No description available.

M.S.

Thesis (MSc (Biochemistry))--University of Stellenbosch, 2009. / A Python package called PySUNDIALS has been developed which provides an interface to the suite of nonlinear di erential/algebraic equation solvers (SUNDIALS) using ctypes as a foreign function interface (FFI). SUNDIALS is a C implementation of a set of modern algorithms for integrating and solving various forms of the initial value problem (IVP). Additionally, arbitrary root nding capabilities, time dependent sensitivity analysis, and the solution of di erential and algebraic systems are available in the various modules provided by SUNDIALS. A signi cant focus of the project was to ensure the python package conforms to Python language standards and syntactic expectations. Multiple examples of the SUNDIALS modules (CVODE, CVODES, IDA and KINSOL) are presented comparing PySUNDIALS to C SUNDIALS (for veri cation of correctness), and comparing PySUNDIALS to various other comparable software packages. The examples presented also provide benchmark comparisons for speed, and code length. Speci c uses of the features of the SUNDIALS package are illustrated, including the modelling of discontinuous events using root nding, time dependent sensitivity analysis of oscillatory systems, and the modelling of equilibrium blocks using a complete set of implicit di erential and algebraic equations. PySUNDIALS is available as open source software for download. It is being integrated into the systems biology software PySCeS as an optional solver set, on an ongoing basis. A brief discussion of potential methods of optimization and the continuation of the project to wrap the parallel processing modules of SUNDIALS is presented.

published_or_final_version / Chemistry / Doctoral / Doctor of Philosophy

Understanding of a global biological network structure by studying its simple local properties through the well-developed field of graph theory is of interest. In particular, in this research an observed biological network was explored through a simulation study. However, one difficulty in such exploration lies on the fitting of graphical models on biological network data. An Exponential Random Graph Model (ERGM) was considered to determine estimations of the several network attributes of complex biological network data. We also compared the estimates of observed network to our random simulated network for both Markov Chain Monte Carlo Maximum Likelihood Estimation (MCMCMLE) and Maximum Pseudo Likelihood Estimation (MPLE) methods under ERGM. The motivation behind this was to determine how different the observed network could be from a randomly simulated network if the physical numbers of attributes were approximately same. Cut-off points of some common attributes of interest for different order of nodes were determined through simulations. We implemented our method to a known regulatory network database of E. coli. / Department of Mathematical Sciences

Sabe-se que em sistemas biológicos, as funções de proteínas e de hormônios estão relacionadas com suas conformações espaciais e que suas estruturas e funções são freqüentemente influenciadas pela interação com os lipídeos das membranas plasmáticas e/ou intracelulares. Devido à importância das interações entre as proteínas e hormônios com as membranas, vários estudos têm sido realizados empregando modelos que simulam as membranas, pois as biológicas são estruturas bastante complexas. Entre esses modelos esta o de micelas reversas que pode ser considerado atualmente como o que melhor reproduz as condições existentes in vivo, pois a água presente nesse sistema e uma ótima representação para a água presente em sistemas biológicos em torno dos receptores de membrana. Visando estudar a interação do hormônio melanócito estimulante (- MSH) e do peptídeo sintético melanotrópico análogo (MSH1) com um modelo de membrana, na tentativa de compreensão de seu papel biológico, usamos micelas reversas preparadas com o anfifílico bis-(2-etilhexil)sulfosucinato de sódio, abreviado AOT. É sabido que - MSH é importante na regulação da pigmentação da pele, alem de estar relacionado a vários processos fisiológicos e neurológicos. Mais recentemente, foram encontradas evidencias de que ele atua também como neurotransmissor ou neuromodulador na aprendizagem, memória e capacidade de concentração. Clinicamente, os peptídeos melanotrópicos podem eventualmente ser utilizados no tratamento de alterações pigmentares e na detecção e erradicação de melanomas. Realizamos medidas de ressonância paramagnética eletrônica e de fluorescência de estado estacionário e resolvida no tempo para estudar a dinâmica interna dos peptídeos melanotrópicos na interação com micelas reversas de AOT. Monitoramos a fluorescência do resíduo Triptofano localizado na nona posição da seqüência de aminoácidos dos peptídeos melanotrópicos. A supressão da fluorescência do resíduo triptofano por acrilamida (que fica no meio micelar) também foi medida para auxiliar na tentativa de localizar a posição do fluoróforo nas micelas reversas. Dos espectros de EPR obtidos com o marcador de spin 5-SASL observamos que, com o aumento do tamanho das micelas reversas pelo aumento da quantidade de água, a região das cabeças polares tende a ficar flexível enquanto que, em oposição, aumenta a rigidez, a polaridade ordem da região das cadeias. Os resultados obtidos para o acréscimo de solução tampão fosfato e para soluções contendo Trp, LTL, -MSH e MSH1 são similares mostrando que essa técnica fornece informações sobre as micelas, independente da interação das mesmas com os peptídeos. Dos resultados obtidos com a fluorescência para o grau de anisotropia, tempo de vida e comprimento de onda de máxima emissão observamos que os fluoróforos utilizados (Trp, LTL, -MSHe MSH1) experimentam uma região menos polar e mais rígida do que a água. Vimos também que com o aumento da quantidade de água nas micelas reversas os peptídeos e o aminoácido tendem a assumir determinadas localizações na interface, sendo que o Triptofano fica no meio mais hidratado que não é a agua bulk. Os espectros de decaimentos associados mostram a ocorrência de conformações com diferentes graus de exposição do Triptofano ao ambiente aquoso. Assim, pudemos perceber que o Trp é o mais exposto à água tendendo a localizar-se na região de água estruturada. O LTL fica ancorado na região da interface e os peptídeos melanotrópicos inserem-se na região das cadeias hidrocarbônicas, sendo que o -MSH insere-se mais profundamente. Observamos também dos espectros de decaimentos associados diferenças das distribuições conformacionais para os hormônios melanotrópicos, especialmente para as micelas reversas maiores que simulam a situação biológica, o que pode estar relacionado com as diferentes atividades bio1ógicas dos mesmos. / The biological function of proteins and hormones is related to their conformations and both structure and function are frequently dependent on the interactions with lipids of plasmatic and intracelular membranes. Due to the complexity of biological membranes, many studies about these interactions employ model membranes. The reverse micelle is a good model, for it offers an adequate representation of the structured water that is present in biological systems around the membrane receptors. We report here studies of the interaction of -melanocyte stimulating hormone (-MSH) and one synthetic analogue (MSH1) with reverse micelles prepared from the amphyphylic sodium bis-(2-ethylhexyl)sulfosuccinate (AOT) in isooctane. The -MSH is important in the regulation of skin pigmentation and is also involved with other physiological process. It was recently found evidences of its action as a neurotransmitter or neuromodulator in learning, memory and attention. It is claimed that potent analogues of melanotropin hormones could be used in the therapy of pigmentary disorders and detection and treatment of melanome. Electron paramagnetic resonance (EPR), steady state fluorescence and time-resolved fluorescence were employed to study the internal dynamics of the melanotropins in interaction with reverse micelles of AOT. We monitored the fluorescence of the residue tryptophan located in the 9 position of the aminoacids sequence of -MSH and MSH-l. The tripeptide Lysil-tryptophyl-Lysine (LTL) and the isolated aminoacid tryptophan were also investigated as simpler molecules interacting with the reverse micelles. It was also measured the fluorescence quenching by acrylamide, to obtain more information about the peptide location in reverse micelles. We monitored the EPR spectra of the spin label 5-doxyl stearate acid (5-SASL) at increasing values of Wo hat is the ratio between the number of water molecules and the number of AOT molecules. The region of the polar head gains flexibility when the size of the reverse micelles increases (due to increase in water content) and, opposite to this, the region of the hydrophobic tail becomes more rigid, showing higher order and polarity. Similar effects were observed upon addition of solutions containing either tryptophan, or LTL, or -MSH and MSH-1, indicating that the EPR measurements gave information about the changes in the micelles promoted by water molecules, independent of the interactions with the peptides. Monitoration of fluorescence parameters like spectral position of emission band, anisotropy and lifetime demonstrated that the environment around the fluorophore, in all compounds, is less polar and more rigid than bulk water. Those parameters reflect the location of the compounds in the heterogeneous isooctane/AOT/water medium and are sensitive to the changes induced in the micelles by the increasing the amount of water. However, in large micelles having wo above 10, the modifications detected by fluorescence re small and the addition of water no more affects the location of the fluorophores. Quenching measurements gave additional support to the data indicating that the different compounds occupy different positions in the large reverse micelles, but in any case they are in the interface region, without dispersing into the bulk water. Decay associated spectra allowed the identification of conformations with various degree of exposition to polar and non polar media. The conformation related to the long lifetime is more exposed to water while that associated to the intermediate lifetime is preferentially stabilised in non polar media. The native hormone -MSH in the large micelles shows predominance of the conformation sensing a non polar environment, with similar results presented by the analogue MSH-1. Those melanotropins are in the region of the hydrocarbon chain, with slightly deep location for the native hormone. The tripeptide LTL is anchored in the interface region, probably stabilised by electrostatic interaction between the charged groups in the peptide and the negative charge in AOT. Finally, the tryptophan is most exposed to water, probably interacting with structural water near to the interface.

In this thesis, we develop and apply top-down, quantitative approaches to gain novel insights into various complex biological systems. Beginning at the multicellular level, we study human gut microbiome dynamics from an ecological perspective. We develop computational frameworks to enable a global understanding of the spatiotemporal variability of gut bacterial abundances. We demonstrate the utility of our frameworks to elucidate the ecological processes governing abundance changes of gut microbiota. We then shift our focus to the intracellular level by investigating the metabolic limitations of cancer cell growth. We use coarse-grained mathematical modeling to identify a major growth limitation of cancer cells associated with electron acceptor deficiency, which we then experimentally validate. Collectively, these set of approaches help to decipher the organizing principles of complex biological systems at both the individual and multicellular levels.

Sabe-se que em sistemas biológicos, as funções de proteínas e de hormônios estão relacionadas com suas conformações espaciais e que suas estruturas e funções são freqüentemente influenciadas pela interação com os lipídeos das membranas plasmáticas e/ou intracelulares. Devido à importância das interações entre as proteínas e hormônios com as membranas, vários estudos têm sido realizados empregando modelos que simulam as membranas, pois as biológicas são estruturas bastante complexas. Entre esses modelos esta o de micelas reversas que pode ser considerado atualmente como o que melhor reproduz as condições existentes in vivo, pois a água presente nesse sistema e uma ótima representação para a água presente em sistemas biológicos em torno dos receptores de membrana. Visando estudar a interação do hormônio melanócito estimulante (- MSH) e do peptídeo sintético melanotrópico análogo (MSH1) com um modelo de membrana, na tentativa de compreensão de seu papel biológico, usamos micelas reversas preparadas com o anfifílico bis-(2-etilhexil)sulfosucinato de sódio, abreviado AOT. É sabido que - MSH é importante na regulação da pigmentação da pele, alem de estar relacionado a vários processos fisiológicos e neurológicos. Mais recentemente, foram encontradas evidencias de que ele atua também como neurotransmissor ou neuromodulador na aprendizagem, memória e capacidade de concentração. Clinicamente, os peptídeos melanotrópicos podem eventualmente ser utilizados no tratamento de alterações pigmentares e na detecção e erradicação de melanomas. Realizamos medidas de ressonância paramagnética eletrônica e de fluorescência de estado estacionário e resolvida no tempo para estudar a dinâmica interna dos peptídeos melanotrópicos na interação com micelas reversas de AOT. Monitoramos a fluorescência do resíduo Triptofano localizado na nona posição da seqüência de aminoácidos dos peptídeos melanotrópicos. A supressão da fluorescência do resíduo triptofano por acrilamida (que fica no meio micelar) também foi medida para auxiliar na tentativa de localizar a posição do fluoróforo nas micelas reversas. Dos espectros de EPR obtidos com o marcador de spin 5-SASL observamos que, com o aumento do tamanho das micelas reversas pelo aumento da quantidade de água, a região das cabeças polares tende a ficar flexível enquanto que, em oposição, aumenta a rigidez, a polaridade ordem da região das cadeias. Os resultados obtidos para o acréscimo de solução tampão fosfato e para soluções contendo Trp, LTL, -MSH e MSH1 são similares mostrando que essa técnica fornece informações sobre as micelas, independente da interação das mesmas com os peptídeos. Dos resultados obtidos com a fluorescência para o grau de anisotropia, tempo de vida e comprimento de onda de máxima emissão observamos que os fluoróforos utilizados (Trp, LTL, -MSHe MSH1) experimentam uma região menos polar e mais rígida do que a água. Vimos também que com o aumento da quantidade de água nas micelas reversas os peptídeos e o aminoácido tendem a assumir determinadas localizações na interface, sendo que o Triptofano fica no meio mais hidratado que não é a agua bulk. Os espectros de decaimentos associados mostram a ocorrência de conformações com diferentes graus de exposição do Triptofano ao ambiente aquoso. Assim, pudemos perceber que o Trp é o mais exposto à água tendendo a localizar-se na região de água estruturada. O LTL fica ancorado na região da interface e os peptídeos melanotrópicos inserem-se na região das cadeias hidrocarbônicas, sendo que o -MSH insere-se mais profundamente. Observamos também dos espectros de decaimentos associados diferenças das distribuições conformacionais para os hormônios melanotrópicos, especialmente para as micelas reversas maiores que simulam a situação biológica, o que pode estar relacionado com as diferentes atividades bio1ógicas dos mesmos. / The biological function of proteins and hormones is related to their conformations and both structure and function are frequently dependent on the interactions with lipids of plasmatic and intracelular membranes. Due to the complexity of biological membranes, many studies about these interactions employ model membranes. The reverse micelle is a good model, for it offers an adequate representation of the structured water that is present in biological systems around the membrane receptors. We report here studies of the interaction of -melanocyte stimulating hormone (-MSH) and one synthetic analogue (MSH1) with reverse micelles prepared from the amphyphylic sodium bis-(2-ethylhexyl)sulfosuccinate (AOT) in isooctane. The -MSH is important in the regulation of skin pigmentation and is also involved with other physiological process. It was recently found evidences of its action as a neurotransmitter or neuromodulator in learning, memory and attention. It is claimed that potent analogues of melanotropin hormones could be used in the therapy of pigmentary disorders and detection and treatment of melanome. Electron paramagnetic resonance (EPR), steady state fluorescence and time-resolved fluorescence were employed to study the internal dynamics of the melanotropins in interaction with reverse micelles of AOT. We monitored the fluorescence of the residue tryptophan located in the 9 position of the aminoacids sequence of -MSH and MSH-l. The tripeptide Lysil-tryptophyl-Lysine (LTL) and the isolated aminoacid tryptophan were also investigated as simpler molecules interacting with the reverse micelles. It was also measured the fluorescence quenching by acrylamide, to obtain more information about the peptide location in reverse micelles. We monitored the EPR spectra of the spin label 5-doxyl stearate acid (5-SASL) at increasing values of Wo hat is the ratio between the number of water molecules and the number of AOT molecules. The region of the polar head gains flexibility when the size of the reverse micelles increases (due to increase in water content) and, opposite to this, the region of the hydrophobic tail becomes more rigid, showing higher order and polarity. Similar effects were observed upon addition of solutions containing either tryptophan, or LTL, or -MSH and MSH-1, indicating that the EPR measurements gave information about the changes in the micelles promoted by water molecules, independent of the interactions with the peptides. Monitoration of fluorescence parameters like spectral position of emission band, anisotropy and lifetime demonstrated that the environment around the fluorophore, in all compounds, is less polar and more rigid than bulk water. Those parameters reflect the location of the compounds in the heterogeneous isooctane/AOT/water medium and are sensitive to the changes induced in the micelles by the increasing the amount of water. However, in large micelles having wo above 10, the modifications detected by fluorescence re small and the addition of water no more affects the location of the fluorophores. Quenching measurements gave additional support to the data indicating that the different compounds occupy different positions in the large reverse micelles, but in any case they are in the interface region, without dispersing into the bulk water. Decay associated spectra allowed the identification of conformations with various degree of exposition to polar and non polar media. The conformation related to the long lifetime is more exposed to water while that associated to the intermediate lifetime is preferentially stabilised in non polar media. The native hormone -MSH in the large micelles shows predominance of the conformation sensing a non polar environment, with similar results presented by the analogue MSH-1. Those melanotropins are in the region of the hydrocarbon chain, with slightly deep location for the native hormone. The tripeptide LTL is anchored in the interface region, probably stabilised by electrostatic interaction between the charged groups in the peptide and the negative charge in AOT. Finally, the tryptophan is most exposed to water, probably interacting with structural water near to the interface.

Abstract not available

In response to organic contaminations pollutating water sources of drinking water, domestic water treatment plants (WTP) were transforming from traditional chlorination disinfecton method to advanced ozone-based disinfection processes. However, the effectiveness of water purification procedures n removing AOC (Assimilable Organic Carbon) and DBPsFP (Disinfection By-Products Formation Potential) can be improved. Additionally, the quality of clean water purified at WTP may deteriorate in the water distribution network for various reasons, primarily resulting from the regrowth of microorganisms in the water distribution pipelines. This study investigates and researches the essential water quality items of effluent before and after the advanced water purification treatment plants and water movement to end users through water distribution networks. The investigation proceeded in four directions: (1) the efficiency of removing AOC from raw water using powdered and granular activated carbon biological systems, and the development of an AOC prediction model based on water quality monitoring items using the AutoNet (6.03) method of the artificial neural network system; (2) removal of the byproducts of disinfection from raw water using powdered activated carbon biological systems; (3) examining the relationship between ozone-based and chlorination-based water disinfection methods by comparing the number of coliform bacteria and total bacteria population in traditional and advanced processing units; (4) regarding the water distribution storage facilities for users, water reservoir towers were examined for water quality sampling and analysis and water tower cleaning frequencies. Regression analysis was performed using SPSS ¡]Statistical Product and Service Solutions¡^ statistical software, with the correlation coefficient denoting the closeness of relationships. We anticipate understanding the water quality situation for current users of tap water, and demands for cleaning frequencies, thereby achieving the purpose of improving drinking water safety. Regarding the efficiency of removing AOC from raw water, the results showed powdered and granular activated carbon biological systems performed well, with the AOC removal rate reaching 53% and 54%, respectively, and the SUVA (Specific Ultraviolet Absorbance) value (showed by UV254/DOC) being reduced by 15-18% and 22-23%, respectively. The correlation analysis of the AOC prediction model shows that the GAC (Granular Activated Carbon) had high predictive and actual value R values (R2 = 0.772) after model regressing, and the PAC (Powder Activated Carbon) had higher predictive and actual value R values (R2 = 0.856) after model regressing as well. That the PAC system AOC prediction model has a slightly higher correlation that may be attributed to water contaminations resulting from domestic sewage, agricultural fertilizers, and livestock excretions. In the use of powdered activated carbon biological systems to remove disinfection byproducts, THMsFP (Trihalomethanes Formation Potential) and HAAsFP (Haloacetic acids Formation Potential) functioned with a certain removal efficiency, with the average effluent concentrations being under the regulatory standard of 80£gg/L, respectively, which reduces carcinogenic risks. Correlation analyses conducted using SUVA on the three water quality concentrations (HAA5FP, HAA9FP, and THMsFP) obtained R2 values of 0.805, 0.820, and 0.823, respectively, indicating high levels of correlation. For the results of microbial assessment using ozone and chlorine to process drinking water, the advanced and conventional WTP achieved a removal rate greater than 99% for microbial removal (coliform bacteria and total bacteria population). The correlation analysis between cleaning frequencies and water quality parameters showed the frequency at which the water reservoirs and towers were cleaned has a significant impact on tap water quality in residential compounds and schools that accommodated more than 100 households or less than 99 households. Higher cleaning frequency (more than four cleanings a year) results in better the water quality.