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Thesis (Ph. D.)--School of Mechanical Engineering, Georgia Institute of Technology, 2004. Directed by Andrei G. Federov. / Vita. Includes bibliographical references (leaves 155-164).

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Developing cultivation methods that yield chemically and isotopically defined fatty acid (FA) compositions within bacterial cytoplasmic membranes establishes an in vivo experimental platform to study membrane biophysics and cell membrane regulation using novel approaches. Yet before fully realizing the potential of this method, it is prudent to understand the systemic changes in cells induced by the labeling procedure itself. In this work, analysis of cellular membrane compositions was paired with proteomics to assess how the proteome changes in response to the directed incorporation of exogenous FAs into the membrane of Bacillus subtilis. Key findings from this analysis include an alteration in lipid headgroup distribution, with an increase in phosphatidylglycerol lipids and decrease in phosphatidylethanolamine lipids, possibly providing a fluidizing effect on the cell membrane in response to the induced change in membrane composition. Changes in the abundance of enzymes involved in FA biosynthesis and degradation are observed; along with changes in abundance of cell wall enzymes and isoprenoid lipid production. The observed changes may influence membrane organization, and indeed the well-known lipid raft-associated protein flotillin was found to be substantially down-regulated in the labeled cells – as was the actin-like protein MreB. Taken as a whole, this study provides a greater depth of understanding for this important cell membrane experimental platform and presents a number of new connections to be explored in regard to modulating cell membrane FA composition and its effects on lipid headgroup and raft/cytoskeletal associated proteins.

Molecular recognition at biomembranes is one of the more poorly understood aspects of fundamental research in physical organic chemistry. Our aim was to improve our understanding of the molecular recognition of polysaccharides at biomembranes, in particular developing synthetic lipids that will recognise and report on the presence of glycosaminoglycans (GAG polysaccharides), like heparin and hyaluronic acid. Elevated levels of hyaluronic acid have been implicated in bladder carcinoma and osteoarthritis, and the use of heparin for medical applications is well documented. We synthesised a boronic acid capped lipid that also bore a fluorinated fluorescent reporter group, which could report on multivalent recognition events at bilayer membranes by fluorescent quenching and changes in the lateral distribution of the reporter groups. These preliminary studies showed these boronic acid capped fluorinated lipids gave a fluorescent signal upon interaction with simple mono- and poly- saccharides, albeit with unexpectedly weak binding to these saccharides. To understand and quantify the weaker binding of saccharides to membrane bound boronic acids a series of novel fluorescent and chromogenic lipids were synthesised that bore the reporter group close to the boronic acid. These studies revealed several underlying factors that had important roles in the recognition of oligosaccharides by boronic acid capped lipids. For the first time the effect of the bilayer on saccharide/boronic acid recognition was quantified, with the membrane weakening the interaction 33-fold. We were able to propose a model for the interaction of saccharides for membrane bound boronic acids that explained many of these unexpected observations.We also devised a parallel approach using GAGs to open or close synthetic membrane channels. Using a GAG to switch on the release of an ion or dye would generate a fluorescent signal that amplifies the original recognition event and improves sensitivity for GAGs. Proof-of-principle studies using palladium ions to open dye-transporting channels were successful and these studies were followed by the synthesis of boronic acid-capped cholates. Incorporation of boronic acid-capped cholates into membranes caused changes in the rate of release of alkali metal ions, which caused an enclosed fluorescent dye to give a signal, in the presence or absence of saccharides. These compounds successfully gave a response to the simple saccharide D-fructose but gave no response to other saccharides tested, including various hyaluronic acids. Although we were not able to develop a selective sensor for GAGs, we have developed a model for saccharide/boronic acid interactions that is a valuable addition to the physical organic chemistry of membranes.

Orientadores: Eneida de Paula, Cleyton Crepaldi Domingues / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-18T17:11:37Z (GMT). No. of bitstreams: 1 Casadei_BrunaRenata_M.pdf: 5692711 bytes, checksum: 9dcfea152b622eb3bd7d81b793794e3e (MD5) Previous issue date: 2011 / Resumo: A visão atual sobre membranas biológicas abarca descrições cada vez mais complexas devido, principalmente, à descoberta de novos papéis atribuídos aos lipídios e sua heterogeneidade. Em particular a associação de esfingolipídios e colesterol, acrescida de proteínas específicas, constitui a base da formação de domínios membranares conhecidos como lipid rafts. Rafts são microdomínios funcionais de biomembranas e estão envolvidos em diversos processos biológicos como reconhecimento celular, endocitose, transdução de sinal, entre outros processos. Uma estratégia experimental para estudar esses domínios é a preparação de frações de membrana parcialmente resistentes ao tratamento com detergentes, a baixa temperatura (4°C). Neste trabalho demonstramos pela primeira vez o preparo e caracterização de frações resistentes a detergente (DRMs) extraídas de membranas de eritrócito humano, a partir do tratamento com os detergentes não iônicos polioxietileno 20-oleil éter (Brij 98) e polioxietileno 20-cetil éter (Brij 58), seguida de separação por ultracentrifugação em gradiente de sacarose. Essas DRMs foram obtidas a 4°C e 37°C, a partir de membranas intactas e com conteúdo reduzido de colesterol (após tratamento com metil-beta-ciclodextrina) e foram comparadas com DRMs de Triton X-100 (TX-100) em relação ao tamanho, conteúdo proteico e lipídico e grau de organização da bicamada. As frações de DRM de Brij mostraram-se enriquecidas em colesterol e fosfolipídios com ácidos graxos de cadeia saturada (em especial ácido lignocérico das esfingomielinas), características consistentes com lipid rafts. No entanto, DRMs de TX-100 apresentaram maior proporção de esfingomielinas/glicerofosfolipídios que as frações obtidas com Brij, além de menor proporção de fosfatidiletanolamina, um lipídio preferencial da monocamada interna da membrana de eritrócitos. Em relação à solubilização proteica, a membrana do eritrócito foi mais resistente ao tratamento com Brij 98 do que aos outros dois detergentes. Flotilina-2 e estomatina foram encontradas nas frações de DRMs de Brij 98 e Brij 58, porém a redução do conteúdo de colesterol da membrana eritrocitária resultou numa menor associação da flotilina-2 àquelas DRMs. Resultados de Ressonância Paramagnética Eletrônica, com uso de marcadores de spin do tipo doxil-estearato não acusaram variação significativa no grau de empacotamento dos lipídios nas bicamadas de DRMs de Brij 98 e Brij 58 em relação à membrana eritrocitária, diferentemente do observado em DRMs de TX-100 e do que seria esperado para domínios lipídicos na fase líquido-ordenada. Em conclusão, DRMs de eritrócitos humanos, com características compatíveis aos domínios funcionais de biomembranas (rafts), foram obtidas tanto a 4ºC quanto a 37ºC; essas frações resistentes aos Brij apresentaram tamanho, composição proteica e lipídica e grau de empacotamento da bicamada diferente das DRMs de TX-100, indicando um processo de extração diferencial dos componentes da membrana eritrocitária induzida por esses detergentes / Abstract: Depiction of biological membranes has been turning more and more complex lately due to the new roles assigned to their lipid components and their heterogeneity. The association between sphingolipids and cholesterol is the basis of lipid rafts formation. Rafts are functional microdomains of biological membranes which have been associated to different biological processes such as cellular recognition, endocytosis and signal transduction, among others. An useful experimental approach to study lipid rafts is the preparation of membrane fractions partially resistant to detergents under low temperature (4ºC). In this work we report the isolation of detergent resistant membranes (DRMs) from human erythrocytes treated with the non-ionic detergents polioxyethylene 20-oleoyl ether (Brij 98) and polioxyethylene 20-cetyl ether (Brij 58) followed by sucrose gradient ultracentrifugation. Such DRMs were obtained at 4°C and 37°C, from cholesterol-depleted (treated with methyl-beta-cyclodextrin) and intact erythrocyte membranes and they compared to DRMs obtained with Triton X-100 (TX-100) regarding the size, protein and lipid content and membrane fluidity. Brij DRMs were found to be enriched in cholesterol and phospholipids containing saturated fatty acids (especially those from sphingomyelin), features commonly associated to lipid rafts. Nevertheless, TX-100 DRMs presented higher sphingomyelin/phospholipid ratios and lower phosphatidylethanolamine content (a glycerophospholipid mainly present in the inner leaflet) than the Brij's. As for protein solubilization, erythrocyte membranes were more resistant to Brij 98 than to the other two detergents. Flotillin-2 and stomatin were found in both Brij 98 and Brij 8 DRMs. However, flotillin-2 was partially solubilized when DRMs were prepared from cholesterol-depleted erythrocyte membrane. Electron paramagnetic resonance experiments, with doxyl stearic acid spin labels incorporated in the DRMs showed no significant changes in the bilayer compactness of Brij 98 and 58 DRMs in comparison to intact membrane, a unexpected result for lipid domains existing in a liquid-ordered phase, and in contrast to results previously observed with TX-100 DRMs. Altogether, these results show the isolation of DRMs from human erythrocytes treated with Brij 98 and Brij 58 at low (4°C) and physiological temperature (37°C). These detergent-resistant membrane fractions, obtained with Brij 98 and 58 presented some lipid rafts features, although with differences in protein and lipid contents, size and membrane fluidity in comparison to TX-100 DRMs. Besides, these results suggest that TX-100, Brij 98 and Brij 58 induced a different solubilization process on the erythrocyte membrane / Mestrado / Bioquimica / Mestre em Biologia Funcional e Molecular

Lipid molecules form thin biological membranes that envelop all living cells, and behave as two-dimensional liquid sheets immersed in bulk water. The interactions of such biomembranes with their environment lay the foundation of a plethora of biological processes rooted in the mesoscopic domain - length scales of 1-1000 nm and time scales of 1-1000 ns. Research in this intermediate regime has for a long time been out of reach for conventional experiments, but breakthroughs in computer simulation methods and scattering experimental techniques have made it possible to directly probe static and dynamic properties of biomembranes on these scales. Biomembranes are soft, with a relatively low energy cost of bending, and are thereby influenced by random, thermal fluctuations of individual molecules. Molecular dynamics simulations show how in-plane (density fluctuations) and out-of-plane (undulations) motions are intertwined in the bilayer in the mesoscopic domain. By novel methods, the fluctuation spectra of lipid bilayers can be calculated withdirect Fourier analysis. The interpretation of the fluctuation spectra reveals a picture where density fluctuations and undulations are most pronounced on different length scales, but coalesce in the mesoscopic regime. This analysis has significant consequences for comparison of simulation data to experiments. These new methods merge the molecular fluctuations on small wavelengths, with continuum fluctuations of the elastic membrane sheet on large wavelengths, allowing electron density profiles (EDP) and area per lipid to be extracted from simulations with high accuracy. Molecular dynamics simulations also provide insight on the small-wavelength dynamics of lipid membranes. Rapidly decaying density fluctuations can be described as propagating sound waves in the framework of linearized hydrodynamics, but there is a slow, dispersive, contribution that needs to be described by a stretched exponential over a broad range of length- and time scales - recent experiments suggest that this behavior can prevail even on micrometer length scales. The origin of this behavior is discussed in the context of fluctuations of the bilayer interface and the molecular structure of the bilayer itself. Connections to recent neutron scattering experiments are highlighted. / QC 20111014 / Modelling of biological membranes

Uranium decontamination gains a great importance with the spread of nuclear waste in both soil and water systems across the planet. All known remediation methods of uranium can be exclusively based either on synthetic materials with high adsorbent power and known physical chemistry or life organisms by which the uranium eventually accumulated inside their tissues. In the present thesis, it was attempted to design a rational approach for uranyl removal primarily from waters using the reducing potential of quercetin, which is a plant-derived small organic molecules, along with its photochemical activities. Such approach, which is neither a fully synthetic nor an organism-based approach, was chosen here to avoid disadvantages with both traditional strategies. Here, complexation experiments were designed to assess the use of uranyl-quercetin complexes for the photoreduction of water-soluble U(VI) to insoluble U(IV) by comparing absorption properties of uranyl-quercetin complexes in acetone, water, and hydrophobic bilayer lipid vesicles. The UV-vis data show that uranyl quercetin complex can form in both hydrophobic and hydrophilic environments. In both cases the B-ring band in quercetin structure becomes reduced, red shifted and a pronounced absorption arises in the 400-500 nm range. Such data suggests that U(VI) binds at the 3-OH and 4-carbonyl of ring C of quercetin. Interestingly, the results of UV-Vis spectroscopy part hint at a crucial role of a stable or transiently ionized hydroxyl for the efficient uranyl-dependent photodegradation of quercetin. FTIR spectroscopy absorption changes further demonstrates that the UV-vis-spectroscopic changes are indeed accompanied by changes in the chemical structure of the complex as expected for a uranyl-dependent photodegradation. IR data thus suggest that U(VI) becomes reduced by the photoreaction, rather than merely changing its coordination shell. The frequency shifts in the C=C and C=O absorption range on the other hand are consistent with changes in force constants rather than bond breakage. Upon illumination condition, uranyl quercetin complex in water forms a dark precipitate. Uranyl precipitation and the disappearance of U(VI) IR absorption bands upon illumination further demonstrate that uranyl acts as a redox partner rather than a catalyst in the photoreaction of quercetin. The formation of uranyl-quercetin complexes in the presence of lipidic phases has been addressed experimentally. The complex is partitioned into the hydrophilic/hydrophobic interface of liposomes. Its electronic absorption properties are influenced by the degree of hydrophobicity provided by the adjacent lipid headgroups. The preference of quercetin to associate with hydrophobic microenvironments can thus be exploited to transfer uranyl to the lipid water biomolecular interface. Illumination of the uranyl-quercetin complex in the presence of different liposomes has been performed in this study for the first time, to the best of my knowledge. The data provide evidence that again uranyl is a redox partner for the photodegradation of quercetin also in this microenvironment. Uranyl in an oxidation state smaller than VI is unsoluble in water. Therefore, its quercetin-mediated photoreduaction of uranium provides a method to transfer soluble uranium to the liposome and stabilize the reduced photoproduct. Thereby, uranyl could be removed from solution in an insoluble form using cheap natural compounds. The binding site assignment of uranyl-quercetin complex in acetone have been verified here using NMR spectra and DFT theory. NMR Spectra showed that the observations of broadened and narrow bands in the NMR spectra of quercetin, upon complexation with uranyl, support an intramolecular exchange or site exchange within the quercetin molecule. Moreover, the complexation takes place around the carbonyl group with U(VI) exhibiting two possibly coordination modes, involving the carbonyl and the adjacent O(H) groups. This has been also confirmed from the DFT calculations. Finally, interaction experiments of uranyl-quercetin complex with DNA have been performed to assess an alternative uranyl-trapping and photoreduction system. The data show that consecutive addition of quercetin and uranyl destabilizes DNA. However, a preformed uranyl quercetin complex has very little effect on DNA structure. On the other hand, quercetin and uranyl appear to bind to DNA as a preformed complex in the loop portion of hairpin DNA. Therefore, also HP DNA is expected to be a suitable but less effective trapping system for the uranyl quercetin complex and its potential photoproducts.

Submitted by Onia Arantes Albuquerque (onia.ufg@gmail.com) on 2018-10-30T13:45:30Z No. of bitstreams: 2 Dissertação - Lorena Damasio Cardoso - 2018.pdf: 3279572 bytes, checksum: 019cc5a3b996db0774fcbab0c3c38770 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2018-10-30T15:16:02Z (GMT) No. of bitstreams: 2 Dissertação - Lorena Damasio Cardoso - 2018.pdf: 3279572 bytes, checksum: 019cc5a3b996db0774fcbab0c3c38770 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2018-10-30T15:16:02Z (GMT). No. of bitstreams: 2 Dissertação - Lorena Damasio Cardoso - 2018.pdf: 3279572 bytes, checksum: 019cc5a3b996db0774fcbab0c3c38770 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2018-10-01 / The loss of tissue because of congenital defects, pathological processes or traumas stimulated the development of tissue engineering, with the aim of repairing or replacing damaged tissues or organs. Due to its elastic properties, cartilaginous tissue has been widely used in reconstructive procedures. The use of this tissue as biomaterial mainly aims at maintaining the three-dimensional properties of the matrix, prioritizing structural, mechanical and biological support for the cells and allowing adequate remodeling. The ideal is to obtain a biomaterial with characteristics of biocompatibility, biofunctionality and mechanical resistance. In this sense, treatments were developed in order to minimize possible inflammatory processes and rejection of the biomembrane at the receptor. The aim of this study was to compare the histological changes in elastic cartilages of the external ear of bovines, submitted to different treatments of conservation with chemical treatment by alkaline solution. The samples were cleaned, standardized and divided into control group and treatment groups. The conservation methods were evaluated with supersaturated salt solution, supersaturated sugar solution, glycerine, formalin and alkaline solution. The samples were maintained in storage media for 60 days and in alkaline solution for 72 hours. After, they underwent preparation, analysis and interpretation on histological slides. In each treatment were evaluated microstructureal parameters, as the maintenance of elastic fibers, fundamental amorphous substance and decellularization. When comparing to the other groups, we verified that the cartilages treated in alkaline solution had better decellularization rate, fundamental amorphous substance removal and mantainance of elastic fibers tridimensional structure. For this reason, this group was considered the most effective method in this study. / A perda de tecidos devido a defeitos congênitos, processos patológicos ou traumas estimulou o desenvolvimento da engenharia tecidual com objetivo de reparo ou substituição de tecidos ou órgãos danificados. Devido às suas propriedades elásticas, o tecido cartilaginoso tem sido bastante utilizado em procedimentos reconstrutivos. A utilização deste tecido como biomaterial se dá principalmente pela manutenção das propriedades tridimensionais da matriz, priorizando sustentação estrutural, mecânica e biológica para as células e permitindo remodelamento adequado. O ideal é que se obtenha um biomaterial com características de biocompatibilidade, biofuncionalidade e resistência mecânica. Neste sentido, foram desenvolvidos tratamentos a fim de minimizar possíveis processos inflamatórios e rejeição da biomembrana no receptor. Objetivou-se comparar as alterações histológicas em cartilagens elásticas de orelha externa de bovinos submetidas a diferentes métodos de conservação com tratamento químico por solução alcalina. As amostras passaram por um processo de dissecação e higienização, sendo posteriormente divididas em grupo controle e grupos de tratamentos. Foram avaliados os métodos de conservação com solução supersaturada de sal, solução supersaturada de açúcar, glicerina, formalina e solução alcalina. As amostras foram mantidas em meios de conservação durante 60 dias e em solução alcalina durante 72 horas. Posteriormente passaram por preparação, análise e interpretação em lâminas histológicas. Em cada tratamento foram avaliados parâmetros microestruturais tais como a manutenção de fibras elásticas, substância fundamental amorfa e descelularização. Em comparação aos demais grupos, foi observado que o grupo do tratamento alcalino apresentou maior descelularização, remoção da substância fundamental amorfa e manutenção da estrutura tridimensional das fibras elásticas. Por isso, este grupo foi considerado o método mais efetivo neste estudo.