Construction of a global map of human gene expression : the process, tools and analysis

This thesis studies human gene expression space using high throughput gene expression data from DNA microarrays. In molecular biology, high throughput techniques allow numerical measurements of expression of tens of thousands of genes simultaneously. In a single study, this data is traditionally obtained from a limited number of sample types with a small number of replicates. For organism-wide analysis, this data has been largely unavailable and the global structure of human transcriptome has remained unknown. This thesis introduces a human transcriptome map of different biological entities and analysis of its general structure. The map is constructed from gene expression data from the two largest public microarray data repositories, GEO and ArrayExpress. The creation of this map contributed to the development of ArrayExpress by identifying and retrofitting the previously unusable and missing data and by improving the access to its data. It also contributed to creation of several new tools for microarray data manipulation and establishment of data exchange between GEO and ArrayExpress. The data integration for the global map required creation of a new large ontology of human cell types, disease states, organism parts and cell lines. The ontology was used in a new text mining and decision tree based method for automatic conversion of human readable free text microarray data annotations into categorised format. The data comparability and minimisation of the systematic measurement errors that are characteristic to each lab- oratory in this large cross-laboratories integrated dataset, was ensured by computation of a range of microarray data quality metrics and exclusion of incomparable data. The structure of a global map of human gene expression was then explored by principal component analysis and hierarchical clustering using heuristics and help from another purpose built sample ontology. A preface and motivation to the construction and analysis of a global map of human gene expression is given by analysis of two microarray datasets of human malignant melanoma. The analysis of these sets incorporate indirect comparison of statistical methods for finding differentially expressed genes and point to the need to study gene expression on a global level.

A role to play: Investigating concepts of masculinity in Australia through theatre

Health professionals, academics, social commentators and the media are increasingly sending the same message – Australian men are in crisis. This message has been supported by documented rises in alcoholism, violence, depression, suicide and crime amongst men in Australia. A major cause of this crisis, it can be argued, is an over-reliance on the out-dated and limited model of hegemonic masculinity that all men are encouraged to imitate in their own behaviour. This paper, as part of a larger study, explores representations of masculinity in selected works of contemporary Australian theatre in order to investigate the concept of hegemonic masculinity and any influence it may have on the perceived ‘crisis of masculinity’. Theatre is but one of the artistic modes that can be used to investigate masculinity and issues associated with identity. The Australia Council for the Arts recognises theatre, along with literature, dance, film, television, inter-arts, music and visual arts, as critical to the understanding and expression of Australian culture and identity. Theatre has been chosen in this instance because of the opportunities available to this study for direct access to specific theatre performances and creators and, also, because of the researcher’s experience, as a theatre director, with the dramatic arts. Through interviews with writers, directors and actors, combined with the analysis of scripts, academic writings, reviews, articles, programmes, play rehearsals and workshops, this research utilises theatre as a medium to explore masculinity in Australia.

Theories of moral education and implementation in Indonesia: Re-energizing cultural identity and addressing future challenges

School is regarded as a site of moral training for the younger generation to encounter nation’s future challenges as well as to re-energize nation’s cultural identity. The more competitive global society led by free market trade in terms of ASEAN Economic Community (AEC), requires the school to adapt and change its curriculum more frequently. Like many other countries, Indonesian Ministry of Education and Culture has introduced and nurtured universal values and traditional values respectively through school curriculum reforms to develop students’ ability to participating in global society. This paper will describe classical and contemporary theories related to moral education that have been implemented in Indonesia’s school curriculum and school activities. The theories developed by Durkheim, Alastair MacIntyre, and Basil Bernstein will be discussed. This includes explaining how far the theories have been adopted in Indonesia and how the approaches are currently being used in Indonesian schooling. This paper suggests despite the implementation of those theories in Indonesian schools, the government needs to optimise the operation of those theories to gain significant outcomes.

Christianity and Christian Identity in the Gospel of Philip (NHC II,3)

Previous scholarship has often maintained that the Gospel of Philip is a collection of Valentinian teachings. In the present study, however, the text is read as a whole and placed into a broader context by searching for parallels from other early Christian texts. Although the Valentinian Christian identity of the Gospel of Philip is not questioned, it is read alongside those texts traditionally labelled as "mainstream Christian". It is obvious from the account of Irenaeus that the boundaries between the Valentinians and other Christians were not as clear or fixed as he probably would have hoped. This study analyzes the Valentinian Christian Gospel of Philip from two points of view: how the text constructs the Christian identity and what kind of Christianity it exemplifies. Firstly, it is observed how the author of the Gospel of Philip places himself and his Christian readers among the early Christianities of the period by emphasizing the common history and Christian features but building especially on particular texts and traditions. Secondly, it is noted how the Christian nature of an individual develops according to the Gospel of Philip. The identity of an individual is built and strengthened through rituals, experiences and teaching. Thirdly, the categorizations, attributes, beliefs and behaviour associated on the one hand with the "insiders", the true Christians, and, on the other, with outsiders in the Gospel of Philip, are analyzed using social identity theory the insiders and outsiders are described through stereotyping in the text. Overall, the study implies that the Gospel of Philip strongly emphasizes spiritual progress and transformation. Rather than depicting the Valentinians as the perfect Christians, it underlines their need for constant change and improvement. Although the author seeks to clearly distinguish the insiders from the outsiders, the boundaries of the categories are in fact fluid in the Gospel of Philip. Outsiders can become insiders and the insiders are also in danger of falling out again.

Rukous on perintöä suvusta sukuun : Ikääntyneet ja uskonto vuosituhannen vaihteen Suomessa

"Prayer, a heritage from generation to generation" The elderly and religion in Finland at the turn of the 21st century The strong demographic changes in Europe mean that research on the elderly is highly needed, and also from the viewpoint of their resources and opportunities. Further, it is important to determine, how the elderly could find a meaningful place as members of the chain of generations in our rapidly changing society. The aim of this study was to find out how the elderly build and perceive their place in the society through religious texts. The study was based on religious texts written by elderly people in the study groups of the Finnish pensioners organization Pension Union (Eläkeliitto). These 943 short prayers, poems, and aphorisms were collected during the Tree of Life (Elämänpuu) project in 1998-1999 and were then analysed applying qualitative content analysis and grounded theory methodology. The social construction of aging and the view of communication as a collective signifying process were used as the mainstays of the research perspective. The themes brought forward by the elderly writers were grouped around three key themes: the self, the world and religion. In this examination religion with its forms of expression appeared to be deeply rooted to each of these themes and thus seems a vital part of the elderly writers' culture. In connection with the theme of the self, the religious forms of expression provided a means of building a coherent and culturally accepted self-image which is further supported by positive views of personal history and current life situation. In relation to the world theme, the elderly writers stressed the importance of close social relationships and at the same time expressed anxiety with regard to the changing world. Concerning the theme of religion, the religious forms of expression were first and foremost used in building and creating a sense of personal safety and a belief in the future. The study suggests that skill in the use of religious language enable the elderly to cope with equivocal life events and cognitive dissonance. At the social level the religious forms of expression seemed to connect the writers to the Finnish linguistic culture and identity, as well as to the collective memory, where religion plays a central part. By using religious language the elderly both exploit and maintain these considerable social resources. The key result of the study is that the elderly were found to have a significant and separate role in the continuity and well-being of society. Bound to the religious tradition, the elderly seem to carry significant information as regards the identity of the Finnish people, information which is essentially passed on to future generations. By sustaining traditions and thus the collective identity, they perform a uniquely productive task and their life experience could be seen as a particular type of capital in the society. This result also raises a grave question: Will the elderly of the future be able to undertake this task that so profoundly requires religious literacy?

(Re)presenting Masculinity: A theatre director's critical observations of, and theatrical experimentation with, (re)presentations of masculinity in selected works of contemporary Australian theatre

Health professionals, academics, social commentators and the media are increasingly sending the same message – Australian men are in crisis. This message has been supported by documented rises in alcoholism, violence, depression, suicide and crime amongst men in Australia. A major cause of this crisis, it can be argued, is an over-reliance on the out-dated and limited model of hegemonic masculinity that all men are encouraged to imitate in their own behaviour. This paper, as part of a larger study, explores representations of masculinity in selected works of contemporary Australian theatre in order to investigate the concept of hegemonic masculinity and any influence it may have on the perceived ‘crisis of masculinity’. Theatre is but one of the artistic modes that can be used to investigate masculinity and issues associated with identity. The Australia Council for the Arts recognises theatre, along with literature, dance, film, television, inter-arts, music and visual arts, as critical to the understanding and expression of Australian culture and identity. Theatre has been chosen in this instance because of the opportunities available to this study for direct access to specific theatre performances and creators and, also, because of the researcher’s experience, as a theatre director, with the dramatic arts. Through interviews with writers, directors and actors, combined with the analysis of scripts, academic writings, reviews, articles, programmes, play rehearsals and workshops, this research utilises theatre as a medium to explore masculinity in Australia.

Factors influencing kinetic and equilibrium behaviour of sodium ion exchange with strong acid cation resin

This study reports an investigation of the ion exchange treatment of sodium chloride solutions in relation to use of resin technology for applications such as desalination of brackish water. In particular, a strong acid cation (SAC) resin (DOW Marathon C) was studied to determine its capacity for sodium uptake and to evaluate the fundamentals of the ion exchange process involved. Key questions to answer included: impact of resin identity; best models to simulate the kinetics and equilibrium exchange behaviour of sodium ions; difference between using linear least squares (LLS) and non-linear least squares (NLLS) methods for data interpretation; and, effect of changing the type of anion in solution which accompanied the sodium species. Kinetic studies suggested that the exchange process was best described by a pseudo first order rate expression based upon non-linear least squares analysis of the test data. Application of the Langmuir Vageler isotherm model was recommended as it allowed confirmation that experimental conditions were sufficient for maximum loading of sodium ions to occur. The Freundlich expression best fitted the equilibrium data when analysing the information by a NLLS approach. In contrast, LLS methods suggested that the Langmuir model was optimal for describing the equilibrium process. The Competitive Langmuir model which considered the stoichiometric nature of ion exchange process, estimated the maximum loading of sodium ions to be 64.7 g Na/kg resin. This latter value was comparable to sodium ion capacities for SAC resin published previously. Inherent discrepancies involved when using linearized versions of kinetic and isotherm equations were illustrated, and despite their widespread use, the value of this latter approach was questionable. The equilibrium behaviour of sodium ions form sodium fluoride solution revealed that the sodium ions were now more preferred by the resin compared to the situation with sodium chloride. The solution chemistry of hydrofluoric acid was suggested as promoting the affinity of the sodium ions to the resin.

State Agent, Identity and the "New World Order" : Reconstructing Polish Defence Identity after the Cold War Era

National identity signifies and makes state s defence- and foreign policy behaviour meaningful. National consciousness is narrated into existence by narratives upon one s own exceptionalism and Otherness of the other nations. While national identity may be understood merely as a self-image of a nation, defence identity refers to the borders of Otherness and issues that have been considered as worth defending for. As national identities and all the world order models are human constructions, they may be changed by the human efforts as well; states and nations may deliberately promote communitarian or even cosmopolitan equality and tolerance without borders of Otherness. The main research question of the thesis is: How does Poland constitute herself as a nation and a state agent in the current world order and to what extent have contextual foreign and defence policy interactions changed the Polish defence identity during the post-Cold War era? The main empirical argument of the thesis is: Poland is a narrated idea of a Christian Catholic nation-state, which the Polish State, the Catholic Church of Poland, the Armed Forces of Poland as well as a majority of the Polish nation share. Polish defence identity has been almost impenetrable to contextual foreign and defence policy interactions during the post-Cold War era. While Christian religious ontology binds corporate Poland together, allowing her to survive any number of military and political catastrophes, it simultaneously brings her closer to the USA, raises tensions in the infidel EU-context, and restrains corporate Poland s pursuit of communitarian, or even cosmopolitan, global equality and tolerance. It is not the case that corporate Poland s foreign and defence policy orientation is instinctively Atlanticist by nature, as has been argued. Rather, it has been the State s rational project to overcome a habituated and reified fear of becoming geopolitically sandwiched between Russian and German Others by leaning on the USA; among the Polish nation, support for the USA has been declining since 2004. It is not corporate Poland either that has turned into a constructive European , as has been argued, but rather the Polish nation that has, at least partly, managed to emancipate itself from its habituation to a betrayal by Europe narrative, since it favours the EU as much as it favours NATO. It seems that in the Polish case a truly common European CFSP vis-à-vis Russia may offer a solution that will emancipate the Polish State from its habituated EU-sceptic role identity and corporate Poland from its narrated borders of Otherness towards Russia and Germany, but even then one cannot be sure whether any other perspective than the Polish one on a common stand towards Russia would satisfy the Poles themselves.

Reconstituting identity and history in post-war Mostar, Bosnia-Herzegovina

This paper by Carl Grodach demonstrates the careful unravelling of complexity, diversity, contestation and contradictions involved in the reconstruction of symbolic urban spaces after violent conflict, and the allied processes of cultural reinterpretation, political reconfiguration and material revaluation which accompany it. The paper analyses the reconstruction and redevelopment of the 16th-century historic centre of Mostar, Bosnia-Herzegovina, following the Bosnian Wars of 1992–1995. Reconstruction efforts centre around Stari Most, the 16th-century Ottoman bridge destroyed by Bosnian Croat military in 1993. In Mostar, both international and local organizations are in the process of reinterpreting Bosnia’s legacy of Ottoman city spaces. This research and analysis illuminates how such spaces can be central to contemporary projects to redefine group identities and conceptions of place. It provides insight into the ways various groups are attempting to reshape outside perceptions of the city—and Bosnia’s ethnic conflict—to articulate a new definition of local identity and ethnic relations and to remake a stable tourist economy through Mostar’s urban spaces.

SOCS3 expression induced by PIM2 requires PKC and PI3K signaling

Initiation of proinflammatory host immunity in response to infection represents as a key event in effective control and containment of the pathogen at the site of infection as well as in elicitation of robust immune memory responses. In the current investigation, we demonstrate that an integral cell wall antigen of the mycobacterial envelope, Phosphatidyl-myo-inositol dimannosides (PIM2) triggers Suppressor of cytokine signaling (SOCS) 3 expression in macrophages in a Toll-like receptor 2 (TLR2)-MyD88 dependent manner. Data derived from signaling perturbations suggest the involvement of phosphoinositide-3 kinase (PI3K) and protein kinase C (PKC) signaling pathways during PIM2 induced SOCS3 expression. Further, pharmacological inhibition of ERK1/2, but not of p38 MAP kinase or JNK abrogated the induced expression of SOCS3. The PIM2 induced activation of ERK1/2 was dependent on the activation of PI3K or PKC signaling which in turn regulated p65 nuclear factor -kappa B (NF-kappa B) nuclear translocation. Overall, current study delineates the role for PI3K-PKC axis and ERK1/2 signaling as key signaling events during PIM2 induced SOCS3 expression in macrophages.

Peroxidases in lignifying xylem of Norway spruce, Scots pine and silver birch

Lignin is a complex plant polymer synthesized through co-operation of multiple intracellular and extracellular enzymes. It is deposited to plant cell walls in cells where additional strength or stiffness are needed, such as in tracheary elements (TEs) in xylem, supporting sclerenchymal tissues and at the sites of wounding. Class III peroxidases (POXs) are secreted plant oxidoreductases with implications in many physiological processes such as the polymerization of lignin and suberin and auxin catabolism. POXs are able to oxidize various substrates in the presence of hydrogen peroxide, including lignin monomers, monolignols, thus enabling the monolignol polymerization to lignin by radical coupling. Trees produce large amounts of lignin in secondary xylem of stems, branches and roots. In this study, POXs of gymnosperm and angiosperm trees were studied in order to find POXs which are able to participate in lignin polymerization in developing secondary xylem i.e. are located at the site of lignin synthesis in tree stems and have the ability to oxidize monolignol substrates. Both in the gymnosperm species, Norway spruce and Scots pine, and in the angiosperm species silver birch the monolignol oxidizing POX activities originating from multiple POX isoforms were present in lignifying secondary xylem in stems during the period of annual growth. Most of the partially purified POXs from Norway spruce and silver birch xylem had highest oxidation rate with coniferyl alcohol, the main monomer in guaiacyl-lignin in conifers. The only exception was the most anionic POX fraction from silver birch, which clearly preferred sinapyl alcohol, the lignin monomer needed in the synthesis of syringyl-guaiacyl lignin in angiosperm trees. Three full-length pox cDNAs px1, px2 and px3 were cloned from the developing xylem of Norway spruce. It was shown that px1 and px2 are expressed in developing tracheids in spruce seedlings, whereas px3 transcripts were not detected suggesting low transcription level in young trees. The amino acid sequences of PX1, PX2 and PX3 were less than 60% identical to each other but showed up to 84% identity to other known POXs. They all begin with predicted N-terminal secretion signal (SS) peptides. PX2 and PX3 contained additional putative vacuolar localization determinants (VSDs) at C-terminus. Transient expression of EGFP-fusions of the SS- and VSD-peptides in tobacco protoplasts showed SS-peptides directed EGFP to secretion in tobacco cells, whereas only the PX2 C-terminal peptide seems to be a functional VSD. According to heterologous expression of px1 in Catharanthus roseus hairy roots, PX1 is a guaicol-oxidizing POX with isoelectric point (pI) approximately 10, similar to monolignol oxidizing POXs in protein extracts from Norway spruce lignifying xylem. Hence, PX1 has characteristics for participation to monolignol dehydrogenation in lignin synthesis, whereas the other two spruce POXs seem to have some other functions. Interesting topics in future include functional characterization of syringyl compound oxidizing POXs and components of POX activity regulation in trees.

Traces from elsewhere: Nomadism, artistic identity and contemporary dance in Ireland

This keynote presentation explores the connections between nomadism and artistic identity formation by interrogating the creativity that migration elicits and the narratives that surround it. It is further situated in the complex role that emigration has in Irish culture questioning whether contemporary dance in particular is emblematic of this socio-cultural phenomenon. These questions are anchored through descriptions of a creative project currently underway that draws together artists from Ireland and Australia to explore how we manage absence and presence in a globalized yet increasingly virtual world.

U12-type Spliceosome: Localization and Effects of Splicing Efficiency on Gene Expression

The removal of non-coding sequences, introns, is an essential part of messenger RNA processing. In most metazoan organisms, the U12-type spliceosome processes a subset of introns containing highly conserved recognition sequences. U12-type introns constitute less than 0,5% of all introns and reside preferentially in genes related to information processing functions, as opposed to genes encoding for metabolic enzymes. It has previously been shown that the excision of U12-type introns is inefficient compared to that of U2-type introns, supporting the model that these introns could provide a rate-limiting control for gene expression. The low efficiency of U12-type splicing is believed to have important consequences to gene expression by limiting the production of mature mRNAs from genes containing U12-type introns. The inefficiency of U12-type splicing has been attributed to the low abundance of the components of the U12-type spliceosome in cells, but this hypothesis has not been proven. The aim of the first part of this work was to study the effect of the abundance of the spliceosomal snRNA components on splicing. Cells with a low abundance of the U12-type spliceosome were found to inefficiently process U12-type introns encoded by a transfected construct, but the expression levels of endogenous genes were not found to be affected by the abundance of the U12-type spliceosome. However, significant levels of endogenous unspliced U12-type intron-containing pre-mRNAs were detected in cells. Together these results support the idea that U12-type splicing may limit gene expression in some situations. The inefficiency of U12-type splicing has also promoted the idea that the U12-type spliceosome may control gene expression, limiting the mRNA levels of some U12-type intron-containing genes. While the identities of the primary target genes that contain U12-type introns are relatively well known, little has previously been known about the downstream genes and pathways potentially affected by the efficiency of U12-type intron processing. Here, the effects of U12-type splicing efficiency on a whole organism were studied in a Drosophila line with a mutation in an essential U12-type spliceosome component. Genes containing U12-type introns showed variable gene-specific responses to the splicing defect, which points to variation in the susceptibility of different genes to changes in splicing efficiency. Surprisingly, microarray screening revealed that metabolic genes were enriched among downstream effects, and that the phenotype could largely be attributed to one U12-type intron-containing mitochondrial gene. Gene expression control by the U12-type spliceosome could thus have widespread effects on metabolic functions in the organism. The subcellular localization of the U12-type spliceosome components was studied as a response to a recent dispute on the localization of the U12-type spliceosome. All components studied were found to be nuclear indicating that the processing of U12-type introns occurs within the nucleus, thus clarifying a question central to the field. The results suggest that the U12-type spliceosome can limit the expression of genes that contain U12-type introns in a gene-specific manner. Through its limiting role in pre-mRNA processing, the U12-type splicing activity can affect specific genetic pathways, which in the case of Drosophila are involved in metabolic functions.