Phototaxis away from blue light by an Escherichia coli mutant accumulating protoporphyrin IX.

The hemH gene of Escherichia coli encodes ferrochelatase (EC 4.99.1.1), the enzyme that catalyzes the last step in the production of heme, namely the synthesis of heme from protoporphyrin IX plus Fe2+. The behavioral responses to light were studied in E. coli carrying a hemH mutation. It was shown that the hemH mutant displayed a tumbling response upon illumination and a running response upon removal of the light. The most effect light to induce a tumbling response in the hemH mutant was blue light (396-450 nm). The chemotaxis machinery was needed for the light-induced tumbling response in the hemH mutant. The bacterial defect is an analog of the human inherited disease erythropoietic protoporphyria.

Two routes of chlorophyllide synthesis that are differentially regulated by light in barley (Hordeum vulgare L.).

NADPH-protochlorophyllide oxidoreductase (POR; EC 1.6.99.1) catalyzes the only known light-dependent step in chlorophyll synthesis of higher plants, the reduction of protochlorophyllide (Pchlide) to chlorophyllide. In barley, two distinct immunoreactive POR proteins were identified. In contrast to the light-sensitive POR enzyme studied thus far (POR-A), levels of the second POR protein remained constant in seedlings during the transition from dark growth to the light and in green plants. The existence of a second POR-related protein was verified by isolating and sequencing cDNAs that encode a second POR polypeptide (POR-B) with an amino acid sequence identity of 75% to the POR-A. In the presence of NADPH and Pchlide, the in vitro-synthesized POR-A and POR-B proteins could be reconstituted to ternary enzymatically active complexes that reduced Pchlide to chlorophyllide only after illumination. Even though the in vitro activities of the two enzymes were similar, the expression of their genes during the light-induced transformation of etiolated to green seedlings was distinct. While the POR-A mRNA rapidly declined during illumination of dark-grown seedlings and soon disappeared, POR-B mRNA remained at an approximately constant level in dark-grown and green seedlings. Thus these results suggest that chlorophyll synthesis is controlled by two light-dependent POR enzymes, one that is active only transiently in etiolated seedlings at the beginning of illumination and the other that also operates in green plants.

Spin boson models for quantum decoherence of electronic excitations of biomolecules and quantum dots in a solvent

We give a theoretical treatment of the interaction of electronic excitations (excitions) in biomolecules and quantum dots with the surrounding polar solvent. Significant quantum decoherence occurs due to the interaction of the electric dipole moment of the solute with the fluctuating electric dipole moments of the individual molecules in the solvent. We introduce spin boson models which could be used to describe the effects. of decoherence on the quantum dynamics of biomolecules which undergo light-induced conformational change and on biomolecules or quantum dots which are coupled by Forster resonant energy transfer.

Oxygen, pH and calcium dynamics and fluxes at the thallus surface under ambient (8.1) and low (7.8) seawater pH and across a range of irradiances

Presently, an incomplete mechanistic understanding of tropical reef macroalgae photosynthesis and calcification restricts predictions of how these important autotrophs will respond to global change. Therefore, we investigated the mechanistic link between inorganic carbon uptake pathways, photosynthesis and calcification in a tropical crustose coralline alga (CCA) using microsensors. We measured pH, oxygen (O2), and calcium (Ca2+) dynamics and fluxes at the thallus surface under ambient (8.1) and low (7.8) seawater pH (pHSW) and across a range of irradiances. Acetazolamide (AZ) was used to inhibit extracellular carbonic anhydrase (CAext), which mediates hydrolysis of HCO3-, and 4,4' diisothiocyanatostilbene-2,2'-disulphonate (DIDS) that blocks direct HCO3- uptake by anion exchange transport. Both inhibited photosynthesis, suggesting both diffusive uptake of CO2 via HCO3- hydrolysis to CO2 and direct HCO3- ion transport are important in this CCA. Surface pH was raised approximately 0.3 units at saturating irradiance, but less when CAext was inhibited. Surface pH was lower at pHSW 7.8 than pHSW 8.1 in the dark, but not in the light. The Ca2+ fluxes were large, complex and temporally variable, but revealed net Ca2+ uptake under all conditions. The temporal variability in Ca2+ dynamics was potentially related to localized dissolution during epithallial cell sloughing, a strategy of CCA to remove epiphytes. Simultaneous Ca2+ and pH dynamics suggest the presence of Ca2+/H+ exchange. Rapid light-induced H+ surface dynamics that continued after inhibition of photosynthesis revealed the presence of a light-mediated, but photosynthesis-independent, proton pump. Thus, the study indicates metabolic control of surface pH can occur in CCA through photosynthesis and light-inducible H+ pumps. Our results suggest that complex light-induced ion pumps play an important role in biological processes related to inorganic carbon uptake and calcification in CCA.

Nonlinear Optics and Carrier Dynamics in Nanostructured and Two-Dimensional Materials

Understanding and measuring the interaction of light with sub-wavelength structures and atomically thin materials is of critical importance for the development of next generation photonic devices.  One approach to achieve the desired optical properties in a material is to manipulate its mesoscopic structure or its composition in order to affect the properties of the light-matter interaction.  There has been tremendous recent interest in so called two-dimensional materials, consisting of only a single to a few layers of atoms arranged in a planar sheet.  These materials have demonstrated great promise as a platform for studying unique phenomena arising from the low-dimensionality of the material and for developing new types of devices based on these effects.  A thorough investigation of the optical and electronic properties of these new materials is essential to realizing their potential.  In this work we present studies that explore the nonlinear optical properties and carrier dynamics in nanoporous silicon waveguides, two-dimensional graphite (graphene), and atomically thin black phosphorus. We first present an investigation of the nonlinear response of nanoporous silicon optical waveguides using a novel pump-probe method. A two-frequency heterodyne technique is developed in order to measure the pump-induced transient change in phase and intensity in a single measurement. The experimental data reveal a characteristic material response time and temporally resolved intensity and phase behavior matching a physical model dominated by free-carrier effects that are significantly stronger and faster than those observed in traditional silicon-based waveguides.  These results shed light on the large optical nonlinearity observed in nanoporous silicon and demonstrate a new measurement technique for heterodyne pump-probe spectroscopy. Next we explore the optical properties of low-doped graphene in the terahertz spectral regime, where both intraband and interband effects play a significant role. Probing the graphene at intermediate photon energies enables the investigation of the nonlinear optical properties in the graphene as its electron system is heated by the intense pump pulse. By simultaneously measuring the reflected and transmitted terahertz light, a precise determination of the pump-induced change in absorption can be made. We observe that as the intensity of the terahertz radiation is increased, the optical properties of the graphene change from interband, semiconductor-like absorption, to a more metallic behavior with increased intraband processes. This transition reveals itself in our measurements as an increase in the terahertz transmission through the graphene at low fluence, followed by a decrease in transmission and the onset of a large, photo-induced reflection as fluence is increased.  A hybrid optical-thermodynamic model successfully describes our observations and predicts this transition will persist across mid- and far-infrared frequencies.  This study further demonstrates the important role that reflection plays since the absorption saturation intensity (an important figure of merit for graphene-based saturable absorbers) can be underestimated if only the transmitted light is considered. These findings are expected to contribute to the development of new optoelectronic devices designed to operate in the mid- and far-infrared frequency range.  Lastly we discuss recent work with black phosphorus, a two-dimensional material that has recently attracted interest due to its high mobility and direct, configurable band gap (300 meV to 2eV), depending on the number of atomic layers comprising the sample. In this work we examine the pump-induced change in optical transmission of mechanically exfoliated black phosphorus flakes using a two-color optical pump-probe measurement. The time-resolved data reveal a fast pump-induced transparency accompanied by a slower absorption that we attribute to Pauli blocking and free-carrier absorption, respectively. Polarization studies show that these effects are also highly anisotropic - underscoring the importance of crystal orientation in the design of optical devices based on this material. We conclude our discussion of black phosphorus with a study that employs this material as the active element in a photoconductive detector capable of gigahertz class detection at room temperature for mid-infrared frequencies.

Efficient photo-induced dielectrophoretic particle trapping on Fe:LiNbO3 for arbitrary two dimensional patterning

1D and 2D patterning of uncharged micro- and nanoparticles via dielectrophoretic forces on photovoltaic z-cut Fe:LiNbO3 have been investigated for the first time. The technique has been successfully applied with dielectric micro-particles of CaCO3 (diameter d = 1-3 ?m) and metal nanoparticles of Al (d = 70 nm). At difference with previous experiments in x- and y-cut, the obtained patterns locally reproduce the light distribution with high fidelity. A simple model is provided to analyse the trapping process. The results show the remarkably good capabilities of this geometry for high quality 2D light-induced dielectrophoretic patterning overcoming the important limitations presented by previous configurations.

In vivo and in vitro models demonstrate a role for caveolin-1 in the pathogenesis of ischaemic acute renal failure

Caveolae and their proteins, the caveolins, transport macromolecules; compartmentalize signalling molecules; and are involved in various repair processes. There is little information regarding their role in the pathogenesis of significant renal syndromes such as acute renal failure (ARF). In this study, an in vivo rat model of 30 min bilateral renal ischaemia followed by reperfusion times from 4 h to 1 week was used to map the temporal and spatial association between caveolin-1 and tubular epithelial damage (desquamation, apoptosis, necrosis). An in vitro model of ischaemic ARF was also studied, where cultured renal tubular epithelial cells or arterial endothelial cells were subjected to injury initiators modelled on ischaemia-reperfusion (hypoxia, serum deprivation, free radical damage or hypoxia-hyperoxia). Expression of caveolin proteins was investigated using immunohistochemistry, immunoelectron microscopy, and immunoblots of whole cell, membrane or cytosol protein extracts. In vivo, healthy kidney had abundant caveolin-1 in vascular endothelial cells and also some expression in membrane surfaces of distal tubular epithelium. In the kidneys of ARF animals, punctate cytoplasmic localization of caveolin-1 was identified, with high intensity expression in injured proximal tubules that were losing basement membrane adhesion or were apoptotic, 24 h to 4 days after ischaemia-reperfusion. Western immunoblots indicated a marked increase in caveolin-1 expression in the cortex where some proximal tubular injury was located. In vitro, the main treatment-induced change in both cell types was translocation of caveolin-1 from the original plasma membrane site into membrane-associated sites in the cytoplasm. Overall, expression levels did not alter for whole cell extracts and the protein remained membrane-bound, as indicated by cell fractionation analyses. Caveolin-1 was also found to localize intensely within apoptotic cells. The results are indicative of a role for caveolin-1 in ARF-induced renal injury. Whether it functions for cell repair or death remains to be elucidated.

Accurately defining the reference condition for summary biotic metrics: A comparison of four approaches

Protocols for bioassessment often relate changes in summary metrics that describe aspects of biotic assemblage structure and function to environmental stress. Biotic assessment using multimetric indices now forms the basis for setting regulatory standards for stream quality and a range of other goals related to water resource management in the USA and elsewhere. Biotic metrics are typically interpreted with reference to the expected natural state to evaluate whether a site is degraded. It is critical that natural variation in biotic metrics along environmental gradients is adequately accounted for, in order to quantify human disturbance-induced change. A common approach used in the IBI is to examine scatter plots of variation in a given metric along a single stream size surrogate and a fit a line (drawn by eye) to form the upper bound, and hence define the maximum likely value of a given metric in a site of a given environmental characteristic (termed the 'maximum species richness line' - MSRL). In this paper we examine whether the use of a single environmental descriptor and the MSRL is appropriate for defining the reference condition for a biotic metric (fish species richness) and for detecting human disturbance gradients in rivers of south-eastern Queensland, Australia. We compare the accuracy and precision of the MSRL approach based on single environmental predictors, with three regression-based prediction methods (Simple Linear Regression, Generalised Linear Modelling and Regression Tree modelling) that use (either singly or in combination) a set of landscape and local scale environmental variables as predictors of species richness. We compared the frequency of classification errors from each method against set biocriteria and contrast the ability of each method to accurately reflect human disturbance gradients at a large set of test sites. The results of this study suggest that the MSRL based upon variation in a single environmental descriptor could not accurately predict species richness at minimally disturbed sites when compared with SLR's based on equivalent environmental variables. Regression-based modelling incorporating multiple environmental variables as predictors more accurately explained natural variation in species richness than did simple models using single environmental predictors. Prediction error arising from the MSRL was substantially higher than for the regression methods and led to an increased frequency of Type I errors (incorrectly classing a site as disturbed). We suggest that problems with the MSRL arise from the inherent scoring procedure used and that it is limited to predicting variation in the dependent variable along a single environmental gradient.

Effect of pupil dilation and constriction on the distribution of bit errors within the iris

Texture information in the iris image is not uniform in discriminatory information content for biometric identity verification. The bits in an iris code obtained from the image differ in their consistency from one sample to another for the same identity. In this work, errors in bit strings are systematically analysed in order to investigate the effect of light-induced and drug-induced pupil dilation and constriction on the consistency of iris texture information. The statistics of bit errors are computed for client and impostor distributions as functions of radius and angle. Under normal conditions, a V-shaped radial trend of decreasing bit errors towards the central region of the iris is obtained for client matching, and it is observed that the distribution of errors as a function of angle is uniform. When iris images are affected by pupil dilation or constriction the radial distribution of bit errors is altered. A decreasing trend from the pupil outwards is observed for constriction, whereas a more uniform trend is observed for dilation. The main increase in bit errors occurs closer to the pupil in both cases.

Dynamic, invivo, real-time detection of retinal oxidative status in a model of elevated intraocular pressure using a novel, reversibly responsive, profluorescent nitroxide probe

Changes to the redox status of biological systems have been implicated in the pathogenesis of a wide variety of disorders including cancer, Ischemia-reperfusion (I/R) injury and neurodegeneration. In times of metabolic stress e.g. ischaemia/reperfusion, reactive oxygen species (ROS) production overwhelms the intrinsic antioxidant capacity of the cell, damaging vital cellular components. The ability to quantify ROS changes in vivo, is therefore essential to understanding their biological role. Here we evaluate the suitability of a novel reversible profluorescent probe containing a redox-sensitive nitroxide moiety (methyl ester tetraethylrhodamine nitroxide, ME-TRN), as an in vivo, real-time reporter of retinal oxidative status. The reversible nature of the probe's response offers the unique advantage of being able to monitor redox changes in both oxidizing and reducing directions in real time. After intravitreal administration of the ME-TRN probe, we induced ROS production in rat retina using an established model of complete, acute retinal ischaemia followed by reperfusion. After restoration of blood flow, retinas were imaged using a Micron III rodent fundus fluorescence imaging system, to quantify the redox-response of the probe. Fluorescent intensity declined during the first 60 min of reperfusion. The ROS-induced change in probe fluorescence was ameliorated with the retinal antioxidant, lutein. Fluorescence intensity in non-Ischemia eyes did not change significantly. This new probe and imaging technology provide a reversible and real-time response to oxidative changes and may allow the in vivo testing of antioxidant therapies of potential benefit to a range of diseases linked to oxidative stress

Variations in the levels of aminoacylation and modified nucleotide content between total tRNAs from chloroplasts and etioplasts in cucumber cotyledons

Total tRNAs isolated from chloroplasts and etioplasts of cucumber cotyledons were compared with respect toamino acid acceptance, isoacceptor distribution and extent of modification. Aminoacylation of the tRNAs with nine different amino acids studied indicated that the relative acceptor activities of chloroplast total tRNAs for four amino acids are significantly higher than etioplast total tRNAs. Two dimensional polyacrylamide gel electrophoresis(2D-PAGE) of chloroplast total tRNAs separated at least 32 spots, while approximately 41 spots were resolved from etioplast total tRNAs. Comparison of the reversed-phase chromatography (RPC-5) profiles of chloroplast and etioplast leucyl-, lysyl-, phenylalanyl-, and valyl-tRNA species showed no qualitative differences in the elution profiles. However, leucyl-, lysyl- and valyl-tRNA species showed quantitative differences in the relative amounts of the isoaccepting species present in chloroplasts and etioplasts. The analysis of modified nucleotides of total tRNAs from the two plastid types indicated that total tRNA from etioplasts was undermodified with respect to ribothymidine, isopentenyladenosine/hydroxy-isopentenyladenosine, 1 -methylguanosine and 2-o-methylguanosine. This indicates that illumination may cause de novo synthesis of chloroplast tRNAmodifying enzymes encoded for by nuclear genes leading to the formation of highly modified tRNAs in chloroplasts. Based on these results, we speculate that the observed decrease in levels of aminoacylation, variations in the relative amounts of certain isoacceptors, and differences in the electrophoretic mobilities of some extra tRNA spots in the etioplast total tRNAs as compared to chloroplast total tRNAs could be due to some partially undermodified etioplast tRNAs. Taken together, the data suggested that the light-induced transformation of etioplasts into chloroplasts is accompanied by increases in the relative levels of some functional chloroplast tRNAs by post transcriptional nucleotide modifications.

Assembly of sol-gel-grown $Li _{(x)} CoO_{2}$ nanocrystals through electromagnetic irradiation

We report the fabrication of assembled nanostructures from the pre-synthesized nanocrystals building blocks through optical means of exciton formation and dissociation. We demonstrate that Li (x) CoO2 nanocrystals assemble to an acicular architecture, upon prolonged exposure to ultraviolet-visible radiation emitted from a 125 W mercury vapor lamp, through intermediate excitation of excitons. The results obtained in the present study clearly show how nanocrystals of various materials with band gaps appropriate for excitations of excitons at given optical wavelengths can be assembled to unusual nanoarchitectures through illumination with incoherent light sources. The disappearance of exciton bands due to Li (x) CoO2 phase in the optical spectrum of the irradiated film comprising acicular structure is consistent with the proposed mechanism of exciton dissociation in the observed light-induced assembly process. The assembly process occurs through attractive Coulomb interactions between charged dots created upon exciton dissociation. Our work presents a new type of nanocrystal assembly process that is driven by light and exciton directed.

Photoinduced DNA and Protein Cleavage Activity of Ferrocene-Appended L-Methionine Reduced Schiff Base Copper(II) Complexes of Phenanthroline Bases

Ferrocene-appended ternary copper(H) complexes of phenanthroline bases having CuN3OS coordination with an axial Cu-S bond derived from L-methionine reduced Schiff base shows red light induced oxidative DNA cleavage activity following a hydroxyl radical pathway. The dipyridophenazine complex, in addition, displays photoinduced oxidative cleavage of bovine serum albumin protein in UV-A light.

External signal-activated liposomal drug delivery systems

Modern drug discovery gives rise to a great number of potential new therapeutic agents, but in some cases the efficient treatment of patient may not be achieved because the delivery of active compounds to the target site is insufficient. Thus, drug delivery is one of the major challenges in current pharmaceutical research. Numerous nanoparticle-based drug carriers, e.g. liposomes, have been developed for enhanced drug delivery and targeting. Drug targeting may enhance the efficiency of the treatment and, importantly, reduce unwanted side effects by decreasing drug distribution to non-target tissues. Liposomes are biocompatible lipid-based carriers that have been studied for drug delivery during the last 40 years. They can be functionalized with targeting ligands and sensing materials for triggered activation. In this study, various external signal-assisted liposomal delivery systems were developed. Signals can be used to modulate drug permeation or release from the liposome formulation, and they provide accurate control of time, place and rate of activation. The study involved three types of signals that were used to trigger drug permeation and release: electricity, heat and light. Electrical stimulus was utilized to enhance the permeation of liposomal DNA across the skin. Liposome/DNA complex-mediated transfections were performed in tight rat epidermal cell model. Various transfection media and current intensities were tested, and transfection efficiency was evaluated non-invasively by monitoring the concentration of secreted reporter protein in cell culture medium. Liposome/DNA complexes produced gene expression, but electrical stimulus did not enhance the transfection efficiency significantly. Heat-sensitive liposomal drug delivery system was developed by coating liposomes with biodegradable and thermosensitive poly(N-(2-hydroxypropyl) methacrylamide-mono/dilactate polymer. Temperature-triggered liposome aggregation and contents release from liposomes were evaluated. The cloud point temperature (CP) of the polymer was set to 42 °C. Polymer-coated liposome aggregation and contents release were observed above CP of the polymer, while non-coated liposomes remained intact. Polymer precipitates above its CP and interacts with liposomal bilayers. It is likely that this induces permeabilization of the liposomal membrane and contents release. Light-sensitivity was introduced to liposomes by incorporation of small (< 5 nm) gold nanoparticles. Hydrophobic and hydrophilic gold nanoparticles were embedded in thermosensitive liposomes, and contents release was investigated upon UV light exposure. UV light-induced lipid phase transitions were examined with small angle X-ray scattering, and light-triggered contents release was shown also in human retinal pigment epithelial cell line. Gold nanoparticles absorb light energy and transfer it into heat, which induces phase transitions in liposomes and triggers the contents release. In conclusion, external signal-activated liposomes offer an advanced platform for numerous applications in drug delivery, particularly in the localized drug delivery. Drug release may be localized to the target site with triggering stimulus that results in better therapeutic response and less adverse effects. Triggering signal and mechanism of activation can be selected according to a specific application.

Non-finite constructions in Old English : with special reference to syntactic borrowing from Latin

My dissertation is a corpus-based study of non-finite constructions in Old English (OE). It revisits the question of Latin influence on the OE syntax, offering a new evaluation of syntactic interference between Latin and OE, and, more generally, of the contact situation in the OE period, drawing on methods used in studying grammaticalization and language contact. I address three non-finite constructions: absolute participial construction, accusative-and-infinitive construction, and nominative-and-infinitive construction, exemplified respectively in present-day English as - She looked like a pixie sometimes, her eyes darting here and there, forever watchful (BNC CCM 98); - My first acquaintance with her was when I heard her sing (BNC CFY 2215); - Charles the Bald was said to resemble his grandfather physically (BNC HPT 175). This study compares data from translated texts against the background of original OE writings, establishing dependencies and differences between the two. Although the contrastive analysis of source and target texts is one of the major methods employed in the study, translation and translation strategies as such are only my secondary foci. The emphasis is rather on what source/target comparison can tell us about the OE non-finite syntax and the typological differences between Latin and OE in this domain, and on whether contact-induced change can originate in translation. In terms of theoretical framework, I have adopted functional-typological approach, which rests on the principles of iconicity and event integration, and to the best of my knowledge, has not been applied systematically to OE non-finite constructions. Therefore one more aim of the dissertation is to test this framework and to see how OE fits into the cross-linguistic picture of non-finites. My research corpus consists of two samples: 1) written OE closely dependent on the Latin originals, based on editions of two gloss texts, five translations, and Latin originals of these texts, representing four text types: hymns, religious regulations, homily/life narrative, and biblical narrative (180,622 words); and 2) written OE as far independent from Latin as possible, based on a selection from the York-Toronto-Helsinki Parsed Corpus of Old English Prose (YCOE) and representing five text types: laws, charters, correspondence, chronicle narrative, and homily/life narrative (274,757 words).