My thesis looks to define a harmonious relationship between architecture and nature. The critical intersection of the realm of land and the realm of building is what has most influenced my design process. This place where building meets nature needs to be both meaningful and balanced. The investigation involves how to respect the current condition and compliment it with an architecture serving as connection for the human experience. / Master of Architecture

The propagation of radiowaves through ionospheric irregularities can lead to random amplitude and phase fluctuations of the signal, otherwise known as scintillation, which can severely impact the performance of Global Navigation Satellite System (GNSS) and communication systems. Research into high latitude scintillation, through statistical analysis and inverse modeling, was completed to provide insight into the temporal and spatial distribution, and irregularity parameters, which can ultimately support the development of impact mitigation techniques, and deepen our understanding of the underlying physics. The work in this dissertation focused on the statistical analysis of Global Positioning System (GPS) scintillation data, data inversion, two-dimensional (2D) and three-dimensional (3D) scintillation modeling. The statistical analysis revealed distinct trends in the distribution of scintillation, while demonstrating that for GPS signals, phase scintillation occurs most frequently and can be treated as stochastic Total Electron Content (TEC); findings which have significant implications for impact mitigation. For the first of two inversion studies, scintillation data associated with a series of Polar Cap Patches (PCPs), which are common large-scale high latitude structures, was inverted to gain insight into the composition of the underlying irregularities. The results of this study suggest that the irregularities can be modeled as rods interbedded with sheets, which is knowledge that is crucial for the anchoring of models used to develop system mitigation techniques. The final study presents the results of modeling and inversion work to identify the conditions under which a 2D analytic version of the 3D numerical Satellite-beacon Ionospheric-scintillation global model of the upper atmosphere (SIGMA) model can be used to perform modeling in high latitude regions. During the study, it was found that the analytic model tends to diverge for electron density variance times irregularity layer thickness values exceeding 2, matched reasonably well for correlation length to thickness ratios up to 0.2, and was incompatible when ratios approached 0.35. An elevation angle limitation was also identified for the 2D model, and inflated values for the electron density variance were observed overall, which are thought to result from the weak scatter limits of the analytic model. These inflated values were particularly acute in the auroral zone during elevated conditions and suggest that the analytic model used in the study is not well suited for modeling the highly elongated irregularities associated with auroral precipitation. / Doctor of Philosophy / The ionosphere is a region of the earth's atmosphere extending from approximately 90 to 1000 km in altitude. Radio wave signals which travel through irregularities in the ionosphere can be distorted in a way that can lead to random amplitude and phase fluctuations of the signal, otherwise known as scintillation, which can severely degrade the performance of navigation and communication systems. Research into high latitude scintillation, through statistical analysis, and data and model matching, was completed to provide insight into the time and space distribution, and irregularity parameters, in order to ultimately deepen our understanding of the physics and to help develop better models. The work in this dissertation focused on the statistical analysis of GPS scintillation data, data and model matching, and 2D and 3D irregularity modeling. The statistical analysis revealed distinct trends in the distribution of scintillation, while demonstrating that for GPS signals, phase scintillation occurs most frequently but the impacts can be corrected if measured; findings which have significant implications for impact mitigation. For the first of two model and data matching studies, scintillation data associated with a series of common large-scale high latitude structures called PCPs, was matched to a model to gain insight into the composition of the underlying irregularities. The results of this study suggest that the irregularities can be modeled as vertical rods oriented along the magnetic field interbedded within flat sheets, which is knowledge that is crucial for having confidence in the models used to develop system mitigation techniques. The final study presents the results of modeling and data matching work to identify the conditions under which a 2D or 3D model can be used to perform irregularity modeling in the high latitude regions. During the study, it was found that the 2D model tends to diverge from the 3D model for significant variations in the ionosphere, and when irregularity rods are highly elongated. A signal propagation path elevation angle limitation was also identified for the 2D model, and inflated values for the predicted ionospheric variations were observed overall, which are thought to result from limits of the 2D model compared to the more general 3D version. These inflated values were particularly acute in the auroral region during elevated conditions and suggest that the 2D model used in the study is not well suited for modeling the highly elongated irregularities associated with aurora effects.

Uveal melanoma (UM) is the most common primary cancer of the eye and its prognosis is strongly influenced by the occurrence of metastases, which are both rapidly developing and mostly fatal. The most frequent driver mutations occur in a small number of genes including GNAQ, GNA11, BAP1, CYSLTR2 and SF3B1. Due to a lack of suitable animal models, the mechanism through which mutations in these genes cause or cooperate in UM initiation and progression is still largely unknown. We aimed at generating transgenic strains expressing the human mutant proteins in zebrafish uveal melanocytes, using the kita promoter. We used the binary Gal4/UAS system to express the mutant genes mentioned above. Moreover, we performed xenotransplantation experiments with uveal melanoma human and zebrafish cell lines in optically-clear, immunocompromised, zebrafish larvae. Transplanted fish developed melanoma near the site of transplantation in two weeks and showed metastatic growth within one month of age. This approach could be used for short-term assays in larvae, and be further developed for long-term uveal melanoma studies. In parallel, we performed a chemical screen using a transgenic model previously generated in our laboratory, where oncogenic RAS is expressed under the kita promoter. As adults transgenic kita:RAS develop cutaneous melanoma with high frequency and uveal melanoma with a much lower percentage. Larvae showed an increased number of melanocytes already at 3 days post fertilization (dpf) as the earliest evidence of abnormal melanocyte growth. Using this model we performed a chemical screen based on automated detection of a reduction of melanocytes number caused by any of the 1280 FDA or EMA approved drugs of the Prestwick library. The analysis showed that 55 molecules were able to reduce by 60% or more the number of melanocytes per embryo. We identified clotrimazole, as the best candidate. The molecule is an azole derivative acting on the energetic metabolism of melanoma cells. We further tested two compounds for each of the 5 pharmacological classes, and a farnesyltransferase inhibitor (lonafarnib), that inhibits an essential post-translational modification of HRAS and suppresses the hyperpigmentation phenotype. Combinations of clotrimazole and lonafarnib showed the most promising results in zebrafish embryos, allowing a dose reduction of both drugs. We performed validation of these observations in the metastatic human melanoma cell line A375M, and in normal human epithelial melanocytes (NHEM) as control cells, in order to investigate the mechanism of action of clotrimazole in blocking the proliferation of transformed melanocytes. Viability assay and analysis of energy metabolism in clotrimazole treated cells show that this drug specifically affects melanoma cells in vitro and transformed melanocytes in vivo, having no effects on NHEM or wild type larvae. Similar effects were observed with another hit of the antifungal class, miconazole. Furthermore, we show that the effects of clotrimazole are mediated by the inhibition of hexokinase activity and suggest further testing of clotrimazole in combinatorial treatments. In conclusion, this thesis investigated different possibilities of modeling the rare cancer uveal melanoma in zebrafish, using both transgenic and transplantation approaches, and developed a pipeline for a high-throughput, semi-automated chemical screen in a zebrafish melanoma that identified clotrimazole and miconazole as targeting a metabolic vulnerability in melanoma cells.

The DNA damage response is a cell-wide response that coordinates repair and cell-cycle progression. Crucial to fidelity of genetic propagation, survival, and apoptosis, dysfunctions in the response are at the root of genome instability syndromes and cancer predisposition in mammalian cells. Within the response lie hubs of coordination, called checkpoints, whose members and organization are ubiquitous amongst eukaryotes. The high conservation of these checkpoints enable the study of their dynamics by proxy via simpler model organisms. We use the budding yeast, Saccharomyces cerevisiae, to study the replication and DNA damage checkpoints --- both implicated in DNA damage repair. Using a yEGFP reporter driven by the RNR3 promoter and reporter-based synthetic genetic array analysis, we created a detector of potential checkpoint activation in response to two doses of MMS, 0.015% and 0.060% (v/v). The high-throughput screens and differential epistasis miniarray analyses (EMAPs) yield unanticipated involvement of oxidative stress response, ribosomal biogenesis, and chromatin remodelling genes.

To ensure that photovoltaics contributes significantly to future world energy production, the cost per watt of producing solar cells needs to be drastically reduced. The use of n-type silicon wafers in conjunction with industrial print technology has the potential to lower the cost per watt of solar cells. The use of n-type silicon is expected to allow the use of cheaper Cz substrates, without a corresponding loss in device efficiency. Printed metallisation is well utilised by the PV industry due to its low cost, yet there are few examples of its application to n-type solar cells. This thesis explores the use of n-type Cz silicon with printed metallisation and diffusion from printed sources in creating industrially applicable solar cell structures. The thesis begins with an overview of existing n-type solar cell structures, previous printed thick film metallisation research and previous research into printed dopant sources. A study of printed thick-film metallisation for n-type solar cells is then presented, which details the fabrication of boron doped p-type emitters followed by a survey of thick film Ag, Al, and Ag/Al inks for making contact to a p-emitter layer. Drawbacks of the various inks include high contact resistance, low metal conductivity or both. A cofire regime for front and rear contacts is established and an optimal emitter selected. A study of printed dopant pastes is presented, with an objective to achieve selective, heavily doped regions under metal contacts without significantly compromising minority carrier lifetime in solar cells. It is found that heavily doped regions are achievable with both boron and phosphorus, but that only phosphorus paste was capable of post-processing lifetime compatible with good efficiencies. The effect of belt furnace processing on n-type silicon wafers is explored, with large losses in implied voltage observed due to contamination of Si wafers from transition metals present in the belt furnace. Due to exposure to chromium in the belt furnace, no significant advantage in using n-type wafers instead of p-type is observed during the belt furnace processing step. Finally, working solar cells with efficiencies up to 16.1% are fabricated utilising knowledge acquired in the earlier chapters. The solar cells are characterised using several new photoluminescence techniques, including photoluminescence with current extraction to measure the quality of metal contacts. The work in this thesis indicates that n-type printed silicon solar cell technology shows potential for good performance at low cost.

<p>Klassisk mus-interaktion har begränsningen att bara en punkt kan aktiveras på skärmen i taget. Interaktionen med de flesta applikationer blir, på grund av detta, sekventiell vilket kan vara en begränsning eftersom människan är van att utforska problem simultant med båda händerna. Flerpunktspekskärmar är en relativt ny teknik som möjliggör nya interaktionsmöjligheter där flera pekpunkter kan vara aktiva simultant. Det här examensarbetet fokuserar på problemen kring att skapa en applikation med användargränssnitt för flerpunktspekskärmar. Applikationen som utvecklats har en grundstruktur vilken är möjlig att vidareutveckla och på så sätt anpassas för att passa nya behov, till skillnad från de implementationer som granskats vid förstudien vilka fokuserar på att lösa specifika problem. Under examensarbetet har också en flerpunktspekskärm byggts av komponenter som kunnat köpas i detaljhandeln.</p> / <p>Classical mouse interaction is limited in that only a single screen point at a time can be activated. Most application interaction is, due to this, performed in a sequential manner. This may be a limiting factor as humans by nature explore problems with both hands simultaneously. Multi-touch screens are a relatively new type of technology that enables new ways of interaction where multiple touch points can exist simultaneously. This thesis focuses on the problem with developing an application with a user interface designed for multi-touch screens. The application that has been developed defines a base structure from which future applications can be developed, unlike implementations examined in the feasibility study which mainly focus on solving specific problems. A multi-touch screen is also built using standard off the shelf components.</p>

Pectic polysaccharides, a class of plant cell wall polymers, form one of the most complex networks known in nature. Despite their complex structure and their importance in plant biology, little is known about the molecular mechanism of their biosynthesis, modification, and turnover, particularly their structure-function relationship. One way to gain insight into pectin metabolism is the identification of mutants with an altered pectin structure. Those were obtained by a recently developed pectinase-based genetic screen. Arabidopsis thaliana seedlings grown in liquid medium containing pectinase solutions exhibited particular phenotypes: they were dwarfed and slightly chlorotic. However, when genetically different A. thaliana seed populations (random T-DNA insertional populations as well as EMS-mutagenized populations and natural variations) were subjected to this treatment, individuals were identified that exhibit a different visible phenotype compared to wild type or other ecotypes and may thus contain a different pectin structure (pec-mutants). After confirming that the altered phenotype occurs only when the pectinase is present, the EMS mutants were subjected to a detailed cell wall analysis with particular emphasis on pectins. This suite of mutants identified in this study is a valuable resource for further analysis on how the pectin network is regulated, synthesized and modified. Flanking sequences of some of the T-DNA lines have pointed toward several interesting genes, one of which is PEC100. This gene encodes a putative sugar transporter gene, which, based on our data, is implicated in rhamnogalacturonan-I synthesis. The subcellular localization of PEC100 was studied by GFP fusion and this protein was found to be localized to the Golgi apparatus, the organelle where pectin biosynthesis occurs. Arabidopsis ecotype C24 was identified as a susceptible one when grown with pectinases in liquid culture and had a different oligogalacturonide mass profile when compared to ecotype Col-0. Pectic oligosaccharides have been postulated to be signal molecules involved in plant pathogen defense mechanisms. Indeed, C24 showed elevated accumulation of reactive oxygen species upon pectinase elicitation and had altered response to the pathogen Alternaria brassicicola in comparison to Col-0. Using a recombinant inbred line population three major QTLs were identified to be responsible for the susceptibility of C24 to pectinases. In a reverse genetic approach members of the qua2 (putative pectin methyltransferase) family were tested for potential target genes that affect pectin methyl-esterification. The list of these genes was determined by in silico study of the pattern of expression and co-expression of all 34 members of this family resulting in 6 candidate genes. For only for one of the 6 analyzed genes a difference in the oligogalacturonide mass profile was observed in the corresponding knock-out lines, confirming the hypothesis that the methyl-esterification pattern of pectin is fine tuned by members of this gene family. This study of pectic polysaccharides through forward and reverse genetic screens gave new insight into how pectin structure is regulated and modified, and how these modifications could influence pectin mediated signalling and pathogenicity. / Pektin Polysaccharide, eine Klasse pflanzlicher Zellwand Polymere, formen eine der komplexesten natürlichen Strukturen. Trotz seiner immensen Bedeutung in der Biologie der Pflanzen sind die Kenntisse über die molekularen Mechanismen der Pektin Biosynthese, dessen Modifikation und Abbau überraschend gering. Eine Möglichkeit neue Einblicke in den pflanzlichen Pektin Metabolismus zu erhalten, ist die Identifizierung von Mutanten mit veränderter Pektinstruktur. Solche Mutanten konnten durch ein neuatiges Selektionsverfahren gefunden werden. Zieht man Keimlinge der Ackerschmalwand (Arabidopsis thaliana) in Flüssigmedium mit Pektinase an, so lässt sich ein typischer Phänotyp beobachten: Die Pflanzen sind kleinwüchsig und leicht chlorotisch. Diesem Verfahren wurden Populationen verschiedener Genotypen (Insertions Linien, EMS Mutanten, natürlich vorkommende Varianten) ausgesetzt. Auf diese Weise wurden Individuen identifiziert, die gegenüber der Pektinase Behandlung eine verminderte oder erhöhte Resistenz aufweisen, was auf eine veränderte Pektinstruktur hindeutet. Die EMS Mutanten wurden einer detaillierten Zellwand Analyse unterzogen. die so in dieser Arbeit identifizierte Kollektion von Mutanten stellt eine wertvolle Ressource für weitere Forschungsansätze zur Regulation, Biosynthese und Modifikation des Pektins dar. Die Lokalisation der Insertionen in den T-DNA Linien führte zur Identifikation interessanter Gene, zu denen der putative Zuckertransporter PEC100 gehört. Dieses Gen steht vermutlich in Verbindung mit der Synthese von Rhamnogalakturonan-I, einem Bestandteil des Pektins. In dieser Arbeit konnte PEC100 im Golgi Apparat, dem Ort der Pektin Biosynthese, lokalisiert werden. Die natürlich vorkommende Variante C24 ist besonders empfindlich gegenüber der Pektinase. Diese Empfindlichkeit konnte anhand rekombinanter Inzucht Linien auf drei bedeutende quantitative Merkmalsloci (QTL) eingegrenzt werden. C24 zeigte zudem ein gegenüber der Referenz verändertes Massenprofil der Oligogalakturonide. Diese werden derzeit als Signalmoleküle in der pflanzlichen Pathogenabwehr diskutiert, was mit der in dieser Arbeit geseigten Resistenz von C24 gegenüber Schwarzfleckigkeit verursachende Pilz (Alternaria brassicicola) korreliert. In einem revers-genetischen Ansatz wurden zudem Mitglieder der Pektin Methyltransferase Familie als potentielle Enzyme getestet, die die Pektin Methylesterifikation beeinflussen könnten. Diese Mutation in einer dieser Methyltransferasen führte zu Veränderungen des Oligogalakturonid Massenprofils. Dies bestätigt die Hypothese, dass Mitglieder dieser Genfamilie an der Regulation der Methylesterifikation von Pektin beteiligt sind. Die vorliegende Studie, in der ein genetishen Selektionverfahren und Methoden der reversen Genetik kombiniert wurden, hat neue Einblicke in die Regulation und Modifikation von Pektin geliefert.

To ensure that photovoltaics contributes significantly to future world energy production, the cost per watt of producing solar cells needs to be drastically reduced. The use of n-type silicon wafers in conjunction with industrial print technology has the potential to lower the cost per watt of solar cells. The use of n-type silicon is expected to allow the use of cheaper Cz substrates, without a corresponding loss in device efficiency. Printed metallisation is well utilised by the PV industry due to its low cost, yet there are few examples of its application to n-type solar cells. This thesis explores the use of n-type Cz silicon with printed metallisation and diffusion from printed sources in creating industrially applicable solar cell structures. The thesis begins with an overview of existing n-type solar cell structures, previous printed thick film metallisation research and previous research into printed dopant sources. A study of printed thick-film metallisation for n-type solar cells is then presented, which details the fabrication of boron doped p-type emitters followed by a survey of thick film Ag, Al, and Ag/Al inks for making contact to a p-emitter layer. Drawbacks of the various inks include high contact resistance, low metal conductivity or both. A cofire regime for front and rear contacts is established and an optimal emitter selected. A study of printed dopant pastes is presented, with an objective to achieve selective, heavily doped regions under metal contacts without significantly compromising minority carrier lifetime in solar cells. It is found that heavily doped regions are achievable with both boron and phosphorus, but that only phosphorus paste was capable of post-processing lifetime compatible with good efficiencies. The effect of belt furnace processing on n-type silicon wafers is explored, with large losses in implied voltage observed due to contamination of Si wafers from transition metals present in the belt furnace. Due to exposure to chromium in the belt furnace, no significant advantage in using n-type wafers instead of p-type is observed during the belt furnace processing step. Finally, working solar cells with efficiencies up to 16.1% are fabricated utilising knowledge acquired in the earlier chapters. The solar cells are characterised using several new photoluminescence techniques, including photoluminescence with current extraction to measure the quality of metal contacts. The work in this thesis indicates that n-type printed silicon solar cell technology shows potential for good performance at low cost.

Hedgehog (Hh) est un morphogène conservé au cours de l’évolution, et qui est impliqué dans un grand nombre de processus développementaux. Ma thèse vise à comprendre comment la sécrétion, et la mise en place du gradient d’Hh sont régulées à partir de son site de production, en utilisant la drosophile comme modèle animal. Pour identifier les régulateurs positifs impliqués dans la maturation du signal Hh, nous avons conçu et réalisé un crible génétique couvrant l’ensemble du génome, par ARNs interférents (ARNi). Grâce à ce crible, nous avons identifié la petite protéine GTPase Rab8 qui serait impliquée spécifiquement dans le routage intracellulaire de Hh. Selon notre modèle proposé, la protéine Hh serait secrétée de 2 façons. Sa sécrétion du coté apical est nécessaire à l'activation de gènes cibles à longue distance, alors que sa sécrétion du coté baso-latéral permettrait l'activation de gènes cibles à courte distance. La façon par laquelle Hh est transportée de la membrane apicale à la membrane basale à l’intérieur des cellules productrices n’est pas connue. La perte de fonction de Rab8 dans les cellules productrices de Hh induit une augmentation de l’activation des gènes cibles à courtes distances, alors l’expression des gènes cibles activés à longues distances est réduite. De plus, en utilisant des expériences sur tissus vivant pour suivre la dynamique de l'internalisation de la protéine endogène d’Hh, nous avons constaté que la perte de Rab8 n'a pas d’effet sur sa sécrétion primaire, mais entraine des défauts dans l’endocytose de Hh, affectant, par la suite, la mise en place du gradient morphogénétique. / Hedgehog (Hh) is a conserved secreted morphogen involved in an array of developmental processes. Using Drosophila as a model, during my thesis we aimed to ask how the secretion, extraction and transport of Hh protein are regulated at the site of its production. To understand the positive regulators of Hh secretion and transport we designed and performed a genome-wide RNAi screen in Drosophila to identify new regulators of Hh transport and identified the small GTPase Rab8 as a novel component required for Hh trafficking. According to our proposed model, there are two pools of secreted Hh. The apical pool is needed for long range target gene activation, and basolateral pool for short range target gene activation. It is not clear how Hh is sorted apico-basally in the producing cells. Interfering with Rab8 function in the Hh producing cells extends Hh short range targets. Conversely, it reduces the long range Hh targets, suggesting that interfering with Rab8 function in the Hh producing cells impairs Hh trafficking, thus hampering the fine tuning between the two secreted pools of Hh. Moreover, using live assays to track the dynamics of endogenous Hh internalization, we observed that loss of Rab8 in Hh producing cells does not affect its primary secretion, but causes defects in Hh endocytosis, subsequently affecting its gradient activity. We hypothesize a model where Hh is targeted for primary secretion to the apical side of the wing disc, which then is internalized, and this internalized Hh is then directed for recycling which is essential for its long range activity.

Klassisk mus-interaktion har begränsningen att bara en punkt kan aktiveras på skärmen i taget. Interaktionen med de flesta applikationer blir, på grund av detta, sekventiell vilket kan vara en begränsning eftersom människan är van att utforska problem simultant med båda händerna. Flerpunktspekskärmar är en relativt ny teknik som möjliggör nya interaktionsmöjligheter där flera pekpunkter kan vara aktiva simultant. Det här examensarbetet fokuserar på problemen kring att skapa en applikation med användargränssnitt för flerpunktspekskärmar. Applikationen som utvecklats har en grundstruktur vilken är möjlig att vidareutveckla och på så sätt anpassas för att passa nya behov, till skillnad från de implementationer som granskats vid förstudien vilka fokuserar på att lösa specifika problem. Under examensarbetet har också en flerpunktspekskärm byggts av komponenter som kunnat köpas i detaljhandeln. / Classical mouse interaction is limited in that only a single screen point at a time can be activated. Most application interaction is, due to this, performed in a sequential manner. This may be a limiting factor as humans by nature explore problems with both hands simultaneously. Multi-touch screens are a relatively new type of technology that enables new ways of interaction where multiple touch points can exist simultaneously. This thesis focuses on the problem with developing an application with a user interface designed for multi-touch screens. The application that has been developed defines a base structure from which future applications can be developed, unlike implementations examined in the feasibility study which mainly focus on solving specific problems. A multi-touch screen is also built using standard off the shelf components.