Allosteric regulation of proteins by reversible ligand binding is essential for regulation of fundamental biological processes. The mechanism by which a binding event alters the function of a distant site in a protein is only poorly understood. In this thesis, I use the Tetracycline Repressor (TetR) as a model system to study ligand induced allostery. The transcription of genes encoding the resistance to the antibiotic, tetracycline (Tc), is repressed by TetR, which is a homodimeric alpha-helical protein possessing a small N-terminal DNA binding domain (DNB domain) and a larger C-terminal tetracycline binding and dimerization domain (TBD domain). Based on previous structural and thermodynamic studies, the DNB domains are thought to exist in two stable, distinct conformations. One conformation is able to bind the Tc resistance operator sequence (tetO) with high affinity, while the other, which is induced by Tc binding, binds very weakly. While most previous studies on TetR have focused on the effects of Tc binding on the DNB domain conformation, here I have investigated the role of the DNB domain in modulating Tc binding. By introducing destabilizing mutations into the DNB domain I ascertained that the conformation and stability of the DNB domain plays an important role in determining Tc binding affinity. I also discovered that in the absence of ligand, the DNB domain exists in an unstable and flexible state with respect to the TBD domain. However, Tc binding to the TBD domain stabilizes the DNB domain, causing it to fold cooperatively with the TBD domain. I have discovered that the behavior of previously isolated non-inducible mutants is caused by the inability of Tc to stabilize the DNB domain in these mutants. Furthermore, reverse TetR mutants, which bind DNA better in the presence of Tc have an unfolded DNB domain that is only partially stabilized by Tc binding. My work suggests a new comprehensive, Tc induced stabilization and domain cooperativity model that can describe the mechanism of allostery in TetR and previously unexplainable mutants. A practical outcome of this research is the creation of a Tc induced folding switch that can be exploited to control the in vivo degradation of a protein of interest.

A sílica obtida da queima de casca de arroz foi convertida nas fases α e β. A estabilização da fase β foi obtida pela introdução de alumínio e cálcio na rede de sílica, 10001100 °C, na proporção CaO:2Al2O3:38SiO2. Foi observado que a transição de fase α→β da cristobalita α tem sua temperatura de transição reduzida de 175°C bem como sua entalpia de transição, de 16,0 J/g para 7,0 J/g. Esse efeito é causado pela introdução de íon K+, presente na casca de arroz, na estrutura da sílica. O processamento empregado nessa conversão usa equipamentos normalmente encontrados em empresas de cerâmica tradicional moinho, atomizador, prensa e forno / Silica generated from burned rice shells has been converted to the β and &#945 phases of cristobalite. The β phase stabilization was acomplished by instilling aluminum and calcium into the silica structure, at 1000-1100 °C, in the following proportion CaO:2Al2O3:38SiO2. The phase transition α→β of the α-cristobalite has a lower transition temperature, as compared with cristobalite made from pure silica, from 270°C to 170°C. Also the transition entalphy was reduced from 16,0 J/g to 7,0 J/g. These changes were attributed to the K+ ion present in the silica structure of the burned silica. The process used in this convertion makes use of standard equipments, regularly used in ceramic producing companies mill, spray dryer, furnaces, and press.

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Typescript (photocopy). / Digitized by Kansas Correctional Industries

Esta pesquisa foi desenvolvida na Estação de Tratamento de Esgoto de Cajati, onde o tratamento é realizado por lagoas de estabilização com sistema australiano. Em amostragens de variação nictemeral e sazonal, observou-se estratificação térmica nas duas lagoas, sendo que esta foi mais acentuada em abril. Em todos os períodos, a coluna de água esteve homogênea às 2h e 8h e estratificada às 14h e 20h. A estratificação térmica resultou na estratificação química (pH e oxigênio dissolvido), sendo que ambas as lagoas foram divididas em dois compartimentos: superior, com maiores temperaturas, pH e oxigênio dissolvido, e outro inferior, com comportamento contrário. A lagoa anaeróbia apresentou concentrações de oxigênio dissolvido de aproximadamente 10,0 mg/L, o que resulta em funcionamento inadequado também foi confirmado pelos resultados de clorofila nesta lagoa, que foram semelhantes aos da facultativa e atingiram até 3,5x\'10 POT.3\' \'mü\'g/L em abril e julho. Além disso, as concentrações de nutrientes e coliformes foram baixas no afluente bruto em relação às obtidas na literatura. Os valores de pH estiveram altos para lagoas de estabilização, com máxima de 12,17 em janeiro. Apenas em abril, o pH esteve menor (6,84-9,86), condizente com a literatura e adequado para fermentação anaeróbia. O menor pH e maiores temperaturas obtidos em abril resultaram em melhores eficiências de redução que nos outros períodos. As estimativas de vazão e carga orgânica revelaram que a ETE vem operando abaixo da carga prevista, o que pode influenciar na eficiência do sistema, pois este não terá tempo suficiente para formar comunidade microbiana estável. Não foi possível observar variabilidade vertical padrão das biomoléculas proteínas, carboidratos e lipídeos, nem ao longo do sistema. Observou-se heterogeneidade espacial e vertical entre as concentrações de nitrogênio e fósforo em todo sistema, onde alguns processos puderam ser identificados e estes foram influenciados por temperatura, pH e oxigênio dissolvido. Houve predomínio de cianobactéria (Synechocystis sp) na ETE Cajati, seguido de clorofícea (Chlorella kessleri). Em ambas as lagoas, o predomínio foi de Eubactéria com baixas concentrações de Arquéias. O efluente final esteve de acordo com os padrões de lançamento de efluentes estabelecidos na Resolução CONAMA 357/2005. / This research was developed in the Cajati wastewater treatment plant, where the treatment is carried through by stabilization ponds with australian system. In samplings of nictemeral and seasonal variation, thermal stratification in the two ponds was observed, and this was more accented in April. In all the periods, the water column was homogeneous at 2 a.m. and 8 a.m. and stratified at 2 p.m. and 8 p.m. Thermal stratification resulted in chemical stratification (pH and dissolved oxygen) and both the ponds had been divided into two compartments: superior, with higher temperatures, pH and dissolved oxygen, and another inferior, to the contrary behavior. The anaerobic pond presented concentrations of dissolved oxygen of approximately 10,0 mg/L that results in functioning inadequate confirmed by the results of chlorophyll in this pond. The anaerobic pond had been similar to the facultative one, which had reached 3,5 x \'10 POT.3\' \'mü\'g/L in April and July. Moreover, the concentrations of nutrients and coliforms had been low in the raw affluent in relation to those described in literature. The pH values had been high for stabilization ponds, with maximum of 12,17 in January. In April, pH was minor (6,84-9,86), according to literature and for anaerobic fermentation. The minor pH and greater temperature taken in April had resulted in better efficiencies of reduction that in the other periods. The estimates of outflow and organic load had disclosed that the plant is operating below the design load, which can influence the efficiency of the system, therefore it will not have enough time to form steady microbial community. Vertical and spatial variability was not observed for proteins, carbohydrates and lipids. Vertical and spatial heterogeneity was observed in nitrogen and phosphorus concentrations, where some processes could have been identified and these had been influenced by temperature, pH and dissolved oxygen. There were predominance of Cyanobacteria (Synechocystis sp) followed by Chlorophycea (Chlorella kessleri). In both ponds, there was predominance of Eubacteria with low concentrations of Archeae. The final effluent was in accordance with the established standards of discharge of effluent - Resolution CONAMA 357/2005.

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Doctor of Philosophy / In this thesis an examination is made of the vibro-replacement technique for the stabilisation of cohesive soils. Improvement is achieved by the formation of stiffer columns of granular material within the soil deposit using a large cylindrical vibrator referred to as a vibroflot. Granular piles (also termed stone columns) are used either singly or in small groups to supoort isolated footings or large numbers are installed in a regular array to support widespread loads. Each of these modes of application are investigated.

This thesis examines the pre and post failure deformation behaviour of landslides in cut, fill and natural soil slopes, and of the deformation behaviour of embankment dams. The deformation behaviour of landslides and embankment dams have been analysed from a database of case studies from a number of classes of slope (and dam) and material type. The database included some 450 landslides in cuts, fills and natural slopes, and some 170 embankment dams. For landslides in soil slopes, methods and guidelines have been developed for use in the analysis, evaluation and prediction of the pre and post failure deformation behaviour. They take into consideration the factors influencing and the mechanics controlling the deformation behaviour for the classes of slope and material types, which are different for pre and post failure. Pre-failure deformations are largely controlled by the effective stress conditions within the slope, changes in the boundary conditions and the response of the soil to those changes in boundary conditions. Whether the soil, under the effective stress conditions imposed within the slope, is contractive (and saturated or near saturated) or dilative on shearing, has a significant influence on the pre failure deformation behaviour. The post failure deformation behaviour is strongly influenced by the mechanics of failure (including whether the soil is contractive or dilative on shearing), the source area slope angle, the downslope geometry, the orientation of the surface of rupture, the material properties and slide volume. Guidelines are presented for prediction of 'rapid' and 'slow' post failure velocity. For embankment dams, methods and guidelines have been developed for evaluation and prediction of the deformation behaviour during and post construction for selected embankment types. They take into consideration the influence of material type and placement methods, material strength and compressibility properties, embankment zoning geometry, embankment height, and reservoir operation, amongst other factors. Guidelines have been developed to assist in the identification of 'abnormal' deformation behaviour, which can be related to internal deformations or a marginal stability condition and the onset to failure.

Thesis (Ph.D.)--Rensselaer Polytechnic Institute, 1996. / Adviser: Ahmed-W. Elgamal. Includes bibliographical references.

This thesis concerns delay-dependent robust stability analysis and stabilization for time-delay system with uncertainties. By choosing new Lyapunov-Krasovskii functional and using methods which can reduce conservativeness of stability condition in the literature, new delay-dependent sufficient stability conditions are obtained in terms of linear matrix inequality. It is shown that the new stability conditions can provide less conservative results than some existing ones. Furthermore, the new stability conditions are also used to design the state feedback controllers. Finally, numerical examples are given to show the derived results and compared with results in the literature.