Deletion mapping suggests that the 1p22 melanoma susceptibility gene is a tumor suppressor localized to a 9-Mb interval

Loss of the short arm of chromosome 1 is frequently observed in many tumor types, including melanoma. We recently localized a third melanoma susceptibility locus to chromosome band 1p22. Critical recombinants in linked families localized the gene to a 15-Mb region between D1S430 and D1S2664. To map the locus more finely we have performed studies to assess allelic loss across the region in a panel of melanomas from 1p22-linked families, sporadic melanomas, and melanoma cell lines. Eighty percent of familial melanomas exhibited loss of heterozygosity (LOH) within the region, with a smallest region of overlapping deletions (SRO) of 9 Mb between D1S207 and D1S435. This high frequency of LOH makes it very likely that the susceptibility locus is a tumor suppressor. In sporadic tumors, four SROs were defined. SRO1 and SRO2 map within the critical recombinant and familial tumor region, indicating that one or the other is likely to harbor the susceptibility gene. However, SRO3 may also be significant because it overlaps with the markers with the highest 2-point LOD score (D1S2776), part of the linkage recombinant region, and the critical region defined in mesothelioma. The candidate genes PRKCL2 and GTF2B, within SRO2, and TGFBR3, CDC7, and EVI5, in a broad region encompassing SRO3, were screened in 1p22-linked melanoma kindreds, but no coding mutations were detected. Allelic loss in melanoma cell lines was significantly less frequent than in fresh tumors, indicating that this gene may not be involved late in progression, such as in overriding cellular senescence, necessary for the propagation of melanoma cells in culture.

Mapping the language of science and science teaching practices : a case study of early childhood school science

Concerns raised in educational reports about school science in terms of students. outcomes and attitudes, as well as science teaching practices prompted investigation into science learning and teaching practices at the foundational level of school science. Without science content and process knowledge, understanding issues of modern society and active participation in decision-making is difficult. This study contended that a focus on the development of the language of science could enable learners to engage more effectively in learning science and enhance their interest and attitudes towards science. Furthermore, it argued that explicit teaching practices where science language is modelled and scaffolded would facilitate the learning of science by young children at the beginning of their formal schooling. This study aimed to investigate science language development at the foundational level of school science learning in the preparatory-school with students aged five and six years. It focussed on the language of science and science teaching practices in early childhood. In particular, the study focussed on the capacity for young students to engage with and understand science language. Previous research suggests that students have difficulty with the language of science most likely because of the complexities and ambiguities of science language. Furthermore, literature indicates that tensions transpire between traditional science teaching practices and accepted early childhood teaching practices. This contention prompted investigation into means and models of pedagogy for learning foundational science language, knowledge and processes in early childhood. This study was positioned within qualitative assumptions of research and reported via descriptive case study. It was located in a preparatory-school classroom with the class teacher, teacher-aide, and nineteen students aged four and five years who participated with the researcher in the study. Basil Bernstein.s pedagogical theory coupled with Halliday.s Systemic Functional Linguistics (SFL) framed an examination of science pedagogical practices for early childhood science learning. Students. science learning outcomes were gauged by focussing a Hallydayan lens on their oral and reflective language during 12 science-focussed episodes of teaching. Data were collected throughout the 12 episodes. Data included video and audio-taped science activities, student artefacts, journal and anecdotal records, semi-structured interviews and photographs. Data were analysed according to Bernstein.s visible and invisible pedagogies and performance and competence models. Additionally, Halliday.s SFL provided the resource to examine teacher and student language to determine teacher/student interpersonal relationships as well as specialised science and everyday language used in teacher and student science talk. Their analysis established the socio-linguistic characteristics that promoted science competencies in young children. An analysis of the data identified those teaching practices that facilitate young children.s acquisition of science meanings. Positive indications for modelling science language and science text types to young children have emerged. Teaching within the studied setting diverged from perceived notions of common early childhood practices and the benefits of dynamic shifting pedagogies were validated. Significantly, young students demonstrated use of particular specialised components of school-science language in terms of science language features and vocabulary. As well, their use of language demonstrated the students. knowledge of science concepts, processes and text types. The young students made sense of science phenomena through their incorporation of a variety of science language and text-types in explanations during both teacher-directed and independent situations. The study informs early childhood science practices as well as practices for foundational school science teaching and learning. It has exposed implications for science education policy, curriculum and practices. It supports other findings in relation to the capabilities of young students. The study contributes to Systemic Functional Linguistic theory through the development of a specific resource to determine the technicality of teacher language used in teaching young students. Furthermore, the study contributes to methodology practices relating to Bernsteinian theoretical perspectives and has demonstrated new ways of depicting and reporting teaching practices. It provides an analytical tool which couples Bernsteinian and Hallidayan theoretical perspectives. Ultimately, it defines directions for further research in terms of foundation science language learning, ongoing learning of the language of science and learning science, science teaching and learning practices, specifically in foundational school science, and relationships between home and school science language experiences.

Demonstration of cellulosic ethanol production from sugarcane bagasse in Australia : the Mackay Renewable Biocommodities Pilot Plant

The ready availability of sugarcane bagasse at an existing industrial facility and the potential availability of extra fibre through trash collection make sugarcane fibre the best candidate for early stage commercialisation of cellulosic ethanol technologies. The commercialisation of cellulosic ethanol technologies in the sugar industry requires both development of novel technologies and the assessment of these technologies at a pre-commercial scale. In 2007, the Queensland University of Technology (QUT) received funding from the Australian and Queensland Governments to construct a pilot research and development facility for the production of bioethanol and other renewable biocommodities from biomass including sugarcane bagasse. This facility has been built on the site of the Racecourse Sugar Mill in Mackay, Queensland and is known as the Mackay Renewable Biocommodities Pilot Plant (MRBPP). This research facility is capable of processing cellulosic biomass by a variety of pretreatment technologies and includes equipment for enzymatic saccharification, fermentation and distillation to produce ethanol. Lignin and fermentation co-products can also be produced in the pilot facility.

Hunters & gatherers : strategies for curriculum mapping and data collection for assurance of learning

Assurance of learning is a predominant feature in both quality enhancement and assurance in higher education. Assurance of learning is a process that articulates explicit program outcomes and standards, and systematically gathers evidence to determine the extent to which performance matches expectations. Benefits accrue to the institution through the systematic assessment of whole of program goals. Data may be used for continuous improvement, program development, and to inform external accreditation and evaluation bodies. Recent developments, including the introduction of the Tertiary Education and Quality Standards Agency (TEQSA) will require universities to review the methods they use to assure learning outcomes. This project investigates two critical elements of assurance of learning: 1. the mapping of graduate attributes throughout a program; and 2. the collection of assurance of learning data. An audit was conducted with 25 of the 39 Business Schools in Australian universities to identify current methods of mapping graduate attributes and for collecting assurance of learning data across degree programs, as well as a review of the key challenges faced in these areas. Our findings indicate that external drivers like professional body accreditation (for example: Association to Advance Collegiate Schools of Business (AACSB)) and TEQSA are important motivators for assuring learning, and those who were undertaking AACSB accreditation had more robust assurance of learning systems in place. It was reassuring to see that the majority of institutions (96%) had adopted an embedding approach to assuring learning rather than opting for independent standardised testing. The main challenges that were evident were the development of sustainable processes that were not considered a burden to academic staff, and obtainment of academic buy in to the benefits of assuring learning per se rather than assurance of learning being seen as a tick box exercise. This cultural change is the real challenge in assurance of learning practice.

Mapping resilience : A framework for changing cities

Urban centres base their resilience on the ability to evolve and adapt as needed throughout their life. Although constantly developing, changing and subsuming nature for its needs, the current age of environmental awareness requires that cities progress in a more conscious and considered way. While they have become the dominant form of human habitation, there now exists a need to integrate 'green' solutions into urban centres to address social, physical and environmental wellbeing. The means of implementing the vast array of possible solutions without negative impacts is not clear; cities are complex systems, layering meaning, history and cultural memory ‐ they are a manifestation of shared cultural values, and as such, they do not allow a tabula rasa approach of 'blanket' solutions. All around us, cities are continuing to develop and change, and although their form is varied ‐ sprawling cities with density and sustainability problems; or collapsing cities with 'dead' centres and dilapidated districts – a common issue is the resilience of the local identity. The strength or resilience of cities lies in the elements which have become fixed points in the urban structure, giving character and identity to a shared urban experience. These elements need to be identified and either maintained or revitalised. Similarly, the identification of urban elements which can most viably be modified without compromising character and identity of place, will assist in making concrete contributions to increasing both the sustainability and experience of cities, making them more resilient. Through an examination of case studies, this paper suggests a framework to inform urban renewal assessing the widespread elements which generate an urban identity, beyond the traditional approach of heritage conservation for cultural or tourist purposes. The rapid contemporary alteration of urban structures requires an innovative methodology which satisfies on one side the need of new sustainable performances and, on the other, the resilience of the local character.

Characterisation of the TaNF-Y family of transcription factors in wheat

Light plays a unique role for plants as it is both a source of energy for growth and a signal for development. Light captured by the pigments in the light harvesting complexes is used to drive the synthesis of the chemical energy required for carbon assimilation. The light perceived by photoreceptors activates effectors, such as transcription factors (TFs), which modulate the expression of light-responsive genes. Recently, it has been speculated that increasing the photosynthetic rate could further improve the yield potential of three carbon (C3) crops such as wheat. However, little is currently known about the transcriptional regulation of photosynthesis genes, particularly in crop species. Nuclear factor Y (NF-Y) TF is a functionally diverse regulator of growth and development in the model plant species, with demonstrated roles in embryo development, stress response, flowering time and chloroplast biogenesis. Furthermore, a light-responsive NF-Y binding site (CCAAT-box) is present in the promoter of a spinach photosynthesis gene. As photosynthesis genes are co-regulated by light and co-regulated genes typically have similar regulatory elements in their promoters, it seems likely that other photosynthesis genes would also have light-responsive CCAAT-boxes. This provided the impetus to investigate the NF-Y TF in bread wheat. This thesis is focussed on wheat NF-Y members that have roles in light-mediated gene regulation with an emphasis on their involvement in the regulation of photosynthesis genes. NF-Y is a heterotrimeric complex, comprised of the three subunits NF-YA, NF-YB and NF-YC. Unlike the mammalian and yeast counterparts, each of the three subunits is encoded by multiple genes in Arabidopsis. The initial step taken in this study was the identification of the wheat NF-Y family (Chapter 3). A search of the current wheat nucleotide sequence databases identified 37 NF-Y genes (10 NF-YA, 11 NF-YB, 14 NF-YC & 2 Dr1). Phylogenetic analysis revealed that each of the three wheat NF-Y (TaNF-Y) subunit families could be divided into 4-5 clades based on their conserved core regions. Outside of the core regions, eleven motifs were identified to be conserved between Arabidopsis, rice and wheat NF-Y subunit members. The expression profiles of TaNF-Y genes were constructed using quantitative real-time polymerase chain reaction (RT-PCR). Some TaNF-Y subunit members had little variation in their transcript levels among the organs, while others displayed organ-predominant expression profiles, including those expressed mainly in the photosynthetic organs. To investigate their potential role in light-mediated gene regulation, the light responsiveness of the TaNF-Y genes were examined (Chapters 4 and 5). Two TaNF-YB and five TaNF-YC members were markedly upregulated by light in both the wheat leaves and seedling shoots. To identify the potential target genes of the light-upregulated NF-Y subunit members, a gene expression correlation analysis was conducted using publically available Affymetrix Wheat Genome Array datasets. This analysis revealed that the transcript expression levels of TaNF-YB3 and TaNF-YC11 were significantly correlated with those of photosynthesis genes. These correlated express profiles were also observed in the quantitative RT-PCR dataset from wheat plants grown under light and dark conditions. Sequence analysis of the promoters of these wheat photosynthesis genes revealed that they were enriched with potential NF-Y binding sites (CCAAT-box). The potential role of TaNF-YB3 in the regulation of photosynthetic genes was further investigated using a transgenic approach (Chapter 5). Transgenic wheat lines constitutively expressing TaNF-YB3 were found to have significantly increased expression levels of photosynthesis genes, including those encoding light harvesting chlorophyll a/b-binding proteins, photosystem I reaction centre subunits, a chloroplast ATP synthase subunit and glutamyl-tRNA reductase (GluTR). GluTR is a rate-limiting enzyme in the chlorophyll biosynthesis pathway. In association with the increased expression of the photosynthesis genes, the transgenic lines had a higher leaf chlorophyll content, increased photosynthetic rate and had a more rapid early growth rate compared to the wild-type wheat. In addition to its role in the regulation of photosynthesis genes, TaNF-YB3 overexpression lines flower on average 2-days earlier than the wild-type (Chapter 6). Quantitative RT-PCR analysis showed that there was a 13-fold increase in the expression level of the floral integrator, TaFT. The transcript levels of other downstream genes (TaFT2 and TaVRN1) were also increased in the transgenic lines. Furthermore, the transcript levels of TaNF-YB3 were significantly correlated with those of constans (CO), constans-like (COL) and timing of chlorophyll a/b-binding (CAB) expression 1 [TOC1; (CCT)] domain-containing proteins known to be involved in the regulation of flowering time. To summarise the key findings of this study, 37 NF-Y genes were identified in the crop species wheat. An in depth analysis of TaNF-Y gene expression profiles revealed that the potential role of some light-upregulated members was in the regulation of photosynthetic genes. The involvement of TaNF-YB3 in the regulation of photosynthesis genes was supported by data obtained from transgenic wheat lines with increased constitutive expression of TaNF-YB3. The overexpression of TaNF-YB3 in the transgenic lines revealed this NF-YB member is also involved in the fine-tuning of flowering time. These data suggest that the NF-Y TF plays an important role in light-mediated gene regulation in wheat.

How long is a tweet? Mapping dynamic conversation networks on Twitter using Gawk and Gephi

Twitter is now well established as the world’s second most important social media platform, after Facebook. Its 140-character updates are designed for brief messaging, and its network structures are kept relatively flat and simple: messages from users are either public and visible to all (even to unregistered visitors using the Twitter website), or private and visible only to approved ‘followers’ of the sender; there are no more complex definitions of degrees of connection (family, friends, friends of friends) as they are available in other social networks. Over time, Twitter users have developed simple, but effective mechanisms for working around these limitations: ‘#hashtags’, which enable the manual or automatic collation of all tweets containing the same #hashtag, as well allowing users to subscribe to content feeds that contain only those tweets which feature specific #hashtags; and ‘@replies’, which allow senders to direct public messages even to users whom they do not already follow. This paper documents a methodology for extracting public Twitter activity data around specific #hashtags, and for processing these data in order to analyse and visualize the @reply networks existing between participating users – both overall, as a static network, and over time, to highlight the dynamic structure of @reply conversations. Such visualizations enable us to highlight the shifting roles played by individual participants, as well as the response of the overall #hashtag community to new stimuli – such as the entry of new participants or the availability of new information. Over longer timeframes, it is also possible to identify different phases in the overall discussion, or the formation of distinct clusters of preferentially interacting participants.

AtBAG7, an Arabidopsis Bcl-2-associated athanogene, resides in the endoplasmic reticulum and is involved in the unfolded protein response

The Bcl-2-associated athanogene (BAG) family is an evolutionarily conserved, multifunctional group of cochaperones that perform diverse cellular functions ranging from proliferation to growth arrest and cell death in yeast, in mammals, and, as recently observed, in plants. The Arabidopsis genome contains seven homologs of the BAG family, including four with domain organization similar to animal BAGs. In the present study we show that an Arabidopsis BAG, AtBAG7, is a uniquely localized endoplasmic reticulum (ER) BAG that is necessary for the proper maintenance of the unfolded protein response (UPR). AtBAG7was shown to interact directly in vivo with themolecular chaperone, AtBiP2, by bimolecular fluorescence complementation assays, and the interaction was confirmed by yeast two-hybrid assay. Treatment with an inducer of UPR, tunicamycin, resulted in accelerated cell death of AtBAG7-null mutants. Furthermore, AtBAG7 knockouts were sensitive to known ER stress stimuli, heat and cold. In these knockouts heat sensitivity was reverted successfully to the wild-type phenotype with the addition of the chemical chaperone, tauroursodexycholic acid (TUDCA). Real-time PCR of ER stress proteins indicated that the expression of the heat-shock protein, AtBiP3, is selectively up-regulated in AtBAG7-null mutants upon heat and cold stress. Our results reveal an unexpected diversity of the plant's BAG gene family and suggest that AtBAG7 is an essential component of the UPR during heat and cold tolerance, thus confirming the cytoprotective role of plant BAGs.

Towards lifelong navigation and mapping in an office environment

This paper addresses the challenge of developing robots that map and navigate autonomously in real world, dynamic environments throughout the robot’s entire lifetime – the problem of lifelong navigation. Static mapping algorithms can produce highly accurate maps, but have found few applications in real environments that are in constant flux. Environments change in many ways: both rapidly and gradually, transiently and permanently, geometrically and in appearance. This paper demonstrates a biologically inspired navigation algorithm, RatSLAM, that uses principles found in rodent neural circuits. The algorithm is demonstrated in an office delivery challenge where the robot was required to perform mock deliveries to goal locations in two different buildings. The robot successfully completed 1177 out of 1178 navigation trials over 37 hours of around the clock operation spread over 11 days.

Outdoor simultaneous localisation and mapping using RatSLAM

In this paper an existing method for indoor Simultaneous Localisation and Mapping (SLAM) is extended to operate in large outdoor environments using an omnidirectional camera as its principal external sensor. The method, RatSLAM, is based upon computational models of the area in the rat brain that maintains the rodent’s idea of its position in the world. The system uses the visual appearance of different locations to build hybrid spatial-topological maps of places it has experienced that facilitate relocalisation and path planning. A large dataset was acquired from a dynamic campus environment and used to verify the system’s ability to construct representations of the world and simultaneously use these representations to maintain localisation.

Mapping intermedia news flows : topical discussions in the Australian and French political blogospheres

The growth of technologies and tools branded as =new media‘ or =Web 2.0‘ has sparked much discussion about the internet and its place in all facets of social life. Such debate includes the potential for blogs and citizen journalism projects to replace or alter journalism and mainstream media practices. However, while the journalism-blog dynamic has attracted the most attention, the actual work of political bloggers, the roles they play in the mediasphere and the resources they use, has been comparatively ignored. This project will look at political blogging in Australia and France - sites commenting on or promoting political events and ideas, and run by citizens, politicians, and journalists alike. In doing so, the structure of networks formed by bloggers and the nature of communication within political blogospheres will be examined. Previous studies of political blogging around the world have focussed on individual nations, finding that in some cases the networks are divided between different political ideologies. By comparing two countries with different political representation (two-party dominated system vs. a wider political spectrum), this study will determine the structure of these political blogospheres, and correlate these structures with the political environment in which they are situated. The thesis adapts concepts from communication and media theories, including framing, agenda setting, and opinion leaders, to examine the work of political bloggers and their place within the mediasphere. As well as developing a hybrid theoretical base for research into blogs and other online communication, the project outlines new methodologies for carrying out studies of online activity through the analysis of several topical networks within the wider activity collected for this project. The project draws on hyperlink and textual data collected from a sample of Australian and French blogs between January and August 2009. From this data, the thesis provides an overview of =everyday‘ political blogging, showing posting patterns over several months of activity, away from national elections and their associated campaigns. However, while other work in this field has looked solely at cumulative networks, treating collected data as a static network, this project will also look at specific cases to see how the blogospheres change with time and topics of discussion. Three case studies are used within the thesis to examine how blogs cover politics, featuring an international political event (the Obama inauguration), and local political topics (the opposition to the =Création et Internet‘, or HADOPI, law in France, the =Utegate‘ scandal in Australia). By using a mixture of qualitative and quantitative methods, the study analyses data collected from a population of sites from both countries, looking at their linking patterns, relationship with mainstream media, and topics of interest. This project will subsequently help to further develop methodologies in this field and provide new and detailed information on both online networks and internet-based political communication in Australia and France.

Cellulosic ethanol from sugarcane bagasse in Australia : exploring industry feasibility through systems analysis, techno-economic assessment and pilot plant development

Overcoming many of the constraints to early stage investment in biofuels production from sugarcane bagasse in Australia requires an understanding of the complex technical, economic and systemic challenges associated with the transition of established sugar industry structures from single product agri-businesses to new diversified multi-product biorefineries. While positive investment decisions in new infrastructure requires technically feasible solutions and the attainment of project economic investment thresholds, many other systemic factors will influence the investment decision. These factors include the interrelationships between feedstock availability and energy use, competing product alternatives, technology acceptance and perceptions of project uncertainty and risk. This thesis explores the feasibility of a new cellulosic ethanol industry in Australia based on the large sugarcane fibre (bagasse) resource available. The research explores industry feasibility from multiple angles including the challenges of integrating ethanol production into an established sugarcane processing system, scoping the economic drivers and key variables relating to bioethanol projects and considering the impact of emerging technologies in improving industry feasibility. The opportunities available from pilot scale technology demonstration are also addressed. Systems analysis techniques are used to explore the interrelationships between the existing sugarcane industry and the developing cellulosic biofuels industry. This analysis has resulted in the development of a conceptual framework for a bagassebased cellulosic ethanol industry in Australia and uses this framework to assess the uncertainty in key project factors and investment risk. The analysis showed that the fundamental issue affecting investment in a cellulosic ethanol industry from sugarcane in Australia is the uncertainty in the future price of ethanol and government support that reduces the risks associated with early stage investment is likely to be necessary to promote commercialisation of this novel technology. Comprehensive techno-economic models have been developed and used to assess the potential quantum of ethanol production from sugarcane in Australia, to assess the feasibility of a soda-based biorefinery at the Racecourse Sugar Mill in Mackay, Queensland and to assess the feasibility of reducing the cost of production of fermentable sugars from the in-planta expression of cellulases in sugarcane in Australia. These assessments show that ethanol from sugarcane in Australia has the potential to make a significant contribution to reducing Australia’s transportation fuel requirements from fossil fuels and that economically viable projects exist depending upon assumptions relating to product price, ethanol taxation arrangements and greenhouse gas emission reduction incentives. The conceptual design and development of a novel pilot scale cellulosic ethanol research and development facility is also reported in this thesis. The establishment of this facility enables the technical and economic feasibility of new technologies to be assessed in a multi-partner, collaborative environment. As a key outcome of this work, this study has delivered a facility that will enable novel cellulosic ethanol technologies to be assessed in a low investment risk environment, reducing the potential risks associated with early stage investment in commercial projects and hence promoting more rapid technology uptake. While the study has focussed on an exploration of the feasibility of a commercial cellulosic ethanol industry from sugarcane in Australia, many of the same key issues will be of relevance to other sugarcane industries throughout the world seeking diversification of revenue through the implementation of novel cellulosic ethanol technologies.

Plant programmed cell death : Can't live with it; Can't live without it

The decision of whether a cell should live or die is fundamental for the wellbeing of all organisms. Despite intense investigation into cell growth and proliferation, only recently has the essential and equally important idea that cells control/programme their own demise for proper maintenance of cellular homeostasis gained recognition. Furthermore, even though research into programmed cell death (PCD) has been an extremely active area of research there are significant gaps in our understanding of the process in plants. In this review, we discuss PCD during plant development and pathogenesis, and compare/contrast this with mammalian apoptosis. © 2008 Blackwell Publishing Ltd.

The Profiling of Property, Plant & Equipment (PPE) Contributions in Australia and Malaysia Public Listed Construction Companies

The purpose of this paper is to study the profiling of property, plant and equipment (PPE) contributions in Australia and Malaysia construction companies. A company’s worth is usually based on the listed share price on the stock exchange. In arriving at the net profit, the contribution of PPE in the company’s assets is somehow being neglected. This paper will investigate the followings; firstly the level of PPE contribution in the construction firms by comparing the PPE contributions to the company’s asset as a whole which includes fixed (non-current) assets and current assets. This will determine the true strength of the companies, rather than relying on the share prices alone. Secondly, the paper will determine the trend of company’s asset ownership to show the company’s performance of the PPE ownership during the period of study. The data is based on the selected construction companies listed on the Australian Stock Exchange (ASX) and Malaysian Stock Exchange, known as Bursa Malaysia. The profiling will help to determine the strength of the construction firms based on the PPE holding, and the level of PPE ownerships in the two countries construction firms during the period of study.