The photophysics of pigments is influenced, to an extent depending on its structure, by the properties of the environment. Proteins represent a very specific environment at least in two aspects: i) they are native to most of the pigments in living systems; ii) they facilitate modifications of pigment configuration, leading to changes not only in its spectroscopic properties, but also in its functional abilities. In studies presented in this thesis, femtosecond pump-probe spectroscopy was used to study predominantly the photosynthetic antenna complexes of bacteria and algae. Based on spectroscopic evidence, the structural modifications of pigments imposed by the protein were deduced or hypothesized, together with their functional relevance.

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Storage ring light sources are in use around the world operating as high brightness photon sources from the infrared to the X-ray photon regimes. Whilst modern light source designs achieve horizontal emittances in the few-nm range, they are only diffraction limited in the vertical plane with emittances as low as 10~pm-rad. To achieve fully diffraction limited light sources in the X-ray regime requires a fundamental change in the design of such machines. Many such designs have been proposed based on the multi-bend achromat (MBA) lattice, which have been shown to achieve the required emittance reduction. However MBA lattices typically have a reduced dynamic acceptance, and consequently shorter beam lifetimes. Whilst this can be ameliorated somewhat through the use of top-up injection schemes, many issues still remain. In this thesis we explore one possible alternative to the multi-bend achromat (MBA) paradigm: the stacked storage ring. We propose a storage ring consisting of two synchrotrons joined via a static magnetic vertical transfer line. One of the rings has a reduced emittance through the use of high field damping wigglers, whilst the other is used for standard user experiments. The cumulative emittance of the combined ring structure is a function of the emittances of the two rings. The stacked ring approach allows for a reduction in the beam emittance without a consequent increase in the machine footprint, as in the case of the MBA lattice. Additionally, we may use the more relaxed lattice structures popular in currently operating 3rd generation light sources to maintain a reasonable dynamic acceptance even with the reduced emittance. We apply the stacked storage ring concept to the design of a low emittance 700~MeV compact light source for low energy vacuum ultraviolet photon output. The desirability of such a low energy photon source for UK science has previously been explored in depth. We examine the design of such a light source based around a strong damping stacked storage ring in the presence of Touschek and Intra-Beam scattering whilst analysing the effects on the dynamic properties of the lattice. We also apply the stacked ring concept to two lattices designed to operate in the high energy X-ray region of the photon spectrum and investigate the potential advantages in this regime, including as an adjunct to further improve proposed MBA concepts.

The control of floral induction in the short day plant, Pharbitis nil, is based on a circadian rhythm. At certain times of the circadian (24 h) cycle, a brief light pulse, acting through the photoreceptor, phytochrome, can cause inhibition of induction, whilst at other time points, a brief light pulse promotes a change in phase of the rhythm. The aim of the research presented in this thesis was to investigate the signal transduction pathway linking perception of light by phytochrome to its physiological action on floral induction in Pharbitis nil, and how the circadian oscillator interacts with and influences this pathway. Experimental evidence has implicated calcium in both the regulation of circadian rhythms and in phytochrome action, and more specifically, in the control of floral induction. It was therefore decided to investigate whether the phosphatidylinositol cycle, which, via the key signalling component, l(l,4,5)P3, releases calcium from intracellular stores in animal cells, is involved in the transduction of light signals physiologically active in floral induction. In physiological studies, the calcium channel blocker Verapamil and the calcium chelator EGT A both enhanced the inhibition of floral induction by a sub-maximal light pulse at the ninth hour of an otherwise inductive period. EGT A applied before an inductive dark period significantly reduced the level of flowering, but did not affect flowering if applied at the end of induction. these findings imply that calcium is necessary for induction to take place. In studies investigating the metabolism of I( 1,4,S)P 3 by a soluble extract from Pharbitis nil cotyledons, elevated calcium levels were found to slow the metabolism of l(l,4,5)P3• Lithium, which blocks inositol-1-phosphatase activity in animal cells, causing inositol phosphates to accumulate and blocking the PI cycle, reduced the sensitivity of the response of inhibition to a night break, and caused a decrease in flowering when given before or after an inductive period. These results were interpreted as being a consequence of the characteristic period lengthening effect of lithium. In studies on the metabolism of I( 1,4,5)P 3 by a soluble extract from Pharbitis nil cotyledons, no effect of LiCl was observed, either on the profile of inositol phosphates obtained, or on the rate of metabolism. Therefore it is likely that the effects of lithium on floral induction are not brought about via perturbation of the PI signal transduction cascade. Components of the PI cycle were identified from Pharbitis nil cotyledons (the inductive organs) by radiolabelling with [32P]-orthophosphate and subsequent separation of the aqueous components by HPLC and the lipid components by TLC, and comparison with authentic standards. However, radiolabelling did not permit identification of any light stimulated changes in levels of I( 1,4,5)P 3• This was because of the large variation found in label uptake by the·seedlings. Use of a radio-ligand binding assay specific for I(l ,4,5)P 3, however, permitted identification of an increase in I( 1,4,5)P 3 in response to a 30 s light pulse at the ninth hour of an inductive dark period, which causes inhibition of flowering without affecting the phase of the rhythm. Light did not affect levels of I( 1,4,5)P 3 when given at the third hour of an inductive period, when it has no physiological effect, or at the sixth hour which causes phase shifting of the circadian rhythm. The implications of these findings, that light acting through phytochrome only instigates an increase in I( 1,4,5)P 3 at certain discrete time points of the circadian cycle, are discussed in relationship to the phytochrome multi-gene family, and the multiple modes of phytochrome action, with the implication that there must be other additional signalling systems for transducing light signals perceived by the photoreceptor phytochrome, and that more than one phytochrome species must be active in the control of floral induction.

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Please read the abstract in the section 00front of this document / Dissertation (Master of Architecture)--University of Pretoria, 2005. / Architecture / unrestricted

BACKGROUND: Intraocular scatter is an important factor when considering the performance of the human eye as it can negatively affect visual performances (e.g. glare). However, and in contrast to other optical factors that also affect vision such as high order aberrations, there is currently no efficient method to measure accurately and objectively the amount and the angular distribution of forward light scatter in the eye. Various methods and instruments exist to assess forward light scatter (FLS) but the relation between these methods has rarely been quantified. In addition, FLS measurements obtained with existing instruments cannot be related to any physiological factors due to the absence of a valid model. PURPOSE: To investigate the relations between some of the main methods to measure forward light scatter, and to develop an experimental set -up for the objective measurement of forward light scatter that could be ideally related to physiological parameters. METHODS: After a short review of intraocular light scatter, the three main methods used to assess forward light scattering are compared. In this sense, the C-quant (CQ) straylight meter is compared to the van den Berg (VDB) straylight meter and the Hartmann-Shack spot pattern analysis obtained from the Hartmann-Shack aberrometer. The potential of the new Oculus Pentacam functionalities for providing information on backward light scatter (BLS) are also investigated. Finally, an innovative prototype for objective assessment of intraocular light scattering together with a scatter model of the eye is presented. RESULTS and DISCUSSION: Although no significant relationship was found between the different instruments considered (VDB straylight meter, CQ, Pentacam), our results allowed us to clarify some possible confusion introduced by previously published results and to illustrate the fact that existing commercial instruments such as aberrometers and the Pentacam cannot be used to measure FLS without at least some major modifications (hardware or software). Preliminary results with the prototype built in this study suggest that it could be used for the objective measurement of intraocular light scatter. Relating this measurement to physiological parameters stays however elusive, a fact that widens the future scope of this research.

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Experiments were designed to study the effects of various intensities and durations of light during early development on meristic variation in kokanee and sockeye salmon (Oncorhynchus nerka), pink salmon (O. gorbuscha) and in rainbow trout (Salmo gairdneri). An experiment with sockeye was designed exclusively to test the period of fixation of vertebrae. Among the salmon species rates of hatching and yolk-sac absorption were fastest under the longer light durations and higher intensities. In sockeye and pink an increasing rate of yolk-sac absorption was correlated with increasing amount of light. In trout the rate of yolk-sac absorption showed the opposite results. Mortalities were high under all the experimental conditions. Although meristic variability observed was deemed to be phenotypic yet the affects of selective mortality could not be entirely excluded. Abnormalities in the vertebral column were prevalent in the ‘pre-urostylic' region. The occurrence of abnormal vertebrae was correlated with light only in sockeye. The activities of the pituitary and thyroid glands of trout showed a positive correlation with higher amounts of light. Sockeye scale counts, along the lateral line and on the oblique rows from the origin of dorsal and anal fins to lateral line, were lowest under conditions of higher light and longer durations. Fin ray numbers in all species were the lowest at high light intensities and longer durations. Vertebral counts were lowest at high light intensities and long durations in pink salmon and rainbow trout, but higher in sockeye. At lower light intensities and durations results were variable. Vertebral counts of sockeye increased with increasing light at temperatures of both 8°C and 12°C. Differences among lots at 8°C were significant but those among comparable lots at 12°C were not. The action of light on meristic variability was weak at the higher temperature. It was found in sockeye that vertebral numbers were not fixed before 142 D° and that the period of sensitivity was prolonged (142 D° to 300 D°). / Science, Faculty of / Zoology, Department of / Graduate