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The ubiquitous nature of symmetry lends itself to be taken for granted, however the breath of research on symmetry encompasses several disciplines. In engineering, studies centered on symmetry often address issues in dynamic systems theory, robotics, and gait rehabilitation. This thesis presents findings on two specific topics dealing with passively induced symmetry; dissimilar rotating systems and human gait. Past studies on passive symmetry in dynamic systems often incorporate physical coupling or a controller. This thesis presents a technique to passively induce symmetry between two dissimilar systems that are not physically connected. This work also presents a human gait study consisting of several elements that merge to provide a unique look at how walking symmetry and altered physical parameters (leg length and added weight) of the lower limbs are related. One aspect of this thesis shows the successful development of a general method to induce synchronization between any two dissimilar, uncoupled, rotating systems given the same degrees of freedom, initial angular dynamics, and applied torque. This method is validated with a simulation and subsequent comparison with two physical experiments. The results are in agreement, with slight variations due to the friction and damping of the physical systems. This is further expanded to include the induced symmetry of two systems that experience an external collision. Due to the highly non-linear nature of such systems, an analytical solution was not found; instead a numerical solution is presented that resulted in partial symmetry between systems. The gait study demonstrated that weighted walking and altered leg length have both independent and combined spatio-temporal effects on lower limb symmetry. While altered leg length alone resulted in higher gait asymmetry, the combination of the two physical changes increases this asymmetry to affect the same limb. This study also showed that cognitive and physically distracted walking does not have an added effect to the gait symmetry with passive physical changes. In addition, this study was able to demonstrate that the arm swinging that occurs during natural walking does not significantly alter spatial or temporal gait parameters.

The present research attempted to use display design as a means to mitigate the occurrence and severity of symptoms of motion sickness and increase performance due to reduced “general effects” in an uncoupled motion environment. Specifically, several visual display manipulations of a 360° indirect vision system were implemented during a target detection task while participants were concurrently immersed in a motion simulator that mimicked off-road terrain which was completely separate from the target detection route. Results of a multiple regression analysis determined that the Dual Banners display incorporating an artificial horizon (i.e., AH Dual Banners) and perceived attentional control significantly contributed to the outcome of total severity of motion sickness, as measured by the Simulator Sickness Questionnaire (SSQ). Altogether, 33.6% (adjusted) of the variability in Total Severity was predicted by the variables used in the model. Objective measures were assessed prior to, during and after uncoupled motion. These tests involved performance while immersed in the environment (i.e., target detection and situation awareness), as well as postural stability and cognitive and visual assessment tests (i.e., Grammatical Reasoning and Manikin) both before and after immersion. Response time to Grammatical Reasoning actually decreased after uncoupled motion. However, this was the only significant difference of all the performance measures. Assessment of subjective workload (as measured by NASA-TLX) determined that participants in Dual Banners display conditions had a significantly lower level of perceived physical demand than those with Completely Separated display designs. Further, perceived iv temporal demand was lower for participants exposed to conditions incorporating an artificial horizon. Subjective sickness (SSQ Total Severity, Nausea, Oculomotor and Disorientation) was evaluated using non-parametric tests and confirmed that the AH Dual Banners display had significantly lower Total Severity scores than the Completely Separated display with no artificial horizon (i.e., NoAH Completely Separated). Oculomotor scores were also significantly different for these two conditions, with lower scores associated with AH Dual Banners. The NoAH Completely Separated condition also had marginally higher oculomotor scores when compared to the Completely Separated display incorporating the artificial horizon (AH Completely Separated). There were no significant differences of sickness symptoms or severity (measured by self-assessment, postural stability, and cognitive and visual tests) between display designs 30- and 60-minutes post-exposure. Further, 30- and 60- minute post measures were not significantly different from baseline scores, suggesting that aftereffects were not present up to 60 minutes post-exposure. It was concluded that incorporating an artificial horizon onto the Dual Banners display will be beneficial in mitigating symptoms of motion sickness in manned ground vehicles using 360° indirect vision systems. Screening for perceived attentional control will also be advantageous in situations where selection is possible. However, caution must be made in generalizing these results to missions under terrain or vehicle speed different than what is used for this study, as well as those that include a longer immersion time.

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Die Endprodukte der Tetrapyrrolbiosynthese sind essentiell für die Schwefel- und Stickstoffassimilation (Sirohäm), der von Photorezeptoren abhängigen Genexpression (Phytochromobilin), Elektronenübertragungsreaktionen (Häm) und der Photosynthese (Chlorophyll). Die Synthese von Chlorophyllen wird durch eine Mg-Chelatase (MgCh) eingeleitet, die durch das GENOMES UNCOUPLED 4 (GUN4) Protein stimuliert wird. GUN4 ist essentiell für die Aktivierung der MgCh und die Synthese von Chlorophyllen. Das GUN4 aus Arabidopsis thaliana wird ausschließlich an der vorletzten Aminosäure (S264) des C-Terminus phosphoryliert. Die in vitro und in vivo MgCh-Aktivität wird hingegen durch phosphoryliertes GUN4 nicht mehr stimuliert. De-phosphoryliertes GUN4 bewirkt die lichtabhängige Aktivierung der MgCh im Übergang von der Nacht zum Tag in Angiospermen. Im Laufe der Evolution photosynthetisch aktiver Organismen hat sich die in den Angiospermen hochkonservierte Phosphorylierungsstelle entwickelt. GUN4-Homologe aus Synechocystis oder Chlamydomonas werden nicht phosphoryliert. Im Rahmen der Suche nach der GUN4-spezifischen Proteinkinase wurden vier in den Plastiden lokalisierte PLASTID PROTEIN KINASE WITH UNKNOWN FUNCTION identifiziert. In dieser Arbeit wurden zusätzlich Experimente zum durch die GUN-Proteine vermittelten retrograden Signalweg durchgeführt. gun Mutanten sind durch eine defizitäre cytosolische Anthocyan-/Flavonoidbiosynthese charakterisiert. Auf der Suche nach Hinweisen für einen Zusammenhang zwischen Anthocyanen und der De-repression von PHOTOSYNTHESIS-ASSOCIATED NUCLEAR GENES wurde eine neue gun Mutante identifiziert. Der knockout der durch TRANSPARENT TESTA 4 (TT4) kodierten CHALCON SYNTHASE führte zu einer mit den gun Mutanten vergleichbaren De-repression der PHANGs nach Norflurazon-Behandlung. Pharmakologische Experimente belegen eine mögliche Funktion der Phenylpropanoidbiosynthese in der durch die GUN-Proteine vermittelten retrograden Kommunikation. / Endproducts of the tetrapyrrole biosynthesis pathway are essential for the assimilation of sulfur and nitrogen (siroheme), photoreceptor mediated control of nuclear gene expression (phytochromobilin), electron transfer reactions (heme) and photosynthesis (chlorophyll). The synthesis of chlorophyll is initiated by a Mg-chelatase (MgCh) which is stimulated by the GUN4 protein. GUN4 is essential for the activation of MgCh and synthesis of chlorophyll. GUN4 from Arabidopsis thaliana is exclusively phosphorylated at the next-to-last amino acid of the C-terminus (S264). The stimulatory impact towards MgCh is reduced upon GUN4 phosphorylation. De-phosphorylated GUN4 stimulates MgCh activity during the transition from night to daytime. The phosphorylation site of GUN4 has evolved in the clade of angiosperms. GUN4 homologs of Synechocystis or Chlamydomonas are not phosphorylated. In an attempt to isolate the GUN4-kinase four formerly unknown PLASTID PROTEIN KINASE WITH UNKNOWN FUNCTION were identified. In addition to the elucidation of the post-translational GUN4 modifications, experiments concerning the GUN-dependent retrograde signaling pathway were performed. Under conditions which lead to a block of chloroplast development the de-repression of PHOTOSYNTHESIS-ASSOCIATED NUCLEAR GENES is paralleled by a reduced accumulation of anthocyanins in the gun mutants. When searching for a correlation between anthocyanin biosynthesis and expression of PHANGs a new gun mutant was identified. The knockout of CHALCONE SYNTHASE encoded by TRANSPARENT TESTA 4 (TT4) leads to a comparable de-repression of PHANGs after norflurazon treatment as it was observed for the gun mutants. Pharmacological modification of phenylpropanoid biosynthesis revealed that an intermediate of the pathway is a component of chloroplast-to-nucleus communication. Hence, first evidences for a function of the phenylpropanoid biosynthesis pathway in mediating the GUN-dependent retrograde signal were obtained.

The first identfied 2-oxoglutarate (2OG) dependent oxygenase was a collagen modifying enzyme in the work by Hutton et al. in 1967. Subsequent work has revealed that 2OG dependent oxygenases are a large family with diverse biological roles. With small molecule substrates, these enzymes catalyse a wide range of oxidative reactions, including those that form part of antibiotic biosynthetic pathways. The currently accepted consensus mechanism for catalysis by 2OG-dependent oxygenases is based on crystallographic data, kinetics and on quantum chemical calculations. The consensus mechanism involves oxidative decarboxylation of 2OG by reaction with an oxygen molecule producing CO₂, succinate and a reactive oxidising species that reacts with the 'prime' substrate. Deacetoxycephalosporin C synthase (DAOCS) is a 2OG-dependent oxygenase involved in cephalosporin biosynthesis. The mechanism of DAOCS is of particular interest because it has recently been proposed to be different from the consensus mechanism. The new mechanism proposal from Valeg ard et al. is primarily based on high-resolution crystallographic data with support from steady-state kinetic experiments and quantum-chemical calculations. The work in discussed in this thesis aimed to test the proposal of Valegård et al. by using a combination of spectroscopic and spectrometric methods analysing enzyme-substrate interactions. Substrate binding was investigated using both protein-observe (Chapter 3) and ligand-observe (Chapter 4.1 and 4.2) methods. Preliminary UV-visible data on enzyme-substrates complex formation was also obtained. The strength of substrate and cosubstrate binding was characterised through dissociation constant measurement. An activity assay (Chapter 2) that allows for direct and simultaneous monitoring of 2OG decarboxylation and penicillin ring expansion was optimised. Both the ligand-observe and protein-observe binding experiments as well as the preliminary UV-visible data indicate that the formation of a ternary complex between DAOCS, 2OG and the penicillin substrate is viable. The activity assay conclusively showed that in the presence of unnatural substrates, such as penicillin G, 2OG oxidation is significantly uncoupled from penicillin oxidation. Uncoupled turnover does not occur in the presence of the natural substrate, penicillin N, which is an aspect that should be considered in the analysis of the steady-state kinetic data. Overall, the results provide evidence that, the consensus mechanism for 2OG-dependent oxygenases is viable for DAOCS, at least in the presence of the natural substrate, penicillin N. It is possible that in the presence of an unnatural substrate, the catalytic process undergoes a more complex mechanism, possibly with the direct involvement of reducing agents in the system.

[pt] Em problemas geotécnicos podem ocorrer grandes deformações devido a chuvas prolongadas, sismos, deslizamentos de encostas, etc. Material point method (MPM) é um método de solução baseado no Método dos Elementos Finitos (MEF) que oferece vantagens para o cálculo estático e dinâmico que envolve deformações desse tipo. O objetivo desta dissertação é utilizar o MPM em problemas geotécnicos em condições estáticas e dinâmicas. Esta pesquisa mostra o procedimento de analises do MPM para a condição não acoplada (só solido sem presença de água) e depois acoplada. Para a revisão matemática de MPM se faz antes um resumo da teoria do MEF na metodologia de conservação de quantidade de movimento. Nestas duas formas de resolver os problemas geotécnicos foram expostos três exemplos simples. O primeiro é uma coluna de solo simulado sob os fundamentos da elasticidade, com o objetivo de verificar o deslocamento vertical pelo peso próprio. Isto foi resolvido mediante quatro diferentes métodos: analítica, MEF por resíduos ponderados, MEF por conservação de quantidade de movimento, e MPM. Todos eles consideram somente a fase solida. No segundo exemplo, tem-se solo na geometria de quadrado de lado 1 metro, onde busca-se obter as poropressões quando atingir a condição permanente enquanto os deslocamentos ocorrem ao longo do tempo; ou seja, a análise é acoplada e é resolvida pelo método MPM. Para uma aplicação mais realista, foi feita a análise (não acoplada) da barragem Palo Redondo, pertencente ao projeto Chavimochic, localizada na região de La Libertad, Perú. Nesta análise dinâmica considerou-se dois modelos constitutivos: Elástico e Mohr Coulomb, além de um sismo. / [en] In geotechnical problems can happen large strains because of prolonged rains, earthquake, slide slope, etc. Material point method is a solution method based on the finite element method (FEM) which offers advantages for static and dynamic calculation that involve that kind of strains. The objective in this dissertation is to use the MPM in geotechnical problems in statics and dynamics conditions. This research shows the analysis procedure of MPM for uncoupled condition (only solids, without water) and then coupled. Before the mathematical theory of MPM, a review of the theory of FEM in the conservation of quantidade de movimento is done. In this two methodology were raised three examples. The first one is a soil column that was modeled elastically, in which the main objective in to analyze the vertical displacement because of own weight. This was solved by four different methods: analytically, FEM weighted residual, FEM conservation of momentum, and MPM. All of them consider only the solid phase. The second example is a square of soil with side 1 meter, where the objective is to know the pore-pressure in the permanent condition and at the same time the vertical displacement were generated, it means that the analysis is coupled and were solved by MPM. In order to make a more realistic application, Palo Redondo dam is analyzed (uncoupled condition), which belongs to the Chavimochic project located in La Libertad, region of Perú. This dynamic analysis was done considering two constitutive models: Elastic and Mohr Coulomb, additionally seismic forces.

In the budding yeast Saccharomyces cerevisiae, the evolutionarily conserved Target of Rapamycin (TOR) signaling network regulates cell growth in accordance with nutrient and stress conditions. In this work, I present evidence that the TOR complex 1 (TORC1)-interacting proteins Nnk1, Fmp48, Mks1, and Sch9 link TOR to various facets of nitrogen metabolism and mitochondrial function. The Nnk1 kinase controlled nitrogen catabolite repression-sensitive gene expression via Ure2 and Gln3, and physically interacted with the NAD+-linked glutamate dehydrogenase Gdh2 that catalyzes deamination of glutamate to alpha-ketoglutarate and ammonia. In turn, Gdh2 modulated rapamycin sensitivity, was phosphorylated in Nnk1 immune complexes in vitro, and was relocalized to a discrete cytoplasmic focus in response to NNK1 overexpression or respiratory growth. The Fmp48 kinase regulated respiratory function and mitochondrial morphology, while Mks1 linked TORC1 to the mitochondria-to-nucleus retrograde signaling pathway. The Sch9 kinase appeared to act as both an upstream regulator and downstream sensor of mitochondrial function. Loss of Sch9 conferred a respiratory growth defect, a defect in mitochondrial DNA transmission, lower mitochondrial membrane potential, and decreased levels of reactive oxygen species. Conversely, loss of mitochondrial DNA caused loss of Sch9 enrichment at the vacuolar membrane, loss of Sch9 phospho-isoforms, and small cell size suggestive of reduced Sch9 activity. Sch9 also exhibited dynamic relocalization in response to stress, including enrichment at mitochondria under conditions that have previously been shown to induce apoptosis in yeast. Taken together, this work reveals intimate connections between TORC1, nitrogen metabolism, and mitochondrial function, and has implications for the role of TOR in regulating aging, cancer, and other human diseases.

In the budding yeast Saccharomyces cerevisiae, the evolutionarily conserved Target of Rapamycin (TOR) signaling network regulates cell growth in accordance with nutrient and stress conditions. In this work, I present evidence that the TOR complex 1 (TORC1)-interacting proteins Nnk1, Fmp48, Mks1, and Sch9 link TOR to various facets of nitrogen metabolism and mitochondrial function. The Nnk1 kinase controlled nitrogen catabolite repression-sensitive gene expression via Ure2 and Gln3, and physically interacted with the NAD+-linked glutamate dehydrogenase Gdh2 that catalyzes deamination of glutamate to alpha-ketoglutarate and ammonia. In turn, Gdh2 modulated rapamycin sensitivity, was phosphorylated in Nnk1 immune complexes in vitro, and was relocalized to a discrete cytoplasmic focus in response to NNK1 overexpression or respiratory growth. The Fmp48 kinase regulated respiratory function and mitochondrial morphology, while Mks1 linked TORC1 to the mitochondria-to-nucleus retrograde signaling pathway. The Sch9 kinase appeared to act as both an upstream regulator and downstream sensor of mitochondrial function. Loss of Sch9 conferred a respiratory growth defect, a defect in mitochondrial DNA transmission, lower mitochondrial membrane potential, and decreased levels of reactive oxygen species. Conversely, loss of mitochondrial DNA caused loss of Sch9 enrichment at the vacuolar membrane, loss of Sch9 phospho-isoforms, and small cell size suggestive of reduced Sch9 activity. Sch9 also exhibited dynamic relocalization in response to stress, including enrichment at mitochondria under conditions that have previously been shown to induce apoptosis in yeast. Taken together, this work reveals intimate connections between TORC1, nitrogen metabolism, and mitochondrial function, and has implications for the role of TOR in regulating aging, cancer, and other human diseases.