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.

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;

Cardiovascular disease is a leading cause of morbidity worldwide. Many cardiomyopathies and developmental defects arise from misregulation of the cardiac extracellular matrix (ECM), a dynamic network of proteins, growth factors, and signaling molecules that form a protective sheath around organs and tissues. Changes in ECM composition are mediated in part by matrix metalloproteinases (MMPs) and tissue inhibitors of MMPs (TIMPs). ECM dysregulation leads to outcomes such as fibrotic scarring, hypertrophy, and myocardial infarction. Although fundamental to heart formation and function, the regulation of ECM integration and remodeling during growth is poorly understood. To investigate this, I developed a novel adaptation of fluorescence recovery after photobleaching (FRAP), which, for the first time, allows us to assess ECM protein incorporation during growth in live, intact Drosophila larvae. As such, recovery of fluorescently tagged proteins is a proxy for addition or relocation of ECM protein. We focus on Collagen IV (Viking), a conserved protein and major constituent of the basement membrane (BM). Integration and stabilization of Collagen IV in the BM is poorly understood, however is known to be mediated in part by Collagen modifying proteins secreted protein acidic and rich in cysteine (SPARC) and lysyl oxidase (Lox) are known. We established a time course for Vkg-GFP fluorescence accretion in the heart and body wall muscle throughout larval development, under normal conditions and those in which mmp2 or timp is overexpressed. We also observed the effects reducing the activity of SPARC and Lox Vkg dynamics in the early third instar cardiac ECM. In wildtype, we report a strong phasic pattern of Vkg accumulation at second to third instar ecdysis, potentially to support growth of the succeeding instar. Heart-specific overexpression of mmp2 and timp, the inhibitor of mmp2, perturbs net fluorescence recovery as well as estimated turnover of Vkg-GFP. Our results suggests that MMPs are positive regulators of Vkg/Col IV turnover in the ECM, which is in alignment with other recent studies (Davis et al., 2022; Töpfer et al., 2022). Loss of SPARC and Lox appears to affect estimated Vkg turnover in the cardiac ECM, consistent with a role for these proteins in integrating and stabilizing Collagen IV in the BM. These findings have implications in cardiac conditions and in other ECM-related disorders and diseases such as connective tissue disorders, muscular dystrophy, fibrosis, and cancer. / Thesis / Doctor of Science (PhD)

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.

Solute diffusion is critical to maintenance of cellular function and matrix integrity in articular cartilage. Nutrient deficiency due to transport limitations is thought to be one of the causes of the pathological degeneration of the cartilage tissue. Thus, a study of diffusion within cartilage will lead to a better understanding of the causes of cartilage degeneration. To accurately estimate diffusion coefficients in cartilage and other hydrated medium, we developed a finite-element based method, the Direct Diffusion Simulation Parameter Estimation method (DDSPE), to be used for quantitative determination of solute diffusivities from Fluorescence Recovery After Photobleaching data. Analyses of simulated and experimental FRAP data demonstrated that this method was more accurate than existing analytical methods, including having a low sensitivity to variations in the spot radius. Subsequently, the roles of extracellular matrix (ECM) composition and tissue orientation in solute diffusion within immature bovine cartilage were explored. Diffusivities were measured through the cartilage depth and in two different orientations (radial and transverse). Diffusivities were then correlated with ECM components. Matrix water content was found to be the best predictor of solute diffusion rates in immature cartilage. Although no specific experiments were done to measure the effect of structure, our results suggested that matrix structure did indeed modulate transport. Diffusional anisotropy, defined as the ratio of the diffusivities in both orientations, was observed to be significant in all the immature cartilage zones. As a consequence, the differences in solute diffusion between immature and mature bovine cartilage were investigated. Diffusion rates and diffusional anisotropy decreased in the mature cartilage superficial zone. The decrease in diffusivities observed in mature cartilage suggests that there may be a reduction in nutrient and growth factor supply to the cells. Nevertheless, healthy adult cartilage can still maintain its normal function even with a reduction in solute diffusion rates as nutrient diffusion distances are shorter in mature cartilage. However, any disruption in the mechanical or biological environment could cause an imbalance in tissue homeostasis, which when combined with decreased diffusivities, could trigger matrix degeneration. Thus, decreased diffusivity may be a necessary but not a sufficient prerequisite of matrix degeneration.

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.

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.<div><br></div><div>Development and improvement in optical instrumentation provides potential solutions to the current limitations of characterization methods by conventional instrumentation. Limitations in speed can be addressed through the use of nonlinear optical (NLO) methods, such as second harmonic generation (SHG) and two-photon excited ultraviolet fluorescence (TPE-UVF) microscopy, or by linear methods such as fluorescence recovery after photobleaching (FRAP). For these methods, a high signal-to-noise ratio (SNR) and a nondestructive nature decrease the overall sample size requirements and collections times of these methods. Furthermore, by combination of these optical techniques with other techniques, such as thermal analysis (e.g. differential scanning calorimetry (DSC)), polarization modulation, or patterned illumination, the collection of more complex and higher quality data is possible while retaining the improved speed of these methods. Thus, this modified instrumentation can allow for improved characterization of properties such as stability, structure, and mobility of pharmaceutical and therapeutic products.<br></div><div><br></div><div>With an increase in data quantity and complexity, improvements to existing methods of analysis, as well as development of new data science methods, is essential. Machine learning (ML) architectures and empirically validated models for the analysis of existing data can provide improved quantification. Using the aforementioned optical instrumentation, auto-calibration of data acquired by SHG microscopy is one such method in which quantification of sample crystallinity is enabled by these ML and empirical models. Additionally, ML approaches utilizing generative adversarial networks (GANs) are able to improve on identification of data tampering in order to retain data security. By use of GANs to tamper with experimentally collected and/or simulated data used in existing spectral classifiers, knowledge of adversarial methods and weakness in spectral classification can be ascertained. Likewise, perturbations in physical illumination can be used to ascertain information on classification of real objects by use of GANs. Use of this knowledge can then be used to prevent further data tampering or by improving identification of data tampering.<br></div>

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<br>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.<br>

<p>The overall time and cost for a drug to go from the drug discovery to the consumer market is  significant,  showing  a  need  for  improved  drug  testing  and  discovery  methods.    Work  on nonlinear  optical  methods  for  both  small  active  pharmaceutical  ingredient  drug  formulation analysis and large biological therapeutic stability testing has been shown to improve testing times for formulation, stability and dissolution testing.  Herein, we review the existing and conventional approaches to address stability testing that the pharmaceutical industry uses, and how leveraging nonlinear optical (NLO) methods can improve the current challenges.  The specificity, sensitivity and low limit of detection of second harmonic generation is discussed in application to crystal formation in small-molecule active pharmaceutical ingredients.  The nonlinear optical methods second harmonic generation and two-photon excited ultraviolet fluorescence are directly compared to  ‘gold  standard’  powder  X-ray  diffraction,  which  is  commonly  used  for  measuring  crystal formation and growth of active pharmaceutical ingredients in amorphous solid dispersions.  In addition, the existing FRAP method (with multiple limitations) is improved upon with the ability to  perform  recovered  diffusion  coefficient  data  analysis  in  the  spatial  Fourier  domain.    The collective results discussed in this thesis are just a small subset of the total breadth of investigations marrying the new challenges in the pharmaceutical industry with the new NLO tools tailored to meet them</p>

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.