Genome-wide identification and expression analysis of the NF-Y family of transcription factors in Triticum aestivum

Nuclear Factor Y (NF-Y) is a trimeric complex that binds to the CCAAT box, a ubiquitous eukaryotic promoter element. The three subunits NF-YA, NF-YB and NF-YC are represented by single genes in yeast and mammals. However, in model plant species (Arabidopsis and rice) multiple genes encode each subunit providing the impetus for the investigation of the NF-Y transcription factor family in wheat. A total of 37 NF-Y and Dr1 genes (10 NF-YA, 11 NF-YB, 14 NF-YC and 2 Dr1) in Triticum aestivum were identified in the global DNA databases by computational analysis in this study. Each of the wheat NF-Y subunit families could be further divided into 4-5 clades based on their conserved core region sequences. Several conserved motifs outside of the NF-Y core regions were also identified by comparison of NF-Y members from wheat, rice and Arabidopsis. Quantitative RT-PCR analysis revealed that some of the wheat NF-Y genes were expressed ubiquitously, while others were expressed in an organ-specific manner. In particular, each TaNF-Y subunit family had members that were expressed predominantly in the endosperm. The expression of nine NF-Y and two Dr1 genes in wheat leaves appeared to be responsive to drought stress. Three of these genes were up-regulated under drought conditions, indicating that these members of the NF-Y and Dr1 families are potentially involved in plant drought adaptation. The combined expression and phylogenetic analyses revealed that members within the same phylogenetic clade generally shared a similar expression profile. Organ-specific expression and differential response to drought indicate a plant-specific biological role for various members of this transcription factor family.

Mapping the building and construction product system : preliminary report

This Preliminary Report has been prepared by researchers at The Australian Expert Group in Industry Studies (AEGIS) for the Commonwealth Department of Industry, Science and Resources. It is intended to provide a preliminary 'product system map' of the building and construction industries which defines the system, identifies the major segments, describes key industry players and institutions and provides the basis for exploring relationships, innovation and information flows within the industries. This Preliminary Report is the first of a series of five which will explore the building and construction product system in some depth. This first report does not present original research, although it does include some new interview data and analysis of a variety of written sources. This report is rather a reformulation of existing statistical and analytical material from a product system-based perspective. It is intended to provide the basis for subsequent studies by putting what is already known into an alternative framework and allowing us to see it through a new lens.

Continuous passive motion applied to whole joints stimulates chondrocyte blosynthesis of PRG4

Continuous passive motion (CPM) is currently a part of patient rehabilitation regimens after a variety of orthopedic surgical procedures. While CPM can enhance the joint healing process, the direct effects of CPM on cartilage metabolism remain unknown. Recent in vivo and in vitro observations suggest that mechanical stimuli can regulate articular cartilage metabolism of proteoglycan 4 (PRG4), a putative lubricating and chondroprotective molecule found in synovial fluid and at the articular cartilage surface. ----- ----- Objectives: (1) Determine the topographical variation in intrinsic cartilage PRG4 secretion. (2) Apply a CPM device to whole joints in bioreactors and assess effects of CPM on PRG4 biosynthesis.----- ----- Methods: A bioreactor was developed to apply CPM to bovine stifle joints in vitro. Effects of 24 h of CPM on PRG4 biosynthesis were determined.----- ----- Results: PRG4 secretion rate varied markedly over the joint surface. Rehabilitative joint motion applied in the form of CPM regulated PRG4 biosynthesis, in a manner dependent on the duty cycle of cartilage sliding against opposing tissues. Specifically, in certain regions of the femoral condyle that were continuously or intermittently sliding against meniscus and tibial cartilage during CPM, chondrocyte PRG4 synthesis was higher with CPM than without.----- ----- Conclusions: Rehabilitative joint motion, applied in the form of CPM, stimulates chondrocyte PRG4 metabolism. The stimulation of PRG4 synthesis is one mechanism by which CPM may benefit cartilage and joint health in post-operative rehabilitation. (C) 2006 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

Performing the unutterable : mapping the experiential in contemporary dance

This research project looks to engage audiences in a variety of experiential ways by reexamining and manipulating the traditional presentation paradigm for viewing Western contemporary dance. It considers how the audience may be situated in the creation and presentation of contemporary dance generally, and specifically in the work The Voyeur, which researched these issues in action. By situating the body of the audience member as a site of understanding and meaning making, this practice-based research considers the audience within the artists’ creative process from the inception of a creative work, rather than after the work has been created. The research questions how a ‘lived experience’ of contemporary dance could be deepened for the audience. It presents a series of ‘tools’ to create alternative frameworks of presentation that challenge the dominant modes of creation, presentation and meaning making in contemporary dance. The five tools established and applied in this research are: site, liminality, agency, proximity and performer authenticity. These tools are framed as a series of calibrated scales that allow choreographers to map decisions made in the studio in relation to potential audience engagement. These scales have the ability to house multiple presentation formats from the traditional to the avant garde and open up possibilities for broad analysis of a wide range of artistic dance works.

Mapping the ethical journey of experienced nurses now practising in rural and remote hospitals in central and south-west Queensland and in domiciliary services in Brisbane : a grounded theory approach

The aim of this thesis has been to map the ethical journey of experienced nurses now practising in rural and remote hospitals in central and south-west Queensland and in domiciliary services in Brisbane. One group of the experienced nurses in the study were Directors of Nursing in rural and remote hospitals. These nurses were “hands on”, “multi-skilled “ nurses who also had the task of managing the hospital. Also there were two Directors of Nursing from domiciliary services in Brisbane. A grounded theory method was used. The nurses were interviewed and the data retrieved from the interviews was coded, categorised and from these categories a conceptual framework was generated. The literature which dealt with the subject of ethical decision making and nurses also became part of the data. The study revealed that all these nurses experienced moral distress as they made ethical decisions. The decision making categories revealed in the data were: the area of financial management; issues as end of life approaches; allowing to die with dignity; emergency decisions; experience of unexpected death; the dilemma of providing care in very difficult circumstances. These categories were divided into two chapters: the category related to administrative and financial constraints and categories dealing with ethical issues in clinical settings. A further chapter discussed the overarching category of coping with moral distress. These experienced nurses suffered moral distress as they made ethical decisions, confirming many instances of moral distress in ethical decision making documented in the literature to date. Significantly, the nurses in their interviews never mentioned the ethical principles used in bioethics as an influence in their decision making. Only one referred to lectures on ethics as being an influence in her thinking. As they described their ethical problems and how they worked through them, they drew on their own previous experience rather than any knowledge of ethics gained from nursing education. They were concerned for their patients, they spoke from a caring responsibility towards their patients, but they were also concerned for justice for their patients. This study demonstrates that these nurses operated from the ethic of care, tempered with the ethic of responsibility as well as a concern for justice for their patients. Reflection on professional experience, rather than formal ethics education and training, was the primary influence on their ethical decision making.

Must see TV : mapping an Australian mediasphere

Australian National Cinema and Australian Television Culture. These two books, magisterial accounts of Australian media cultures, are very different. The first analyses (according to its cover blurb) 'the distinct and diverse nature of Australian cinema'; the second offers 'a picture of Australian television'. The books share an author.2 Despite this, their objects of study are constituted very differently. The first is replete with examples of particular films, analyses of their representational strategies, and links to the social context of production. The second addresses almost no programs and those that are mentioned appear only in passing. There is no analysis of any particular television text. The difference between these books cannot be explained in terms of authorial fickleness: rather, it represents the different ways in which television and film have been constructed as objects of study. While film has a recognised canon and a tradition of close textual analysis, in the study of television the programs themselves have tended to vanish - as they do in Australian Television Culture. Most academic work on Australian television is not interested in its programs. Writers have tended to find other aspects more rewarding: industries, institutions, ownership, legislation, technology and production.3 Australian Television Culture is part of this tradition; and an example of how such work, done well, can be a useful contribution to understanding the medium.

Defining and mapping teacher practice in technology classrooms

The indecision surrounding the definition of Technology extends to the classroom as not knowing what a subject “is” affects how it is taught. Similarly, its relative newness – and consequent lack of habitus in school settings - means that it is still struggling to find its own place in the curriculum as well as resolve its relationship with more established subject domains, particularly Science and Mathematics. The guidance from syllabus documents points to open-ended student-directed projects where extant studies indicate a more common experience of teacher –directed activities and an emphasis on product over process. There are issues too for researchers in documenting classroom observations and in analysing teacher practice in new learning environments. This paper presents a framework for defining and mapping classroom practice and for attempting to describe the social practice in the Technology classroom. The framework is a bricolage which draws on contemporary research. More formally, the development of the framework is consonant with the aim of design-based research to develop a flexible, adaptive and generalisable theory to better understanding a teaching domain where promise is not seen to match current reality. The framework may also inform emergent approaches to STEM (Science, Technology, Education and Mathematics) in education.

Multiple evolutionary rate classes in animal genome evolution

The proportion of functional sequence in the human genome is currently a subject of debate. The most widely accepted figure is that approximately 5% is under purifying selection. In Drosophila, estimates are an order of magnitude higher, though this corresponds to a similar quantity of sequence. These estimates depend on the difference between the distribution of genomewide evolutionary rates and that observed in a subset of sequences presumed to be neutrally evolving. Motivated by the widening gap between these estimates and experimental evidence of genome function, especially in mammals, we developed a sensitive technique for evaluating such distributions and found that they are much more complex than previously apparent. We found strong evidence for at least nine well-resolved evolutionary rate classes in an alignment of four Drosophila species and at least seven classes in an alignment of four mammals, including human. We also identified at least three rate classes in human ancestral repeats. By positing that the largest of these ancestral repeat classes is neutrally evolving, we estimate that the proportion of nonneutrally evolving sequence is 30% of human ancestral repeats and 45% of the aligned portion of the genome. However, we also question whether any of the classes represent neutrally evolving sequences and argue that a plausible alternative is that they reflect variable structure-function constraints operating throughout the genomes of complex organisms.

From Greek temple to bird's nest : mapping, assessing and understanding national integrity systems

In this paper, I would like to outline the approach we have taken to mapping and assessing integrity systems and how this has led us to see integrity systems in a new light. Indeed, it has led us to a new visual metaphor for integrity systems – a bird’s nest rather than a Greek temple. This was the result of a pair of major research projects completed in partnership with Transparency International (TI). One worked on refining and extending the measurement of corruption. This, the second, looked at what was then the emerging institutional means for reducing corruption – ‘national integrity systems’

Identification of a cryptic Prokaryotic promoter within the cDNA encoding the 5′ End of Dengue Virus RNA Genome

Infectious cDNA clones of RNA viruses are important research tools, but flavivirus cDNA clones have proven difficult to assemble and propagate in bacteria. This has been attributed to genetic instability and/or host cell toxicity, however the mechanism leading to these difficulties has not been fully elucidated. Here we identify and characterize an efficient cryptic bacterial promoter in the cDNA encoding the dengue virus (DENV) 5′ UTR. Following cryptic transcription in E. coli, protein expression initiated at a conserved in-frame AUG that is downstream from the authentic DENV initiation codon, yielding a DENV polyprotein fragment that was truncated at the N-terminus. A more complete understanding of constitutive viral protein expression in E. coli might help explain the cloning and propagation difficulties generally observed with flavivirus cDNA.

Linkage to chromosome 2q32.2-q33.3 in familial serrated neoplasia (Jass syndrome)

Abstract Causative genetic variants have to date been identified for only a small proportion of familial colorectal cancer (CRC). While conditions such as Familial Adenomatous Polyposis and Lynch syndrome have well defined genetic causes, the search for variants underlying the remainder of familial CRC is plagued by genetic heterogeneity. The recent identification of families with a heritable predisposition to malignancies arising through the serrated pathway (familial serrated neoplasia or Jass syndrome) provides an opportunity to study a subset of familial CRC in which heterogeneity may be greatly reduced. A genome-wide linkage screen was performed on a large family displaying a dominantly-inherited predisposition to serrated neoplasia genotyped using the Affymetrix GeneChip Human Mapping 10 K SNP Array. Parametric and nonparametric analyses were performed and resulting regions of interest, as well as previously reported CRC susceptibility loci at 3q22, 7q31 and 9q22, were followed up by finemapping in 10 serrated neoplasia families. Genome-wide linkage analysis revealed regions of interest at 2p25.2-p25.1, 2q24.3-q37.1 and 8p21.2-q12.1. Finemapping linkage and haplotype analyses identified 2q32.2-q33.3 as the region most likely to harbour linkage, with heterogeneity logarithm of the odds (HLOD) 2.09 and nonparametric linkage (NPL) score 2.36 (P = 0.004). Five primary candidate genes (CFLAR, CASP10, CASP8, FZD7 and BMPR2) were sequenced and no segregating variants identified. There was no evidence of linkage to previously reported loci on chromosomes 3, 7 and 9.