Thesis (PhD (Biochemistry))--University of Stellenbosch, 2009. / ENGLISH ABSTRACT: The sugarcane stalk, besides being the main structural component of the plant, is also the major storage organ for carbohydrates. Sucrose forms the bulk of stored carbohydrates. Previous studies have modelled the sucrose accumulation pathway in the internodal storage parenchyma of sugarcane using kinetic models cast as systems of ordinary differential equations. Typically, results were analysed with methods such as metabolic control analysis. The present study extends those original models within an advection-diffusion-reaction framework, requiring the use of partial differential equations to model sucrose metabolism coupled to phloem translocation. Let N be a stoichiometric matrix, v a vector of reaction rates, s a vector of species concentrations and r the gradient operator. Consider a coupled network of chemical reactions where the species may be advected with velocities, U, or diffuse with coefficients, D, or both. We propose the use of the dynamic system, s + r (Us) + r (Drs) = Nv; for a kinetic model where species can exist in different compartments and can be transported over long distances in a fluid medium, or involved in chemical reactions, or both. Darcy’s law is used to model fluid flow and allows a simplified, phenomenological approach to be applied to translocation in the phloem. Similarly, generic reversible Hill equations are used to model biochemical reaction rates. These are also phenomenological equations, where all the parameters have operationally defined interpretations. Numerical solutions to this formulation are demonstrated with time-courses of two toy models. The first model uses a simple “linear” pathway definition to study the impact of the system geometry on the solutions. Although this is an elementary model, it is able to demonstrate the up-regulation of photosynthesis in response to a change in sink demand. The second model elaborates on the reaction pathway while keeping the same geometry definition as the first. This pathway is designed to be an abstracted model of sucrose metabolism. Finally, a realistic model of sucrose translocation, metabolism and accumulation is presented, spanning eight internodes and four compartments. Most of the parameters and species concentrations used as initial values were obtained from experimental measurements. To analyse the models, a method of sensitivity analysis called the Fourier Amplitude Sensitivity Test (FAST) is employed. FAST calculates the contribution of the possible variation in a parameter to the total variation in the output from the model, i.e. the species concentrations and reaction rates. The model predicted that the most important factors affecting sucrose accumulation are the synthesis and breakdown of sucrose in futile cycles and the rate of cross-membrane transport of sucrose. The models also showed that sucrose moves down a concentration gradient from the leaves to the symplast, where it is transported against a concentration gradient into the vacuole. There was a net gain in carbohydrate accumulation in the realistic model, despite an increase in futile cycling with internode maturity. The model presented provides a very comprehensive description of sucrose accumulation and is a rigorous, quantitative framework for future modelling and experimental design. / AFRIKAANSE OPSOMMING: Benewens sy strukturele belang, is die suikerrietstingel ook die primêre bergingsorgaan vir koolhidrate. Die oorgrote meerderheid van hierdie koolhidrate word as sukrose opgeberg. Studies tot dusver het die metabolisme rondom sukroseberging in die parenchiem van die onderskeie stingellitte as stelsels gewone differensiaalvergelykings gemodelleer. Die resultate is ondermeer met metaboliese kontrole-analise geanaliseer. Hierdie studie brei uit op die oorspronklike modelle, deur gebruik te maak van ’n stromings-diffusie-reaksie-raamwerk. Parsiële differensiaalvergelykings is geformuleer om die metabolisme van sukrose te koppel aan die vloei in die floëem. Gestel N is ’n stoichiometriese matriks, v ’n vektor van reaksiesnelhede, s ’n vektor van spesie-konsentrasies en r die differensiaalvektoroperator. Beskou ’n netwerk van gekoppelde reaksies waar die onderskeie spesies stroom met snelhede U, of diffundeer met koëffisiënte D, of onderhewig is aan beide prosesse. Dit word voorgestel dat die dinamiese stelsel, _s + r (Us) + r (Drs) = Nv; gebruik kan word vir ’n kinetiese model waar spesies in verskeie kompartemente kan voorkom en vervoer kan word oor lang afstande saam met ’n vloeier, of kan deelneem aan chemiese reaksies, of albei. Darcy se wet word gebruik om die vloeier te modeller en maak dit moontlik om ’n eenvoudige, fenomenologiese benadering toe te pas op floëem-vervoer. Eweneens word generiese, omkeerbare Hill-vergelykings gebruik om biochemiese reaksiesnelhede te modelleer. Hierdie vergelykings is ook fenomenologies van aard en beskik oor parameters met ’n duidelike fisiese betekenis. Hierdie omvattende raamwerk is ondermeer gedemonstreer met behulp van numeriese oplossings van twee vereenvoudigde modelle as voorbeelde. Die eerste model het bestaan uit ’n lineêre reaksienetwerk en is gebruik om die geometrie van die stelsel te bestudeer. Alhoewel hierdie ’n eenvoudige model is, kon dit die toename in fotosintese as gevolg van ’n verandering in metaboliese aanvraag verklaar. Die tweede model het uitgebrei op die reaksieskema van die eerste, terwyl dieselfde stelselgeometrie behou is. Hierdie skema is ontwerp as ’n abstrakte weergawe van sukrosemetabolisme. Ten slotte is ’n realistiese model van sukrosevervoer, metabolisme en berging ontwikkel wat agt stingellitte en vier kompartemente omvat. Die meeste parameters en konsentrasies van biochemiese spesies wat as aanvanklike waardes in die model gebruik is, is direk vanaf eksperimentele metings verkry. Die Fourier Amplitude Sensitiwiteits-Toets (FAST) is gebruik om die modelle te analiseer. FAST maak dit moontlik om die bydrae van parameters tot variasie in modeluitsette soos reaksiesnelhede en die konsentrasies van chemiese spesies te bepaal. Die model het voorspel dat sintese en afbraak van sukrose in ’n futiele siklus, asook transmembraan sukrosevervoer, die belangrikste faktore is wat sukrose-berging beïnvloed. Die model het ook getoon dat sukrose saam met ’n konsentrasiegradiënt beweeg vanaf die blare tot by die stingelparenchiem-sitoplasma, van waar dit teen ’n konsentrasiegradiënt na die vogselholte (vakuool) vervoer word. Volgens die realistiese model was daar ’n netto toename in die totale hoeveelheid koolhidrate, ten spyte van ’n toename in die futile siklus van sukrose in die ouer stingellitte. Die model wat in hierdie proefskrif voorgestel word verskaf ’n uitgebreide, omvattende beskrywing van sukroseberging. Voorts stel dit ’n rigiede kwantitatiewe raamwerk daar vir toekomstige modellering en eksperimentele ontwerp.

Les conséquences sanitaires et environnementales de la pollution atmosphérique sont devenues au cours des dernières décennies un des problèmes majeurs de notre société. Sensibilisée à cette problématique, la région Nord Pas-de-Calais a été l'une des premières régions à soutenir et à valoriser la biosurveillance végétale de la qualité de l'air. Les travaux scientifiques réalisés dans le cadre de cette thèse ont pour objectif d'étudier les phénomènes d'accumulation et les impacts des composés organiques volatils (COV) chez les bryophytes. Articulées autour de deux axes, les recherches menées visaient à étudier, d'une part, l'accumulation des benzène, toluène, ethylbenzène et xylènes (BTEX), d'autre part, des effets au niveau cellulaire, du benzène chez Tortula ruralis, par l'analyse des variations de l'expression de biomarqueurs de stress oxydant. Des expérimentations complémentaires in situ , sur le littoral dunkerquois, et en conditions contrôlées ont permis d'établir des phénomènes d'équilibre des concentrations en BTEX entre notre modèle végétal et l'air. In situ, les teneurs en BTEX chez les mousses sont fortement conditionnées par les paramètres météorologiques, et principalement la force des vents. De plus, les concentrations atmosphériques en particules PM10 favoriseraient l'accumulation des BTEX chez la mousse. Mais d'une manière générale, les mousses n'accumulent pas les BTEX de façon corrélée aux teneurs dans l'atmosphère. Concernant l'expression des biomarqueurs de stress oxydant, des variations naturelles des paramètres biologiques mesurés sont observées chez la mousse. Ces variations seraient liées à la nature poïkilohydrique des mousses, leur capacité de reviviscence et aux aptitudes qu'elles ont développées pour résister aux variations de leur état d'hydratation. Ainsi, les biomarqueurs de stress oxydant souvent recherchés dans les études d'écotoxicologie, ne seraient pas adaptés pour l'étude des effets chez les bryophytes terrestres.

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This thesis uses palaeolimnological records to reconstruct Holocene ontogeny trends from four lakes in south western Greenland. The research addresses four hypotheses investigating how Holocene lake ontogeny trends vary under different climatic settings, how long-term changes in ontogeny relate to periods of established climatic change in the region, the similarities between proxies within the lakes and between the lakes, and the role of vegetation in lake ontogeny. The study region occupies the widest ice-free area of south western Greenland and is characterised by a climatic gradient. The area inland and nearer to the ice-margin is arid, receives less precipitation and is warmer relative to the coastal areas. A paired lake approach, using lake records from two inland lakes and two coastal lakes, was adopted to examine the role of climatic setting upon lake development trajectories. Specifically, diatoms were used to reconstruct DI-alkalinity from the lakes using a DI-alkalinity model created from existing training sets in the region (WA Cla model, r2boot = 0.76, RMSEP = 0.28 log alkalinity units), sedimentary pigments to investigate trends in production and sedimentary parameters to reconstruct organic and minerogenic accumulation rates. All four lakes experienced comparable Holocene long-term ontogeny trajectories; maximum alkalinity in the first ~ 1000 cal. year BP of deglaciation followed by maximum production during the peak of Holocene Thermal Maximum (HTM) warming (~7000 -6000 cal. years BP). Following the HTM, all lakes demonstrated oligotrophication and a decline in pH. Vegetation development and catchment stabilisation at the end of the HTM may be important in determining the onset of oligotrophication in vegetated catchments. However, the impact of vegetation development on lake ontogeny cannot be isolated from the changes in the lakes associated with the colder and wetter climate which occurred at the end of the peak HTM warming. The timings of the large transitions in the ontogeny trajectories are comparable with established periods of Holocene climatic variability in the region; climate forcing drives ontogeny in these lakes. However, there are short-term differences between the lakes indicating that lakes have different thresholds of ecological change and may respond differently to the same climate forcing. It is concluded that ontogeny is driven by climate but lakes may respond differently to forcing depending on catchment specific characteristics which can filter out the climate signal or cause climate to influence the lake in a more direct way.

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal.

My work is my critique of a generation that is dependent upon the conveniences of consumerism. Consumerism in our culture is almost inescapable. I do not condemn or celebrate this way of life because it is the only one I know. There are many things about consumerism that I hate such as the waste it creates or class system it creates. At the same time I enjoy the ease and the comforts that it allows us. This is one of the problems with our generation; we do not take a stand either way because we are so dependent on consumerism. No matter how self reliant we may think we are our culture still desires consumerism.

The novel trinuclear complex, BBR3464 has undergone Phase II clinical trials and been shown to have greater cytotoxicity and cellular uptake than clinical anticancer platinum drugs such as cisplatin, oxaliplatin and carboplatin. The clinical efficacy of cisplatin, oxaliplatin and carboplatin is limited due to acquired resistance and dose limiting side effects. The three major pharmacological factors contributing to the intrinsic cytotoxicity of, and cellular resistance to, platinum drugs are (i) cellular uptake and efflux of platinum; (ii) the frequency and nature of Pt-DNA adducts; and (iii) deactivating metabolic reactions with sulfur-containing nucleophiles. Since decreased cellular uptake of platinum drugs is a common feature of resistant cells, investigating mechanisms of cellular uptake and efflux is of a great importance in the field of cancer biology. The mechanisms of uptake of Platinum drugs are diverse and complex. Similar to cisplatin, BBR3464 v as shown to use copper transporter hCTR1 and ATP7B for influx and efflux respectively. Organic cation transporters (OCT) did not play an important role in BBR3464 cellular uptake, however, desipramine, an OCT inhibitor had synergistic effects on platinun drugs-induced cytotoxicity. This effect is of high clinical relevance since desipramine, an antidepressant, is being used in prostate cancer patients for the treatment of neuropathic pain. The mechanism of this interaction was further addressed.Due to the high charge of BBR3464, studies have shown that its DNA binding has a non-covalent component. To examine the non covalent component, labile chloride leaving groups were replaced by non labile ammonia groups. Besides having higher cellular accumulation than BBR3464, the non covalent analogue, AH78, had a different mechanism of action in cells and showed promising results in vivo. These data confirm the validity of searching for new chemotypes outside the cisplatin structural class to aid in the treatment of recurrent, cisplatin-resistant cancers.

Porphyromonas gingivalis, a gram-negative anaerobic bacterium, is implicated as a major etiological agent in the initiation and progression of severe forms of periodontal disease. It has been reported that gingivitis and periodontal disease affect roughly 50.3% and 35% of the adult population, respectively. Therefore, approximately over 85% of the adult population may suffer from some form of gingival disease. Porphyromonas gingivalis, an established periodontopathogen, requires hemin for growth. Although multiple hemin uptake systems appear to be present in this organism, their specific role in hemin uptake and virulence remains unknown. Pigmentation is thought to result from the accumulation of iron protoporphyrin IX (FePPIX) derived from erythrocyte hemoglobin. It has been observed that mutations abolishing activity of the Lys-X specific cysteine protease, Kgp, resulted in loss of black pigmentation of P. gingivalis W83; they were less virulent than their wild-type counterparts. Thus, we have observed that Kgp degradation of fibrinogen deregulates the clotting cascade, thereby minimizing the availability of free erythrocytes. Additionally, Kgp binds erythrocytes and degrades them, releasing hemoglobin. The interference with mechanisms involved in the accumulation of black pigmentation may be significant in controlling the pathogenic potential of P. gingivalis. These results suggest that Lys-gingipain protease is a principal protein involved in acquisition of hemin from hemoglobin as well as a major factor in transport, by affecting the accumulation of FePPIX on the bacterial cell surface. Microarray analysis indicates a change in the expression of key enzymes and proteins required for hemin uptake, iron storage, electron transport and oxidative stress. Therefore, interference with mechanisms involved in accumulation of black pigmentation may be significant in controlling the pathogenic potential of P. gingivalis.

Through my art process and material selection, I investigate how interior spaces long to accumulate memories and possessions. I am interested in encroaching floor to ceiling build-up of collected goods kept in the homes of individuals unable to discard or part with possessions. These individual’s daily movements through their space and their denial of the surrounding mass informs my work. My work is larger than human scale, made of multiple units, and dense; yet understated by the subtle use of color and repeated materials. When I make an installation it often begins with creating a wall or a floor that delineates itself from the actual architecture of a room. I procure discarded domestic fragments such as carpet, shingles, and blinds. I select one material for each project to emphasize excessive quantities. I seek out donated goods and trash piles, heaps on the edge of consumer waste. The sourcing of these materials is serendipitous. I elevate these mundane materials by taking them out of their original context. The cycle of regeneration moves from material to “art object” back to material again as the work is displayed and dispersed back into the cycle of waste. In this thesis I will discuss how through my process and materials, I investigate interior spaces where memory and possessions accumulate.