Estudos têm demonstrado o potencial da terapia fotodinâmica antimicrobiana (aPDT) na inativação de diferentes células microbianas. No geral, são três as fases de crescimento dos microrganismos: fase lag, exponencial e estacionária. Os objetivos deste estudo foram avaliar a susceptibilidade de células de Candida albicans em diferentes fases de crescimento, submetidas à aPDT, associando azul de metileno (50 μM) e luz de emissão vermelha (λ= 660 nm) e investigar alterações morfológicas, mecânicas e bioquímicas, antes e depois da aPDT, por microscopia eletrônica de varredura, de força atômica e por espectroscopia no infravermelho por transformada de Fourier. Os resultados obtidos sugerem que, em parâmetros letais, células em fase estacionária de crescimento (48 h) são menos susceptíveis à aPDT, quando comparadas àquelas em fases lag (6 h) e ex-ponencial (24 h) de crescimento. Entretanto, em parâmetros subletais, células de 6 h e 48 h mostraram a mesma susceptibilidade à aPDT. Em sequência, os experimentos foram realizados em parâmetros considerados subletais para células crescidas por 6 e 48 h. A avaliação morfológica mostrou menor quantidade de matriz extracelular em células de 6 h comparada àquelas de 48 h. A espectroscopia de força atômica mostrou que células em fase lag perderam a rigidez após a aPDT, enquanto que células em fase estacionária mostraram comportamento in-verso. Ainda, células de 48 h diminuíram sua adesividade após a aPDT, enquanto que células de 6 h e 24 h tornaram-se mais adesivas. Os resultados bioquímicos revelaram que as diferenças mais significativas entre as células fúngicas de 6 h e 48 h ocorreram na região de DNA e carboidratos. A aPDT promoveu mais alterações bioquímicas na região de DNA e carboidratos em células de 6 h e em lipídios e ácidos graxos em células de 48 h. Nossos resultados indicam que a fase de crescimento celular desempenha papel importante no sítio de ação da aPDT em células de C. albicans. / Studies have demonstrated the potential of antimicrobial photodynamic therapy (aPDT) on the inactivation of different microbial cells. Overall, there are three phases of cell growth: lag phase, exponential phase and stationary phase. The objectives of this study were to evaluate the susceptibility of Candida albicans in different growth stages submitted to aPDT, with methylene blue (50μM) and red light (λ = 660 nm) and to investigate morphological, mechanical and biochemical changes before and after aPDT, by scanning electron microscopy, atomic force microscopy and by Fourier transform infrared spectroscopy. The results suggested that with lethal parameters, cells in stationary phase (48 h) are less susceptible to aPDT, compared to those in lag phase (6 h) and exponential phase (24 h). However, in sub-lethal parameters 6 h and 48 h cells showed the same susceptibility to aPDT. The following results were obtained in sub-lethal parameters. The morphological evaluation showed lower amount of extra-cellular matrix at 6 h compared to cells growth for 48 h. The atomic force spectroscopy showed that cells in lag phase lost cell wall rigidity after aPDT, while cells in stationary phase showed a reverse behavior. Furthermore, 48 h cells presented a decrease in their adhesiveness after aPDT, whereas cells growth for 6 h and 24 h become more adhesive. The biochemical evaluation showed that the most significant differences among the fungal cells growth for 6 h and 48 h in DNA and carbohydrates. The aPDT caused more expressive alterations on DNA and carbohydrates in cells growth for 6 h, while cells growth for 48 h presented significant alterations on lipids and fatty acids. Our results indicate that cell growth phase play an important role on the target sites affected by aPDT in C. albicans cells.

Orientador: Mônica Alonso Cotta / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Física Gleb Wataghin / Made available in DSpace on 2018-08-19T11:07:57Z (GMT). No. of bitstreams: 1 MurilloMunar_DuberMarcel_M.pdf: 2543124 bytes, checksum: 3cf9b797cba5e450d6c025e609885768 (MD5) Previous issue date: 2011 / Resumo: Este trabalho tem como finalidade mostrar a importância dos diferentes modos da Microscopia de Varredura por Ponta de Prova (SPM) numa abordagem complementar para o estudo de dois diferentes sistemas biológicos. O processo de formação de biofilmes da bactéria fitopatogênica Xylella fastidiosa (Xf) foi o primeiro sistema abordado neste trabalho. Neste caso nosso objetivo é levantar informações que possam complementar o modelo mais aceito atualmente e corroborar os resultados obtidos anteriormente em nosso grupo. As amostras foram preparadas sobre substratos de silício recoberto com ouro e cultivadas durante tempos de crescimento de 7, 14 e 21 dias. O principal modo utilizado foi a Microscopia de Força Atômica por Kelvin Probe por modulação de amplitude (AM-KPFM) que fornece o potencial de superfície com resolução nanométrica. Imagens por KPFM foram adquiridas simultaneamente com as de topografia e fase obtidas por Microscopia de Força Atômica no modo não-contato (NC-AFM). Os resultados obtidos revelaram um processo de recobrimento gradual das bactérias por um filme de substância polimérica extracelular (EPS), concordando com os modelos propostos na literatura, porém ainda não comprovados. Imagens adquiridas por microscopia óptica (MO) mostram um desenvolvimento mais lento dos biofilmes (BF) em comparação aos resultados de G. S. Lorite para BF sobre substratos de silício obtidos anteriormente em nosso grupo. Isto está de acordo com a preferência das bactérias por superfícies com potenciais mais altos. Um resultado original está na observação de protuberâncias encontradas nas extremidades das bactérias, que mostram sinal elétrico diferenciado do resto da célula. Acreditamos que estas estruturas estão relacionadas ao processo de reprodução, pois aparecem tanto em bactérias isoladas como nas que estão no BF para todos os tempos de crescimento. O segundo sistema estudado foi a formação de estrutura quadrúplex-G de DNA. As amostras de DNA foram preparadas sobre mica e medidas no modo NC-AFM. Embora o DNA seja um sistema muito estudado em AFM, o protocolo de preparação das amostras muda segundo o tipo de estrutura que se queira visualizar. Assim, a maior parte do trabalho neste caso consistiu em desenvolver este protocolo de preparação que permitisse a visualização por AFM das estruturas de interesse. Usando concentrações altas de DNA (5ng/µL) as imagens apresentaram estruturas auto-organizadas que impedem a visualizaçã da estrutura quadrúlex·G. Para concentraçõs menores que 0,5ng/µL conseguimos visualizar moléulas isoladas, mas ainda assim as moléulas nã ficaram num estado relaxado. Um resultado interessante foi encontrado nas imagens de fase de moléulas isoladas (com concentraçã de DNA de 0,1ng/µL) onde se observam diferençs estruturais no interior das moléulas, possivelmente devido àformaçã da estrutura quadrúlex-G. Estas diferençs de fase representam um resultado original e mostram a importâcia da complementaridade dos modos AFM na observaçã de fenôenos biolóicos / Abstract: The aim of this work is to show the importance of different modes of Scanning Probe Microscopy (SPM) in a complementary approach to the study of two different biological systems. The process of biofilm formation of the phytopathogenic bacterium Xylella fastidiosa (Xf) was the first system discussed in this work. In this case our goal is to gather information that complements the currently most accepted model and corroborates the results obtained previously in our group. The samples were prepared on silicon substrates coated with gold and cultivated during 7, 14 and 21 days. The main results were obtained using Kelvin Probe Atomic Force Microscopy with amplitude modulation (AM-KPFM) which provides the surface potential with a nanometric resolution. Images were acquired by KPFM simultaneously with topography and phase images obtained by Atomic Force Microscopy in non-contact mode (NC-AFM). The results revealed a process of gradual coating of the bacteria by a film of extracellular polymeric substance (EPS), in agreement with the models proposed in the literature, but not yet proven. Images acquired by optical microscopy (OM) show a slower development of the biofilms (BF) compared to the results of G. S. Lorite for BF on silicon substrates obtained previously in our group. This result agrees with the preference of the bacteria for surfaces with large potentials. An original result is the observation of lumps found at the extremities of the bacteria, which show electrical signal different from the rest of the cell. We believe that these structures are related to the reproduction process as they appear both in isolated bacteria and those on BF for all growth times. The second system studied was the formation of G-quadruplex structure of DNA. DNA samples were prepared on mica and measured in the NC-AFM mode. Although DNA is a well studied system in AFM, the sample preparation protocol changes depending on the type of structure to be viewed. Thus, most of the work described here was to develop the preparation protocol that allows the visualization of the structures of interest by AFM. Using high concentrations of DNA (5ng/µL) the images showed self-organized structures that prevent visualization of G-quadruplex structure. For concentrations less than 0.5 ng/mL we got isolated molecules, but still the molecules were not in a relaxed state. An interesting result was found in the phase images of isolated molecules (with DNA concentration of 0.1 ng/mL) where structural differences are observed within the molecules, possibly due to the formation of G-quadruplex structure. These phase differences represent an original result and show the importance of the complementarity of AFM modes in the observation of biological phenomena / Mestrado / Mestre em Física

Organic crystals are found in everyday goods such as foods, drugs, dyes, and agricultural products. To better understand the solid-state behaviour of organic crystals, the study of their surfaces is crucial, as several reactions occur at the interface between the crystal surface and its immediate environment. While atomic force microscopy (AFM) is a useful tool for studying surfaces, it is not a common technique for studying organic crystals. The rst part of this report aims to address problems of imaging organic crystals by AFM which arise from the nature of the imaging technique and the material property of organic crystals. Methods of detecting and predicting the likelihood of the problems encountered in imaging organic crystals are suggested in order for a more accurate interpretation of the information obtained by this technique. The e ect of humidity on aspirin crystal surfaces is then investigated by AFM. The growth of new features on the surface is believed to be a result of the hydrolysis of aspirin molecules. Mechanisms are suggested based on the observed surface response of aspirin, where surface defects and the mobility of surface molecules are believed to be important factors a ecting reactivity. The last section investigates the solid-state photochemical reaction of anthracene, which is a reaction that should not occur according to the topochemical postulate. The surface response of anthracene crystals to UV light was studied, and the results indicate strong reactivity at sites of surface defects, which is likely due to photodimerisation. A similar mechanism that described the behaviour of aspirin surfaces was suggested for this reaction. In summary, both reactions that were studied provided a better insight towards understanding the solid-state reactivity of organic crystals. The proposed surface mechanisms imply that surface defects and the presence of humidity or solvent vapour are very likely to play a role in determining reactivity. Further studies on the origin of defects are suggested in order to better control the behaviour of organic crystals in the solid-state.

This thesis is concerned with the chemistry and physics of C(100) surfaces of diamond. The polished and cleaned C(100) surface is examined by surface microscopy (Atomic-force Microscopy), electron diffraction (Low-energy Electron Diffraction) and photoemission (X-ray Photoelectron Spectroscopy and Ultra-violet Photoelectron Spectroscopy). Results are presented on the presence of oxygen, nitrogen and hydrogen/deuterium on the C(100) surface. Finally, the valence band structure of diamond is probed by angle-resolved photoemission. We have confirmed by AFM that the grooves from the soft polishing process are present on a polished C(100) surface and found sporadic traces of hard polish on a surface polished in the soft polishing direction. XPS studies have verified heating cycles by electron beam bombardment as a suitable cleaning procedure for pure reconstructed C(100) surfaces. By allowing the crystal to cool slowly, the first experimental evidence of quarter-order LEED spots have been found, which suggest that buckled dimerisation might have occurred similar to those on Si(100) and Ge(100). We present the first experimental electron spectroscopy results for a nitrogen impurity in diamond by showing the N KLL Auger spectrum. An attempt to smooth a C(100) surface of diamond by an atomic hydrogen plasma did not succeed. AFM studies showed no evidence for the surface smoothing reported in other studies, but the results enable us to explain the different plasma published in the literature. The valence band of diamond is investigated by off-normal ARUPS. The features observed are consistent with possible transitions, which are determined using bulk band structure calculations and comparison with the experimental binding energies.

Probe microscopy techniques (Atomic Force Microscopy and Kelvin Force Microscopy) have been shown to be instrumental in the analysis of samples; such as resists and nanostructured materials. Through these techniques detailed surface information has been derived, including information such as surface roughness and surface charge distribution. Poly(Methylmethacrylate) (PMMA), remains at the forefront of resists utilised in e-beam lithography in the electronics industry. Surface morphology (specifically roughness) analysis remains a key parameter of investigation, particularly in the examination of polymeric films. This research aimed to investigate PMMA based electron beam resists as well as a novel (SML) resist material in terms of suitability for electron-beam lithography. Various concentrations (5, 7, 8, 9 and 11% w/v) of both PMMA and the novel resist material were spin-coated onto silica substrates. Samples were baked at 180oC for 3 minutes and examined under ultra-high vacuum using Omicron AFM/SPM to derive RMS values in order to assess roughness in addition to thickness measurements taken. SML resists were then utilised in the development of a new digital etch onto InGaAs/InAlAs wafer. The novel, SML resist material was found to offer smoother resist surface even at higher concentrations of polymer, a difference which was observed to be statistically significant (p<0.01). The SML resist was also notably thicker than the comparable PMMA resist (p>0.05) indicating that lower concentrations of the novel resist would be required to achieve the required resist thickness. Digital etching rates were found to be in agreement with previously documented findings. SML was concluded to be a superior resist in terms of thickness and smoothness, with AFM being further established as an essential characterization technique.

Dizertační práce je obecně zaměřena na problematiku mikroskopie atomárních sil (AFM), a to jak vývoje částí těchto mikroskopů, tak i jejich obecnému využití v oblasti výzkumu povrchů, ultratenkých vrstev a nanostruktur. Na Ústavu fyzikálního inženýrství jsou vyvíjena zařízení umožňující aplikovat uvedenou mikroskopickou metodu. V těchto mikroskopech jsou využívány piezoelektrické motory pro zajištění pohybu vzorku a ladicích zrcátek v optickém detekčním systému. Práce se v části věnované vývoji AFM zabývá studiem parametrů řídicích pulzů za účelem optimalizace funkce těchto komponent. Měřením vlivu tvaru pulzů a opakovací frekvence byl jejich pohyb optimalizován z hlediska stability a rychlosti posuvu. V části věnované výzkumu povrchů byly experimentálně zkoumány morfologické změny ultratenkých vrstev zlata na povrchu oxidu křemičitého za zvýšených teplot. Bylo zjištěno, že vhodná povrchová modifikace způsobuje vznik preferenčních trhlin ve vrstvě zlata. Řízeným rozdělením polykrystalické vrstvy na oddělené oblasti je možné významně ovlivnit proces tvorby ostrůvků zlata vznikajících při žíhání. S využitím metod elektronové litografie je možná příprava uspořádaných polí zlatých ostrůvků o velikostech 50 – 400 nm. Dále bylo ukázáno, že zvýšením teploty žíhání na 1000 °C dochází k postupnému zanořování ostrůvků zlata do povrchu. Tento jev je pravděpodobně způsoben přesunem oxidu křemičitého z oblasti pod zlatým ostrůvkem do těsného okolí vzniklého kráteru, kde tvoří tzv. límec. V těchto studiích vedle metody AFM byla s výhodou používána rovněž elektronová mikroskopie (SEM).

We use time-lapse AFM to visualize collagen fibrils self-assembly. A solution of acid-solubilized collagen was injected into the AFM fluid cell and fibril formation was observed in vitro. Single fibrils continuously grew and fused with each other until the supporting surface was completely covered by a nanoscopically well-defined collagen matrix. Laterally, the fibrils grew in steps of ~4 nm suggesting a two-step mechanism. In a first step, collagen molecules associated together. In the second step, these molecules rearranged into a structure called a microfibril. High-resolution AFM topographs revealed substructural details of the D-band architecture. These substructures correlated well with those revealed from positively stained collagen fibers imaged by transmission electron microscopy. Secondly, a covalent assembly approach to prepare membrane protein for AFM imaging that avoids crystallization was proposed. High-resolution AFM topographs can reveal structural details of single membrane proteins but, as a prerequisite, the proteins must be adsorbed to atomically flat mica and densely packed in a membrane to restrict their lateral mobility. Atomically flat gold, engineered proteins, and chemically modified lipids were combined to rapidly assemble immobile and fully oriented samples. The resulting AFM topographs of single membrane proteins were used to create averaged structures with a resolution approaching that of 2D crystals. Finally, the contribution of specific amino acid residues to the stability of membrane proteins was studied. Two structurally similar proteins sharing only 30% sequence identity were compared. Single-molecule atomic force microscopy and spectroscopy was used to detect molecular interactions stabilizing halorhodopsin (HR) and bacteriorhodopsin (BR). Their unfolding pathways and polypeptide regions that established stable segments were compared. Both proteins unfolded exactly via the same intermediates. This 3 Molecular Assemblies observed by AFM observation implies that these stabilizing regions result from comprehensive contacts of all amino acids within them and that different amino acid compositions can establish structurally indistinguishable energetic barriers. However, one additional unfolding barrier located in a short segment of helix E was detected for HR. This barrier correlated with a Pi-bulk interaction, which locally disrupts helix E and divides into two stable segments.

Atomic force microscopy (AFM) is a powerful technique that enables to study biological macromolecules and dynamic biological processes at different scales. It is an excellent tool for imaging of biological objects under various conditions at a nanometer resolution. Force mode of AFM, so called single molecule force spectroscopy (SMFS), allows for investigation of the strength of molecular interactions of different origins established between and within biological molecules. In the present work, SMFS was used to detect and locate structurally and functionally important interactions of sodium/glycine betaine transporter BetP of Corynebacterium glutamicum, which serves as a model system for this class of proteins. Mechanical pulling of BetP molecules embedded into the lipid membranes resulted in a step-wise unfolding of the protein and revealed insights into its structural stability. Effect of the lipid environment, N- and C-terminal extensions on inramolecular interactions of BetP as well as protein activation and ligand binding were investigated in great detail. In another part of this work, I demonstrate an application of the AFM based technique that can record unfolding of a protein under force-clamp conditions. This method directly measures the kinetics of the protein unfolding, allowing for the use of simple methods to analyze the data. For the first time the force-clamp technique was used to describe in detail unfolding kinetics of the membrane protein, i. e. Na+/H+-antiporter NhaA from Escherichia coli. Performed here experiments on NhaA in its functionally active and inactive states demonstrated the advantages of examining unfolding kinetics at the single-molecule level. It was possible to observe unfolding events for pH-activated conformation of NhaA that due to the low frequency of occurrence were not represented in the ensemble average of the single-molecule measurements. As mechanical unfolding, similarly to bond rupture, is a force-dependent process, force-clamp technique can allow for a more direct way of probing protein unfolding and is anticipated to be also useful to examine the folding/unfolding kinetics of other membrane proteins.

The work presented here has a multidisciplinary character, having as a common factor the characterization of self-assembled nanostructures through force spectroscopy. Exploring AFM as a tool for characterizing self-assembly and interaction forces in soft matter nanostructures, three different Bio and nonbiological systems where investigated, all of them share the common characteristic of being soft matter molecular structures at the nanoscale. The studied systems in question are: a) Polyelectrolyte – lipid nanocomposites. Single polyelectrolyte adsorption-desorption from supported lipid bilayers, b) Polyelectrolyte brushes and c) Virus-Like particles (VLPs). The scientific interest and industrial applications for each of these different nanostructures is broad, and their potential uses in the near future ranges from smart nanocontainers for drug and gene delivery, surface platforms for molecular recognition to the development of new nanodevices with ultrasensitive external stimuli responsiveness. These nano-structures are constructed following assembly of smaller subunits and belong to representative examples of soft matter in modern nanotechnology. The stability, behavior, properties and long term durability of these self-organized structures depends strongly on the environmental conditions to which they are exposed since their building mechanism is a balance between attractive noncovalent interactions and momentum transmitted collisions due Brownian motion of the solvent molecules. For example a set of long chain molecules firmly attached to one end to a surface will alter their conformation as the space between them is reduced or the environmental conditions are modified (i.e. ionic strength, pH or temperature). For a highly packed condition, this fuzzy surface known as a polyelectrolyte brush will then behave as a responsive material with tunable responsiveness. Thus the objective in the present case was to investigate the change in morphology and the mechanical response of a polyelectrolyte brush to external forces by application of AFM nanoindentations under different ionic strength conditions. The degree of penetration of the AFM tip through the brush will provide insights into the forces exerted by the brush against the tip. Compressions on the brush should aid to characterize its changes in compressibility for different salt concentrations. For the second chosen system, the interaction between two assembled interfaces was investigated at the single molecular level. A multilayered film formed by the consecutive assembly of oppositely charged polyelectrolytes and subsequently coated with a lipid membrane represents a fascinating soft composite material resembling more than a few structural components emerging in living organisms. The fluid bilayer, thus provide a biocompatible interface where additional functionalities can further be integrated (fusion peptides for instance). The smooth polymer cushion confers not only structural flexibility but also adaptability of the chosen substrate properties to be coated. This type of interface could be useful in the development of novel molecular biosensors with single molecule recognition capacities or in the fabrication of assays against pathogenic agents. The aim of this project was to study the molecular binding mechanism between the last polyelectrolyte layer and the lipid head group of the lower lipid leaflet. Understanding this adsorption mechanism between both interfaces, should likewise contribute to improve the fabrication of lipid coated polymeric nano/micro capsules with targeting properties. For example this could be critical in the field of nonviral gene therapy, where the improvement in the design of condensates of nucleic acids and other polymers with lipids (lipoplexes) are of main interest for its posterior use as delivery vectors. Finally, viral capsids were investigated. These naturally occurring assembled nanocontainers within living organisms stand for a remarkable example of nature’s morphological designs. These structures self-assemble from a small number of different proteins occurring in identical copies. The capsid as a self-assembled structure carries multiple functions: compaction of the genome, protection against external chemical threats, target recognition, structural support and finally facilitating the release of the genome into the host cell. It is highly interesting how these different functions are organized within the capsid which consists, for example, in the case of the norovirus of 180 identical copies of one single protein. Therefore, the mechanical stability and elastic properties of virus-like particles of Rubella and Norovirus were investigated by external application of loading forces with an AFM tip. The measurements were performed under conditions relevant for the virus infection mechanism. The applied compressions on these protein shells at pH values mimicking the virus life cycle will aid to learn about possible internal transitions among proteins which may be important for switching between the various functions of the capsid. The choice of two unrelated viral systems with different entry pathways into the cell and with different morphological architectures is expected to reveal crucial information about the stability and mechanical resistance to deformation of these empty membrane-coated and bare viral capsids. This last might provide clues on the stage of particle disassembly and cargo release during the final step of the infection process.

京都大学 / 0048 / 新制・課程博士 / 博士(エネルギー科学) / 甲第21886号 / エネ博第387号 / 新制||エネ||75(附属図書館) / 京都大学大学院エネルギー科学研究科エネルギー基礎科学専攻 / (主査)教授 森井 孝, 教授 木下 正弘, 教授 片平 正人 / 学位規則第4条第1項該当 / Doctor of Energy Science / Kyoto University / DGAM