Polyhedral oligomeric silsesquioxanes (POSS) have attracted substantial academic interest for many years as hybrid materials and nanofillers for controlling thermal and mechanical properties, and providing thermal and chemical resistance while retaining ease of processing. A natural extension of these studies has been POSS-based amphiphiles and thin film coatings. Studies at the air/water (A/W) interface have shown that trisilanol-POSS derivatives are amphiphilic and form uniform Langmuir films, whereas closed-cage POSS derivatives are hydrophobic and aggregate. In previous work, a triester (POSS-triester) and a triacid (POSS-triacid) were synthesized from PSS-(3-hydroxypropyl)-heptaisobutyl (POSS-OH) and Weisocyanate and fully characterized by surface pressure – area per molecule (Π-A) isotherm and Brewster angle microscopy (BAM) studies at the A/W interface. The results indicated that POSS-triester is surface active forming a liquid expanded (LE) monolayer, whereas POSS-triacid forms a liquid condensed (LC) monolayer that is only weakly affected by pH. A face-on conformation was proposed and examined to understand the packing of POSS-based amphiphilic molecules at the A/W interface. The face-on/vertex-on comparison is rarely discussed for Langmuir monolayers at the A/W interface. In this thesis, three other POSS-based esters were synthesized from POSS-OH and aminopropylisobutyl-POSS (POSS-NH₂) using Weisocyanate and a similar isocyanate containing two tert-butyl protected carboxylic acids. The synthesized materials are characterized by Π-A isotherm and BAM. For POSS-OH based diester (PAlDE) and POSS-NH2 based diester (PAmDE), LE/LC phase transitions were observed in Π-A isotherms over part of the experimentally accessible temperature range and were attributed to a change from a vertex-on to face-on conformation. Apparent BAM images confirmed LC islands coexisted with the LE phase. The experimentally observed dynamic estimates of the critical temperatures (Tc) were estimated from a two-dimensional Clausius-Clapeyron analysis and were consistent with the temperature dependence of the Π-A isotherms. These LE/LC phase transitions are the first observed for POSS amphiphiles. / Ph. D.

Polyhedral oligomeric silsesquioxanes (POSS) have attracted substantial academic interest for many years as hybrid materials and nanofillers for controlling thermal and mechanical properties, and for providing thermal and chemical resistance while retaining ease of processing. A natural extension of these studies has been working on POSS-based amphiphiles and thin film coatings. Studies at the air/water (A/W) interface have shown that trisilanol-POSS derivatives are amphiphilic and form uniform Langmuir films, whereas closed-cage POSS derivatives are hydrophobic and aggregate. In this study, two novel POSS derivatives were synthesized from PSS-(3-hydroxypropyl)-heptaisobutyl substituted (POSS-OH) and completely characterized. Weisocyanate reacted with POSS-OH, and a POSS-based triester (POSS-triester) was obtained. Trifluoroacidolysis of the POSS-triester at room temperature afforded the corresponding triacid (POSS-triacid). Purified POSS-OH, POSS-triester, and POSS-triacid were studied by using surface pressure - area per molecule (? -A) isotherms as well as Brewster angle microscopy (BAM) at the air/water (A/W) interface. Compared with previous work on trisilanol-POSS derivatives, the results indicated that POSS-triester was surface active and formed a liquid-expanded (LE) monolayer. In contrast, POSS-triacid monolayers were more condensed (LC) and were not dramatically affected by changes in pH. Results for the lift-off areas (Alift-off), limiting areas (A0), collapse areas (Ac), and collapse pressures (? c) of POSS-OH, POSS-triester, and POSS-triacid were compared to trisilanolisobutyl-POSS (TiBP) and were interpreted in terms of possible molecular conformations. Whereas, TiBP has been hypothesized to exist in a vertex-on conformation, POSS-OH and POSS-triacid packing at the A/W interface was consistent with face-on conformations. For POSS-triester, the isotherm was consistent with a vertex-on conformation at low ? , but a face-on conformation at high ? . / Master of Science

Les protéines membranaires sont particulièrement riches en acides aminés aromatiques, tels que le tryptophane (W). On retrouve cette originalité dans beaucoup de peptides antimicrobiens et dans les protéines de fusion virales. La glycoprotéine de l'enveloppe de HIV-1, gp41, en est un exemple. Manifestement, les résidus W sont impliqués dans la perturbation des membranes et la formation des pores. L'objectif de ce travail est d'étudier le rôle des résidus W dans de telles activités en utilisant l'optique non linéaire. Pour cela, nous avons préalablement déterminé l'hyperpolarisabilité (le potentiel non linéaire) du W par la diffusion Hyper Raleigh (HRS). Puis nous avons montré une évolution de la réponse non linéaire de petits peptides synthétiques en fonction du nombre croissant de leurs résidus W. Ces résultats ont permis de suivre l'implication des tryptophanes de deux peptides K3W et gp41W, lors de leurs interactions avec des monocouches lipidiques à l'interface air-eau par la génération de second harmonique (SHG). D'autre part, l'influence de telles interactions sur la structure secondaire et l'orientation des peptides a été déterminée par le PM-IRRAS. Nous avons ainsi montré la cohérence entre les modifications du signal SHG, liées à des changements d'orientation des tryptophanes et celles des spectres de PM-IRRAS, dues à des changements d'orientation de la structure secondaire de gp41W / Membrane proteins are extremely rich in aromatic amino acids, like tryptophan (W). This particularity is found in many antimicrobial peptides and in several virus fusion proteins. An example of these fusion proteins is the HIV-1 envelop glycoprotein, the gp41. It is clear that the W residues are implicated in membrane perturbation and pore formation. The aim of this work was the investigation of the W residue role in such activities, using the nonlinear optic. First, we determined the W hyperpolarizabilité (nonlinear potential) by the Hyper Rayleigh Scattering (HRS). Then, the evolution of the nonlinear signal of small synthetic peptides, as function of the increasing number of their W residues, was demonstrated. These results allowed us to follow the W residue involvement of two peptides, K3W4 and gp41W, in the interaction with lipids monolayer at the air-water interface, using the second harmonic generation (SHG). The influence of such interaction in the peptide structure and orientation was determined using the PM-IRRAS. In conclusion, we showed the coherence between the SHG signal variation, due to the W orientation changes, and the PMIRRAS spectra modification, due to the gp41W helix orientation changes

La protéine BamB est une lipoprotéine de membrane externe appartenant au complexe BAM (β-Barrel Assembly Machinery) et impliquée dans l’assemblage des protéines de membrane externe (PME), la sensibilité aux antibiotiques, le contrôle de l’expression des trois systèmes de sécrétion de type III (T3SS) et la virulence de Salmonella. Chez E. coli, au sein du complexe BAM, elle interagit directement avec la protéine BamA. De plus, chez cette bactérie, BamB présente une activité sérine-thréonine kinase. Afin de mieux caractériser le rôle de BamB, nos objectifs ont été d’étudier (1) l’impact de l’altération de l’interaction de BamB avec le complexe BAM ou de sa séquestration dans le cytoplasme sur l’ensemble des rôles décrits de BamB et (2) l’activité kinase putative de BamB chez Salmonella. Nos résultats montrent que certains rôles de BamB sont dissociables entre eux et que l’interaction BamA/BamB n’est pas requise pour le rôle de BamB dans le contrôle de l’expression des T3SS, la virulence de Salmonella et l’assemblage des PME à la membrane externe. Aucune activité kinase ni aucune activité cytoplasmique de la protéine n’a pu être formellement démontrée. / BamB is an outer-membrane lipoprotein belonging to the BAM complex (β-Barrel Assembly Machinery). In Salmonella, it is involved in the assembly of outer membrane proteins (OMP), in antibiotic susceptibility, in the transcriptional control of the three Type-Three-Secretion-Systems (T3SS) related genes and also in virulence. In E. coli, BamB interacts directly with the BamA protein. Moreover, BamB has been shown to have a serine-threonin kinase activity in this bacterium. In order to better characterize the roles of the BamB protein, our purposes were to study (1) the impact of the alteration of the interaction of BamB with the BAM complex or of its cytoplasmic sequestration and (2) its putative kinase activity in Salmonella. Our results show that some of the BamB roles are dissociable and that the BamA/BamB interaction is not required for T3SS expression, Salmonella virulence or OMP assembly in the outer membrane. Currently, neither a kinase activity nor a cytoplasmic activity has been clearly demonstrated for this protein.

Outer membrane proteins (OMPs) maintain the viability of Gram-negative bacteria by functioning as receptors, transporters, ion channels, lipases, and porins. Folding and assembly of OMPs involves synchronized action of chaperones and multi-protein machineries which escort the highly hydrophobic polypeptides to their target outer membrane in a folding competent state. Previous studies have identified proteins and their involvement along the OMP biogenesis pathway. Yet, the mechanisms of action and the intriguing ability of all these molecular machines to work without the typical cellular energy source of ATP, but solely based on thermodynamic principles, are still not well understood. Here, we highlight how different single-molecule studies can shed additional light on the mechanisms and kinetics of OMP biogenesis.

The main theme of this thesis research is concerned with developing a computational pipeline for processing Next-generation RNA sequencing (RNA-seq) data. RNA-seq experiments generate tens of millions of short reads for each DNA/RNA sample. The alignment of a large volume of short reads to a reference genome is a key step in NGS data analysis. Although storing alignment information in the Sequence Alignment/Map (SAM) or Binary SAM (BAM) format is now standard, biomedical researchers still have difficulty accessing useful information. In order to assist biomedical researchers to conveniently access essential information from NGS data files in SAM/BAM format, we have developed a Graphical User Interface (GUI) software tool named SAMMate to pipeline human transcriptome quantification. SAMMate allows researchers to easily process NGS data files in SAM/BAM format and is compatible with both single-end and paired-end sequencing technologies. It also allows researchers to accurately calculate gene expression abundance scores.

The integration of disabled children into regular schools is a current educational and social issue causing widespread interest, concern and debate throughout Australia. The most controversial and innovative adoption of integration policy has occurred in Victoria since the release of the Collins Report in 1984. The present study was conducted in 26 State primary schools in the Bendigo area of the Loddon Campaspe Mallee region of Victoria where disabled children had been integrated in regular classrooms with the assistance of a paid teacher aide during 1988. The purpose of the study was to survey the concerns of those teachers into whose classes children with disabilities had been integrated. The Stages of Concern (SoC) dimension of the Concerns-Based Adoption Model (C-BAM) was chosen as the research methodology. C-BAM was developed at the Research and Development Center for Teacher Education, University of Texas at Austin, and for the purpose of this study, the methodology consisted of a questionnaire of 35 standardized items (the Stages of Concern Questionnaire), and a School Survey. The study set out to identify the concerns of teachers (ii) toward integration, and to establish reasons why teachers are at particular stages of concern. Factors included teachers' age, gender, number of years of teaching experience, qualifications and in-service training. Other issues related to the disabled children themselves, the school, and factors such as availability of resources, funding levels, and access to support systems. This study developed from the policy document Integration in Victorian Education (the Collins Report, 1984). Since then, the Ministry of Education has published two additional booklets (in January and February, 1987), which partly address some of the issues included in this thesis. These include resourcing, in-servicing and the legal implications of the innovation. The analysis of the data points to major shortcomings which will jeopardize the implementation process and the likely success of the innovation. A number of recommendations have been suggested, with particular reference to the pre-service and in-service training of teachers, and issues relating to funding and resources. The findings have implications for all classroom teachers, as potentially all are required to accept disabled children into their classes. The results and recommendations also have relevance for the Ministry of Education, whose responsibility it is to ensure that the integration of disabled children into regular classes is fully supported at a government level, and for training institutions, whose task it is to provide appropriate pre-service and in-service programs for present and future classroom teachers.

Natural hazards kill 82,500 people globally in a typical year, with earthquakes as the largest cause of death amongst all natural hazards in Central and Southern America, East Asia, Europe, and the Near East. Damages are highest in middle-income countries due to lack of resources for hazard prevention and mitigation. Dancing to the Desert concentrates on Bam, Iran, as a typical post earthquake city, searching for architecture appropriate for post-disaster cities of hot-arid climates. Dancing to the Desert is a discourse on current seismic, urban, and architectural design conditions in hot-arid climates of the globe, and searches for an appropriate architecture for post-disaster cities in developing regions of the desert climate. Chapter One includes analysis on global seismic hazard conditions, focusing on the hot-arid climates in the world and concentrating on the city of Bam, Iran. Chapter Two includes a detailed analysis of the traditional as well as contemporary architecture of Bam, searching for appropriate architectural elements to use in the proposed architecture. Chapter Three proposes a Pilot Project for an orphanage in Bam, based on the architectural elements and strategies discussed in Chapter Two. Through scientific research, case studies, a site visit to Bam, and discussions with local residents, this thesis finds an appropriate proposal adaptable to all post-disaster cities of the hot-arid climate. It also suggests various strategies for disaster prevention and mitigation through public education. These strategies educate the public in employing cultural and environmental friendly resilient architecture, which will subsequently reduce damage and fatalities on brisk of disaster. It also familiarizes the public with the proposed disaster prevention and mitigation strategies and facilitates the adoption of the proposed design in future post-disaster conditions.

Boundary Approximation Method (BAM), or the Collocation Trefftz Method called in the literature, is the most efficient method to solve elliptic boundary value problems with singularities. There are several versions of BAM in practical computation, including the Numerical BAM, Symbolic BAM and their variants. It is known that the Symbolic BAM is much slower than Numerical counterpart. In this thesis, we improve the Symbolic BAM to become the fastest method among all versions of BAM. We prove several important lemmas to reduce the computing time, and a recursive procedure is found to expedite the evaluation of major integrals. Another drawback of the Symbolic BAM is its large condition number. We find a good and easy preconditioner to significantly reduce the condition number. The numerical experiments and comparison are also provided for the Motz problem, a prototype of Laplace boundary value problem with singularity, and the Schiff's Model, a prototype of biharmonic boundary value problem with singularity.

Natural hazards kill 82,500 people globally in a typical year, with earthquakes as the largest cause of death amongst all natural hazards in Central and Southern America, East Asia, Europe, and the Near East. Damages are highest in middle-income countries due to lack of resources for hazard prevention and mitigation. Dancing to the Desert concentrates on Bam, Iran, as a typical post earthquake city, searching for architecture appropriate for post-disaster cities of hot-arid climates. Dancing to the Desert is a discourse on current seismic, urban, and architectural design conditions in hot-arid climates of the globe, and searches for an appropriate architecture for post-disaster cities in developing regions of the desert climate. Chapter One includes analysis on global seismic hazard conditions, focusing on the hot-arid climates in the world and concentrating on the city of Bam, Iran. Chapter Two includes a detailed analysis of the traditional as well as contemporary architecture of Bam, searching for appropriate architectural elements to use in the proposed architecture. Chapter Three proposes a Pilot Project for an orphanage in Bam, based on the architectural elements and strategies discussed in Chapter Two. Through scientific research, case studies, a site visit to Bam, and discussions with local residents, this thesis finds an appropriate proposal adaptable to all post-disaster cities of the hot-arid climate. It also suggests various strategies for disaster prevention and mitigation through public education. These strategies educate the public in employing cultural and environmental friendly resilient architecture, which will subsequently reduce damage and fatalities on brisk of disaster. It also familiarizes the public with the proposed disaster prevention and mitigation strategies and facilitates the adoption of the proposed design in future post-disaster conditions.