Dissertations / Theses on the topic 'Fluorescence Recovery while photobleaching'

In a living cell, signals are usually transmitted from outside to the intracellular machinery through receptors on the cell membrane. Once bound to their ligand (e.g. a hormone or another protein), receptors become activated and trigger chemical reactions inside the cell. To stop the response, receptors are often removed from the cell membrane (internalization). A protein called arrestin binds to the receptor and targets it to a vesicle, which detaches from the membrane and fuses with other vesicles to form an endosome, a sphere-like structure containing many receptors. After internalization, arrestin must dissociate from the receptor before the latter returns to the membrane or is degraded. By using fluorescence recovery after photobleaching data and a reaction-diffusion model, we estimate the in vivo affinity of arrestin for bradykinin type 2 receptor. We use the Hough transform to automate fluorescence quantification and a Bayesian approach to fit the model to the data.

The Bcl-2 family of proteins strictly regulates the intrinsic pathway of apoptosis. Direct physical interactions between Bcl-2 proteins regulate mitochondrial outerpermeabilisation (MOMP), which occurs in response to various cell stresses andapoptotic stimuli. How changes in Bcl-2 protein activity regulate apoptosiscommitment is still unclear, especially with regard to how they interact with eachother within the context of the mitochondrial membrane. Recent studies haveshown that Bcl-2 proteins exist in a dynamic equilibrium between the mitochondriaand the cytosol. In this thesis, by using FRAP, I have measured changes in Bcl-XLand Mcl-1 dynamics in single cells. Surprisingly, individual cells within a populationshow widely differing Bcl-XL and Mcl-1 dynamics. There is a corelation betweenBcl-XL and Mcl-1 dynamics with BH3-only protein expression. Anti-apoptotic andpro-apoptotic Bcl-2 proteins stabilise each other on the OMM. Together, theseresults indicate that cells constantly fine tune mitochondrial priming and thatanalysing anti-apoptotic Bcl-2 proteins by FRAP allows this to be measured at asingle cell level in real time before MOMP.

Thesis (Ph.D. in Neuroscience) -- University of Colorado Denver, 2007.
Typescript. Includes bibliographical references (leaves 84-93). Free to UCD affiliates. Online version available via ProQuest Digital Dissertations;

Low back pain represents a significant concern in the United States, with 70% of individuals experiencing symptoms at some point in their lifetime. Although the specific cause of low back pain remains unclear, symptoms have been strongly associated with degeneration of the intervertebral disc. Insufficient nutritional supply to the disc is believed to be a major mechanism for tissue degeneration. Understanding nutrients' transport in intervertebral disc is crucial to elucidate the mechanisms of disc degeneration, and to develop strategies for tissue repair (in vivo), and tissue engineering (in vitro). Transport in intervertebral disc is complex and involves a series of electromechanical, chemical and biological coupled events. Despite of the large amount of studies performed in the past, transport phenomena in the disc are still poorly understood. This is partly due to the limited number of available experimental techniques for investigating transport properties, and the paucity of theoretical or numerical methods for systematically predicting the mechanisms of solute transport in intervertebral disc. In this dissertation, a theoretical and experimental approach was taken in order to investigate the mechanisms of solute transport and binding interactions in intervertebral disc. New imaging techniques were developed for the experimental determination of diffusive and binding parameters in biological tissues. The techniques are based on the principle of fluorescence recovery after photobleaching, and allow the determination of the anisotropic diffusion tensor, and the rates of binding and unbinding of a solute to the extracellular matrix of a biological tissue. When applied to the characterization of transport properties of intervertebral disc, these methods allowed the establishment of a relationship between solute anisotropic and inhomogeneous diffusivity and the unique morphology of human lumbar annulus fibrosus. A mixture theory for charged hydrated soft tissues was presented as a framework for theoretical investigations on solute transport and binding interactions in cartilaginous tissues. Based on this theoretical framework and on experimental observations, a finite element model was developed to predict solute diffusive-convective-reactive transport in cartilaginous tissues. The numerical model was applied to simulate the effect of mechanical loading on solute transport and binding interactions in cartilage explants and intervertebral disc.

Maintenance of apico-basal polarity is essential for epithelial integrity and requires particular reinforcement during tissue morphogenesis, when cells are reorganised, undergo shape changes and remodel their junctions. It is well established that epithelial integrity during morphogenetic processes depends on the dynamic exchange of adherens junction components, but our knowledge on the dynamics of other proteins and their dynamics during these processes is still limited. The early Drosophila embryo is an ideal system to study membrane dynamics during morphogenesis. Here, morphogenetic activities differ along the anterior-posterior axis, with the extending germband showing a high degree of epithelial remodelling. We developed a Fluorescence Recovery After Photobleaching (FRAP) assay with a higher temporal resolution, which allowed the distinction between a fast and a slow component of recovery of membrane proteins during the germband extension stage. We show for the first time that the recovery kinetics of a general membrane marker, SpiderGFP, differs in the anterior and posterior parts of the embryo, which correlates well with the different morphogenetic activities of the respective embryonic regions. Interestingly, absence of crumbs, a polarity regulator essential for epithelial integrity in the Drosophila embryo, decreases the fast component of SpiderGFP and of the apical marker Stranded at Second-Venus specifically in the anterior region. We suggest that the defects in kinetics observed in crumbs mutant embryos are the first signs of tissue instability in this region, explaining the earlier breakdown of the head epidermis in comparison to that of the trunk, and that diffusion in the plasma membrane is affected by the absence of Crumbs.

Dans de nombreux cas, le développement de surfaces aux propriétés adhésives spécifiques fait appel à l’utilisation « d’interfaces décorées ». Ces interfaces sont composées d’un substrat solide sur lequel des chaînes de polymère sont plus ou moins bien ancrées. Ces chaînes se couplent mécaniquement au matériau environnant et contrôlent la transmission des contraintes de friction et d'adhésion aux interfaces. Ce couplage dépend en particulier de la pénétration des chaînes de surface dans la matrice et de leur dynamique. Dans cette thèse, les systèmes que nous avons étudiés sont constitués d’une couche de chaînes de polymère dont une extrémité est liée de manière covalente à un substrat solide. Ces brosses de polymère, constituent un système modèle pour des interfaces décorées. Notre objectif a été d’étudier la conformation et la dynamique de ces chaînes greffées lorsque ces dernières sont soumises à différents types de sollicitations afin de comprendre les mécanismes moléculaires régissant les propriétés d’adhésion et de friction de ce type d’interface. Dans un premier volet, nous avons étudié par réflectivité de neutrons la cinétique de cicatrisation d'une interface composée initialement de chaînes greffées recroquevillées sur un substrat et en contact avec un fondu. Lorsque le système est amené à une température supérieure à la température de transition vitreuse, les chaînes de polymère retrouvent une mobilité non nulle permettant ainsi la pénétration des chaînes greffées dans le fondu de polymère. La réflectivité de neutrons nous a permis d'une part de sonder à l'échelle moléculaire la cinétique de cicatrisation de ce type d’interface et d'autre part de la quantifier. L'influence des paramètres moléculaires sur cette cinétique de cicatrisation a pu être observée, ce qui nous a permis de proposer un modèle en loi d'échelle permettant d'apporter une interprétation physique au phénomène étudié. La deuxième partie de ce travail de thèse a consisté en l'élaboration d'un dispositif expérimental permettant de cisailler un système brosse/fondu au-dessus de la température de la température transition vitreuse et de geler la conformation des chaînes greffées dans leur configuration cisaillée. L'inversion des spectres de réflectivité neutrons associés a permis de mettre en évidence l'influence du cisaillement sur le degré d'interpénétration entre la brosse et le fondu qui régit la transmission des contraintes de friction sur ce type d'interface. De plus, nous avons pu mesurer la cinétique de relaxation de chaînes greffées, cisaillées au préalable, et la comparer aux expériences d’interdigitation simple. Cette comparaison a permis de divulguer l’importance du type de sollicitation sur la cinétique de relaxation d’une interface brosse / fondu.Nous avons également observé que la cinétique de relaxation et la conformation de chaînes greffées peuvent être altérées lorsque ces dernières sont confinées dans un film d'épaisseur comparable au rayon de giration des chaînes. Une étude systématique par réflectivité de neutrons a permis de mettre en évidence une accélération de la cinétique de relaxation du système en dessous d'une épaisseur critique qui pourrait être interprétée en termes de déplacement de la température de transition vitreuse. Dans un deuxième temps, nous avons étudié le glissement de solutions de polymères sur une surface greffée. La fraction volumique en chaînes libres dans la solution est un paramètre supplémentaire aux trois cas précédents qui contrôle ici le degré d'interpénétration entre chaînes libres et chaînes greffées. Une première approche théorique a permis de dissocier différents régimes de glissements à la paroi en fonction de fraction volumique. Nous avons entrepris une première série d'expériences de vélocimétrie laser après photolyse afin de mesurer le glissement à la paroi de solutions de polymère et de confronter les résultats expérimentaux avec notre approche théorique
In many cases, the development of surfaces with specific adhesive properties involves the use of "decorated interfaces." These interfaces consist of a solid substrate on which polymer chains are more or less well anchored. These chains are mechanically coupled to the surrounding material and control the transmission of friction and adhesion stresses at the interfaces. This coupling depends particularly on the penetration of the surface chains within the matrix and on their own dynamics. In this thesis, the systems we investigated are composed of a layer of polymer chains whose end is covalently linked to a solid substrate. These, so called, polymer brushes, provide a model system for decorated interfaces. Our objective was to study the conformation and dynamics of these grafted chains when they are subjected to different types of stress in order to understand the molecular mechanisms governing the adhesion and friction properties of this type of interface.In the first part, we investigated the healing kinetics of an interface composed initially of grafted chains collapsed on a substrate and in contact with a molten by using neutron reflectivity. When the system is brought above the glass transition temperature, the polymer chains mobility is high enough to allow the penetration of the grafted chains within the polymer melt. Neutrons reflectivity allowed us to probe at the molecular scale and to quantify the healing kinetics of this type of interface. The influence of molecular parameters on this healing kinetics was observed, which allowed us to propose a scaling law model to give a physical interpretation to the phenomenon studied.The second part of this thesis consisted in the development of an experimental setup which is able to shear a brush / melt interface above the glass transition temperature and to freeze the conformation of chains grafted in their sheared conformation. The inversion of the associated neutron reflectivity spectra made it possible to demonstrate the influence of shear on the degree of interpenetration between the brush and the melt which governs the transmission of stresses. In addition, we measured the kinetics of relaxation of grafted chains previously sheared and we compared it to the interdigitation experiments. This comparison highlighted the influence of the kind of solicitation on the relaxation kinetics of a brush/melt interface.We also observed that the relaxation kinetics and the conformation of the grafted chains may be altered when they are confined in a film which thickness is comparable to the radius of gyration of the chains. A systematic study using neutron reflectivity was conducted and highlighted an acceleration of the relaxation kinetics of the system below a critical thickness which could be interpreted in terms of a shift in the glass transition temperature.Secondly, we studied the slip of polymer solutions onto a grafted surface. The volume fraction of free chains in solution is an additional parameter which controls the degree of interpenetration between free chains and grafted chains. A first theoretical approach showed that different slip regimes can occur as a function of volume fraction. We have undertaken a first series of experiments using laser velocimetry after photobleaching to measure the surface velocity of flowing polymer solutions and to compare the experimental results to our theoretical approach

Maintenance of apico-basal polarity is essential for epithelial integrity and requires particular reinforcement during tissue morphogenesis, when cells are reorganised, undergo shape changes and remodel their junctions. It is well established that epithelial integrity during morphogenetic processes depends on the dynamic exchange of adherens junction components, but our knowledge on the dynamics of other proteins and their dynamics during these processes is still limited. The early Drosophila embryo is an ideal system to study membrane dynamics during morphogenesis. Here, morphogenetic activities differ along the anterior-posterior axis, with the extending germband showing a high degree of epithelial remodelling. We developed a Fluorescence Recovery After Photobleaching (FRAP) assay with a higher temporal resolution, which allowed the distinction between a fast and a slow component of recovery of membrane proteins during the germband extension stage. We show for the first time that the recovery kinetics of a general membrane marker, SpiderGFP, differs in the anterior and posterior parts of the embryo, which correlates well with the different morphogenetic activities of the respective embryonic regions. Interestingly, absence of crumbs, a polarity regulator essential for epithelial integrity in the Drosophila embryo, decreases the fast component of SpiderGFP and of the apical marker Stranded at Second-Venus specifically in the anterior region. We suggest that the defects in kinetics observed in crumbs mutant embryos are the first signs of tissue instability in this region, explaining the earlier breakdown of the head epidermis in comparison to that of the trunk, and that diffusion in the plasma membrane is affected by the absence of Crumbs.

Des solutions d'isolat de protéine de lactosérum (WPI) et d'isolat de protéine de soja (SPI) ont été chauffées à différentes concentrations en protéines conduisant à la formation d'agrégats fractals polydisperses de taille moyenne variable. Lastructure des solutions a été analysée par diffusion de la lumière en fonction de la concentration en protéine. La compressibilité osmotique et la longueur de corrélation dynamique diminuent quand la concentration augmente deviennent indépendantes de la taille initiale des agrégats pour les suspensions denses. Pour une taille d'agrégat donnée, la viscosité augmente initialement exponentiellement avec la concentration croissante puis diverge. Plus lesagrégats sont grands, plus l’augmentation de la viscosité apparaît à des concentrations faibles. La dépendance avec la concentration de la viscosité des solutions d'agrégats fractals est beaucoup plus forte que celle de microgels. Le comportement de mélanges de différents types d’agrégats (fractals/fractals ; fractals/microgels et WPI/SPI) a étéétudié principalement par rhéologie.Le recouvrement de fluorescence après photoblanchiment (FRAP) a été utilisé pour étudier la diffusion de chaînes de dextran marquées par des fluorophores dans des solutions d’agrégats et des gels de WPI. Une diffusion brownienne estobservée dans des suspensions d’agrégats et des gels faibles formés juste au-delà de Cg avec un coefficient de diffusion (D) qui diminue avec l'augmentation de la concentration mais, avec une dépendance plus faible que celle de la viscosité (). A des concentrations plus élevées, des gels densément réticulés sont formés, ce qui induit une forte diminution de la mobilité des chaînes de dextran. Pour ces systèmes, la recouvrance de la fluorescence est logarithmique avec le temps,suggérant une distribution exponentielle des coefficients de diffusion. La diffusion des chaînes de dextran a également été étudiée en fonction de la concentration en protéines pour les suspensions de trois types d'agrégats de WPI (petits et grands fractals et microgels)
Polydisperse fractal aggregates of varying average sizes were formed when solutions of whey protein isolate and soy protein isolate were heated at different protein concentrations and at neutral pH. The structure of these fractals aggregates solutions was analyzed by light scattering as a function of protein concentration. In dense suspension, the osmotic compressibility and the correlation length decreases with increasing concentration and become independent of the initial aggregate size. In this concentration regime, the aggregates are strongly interpenetrated and can be visualized as a set of "blobs". For a fixed aggregate size, the viscosity initially increases exponentially with increasing concentration and then diverges at the gel point. Larger fractal aggregates show a more important increase of the viscosity with increasing concentration than smaller aggregates, because they are less dense. The increase of the viscosity was much stronger for large fractal aggregates than for homogeneous microgels (microgels were formed by heating the WPI solution in present of CaCl2) of the same size.Dynamic light scattering, rheology and FRAP measurements were performed to investigate mixtures of different type of aggregates of WPI (fractals/fractals, fractals/microgels) and fractals of mixtures of WPI and SPI. Flow measurements were used to characterise the rheological properties of the aggregate suspension whereas Fluorescence recovery after Photobleaching (FRAP) was used to determine the self diffusion of fluorophore-labelled dextrans chains in mixtures over a wide range of concentrations. The results were compared to the concentration dependence of zero shear viscosity, gel stiffness, osmotic compressibility and correlation length. Brownian diffusion of the dextran chains was observed in aggregate suspensions and weak gels formed just above the gel point with a diffusion coefficient that decreased with increasing concentration, but the dependence was weaker than that of the viscosity. At higher concentrations, densely crosslinked gels were formed, which induced a sharp decrease in the mobility of the dextran chains. For these systems, the recovery of fluorescence was logarithmic over time, suggesting an exponential distribution of diffusion coefficients

Thesis (Ph.D)--Biomedical Engineering, Georgia Institute of Technology, 2008.
Committee Chair: Levenston, Marc; Committee Member: Garcia, Andres; Committee Member: Koros, William; Committee Member: Sambanis, Athanassios; Committee Member: Temenoff, Johnna; Committee Member: Vidakovic, Brani.

Les pathologies inflammatoires vasculaires (PV) et articulaires (PA) représentent aujourd'hui la cause principale de la mortalité et d’invalidité dans les pays industrialisés. Comme les causes exactes favorisant leur apparition restent inconnues, le présent travail a proposé de nouvelles méthodes physiques susceptibles de détecter les premiers stades inflammatoires en utilisant des marqueurs spécifiques et d'étudier les changements mécaniques et structuraux subis par les tissus vasculaires et le liquide synovial (LS). Les PV peuvent être détectées en utilisant les examens IRM. Afin d’améliorer l’efficacité des agents de contraste IRM ceux-ci peuvent être greffés avec des anticorps. En utilisant la Spectroscopie de Force (SF), un mode de la Microscopie à Force Atomique, l’affinité établie entre un nouvel anticorps, le Fucoidan, et le marqueur spécifique P-Selectine a été analysé. L’étude sur PV a été finalisée en utilisant les mêmes techniques SF en mesure d’indentation afin de connaitre les changements de propriétés mécaniques entre les tissus vasculaires sains et pathologiques. Les modifications dans la dynamique du LS déclenchées par l'une des molécules incapables de réagir selon leur fonctionnalité peuvent conduire aux PA. Aussi la technique SF a été utilisée pour étudier le comportement de chaque composant moléculaire du LS. Il a été prouvé l’affinité de ces composants pour les bicouches lipidiques (BL), fréquemment rencontrées dans le corps humain. L’étude a été complétée par l’analyse des changements intervenant dans la dynamique des BL en présence/absence des composants principaux de LS. Les investigations ont été réalisées par un test de Récupération de Fluorescence Après Photoblanchiment. Enfin un test tribologique a été conduit pour étudier la variation du coefficient de frottement entre les BL et les composants du LS
As vascular (VP) and articular (AP) inflammatory pathologies represent nowadays the principal cause of mortality and disability in industrialized countries, the exact causes favoring their occurrence remain still unknown. The present work aimed at proposing new physical methods to detect the early inflammatory stages through recognition of specific markers and to study the structural and mechanical changes undergone by pathological vascular tissues and synovial fluid (SF). Vascular pathologies can be detected through contrasted MRI pictures. In order to improve the capacity of contrast agents to target specific markers they can be antibody-grafted. Atomic Force Microscopy’s mode Force Spectroscopy (AFM-FS) was used to evaluate the affinity between the Fucoidan as a new antibody, and the P-Selectin vascular inflammatory marker, for capacity to target that marker. Further study of VP used the FS techniques for nanoindentation to study changes in mechanical properties between healthy and pathological vascular tissues. Modifications in SF’s dynamics triggered by one of the molecular component not fulfilling its role may lead to AP. To investigate this issue, each of the main SF’s molecular components had their affinity tested versus the ever-present lipid bilayers using AFM-FS techniques. Furthermore changes in lipid bilayers’ dynamics in the presence/absence of the main SF components were analyzed by Fluorescence Recovery After Photobleaching technique. Finally a tribological test was performed to study the variation of the friction coefficient between the lipid bilayers and SF’s main components

In addition to classical adhesion structures like filopodia or focal adhesions, dendritic cells similar to macrophages and osteoclasts assemble highly dynamic F-actin structures called podosomes. They are involved in cellular processes such as extracellular matrix degradation, bone resorption by osteoclasts, and trans-cellular diapedesis of lymphocytes. Besides adhesion and migration, podosomes enable dendritic cells to degrade connective tissue by matrix metalloproteinases. SWAP-70 interacts with RhoGTPases and F-actin and regulates migration of dendritic cells. SWAP-70 deficient osteoclasts are impaired in F-actin-ring formation and bone resorption. In the present study, we demonstrate that SWAP-70 is not required for podosome formation and F-actin turnover in dendritic cells. Furthermore, we found that toll-like receptor 4 ligand induced podosome disassembly and podosome-mediated matrix degradation is not affected by SWAP-70 in dendritic cells. Thus, podosome formation and function in dendritic cells is independent of SWAP-70.

In addition to classical adhesion structures like filopodia or focal adhesions, dendritic cells similar to macrophages and osteoclasts assemble highly dynamic F-actin structures called podosomes. They are involved in cellular processes such as extracellular matrix degradation, bone resorption by osteoclasts, and trans-cellular diapedesis of lymphocytes. Besides adhesion and migration, podosomes enable dendritic cells to degrade connective tissue by matrix metalloproteinases. SWAP-70 interacts with RhoGTPases and F-actin and regulates migration of dendritic cells. SWAP-70 deficient osteoclasts are impaired in F-actin-ring formation and bone resorption. In the present study, we demonstrate that SWAP-70 is not required for podosome formation and F-actin turnover in dendritic cells. Furthermore, we found that toll-like receptor 4 ligand induced podosome disassembly and podosome-mediated matrix degradation is not affected by SWAP-70 in dendritic cells. Thus, podosome formation and function in dendritic cells is independent of SWAP-70.

Mammalian hearing exhibits exquisite sensitivity and frequency selectivity attributed to the unique properties of cochlear outer hair cells (OHCs). These sensory epithelial cells are electro-mechanical transducers, capable of converting sound-induced electrical signals into mechanical forces which provide feedback via a mechanism known as the cochlear amplifier. In a process aptly termed electromotility, electro-mechanical transduction manifests as whole-cell axial length changes in OHCs that occur in response to changes in the transmembrane potential. The polytopic motor protein prestin functions as the voltage sensor and molecular motor, both in OHCs and when expressed in heterologous systems. As the molecular mechanism(s) of electromotility remain unknown, examining the structure and function of prestin is a major focus of ongoing research. Since changes in membrane composition and biophysical properties affect protein function and organization, we are particularly interested in membrane-protein interactions. Recent studies suggest that manipulations in membrane cholesterol levels reversibly shift the membrane microdomain distribution of prestin, modulate prestin oligomerization states, and alter prestin function, thus regulating electromotility through membrane-protein interactions. Measurements of protein and lipid lateral mobility provide a powerful tool to dynamically examine such interactions. We hypothesize that OHC plasma membrane cholesterol levels affect electromotility either through microdomain-mediated mechanisms that cluster or segregate prestin molecules or via alterations in the material properties of the membrane, which in turn affect the resident proteins. Using fluorescence recovery after photobleaching (FRAP), we evaluated the lateral mobility of both protein and lipid components of the OHC. Then we showed that the diffusion of both prestin in HEK cells and lipids in OHCs is altered in response to changes in membrane cholesterol concentration. Cumulatively, this work demonstrates the complexity of prestin-membrane interactions and highlights the importance of their inclusion in current models of prestin function and electromotility.

A thorough understanding of pharmaceutical and therapeutic products and materials is important for an improved quality of life. By probing the complex behaviors and properties of these systems, new insights can allow for a better understanding of current treatments, improved design and synthesis of new drug products, and the development of new treatments for various health conditions. Often, the impact of these new insights are limited by current technology and instrumentation and by the methods in which existing data is processed. Additionally, current standards for characterization of pharmaceuticals and therapeutics are time-consuming and can delay the timeline in which these products become available to the consumer. By addressing the limitations in current instrumentation and data science methods, faster and improved characterization is possible.

Measurement science has seen fast growth of data in both volume and complexity in recent years, new algorithms and methodologies have been developed to aid the decision
making in measurement sciences, and this process is automated for the liberation of labor. In light of the adversarial approaches shown in digital image processing, Chapter 2 demonstrate how the same attack is possible with spectroscopic data. Chapter 3 takes the question presented in Chapter 2 and optimized the classifier through an iterative approach. The optimized LDA was cross-validated and compared with other standard chemometrics methods, the application was extended to bi-distribution mineral Raman data. Chapter 4 focused on a novel Artificial Neural Network structure design with diffusion measurements; the architecture was tested both with simulated dataset and experimental dataset. Chapter 5 presents the construction of a novel infrared hyperspectral microscope for complex chemical compound classification, with detailed discussion in the segmentation of the images and choice of a classifier to choose.