In vitro functional characterisation of IGF-I : VN-induced breast cancer progression

Members of the insulin-like growth factor (IGF) family have been shown to play critical roles in normal growth and development, as well as in tumour biology. The IGF system is complex and the biological effects of the IGFs are determined by their diverse interactions between many molecules, including their interactions with extracellular matrix (ECM) proteins. Recent studies have demonstrated that IGFs associate with the ECM protein vitronectin (VN) through IGF-binding proteins (IGFBP) and that this interaction modulates IGF-stimulated biological functions, namely cell migration and cell survival through the cooperative involvement of the type-I IGF receptor (IGF-1R) and VN-binding integrins. Since IGFs play important roles in the transformation and progression of breast cancer and VN has been found to be over-expressed at the leading edge of breast tumours, this project aimed to describe the effects of IGF-I:VN interactions on breast cell function. This was undertaken to dissect the molecular mechanisms underlying IGF-I:VN-induced responses and to design inhibitors to block the effects of such interactions. The studies described herein demonstrate that the increase in migration of MCF-7 breast cancer cells in response to the IGF-I:IGFBP-5:VN complex is accompanied by differential expression of genes known to be involved in migration, invasion and/or survival, including Tissue-factor (TF), Stratifin (SFN), Ephrin-B2, Sharp-2 and PAI-1. This „migration gene signature‟ was confirmed using real-time PCR analysis. Substitution of the native IGF-I within the IGF-I:IGFBP:VN complex with the IGF-I analogue, \[L24]\[A31]-IGF-I, which has a reduced affinity for the IGF-1R, failed to stimulate cell migration and interestingly, also failed to induce the differential gene expression. This supports the involvement of the IGF-1R in mediating these changes in gene expression. Furthermore, lentiviral shRNA-mediated stable knockdown of TF and SFN completely abrogated the increased cell migration induced by IGF-I:IGFBP:VN complexes in MCF-7 cells. Indeed, when these cells were grown in 3D Matrigel™ cultures a decrease in the overall size of the 3D spheroids in response to the IGF-I:IGFBP:VN complexes was observed compared to the parental MCF-7 cells. This suggests that TF and SFN have a role in complex-stimulated cell survival. Moreover, signalling studies performed on cells with the reduced expression of either TF or SFN had a decreased IGF-1R activation, suggesting the involvement of signalling pathways downstream of IGF-1R in TF- and/or SFN-mediated cell migration and cell survival. Taken together, these studies provide evidence for a common mechanism activated downstream of the IGF-1R that induces the expression of the „migration gene signature‟ in response to the IGF-I:IGFBP:VN complex that confers breast cancer cells the propensity to migrate and survive. Given the functional significance of the interdependence of ECM and growth factor (GF) interactions in stimulating processes key to breast cancer progression, this project aimed at developing strategies to prevent such growth factor:ECM interactions in an effort to inhibit the downstream functional effects. This may result in the reduction in the levels of ECM-bound IGF-I present in close proximity to the cells, thereby leading to a reduction in the stimulation of IGF-1R present on the cell surface. Indeed, the inhibition of IGF-I-mediated effects through the disruption of its association with ECM would not alter the physiological levels of IGF-I and potentially only exert effects in situations where abnormal over expression of ECM proteins are found; namely carcinomas and hyperproliferative diseases. In summary, this PhD project has identified novel, innovative and realistic strategies that can be used in vitro to inhibit the functions exerted by the IGF-I:IGFBP:VN multiprotein complexes critical for cancer progression, with a potential to be translated into in vivo investigations. Furthermore, TF and SFN were found to mediate IGF-I:IGFBP:VN-induced effects, thereby revealing their potential to be used as therapeutic targets or as predictive biomarkers for the efficacy of IGF-1R targeting therapies in breast cancer patients. In addition to its therapeutic and clinical scope, this PhD project has significantly contributed to the understanding of the role of the IGF system in breast tumour biology by providing valuable new information on the mechanistic events underpinning IGF-I:VN-mediated effects on breast cell functions. Furthermore, this is the first instance where favourable binding sites for IGF-II, IGFBP-3 and IGFBP-5 on VN have been identified. Taken together, this study has functionally characterised the interactions between IGF-I and VN and through innovative strategies has provided a platform for the development of novel therapies targeting these interactions and their downstream effects.

Circulating microRNAs involved in multiple sclerosis

Multiple sclerosis (MS) is an immune-mediated, demyelinating and neurodegenerative disease of the central nervous system. After traumatic brain injury, it is the leading cause of neurology disability in young adults. Considerable advances have been made in identifying genes involved in MS but the genetic and phenotypic complexity associated with this disease significantly hinders any progress. A novel class of small RNA molecules, microRNAs (miRNAs) has acquired much attention because they regulate the expression of up to 30% of protein-coding genes and may play a pivotal role in the development of many, if not all, complex diseases. Seven published studies investigated miRNAs from peripheral blood mononuclear cells, CD4+, CD8+ T cell, B lymphocytes, peripheral blood leukocytes, whole blood and brain astrocytes with MS risk. The absence of MS studies investigating plasma miRNA prompted the current investigation of identifying a circulating miRNA signature in MS. We conducted a microarray analysis of over 900 known miRNA transcripts from plasma samples collected from four MS individuals and four sex-aged and ethnicity matched healthy controls. We identified six plasma miRNA (miR-614, miR-572, miR-648, miR-1826, miR-422a and miR-22) that were significantly up-regulated and one plasma miRNA (miR-1979) that was significantly down-regulated in MS individuals. Both miR-422a and miR-22 have previously been implicated in MS. The present study is the first to show a circulating miRNA signature involved in MS that could serve as a potential prognostic and diagnostic biomarker for MS.

Integrative genomic profiling reveals conserved genetic mechanisms for tumorigenesis in common entities of non-Hodgkin's lymphoma

Recent developments in genomic technologies have resulted in increased understanding of pathogenic mechanisms and emphasized the importance of central survival pathways. Here, we use a novel bioinformatic based integrative genomic profiling approach to elucidate conserved mechanisms of lymphomagenesis in the three commonest non-Hodgkin's lymphoma (NHL) entities: diffuse large B-cell lymphoma, follicular lymphoma, and B-cell chronic lymphocytic leukemia. By integrating genome-wide DNA copy number analysis and transcriptome profiling of tumor cohorts, we identified genetic lesions present in each entity and highlighted their likely target genes. This revealed a significant enrichment of components of both the apoptosis pathway and the mitogen activated protein kinase pathway, including amplification of the MAP3K12 locus in all three entities, within the set of genes targeted by genetic alterations in these diseases. Furthermore, amplification of 12p13.33 was identified in all three entities and found to target the FOXM1 oncogene. Amplification of FOXM1 was subsequently found to be associated with an increased MYC oncogenic signaling signature, and siRNA-mediated knock-down of FOXM1 resulted in decreased MYC expression and induced G2 arrest. Together, these findings underscore genetic alteration of the MAPK and apoptosis pathways, and genetic amplification of FOXM1 as conserved mechanisms of lymphomagenesis in common NHL entities. Integrative genomic profiling identifies common central survival mechanisms and highlights them as attractive targets for directed therapy.

Relative abundance of full-length and truncated FOXP1 isoforms is associated with differential NFκB activity in Follicular Lymphoma

FOXP1 is a transcriptional repressor that has been proposed to repress the expression of some NFκB-responsive genes. Furthermore, truncated forms of FOXP1 have been associated with a subtype of Diffuse Large B-cell Lymphoma characterised by constitutive NFκB activity, indicating that they may inhibit this repression. We have shown that FL tumors have increased relative abundance of truncated FOXP1 isoforms and this is associated with increased expression of NFκB-associated genes. Our results provide strong evidence that relative FOXP1 isoform abundance is associated with NFκB activity in FL, and could potentially be used as a marker for this gene signature.

Heritage language for Chinese Australians : negotiating 'Chineseness' and, capitalising on resources in the lived world

The ethnic identity and commitment of Heritage Language Learners play salient roles in Heritage Language learning process. The mutually constitutive effect amongst Heritage Language Learner's ethnic identity, commitment, and Heritage Language proficiency has been well documented in social psychological and poststructuralist literatures. Both social psychological and poststructural schools offer meaningful insights into particular contexts but receive critiques from other contexts. In addition, the two schools largely oppose each other. This study uses Bourdieu's sociological triad of habitus, capital, and field to reconcile the two schools through the examination of Chinese Heritage Language Learners in Australia, an idiosyncratic social, cultural, and historical context for these learners. Specifically, this study investigates how young Chinese Australian adults (18-35 in age) negotiate their 'Chineseness' and capitalise on resources through Chinese Heritage Language learning in the lived world. The study adopts an explanatory mixed methods design to combine the quantitative approach with the qualitative approach. The initial quantitative phase addresses the first research question: Is Chinese Heritage Language proficiency of young Chinese Australian adults influenced by their investment of capital, the strength of their habitus of 'Chineseness', or both? The subsequent qualitative phase addresses the second research question: How do young Chinese Australian adults understand their Chinese Heritage Language learning in relation to (potential) profits produced by this linguistic capital in given fields? The initial quantitative phase applies Structural Equation Modelling to analyse the data from an online survey with 230 respondents. Findings indicate the statistically significant positive contribution made by the habitus of 'Chineseness' and by investment of capital to Chinese Heritage Language proficiency (r = .71 and r = .86 respectively). Subsequent multiple regression analysis demonstrates that 62% of the variance of Chinese Heritage Language proficiency can be accounted for by the joint contribution of 'Chineseness' and 'capital'. The qualitative phase of the study uses multiple interviews with five participants. It reveals that Chinese Heritage Language offers meaningful benefits for participants in the forms of capital production and habitus capture or recapture. Findings from the two phases talk to each other in terms of the inherent entanglement amongst habitus of 'Chineseness', investment of capital, and Chinese Heritage Language proficiency. The study offers important contributions. Theoretically, by virtue of Bourdieu's signature concepts of habitus, capital, and field, the study provides answers to questions that both social psychological and poststructuralist theories have long been struggling to answer. Methodologically, the position of 'pluralism' talks back to Bourdieu's theory and forwards to the mixed methods design. Particularly, the study makes a methodological breakthrough: A set of instruments was developed and validated to quantify Bourdieu's key concepts of capital and habitus within certain social fields. Practically, understanding Chinese Australians' heterogeneity and the potential drivers behind Chinese Heritage Language learning contributes to the growing interest in Chinese Australians' contemporary life experiences and helps to better accommodate linguistically diverse Chinese Heritage Language Learners in Chinese language courses. In addition, this study is very timely. It resonates with the recently released Australia in the Asian Century White Paper: Chinese Australians, with sound knowledge of Chinese culture and language obtained through negotiating their 'Chineseness' and capitalising on diverse resources for learning, will help to serve Australia's economic, social, and political needs in unique ways.

Gene expression profiling in human breast cancer – toward personalised therapeutics?

The most integrated approach toward understanding the multiple molecular events and mechanisms by which cancer may develop is the application of gene expression profiling using microarray technologies. As molecular alterations in breast cancer are complex and involve cross-talk between multiple cellular signalling pathways, microarray technology provides a means of capturing and comparing the expression patterns of the entire genome across multiple samples in a high throughput manner. Since the development of microarray technologies, together with the advances in RNA extraction methodologies, gene expression studies have revolutionised the means by which genes suitable as targets for drug development and individualised cancer treatment can be identified. As of the mid-1990s, expression microarrays have been extensively applied to the study of cancer and no cancer type has seen as much genomic attention as breast cancer. The most abundant area of breast cancer genomics has been the clarification and interpretation of gene expression patterns that unite both biological and clinical aspects of tumours. It is hoped that one day molecular profiling will transform diagnosis and therapeutic selection in human breast cancer toward more individualised regimes. Here, we review a number of prominent microarray profiling studies focussed on human breast cancer and examine their strengths, their limitations, clinical implications including prognostic relevance and gene signature significance along with potential improvements for the next generation of microarray studies.

Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma

We characterized the mutational landscape of melanoma, the form of skin cancer with the highest mortality rate, by sequencing the exomes of 147 melanomas. Sun-exposed melanomas had markedly more ultraviolet (UV)-like C>T somatic mutations compared to sun-shielded acral, mucosal and uveal melanomas. Among the newly identified cancer genes was PPP6C, encoding a serine/threonine phosphatase, which harbored mutations that clustered in the active site in 12% of sun-exposed melanomas, exclusively in tumors with mutations in BRAF or NRAS. Notably, we identified a recurrent UV-signature, an activating mutation in RAC1 in 9.2% of sun-exposed melanomas. This activating mutation, the third most frequent in our cohort of sun-exposed melanoma after those of BRAF and NRAS, changes Pro29 to serine (RAC1P29S) in the highly conserved switch I domain. Crystal structures, and biochemical and functional studies of RAC1P29S showed that the alteration releases the conformational restraint conferred by the conserved proline, causes an increased binding of the protein to downstream effectors, and promotes melanocyte proliferation and migration. These findings raise the possibility that pharmacological inhibition of downstream effectors of RAC1 signaling could be of therapeutic benefit.

Behind the cane

Composed by David Bridie and Andree Greenwell with script and lyrics by Margery Forde and Michael Forde, BEHIND THE CANE was community-driven music theatre, commissioned specially as the signature work the 2011 Queensland Music Festival. Co-presented by the QMF and the Whitsunday Regional Council in association with QUT Creative Industries, BEHIND THE CANE was created with and performed by over 180 Bowen residents and told the story of the South Sea Islanders who were brought to Australia to work in the cane fields in the 19 century and the journey of their descendants through the succeeding generations, through racial discrimination and economic hardship, to the present day. The large-scale spectacle event was performed the Sound shell on the Bowen harbour foreshore to audiences of 8,000 over 3 performances and included many of the descendants in featured roles.

Practical Modbus flooding attack and detection

The Modicon Communication Bus (Modbus) protocol is one of the most commonly used protocols in industrial control systems. Modbus was not designed to provide security. This paper confirms that the Modbus protocol is vulnerable to flooding attacks. These attacks involve injection of commands that result in disrupting the normal operation of the control system. This paper describes a set of experiments that shows that an anomaly-based change detection algorithm and signature-based Snort threshold module are capable of detecting Modbus flooding attacks. In comparing these intrusion detection techniques, we find that the signature-based detection requires a carefully selected threshold value, and that the anomaly-based change detection algorithm may have a short delay before detecting the attacks depending on the parameters used. In addition, we also generate a network traffic dataset of flooding attacks on the Modbus control system protocol.

Efficient top-k retrieval with signatures

This paper describes a new method of indexing and searching large binary signature collections to efficiently find similar signatures, addressing the scalability problem in signature search. Signatures offer efficient computation with acceptable measure of similarity in numerous applications. However, performing a complete search with a given search argument (a signature) requires a Hamming distance calculation against every signature in the collection. This quickly becomes excessive when dealing with large collections, presenting issues of scalability that limit their applicability. Our method efficiently finds similar signatures in very large collections, trading memory use and precision for greatly improved search speed. Experimental results demonstrate that our approach is capable of finding a set of nearest signatures to a given search argument with a high degree of speed and fidelity.

A Human identification technique using images of the iris and wavelet transform

A new approach for recognizing the iris of the human eye is presented. Zero-crossings of the wavelet transform at various resolution levels are calculated over concentric circles on the iris, and the resulting one-dimensional (1-D) signals are compared with model features using different dissimilarity functions.

Estrogen receptor β activation impairs mitochondrial oxidative metabolism and affects malignant mesothelioma cell growth in vitro and in vivo

Estrogen receptor (ER)-β has been shown to possess a tumor suppressive effect, and is a potential target for cancer therapy. Using gene-expression meta-analysis of human malignant pleural mesothelioma, we identified an ESR2 (ERβ coding gene) signature. High ESR2 expression was strongly associated with low succinate dehydrogenase B (SDHB) (which encodes a mitochondrial respiratory chain complex II subunit) expression. We demonstrate that SDHB loss induced ESR2 expression, and that activated ERβ, by over-expression or by selective agonist stimulation, negatively affected oxidative phosphorylation compromising mitochondrial complex II and IV activity. This resulted in reduced mitochondrial ATP production, increased glycolysis dependence and impaired cell proliferation. The observed in vitro effects were phenocopied in vivo using a selective ERβ agonist in a mesothelioma mouse model. On the whole, our data highlight an unforeseen interaction between ERβ-mediated tumor suppression and energy metabolism that may be exploited to improve on the therapy for clinical management of malignant mesothelioma.

Towards robotic visual and acoustic stealth for outdoor dynamic target tracking

Covertly tracking mobile targets, either animal or human, in previously unmapped outdoor natural environments using off-road robotic platforms requires both visual and acoustic stealth. Whilst the use of robots for stealthy surveillance is not new, the majority only consider navigation for visual covertness. However, most fielded robotic systems have a non-negligible acoustic footprint arising from the onboard sensors, motors, computers and cooling systems, and also from the wheels interacting with the terrain during motion. This time-varying acoustic signature can jeopardise any visual covertness and needs to be addressed in any stealthy navigation strategy. In previous work, we addressed the initial concepts for acoustically masking a tracking robot’s movements as it travels between observation locations selected to minimise its detectability by a dynamic natural target and ensuring con- tinuous visual tracking of the target. This work extends the overall concept by examining the utility of real-time acoustic signature self-assessment and exploiting shadows as hiding locations for use in a combined visual and acoustic stealth framework.

Acoustic Masking of a Stealthy Outdoor Robot Tracking a Dynamic Target

This work is motivated by the desire to covertly track mobile targets, either animal or human, in previously unmapped outdoor natural environments using off-road robotic platforms with a non-negligible acoustic signature. The use of robots for stealthy surveillance is not new. Many studies exist but only consider the navigation problem to maintain visual covertness. However, robotic systems also have a significant acoustic footprint from the onboard sensors, motors, computers and cooling systems, and also from the wheels interacting with the terrain during motion. All these can jepordise any visual covertness. In this work, we experimentally explore the concepts of opportunistically utilizing naturally occurring sounds within outdoor environments to mask the motion of a robot, and being visually covert whilst maintaining constant observation of the target. Our experiments in a constrained outdoor built environment demonstrate the effectiveness of the concept by showing a reduced acoustic signature as perceived by a mobile target allowing the robot to covertly navigate to opportunistic vantage points for observation.

Anatomy of sand beach ridges : evidence from severe Tropical Cyclone Yasi and its predecessors, northeast Queensland, Australia

[1] Four well-identified tropical cyclones over the past century have been responsible for depositing distinct units of predominantly quartzose sand and gravel to form the most seaward beach ridge at several locations along the wet tropical coast of northeast Queensland, Australia. These units deposited by tropical cyclones display a key sedimentary signature characterized by a sharp basal erosional contact, a coarser grain size than the underlying facies and a coarse-skewed trend toward the base. Coarse-skewed distributions with minimal change in mean grain size also characterize the upper levels of the high-energy deposited units at locations within the zone of maximum onshore winds during the tropical cyclone. These same coarse skew distributions are not apparent in sediments deposited at locations where predominantly offshore winds occurred during the cyclone, which in the case of northeast Australia is north of the eye-crossing location. These sedimentary signatures, along with the geochemical indicators and the degraded nature of the microfossil assemblages, have proven to be useful proxies to identify storm-deposited units within the study site and can also provide useful proxies in older beach ridges where advanced pedogenesis has obscured visual stratigraphic markers. As a consequence, more detailed long-term histories of storms and tropical cyclones can now be developed.