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The rapid development of micro/nanofabrication techniques have enabled engineering of material interfacial properties. Micro/nanostructures with unique electrical, mechanical, thermal, magnetic, optical, and biological properties, have found applications in a wide range of fields such as electronics, photonics, biological/chemical sensing, tissue engineering, and diagnostics, etc. As such, numerous strategies have been developed for structuring materials into micro/nano- scale. However, the challenge still lies in the high cost, low throughput, complexity in fabrication, and difficulty in scaling up. This thesis aims to explore fabrication strategies for micro/nanostructured surfaces that are versatile, simple, and inexpensive. The thin film stencil lift-off technique with both Parylene and self-adhesive vinyl has been explored for this purpose. Further applications of the resulted micro/nanostructured surfaces are also presented in this thesis. Through improved Parylene stencil fabrication process, both spontaneously phase-segregated and arbitrary binary supported lipid bilayer patterns have been achieved. Also, the microstructured Parylene surfaces have been ddemonstrated for patterning stacked SLBs that are either homogeneous or phase-segregated. Without any lithography technique involved, vinyl stencil lift-off offers as a facile and inexpensive benchtop method for patterning thin films such as metal and glassy films. Combining the thermal shrinking of shape memory polymer, the patterned feature sizes are further decreased by 60% in both x and y dimensions, pushing the patterning resolution to down to sub-100 μm range. In addition, the shrinking process induces micro/nanostructures onto the deposited thin film, and the structure sizes are easily tunable with film thickness deposited. Further applications of such patterned micro/nanostructured surfaces has also been explored. The structured gold films have served as high-surface-area electrodes for electrochemical sensing. By introducing photoresist as a sacrificial layer, the structured gold thin films can be lifted off and transferred onto elastomeric substrate, and serve stretchable and flexible sensors. Such sensing devices exhibit great stability and reproducibility even when working under external strain. Finally, the micro/nanostructured glassy surfaces have been employed as substrate for cell growth to study topographical effect on cell morphology. It has been concluded that rougher surfaces lead to cell elongation, and finer structures promote filopodia generation. These results underscore the strength and suitability of thin film stencil lift-off as a powerful technique for creating micro- and nanostructured surfaces. These structured surfaces could find applications in many other areas, due to their great properties such as tunable structure size, high surface area, flexibility, and long-term stability. / Thesis / Doctor of Philosophy (PhD)

<p>One promising HIV-1 vaccine target is the membrane-proximal external region (MPER) of viral gp41. MPER is poorly immunogenic, however, the two rare neutralizing antibodies (NAbs), 2F5 and 4E10, bind to MPER with great neutralizing ability. Although their neutralizing mechanism represents a promising framework for the design of new HIV-1 liposomal vaccine candidates, this mechanism remains poorly understood. It is known that 2F5 and 4E10 are required to first associate with HIV-1 lipids before binding to the target MPER antigen, however, little is known about how lipid membranes contribute to NAb-antigen binding. To this end we have developed model membrane systems to study NAb and antigen lipid interactions. </p><p>We first created a surface plasmon resonance (SPR) spectroscopy based assay that monitors antibody binding to thiol monolayers, which mimic the surface chemical properties of lipid membranes. Next, we focused on mimicking the lipid phase organization (i.e., domain formation) of native membranes by using supported lipid bilayers (SLBs). We used simple SLB compositions to model the liquid-disordered (Ld) and gel phases. To model the HIV-1 envelope, we used a complex SLB composition that contains an Ld and liquid-ordered (Lo) phase. To reliably create model HIV-1 SLBs, we developed an SLB formation technique that uses amphipathic, &#945;-helical peptides as a catalyst to generate complex SLBs that have a high cholesterol content and contain multiple lipid types. For all SLB surfaces we used atomic force microscopy (AFM) to visualize membrane domains, antigen presentation, and antibody-membrane interactions.</p><p>Results from experiments using thiol surfaces showed that NAb binding to hydrophobic thiol surfaces was significantly greater than that of control monoclonal antibodies. This supports the hypothesis that these NAbs embed into the hydrophobic membrane core. Our results demonstrate that 2F5/4E10 do not interact with the highly ordered gel and Lo domains in the SLB but exclusively bind to the Ld phase. This suggests that 2F5/4E10 require low membrane order and weak lateral lipid-lipid interactions to insert into the hydrophobic membrane interior. Thus, vaccine liposomes that primarily contain an Ld phase are more likely to elicit the production of lipid reactive, 2F5- and 4E10-like antibodies, compared to liposomes that contain an Lo or gel phase. In the context of liposomal antigen presentation, our results show that the presence of the MPER656 antigen can severely limit the Ld area available for antibody interactions. Subsequently, this reduces the amount of MPER656 that is accessible for 2F5/4E10 binding, since MPER656 preferentially localizes to the Ld area. If Ld forming lipid components are used in vaccine liposomes, it is important to ensure that the presence of antigen does not inhibit large-scale Ld formation.</p> / Dissertation

abstract: Biological membranes are critical to cell sustainability by selectively permeating polar molecules into the intracellular space and providing protection to the interior organelles. Biomimetic membranes (model cell membranes) are often used to fundamentally study the lipid bilayer backbone structure of the biological membrane. Lipid bilayer membranes are often supported using inorganic materials in an effort to improve membrane stability and for application to novel biosensing platforms. Published literature has shown that a variety of dense inorganic materials with various surface properties have been investigated for the study of biomimetic membranes. However, literature does not adequately address the effect of porous materials or supports with varying macroscopic geometries on lipid bilayer membrane behavior. The objective of this dissertation is to present a fundamental study on the synthesis of lipid bilayer membranes supported by novel inorganic supports in an effort to expand the number of available supports for biosensing technology. There are two fundamental areas covered including: (1) synthesis of lipid bilayer membranes on porous inorganic materials and (2) synthesis and characterization of cylindrically supported lipid bilayer membranes. The lipid bilayer membrane formation behavior on various porous supports was studied via direct mass adsorption using a quartz crystal microbalance. Experimental results demonstrate significantly different membrane formation behaviors on the porous inorganic supports. A lipid bilayer membrane structure was formed only on SiO2 based surfaces (dense SiO2 and silicalite, basic conditions) and gamma-alumina (acidic conditions). Vesicle monolayer adsorption was observed on gamma-alumina (basic conditions), and yttria stabilized zirconia (YSZ) of varying roughness. Parameters such as buffer pH, surface chemistry and surface roughness were found to have a significant impact on the vesicle adsorption kinetics. Experimental and modeling work was conducted to study formation and characterization of cylindrically supported lipid bilayer membranes. A novel sensing technique (long-period fiber grating refractometry) was utilized to measure the formation mechanism of lipid bilayer membranes on an optical fiber. It was found that the membrane formation kinetics on the fiber was similar to its planar SiO2 counterpart. Fluorescence measurements verified membrane transport behavior and found that characterization artifacts affected the measured transport behavior. / Dissertation/Thesis / Ph.D. Chemical Engineering 2011

<p dir="ltr">The modern view of the plasma membrane is that of a complex, highly dynamic, compartmentalized system that critically impacts multiple important cellular functions. Supported model membranes of well-defined compositions have emerged as attractive experimental platforms to determine the underlying molecular processes that regulate membrane-associated cellular functions using advanced biophysical detection methods with up to single molecule resolution. However, membrane properties of previously employed supported membrane systems, such as solid-supported lipid bilayer (SLB) and polymer-supported lipid bilayer with a polymer layer thickness of several nm, were found to be perturbed by the nearby solid substrate. To overcome this limitation, the present work describes for the first time the capillary-assisted formation of a lipid bilayer (CA-PGB) on the surface of a fully hydrated, several micrometers thick polyacrylamide gel. CA-PGB formation can be accomplished by physisorption or specific chemical linkages (tethering) between polymer gel and bilayer. Not dissimilar to conditions found in plasma membranes, membrane properties of CA-PGB are found to be solely influenced by the attached polymer layer. The successful formation and lipid fluidity of CA-PGB is confirmed using confocal microscopy and fluorescence correlation spectroscopy (FCS). Lipid bilayer spreading on the hydrogel surface by capillary-assisted assembly is not altered when the polymer gel stiffness or bilayer bending stiffness are varied, illustrating the robustness and versatility of the assembly process. This work also shows that, unlike other supported membrane systems, the capillary-assisted assembly approach causes the formation of a lipid reservoir at the edge of the capillary. This lipid reservoir provides a lipid supply for the CA-PGB, enabling bilayer self-healing and superior bilayer stability relative to SLB. Experimental data are presented that support an assembly process, in which bilayer spreading on the gel surface inside the water capillary between two substrates is caused by monolayer collapse of suddenly accumulated lipids at the air-water interface of the capillary during sandwiching. A key aspect of the monolayer collapse-induced bilayer spreading is its rapid kinetics, which appears to be faster than the polymer gel swelling kinetics. The importance of the fast kinetics of bilayer spreading during capillary-assisted assembly is supported by the observation that attempts to build polymer gel-supported lipid bilayer using traditional lipid assembly methods [i. e., Langmuir-Blodgett (LB)/Langmuir-Schaefer (LS), LB- vesicle fusion, and spontaneous bilayer spreading from a hydrated lipid source], characterized by slower bilayer spreading kinetics, are unable to form a homogeneous fluid lipid bilayer on the polymer gel surface. The experimental results obtained in this work strongly suggest that the CA-PGB not only represents a powerful experimental model membrane platform for the analysis of membrane-associated processes relevant in cellular membranes, but also serves as promising cell surface mimetic to probe the cellular mechanosensitivity of adherend cells.</p>

Systemisch applizierte Therapeutika können erhebliche Nebenwirkungen auslösen, welche auf Grund eines unspezifischen Transports oder einer hohen Dosis von appliziertem Wirkstoff auftreten. Daher bedarf es der Entwicklung neuartiger Wirkstoff-Transportsysteme (Drug Delivery Systems) welche in der Lage sind, Wirkstoffe in genau definierbaren Dosen gezielt in die adressierte Zelle zu transportieren. Ein vielversprechender Ansatz, welcher diesen Anforderungen nachkommt, findet sich in der Layer-by-Layer-Technik (LbL), d.h. der wechselseitigen Assemblierung von Polymeren/Wirkstoffen auf soliden sphärischen Templaten, eines funktionellen Supported Lipid Bilayers sowie der Oberflächenfunktionalisierung mit spezifischen Antikörpern. Dabei ist die Homogenität und Regularität des Supported Lipid Bilayers von großer Bedeutung, um in biomedizinischen Anwendungen eine ungewollte Interaktion mit Serumkomponenten sowie eine Opsonierung zu verhindern. Insbesondere die funktionelle Lipidkomponente besitzt allerdings maßgebliche Auswirkungen auf diese Parameter. In dieser Arbeit wurde die Idee der Oberflächenfunktionalisierung von LbL-beschichteten Silica-Mikropartikeln (SiO2) mit einem funktionellen Supported Lipid Bilayer aufgegriffen und weiterentwickelt, wobei insbesondere die Homogenität des Supported Lipid Bilayers auch auf sehr kleinen Längenskalen (wenige Nanometer) bestimmt wurde. In einem letzten Schritt konnte anhand zweier verschiedener Zelllinien (3T3 und Vero) die Adaptivität und Effektivität des entwickelten Drug Delivery Systems nachgewiesen werden.

Systemisch applizierte Therapeutika können erhebliche Nebenwirkungen auslösen, welche auf Grund eines unspezifischen Transports oder einer hohen Dosis von appliziertem Wirkstoff auftreten. Daher bedarf es der Entwicklung neuartiger Wirkstoff-Transportsysteme (Drug Delivery Systems) welche in der Lage sind, Wirkstoffe in genau definierbaren Dosen gezielt in die adressierte Zelle zu transportieren. Ein vielversprechender Ansatz, welcher diesen Anforderungen nachkommt, findet sich in der Layer-by-Layer-Technik (LbL), d.h. der wechselseitigen Assemblierung von Polymeren/Wirkstoffen auf soliden sphärischen Templaten, eines funktionellen Supported Lipid Bilayers sowie der Oberflächenfunktionalisierung mit spezifischen Antikörpern. Dabei ist die Homogenität und Regularität des Supported Lipid Bilayers von großer Bedeutung, um in biomedizinischen Anwendungen eine ungewollte Interaktion mit Serumkomponenten sowie eine Opsonierung zu verhindern. Insbesondere die funktionelle Lipidkomponente besitzt allerdings maßgebliche Auswirkungen auf diese Parameter. In dieser Arbeit wurde die Idee der Oberflächenfunktionalisierung von LbL-beschichteten Silica-Mikropartikeln (SiO2) mit einem funktionellen Supported Lipid Bilayer aufgegriffen und weiterentwickelt, wobei insbesondere die Homogenität des Supported Lipid Bilayers auch auf sehr kleinen Längenskalen (wenige Nanometer) bestimmt wurde. In einem letzten Schritt konnte anhand zweier verschiedener Zelllinien (3T3 und Vero) die Adaptivität und Effektivität des entwickelten Drug Delivery Systems nachgewiesen werden.

Lipid structures, such as liposomes or micelles, are of high interest as an approach to support the transport and delivery of active agents as a drug delivery system. However, there are many open questions regarding their uptake and impact on cellular metabolism. In this study, lipid structures were assembled as a supported lipid bilayer on top of biopolymer-coated microcarriers based on the Layer-by-Layer assembly strategy. The functionalized microcarriers were then applied to various human and animal cell lines in addition to primary human macrophages (MΦ). Here, their influence on cellular metabolism and their intracellular localization were detected by extracellular flux analysis and immunofluorescence analysis, respectively. The impact of microcarriers on metabolic parameters was in most cell types rather low. However, lipid bilayer-supported microcarriers induced a decrease in oxygen consumption rate (OCR, indicative for mitochondrial respiration) and extracellular acidification rate (ECAR, indicative for glycolysis) in Vero cells. Additionally, in Vero cells lipid bilayer microcarriers showed a more pronounced association with microtubule filaments than polymer-coated microcarrier. Furthermore, they localized to a perinuclear region and induced nuclei with some deformations at a higher rate than unfunctionalized carriers. This association was reduced through the application of the microtubule polymerization inhibitor nocodazole. Thus, the effect of respective lipid structures as a drug delivery system on cells has to be considered in the context of the respective target cell, but in general can be regarded as rather low.

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Biological systems carry inherent complexity, which pose difficulties observing behavioural properties, such as diffusion coefficients, kinetic constants and state switching occurrences. With constantly improving computing power and microscopy technologies, single molecule methods have become a viable alternative when probing the behaviour of proteins, enzymes, lipids and other molecules. Processed microscopy images and videos provide information such as particle intensities and trajectories, avoiding ensemble averaging and therefore allowing for a detailed breakdown of particle mobility and interactions. A single particle tracking (SPT) algorithm was developed which implements detection, localization and position linking on image stacks. Sub-pixel precise detection is done via either centroid determination, Gaussian fit, or radial symmetry centres, while tracking makes use of distance based global cost optimization. The detection algorithm is also used for single particle spectroscopy, where intensity information is used to determine the size of oligomers, as well as their interaction with other molecules through channel intensity cross-correlation. The algorithm underwent benchmarking with simulated videos and was applied to three different biological systems with comparison to other established methods of analysis. The first system studied was the diffusion of the fluorescent lipophilic dye DiD in a five-component mitochondria-like solid-supported lipid bilayer. Comparing line-scanning fluorescence correlation spectroscopy (FCS) and single particle tracking, the measured diffusion coefficients were found to be statistically different, with DFCS = 3 μm2s-1 and DSPT = 2 μm2s-1, indicating different operational ranges for the two methods. FCS outperforms SPT when the diffusion coefficient exceeds 1 μm2s-1, making it ideal for lipid diffusion in fluid membranes and proteins in solution with weak membrane interaction. SPT is best suited for mobile and immobile membrane inserted proteins, as well as lipid diffusion in viscous membranes. The second system studied was the interaction between the two proteins Bax and Bid when inserted in a membrane. Bax and Bid are both members of the Bcl-2 family of proteins, which plays a vital role in the apoptosis mechanism, by inducing mitochondrial outer membrane permeabilization. To study this system with single particle spectroscopy, fluorescently labelled Bax and truncated Bid (tBid) were imaged when interacting with a mitochondria-like supported lipid bilayer with confocal microscopy. Immobile and mobile particles were detected and distinguished based on the eccentricity of the observed fluorescence spot. The intensity of the particle signal was used to determine oligomer type (homo-oligomerization) while the interaction with the particles' counterpart (hetero-oligomerization) was determined by channel cross-correlation. This allowed the measurement of the 2D-KD values for mobile (0.6 μm-2) and immobile (0.08 μm-2) Bax/tBid complexes, showing that the degree of insertion of the proteins in the membrane greatly affect their affinity for each other. The third and final system studied was the motion of cellulases on cellulose fibers. Enzymatic hydrolysis of crystalline cellulose is a costly step in the generation of fermentable sugars for biofuel production. Due to the complex structure and many possible interaction states of the enzymes with cellulose, single particle tracking is a well-adapted technique to the gathering of information on the enzyme dynamics, which is essential for process optimization. The movement of cellulases on cellulose substrate was observed via labelled Thermobifidia fusca Cel5A, Cel6B and Cel9A on bacterial micro-crystalline cellulose substrate. The detected trajectories were analyzed using multiple diffusion models. A simple one-state diffusion model was insufficient to describe the observed radial displacement distributions and so a two-state model was introduced and confronted with the data using conventional least-squares fits , as well as a hidden Markov approach. The diffusion coefficients of the two states are found to be on the order of Dfast = 10-3 μm2s-1 and Dslow = 10-4 μm2s-1, with the slow state being more stable and therefore more likely to occur. Single particle tracking can give us better insight into complex interactions, such as synergistic binding of proteins existing in several different states and processive enzymatic behaviour, where ensemble averaging techniques can fall short. The uses of single molecule methods are plentiful and with the current rise of machine learning, higher levels of abstraction will provide us with more detailed insights into biological processes, driving promising developments in the medical field, as well as new technologies in many sectors of industry. / Thesis / Doctor of Science (PhD) / Proteins are the motors that drive most cellular processes, for example steering a cell’s life cycle, or decomposing sources of nutrients. Being able to observe the motion of individual proteins is key to understanding their behaviour. In this work a single particle tracking (SPT) program was developed to extract protein trajectories from fluorescence microscopy experiments. With this tool-set we investigated the following two systems. The first system of interest is the Bcl-2 protein family, which is vital during the pro- grammed cell death at the end of each cell’s life span. The failure of a controlled cell death can have dire consequences, such as necrosis and cancer. The Bcl-2 family proteins Bid and Bax are active on the outer membrane of the mitochondria, where they initiate the process of terminating the cell’s functions by forming pores. For our experiments we ar- tificially mimicked the outer membrane of the mitochondria, introduced Bid and Bax and observed their preferential groupings on the membrane surface. This provided indications of the mechanisms involved during binding and pore formation. The motivation behind the investigation of the second system is the improvement of biofuel generation from a renewable source: plant-based biomass. Cellulases are enzymes from bacteria or fungi that break down cellulose – one of the main building blocks of all plant cell walls – into fermentable sugars. In fluorescence microscopy experiments a purified cellulose substrate was used to monitor the motion of three types of cellulases. The insight which we gained into the cellulase behaviour may allow the optimization of the process of cellulose decomposition.