Molecular and cellular effects of ultraviolet light-induced genotoxicity

Exposure to the solar ultraviolet spectrum that penetrates the Earth's stratosphere (UVA and UVB) causes cellular DNA damage within skin cells. This damage is elicited directly through absorption of energy (UVB), and indirectly through intermediates such as sensitizer radicals and reactive oxygen species (UVA). DNA damage is detected as strand breaks or as base lesions, the most common lesions being 8-hydroxydeoxyguanosine (8OHdG) from UVA exposure and cyclobutane pyrimidine dimers from UVB exposure. The presence of these products in the genome may cause misreading and misreplication. Cells are protected by free radical scavengers that remove potentially mutagenic radical intermediates. In addition, the glutathione-S-transferase family can catalyze the removal of epoxides and peroxides. An extensive repair capacity exists for removing (1) strand breaks, (2) small base modifications (8OHdG), and (3) bulky lesions (cyclobutane pyrimidine dimers). UV also stimulates the cell to produce early response genes that activate a cascade of signaling molecules (e.g., protein kinases) and protective enzymes (e.g., haem oxygenase). The cell cycle is restricted via p53-dependent and -independent pathways to facilitate repair processes prior to replication and division. Failure to rescue the cell from replication block will ultimately lead to cell death, and apoptosis may be induced. The implications for UV-induced genotoxicity in disease are considered.

Advanced fibre gratings fabricated in standard and infrared glass fibres by ultraviolet and near-infrared-femtosecond lasers

In this thesis, I describe studies on fabrication, spectral characteristics and applications of tilted fibre gratings (TFGs) with small, large and 45° tilted structures and novel developments in fabrication of fibre Bragg gratings (FBGs) and long period gratings (LPGs) in normal silica and mid-infrared (mid-IR) glass fibres using near-IR femtosecond laser. One of the major contributions presented in this thesis is the systematic investigation of structures, inscription methods and spectral, polarisation dependent loss (PDL) and thermal characteristics of TFGs with small (<45°), large (>45°) and 45° tilted structures. I have experimentally characterised TFGs, obtaining relationships between the radiation angle, central wavelength of the radiation profile, Bragg resonance and the tilt angle, which are consistent with theoretical simulation based on the mode-coupling theory. Furthermore, thermal responses have been measured for these three types of TFGs, showing the transmission spectra of large and 45° TFGs are insensitive to the temperature change, unlike the normal and small angle tilted FBGs. Based on the distinctive optical properties, TFGs have been developed into interrogation system and sensors, which form the other significant contributions of the work presented in this thesis. The 10°-TFG based 800nm WDM interrogation system can function not just as an in-fibre spectrum analyser but also possess refractive index sensing capability. By utilising the unique polarisation properties, the 81 °-TFG based sensors are capable of sensing the transverse loading and twisting with sensitivities of 2.04pW/(kg/m) and 145.90pW/rad, repectively. The final but the most important contribution from the research work presented in this thesis is the development of novel grating inscription techniques using near-IR femtosecond laser. A number of LPGs and FBGs were successfully fabricated in normal silica and mid-IR glass fibres using point-by-point and phase-mask techniques. LPGs and 1st and 2nd order FBGs have been fabricated in these mid-IR glass fibres showing resonances covering the wavelength range from 1200 to 1700nm with the strengths up to 13dB. In addition, the thermal and strain sensitivities of these gratings have been systematically investigated. All the results from these initial but systematic works will provide useful function characteristics information for future fibre grating based devices and applications in mid-IR range.

(Table 1) Salinity, dissolved organic carbon and absorption characteristics of surface river waters around Hudson Bay

Composition and concentration of colored dissolved organic matter (CDOM) have been determined in Hudson Bay and Hudson Strait by excitation emission matrix spectroscopy (EEM) and parallel factor analysis (PARAFAC). Based on 63 surface samples, PARAFAC identified three fluorescent components, which were attributed to two humic- and one protein-like components. One humic-like component was identified as representing terrestrial organic matter and showed a conservative behaviour in Hudson Bay estuaries. The second humic-like component, traditionally identified as peak M, originated both from land and produced in the marine environment. Component 3 had spectra resembling protein-like material and thought to be plankton-derived. The distribution and composition of CDOM were largely controlled by water mass mixing with protein-like component being the least affected. Distinctive fluorescence patterns were also found between Hudson Bay and Hudson Strait, suggesting different sources of CDOM. The optically active fraction of DOC (both absorbing and fluorescing) was very high in the Hudson Bay (up to 89%) suggesting that fluorescence and absorbance can be used as proxies of the DOC concentration.

Investigating the potential magnetic origin of wind variability in OB stars

In this thesis, the origin of large-scale structures in hot star winds, believed to be responsible for the presence of discrete absorption components (DACs) in the absorption troughs of ultraviolet resonance lines, is constrained using both observations and numerical simulations. These structures are understood as arising from bright regions on the stellar surface, although their physical cause remains unknown. First, we use high quality circular spectropolarimetric observations of 13 well-studied OB stars to evaluate the potential role of dipolar magnetic fields in producing DACs. We perform longitudinal field measurements and place limits on the field strength using Bayesian inference, assuming that it is dipolar. No magnetic field was detected within this sample. The derived constraints statistically refute any significant dynamical influence from a magnetic dipole on the wind for all of these stars, ruling out such fields as a cause for DACs. Second, we perform numerical simulations using bright spots constrained by broadband optical photometric observations. We calculate hydrodynamical wind models using three sets of spot sizes and strengths. Co-rotating interaction regions are yielded in each model, and radiative transfer shows that the properties of the variations in the UV resonance lines synthesized from these models are consistent with those found in observed UV spectra, establishing the first consistent link between UV spectroscopic line profile variability and photometric variations and thus supporting the bright spot paradigm (BSP). Finally, we develop and apply a phenomenological model to quantify the measurable effects co-rotating bright spots would have on broadband optical photometry and on the profiles of photopheric lines in optical spectra. This model can be used to evaluate the existence of these spots, and, in the event of their detection, characterize them. Furthermore, a tentative spot evolution model is presented. A preliminary analysis of its output, compared to the observed photometric variations of xi Persei, suggests the possible existence of “active longitudes” on the surface of this star. Future work will expand the range of observational diagnostics that can be interpreted within the BSP, and link phenomenology (bright spots) to physical processes (magnetic spots or non-radial pulsations).

The crowded magnetosphere of the post-common-envelope binary QS Virginis

We present high-speed photometry and high-resolution spectroscopy of the eclipsing post-common-envelope binary QS Virginis (QS Vir). Our Ultraviolet and Visual Echelle Spectrograph (UVES) spectra span multiple orbits over more than a year and reveal the presence of several large prominences passing in front of both the M star and its white dwarf companion, allowing us to triangulate their positions. Despite showing small variations on a time-scale of days, they persist for more than a year and may last decades. One large prominence extends almost three stellar radii from the M star. Roche tomography reveals that the M star is heavily spotted and that these spots are long-lived and in relatively fixed locations, preferentially found on the hemisphere facing the white dwarf. We also determine precise binary and physical parameters for the system. We find that the 14 220 ± 350 K white dwarf is relatively massive, 0.782 ± 0.013 M⊙, and has a radius of 0.010 68 ± 0.000 07 R⊙, consistent with evolutionary models. The tidally distorted M star has a mass of 0.382 ± 0.006 M⊙ and a radius of 0.381 ± 0.003 R⊙, also consistent with evolutionary models. We find that the magnesium absorption line from the white dwarf is broader than expected. This could be due to rotation (implying a spin period of only ˜700 s), or due to a weak (˜100 kG) magnetic field, we favour the latter interpretation. Since the M star's radius is still within its Roche lobe and there is no evidence that it is overinflated, we conclude that QS Vir is most likely a pre-cataclysmic binary just about to become semidetached.

Exploring Habitability Markers, Biosignatures, and Their False Positives Using Spectral Models of Terrestrial Exoplanets

Thesis (Ph.D.)--University of Washington, 2016-08

Pulling Back the Veil: The Characterization and Habitability of Enshrouded Worlds

Thesis (Ph.D.)--University of Washington, 2016-08

Dynamics of coupled modes in two-section semiconductor lasers with saturable absorption

Semiconductor lasers have the potential to address a number of critical applications in advanced telecommunications and signal processing. These include applications that require pulsed output that can be obtained from self-pulsing and mode-locked states of two-section devices with saturable absorption. Many modern applications place stringent performance requirements on the laser source, and a thorough understanding of the physical mechanisms underlying these pulsed modes of operation is therefore highly desirable. In this thesis, we present experimental measurements and numerical simulations of a variety of self-pulsation phenomena in two-section semiconductor lasers with saturable absorption. Our theoretical and numerical results will be based on rate equations for the field intensities and the carrier densities in the two sections of the device, and we establish typical parameter ranges and assess the level of agreement with experiment that can be expected from our models. For each of the physical examples that we consider, our model parameters are consistent with the physical net gain and absorption of the studied devices. Following our introductory chapter, the first system that we consider is a two-section Fabry-Pérot laser. This example serves to introduce our method for obtaining model parameters from the measured material dispersion, and it also allows us to present a detailed discussion of the bifurcation structure that governs the appearance of selfpulsations in two-section devices. In the following two chapters, we present two distinct examples of experimental measurements from dual-mode two-section devices. In each case we have found that single mode self-pulsations evolve into complex coupled dualmode states following a characteristic series of bifurcations. We present optical and mode resolved power spectra as well as a series of characteristic intensity time traces illustrating this progression for each example. Using the results from our study of a twosection Fabry-Pérot device as a guide, we find physically appropriate model parameters that provide qualitative agreement with our experimental results. We highlight the role played by material dispersion and the underlying single mode self-pulsing orbits in determining the observed dynamics, and we use numerical continuation methods to provide a global picture of the governing bifurcation structure. In our concluding chapter we summarise our work, and we discuss how the presented results can inform the development of optimised mode-locked lasers for performance applications in integrated optics.

Analysis and control of transient spectra using time-dependent density functional theory.

215 p.

Processing Bio-Argo nitrate concentration at the DAC Level

The only method used to date to measure dissolved nitrate concentration (NITRATE) with sensors mounted on profiling floats is based on the absorption of light at ultraviolet wavelengths by nitrate ion (Johnson and Coletti, 2002; Johnson et al., 2010; 2013; D’Ortenzio et al., 2012). Nitrate has a modest UV absorption band with a peak near 210 nm, which overlaps with the stronger absorption band of bromide, which has a peak near 200 nm. In addition, there is a much weaker absorption due to dissolved organic matter and light scattering by particles (Ogura and Hanya, 1966). The UV spectrum thus consists of three components, bromide, nitrate and a background due to organics and particles. The background also includes thermal effects on the instrument and slow drift. All of these latter effects (organics, particles, thermal effects and drift) tend to be smooth spectra that combine to form an absorption spectrum that is linear in wavelength over relatively short wavelength spans. If the light absorption spectrum is measured in the wavelength range around 217 to 240 nm (the exact range is a bit of a decision by the operator), then the nitrate concentration can be determined. Two different instruments based on the same optical principles are in use for this purpose. The In Situ Ultraviolet Spectrophotometer (ISUS) built at MBARI or at Satlantic has been mounted inside the pressure hull of a Teledyne/Webb Research APEX and NKE Provor profiling floats and the optics penetrate through the upper end cap into the water. The Satlantic Submersible Ultraviolet Nitrate Analyzer (SUNA) is placed on the outside of APEX, Provor, and Navis profiling floats in its own pressure housing and is connected to the float through an underwater cable that provides power and communications. Power, communications between the float controller and the sensor, and data processing requirements are essentially the same for both ISUS and SUNA. There are several possible algorithms that can be used for the deconvolution of nitrate concentration from the observed UV absorption spectrum (Johnson and Coletti, 2002; Arai et al., 2008; Sakamoto et al., 2009; Zielinski et al., 2011). In addition, the default algorithm that is available in Satlantic sensors is a proprietary approach, but this is not generally used on profiling floats. There are some tradeoffs in every approach. To date almost all nitrate sensors on profiling floats have used the Temperature Compensated Salinity Subtracted (TCSS) algorithm developed by Sakamoto et al. (2009), and this document focuses on that method. It is likely that there will be further algorithm development and it is necessary that the data systems clearly identify the algorithm that is used. It is also desirable that the data system allow for recalculation of prior data sets using new algorithms. To accomplish this, the float must report not just the computed nitrate, but the observed light intensity. Then, the rule to obtain only one NITRATE parameter is, if the spectrum is present then, the NITRATE should be recalculated from the spectrum while the computation of nitrate concentration can also generate useful diagnostics of data quality.

Thermal Treatments of Fe—Mn Alkoxide of Glycerol: Infrared absorption and emission

Synthetic Fe—Mn alkoxide of glycerol samples are submitted to controlled heating conditions and examined by IR absorption spectroscopy. On the other hand, the same sample is studied by infrared emission spectroscopy (IRES), upon heating in situ from 100 to 600°C. The spectral techniques employed in this contribution, especially IRES, show that as a result of the thermal treatments ferromagnetic oxides (manganese ferrite) are formed between 350 and 400°C. Some further spectral changes are seen at higher temperatures.

The Behavior of Hydroxyl Units of Synthetic Goethite and its Dehydroxylated Product Hematite

The behavior of the hydroxyl units of synthetic goethite and its dehydroxylated product hematite was characterized using a combination of Fourier transform infrared (FTIR) spectroscopy and X-ray diffraction (XRD) during the thermal transformation over a temperature range of 180-270 degrees C. Hematite was detected at temperatures above 200 degrees C by XRD while goethite was not observed above 230 degrees C. Five intense OH vibrations at 3212-3194, 1687-1674, 1643-1640, 888-884 and 800-798 cm(-1), and a H2O vibration at 3450-3445 cm(-1) were observed for goethite. The intensity of hydroxyl stretching and bending vibrations decreased with the extent of dehydroxylation of goethite. Infrared absorption bands clearly show the phase transformation between goethite and hematite: in particular. the migration of excess hydroxyl units from goethite to hematite. Two bands at 536-533 and 454-452 cm(-1) are the low wavenumber vibrations of Fe-O in the hematite structure. Band component analysis data of FTIR spectra support the fact that the hydroxyl units mainly affect the a plane in goethite and the equivalent c plane in hematite.

Vibrational spectroscopy of phthalocyanine and naphthalocyanine in sandwich-type (na)phthalocyaninato and porphyrinato rare earth complexes : (Part 10) The infrared and Raman characteristics of phthalocyanine in heteroleptic bis(phthalocyaninato) rare earth complexes with decreased molecular symmetry

The infrared (IR) spectroscopic data for a series of eleven heteroleptic bis(phthalocyaninato) rare earth complexes MIII(Pc)[Pc(α-OC5H11)4] (M = Sm–Lu, Y) [H2Pc = unsubstituted phthalocyanine, H2Pc(α-OC5H11)4 = 1,8,15,22-tetrakis(3-pentyloxy)phthalocyanine] have been collected with 2 cm−1 resolution. Raman spectroscopic properties in the range of 500–1800 cm−1 for these double-decker molecules have also been comparatively studied using laser excitation sources emitting at 632.8 and 785 nm. Both the IR and Raman spectra for M(Pc)[Pc(α-OC5H11)4] are more complicated than those of homoleptic bis(phthalocyaninato) rare earth analogues due to the decreased molecular symmetry of these double-decker compounds, namely C4. For this series, the IR Pc√− marker band appears as an intense absorption at 1309–1317 cm−1, attributed to the pyrrole stretching. With laser excitation at 632.8 nm, Raman vibrations derived from isoindole ring and aza stretchings in the range of 1300–1600 cm−1 are selectively intensified. In contrast, when excited with laser radiation of 785 nm, the ring radial vibrations of isoindole moieties and dihedral plane deformations between 500 and 1000 cm−1 for M(Pc)[Pc(α-OC5H11)4] intensify to become the strongest scatterings. Both techniques reveal that the frequencies of pyrrole stretching, isoindole breathing, isoindole stretchings, aza stretchings and coupling of pyrrole and aza stretchings depend on the rare earth ionic size, shifting to higher energy along with the lanthanide contraction due to the increased ring-ring interaction across the series. The assignments of the vibrational bands for these compounds have been made and discussed in relation to other unsubstituted and substituted bis(phthalocyaninato) rare earth analogues, such as M(Pc)2 and M(OOPc)2 [H2OOPc = 2,3,9,10,16,17,23,24-octakis(octyloxy)phthalocyanine].