells each, rather than into larger single macropellets, enhances chondrogenic redifferentiation. In this study, we describe the development of a cost effective fabrication strategy to manufacture a microwell surface for the large-scale production of micropellets. The thousands of micropellets were manufactured using the microwell platform, which is an array of 360×360 µm microwells cast into polydimethylsiloxane (PDMS), that has been surface modified with an electrostatic multilayer of hyaluronic acid and chitosan to enhance micropellet formation. Such surface modification was essential to prevent chondrocyte spreading on the PDMS. Sulfated glycosaminoglycan (sGAG) production and collagen II gene expression in chondrocyte micropellets increased significantly relative to macropellet controls, and redifferentiation was enhanced in both macro and micropellets with the provision of a hypoxic atmosphere (2% O2). Once micropellet formation had been optimized, we demonstrated that micropellets could be assembled into larger cartilage tissues. Our results indicate that micropellet amalgamation efficiency is inversely related to the time cultured as discreet microtissues. In summary, we describe a micropellet production platform that represents an efficient tool for studying chondrocyte redifferentiation and demonstrate that the micropellets could be assembled into larger tissues, potentially useful in cartilage defect repair.

Humanised xenograft models of bone metastasis revisited : novel insights into species-specific mechanisms of cancer cell osteotropism

The determinants and key mechanisms of cancer cell osteotropism have not been identified, mainly due to the lack of reproducible animal models representing the biological, genetic and clinical features seen in humans. An ideal model should be capable of recapitulating as many steps of the metastatic cascade as possible, thus facilitating the development of prognostic markers and novel therapeutic strategies. Most animal models of bone metastasis still have to be derived experimentally as most syngeneic and transgeneic approaches do not provide a robust skeletal phenotype and do not recapitulate the biological processes seen in humans. The xenotransplantation of human cancer cells or tumour tissue into immunocompromised murine hosts provides the possibility to simulate early and late stages of the human disease. Human bone or tissue-engineered human bone constructs can be implanted into the animal to recapitulate more subtle, species-specific aspects of the mutual interaction between human cancer cells and the human bone microenvironment. Moreover, the replication of the entire "organ" bone makes it possible to analyse the interaction between cancer cells and the haematopoietic niche and to confer at least a partial human immunity to the murine host. This process of humanisation is facilitated by novel immunocompromised mouse strains that allow a high engraftment rate of human cells or tissue. These humanised xenograft models provide an important research tool to study human biological processes of bone metastasis.

Stage-specific embryonic antigen-4 is not a marker for chondrogenic and osteogenic potential in cultured chondrocytes and mesenchymal progenitor cells

One important challenge for regenerative medicine is to produce a clinically relevant number of cells with consistent tissue-forming potential. Isolation and expansion of cells from skeletal tissues results in a heterogeneous population of cells with variable regenerative potential. A more consistent tissue formation could be achieved by identification and selection of potent progenitors based on cell surface molecules. In this study, we assessed the expression of stage-specific embryonic antigen-4 (SSEA-4), a classic marker of undifferentiated stem cells, and other surface markers in human articular chondrocytes (hACs), osteoblasts, and bone marrow-derived mesenchymal stromal cells (bmMSCs) and characterized their differentiation potential. Further, we sorted SSEA-4-expressing hACs and followed their potential to proliferate and to form cartilage in vitro. Cells isolated from cartilage and bone exhibited remarkably heterogeneous SSEA-4 expression profiles in expansion cultures. SSEA-4 expression levels increased up to approximately 5 population doublings, but decreased following further expansion and differentiation cultures; levels were not related to the proliferation state of the cells. Although SSEA-4-sorted chondrocytes showed a slightly better chondrogenic potential than their SSEA-4-negative counterparts, differences were insufficient to establish a link between SSEA-4 expression and chondrogenic potential. SSEA-4 levels in bmMSCs also did not correlate to the cells' chondrogenic and osteogenic potential in vitro. SSEA-4 is clearly expressed by subpopulations of proliferating somatic cells with a MSC-like phenotype. However, the predictive value of SSEA-4 as a specific marker of superior differentiation capacity in progenitor cell populations from adult human tissue and even its usefulness as a stem cell marker appears questionable.

Construct Redundancy in Process Modeling Grammars: Improving the Explanatory Power of Ontological Analysis

Conceptual modelling supports developers and users of information systems in areas of documentation, analysis or system redesign. The ongoing interest in the modelling of business processes has led to a variety of different grammars, raising the question of the quality of these grammars for modelling. An established way of evaluating the quality of a modelling grammar is by means of an ontological analysis, which can determine the extent to which grammars contain construct deficit, overload, excess or redundancy. While several studies have shown the relevance of most of these criteria, predictions about construct redundancy have yielded inconsistent results in the past, with some studies suggesting that redundancy may even be beneficial for modelling in practice. In this paper we seek to contribute to clarifying the concept of construct redundancy by introducing a revision to the ontological analysis method. Based on the concept of inheritance we propose an approach that distinguishes between specialized and distinct construct redundancy. We demonstrate the potential explanatory power of the revised method by reviewing and clarifying previous results found in the literature.

Mapping semantic knowledge for unsupervised text categorisation

Text categorisation is challenging, due to the complex structure with heterogeneous, changing topics in documents. The performance of text categorisation relies on the quality of samples, effectiveness of document features, and the topic coverage of categories, depending on the employing strategies; supervised or unsupervised; single labelled or multi-labelled. Attempting to deal with these reliability issues in text categorisation, we propose an unsupervised multi-labelled text categorisation approach that maps the local knowledge in documents to global knowledge in a world ontology to optimise categorisation result. The conceptual framework of the approach consists of three modules; pattern mining for feature extraction; feature-subject mapping for categorisation; concept generalisation for optimised categorisation. The approach has been promisingly evaluated by compared with typical text categorisation methods, based on the ground truth encoded by human experts.

Limbal mesenchymal stromal cells (L-MSC) display immunosuppressive properties across donor and species boundaries

Purpose: We have evaluated the immunosuppressive properties of L-MSC with the view to using these cells in allogeneic cell therapies for corneal disorders. We hypothesized that L-MSC cultures would suppress T-cell activation, in a similar way to those established from human bone marrow (BM-MSC). Methods: MSC cultures were established from the limbal stroma of cadaveric donor eye tissue (up to 1 week postmortem) using either conventional serum-supplemented growth medium or a commercial serum-free medium optimized for bone marrow derived MSC (MesenCult-XF system). The MSC phenotype was examined by flow cytometry according to current and emerging markers for human MSC. Immunosuppressive properties were assessed using a mixed lymphocyte reaction (MLR) assay, whereby the white cell fraction from two immunologically incompatible blood donors are cultured together in direct contact with growth arrested MSC. T-cell activation (proliferation) was measured by uptake of tritiated thymidine. Human L-MSC were tested in parallel with human BM-MSC and rabbit L-MSC. Human and rabbit L-MSC were also tested for their ability to stimulate the growth of limbal epithelial (LE) cells in colony formation assays (for both human as well as rabbit LE cells). Results: L-MSC cultures were >95% negative for CD34, CD45 and HLA-DR and positive for CD73, CD90, CD105 and HLA-ABC. Modest levels (30%) of CD146 expression were observed for L-MSC cultures grown in serum-supplemented growth medium, but not those grown in MesenCult-XF. All MSC cultures derived from both human and rabbit tissue suppressed T-cell activation to varying degrees according to culture technique and species (MesenCult-XF >> serum-fed cultures, rabbit L-MSC >> human L-MSC). All L-MSC stimulated colony formation by LE cells irrespectively of the combination of cell species used. Conclusions: L-MSC display immunosuppressive qualities, in addition to their established non-immunogenic cell surface marker profile, and stimulate LE cell growth in vitro across species boundaries. These results support the potential use of allogeneic or even xenogeneic L-MSC in the treatment of corneal disorders.

Indigenous/digital heterogeneities : an actor-network-theory approach

This thesis analysed the theoretical and ontological issues of previous scholarship concerning information technology and indigenous people. As an alternative, the thesis used the framework of actor-network-theory, especially through historiographical and ethnographic techniques. The thesis revealed an assemblage of indigenous/digital enactments striving for relevance and avoiding obsolescence. It also recognised heterogeneities- including user-ambivalences, oscillations, noise, non-coherences and disruptions - as part of the milieu of the daily digital lives of indigenous people. By taking heterogeneities into account, the thesis ensured that the data “speaks for itself” and that social inquiry is not overtaken by ideology and ontology.