Dissertations / Theses on the topic 'Metabolic architecture'

Deinococcus geothermalis est un organisme non-model intéressant pour les bio-productions de part sa résistance extrême et ses capacités de fermentation partant de diverses sources de carbone. Cependant les outils d’ingénierie permettant une fine maîtrise des voix métaboliques restent limités pour cet organisme. Le but de ce travail de thèse, est d’essayer de surpasser cet obstacle à travers l’observation des motifs génétiques et de leur organisation. L’analyses de ces motifs a été menée via deux approches. La première est l’étude de l’impact de la position dans le génome sur l’expression d’une cassette reportrice. Grâce à une collection de 150 souches, nous avons observé que l’expression est plus forte au niveau de l’origine de réplication que du terminus. Une autre observation concerne la présence de zone de forte expression réparties symétriquement le long du chromosome. La seconde approche est l’analyse des motifs génétiques en cas de stress grace outil GREAT:SCAN:patterns. Ces motifs sont fortement liés régulation de l’expression des gènes et sont des points intéressant pour l’ingénierie du génome. En analysant les résultats de différentes conditions de stress ainsi que les régulons décrits dans la littérature, nous avons pu observer que des stress voisins partagent les mêmes motifs et que ces motifs semblent conservés chez des organismes distants. Ces deux approches ont permis de déterminer des positions d’insertion dans le génome intéressantes pour l’ingénierie métabolique
Deinococcus geothermalis is a non-model organism of high interest for bio-manufacturing since it shows a extreme resistance and good capacities for fermentation process on different carbon sources. However the engineering tools are limited to finely tuned metabolic pathways for bio-productions. This PhD work aims at contributing to overcome this obstacle through a whole-genome approach to the issue of understanding the genomic organization of D. geothermalis and defined interesting genomic locations. The whole-genome approach is based on the existence of genome-scale patterns that were analyzed in two different ways. A first approach consisted of studying the influence of the genome location on the expression of a reporter cassette. On a library of over 150 strains, the expression is higher near the origin of replication than near the terminus, a common observation. However, other hot spots of expression along the genome additionally appeared with a symmetric distribution about the origin of replication. The second approach consisted of analyzing the genomic patterns under stress through the in-house GREAT:SCAN:patterns software. These patterns interrelate with gene expression regulation and are an interesting key for genome engineering. Testing different stress conditions and considering the matching regulons as described in the literature, it appeared that related stresses share genomic patterns. Moreover these patterns tend to be conserved between distant organisms. These two approaches lead to define interesting genome loci for inserting genes encoding the enzymes of a pathway, with a view to metabolic engineering

There is a huge demand for analysis and visualization of the biological models. PathwayPioneer is a web-based tool to analyze and visually represent complex biological models. PathwayPioneer generates the initial layout of the model and allows users to customize it. It is developed using .net technologies (C#) and hosted on the Internet Information Service (IIS) server. At back-end it interacts with python-based COBRApy library for biological calculations like Flux Balance Analysis (FBA). We have developed a parallel processing architecture to accommodate processing of large models and enable message-based communication between the .net webserver and python engine. We compared the performance of our online system by loading a website with multiple concurrent dummy users and performed different time intensive operations in parallel. Given two metabolites of interest, millions of pathways can be found between them even in a small metabolic network. Depth First Search or Breadth First search algorithm retrieves all the possible pathways, thereby requiring huge computational time and resources. In Pathway Search using Informed Method, we have implemented, compared, and analyzed three different informed search techniques (Selected Subsystem, Selected Compartment, and Dynamic Search) and traditional exhaustive search technique. We found that the Dynamic approach performs exceedingly well with respect to time and total number of pathways searches. During our implementation we developed a SBML parser which outperforms the commercial libSBML parser in C#.

Urban areas cover 2% of the Earth’s land surface, host more than 50% of global population and are estimated to account for around 75% of CO2 emissions from global energy use. In order to mitigate existing and future direct and indirect environmental pressures resulting from urban resource use, it is necessary to investigate and better understand resource and pollution flows associated with urban systems.Current urban environmental assessment methodologies enable the quantification of resource use and pollution emissions flows entering, becoming stocked and exiting urban areas. While these methodologies enable to estimate the environmental effect of cities, they often consider urban areas as being static and homogeneous systems. This partial and simplistic representation shadows the complex spatio-temporal interrelationships between the local context and its associated local and global environmental pressures. This characterisation of urban systems is a significant limitation, not only for the urban environmental assessments, but also for the identification of their drivers as it may lead to inadequate urban environmental policies. To overcome this limitation and effectively reduce glocal urban environmental pressures, it is necessary to better understand the complex functioning of cities and identify their drivers.This research developed a comprehensive urban environmental assessment framework that helps to better explicit and understand the complex relationship between an urban system and its environmental profile in a systemic and systematic way. This framework was applied to the case study of Brussels Capital Region (BCR).Results from the application of this framework show that urban systems are neither static nor homogeneous. In fact, different relationships between the urban and metabolic profiles appear when considering different spatial scales and temporal intervals as well as different urban and metabolic metrics. The establishment of BCR’s urban profile showed that components that shape the urban system evolve in an organic way over time. Moreover, the spatial expression of an urban system portrays its heterogeneous aspect and how different metrics of the same urban indicator can reveal distinct facets and challenges for an urban area or a neighbourhood. Finally, it was demonstrated that the relationship between urban indicators is different for each spatial scale and therefore knowledge from one spatial scale is not necessarily transferable from one scale to another. The establishment and analysis of BCR’s metabolic profile also underlined the complex functioning of cities as each flow has a different temporal evolution and spatial expression. Due to the multifaceted and intertwined aspect of metabolic flows it becomes clear that no single parameter enables to explain or predict their behaviour. This leads to the conclusion that a great number of questions still need to be considered, understood and answered before effectively and coherently reducing environmental pressures from cities. The developed framework proposes a number of concrete steps that enable existing and new cities to better understand their metabolic functioning and ultimately transition towards less environmentally harmful futures.
Doctorat en Art de bâtir et urbanisme (Polytechnique)
info:eu-repo/semantics/nonPublished

The world’s population is increasing and every day, more people are coming to the cities. People are constantly relocating their houses for meeting their needs. As societies are growing and mobility in cities is raising, cities would face challenges like accommodating the population inexpensively and providing good quality of life and stable social and environmental infrastructure for them. However, due to the fixed regulated and unadaptable construction market, the architecture doesn’t meet the changing needs of inhabitants, therefore, every day the housing market is more unaffordable because of the high demand for housing developments, lands scarce, etc. Architecture needs to be flexible to adjust itself to the current market. Since most of the relocations and high demands for building new housing projects occur when built spaces fail to meet their occupants’ growing needs. This thesis tries to find an alternative framework for designing a flexible one whereby architecture is shaped by the user’s needs and can adjust itself in a long period. This thesis also works on designing an environment that responds to the social, economic, and environmental needs of residents as one united community. Therefore, it uses a shared living idea as an affordable alternative for making houses cheaper and creating a more stable social environment for inhabitants. The content of this thesis is categorized upon the following narrative. Firstly, this thesis is trying to deepen its understanding of the matter of shared living and its possible advantages and disadvantages for producing stable social and economical infrastructure. For this purpose, it analyses a notion of shared living and shared economy through studying successful case studies. Secondly, by studying and utilizing metabolic design criteria, the thesis will form an understanding of a more sustainable approach toward architecture and built environment to design an affordable housing system that provides high quality of life for inhabitants through responding to their needs. Thirdly, the thesis will frame its design strategy based on shared living perspective and metabolic design criteria. The thesis then will illustrate its steps and methods to achieve flexible architecture through designing its module, structure, and material. Lastly, it will discuss its findings on how the shared living approach and metabolic philosophy can aid architects to design more sustainable housing units that can meet their resident’s needs through a long period and make strong social, economic, and environmental infrastructure.

Si l’obésité a longtemps été considérée comme protectrice pour le squelette, sa prise en charge nutritionnelle s’accompagne d’une perte osseuse. Dans le but d’étudier les mécanismes liant le tissu adipeux et le tissu osseux, des rats ont été nourris avec un régime riche en graisse et en sucre afin d’induire une obésité et ses complications métaboliques. Puis, ces rats ont suivi un programme de prise en charge de l’obésité associant un rééquilibrage nutritionnel à de l’activité physique. Des investigations de la densité, de la micro architecture trabéculaire, de la qualité corticale, des propriétés biomécaniques et des paramètres cellulaires du tissu osseux ont été réalisées sur le squelette des rats. L’obésité induite a amélioré les paramètres densitométriques et corticaux des rats. La prise en charge de l’obésité a entraîné des effets contrastés. Le rééquilibrage de l’alimentation n’a pas altéré la densité ni les paramètres biomécaniques et corticaux du tissu osseux des rats en dépit d’altérations de la micro architecture et des perturbations l’activité cellulaire osseuse. L’exercice a augmenté la densité minérale osseuse du tibia des rats. Nos résultats montrent que l’inclusion de l’exercice dans un programme de prise en charge de l’obésité permet de potentialiser la perte de masse grasse et de maintenir l’intégrité du squelette. En étudiant l’impact d’un régime obésogène et de la prise en charge de l’obésité sur le tissu osseux chez le rat, ce travail de thèse apporte sa contribution dans la compréhension des mécanismes liant le tissu adipeux et le tissu osseux
While obesity has long been considered protective of bone tissue, its nutritional management is linked to a concomitant bone loss. In order to access these mechanisms, male rats were given a high fat / high sucrose diet to induce obesity and its resulting metabolic disorders. Then, these rats participated in a well balanced nutritional program combined, or not, with physical activity in order to treat their obesity. Investigations on density, trabecular micro-architecture, cortical quality, biomechanical properties and cellular parameters of bone tissue were performed on rat’s skeleton. Obesity had improved the bone density and cortical parameters of rats. Obesity management had induced mixed effects. The well balanced diet did alter neither the bone density nor biomechanical and cortical parameters despite the presence of alterations in the trabecular micro architecture and some disturbances of bone cellular activity. Exercise by itself had increased the tibia bone mineral density. Our results show that including exercise in obesity management allows increasing the fat mass loss and maintaining the skeleton integrity. By studying the impact of an obesogenic diet and obesity treatment on bone tissue in rats, this study brings its contribution to the understanding of the mechanisms linking adipose tissue and bone tissue

Thesis: S.M., Massachusetts Institute of Technology, Department of Architecture, 2016.
Cataloged from PDF version of thesis.
Includes bibliographical references (pages 133-145).
Coastal areas are home to more than half of the world's population and many of its most populated urban areas. Coastal urbanism remains very much in demand despite major risk factors such as sea level rise, longterm shoreline erosion, storm surges, land liquefaction, and subsidence. City-building on reclaimed land is an ambitious form of development yet prevalent around the world, especially where an economic growth agenda is pursued aggressively against the availability of land resources. This thesis develops a critical design agenda to respond to how pro-growth forces and environmental change can be negotiated towards a reconsidered coastal urbanism. The thesis argument is that coastal urban and territorial form should not follow a static master plan based on a risk model; instead, it should employ/follow a dynamic gradient of permanence and ephemerality in multiple time scales, following coastal succession as a design analogy. Tokyo Bay is the site of experimentation. The world's largest metropolitan area has a long history of land reclamation debates and projects, which resulted in a highly articulated urban coast with reclaimed shorelines, and near- and off-shore artificial islands with a mix of uses. The on-going construction of the urban archipelago is an outcome of urban and regional metabolisms, where incinerated solid waste, dredged sediment, excavated soil, and demolished buildings are deposited to make new land. Demand for post-industrial urban development and land reclamation is still alive in coastal Tokyo despite the vulnerabilities of flooding and seismic events. Large waterfront sites are now available for new development. The construction of permanent and temporary facilities in Tokyo Bay for the 2020 Summer Olympics offers an opportunity to develop a succession- based design strategy-not only for the 2020 peak condition, but also in anticipation of future transformations. The design exploration establishes, via strategic cartography, a resiliency district framework based on a gradient of permanence and flexibility in the ground condition. The sharply delineated boundary between land and sea is rethought as a dynamic frontier zone of flexibility that adapts to flooding and sea level rise and as an active site for coastal deposition and submersion. A second, elevated ground level is proposed to serve as a pedestrian and emergency thoroughfare, as well as an extension of transportation and logistics infrastructure. The Metabolist imaginary envisioned Tokyo Bay as a site of continuous urban growth towards a mega-scale climax state; ground was taken for granted and the possibilities of urban decline or reconstruction were hardly considered within the same design utopia. This project argues for a New Metabolism in which the ground is conceived as an indeterminate landscape of change. The uncertainties of the ground are addressed by an 'artificial land' infrastructure which organizes and facilitates transformation over time.
by Caner Oktem.
S.M.

Includes abstract.
Includes bibliographical references.
One of my initial research questions was to answer how informal settlements can pioneer the mitigation of greenhouse gas emissions in Cape Town. The objectives included understanding energy usage in informal settlements, invetigating current energy technologies and innovating an architectural typology which can support multiple renewable fuel sources and create positive, urban space in these communities.

In this dissertation, I conduct a reflection on the effects of disaster on time perceptions and their consequences on architecture as a vessel of social and individual values, through a study of two major paradigmatic disasters spaces – Post World War II Japan and Post-earthquake Haiti. While on the surface these two cases do not have many points in common, both are instrumental to establishing the manifestation of disasters' impacts on the culture of construction and on the architectural theories that ensue from them. The first case, Japan after the Second World War, establishes the long term influences and changes in social and architectural thought that occur after a disaster, while Haiti, examines the role of the architect in the reconstruction phases and attempts to register the immediate impressions of local architects on the disaster's impact on their practice. I show that both cases exhibit manifestations of the importance of the architect's role of not only building back, but moving forward while capitalizing on the events and social changes that happened.
Ph. D.

This thesis aimed to investigate several fundamental and perplexing questions relating to the phloem loading and transport mechanisms of Cucurbita maxima, by combining metabolomic analysis with cell biological techniques. This putative symplastic loading species has long been used for experiments on phloem anatomy, phloem biochemistry, phloem transport physiology and phloem signalling. Symplastic loading species have been proposed to use a polymer trapping mechanism to accumulate RFO (raffinose family oligosaccharides) sugars to build up high osmotic pressure in minor veins which sustains a concentration gradient that drives mass flow. However, extensive evidence indicating a low sugar concentration in their phloem exudates is a long-known problem that conflicts with this hypothesis. Previous metabolomic analysis shows the concentration of many small molecules in phloem exudates is higher than that of leaf tissues, which indicates an active apoplastic loading step. Therefore, in the view of the phloem metabolome, a symplastic loading mechanism cannot explain how small molecules other than RFO sugars are loaded into phloem.

Most studies of phloem physiology using cucurbits have neglected the possible functions of vascular architecture in phloem transport. It is well known that there are two phloem systems in cucurbits with distinctly different anatomical features: central phloem and extrafascicular phloem. However, mistaken conclusions on sources of cucurbit phloem exudation from previous reports have hindered consideration of the idea that there may be important differences between these two phloem systems.

The major results are summarized as below:
1) O-linked glycans in C.maxima were structurally identified as beta-1,3 linked glucose polymers, and the composition of glycans in cucurbits was found to be species-specific. Inter-species grafting experiments proved that these glycans are phloem mobile and transported uni-directionally from scion to stock.
2) As indicated by stable isotopic labelling experiments, a considerable amount of carbon is incorporated into small metabolites in phloem exudates. However, the incorporation of carbon into RFO sugars is much faster than for other metabolites.
3) Both CO2 labelling experiments and comparative metabolomic analysis of phloem exudates and leaf tissues indicated that metabolic processes other than RFO sugar metabolism play an important role in cucurbit phloem physiology.
4) The underlying assumption that the central phloem of cucurbits continuously releases exudates after physical incision was proved wrong by rigorous experiments including direct observation by normal microscopy and combined multiple-microscopic methods. Errors in previous experimental confirmation of phloem exudation in cucurbits are critically discussed.
5) Extrafascicular phloem was proved to be functional, as indicated by phloem-mobile carboxyfluorescein tracer studies. Commissural sieve tubes interconnect phloem bundles into a complete super-symplastic network.
6) Extrafascicular phloem represents the main source of exudates following physical incision. The major transported metabolites by these extrafacicular phloem are non-sugar compounds including amino acids, O-glycans, amines.
7) Central phloem contains almost exclusively RFO sugars, the estimated amount of which is up to 1 to 2 molar. The major RFO sugar present in central phloem is stachyose.
8) Cucurbits utilize two structurally different phloem systems for transporting different group of metabolites (RFO sugars and non-RFO sugar compounds). This implies that cucurbits may use spatially separated loading mechanisms (apoplastic loading for extrafascicular phloem and symplastic loading for central phloem) for supply of nutrients to sinks.
9) Along the transport systems, RFO sugars were mainly distributed within central phloem tissues. There were only small amounts of RFO sugars present in xylem tissues (millimolar range) and trace amounts of RFO sugars in cortex and pith. The composition of small molecules in external central phloem is very different from that in internal central phloem.
10) Aggregated P-proteins were manually dissected from central phloem and analysed by both SDS-PAGE and mass spectrometry. Partial sequences of peptides were obtained by QTOF de novo sequencing from trypsin digests of three SDS-PAGE bands. None of these partial sequences shows significant homology to known cucurbit phloem proteins or other plant proteins. This proves that these central phloem proteins are a completely new group of proteins different from those in extrafascicular phloem. The extensively analysed P-proteins reported in literature to date are therefore now shown to arise from extrafascicular phloem and not central phloem, and therefore do not appear to be involved in the occlusion processes in central phloem.
Phloem transportiert ein ausgedehntes Spektrum an Molekülen zwischen Pflanzenorganen, um Wachstum und Entwicklung zu koordinieren. Folglich ist eine umfassende und unvoreingenommene Metabolom-Analyse notwendig, um unser Verständnis über den Transport von Stoffwechselprodukten sowie über Phloemtransport zu vertiefen. Phloemexsudate von Kürbispflanzen werden unter Verwendung der Metabolom-Analyse analysiert. Bei diesen Pflanzen wird angenommen, dass sie symplastische Beladungswege verwenden, um Photoassmilate als Ausgangsschritt des Phloemtransportes zu konzentrieren. Zwei neue Familien Callose-verwandter Substanzen, 1,3-Overknüpfte Glycane, sowie eine Reihe anderer kleinerer Metabolite werden in den Phloemexsudaten detektiert. Metabolom-Daten und physiologische Experimente widersprechen früher berichtetem Verständnis des Phloemexsudationsprozesses in Kürbispflanzen. Folglich bestätigt sich der Phloemexsudationsprozeß durch Kombination unterschiedlicher mikroskopischer Techniken. Kürbispflanzen besitzen zwei Phloemsysteme mit eindeutigen anatomischen Eigenschaften. Es zeigt sich, daß Phloemexsudate in Kürbissen hauptsächlich vom extrafaszikulären Phloem, nicht vom zentralen Phloem, stammen. In den letzten Jahrzehnten wurde gewöhnlich mißverstanden, daß Phloemexsudate vom zentralen Phloem stammen. Die eindeutigen metabolischen Profile der unterschiedlichen Phloemsysteme, die durch Metabolom-Analysen in der räumlichen Auflösung beobachtet werden, bestätigen die unterschiedlichen physiologischen Funktionen der zwei unterschiedlichen Phloemsysteme: das zentrale Phloem transportiert hauptsächlich Zucker, während das extrafaszikuläre Phloem ein ausgedehntes Spektrum von Metaboliten transportiert. Es kann auch ein unterschiedliches metabolisches Profil kleiner Moleküle zwischen internem und externem zentralem Phloem beobachtet werden. Von Strukturproteinen des zentralen Phloems wurden auch Proben genommen und mittels Massenspektrometrie analysiert. Diese Proteine erweisen sich als neuartige Proteine, die sich zu denen im extrafaszikulären Phloem unterscheiden. Dies bestätigt ferner den Funktionsunterschied der unterschiedlichen Phloemsysteme in Kürbispflanzen. Basierend auf diesen neuartigen Entdeckungen des Phloem-Metaboloms und dem vorhergehenden Wissen über den Phloemtransport in Kürbispflanzen, wird ein neues Modell vorgeschlagen, um den Mechanismus des Phloemtransports in der symplastischen Beladung zu verstehen.

This thesis confronts the ultimate limits of perceiving the constructed world and the limits of our ability to experience architecture. The imperative of architecture is poetic: to and project encounters between matter and energy that shape the existing and bring forth the as yet unimagined to form a continuing human world. This is explored through the imagining of a habitat and vessel that projects the human endeavor of architecture into the formless depth of space. In drawing the physical from the void, the page becomes a way to move architecture from non-existence into the real by means of the imagination. An imagined wold is drawn from the void in search of the center for a universal and humanist architecture. The thesis is conceived as a vehicle for drawing the limits of perception when we attempt to imagine that which is greater than ourselves.
Master of Architecture

Esta dissertação visa entender as implicações do projeto arquitetônico no momento da execução de obras efêmeras, bem como busca elucidar os paradigmas essenciais a este projeto frente ao estágio avançado de depredação dos meios naturais em que o planeta se encontra. Entretanto, ainda que com a escassez de referências bibliográficas sobre o tema, na busca por esse pensamento analisaremos três pavilhões de verão da Galeria Serpentine executados por arquitetos de grande importância no cenário atual acreditamos que o conceito em arquitetura fica plasmado na obra. A leitura desses objetos, organizados não verbalmente, necessita de um referencial capaz de elucidar a sintaxe do pensamento que o orienta, revelando através de dados icônicos e indiciais o repertório de seu projetista. Neste momento mostra-se fecunda a teoria da semiótica de Charles Sanders Peirce, não apenas para revelar o repertório do arquiteto e os paradigmas de projeto que o orientam, mas também para pesquisar de que maneira estes profissionais materializam seus pensamentos através da linguagem não-verbal da arquitetura. Por outro lado, o que se vê à exaustão em eventos comerciais é a utilização de semelhantes sistemas construtivos industrializados, dos quais o OCTANORM é o mais conhecido, o que garante a continuidade do processo moderno e a elevação da capacidade de montagem e desmontagem como valor principal da obra. As hipóteses aqui levantadas tomam estes sistemas como uma manifestação da continuidade e apontam para outras arquiteturas, ainda efêmeras, mas alheias a essa dinâmica e com especificidades que caracterizam um campo particular de estudo. A base epistemológica deste trabalho veicula muito a semiótica peirciana e a bibliografia fundamental que dá orientação à pesquisa tem origem na filosofia da arquitetura e na psicologia da percepção com diversos teóricos.
This dissertation intends to understand the architectural project implications in the moment of the execution of ephemeral works, and tries to elucidate the essential paradigms to this project due to the advanced stage of depredation found within the planets natural resources. However, even facing a bibliographic shortage on the theme, searching this thought, we will analyze three summer pavilions inside Serpentine Gallery, executed by well-known architects we believe that the concept in architecture remains in this work. The reading of these objects, non-verbally organized, needs a reference capable of elucidating the thought syntax that guides it, revealing the designer repertory through iconic and inkling data. In this moment, Charles Sanders Peirces theory is shown to be abundant, not only to reveal the architectural repertory and the projects paradigms that guide it, but also to find the way that these professionals turn their thoughts into matter through non-verbal architectural language. On the other hand, what is exhaustively seen throughout commercial events is the use of similar industrialized constructive systems, from which OCTANORM is the most known, what guarantees the continuity of the modern process and the elevation of the mounting an dismounting capability as the main value of the work. The hypotheses raised in here consider these systems as a manifestation of continuity and point to other architectures, still ephemeral, but disconnected to this dynamic and owners of specificities that characterize a particular field of study. The basis of this work, regarding the use of epistemology, features peircians semiotics a lot and, the fundamental bibliography, that gives the research an orientation, has its origin in the architecture philosophy and in the psychology of perception defended by many theorists.

Les plantes sont des organismes immobiles qui doivent répondre et s’adapter à des contraintes abiotiques et biotiques. Parmi les stress biotiques, les maladies virales, établies ou émergentes, peuvent être responsables de pertes de rendement majeures aux conséquences économiques importantes. Face aux phytovirus la lutte génétique constitue le moyen de lutte le plus efficace, le plus respectueux de l’environnement et du consommateur. Comprendre l’interaction entre les plantes et les virus reste indispensable pour rechercher de nouvelles sources de résistances. Ce travail de thèse s’intéresse à l’étude du pathosystème naturel Arabidopis thaliana/Turnip mosaic virus (TuMV). Les essais ont été menés majoritairement en conditions extérieures permettant une analyse de l’interaction dans un environnement multistress. La réponse d’A. thaliana a été explorée par l’étude de traits liés à la maladie et par la variation en métabolites primaires et secondaires. Ce travail a permis i) de caractériser de façon fine la réponse d’A. thaliana au TuMV en conditionsmultistress en exploitant la diversité naturelle d’une population mondiale et française ii) de déterminer l’architecture génétique de cette interaction par des approches de génétique d’association et de QTL mapping. Plusieurs nouveaux loci potentiellement impliqués dans la réponse ont été identifiés iii) de montrer l’intérêt du phénotypage métabolique pour discriminer les accessions en fonction de leur sensibilité au TuMV. La multidisciplinarité des approches constitue la richesse de ce travail de thèse qui contribue à une meilleure caractérisation et compréhension de la réponse des plantes lors d’une infection virale
Plants are immobile organisms which have to adapt to abiotic and biotic constraints. Among bioticstress, established or emerging viral diseases, may be responsible for major yield losses withsignificant consequences. Genetic control is the most effective, environmentally and consumerfriendlyway to control viral infections. Understanding plant/virus interactions remains essential tosearch for new sources of resistance. This work, focuses on the study of the natural pathosystemArabidopsis thaliana/Turnip mosaic virus (TuMV). Most of the trials were conducted in commongarden conditions allowing the analysis of the interaction in a multistress environment. A. thaliana’sresponse was explored through the study of disease-related traits and the variations in primary andsecondary metabolites. This work allows i) the fine characterization of A. thaliana’s response toTuMV in multistress conditions through the exploration of the natural diversity of a world and Frenchpopulation ii) to determine the genetic architecture of this interaction by genome wide associationsand QTL mapping. Several new loci potentially involved in the response have been identified iii) tohighlight the interest of metabolic phenotyping to discriminate accessions according to theirsusceptibility to TuMV. The multidisciplinary approaches contribute to a better characterization andunderstanding of plant-virus interaction

Contemporary towns and cities in developing countries are faced with myriads of challenges. And, scholars have been suggesting various approaches, methods and tools to improve local resilience against these challenges. Some of the approaches and movements that proliferated recently in urban studies are Urban Metabolism, Sustainable Spatial Planning, the specified resilience approach, and the circular economy. Although these movements played an important role in improving local resilience and sustainability in the western world, their impacts on towns and cities of the developing world remains minimal. This is mainly because these movements were conceived and born in western countries and most of them are targeted at solving their own local problems. So, there is a very strong need to contextualize and modify them so that they fit into the existing local conditions in towns and cities of developing countries. In addition, lack of institutions and usable data makes it very difficult to undertake similar studies in countries like Ethiopia. That is why contextualizing these movements and searching resource efficient paths to local resilience and sustainability have become important tasks in recent years. In addition, developing a methodology that helps to operationlize and spatialize these concepts (resilience and sustainability - concepts usually criticized for being too general and normative) is also very crucial.This research, therefore, developed a robust diagnostic and analytical tool to study the nexus between major challenges (in small towns) and their impact on local resilience and sustainability in Ethiopia. The urban metabolism approach is mainly used (as a tool) to understand the nature of these challenges and to diagnose resilience in small towns. It specifically focuses on the flow food and housing construction materials (the two most stressed flows) in the case towns. These case towns are selected to represent the two ends of the sustainable town planning continuum in Ethiopia (Amdework is an organically growing old town and BuraNEST is a new planned town based on principles of sustainability). This research is mainly conducted at three stages: at regional level, at local level and at sub-system level. The first task done to achieve this objective is, therefore, characterization of the role of the case town in the regional urban system. This is done mainly using the urban metabolism approach. The deployment of this tool helped the researcher to pinpoint weak links, unsustainable flows, and vulnerable paths that simultaneously impact local resilience and sustainability in the case towns. This preliminary exploratory research clearly indicated the role of the town in the regional urban system and revealed the two most stressed (but important) sub-systems in the localities: the food and the housing sub-systems.Following this preliminary finding, the research has been narrowed down to the aforementioned two most stressed sub-systems. The food sub-system is first studied using the urban metabolism and the 'specified resilience' approaches. The research adopts a tri-tiered method (resilience at the source, resilience in the chain and resilience in consumption) to investigate local food resilience and metabolism and their relationship with the spatial configuration of the case town. The deployment of this method helps to operationalize and reduce the normative content of the concept (of resilience). This study reveals that urban agriculture is a highly marginalized agenda at all the three stages. Furthermore, the research investigates various bottom-up informal initiatives in the case town and other innovative planning endeavors (such as the planning of BuraNEST) that are aimed at improving sustainability and resilience in the food sub-system. The other focus area of the research is the housing sub-system. The urban metabolism approach, again, is primarily used to characterize, map and quantify the flow of materials used in the construction of residential houses in the town. The research developed a new bottom-up data generation technique to undertake this analysis. This method dominantly relied on estimations and conversions (of traditional measurements to the metric system) to get quantified data that was finally used as an input to develop metabolic models. Models (Sankeys) developed in this research reveal that the vast majority of inputs used in the construction are sourced locally. However, certain recent worrisome trends challenging sustainability have been observed in the housing sub-system due to the increased tendency of transporting important construction inputs from distant sources (mainly due to local construction regulations). The research, on the other hand, found that housing in BuraNEST, a town claimed to have been planned based on principles of sustainability, is more reliant on local sources and recognizes local needs and challenges. However, there are some critical pending questions (related with governance and affordability) that need to be addressed to improve sustainability in the housing sub-system in the long-run. Lastly, the research also investigates planning system challenges in small towns of Ethiopia. This is done mainly because many of the challenges found in the previous two analyses point to the presence of certain systemic problems in the policies, laws and manuals used in the planning of small town of Ethiopia. Such disorientations obviously negatively impact local resilience and sustainability in the long-run. Various definitions, wordings, phrases, and criteria identified in the federal planning law and manual were found to be on a direct collision course with principles of sustainability in many instances. By doing these, this research, therefore, systematically analyzed how the nexus between population pressure, resource flows and planning system challenges impact local resilience and sustainability (in the food and housing sub-systems) in small towns of Ethiopia. More importantly, it successfully spatialized and operationalized critical concepts such as urban resilience and sustainability using a new bottom-up approach. Clarity of the methodology vividly spells out the starting point when dealing with such important topics. This research can, therefore, serve as an important material to other researchers who are interested to study issues related to urban resilience and metabolism in small towns of developing countries. It clearly shows how the urban metabolism (as a tool) can be deployed to diagnose resilience in specific systems and sub-systems of towns and cities. It also provides a step-by-step procedure on how to generate data in data poor contexts and build metabolic models that can be used to study resilience in urban areas.
Les villes contemporaines des pays en développement sont confrontées à une multitude de défis. Les chercheurs ont suggéré diverses approches, méthodes et outils pour améliorer la résilience locale face à ces défis et parmi les approches qui ont proliféré récemment dans les études urbaines, nous pouvons citer le Métabolisme Urbain, l’urbanisme durable, l'approche de la Résilience Spécifiée et l'économie Circulaire. Bien que ces mouvements et ces outils aient joué un rôle important dans l'amélioration de la résilience et de la durabilité locales dans le monde occidental, leur application et leur impact sur les villes des pays en développement sont négligeables. Cela est principalement dû au fait que ces mouvements ont été conçus et sont nés dans les pays occidentaux et que, par conséquent, la plupart d'entre eux visent à résoudre des problèmes qui leur sont propres. Il existe donc un besoin important de contextualiser et d'adapter ces outils, mouvements et méthodologies pour étudier, comprendre et résoudre les problèmes des villes du monde en développement. En outre, le manque d'institutions et de données utilisables rend difficile la réalisation d'études similaires dans des pays comme l'Éthiopie. La recherche de chemins efficaces pour la résilience et la durabilité locale est donc une tâche difficile dans les pays en développement. De plus, il est très important de développer une méthodologie qui aide à opérationnaliser et à spatialiser ces concepts (résilience et durabilité, des concepts généralement critiqués pour être trop généraux et normatifs).Cette recherche a donc permis de mettre au point un solide outil de diagnostic et d'analyse pour étudier le lien entre les principaux défis et leur impact sur la résilience et la durabilité locale dans les petites villes d'Éthiopie. L'approche du métabolisme urbain est principalement utilisée pour comprendre la nature des défis urbains et diagnostiquer la résilience dans les villes concernées. Cette approche se concentre spécifiquement sur les flux des deux sous-systèmes les plus sollicités :les flux de nourriture et de matériaux de construction de logements. Les deux villes étudiées sont sélectionnées pour représenter les deux extrêmes du continuum de la planification urbaine durable en Éthiopie :une nouvelle ville planifiée (BuraNEST) et une vieille ville à croissance organique (Amdework). Cette recherche est organisée selon trois échelles :au niveau régional, au niveau local et au niveau des sous-systèmes. La première tâche effectuée pour atteindre cet objectif a donc été de caractériser le rôle de la ville prise comme cas d’étude dans le système urbain régional, en s’appuyant sur l'approche du métabolisme urbain. Le déploiement de cet outil a permis d'identifier les trajectoires non durables, les flux vulnérables et les activités qui ont simultanément un impact sur la résilience locale et sur la durabilité des villes étudiées. Cette recherche exploratoire préliminaire a clairement souligné le rôle de la ville dans le système urbain régional et a révélé deux sous-systèmes particulièrement sous tension: les sous-systèmes de l'alimentation et du logement.Suite à cette première constatation, la recherche se concentre sur ces deux sous-systèmes. Le sous-système alimentaire est d'abord étudié en utilisant le métabolisme urbain et les approches de « résilience spécifiée ». La recherche adopte une méthode suivant trois niveaux (résilience à la source, résilience dans la chaîne et résilience dans la consommation) pour étudier la résilience alimentaire locale et sa relation avec la configuration spatiale urbaine. Le déploiement de cette méthode permet d’opérationnaliser et de réduire le contenu normatif du concept de résilience. La recherche révéle que l'agriculture urbaine est un programme très marginalisé aux trois stades du métabolisme alimentaire. En outre, la recherche examine diverses initiatives informelles ascendantes dans la ville en question et d'autres initiatives de planification innovantes (telles que la planification de BuraNEST) qui visent à améliorer la durabilité et la résilience du sous-système alimentaire.Le second domaine d'étude de la recherche concerne le sous-système du logement. L'approche du métabolisme urbain est utilisée pour caractériser, cartographier et quantifier le flux de matériaux utilisés dans la construction des bâtiments résidentielles. La recherche développe une nouvelle technique de génération de données ascendantes pour entreprendre cette analyse. Cette méthode repose principalement sur de nombreuses estimations et conversions (des mesures traditionnelles vers le système métrique) pour obtenir des données quantifiées qui peuvent être utilisées comme intrants pour développer des modèles métaboliques. Les modèles (Sankeys) développés dans le cadre de cette recherche ont révélé que la grande majorité des matériaux intrants utilisés dans la construction proviennent de sources locales. Cependant, certaines tendances récentes inquiétantes remettant en cause la durabilité ont été observées dans le sous-système de logement en raison de la tendance croissante à importer d'importants éléments de construction provenant de sources éloignées (principalement en raison des réglementations locales en matière de construction). D'autre part, la recherche a révélé que les logements de BuraNEST, une ville qui déclare avoir été planifiée sur la base des principes de durabilité, dépendent davantage des ressources locales et considèrent les besoins et défis locaux. Cependant, le programme de logement de BuraNEST suscite d'importantes préoccupations en raison de la présence de quelques enjeux la gouvernance et l’économie de la construction des maisons, qui peuvent menacer la durabilité du programme à long terme. Enfin, la recherche s'est également penchée sur les problèmes liés au système de planification dans les petites villes d'Éthiopie. Cela est principalement dû au fait que de nombreuses questions relevées dans les deux analyses précédentes indiquent la présence de certains problèmes systémiques dans les politiques, les lois et les manuels utilisés dans la planification des petites villes d'Éthiopie. De telles désorientations ont évidemment un impact négatif sur la résilience et la durabilité locales à long terme. Dans de nombreux cas, diverses définitions, formulations, phrases et critères identifiés dans la loi et les règles de planification fédérale se sont révélés être en conflit direct avec les principes de durabilité.Par conséquent, cette recherche analyse de manière systématique le lien entre la pression démographique, les flux de ressources et les défis du système de planification qui ont un impact sur la résilience et la durabilité des petites villes d'Éthiopie. Plus important encore, cette recherche a réussi à spatialiser et à opérationnaliser des concepts critiques tels que la résilience et la durabilité urbaines en utilisant une nouvelle approche bottom-up. La rigueur de la méthodologie définit clairement le point de départ lorsqu'il s'agit de traiter des sujets aussi importants. Cette recherche peut donc constituer un matériel important pour les chercheurs qui souhaitent étudier les questions liées à la résilience et au métabolisme urbains dans les petites villes des pays en développement. Elle montre clairement comment le métabolisme urbain, en tant qu'outil, peut être déployé pour diagnostiquer la résilience dans les systèmes et sous-systèmes spécifiques des villes. Il fournit également une procédure étape par étape sur la façon de générer des données dans des contextes de manque d’information ,permettant ainsi deconstruire des modèles métaboliques qui peuvent être utilisés pour étudier la résilience dans les zones urbaines.
Doctorat en Art de bâtir et urbanisme (Polytechnique)
info:eu-repo/semantics/nonPublished

La cellule cardiaque requiert un apport énergétique conséquent qui exige une production et un transfert énergétiques efficaces. Si la production de l’énergie dépend essentiellement des propriétés intrinsèques des mitochondries, il semblerait que l’efficacité du transfert d’énergie du site de production vers les sites consommateurs (ATPases) pourrait être liée à l’architecture spécifique du cardiomyocyte qui conduit à une organisation spatiale singulière des structures internes (mitochondries, réticulum sarcoplasmique, myofilaments). Pour comprendre ce qui lie la cytoarchitecture, la compartimentation cellulaire et la fonction contractile, il a été entrepris d’étudier l’architecture cellulaire et la signalisation énergétique de cardiomyocytes au cours du processus de maturation de la cytoarchitecture et dans un modèle présentant une désorganisation des structures intracellulaires. La première partie de ce travail, réalisée durant le développement postnatal de la souris, a permis de démontré qu’il existe une synchronisation parfaite entre la mise en place de la cytoarchitecture et la maturation fonctionnelle du transfert d’énergie par canalisation directe des nucléotides adényliques entre les mitochondries et les ATPases. Si cette étude apporte un élément qui tendrait à démontrer l’implication de l’architecture cellulaire dans l’efficacité des transferts d’énergie, elle a également mis en avant la maturation très précoce de l’énergétique cellulaire. La mitochondrie faisant partie intégrante de cette architecture et étant modelée par des mécanismes de fusion et de fission, la deuxième étape de ce travail de thèse a consisté à étudier l’implication de la morphologie mitochondriale dans l’énergétique du cardiomyocyte. Il a ainsi été montré que, chez la souris, la diminution d’expression de la protéine OPA1, impliquée dans la fusion mitochondriale, conduit à des perturbations de la morphologie mitochondriale qui n’affectent pas la fonction intrinsèque mitochondriale mais qui altèrent le système de canalisation directe entre les mitochondries et les ATPases des myofilaments. De manière générale, ces résultats démontrent clairement une dépendance des transferts d’énergie à l’architecture cellulaire spécifique de la cellule musculaire cardiaque
The cardiac cell function requires a large amount of energy and therefore needs a high efficiency of energetic production and energetic transfer. While the energy production depends on the intrinsic properties of the mitochondria, it appears that the efficiency of energetic transfers from the main producers (mitochondria) to consumers (ATPases) could be related to the specific architecture of the cardiomyocyte, which ensures a unique spatial organization of internal structures (mitochondria, sarcoplasmic reticulum, myofilaments). In order to reveal the role of mitochondrial network organization in cardiac energy metabolism, we studied the cellular architecture and the energetic signalling of cardiomyocytes in the process of maturation of the cytoarchitecture and in a model which exhibits a perturbation of the mitochondrial dynamics. The first part of this work, which was performed during postnatal development of the mouse, showed the perfect synchronisation between the establishment of the cytoarchitecture and the maturation of the transfer of energy by direct channelling of adenine nucleotides between mitochondria and ATPases. While this study provides an element which would demonstrate the involvement of cellular architecture in the efficiency of energy transfer, it also highlighted the very early maturation of the energetic system of the cell. Knowing that the mitochondria are an integral part of the cell architecture and that the mitochondrial network is controlled by fusion and fission mechanisms, the second step of this work consisted in investigating the involvement of mitochondrial dynamics in cardiomyocyte energetics. Our work has shown that a decrease in expression of OPA1, a protein responsible for mitochondrial fusion, leads to disruption of mitochondrial morphology which does not affect intrinsic mitochondrial function but affects the direct channelling of ATP and ADP between mitochondria and ATPases of the myofilaments. Overall, these results clearly demonstrate that energy transfer in cardiomyocytes strictly depends on specific cellular architecture

Acidophilic iron oxidizing bacteria of the betaproteobacterial genus “Ferrovum” are ubiquitously distributed in acid mine drainage (AMD) habitats worldwide. Since their isolation and maintenance in the laboratory has proved to be extremely difficult, members of this genus are not accessible to a “classical” microbiological characterization with exception of the designated type strain “Ferrovum myxofaciens” P3G. The present study reports the characterization of “Ferrovum” strains at genome and transcriptome level. “Ferrovum” sp. JA12, “Ferrovum” sp. PN-J185 and “F. myxofaciens” Z-31 represent the iron oxidizers of the mixed cultures JA12, PN-J185 and Z-31. The mixed cultures were derived from the mine water treatment plant Tzschelln close to the lignite mining site in Nochten (Lusatia, Germany). The mixed cultures also contain a heterotrophic strain of the genus Acidiphilium. The genome analysis of Acidiphilium sp. JA12-A1, the heterotrophic contamination of the mixed culture JA12, indicates an interspecies carbon and phosphate transfer between Acidiphilium and “Ferrovum” in the mixed culture, and possibly also in their natural habitat. The comparison of the inferred metabolic potentials of four “Ferrovum” strains and the analysis of their phylogenetic relationships suggest the existence of two subgroups within the genus “Ferrovum” (i.e. the operational taxonomic units OTU-1 and OUT-2) harboring characteristic metabolic profiles. OTU-1 includes the “F. myxofaciens” strains P3G and Z-31, which are predicted to be motile and diazotrophic, and to have a higher acid tolerance than OTU-2. The latter includes two closely related proposed species represented by the strains JA12 and PN-J185, which appear to lack the abilities of motility, chemotaxis and molecular nitrogen fixation. Instead, both OTU-2 strains harbor the potential to use urea as alternative nitrogen source to ammonium, and even nitrate in case of the JA12-like species. The analysis of the genome architectures of the four “Ferrovum” strains suggests that horizontal gene transfer and loss of metabolic genes, accompanied by genome reduction, have contributed to the evolution of the OTUs. A trial transcriptome study of “Ferrovum” sp. JA12 supports the ferrous iron oxidation model inferred from its genome sequence, and reveals the potential relevance of several hypothetical proteins in ferrous iron oxidation. Although the inferred models in “Ferrovum” spp. share common features with the acidophilic iron oxidizers of the Acidithiobacillia, it appears to be more similar to the neutrophilic iron oxidizers Mariprofundus ferrooxydans (“Zetaproteobacteria”) and Sideroxydans lithotrophicus (Betaproteobacteria). These findings suggest a common origin of ferrous iron oxidation in the Beta- and “Zetaproteobacteria”, while the acidophilic lifestyle of “Ferrovum” spp. may have been acquired later, allowing them to also colonize acid mine drainage habitats.

La croissance de la consommation par les villes de ressources naturelles est un facteur déterminant dans l'altération de la biosphère. Pour comprendre le processus du changement du rapport entre la ville et la biosphère, transition socioécologique dans le cas particulier de la ville, nous avons caractérisé la ville comme étant tributaire de la ressource 1 externe en termes matériel et écologique. On s'intéresse dans ce travail à la relation entre la demande en énergie de la ville, l'évolution du système d'approvisionnement urbain et extra urbain en énergie, et le bassin d'approvisionnement en ressource énergétique avec le cas de l'agglomération parisienne. Pour ce faire, nous avons d'une pan tenté d'évaluer la pression environnementale effectuée pour la consommation énergétique urbaine. métabolisme urbain, en utilisant la. méthode d'analyse de flux d'énergie et de matière (AFME). L'AFME s'intéresse à mesurer le métabolisme d'une société et inclut par conséquent la consommation énergétique technique (pour le chauffage, le transport, l'industrie) 1 ainsi que l'alimentation humaine et animale consommée dans la ville. La consommation énergétique urbaine est évaluée par la demande énergétique totale (DET), indicateur de pression environnementale. dans le but de mesurer la 1 consommation d'énergie primaire en amont pour l'approvisionnement en énergie finale du territoire. On essaie ensuite de mettre en parallèle l'évolution de la DET pour l'énergie technique et l'évolution du rayon d'approvisionnement de i cette dernière au fur et à mesure de la croissance urbaine.

Expanding on the fields of bio-mimicry, morpho-ecologies, and dynamics and fluidity in architecture, this thesis proposes architecture as organism. It suggests that as organism, architecture is inherently responsive to the thresholds it exists on and within, thresholds which are composed not just of the physical but of the ephemeral; of time and of space. The existence, metabolism and morphology of an architectural organism becomes a function of the dynamic world into which it is born, inextricable from the ecology of the space it will inhabit. This thesis explores the architectural organism in the context of a visibly and significantly changing threshold, how connections are made between it and the world around it, and how it might engage those who are its inhabitants. The thesis is located in Nova Scotia’s Bay of Fundy, at the mouth of the Gaspereau River.

Cells require adenosine triphosphate (ATP) to drive the myriad processes associated with growth, replication, and homeostasis. Eukaryotic cells rely on mitochondria to produce the vast majority of their ATP. Mitochondria consist of a relatively smooth outer mitochondrial membrane (OMM) and a highly complex inner mitochondrial membrane (IMM), containing numerous invaginations, called cristae, which house the molecular machinery of oxidative phosphorylation (OXPHOS). Although mitochondrial form and function are intimately connected, limitations in the resolution of live-cell imaging have hindered the ability to directly visualize the relationship between the architecture of the IMM and its associated bioenergetic properties. Using advanced imaging technologies, including Airyscan, stimulated emission depletion (STED), and structured illumination microscopy (SIM), we developed an approach to image the IMM in living cells. Staining mitochondria with various ΔΨm-dependent dyes, we found that the fluorescence pattern along the IMM was heterogeneous, with cristae possessing a significantly greater fluorescence intensity than the contiguous inner boundary membrane (IBM). Applying the Nernst equation, we determined that the ΔΨm of cristae is approximately 12 mV stronger than that of IBM, indicating that the electrochemical gradient that drives ATP synthesis is compartmentalized in cristae membranes. Notably, deletion of key components of the mitochondrial contact site and cristae organizing system (MICOS), as well as OPA1, which regulate crista junctions (CJs), decreased ΔΨm heterogeneity. Complementing our super-resolution imaging of cristae in living cells, we also developed a machine-learning protocol to quantify IMM architecture. Tracking real-time changes in cristae density, size, and shape, we determined that cristae dynamically remodel on a scale of seconds. Furthermore, we found that cristae move away from sites of mitochondrial fission, and, prior to mitochondrial fusion, the IMM forms finger-like protrusions bridging the membranes of the fusing organelles. Lastly, we investigated the role of the motor adaptor protein, Milton1/TRAK1, in mitochondrial dynamics. Patient-derived Milton1-null fibroblasts not only had impaired mitochondrial motility but exhibited fragmentation corresponding to a roughly 40% decrease in mitochondrial aspect ratio and a 17% increase in circularity, associated with increased DRP1 activity. Conversely, we found that overexpression of Milton1 led to mitochondrial hyperfusion, decreased DRP1 activity, and aberrant clustering of mtDNA. Overall, our studies directly demonstrate that maintaining mitochondrial architecture is essential for preserving the functionality of mitochondria, the hubs of eukaryotic metabolism.

In this research, I aim to investigate the interrelationships between people, architecture and the landscape, by asking the question "what is the architect's role in curating place'. The goal of this body of work is to challenge the role of the ‘architect' when working within the context of place. This research, and the design intervention developed a process that challenges the profession by asking: “Should an architect be solely the creator of place, or is the architect a curator of place? The research analyzes existing theories related to the definition and concept of place approached from a wide spectrum of professional expertise overtime to attempt to grasp human being's passion related to the dynamic topic of place. The intent is to create a framework for design that can be adopted, implemented and layered upon any place, to unearth, distill, and better understand its essence. The rural post-industrial landscape of Western Massachusetts specifically focused around the former paper mill village of Woronoco is the stage for this inquiry. place is anchored equally in the qualitative and quantitative forces that shape it and thus requires an attentive observer, a trained observer, but most importantly a local, inspired observer who is fundamentally attached to that place. As both a landscape architect and architect, I offer a heightened awareness of the patterns and processes or ecology of place especially concerning the occupation and physical impact of humans on the landscape through the built environment. The proposed design interventions will attempt to treat place as a living organism, one that is continuously changing and whose dynamics are interconnected and responsive to a broad range of forces that shape it. A place curation design approach has led me to offer a series of design interventions, and not a proposal for a single building. These interventions will not fulfill a single program or fulfill one specific functional purpose; it will not focus on creating a design typology or use a consistent design language or material palette. Instead, the design will introduce multiple architectonic interventions that are derived almost organically in the landscape, in a manner that will stimulate the continued use and engagement with this place. Human interaction, engagement and interpretation is the essential component to ensuring the longterm sustainability of place, allowing it to continuously evolve and be relevant to future generations.

Duchenne Muscular Dystrophy (DMD) is a severe and progressive skeletal muscle wasting disease characterised by [Ca2+]-induced hyper-catabolism, and subsequently, a higher demand for energy production to modulate intracellular Ca2+ homeostasis, and protein degradation and synthesis pathways. The broad aim of this thesis was to elucidate potential defects in metabolism of the C57BL/10 mdx mouse model of DMD, and to determine the role of Ca2+ in any such defects. In particular, this thesis has examined the efficacy of the nutritional supplements creatine (Cr) and to a lesser extent, isolated whey protein (WP), in improving intracellular Ca2+ regulation, energy and protein balance and tissue architecture, thus alleviating a degree of the dystrophic pathology. 1. Whether the ATP-producing capacity of dystrophic mitochondria is defective remains largely contentious, and no study to date has directly quantified and contrasted ATP-production rate under the major macronutrient pathways feeding the mitochondria in either mdx hind limb or the more human DMD phenotype-like diaphragm. Chapter Three has demonstrated severely depressed mitochondrial ATP production rate (MAPR) of mdx diaphragm across all macronutrient substrate pathways, but to a lesser extent under protein metabolism, and in tibialis anterior (TA) across the sum of all macronutrient substrate pathways. Function of the electron transport chain complex II was not impaired in dystrophic diaphragm, but was notably depressed in TA. Citrate synthase activity was comparable to controls in both muscles, as was mitochondrial protein content. However, the susceptibility of dystrophic mitochondrial to mechanical damage during the mitochondria isolation process was significantly greater in mdx compared to controls, and in diaphragm compared to TA. It is postulated that mdx skeletal muscle has an intrinsic inability to utilise macronutrient substrates leading to substrate “back-up” and inhibition/down-regulation of key Krebs’ cycle enzymes, thus creating an intracellular “starvation” scenario. That protein metabolism was less affected than the other macronutrient substrate pathways suggests that a portion of the muscle hyper-catabolism observed in DMD may occur due to autophagy to increase amino acid funnelling to mitochondria for ATP production. 2. Supplementation of the high-energy storage nutrient Cr is demonstrably beneficial in maintaining muscle function, energy status and cell survival rate in human DMD and dystrophic mdx skeletal muscle. Long-term chronic dose supplementation regimes, however, have been associated with down-regulation of creatine transporter (CreaT) expression thus making such regimes futile in maintaining consistently high intramuscular PCr stores. Chapter Four has demonstrated successful prevention of CreaT mRNA down-regulation by a chronic dose in utero and life-long Cr supplementation protocol, and subsequently persistently elevated [PCr] compared to unsupplemented mdx skeletal muscle. This was associated with a drastically reduced amount of muscle damage as depicted by Evan’s blue dye (EBD) uptake into myofibres, and a lesser degree of damage to those fibres that were permeant to EBD. This unequivocally demonstrates that muscle wasting occurs secondary to metabolic compromise and failure to maintain ATP supply to intracellular mechanisms that promote cell survival. 3. Effective intracellular Ca2+ regulation by the sarcoplasmic reticulum (SR) is integral to muscle function and becomes of paramount importance to the maintenance of cell survival in conditions of increasing [Ca2+]i such as that evident in DMD. Chapter Five details an optimised method for the fluorometric quantitation of SR Ca2+ flux kinetics currently utilised by our laboratory. It was demonstrated that the SR Ca2+ ATPase (SERCA) preferentially utilises ATP produced by a linked creatine kinase (CK) system over both exogenously administered ATP and ATP produced by SR-linked glycolytic enzymes, and as such, SR Ca2+ uptake rate was considerably faster under these conditions. It was also demonstrated that high [ADP] proximal to the SR vesicles impairs the binding of Ca2+ to Fura-2 and that the presence of 25mM PCr and low [ADP] drastically reduces passive Ca2+ leak from the SR. Thus, this study provides sound rationale for the use of Cr supplementation to improve intracellular Ca2+ handling by the SR subsequent to increasing PCr stores and the buffering of rising [ADP] during metabolic compromise. 4. It has been suggested that the beneficial effects observed in human DMD and dystrophic mdx skeletal muscle following Cr supplementation result from an improved capacity for intracellular Ca2+ handling by the SR and, therefore, delayed degenerative progression. Chapter Six has demonstrated no direct modulatory effect for Cr supplementation on SERCA or RyR function such to increase/decrease SR Ca2+ uptake, leak or release rates, but postulates that the benefit imparted by Cr supplementation is in maintaining maximum uptake (and subsequently release) velocity secondary to buffering rising [ADP] and collapse of the ATP:ADP ratio proximal to the SR. This study has also investigated the effects of supplementation with WP and a Cr+WP combination. As with Cr supplementation, WP induced no direct modulation of SR Ca2+ flux kinetics. Both supplements were shown to modulate differential expression of specific intracellular protein pools, although not necessarily net protein accretion. It is speculated that modification of expressed intracellular protein pools permits the “switching” of dystrophic mdx skeletal muscle from a “functional” phenotype to a “cell survival” phenotype, and that this is inhibited in unsupplemented muscle by a lack of amino acid and energy resources. It was also apparent that Cr and WP supplementation exerted different effects on tissue architecture maintenance. Cr supplementation increased the proportional area of functional muscle tissue and decreased non-muscle “gap” areas thus suggesting a role in muscle hypertrophy, where as Cr+WP combined increased active/recent degeneration and regeneration and the proportion of centrally-nucleated previously damaged fibres compared to peripherally-nucleated undamaged fibres in functional muscle tissue, thus indicating a potentially damaging effect. Collectively, the studies comprising this thesis indicate that the progressive skeletal muscle wasting evident in DMD is closely related to dissipating energy stores, and that the primary disease pathology may, therefore, be an intrinsic metabolic defect caused by the DMD genotype that subsequently induces Ca2+ dys-regulation. Cr supplementation was shown to provide several benefits to dystrophic mdx skeletal muscle architecture, including reduced severity of degenerative cycles, maintenance of muscle tissue and reduced proportional area of non-muscle tissue secondary to increased intramuscular [PCr]. The findings of Chapter Five suggest that Cr supplementation modulates its effect by maintaining normal [PCr] and a high ATP:ADP and PCr:Cr proximal to the SR, such to maintain maximum Ca2+ uptake velocity and reduce passive Ca2+ leak. Both Cr and WP supplementation also seem to modulate intracellular protein synthesis such to increase the capacity for myofibre survival. Thus, these supplements could be of benefit in the adjunct treatment of DMD, and warrant further investigation as to their long-term and mechanistic efficacy.

Disasters due to war and conflict or natural forces are responsible for the 26 million people displaced across the world today. The crisis extends into the temporary, yet indefinite, displacement camps where people live in congested living arrangements, vulnerable to an increased risk of disease, death, and social violence (spousal abuse, rape). Even when chaos subsides, social and physical networks have frayed rendering the temporary displacement camp a permanent home for some. Often, despite this “permanence”, access to adequate services and infrastructure and hence social and economic growth remains in a state of emergency. This thesis proposes that water infrastructure is the key social catalyst for developing these displacement camps into permanent sustainable communities. An urban displacement camp in the town of Gulu, Northern Uganda, is the case study location for a speculative design intervention. During rebel activities from 1996 to 2004, the town of Gulu more than tripled in size, absorbing almost 100,000 displaced people forced to flee their land. These people settled in displacement camps next to, and within the wetlands that border the town on all sides. The urban metabolism of the town has become polluted as the displaced people use, alter and degrade the wetlands because they have no other alternatives. Following the instigation of a peace process in 2006, some people have begun the journey home. However, it is estimated that just over half of these people will continue to live in the squalid camps, without an opportunity to prosper. A strategy is proposed for addressing and subsequently re-defining this urban metabolism. By synthesizing the existing urban fabric with strategies for harnessing the natural landscape, varying scales of water infrastructure are proposed. New opportunities for agricultural production is supported, while the spatial relationships created by the physical structuring of the water infrastructure renews the influence that water collection and distribution has in creating the social locus of a community.