No description available.

No description available.

The work presented in this thesis leads to the formulation of a dynamic mathematical model of an immersed membrane bioreactor (iMBR) for wastewater treatment. This thesis is organised into three parts, each one describing a different set of tasks associated with model development and simulation. In the first part, the Author qualitatively and quantitatively compares various published activated sludge models, i.e. models of biochemical processes associated with bacterial growth, decay, lysis and substrate utilisation in activated sludge systems. As the thesis is focused on modelling membrane bioreactors (MBRs) which are known to experience membrane fouling as a result of adsorption of biopolymers present in the bulk liquid onto and within the membrane, all activated sludge models considered in this thesis are able to predict, with various levels of accuracy, the concentrations of biopolymeric substances, namely soluble microbial products (SMP) and extracellular polymeric substances (EPS). Some of the published activated sludge models dedicated to modelling SMP and EPS kinetics in MBR systems were unable to predict the SMP and EPS concentrations with adequate levels of accuracy, without compromising the predictions of other sludge and wastewater constituents. In other cases, the model equations and the assumptions made by their authors were questionable. Hence, two new activated sludge models with SMP and EPS as additional components have been formulated, described, and simulated. The first model is based on the Activated Sludge Model No. 1 (ASM1) whereas the second model is based on the Activated Sludge Model No. 3 (ASM3). Both models are calibrated on two sets of data obtained from a laboratory-scale system and a full-scale system and prove to be in very good agreement with the measurements. The second part of this thesis explains the development of two membrane fouling models. These models are set to describe the loss of membrane permeability during filtration of various solutions and suspensions. The main emphasis is placed on filtration of activated sludge mixtures, however the models are designed to be as general as feasibly possible. As fouling is found to be caused by a large number of often very complex processes which occur at different spatial as well as temporal scales, the two fouling models developed here have to consider a number of significant simplifications and assumptions. These simplifications are required to balance the model's accuracy, generality and completeness with its usability in terms of execution times, identifiability of parameters and ease of implementation in general purpose simulators. These requirements are necessary to ascertain that long term simulations as well as optimisation and sensitivity studies performed in this thesis either individually on fouling models or on the complete model of a MBR can be carried out within realistic time-scales. The first fouling model is based on an idea that fouling can be subdivided into just two processes: short-term reversible fouling and long-term irreversible fouling. These two processes are described with two first order ordinary differential equations (ODEs). Whilst the first model characterises the membrane filtration process from an observer's input-output point of view without any rigorous deterministic description of the underlying mechanisms of membrane fouling, the second model provides a more theoretical and in-depth description of membrane fouling by incorporating and combining three classical macroscopic mechanistic fouling equations within a single simulation framework. Both models are calibrated on a number of experimental data and show good levels of accuracy for their designated applications and within the intended ranges of operating conditions. In the third part, the first developed biological model (CES-ASM1) is combined with the behavioural fouling model and the links between these two models are formulated to allow complete simulation of a hollow fibre (HF) immersed membrane bioreactor (iMBR). It is assumed that biological processes affect the membrane through production of mixed liquor suspended solids (MLSS), SMP and EPS which cause pore blockage, cake formation, pore diameter constriction, and affect the specific cake resistance (SCR). The membrane, on the other hand, has a direct effect on the bulk liquid SMP concentration due to its SMP rejection properties. SMP are assumed to be solely responsible for irreversible fouling, MLSS is directly linked to the amount of cake depositing on the membrane surface, whereas EPS content in activated sludge affects the cake's SCR. Other links provided in the integrated MBR model include the effects of air scouring on the rate of particle back-transport from the membrane surface and the effects of MLSS concentration on oxygen mass transfer. Although backwashing is not described in great detail, its effects are represented in the model by resetting the initial condition in the cake deposition equation after each backwash period. The MBR model was implemented in Simulink® using the plant layout adopted in the MBR benchmark model of Maere et al. [160]. The model was then simulated with the inputs and operational parameters defined in [36, 160]. The results were compared against the MBR benchmark model of Maere et al. [160] which, contrary to this work, does not take into account the production of biopolymers, the membrane fouling, nor any interactions between the biological and the membrane parts of an MBR system.

Thesis advisor: Mary F. Roberts / Thesis advisor: Eranthie Weerapana / Peripheral proteins from mammals often exhibit multi-domain structures and require metal ions such as calcium as co-factors. This dissertation investigates two types of such proteins -- pulmonary collectins (surfactant proteins A and D) and phosphatidylinositol-specific phospholipase C (PLC) delta1 -- and their interactions with model membranes. One approach to work around the complexity brought upon by such multi-domain protein structure is to use a truncated construct or an isolated single domain. For pulmonary collectins, homotrimers consisting of the neck domain and the carbohydrate recognition domain were used in a novel NMR assay for better understanding of their lipid-specific interactions with the membranes. For PLC delta1, we were particularly interested in the role of the EF-hand domain. The isolated EF-hand domain of PLC delta1 was first used to characterize its interactions with membranes and identify key residues responsible for such interactions. These key residues in the N terminal lobe of the EF-hand domain, either cationic or hydrophobic, were then found to affect the hydrolysis activity of the full-length enzyme. A common role for this region of the PLC in facilitating proper membrane association was thus proposed. / Thesis (PhD) — Boston College, 2013. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

The bilayer disc is a flat, lipid aggregate structure in the nanometre regime. It is composed of a bilayer of amphiphilic molecules with micelle-forming amphiphilic molecules supporting the rim, which prevent disc fusion and self-closure. Stable discs have been found in lipid mixtures containing polyethylene glycol (PEG)-lipids as a rim-stabilizing component. One of the aims of the work described in this thesis was to increase the fundamental knowledge and understanding of the systems in which these discs are formed. Other micelle-forming surfactants apart from PEG-lipids were also explored to see if they could be used to stabilize the disc aggregate structure. Due to the similarities of these lipid discs with natural membranes it was hypothesized that they could be used as models for biological membranes. It was demonstrated that discs are formed in PEG-lipid/lipid systems when the lipid mixture contains components that reduce the spontaneous curvature and increase the monolayer bending rigidity. Discoidal structures are furthermore preferred when the lipids are in the gel phase, probably due to a combination of high bending rigidity and reduced PEG-lipid/lipid miscibility. The disc size could be varied by changing the PEG-lipid concentration. The size and size homogeneity of the discs could also be varied by changing the preparation path. Generally, the preferences of certain lipid systems to form discs remained when the PEG-lipid was replaced by more conventional surfactants. However, discs prepared in PEG-lipid/lipid systems are more useful as model membranes because of their relatively large size and good temperature, dilution and long-term stability. Data obtained with isothermal titration calorimetry and drug partition chromatography indicate that these bilayer discs may serve as an attractive and sometimes superior alternative to liposomes in studies of drug-membrane interactions.

Lipodisks, also referred to as polyethylene glycol (PEG)-stabilized bilayer disks, have previously been demonstrated to hold great potential as model membranes in drug partition studies. In this study, an HPLC-MS system with stably immobilized lipodisks is presented. Functionalized lipodisks were immobilized on two different HPLC support materials either covalently by reductive amination or by streptavidin-biotin binding. An analytical HPLC column with immobilized lipodisks was evaluated by analysis of mixtures containing 15 different drug compounds. The efficiency, reproducibility, and stability of the system were found to be excellent. In situ incorporation of cyclooxygenase-1 (COX-1) in immobilized lipodisks on a column was also achieved. Specific binding of COX-1 to the immobilized lipodisks was validated by interaction studies with QCM-D. These results, taken together, open up the possibility of studying ligand interactions with membrane proteins by weak affinity chromatography. / <p>De två (2) första författarna delar förstaförfattarskapet.</p>

No description available.

Os hormônios peptídicos Angiotensina II (Ang II) e bradicinina (BK) ativam transdução de sinal através da ligação a Receptores Acoplados a Proteínas G (GPCR). Este trabalho propõe o estudo de propriedades conformacionais, através de espectroscopia de fluorescência da Ang II e BK e de seus análogos contendo o marcador de spin ácido 2,2,6,6-tetrametilpiperidina-1-oxil-4-amino-4-carboxílico, TOAC (TOAC1-Ang II, TOAC3-Ang II, TOAC0-BK, TOAC3-BK). Os peptídeos foram estudados em solução (efeito do pH) e também na presença de membranas modelo, micelas e bicamadas, formadas por anfifílicos zwitteriônicos ou aniônicos. Foi monitorada a fluorescência intrínseca dos resíduos aromáticos (Tyr4 na Ang II e Phe5 e Phe8 na BK). O efeito de supressão da fluorescência pelo TOAC foi utilizado para obter informação sobre a proximidade desse resíduo aos grupos fluoróforos. Foi observada dependência da fluorescência com o pH e regiões de pKs dos grupamentos ionizáveis. Os espectros evidenciaram também a interação peptídeo-membrana modelo. Interações mais fortes ocorreram entre os peptídeos e membranas com carga superficial negativa, evidenciando a importância de interações eletrostáticas para a ligação. Porém, interações hidrofóbicas também estão envolvidas, como verificado pela ligação dos peptídeos a membranas zwitteriônicas. Estudos com variação de pH também mostraram o papel dessa variável na interação peptídeo-membrana e a alteração de pKs de resíduos ionizáveis decorrentes da interação. A titulação com concentrações crescentes de membranas permitiu o cálculo das constantes de associação. A ligação a membranas é função da conformação dos peptídeos. Em particular, a presença de TOAC na posição 3 parece diminuir a afinidade desses análogos por membranas. Supressão de fluorescência foi efetuada empregando três diferentes abordagens: 1) supressão pela molécula aquossolúvel acrilamida, 2) supressão da fluorescência de fosfolipídeos contendo o fluoróforo NBD em diferentes posições da molécula pelos análogos marcados com TOAC, 3) supressão da fluorescência dos peptídeos por ésteres metílicos do ácido esteárico contendo o grupamento nitróxido em diferentes posições da cadeia. Esses estudos permitiram determinar a localização dos peptídeos na interface água-membrana. Medidas de anisotropia de fluorescência também evidenciaram a ligação dos peptídeos a membranas, revelando maior imobilidade dos mesmos nessas condições. Foi ainda estudado um peptídeo que contém os resíduos 92-100 (fEL1) do receptor AT1 de Ang II humano. Predições baseadas na estrutura cristalina da rodopsina estimam que essa seqüência localiza-se na primeira alça extra-celular do receptor. A seqüência contém a Tyr92, considerada um resíduo importante para a ligação hormônio-receptor. Resultados preliminares sugeriram que fEL1 interage com Ang II e TOAC1-Ang II, mas não com TOAC3-Ang II. Este último resultado provavelmente deve-se à dobra causada por TOAC que restringe a liberdade de movimento do esqueleto peptídico. Essa característica provavelmente determina a falta de atividade biológica de TOAC3-Ang II e TOAC3-BK, enquanto os análogos marcados no N-terminal retém atividade parcial (Nakaie et al., 2002). Tem sido proposto que peptídeos ligantes de GPCR se ligariam à bicamada lipídica e atingiriam seu receptor através da difusão pela bicamada. Em solução aquosa essas moléculas são flexíveis, existindo um equilíbrio dinâmico entre várias conformações. A ligação à bicamada lipídica estabilizaria uma ou algumas conformações, entre elas aquela que o ligante adota ao ligar-se ao receptor. O presente estudo contribui para a compreensão, a nível molecular, do processo de interação entre os hormônios peptídicos e membranas lipídicas. / The peptide hormones Angiotensin II (Ang II) and bradykinin (BK) trigger signal transduction by binding to G Protein Coupled Receptors (GPCR). This work proposes the study of conformational properties of Ang II and BK, as well as their analogues containing the spin label 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid, TOAC (TOAC1-Ang II, TOAC3-Ang II, TOAC0-BK, TOAC3-BK) making use of fluorescence spectroscopy. Studies were performed in solution (effect of pH) and also of the interaction between the peptides and model membranes - micelles and bilayers - formed by amphiphiles, either zwitterionic or negatively charged. The intrinsic fluorescence of aromatic residues (Tyr4 in Ang II and Phe5 and Phe8 in BK) was monitored. Fluorescence quenching by the TOAC-carrying analogues provided information about the proximity between TOAC and the fluorophores. The fluorescence was pH-dependent and evinced regions corresponding to pKs of ionizable groups. Peptide-model membrane interactions were also examined. Stronger interactions were detected between the peptides and membranes formed by negatively charged amphiphiles, pointing to the importance of electrostatic interactions for binding. However, hydrophobic interactions were also involved, as suggested by the fact that the peptides also bound to zwitterionic membranes. Variable pH studies showed the effect of this parameter on peptide-membrane interaction. The peptide-membrane interactions promoted changes in the pKs of ionizable residues. Titrations with increasing membrane concentrations allowed calculation of binding constants. Binding to membranes is a function of peptide conformation. In particular, TOAC at position 3 seems to decrease the affinity of both Ang II and BK for membranes. Fluorescence quenching studies made use of three different approaches: 1) quenching by water soluble acrylamide, 2) quenching of the fluorescence of phospholipids carrying the fluorescent group NBD in different positions by the spin-labeled TOAC-bearing analogues, 3) quenching of the peptides fluorescence by methyl esters of stearic acid containing the nitroxide moiety at different positions in the acyl chain. These studies indicated that the peptides are located at the water-membrane interface. Measurements of fluorescence anisotropy also evinced binding of the peptides to the membranes and showed that the peptides undergo more restricted motion under these conditions. A peptide containing residues 92-100 (fEL1) of the Ang II AT1 human receptor was also studied. Predictions based on rhodopsin crystalline structure estimate that this sequence is located in the receptor´s first extra-cellular loop. Preliminary results suggest that fEL1 interacts with Ang II and TOAC1-Ang II, but not TOAC3-Ang II. This latter result is probably due to the TOAC-induced bend that restricts the freedom of motion of the peptide backbone. This feature is probably the cause of lack of biological activity of TOAC3-Ang II and TOAC3-BK, while the N-terminally labeled analogues retain partial activity (Nakaie et al., 2002). GPCR-binding peptides have been proposed to bind to the lipid bilayer and reach their receptors by diffusion in the bilayer. In aqueous solution these molecules exist as a dynamic equilibrium between various flexible conformations, among them, the receptor-bound conformation. The present study provides contributions for the understanding, at the molecular level, of the interaction between the peptide hormones and lipid membranes.

O entendimento em nível molecular da interação tanto de vírus causadores de doenças (ou parte deles, como proteínas e peptídeos) quanto de moléculas candidatas a fármacos, é de suma importância para a terapia e tratamento de doenças. Neste trabalho, utilizamos técnicas biofísicas e bioquímicas para o estudo da interação entre miméticos de membrana e dois grupos de pequenas moléculas. A primeira relacionada a uma doença, o peptídeo de fusão da Dengue, sequência putativa da glicoproteína E do vírus da Dengue, e que se conserva entre outros flavivírus, como o vírus da Zika. Já o segundo grupo é formado por compostos de coordenação de cobre, Fenantrolina e os dipeptídeos Ala-Gly e Ala-Phe: Cu(L-dipeptídeo)(Fenantrolina), e que são potenciais candidatos a fármacos antitumorais. Nossos resultados mostram que as moléculas de ambos os grupos são capazes de interagir e modificar as propriedades do sistema mimético de membrana. Indicando que, por um lado, se pode pensar em estratégias de bloqueio da interação para evitar infecção pelo vírus e, por outro lado, se pode usar nossos resultados para melhor planejar formas de potencializar a interação em mecanismos de entrega de fármaco e/ou de difusão pela barreira física representada pelo sistema de membranas da célula tumoral / The understanding at the molecular level of the interaction of both disease-causing viruses (or part thereof, such as proteins and peptides) and drug-candidate molecules is of paramount importance for the therapy and treatment of such diseases. In this work, we use biophysical techniques to study the interaction between membrane mimetics and two groups of small molecules. The first one is related to a disease, the Dengue fusion peptide, putative sequence of Dengue virus glycoprotein E, which is conserved among other flaviviruses, such as the Zika virus. The second group consists of coordination compounds of copper, Phenantroline and the dipeptides Ala-Gly and Ala-Phe: Cu (L-dipeptide) (phenanthroline), which are potential candidates for antitumor drugs. Our results show that the molecules form both groups are capable of interacting and modifying the physic-chemical properties of the mimetic membrane system. This indicates that, on one hand, one can think in strategies of blocking the interaction to avoid virus infection and, on the other hand, one can use our results to improve membrane interaction in drug delivery mechanisms and/or for facilitating diffusion through the physical barrier represented by the membranes in tumor cells

O entendimento em nível molecular da interação tanto de vírus causadores de doenças (ou parte deles, como proteínas e peptídeos) quanto de moléculas candidatas a fármacos, é de suma importância para a terapia e tratamento de doenças. Neste trabalho, utilizamos técnicas biofísicas e bioquímicas para o estudo da interação entre miméticos de membrana e dois grupos de pequenas moléculas. A primeira relacionada a uma doença, o peptídeo de fusão da Dengue, sequência putativa da glicoproteína E do vírus da Dengue, e que se conserva entre outros flavivírus, como o vírus da Zika. Já o segundo grupo é formado por compostos de coordenação de cobre, Fenantrolina e os dipeptídeos Ala-Gly e Ala-Phe: Cu(L-dipeptídeo)(Fenantrolina), e que são potenciais candidatos a fármacos antitumorais. Nossos resultados mostram que as moléculas de ambos os grupos são capazes de interagir e modificar as propriedades do sistema mimético de membrana. Indicando que, por um lado, se pode pensar em estratégias de bloqueio da interação para evitar infecção pelo vírus e, por outro lado, se pode usar nossos resultados para melhor planejar formas de potencializar a interação em mecanismos de entrega de fármaco e/ou de difusão pela barreira física representada pelo sistema de membranas da célula tumoral / The understanding at the molecular level of the interaction of both disease-causing viruses (or part thereof, such as proteins and peptides) and drug-candidate molecules is of paramount importance for the therapy and treatment of such diseases. In this work, we use biophysical techniques to study the interaction between membrane mimetics and two groups of small molecules. The first one is related to a disease, the Dengue fusion peptide, putative sequence of Dengue virus glycoprotein E, which is conserved among other flaviviruses, such as the Zika virus. The second group consists of coordination compounds of copper, Phenantroline and the dipeptides Ala-Gly and Ala-Phe: Cu (L-dipeptide) (phenanthroline), which are potential candidates for antitumor drugs. Our results show that the molecules form both groups are capable of interacting and modifying the physic-chemical properties of the mimetic membrane system. This indicates that, on one hand, one can think in strategies of blocking the interaction to avoid virus infection and, on the other hand, one can use our results to improve membrane interaction in drug delivery mechanisms and/or for facilitating diffusion through the physical barrier represented by the membranes in tumor cells