Phylogeny, Heat-Stress and Enzymatic Heat-Sensitivity in the Antarctic Psychrophile, Chlamydomonas sp. UWO 241

Psychrophilic species, micro-organisms which are unable to grow at temperatures of or above 20°C, are abundant in perennially cold ecosystems across the globe. Intensifying scientific investigation of these organisms from ecological to molecular scales has underscored the ability of life on Earth to adapt to environments which seem inhospitable due to high or low temperatures, high salinity, pressure and light, and ultra-low nutrient availability. Psychrophilic organisms that are also photosynthetic represent a much more limited group than psychrophiles generally, as their habitats must be well buffered against the warming influence of the infra-red energy accompanying sunlight. Photosynthetic psychrophiles face the added challenge of balancing the biophysical capture and biochemical transformation of light energy. The psychrophilic green alga Chlamydomonas sp. UWO 241 (hereafter UWO 241) has been the subject of numerous publications, however these are mainly focused on adaptations which facilitate life at low temperature as opposed to restricting it from moderate ones. In this thesis I critically examine previously published phylogenies placing UWO 241 as a strain of Chlamydomonas raudensis, investigate the changes in mRNA abundance in UWO 241 in response to high steady-state growth temperatures and heat shock using targeted and transcriptome-wide approaches, and investigate the regulatory enzymes of the carbon-fixing Calvin-Benson-Bassham (CBB) cycle for signs of heat sensitivity using the techniques of Homology Modelling and Molecular Dynamics. These investigations revealed that, contrary to previously published reports, UWO 241 is not closely related to C. raudensis SAG 49.72. Here, I also show that mRNA abundance in UWO 241 does not respond to different steady-state growth temperatures or a heat-shock temperature shift regime in ways similar to the related mesophile, Chlamydomonas reinhardtii. Additionally, analysis of the regulatory CBB cycle enzymes of UWO 241 for indications of heat-lability indicated that glyceraldehyde-3-phosphate dehydrogenase may be the heat-limited enzyme in this pathway. These findings deepen our understanding of the reasons that this Antarctic alga is unable to grow at moderate temperatures

Emergent resonances in a thin film tailored by optically-induced small permittivity asymmetries

Resonances are usually associated with finite systems - the vibrations of clamped strings in a guitar or the optical modes in a cavity defined by mirrors. In optics, resonances may be induced in infinite continuous media via periodic modulations of their optical properties. Here we demonstrate that periodic modulations of the permittivity of a featureless thin film can also act as a symmetry breaking mechanism, allowing the excitation of photonic $\textit{quasi}$-bound states in the continuum ($\textit{q}$BICs). By interfering two ultrashort laser pulses in the unbounded film, transient resonances can be tailored through different parameters of the pump beams. We show that the system offers resonances tunable in wavelength and quality-factor, and spectrally selective enhancement of third harmonic generation. Due to a fast decay of the permittivity asymmetry, we observe ultrafast dynamics, enabling time-selective near-field enhancement with picosecond precision. Optically-induced permittivity asymmetries may be exploited in on-demand weak to ultrastrong light-matter interaction regimes and light manipulation at dynamically chosen wavelengths in lithography-free metasurfaces

Retinoic acid is a key regulatory switch determining the difference between lung and thyroid fates in Xenopus laevis

<p>Abstract</p> <p>Background</p> <p>The lung and thyroid are derived from the anterior endoderm. Retinoic acid and Fgf signalling are known to be essential for development of the lung in mouse but little is known on how the lung and thyroid are specified in <it>Xenopus</it>.</p> <p>Results</p> <p>If either retinoic acid or Fgf signalling is inhibited, there is no differentiation of the lung as assayed by expression of <it>sftpb</it>. There is no change in expression of thyroid gland markers when retinoic acid signalling is blocked after gastrulation and when Fgf signalling is inhibited there is a short window of time where <it>pax2 </it>expression is inhibited but expression of other markers is unaffected. If exogenous retinoic acid is given to the embryo between embryonic stages 20 and 26, the presumptive thyroid expresses <it>sftpb </it>and <it>sftpc</it>, specific markers of lung differentiation and expression of key thyroid transcription factors is lost. When the presumptive thyroid is transplanted into the posterior embryo, it also expresses <it>sftpb</it>, although <it>pax2 </it>expression is not blocked.</p> <p>Conclusions</p> <p>After gastrulation, retinoic acid is required for lung but not thyroid differentiation in <it>Xenopus </it>while Fgf signalling is needed for lung but only for early expression of <it>pax2 </it>in the thyroid. Exposure to retinoic acid can cause the presumptive thyroid to switch to a lung developmental program.</p

Comparison of Harmonic Generation from Crystalline and Amorphous Gallium Phosphide Nanofilms

Gallium phosphide (GaP) is a promising material for nanophotonics, given its large refractive index and a transparency over most of the visible spectrum. However, since easy phase-matching is not possible with bulk GaP, a comprehensive study of its nonlinear optical properties for harmonic generation, especially when grown as thin films, is still missing. Here, second harmonic generation is studied from epitaxially grown GaP thin films, demonstrating that the absolute conversion efficiencies are comparable to a bulk wafer over the pump wavelength range from 1060 to 1370 nm. Furthermore, the results are compared to nonlinear simulations, and the second order nonlinear susceptibility is extracted, showing a similar dispersion and magnitude to that of the bulk material. Furthermore, the third order nonlinear susceptibility of amorphous GaP thin films is extracted from third harmonic generation to be more than one order of magnitude larger than that of the crystalline material, and generation of up to the fifth harmonic is reported. The results show the potential of crystalline and amorphous thin films for nonlinear optics with nanoantennas and metasurfaces, particularly in the visible to near infrared part of the spectrum

Imaging Lipid Distributions in Model Monolayers by ToF-SIMS with Selectively Deuterated Components and Principal Components Analysis

Abstract Time of Flight Secondary Ion Mass Spectrometry (ToF-SIMS) provides the capability to image the distribution of molecular ions and their associated fragments that are emitted from monolayer films. ToF-SIMS can be applied to the analysis of monolayers of complex lipid mixtures that act as a model to understand the organization of cell membranes into solid-like domains called lipid rafts. The ability to determine the molecular distribution of lipids using ToF-SIMS in monolayer films is also important in studies of the function of pulmonary surfactant. One of the limitations of the use of ToF-SIMS to studies of complex lipid mixtures found in biological systems, arises from the similarity of the mass fragments that are emitted from the components of the lipid mixture. The use of selectively deuterated components in a mixture overcomes this limitation and results in an unambiguous assignment of specific lipids to particular surface domains. The use of deuterium labeling to identify specific lipids in a multi-component mixture can be done by the deuteration of a single lipid or by the addition of more than one lipid with selectively deuterated components. The incorporation of deuterium into the lipid chains does not alter the miscibility or phase behavior of these systems. The use of deuterium labeling to identify lipids and determine their distribution in monolayer films will be demonstrated using two biological systems. Principal components analysis (PCA) is used to further analyze these deuterated systems checking for the origin of the various mass fragments present