Developments in the Theory of X-ray Absorption and Compton Scattering.

Thesis (Ph.D.)--University of Washington, 2016-06

Dynamic and regulated association of caveolin with lipid bodies: Modulation of lipid body motility and function by a dominant negative mutant

Caveolins are a crucial component of caveolae but have also been localized to the Golgi complex, and, under some experimental conditions, to lipid bodies (LBs). The physiological relevance and dynamics of LB association remain unclear. We now show that endogenous caveolin-1 and caveolin-2 redistribute to LBs in lipid loaded A431 and FRT cells. Association with LBs is regulated and reversible; removal of fatty acids causes caveolin to rapidly leave the lipid body. We also show by subcellular fractionation, light and electron microscopy that during the first hours of liver regeneration, caveolins show a dramatic redistribution from the cell surface to the newly formed LBs. At later stages of the regeneration process (when LBs are still abundant), the levels of caveolins in LBs decrease dramatically. As a model system to study association of caveolins with LBs we have used brefeldin A (BFA). BFA causes rapid redistribution of endogenous caveolins to LBs and this association was reversed upon BFA washout. Finally, we have used a dominant negative LB-associated caveolin mutant (cav(DGV)) to study LB formation and to examine its effect on LB function. We now show that the cav(DGV) mutant inhibits microtubule-dependent LB motility and blocks the reversal of lipid accumulation in LBs.

Stationary scattering from a nonlinear network

Transmission through a complex network of nonlinear one-dimensional leads is discussed by extending the stationary scattering theory on quantum graphs to the nonlinear regime. We show that the existence of cycles inside the graph leads to a large number of sharp resonances that dominate scattering. The latter resonances are then shown to be extremely sensitive to the nonlinearity and display multistability and hysteresis. This work provides a framework for the study of light propagation in complex optical networks.

Ultra-long raman laser with a feedback based on the Rayleigh scattering

This paper reports the Rayleigh scattering effects in ultra-long Raman fibre laser. It has been found that in a long fibre cavity (-100 km) the distributed feedback due to Rayleigh back scattering at propagation of light between fibre Bragg grating reflectors may be comparable with the lumped feedback provided by the FBG itself. As a result, Raman lasing in the fibre span limited by lumped (FBG) reflector at one side only appears possible due to significant reflection from the RS-based "random" distributed mirror at the other side. Thus, it concludes that a distributed Rayleigh scattering "random" mirror can form a cavity together with a single FBG spliced to the opposite cavity end.

The investigation of the sensitivity gradient of the visual field, as a function of stimulus dynamic range, in the normal and abnormal eye

The study utilized the advanced technology provided by automated perimeters to investigate the hypothesis that patients with retinitis pigmentosa behave atypically over the dynamic range and to concurrently determine the influence of extraneous factors on the format of the normal perimetric sensitivity profile. The perimetric processing of some patients with retinitis pigmentosa was considered to be abnormal in either the temporal and/or the spatial domain. The standard size III stimulus saturated the central regions and was thus ineffective in detecting early depressions in sensitivity in these areas. When stimulus size was scaled in inverse proportion to the square root of ganglion cell receptive field density (M-scaled), isosensitive profiles did not result, although cortical representation was theoretically equivalent across the visual field. It was conjectured that this was due to variations in the ganglion cell characteristics with increasing peripheral angle, most notably spatial summation. It was concluded that the development of perimetric routines incorporating stimulus sizes adjusted in proportion to the coverage factor of retinal ganglion cells would enhance the diagnostic capacity of perimetry. Good general and local correspondence was found between perimetric sensitivity and the available retinal cell counts. Intraocular light scatter arising both from simulations and media opacities depressed perimetric sensitivity. Attenuation was greater centrally for the smaller LED stimuli, whereas the reverse was true for the larger projected stimuli. Prior perimetric experience and pupil size also demonstrated eccentricity-dependent effect on sensitivity. Practice improved perimetric sensitivity for projected stimuli at eccentricities greater than or equal to 30o; particularly in the superior region. Increase in pupil size for LED stimuli enhanced sensitivity at eccentricities greater than 10o. Conversely, microfluctuation in the accommodative response during perimetric examination and the correction of peripheral refractive error had no significant influence on perimetric sensitivity.

Ultra-long raman laser with a feedback based on the Rayleigh scattering

This paper reports the Rayleigh scattering effects in ultra-long Raman fibre laser. It has been found that in a long fibre cavity (-100 km) the distributed feedback due to Rayleigh back scattering at propagation of light between fibre Bragg grating reflectors may be comparable with the lumped feedback provided by the FBG itself. As a result, Raman lasing in the fibre span limited by lumped (FBG) reflector at one side only appears possible due to significant reflection from the RS-based "random" distributed mirror at the other side. Thus, it concludes that a distributed Rayleigh scattering "random" mirror can form a cavity together with a single FBG spliced to the opposite cavity end.

The pupillary light reflex in migraine

The literature suggests that there may be pupil size and response abnormalities in migraine headache sufferers. We used an infra-red pupillometer to measure dynamic pupil responses to light in 20 migraine sufferers (during non-headache periods) and 16 non-migraine age and gender matched controls. There was a significant increase in the absolute inter-ocular difference of the latency of the pupil light response in the migraine group compared with the controls (0.062 s vs 0.025 s, p = 0.014). There was also a significant correlation between anisocoria and lateralisation of headache such that migraine sufferers with a habitual head pain side have more anisocoria (r= 0.59, p < 0.01), but this was not related to headache laterally. The pupil changes were not correlated with the interval since the last migraine headache, the severity of migraine headache or the number of migraine headaches per annum. We conclude that subtle sympathetic and parasympathetic pupil abnormalities persist in the inter-ictal phase of migraine. © 2005 The College of Optometrists.

Dynamic strain sensor using a vcsel and a polymer fiber bragg grating in a multimode fiber

We have implemented a dynamic strain sensor using a Polymer Optical Fiber Bragg Grating (POFBG). In this paper, we have investigated an approach for making such systems cheaper through the use of easy to handle multimode fiber. A Vertical-Cavity Surface-Emitting Laser is used to decrease the cost of the interrogation system and a photodetector converts the reflected light into an electrical signal.

Abaxial Anthocyanin Layer in Leaves of Tropical Rain Forest Plants: Enhancer of Light Capture in Deep Shade

The permanent pigmentation of the leaves of tropical rain forest herbs with anthocyanin has traditionally been viewed as a mechanism for enhancing transpiration by increased heat absorption. We report measurements to ?+0.1?0C on four Indo-mal- esian forest species polymorphic with respect to color. There were no detectable differences in temperature between cyanic and green leaves. In deeply shaded habitats, any temperature difference would arise from black-body infrared radiation which all leaves absorb and to which anthocyanins are transparent. Reflectance spectra of the lower leaf surfaces of these species re- vealed increased reflectance around 650-750 nm for cyanic leaves compared with green leaves of the same species. In all spe- cies anthocyanin was located in a single layer of cells immediately below the photosynthetic tissue. These observations provide empirical evidence that the cyanic layer can improve photosynthetic energy capture by back-scattering additional light through the photosynthetic tissue.

Modelagem dos efeitos da irradiação luminosa no cérebro de camundongos e rastreamento de neurônios durante experimentos de microscopia de fluorescência

The fluorescent proteins are an essential tool in many fields of biology, since they allow us to watch the development of structures and dynamic processes of cells in living tissue, with the aid of fluorescence microscopy. Optogenectics is another technique that is currently widely used in Neuroscience. In general, this technique allows to activate/deactivate neurons with the radiation of certain wavelengths on the cells that have ion channels sensitive to light, at the same time that can be used with fluorescent proteins. This dissertation has two main objectives. Initially, we study the interaction of light radiation and mice brain tissue to be applied in optogenetic experiments. In this step, we model absorption and scattering effects using mice brain tissue characteristics and Kubelka-Munk theory, for specific wavelengths, as a function of light penetration depth (distance) within the tissue. Furthermore, we model temperature variations using the finite element method to solve Pennes’ bioheat equation, with the aid of COMSOL Multiphysics Modeling Software 4.4, where we simulate protocols of light stimulation tipically used in optogenetics. Subsequently, we develop some computational algorithms to reduce the exposure of neuron cells to the light radiation necessary for the visualization of their emitted fluorescence. At this stage, we describe the image processing techniques developed to be used in fluorescence microscopy to reduce the exposure of the brain samples to continuous light, which is responsible for fluorochrome excitation. The developed techniques are able to track, in real time, a region of interest (ROI) and replace the fluorescence emitted by the cells by a virtual mask, as a result of the overlay of the tracked ROI and the fluorescence information previously stored, preserving cell location, independently of the time exposure to fluorescent light. In summary, this dissertation intends to investigate and describe the effects of light radiation in brain tissue, within the context of Optogenetics, in addition to providing a computational tool to be used in fluorescence microscopy experiments to reduce image bleaching and photodamage due to the intense exposure of fluorescent cells to light radiation.

Dynamic control of laser driven proton beams by exploiting self-generated, ultrashort electromagnetic pulses

As part of the ultrafast charge dynamics initiated by high intensity laser irradiations of solid targets,high amplitude EM pulses propagate away from the interaction point and are transported along anystalks and wires attached to the target. The propagation of these high amplitude pulses along a thinwire connected to a laser irradiated target was diagnosed via the proton radiography technique,measuring a pulse duration of 20 ps and a pulse velocity close to the speed of light. The strongelectric field associated with the EM pulse can be exploited for controlling dynamically the protonbeams produced from a laser-driven source. Chromatic divergence control of broadband laser drivenprotons (upto 75% reduction in divergence of >5 MeV protons) was obtained by winding the supportingwire around the proton beam axis to create a helical coil structure. In addition to providingfocussing and energy selection, the technique has the potential to post-accelerate the transiting protonsby the longitudinal component of the curved electric field lines produced by the helical coil lens.

Neutron Scattering Studies on Complex Magnetic Structures in Magnetoelectric Materials

In this thesis, the magnetic properties of four transition-metal oxides are presented. Their multiferroic and magnetoelectric phases have been investigated by means of different neutron scattering techniques. The materials TbMnO3 and MnWO4 belong to the group of spin-induced multiferroics. Their ferroelectric polarization can be explained by the inverse DzyaloshinskiiMoriya interaction. Another common feature of both materials is the presence of subsequent magnetic transitions from a spin-density wave to a spin spiral. The features of the phase transitions have been studied in both materials and it could be shown that diffuse magnetic scattering from the spin spiral is present even in the ordered spin-density wave phase. The excitation spectrum in the multiferroic phase of TbMnO3 was investigated in detail and a comprehensive dataset was obtained using time-of-flight spectroscopy. A spin-wave model could be obtained which can quantitatively describe the full dispersion. Furthermore, the polarization of the zone-center excitations could be derived which fit well to data from inelastic neutron spectroscopy and infrared spectroscopy. With the combination of spherical neutron polarimetry and a poling of the sample by an electric field, it was possible to observe the chiral magnetic component of the magnetic excitations in TbMnO3 and MnWO4. The spin-wave model for TbMnO3 obtained in this thesis is able to correctly describe the dispersion of this component. The double tungstate NaFe(WO4)2 is isostructural to the multiferroic MnWO4 and develops a complex magnetic phase diagram. By the use of neutron diffraction techniques, the zero-field structure and high-field structures in magnetic field applied along the b-axis could be determined. The data reveal a direct transition into an incommensurate spin-spiral structure. The value of the incommensurability is driven by anharmonic modulations and shows strong hysteresis effects. The static and dynamic properties in the magnetoelectric spin-glass phase of Ni0.42Mn0.58TiO3 were studied in detail. The spin-glass phase is composed of short-ranged MnTiO3 and NiTiO3-type order. The antiferromagnetic domains could be controlled by crossed magnetic and electric fields, which was visualized using spherical neutron polarimetry. A comprehensive dataset of the magnetic excitations in the spin-glass phase was collected. The dataset revealed correlations in the hexagonal plane which are only weakly coupled along the c-axis. The excitation spectra could be simulated by taking into account the MnTiO3-type order.

Dynamic Coculture of a Prevascularized Engineered Bone Construct

The generation of functional, vascularized tissues is a key challenge for the field of tissue engineering. Before clinical implantations of tissue engineered bone constructs can succeed, in vitro fabrication needs to address limitations in large-scale tissue development, including controlled osteogenesis and an inadequate vasculature network to prevent necrosis of large constructs. The tubular perfusion system (TPS) bioreactor is an effective culturing method to augment osteogenic differentiation and maintain viability of human mesenchymal stem cell (hMSC)-seeded scaffolds while they are developed in vitro. To further enhance this process, we developed a novel osteogenic growth factors delivery system for dynamically cultured hMSCs using microparticles encapsulated in three-dimensional alginate scaffolds. In light of this increased differentiation, we characterized the endogenous cytokine distribution throughout the TPS bioreactor. An advantageous effect in the ‘outlet’ portion of the uniaxial growth chamber was discovered due to the system’s downstream circulation and the unique modular aspect of the scaffolds. This unique trait allowed us to carefully tune the differentiation behavior of specific cell populations. We applied the knowledge gained from the growth profile of the TPS bioreactor to culture a high-volume bone composite in a 3D-printed femur mold. This resulted in a tissue engineered bone construct with a volume of 200cm3, a 20-fold increase over previously reported sizes. We demonstrated high viability of the cultured cells throughout the culture period as well as early signs of osteogenic differentiation. Taking one step closer toward a viable implant and minimize tissue necrosis after implantation, we designed a composite construct by coculturing endothelial cells (ECs) and differentiating hMSCs, encouraging prevascularization and anastomosis of the graft with the host vasculature. We discovered the necessity of cell to cell proximity between the two cell types as well as preference for the natural cell binding capabilities of hydrogels like collagen. Notably, the results suggested increased osteogenic and angiogenic potential of the encapsulated cells when dynamically cultured in the TPS bioreactor, suggesting a synergistic effect between coculture and applied shear stress. This work highlights the feasibility of fabricating a high-volume, prevascularized tissue engineered bone construct for the regeneration of a critical size defect.