Le ribosome est un organite essentiel de la cellule qui assure la synthèse des protéines. C'est une structure très conservée, composée d'ARN et de protéines ribosomiques organisés en deux sous-unités. Les expériences de reconstitution in vitro du ribosome d'E. coli ont montré que l'assemblage est un processus coordonné impliquant de nombreuses interactions entre les différents constituants. En particulier, les premières étapes de l'assemblage de la grande sous-unité dépendent fortement de la fixation coopérative de cinq protéines ribosomiques à l'ARN 23S, mais les mécanismes moléculaires sous-jacents sont mal connus.Cette étude à l'échelle de la molécule unique vise à préciser ces mécanismes et porte sur un fragment constitué des hélices H18, H19 et H20 du domaine I de l'ARN ribosomique 23S contenant les sites de fixation des protéines uL24 et uL4. Ce fragment d'ARN a été préparé dans une configuration qui permet la mesure de force via un double piège optique. Les courbes de force obtenues ont permis de dresser une cartographie de la stabilité des structures du fragment d'ARN.Ces cartes ont été comparées en absence et en présence des protéines ribosomiques uL24 et/ou uL4, démontrant ainsi que le fragment d'ARN est stabilisé par la fixation des protéines uL24 et/ou uL4. Leur fixation est coopérative et la présence conjointe des deux protéines sur-stabilise les structures du fragment d'ARN.Ces résultats sont discutés dans la perspective de préciser le rôle du fragment d'ARN et des protéines ribosomiques uL24 et uL4 dans l'assemblage de la grande sous-unité du ribosome. / Ribosomes are essential organelles of the cell responsible for the synthesis of proteins. Their well conserved structure made of RNA and proteins is organized into two subunits. In vitro reconstitution of E. coli ribosomes showed that their assembly is a coordinated process which involves many interactions between the components. More specifically, the early stages of the large subunit assembly depend strongly on the cooperative binding of five ribosomal proteins to the 23S RNA. The underlying molecular mechanisms however remain poorly understood.The aim of this study is to shine new light on these mechanisms at the single molecule level. It focuses on a 23S ribosomal RNA fragment composed of the helices H18, H19 and H20 in domain I which encompasses the binding sites of the ribosomal proteins uL24 and uL4. This RNA fragment has been prepared in a dumbbell configuration and force versus displacement measurements have been performed using a dual optical trap. From these measurements, a map summarizing the mechanical stability of the RNA fragment has been determined.The maps obtained in absence and in presence of the ribosomal proteins uL24 and/or uL4 have been compared consequently demonstrating mechanical stabilization of the RNA fragment induced by the binding of uL24 and/or uL4. Moreover, their binding is cooperative and when both are present, the mechanical stabilization of the RNA fragment is enhanced.These results are discussed to specify the role of the RNA fragment and proteins uL24 and uL4 in the large ribosomal subunit assembly.

Desde o desenvolvimento dos primeiros métodos de controle do movimento e posição de partículas usando lasers, ainda no início da década de 1970, até o reconhecimento com o prêmio Nobel de Física de 2018, uma das principais e mais versáteis ferramentas de manipulação óptica, as chamadas pinças ópticas, têm sido usadas majoritariamente para explorar objetos em dois regimes de tamanho: o limite das partículas sub-nanométricas (átomos e moléculas simples) e o limite das partículas micrométricas (com aplicações especialmente em sistemas biológicos). Nesse trabalho, foi desenvolvido e construído um aparato experimental para aprisionar micro e nanopartículas numa pinça óptica, que pode ser controlada de forma dinâmica usando modulação acusto-óptica do feixe de aprisionamento. A calibração da pinça óptica foi feita por diversos métodos, incluindo o método de equipartição de energia e análise do potencial óptico, resultando em forças de aprisionamento da ordem de piconewtons por micrometros. Ademais, simulações computacionais de modelos estocásticos foram realizadas com o intuito de comparar os resultados experimentais com àqueles previstos teoricamente e guiar estudos futuros. / Since the development of early methods for controlling the motion and position of particles using lasers, in the 1970s, to the recognition with the 2018 Nobel Prize for Physics, one of the most versatile optical manipulation tools, the so-called optical tweezers, have been used mostly to explore objects in two limits of sizes: the sub nanometric particles (atoms and simple molecules) and the micrometric particles (with applications especially in biological systems). In this work, an experimental apparatus was developed and built to trap micro and nanoparticles in an optical tweezer that can be dynamically controlled, using acoustic-optical modulation of the trapping beam. The calibration of the optical tweezer was done using several methods, including the energy equipartition method and optical potential analysis, resulting in trapping forces on the order of piconewtons per micrometers. In addition, computational simulations of stochastic models were performed with the purpose of comparing the experimental results with those predicted theoretically and guiding future studies.

In an effort to develop an optical-acoustical understanding of ultrasound contrast agent microbubble dynamics in a micro-environment that resembles blood vessels, this thesis presents experimental work on optical trapping and acoustical probing of ultrasound contrast agent microbubbles confined in regenerated cellulose capillaries. First, we showed by acoustical means that the pressure threshold of an individual microbubble shell rupture increases significantly when confined in regenerated cellulose capillaries. We report that the shell rupture threshold in regenerated cellulose capillaries increased by at least 0.3 MPa from 0.8 MPa for unconfined microbubbles. Second, we achieved optical trapping and manipulation of ultrasound contrast agent microbubbles confined in capillaries using Hermite-Gaussian laser beams. / Graduation date: 2012

This dissertation combines various holographic techniques with application on the two- and three-dimensional imaging of ophthalmic tissue, fingerprints, and microsphere samples with micrometer resolution. Digital interference holography (DIH) uses scanned wavelengths to synthesize short-coherence interference tomographic images. We used DIH for in vitro imaging of human optic nerve head and retina. Tomographic images were produced by superposition of holograms. Holograms were obtained with a signal-to-noise ratio of approximately 50 dB. Optic nerve head characteristics (shape, diameter, cup depth, and cup width) were quantified with a few micron resolution (4.06 -4.8 microns). Multiple layers were distinguishable in cross-sectional images of the macula. To our knowledge, this is the first report of DIH use to image human macular and optic nerve tissue. Holographic phase microscopy is used to produce images of thin film patterns left by latent fingerprints. Two or more holographic phase images with different wavelengths are combined for optical phase unwrapping of images of patent prints. We demonstrated digital interference holography images of a plastic print, and latent prints. These demonstrations point to significant contributions to biometry by using digital interference holography to identify and quantify Level 1 (pattern), Level 2 (minutia points), and Level 3 (pores and ridge contours). Quantitative studies of physical and biological processes and precise non-contact manipulation of nanometer/micrometer trapped objects can be effectuated with nanometer accuracy due to the development of optical tweezers. A three-dimensional gradient trap is produced at the focus position of a high NA microscope objective. Particles are trapped axially and laterally due to the gradient force. The particle is confined in a potential well and the trap acts as a harmonic spring. The elastic constant or the stiffness along any axis is determined from the particle displacements in time along each specific axis. Thus, we report the sensing of small particles using optical trapping in combination with the digital Gabor holography to calibrate the optical force and the position and of the copolymer microsphere in the x, y, z direction with nm precision.

Von Willebrand factor (VWF) is a multimeric glycoprotein that critically supports platelet aggregation in hemostasis. Disordered VWF function causes both thrombotic and bleeding disorders, and genetic defects in VWF are responsible for von Willebrand’s disease (VWD), the most common inherited bleeding disorder in humans. Very large VWF multimers exhibit the greatest thrombogenic activity, which is attenuated by ADAMTS13 cleavage in the A2 domain. A2 cleavage is regulated by mechanical force, and pathologically high shear forces are known to enhance proteolysis and cause bleeding in patients. Enhanced cleavage is also described in patients with VWD 2A mutations. In contrast, VWF A2 is stabilized against cleavage by a calcium binding site within A2. Single molecule studies have demonstrated that mechanical unfolding is required for A2 cleavage to expose the scissile bond. In this dissertation, we aim to better understand the mechanosensitivity of A2 cleavage by characterizing the force sensitivity of A2 unfolding and refolding. We first characterized the interaction between VWF A2 and calcium using bulk isothermal calorimetry and thermal denaturation assays. In parallel, we used single molecule optical tweezers to characterize A2 unfolding and refolding. Calcium was found to bind A2 with high affinity, stabilize A2 against thermal denaturation, and enhance domain refolding. In contrast, we found that VWD 2A mutations destabilize the A2 domain against thermal denaturation. R1597W, the most common VWD 2A mutation, lies within the calcium binding loop and exhibited diminished calcium stabilization against thermal denaturation. Using optical tweezers, we found that R1597W also diminished A2 refolding. R1597W refolding in the presence of calcium was similar to that of wild-type A2 in the absence of calcium, suggesting that loss of calcium stabilization contributes to the disease mechanism of R1597W. Other VWD 2A mutations lying outside the calcium binding loop also destabilized A2, but retained calcium mediated stabilization. These studies provide a better understanding of VWD 2A pathophysiology and offer structural insights into A2 unfolding and refolding pathways. By exploring the role of mechanical force in regulating VWF cleavage, this work moves towards a better understanding of how hydrodynamic forces within the vasculature regulate VWF function in hemostasis and thrombosis.

In dieser Dissertation werden die Bindungseigenschaften von Rezeptor-Ligand-Komplexen mit Hilfe von Optischen Pinzetten untersucht. Aufgrund ihrer außerordentlichen Orts- (2nm) und Kraftauflösung (0,2pN) ist es möglich, diese spezifischen Interaktionen anhand einzelner Bindungsereignisse zu charakterisieren. Als Modellsysteme dienen die Wechselwirkungen zwischen den phosphorylierungsspezifischen, monoklonalen Antikörpern HPT-101 und HPT-104 und dem Morbus Alzheimer relevanten Tau-Peptid. Dieses pathogen veränderte Peptid wird krankheitsspezifisch an den Aminosäuren Threonin231 und Serin235 phosphoryliert, sodass die Detektion dieses Phosphorylierungsmusters mit Hilfe von monoklonalen Antikörpern eine mögliche Früherkennung der Alzheimer-Krankheit darstellt. Eine notwendige Voraussetzung dafür ist jedoch die exakte Kenntnis der Bindungsstellen des Liganden am Rezeptor. Ziel des ersten Teils dieser Arbeit ist es, das Epitop des monoklonalen Antikörpers HPT-101 zu bestimmen. Dazu werden mögliche bindungsrelevante Aminosäuren durch ein Alanin ausgetauscht (Alanin-Scan) und so insgesamt sieben neue Tau-Isoformen aus dem ursprünglichen doppelt-phosphorylierten Peptid Tau[pThr231/pSer235] hergestellt. Die jeweiligen Interaktionen zwischen den modifizierten Peptiden und dem Antikörper werden mit der dynamischen Kraftspektroskopie untersucht und mit Hilfe eines literaturbekannten Modells analysiert. Die sich daraus ergebenden Bindungsparameter (Lebensdauer der Bindung, charakteristische Bindungslänge, freie Aktivierungsenergie und Affinitätskonstante) werden zusammen mit den relativen Bindungshäufigkeiten erstmals genutzt, um Kriterien für essentielle, sekundäre und nicht-essentielle Aminosäuren im Tau-Peptid zu definieren. Bemerkenswerterweise existieren für insgesamt drei dieser Parameter (Bindungslebensdauer, Bindungslänge und Affinitätskonstante) scharfe Klassengrenzen, mit denen eine objektive Einteilung des Epitops von Antikörper HPT-101 möglich ist. Die erhaltenen Ergebnisse sind in überzeugender Weise im Einklang mit ELISA-Messungen zu diesem Antikörper-Peptid-Komplexen, sie liefern jedoch einen tieferen Einblick in die Natur einer spezifischen Bindung, da den kraftspektroskopischen Messungen auch die Bindungskinetik zugänglich ist. Das zweite Projekt der vorliegenden Dissertation etabliert eine Methodik, um die Datenvarianz in der Bestimmung der relativen Bindungshäufigkeit zu reduzieren. Anhand einer Kombination aus Fluoreszenz- und kraftspektroskopischen Messungen werden die Wechselwirkungen zwischen dem monoklonalen Antikörper HPT-104 und dem fluoreszenzmarkierten Peptid Tau[Fl-pThr231] untersucht. Es wird gezeigt, dass durch Vorsortieren der Peptid-beschichteten Kolloide, entsprechend ihrer Oberflächenbeladung, die Datenvarianz in den Bindungshäufigkeitsmessungen signifikant reduziert wird.

Colloidal particles are small particles ranging in size from nanometres to micrometres suspended in a fluid. Amongst many scientific and biological applications, they have been used to model crystallisation, vitrification, and particle interactions along with the use of colloidal model systems for the study of the fundamental nature of the fluid-crystal and fluid-glass phase transitions. It has been shown that colloidal particles can be trapped and manipulated using strongly-focused light beams known as optical tweezers, and this has paved the way for research into the area of micromanipulation using optical trapping. Holographic elements can replace multiple lenses in creating large numbers of optical tweezers and this is known as holographic optical trapping (HOT). A computer generated hologram can be designed to create large structured light fields, consisting of multiple foci, to enable trapping of multiple particles in arbitrary configurations. The overall aim of this project was to design, develop and test the suitability of a simple, inexpensive optical trapping arrangement suitable for multiple optical trapping. To achieve this, a theoretically-exact expression for the wavefront of a single point source was implemented in the coding scheme, allowing for the fast creation of multiple point sources suitable for holographic optical trapping experiments. Compensation for the spherical aberration present in the focusing optics was implemented into the coding scheme. Kodalith photographic film was chosen as the holographic recording medium for its high contrast and availability. The film has proven to be a successful medium, when used to record photographically-reduced images of high-quality printouts of the computed diffraction pattern, as it was able to successfully reproduce complex light fields. It is believed that this will be the first time that this film has been implemented for optical trapping purposes. The main limitations concerning the performance of the holograms recorded on Kodalith were the phase nonuniformities caused by unevenness in the film thickness which resulted in a failure to separately resolve light traps separated by less than about 5 (Mu)m. Index matching of the film between sheets of flat glass helped to compensate for these limitations. Holographic optical trapping was successfully observed using a variety of different initial beam powers, holographic aperture settings and light field configurations. Trapping experiments on of two types of particles (PMMA and polystyrene) were successfully conducted, with as little as ~ 150 (Mu)W per trap being required for multiple polystyrene trapping. However, particles were weakly trapped and were easily dislodged at these powers, and a higher power per trap of around 1 mW is preferred. The use of a relatively low numerical aperture (NA) 50 mm SLR lens for focusing the holographic optical traps was successful, proving that optical trapping can be conducted without the use of high NA microscope-objective lenses commonly used in other set ups. Holographic trapping of colloidal particles was successfully conducted at RMIT University for the first time proving the validity of the coding scheme, the recording method and the trapping arrangement.

Optical tweezers using highly focussed laser beams can be used to exert forces and torques and thus drive micromachines. This opens up a new field of microengineering, whose potential has yet to be fully realized. Until now, methods that have been used for modelling optical tweezers are limited to scatterers that are homogeneous or that have simple geometry. To aid in designing more general micromachines, I developed and implemented two main methods for modelling the micromachines that we use. These methods can be used for further proposed structures to be fabricated. The first is a FDFD/T-matrix hybrid method that incorporates the finite difference frequency domain (FDFD) method, which is used for inhomogeneous and anisotropic media, with vector spherical wave functions (VSWF) to formulate the T-matrix. The T-matrix is then used to calculate the torque of the trapped vaterite sphere, which is apparently composed of birefringent unit crystals but the bulk structure appears to be arranged in a sheaf-of-wheat fashion. The second method is formulating the T-matrix via discrete dipole approximation (DDA) of complex arbitrarily shaped mesoscale objects and implementing symmetry optimizations to allow calculations to be performed on high-end desktop PCs that are otherwise impractical due to memory requirements and calculation time. This method was applied to modelling microrotors. The T-matrix represents the scattering properties of an object for a given wavelength. Once it is calculated, subsequent calculations with different illumination conditions can be performed rapidly. This thesis also deals with studies of other light scattering phenomena including the modelling of scattered fields from protein molecules subsequently used to model FRET resonance, determining the limits of trappability, interferometric Brownian motion and the comparison between integral transforms by direct numerical integration and overdetermined point-matching.

Optical tweezers using highly focussed laser beams can be used to exert forces and torques and thus drive micromachines. This opens up a new field of microengineering, whose potential has yet to be fully realized. Until now, methods that have been used for modelling optical tweezers are limited to scatterers that are homogeneous or that have simple geometry. To aid in designing more general micromachines, I developed and implemented two main methods for modelling the micromachines that we use. These methods can be used for further proposed structures to be fabricated. The first is a FDFD/T-matrix hybrid method that incorporates the finite difference frequency domain (FDFD) method, which is used for inhomogeneous and anisotropic media, with vector spherical wave functions (VSWF) to formulate the T-matrix. The T-matrix is then used to calculate the torque of the trapped vaterite sphere, which is apparently composed of birefringent unit crystals but the bulk structure appears to be arranged in a sheaf-of-wheat fashion. The second method is formulating the T-matrix via discrete dipole approximation (DDA) of complex arbitrarily shaped mesoscale objects and implementing symmetry optimizations to allow calculations to be performed on high-end desktop PCs that are otherwise impractical due to memory requirements and calculation time. This method was applied to modelling microrotors. The T-matrix represents the scattering properties of an object for a given wavelength. Once it is calculated, subsequent calculations with different illumination conditions can be performed rapidly. This thesis also deals with studies of other light scattering phenomena including the modelling of scattered fields from protein molecules subsequently used to model FRET resonance, determining the limits of trappability, interferometric Brownian motion and the comparison between integral transforms by direct numerical integration and overdetermined point-matching.

Following the first demonstration in 1987 by Arthur Ashkin of trapping of biological objects with infrared laser light, optical tweezers have become increasingly useful and versatile tool in a variety of non-contact micromanipulation experiments in biological applications. In this thesis we demonstrated various applications of optical tweezers in botanical sciences, chemical engineering and anatomical sciences. The investigation of the three-dimensional shape of spinach chloroplasts has been accomplished. This was done using a steerable and a stationary trap system. A trapped rotating calcite crystal positioned close to a chloroplast provided means for inducing the rotation and orientation of chloroplast. The utility of rotating birefringent particles is demonstrated for the first time in biological applications. The stirrer method is a versatile method in orienting any biological object to study its shape and/or structure. Also, we demonstrated the ability of optical tweezers to fix and displace chloroplasts inside a living spinach plant cell. In the second part of the work described in this thesis, the steerable trap was used to study the viscoelastic properties of a polymeric filament that connects a single bacterium to an activated sludge floc. Also we estimated the minimum bonding force that can cause a weak interaction between the bacterium surface and the filament using optical tweezers as a transducer. This force was estimated to be at least 10 pN. These measurements are of value in improving activated sludge flocculation and ultimately the wastewater treatment process. In addition, the steerable trap was used to move small organelles inside large bacteria cells. The repositioning of organelles resulted in creating new internal cell structure. In the final part of the thesis, experiments are described where the laser tweezers system was combined with a cw argon-ion laser microbeam to investigate the fusion of smooth muscle cells and macrophages. In order to minimize the optical damage to the cells, a special arrangement was established to create short pulses for cutting the contact of the cell membrane of the two-fusion cell partners. The effectiveness of the cutting function of the pulsed system when used at 488 nm wavelength varied from cell to cell. The laser parameters such as laser power, pulse duration and repetition rate were varied in order to obtain the best working function of the setup. But overall the results indicate that the relatively long (ms) pulses possible may not be well suited to such applications.