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This research integrates the theoretical implications of risk perception, the social amplification of risk, and the role of place-specific contexts, in order to explore the various perceptions surrounding Florida red tides. Florida red tides are a naturally-occurring event, yet most scientists agree that they are increasing in frequency, duration, and severity. This has profound implication for public health, the local economy, and the biological community. While many of the negative impacts are not easily controllable at this time, some of the secondary impacts can be mitigated through individuals' responses. Unfortunately, public perceptions and consequent reactions to red tides have not been investigated. This research uses questionnaire surveys, semi-structured interviews, and newspaper content analysis to explore the various perceptions of risk surrounding red tides. Surveys and interviews were conducted along two Florida west coast beaches, Fort De Soto Park and Siesta Key. Results indicate that the underlying foundations of the social amplification of risk framework are applicable to understanding how individuals form perceptions of risk relative to red tide events. There are key differences between the spatial locations of individuals and corresponding perceptions, indicating that place-specific contexts are essential to understanding how individuals receive and interpret risk information. The results also suggest that individuals may be lacking efficient and up-to-date information about red tides and their impacts due to inconsistent public outreach. Overall, particular social and spatial factors appear to be more influential as to whether individuals amplify or attenuate the risks associated with red tides.

Despite significant advances in diagnosis and treatment, breast cancer remains the leading cause of cancer-related deaths in Australian women. Colorectal cancer is the second most common cancer in both males and females; after prostate and breast cancer, respectively, and excluding non-melanocytic skin cancer. Both breast cancer and colorectal cancer follow a common progressive course of illness; presenting (at least initially) with benign symptoms that can be treated by ablation (or removal) of the affected area. Cancer progression is associated with breakdown of tissue barriers (such as basement membranes), leading to the spread of cancer cells (via the vasculature or lymphatic system), and the establishment of secondary metastatic disease at green-field sites. Secondary tumours presenting in the lungs, ovaries, liver, bone, or brain are associated with chronic-debilitating symptoms that are difficult to treat, and will result in death. In the case of breast and colon cancer, effective early therapeutic intervention does have a significant impact upon patient survival. Tumour progression in breast and colon carcinomas is characterised by invasion of the surrounding stroma, and the acquisition of stromal characteristics, by previously epithelial cells. This progression is associated with the expression of extracellular proteases (ECPs) and increased motility. The process of mesenchymal transformation that tumour cells undergo is also referred to as the epithelial to mesenchymal transition (EMT). In general terms the aim of the study, presented in this thesis, was to investigate gene expression in cancer biology; and to characterise changes in breast cancer and colon cancer, with a focus on those genes, and gene products that may play a role in metastasis, including a family of ECPs, the matrix metalloproteinases (MMPs). In our laboratory, we have applied methods in microdissection, differential display polymerase chain reaction amplification (DD-PCR), and array hybridisation analysis to identify gene expression patterns in late stage archival formalin fixed paraffin embedded (FFPE) breast tumour biopsies that may be indicative of the EMT; or the response to the surrounding stroma/interstitium to the presence of the tumour.' The quality of nucleic acid obtainable from FFPE material presents a considerable challenge for gene expression studies. In order to identify tissue specific gene expression patterns, DD-PCR products, amplified from message obtained following segregation of tumour tissue from surrounding stroma, was hybridised to arrayed cDNA libraries created from stromal tumours, or sarcomas. In this way, 21 known genes, or expressed sequence tags (ESTs), were identified. These included the cytoskeletal element and EMT marker, vimentin, the mammary developmental factor and, signal transducer and activator of transcription (STAT)-3, and the cargo selection protein (TIP47). Seventeen genes showed differential expression in either the tumour, or stromal fractions. When applied to transformed breast cancer cell lines (MDA-MB-435 & T47D) DD-array analysis revealed a further 17 genes that were differentially regulated in invasive cells, compared with those displaying a less invasive phenotype. Six of the ESTs identified by DD-PCR array analysis, had no known (or predicted) function. For example, bcaf-2 was identified as the 3'-end of a putative open reading frame (ORF) localised to chromosome 6, while bcaf-10 showed homology with a known ORF. In order to analyse the expression of these bcafs further, a stromal cell culture model, representative of the original osteosarcoma cDNA libraries from which they were obtained, was used. In this model, CD14' (or adherent) peripheral blood mononuclear cells (PBMCs) treated with macrophage colony stimulating factor (M-CSF), can be allowed to differentiate into macrophage-like (ML) cells; while cells treated with M-CSF, and the receptor activator of NF-KB ligand (RANKL) will differentiate into multinucleate osteoclast-like (OCL) multinucleate giant cells. Uniquely, the stromal EST, bcaf-2 was expressed only by RANKL-treated (or OCL) cells. bcaf-2 and other ESTs, identified by DD-PCR analysis (and recently published) are the subject of on going research in our laboratory. The role of RANKL in mammary gland development and bone metastasis suggested that the identification of a RANKL-regulated stromal factor in breast tissue (bcaf-2) was not an artefact. RANKL is a membrane-bound, member of the tumour necrosis factor (TNF)-a cytokine super family. In order to test the hypothesis that RANKL might act as an inflammatory cytokine to regulate clinically significant stromal gene expression in the breast, we employed quantitative real time PCR analysis to examine the relative levels of selected members of a group of metal dependent ECPs, the matrix metalloproteinases (MMPs). RNA was extracted from ML cells and OCL cells, as well as RANK positive breast cancer cell lines (T47D, MDA-MB-435 & MCF-7). When the relative levels of protease mRNA were compared we demonstrated a significant (>20- fold) specific increase in collagenase (collagenase 2lMMP-8 and collagenase 3lMMP-13), and the tissue inhibitor of MMP (TIMP)-2 expression in M-CSF and RANKL treated PBMCs cells. When the assay was applied to RANKL treated breast cancer cell lines (MCF-7, T47D & MDAMB- 231), minor (40-fold) but potentially significant alterations in stromal protease gene expression were observed. The changes observed did not however, support the hypothesis that RANKL might act as an inflammatory cytokine to induce significant alterations in ECP expression in breast cancer cells. To investigate the role of RANKL as a driver of EMT in aberrant breast epithelium, total message (mRNNcDNA) from T47D, MCF-7, MDA-MB-231 cells, and message from the same cell lines treated with RANKL were compared by comparative fluorescent cDNA microarray analysis. Of the 1,700 targets available on the arrays, this study identified 160 that were differentially expressed in RANKL treated cells. The results suggest that RANKL may promote rather than suppress a mammary epithelial phenotype in breast cancer. In fact a putative mesenchymal to epithelial transition (MET) was observed following microscopic analysis, and this finding is the subject of on going research in our laboratory. Sporadic structural alterations in certain mitogenic factors represent important early events in cancer progression, while inherited mutations govern familial susceptibility to disease. In colon cancer, a close link exists between Winglessllnt (WNT) signalling, disease pathology, and the expression of MMPs. To examine the relationship between protease expression and structural genetic alterations in this EMT-linked signalling pathway, and others, we applied combined QPCR analysis of MMP expression and PCR-Single Strand Conformation Analysis (SSCA) to 26 colonic tumours, and patient-matched normal colonic mucosa. In this study, significant correlations between the expression of ECPs, and a key mediator of WNT signalling (p-catenin) were identified. While tumours possessing specific functional mutations in K-Ras, were found to group with phenotypic clustering based on protease gene expression. This result may be due to an interruption of normal interactions between RasIRaf signalling and transforming growth factor (TGF) P signalling, via Sma- and Mad- related protein (SMAD) signalling. These results demonstrate that the already identified link between mutations in kinase signalling, and aspects of gross colon tumour morphology (such as dysplasia) may be due to aberrant MMP expression patterning. The final aim of this research was to utilise methods developed in microdissection and specific Q-PCR analysis, to identify whether tumour-stroma differences in MMP gene expression might be used as markers of disease pathology. Total RNA from tumour, and biopsy-matched adjacent stromal tissue were segregated from 35 FFPE archival breast tumour biopsies. Comparison with stroma identified specific associations between TIMP-2 expression in the stroma and lymph node involvement, as well as stromelysin-3 (MMP-I I ) and TIMP-I expression and calcification of the tumour. Furthermore, a significant correlation was identified in the pattern of gelatinase (gelatinase AIMMP-2 & gelatinaseB1MMP-9) expression; while no significant correlation was identified in tumour-stroma MMP gene expression differences, and tumour grade, or hormone receptor status. These results suggest that coordinated changes within the tumour, and proximal stromal tissues (rather than tissue specific changes per se), regulate pathologically significant changes in breast carcinogenesis. In conclusion, this thesis describes the use of novel techniques in specific and global gene expression analysis that permitted examination of stromal gene expression changes in epithelial tumour progression. Microdissection facilitated localisation of expression to particular tissues, while cell culture models provided material with which to optimise and demonstrate the efficacy of techniques used (where tumour material itself was not abundant). Furthermore, we have identified significant and specific correlations between general stromal protease gene expression changes, a putative mammary epithelial differentiation factor (RANKL), alterations in growth factor signalling, and epithelial tumour pathology in the breast and colon. The combination of techniques developed in this study may assist in improvement of categorisation of tumours in clinical pathology. Specifically, the development of novel grading systems that link underlying molecular genetic changes with changes in tumour pathology. These processes may assist to improve diagnosis and provide more effective patient/tumour-specific drug therapies.

Ce mémoire présente la génération de similaritons dans un amplificateur Raman à dispersion normale aux longueurs d'onde des télécommunications optiques. Les profils temporels expérimentaux obtenus par caractérisation FROG mettent en évidence un profil d'intensité parabolique associé à une dérive de fréquence linéaire, en accord avec les résultats d'un modèle numérique.<br />Différentes propriétés théoriques des similaritons sont ensuite vérifiées expérimentalement. La dynamique de deux impulsions similaritons à des longueurs d'ondes centrales identiques ou différentes est également étudiée : les similaritons sont robustes vis-à-vis des collisions alors que l'interaction de deux similaritons entraîne la génération d'un train de solitons noirs à haut-débit.<br />Dans une dernière partie, nous évoquons l'application des similaritons à trois domaines : la génération d'impulsions ultracourtes, la mise en forme d'impulsions et enfin la régénération optique de signaux télécom à haut-débit.

Ce travail de thèse constitue une contribution théorique et expérimentale aux études sur les effets d'optique non linéaires dans les cristaux photoniques en semiconducteurs III-V. Les cristaux photoniques sont des matériaux artificiels présentant une modulation périodique de l'indice de réfraction à l'échelle de la longueur d'onde de la lumière. En contrôlant les paramètres physiques de ces structures (périodicité, motifs, facteur de remplissage en air...), il est possible de réaliser une véritable ingénierie des propriétés dispersives de la matière pour, par exemple, empêcher la lumière de se propager dans toutes les directions de l'espace. L'objectif de cette thèse est de combiner les propriétés dispersives uniques des cristaux photoniques aux propriétés non linéaires très intéressantes des semiconducteurs III-V afin d'exalter les interactions non linéaires entre la lumière et la matière. Nous verrons que les cristaux photoniques 1D et 2D sont adéquats pour obtenir des effets non linéaires du second ordre (génération de seconde harmonique) efficaces sur de courtes distances car ils permettent de réaliser la condition d'accord de phase dans des matériaux fortement non linéaires comme l'AlxGa1-xAs tout en ralentissant la lumière. Nous montrerons également que les cristaux photoniques 2D en semiconducteurs III-V permettent de réaliser les briques de bases actives pour le traitement du signal tout optique comme des sources lasers, des amplificateurs, des commutateurs ultrarapides...

Ce travail de thèse vise l'étude des interactions entre les plasmas utilisés en microélectronique et les résines à amplification chimique. Les procédés de fabrication employés en microélectronique nécessitent l'utilisation de matériaux polymères. Ces matériaux permettent dans un premier temps de définir des motifs représentant les différentes parties des composants électroniques, grâce à une étape de lithographie. Dans la suite du procédé de fabrication, ils jouent le rôle de masque afin de traiter les surfaces sous-jacentes aux endroits désirés. Une de ces étapes pour laquelle le polymère joue le rôle de masque est la gravure sèche par plasma, qui permet de transférer les motifs créés par lithographie dans le substrat et ainsi obtenir la structure du circuit intégré. Ainsi les résines employées doivent être suffisamment résistantes afin de remplir efficacement leur rôle de masque à la gravure. L'objectif principal de ce travail de thèse a donc été d'étudier la résistance à la gravure des résines à amplification chimique de dernière génération (193 nm) afin de mettre en évidence les dégradations de ces matériaux pendant les étapes de gravure, et de trouver des moyens d'améliorer leur résistance. Dans un premier temps le comportement des résines 193 nm a été comparé à une résine de référence plus résistante. Des analyses physico-chimiques (FTIR, XPS, DSC et TGA) ont permis de mettre en évidence les faiblesses des résines 193 nm liées à leur structure acrylique. La chimie des résines 193 nm étant complexe et devant répondre à de nombreux critères notamment pour l'étape de lithographie, il est préférable de les renforcer en tentant de contrôler les dégradations observées. Ainsi le deuxième objectif de la thèse a été d'étudier le renforcement des résines par des procédés plasma en utilisant des conditions particulières différentes des étapes de gravure. Les modifications spécifiques apportées par ces traitements sur les résines ont donc été mises en évidence, et le rôle prépondérant des émissions UV a notamment pu être prouvé. Enfin ces traitements plasma ont été appliqués sur des lignes de résines afin de montrer le fort potentiel applicatif de ces procédés pour améliorer deux points critiques : la vitesse de gravure et la rugosité des motifs.

Nous avons consacré cette thèse à l'étude des différents processus non-linéaires de l'interaction rayonnement-matière et en particulier à la génération des solitons de gap dans les milieux non-linéaires à bandes interdites. Dans la première partie nous avons utilisé un modèle semi-classique de Maxwell-Bloch pour décrire l'interaction d'un milieu à deux niveaux quantiques avec charges avec un champ électromagnétique classique à travers la densité de population, qui est à l'origine même de la non-linéarité. Le couplage non-linéaire qui en résulte génère des phénomènes particulièrement intéressants (génération et diffusion des solitons de gap) à la résonance, quand la pulsation du champ appliqué est proche de la fréquence de transition du milieu à deux niveaux. La dynamique non-linéaire observée numériquement est expliquée à l'aide d'un modèle de Schrödinger non-linéaire dans un potentiel lié aux charges du milieu. La deuxième partie concerne l'étude théorique de la dynamique des solitons quadratiques dans les amplificateurs paramétriques optiques (OPA). Les équations décrivant l'interaction à trois ondes dégénérée dans un cristal biréfringent non-linéaire ont été établies en prenant en compte la diffraction transverse et le walk-off spatial. Nous avons proposé une méthode pour résoudre le problème ardu de la détermination du seuil de supratransmission non-linéaire dans les OPA et nous avons généralisé les résultats obtenus à une grande classe de systèmes non-linéaires non-intégrables à composantes multiples.

With the full sequence of the human genome now available, anexciting era in biomedical research has started. The sequenceprovides information about all our genes and greatly increasesthe scope to compare genetic activities in different cells, toanalyze genetic variation between individuals and betweendifferent species and, most importantly, to investigatesystematically the whole genome in a gene-by-gene manner, andthus increase our understanding of gene function. This thesis describes studies in which developments weremade in several areas of functional genomics. Messenger RNAlevels were analyzed by the use of an amplification procedure,in which the 3´-ends of the transcripts were selected inorder to amplify the mRNA population in an unbiased fashion. Bysonicating cDNA originating from expressed mRNA, uniformlysized representatives of the transcripts,“signaturetags”, were obtained. The mRNA levels in the original mRNApopulation correlated well with the levels in the amplifiedmaterial, as verified by microarray analysis and realtimequantitative PCR. The expressed transcripts can be identifiedusing pyrosequencing, by comparing the obtained sequenceinformation from the signature tags to information contained invarious sequence databases. In one of the articles, the use ofpyrosequencing is illustrated by efforts to find genes involvedin the disease progression of atherosclerosis. More challenging than the study of mRNA levels is to analyzewhen, where and how proteins fulfill their wide-ranging rolesin all the various cellular processes. Proteins are morecomplex biomolecules than mRNA, each having unique properties.Current techniques for studying proteins need much improvement,and are often limited to investigations of a specific portionof the proteome. One approach for studying the whole proteomeis to systematically generate reagents with specific affinityfor the proteins encoded by the genome, one by one. Theaffinity reagents can be used as flags for their targets,providing a flag-specific detection system, so that the targetproteins can be sub-cellularly localized in the majority ofhuman tissues in an array format. One of the articles includedin the thesis presents a pilot project for large-scale affinityreagent production. The aim was to provide a sound basis forwhole proteome studies, but as a pilot study this investigationwas limited to the proteins encoded by human chromosome 21. Allputative genes on the chromosome were subjected to antibodygeneration in a systematic manner. Small, uniform, and easilyproduced representative portions of the full-length proteinswere expressed. These were denoted“Protein EpitopeSignature Tags”and were designed to be unique for theirfull-length counterparts. The antibodies were produced inrabbits and two of the articles in the thesis discuss differentapproaches for affinity purification of the antibodies toachieve the highest possible specificity towards the targets.The resulting“mono-specific”, but still“multi-epitope”, antibodies can be used for a widerange of additional biochemical studies, such as protein arrayand protein pull-out analyses. <b>Keywords:</b>functional genomics, 3´-end signaturetags, pyrosequencing, amplification, PrEST, chromosome 21,polyclonal antibodies, dual expression, affinitypurification.