Molecular Tuning of Rhodopsins for High Visual Sensitivity in Different Light Environments : Variation in Absorbance Spectrum and Opsin Sequence within and between Species

Visual pigments of different animal species must have evolved at some stage to match the prevailing light environments, since all visual functions depend on their ability to absorb available photons and transduce the event into a reliable neural signal. There is a large literature on correlation between the light environment and spectral sensitivity between different fish species. However, little work has been done on evolutionary adaptation between separated populations within species. More generally, little is known about the rate of evolutionary adaptation to changing spectral environments. The objective of this thesis is to illuminate the constraints under which the evolutionary tuning of visual pigments works as evident in: scope, tempo, available molecular routes, and signal/noise trade-offs. Aquatic environments offer Nature s own laboratories for research on visual pigment properties, as naturally occurring light environments offer an enormous range of variation in both spectral composition and intensity. The present thesis focuses on the visual pigments that serve dim-light vision in two groups of model species, teleost fishes and mysid crustaceans. The geographical emphasis is in the brackish Baltic Sea area with its well-known postglacial isolation history and its aquatic fauna of both marine and fresh-water origin. The absorbance spectrum of the (single) dim-light visual pigment were recorded by microspectrophotometry (MSP) in single rods of 26 fish species and single rhabdoms of 8 opossum shrimp populations of the genus Mysis inhabiting marine, brackish or freshwater environments. Additionally, spectral sensitivity was determined from six Mysis populations by electroretinogram (ERG) recording. The rod opsin gene was sequenced in individuals of four allopatric populations of the sand goby (Pomatoschistus minutus). Rod opsins of two other goby species were investigated as outgroups for comparison. Rod absorbance spectra of the Baltic subspecies or populations of the primarily marine species herring (Clupea harengus membras), sand goby (P. minutus), and flounder (Platichthys flesus) were long-wavelength-shifted compared to their marine populations. The spectral shifts are consistent with adaptation for improved quantum catch (QC) as well as improved signal-to-noise ratio (SNR) of vision in the Baltic light environment. Since the chromophore of the pigment was pure A1 in all cases, this has apparently been achieved by evolutionary tuning of the opsin visual pigment. By contrast, no opsin-based differences were evident between lake and sea populations of species of fresh-water origin, which can tune their pigment by varying chromophore ratios. A more detailed analysis of differences in absorbance spectra and opsin sequence between and within populations was conducted using the sand goby as model species. Four allopatric populations from the Baltic Sea (B), Swedish west coast (S), English Channel (E), and Adriatic Sea (A) were examined. Rod absorbance spectra, characterized by the wavelength of maximum absorbance (λmax), differed between populations and correlated with differences in the spectral light transmission of the respective water bodies. The greatest λmax shift as well as the greatest opsin sequence difference was between the Baltic and the Adriatic populations. The significant within-population variation of the Baltic λmax values (506-511 nm) was analyzed on the level of individuals and was shown to correlate well with opsin sequence substitutions. The sequences of individuals with λmax at shorter wavelengths were identical to that of the Swedish population, whereas those with λmax at longer wavelengths additionally had substitution F261F/Y in the sixth transmembrane helix of the protein. This substitution (Y261) was also present in the Baltic common gobies and is known to redshift spectra. The tuning mechanism of the long-wavelength type Baltic sand gobies is assumed to be the co-expression of F261 and Y261 in all rods to produce ≈ 5 nm redshift. The polymorphism of the Baltic sand goby population possibly indicates ambiguous selection pressures in the Baltic Sea. The visual pigments of all lake populations of the opossum shrimp (Mysis relicta) were red-shifted by 25 nm compared with all Baltic Sea populations. This is calculated to confer a significant advantage in both QC and SNR in many humus-rich lakes with reddish water. Since only A2 chromophore was present, the differences obviously reflect evolutionary tuning of the visual protein, the opsin. The changes have occurred within the ca. 9000 years that the lakes have been isolated from the Sea after the most recent glaciation. At present, it seems that the mechanism explaining the spectral differences between lake and sea populations is not an amino acid substitution at any other conventional tuning site, but the mechanism is yet to be found.

Analysis of integrated optofluidic lab-on-a-chip sensor based on refractive index and absorbance sensing

The analysis of a fully integrated optofluidic lab-on-a-chip sensor is presented in this paper. This device is comprised of collinear input and output waveguides that are separated by a microfluidic channel. When light is passed through the analyte contained in the fluidic gap, optical power loss occurs owing to absorption of light. Apart from absorption, a mode-mismatch between the input and output waveguides occurs when the light propagates through the fluidic gap. The degree of mode-mismatch and quantum of optical power loss due to absorption of light by the fluid form the basis of our analysis. This sensor can detect changes in refractive index and changes in concentration of species contained in the analyte. The sensitivity to detect minute changes depends on many parameters. The parameters that influence the sensitivity of the sensor are mode spot size, refractive index of the fluid, molar concentration of the species contained in the analyte, width of the fluidic gap, and waveguide geometry. By correlating various parameters, an optimal fluidic gap distance corresponding to a particular mode spot size that achieves the best sensitivity is determined both for refractive index and absorbance-based sensing.

Multivalent Cu-Doped ZnO Nanoparticles with Full Solar Spectrum Absorbance and Enhanced Photoactivity

Full solar spectrum absorbers are widely pursued for applications related to photocatalysis and photovoltaics. Here we report multivalent Cu-doped ZnO nanoparticles which exhibit full solar spectrum absorbance and high photoactivity. Metathesis-based, green-chemical approaches with synthesis yield of similar to 100% are used. Cu incorporation in ZnO results in an increase of average solar spectrum absorbance from a mere 0.4% to 34%. On the other hand, (Zn, Cu)0 composites result in materials with up to 64% average solar spectrum absorbance. Doped systems operate well under both visible and UV illumination. The nanomaterials prepared are characterized by using X-ray powder diffraction (XRD), scanning electron microscopy (SEM), Brunauer-Emmett-Teller (BET) surface area analysis, and X-ray photoelectron spectroscopy (XPS). Photocatalysts explored have particle sizes >= 50 nm. This is deliberately done in order to avoid the nanotoxic size regime of ZnO. Despite the large particle size and low specific surface area (<20 m(2).g(-1)), the best catalyst reported here compare favorably with recent reports on ZnO based systems. Using X-photoelectron spectroscopy and synthesis property correlations, we infer that the presence of multivalent Cu (most likely in the form of Cu1+delta) on ZnO surface is responsible for the observed photoactivity enhancement.

Single-Cell Optical Absorbance Characterization With High-Throughput Microfluidic Microscopy

Morphological changes in cells associated with disease states are often assessed using clinical microscopy. However, the changes in chemical composition of cells can also be used to detect disease conditions. Optical absorption measurements carried out on single cells using inexpensive sources, detectors can help assess the chemical composition of cells; thereby enable detection of diseases. In this article, we present a novel technique capable of simultaneously detecting changes in morphology and chemical composition of cells. The presented technique enables characterization of optical absorbance-based methods against microscopy for detection of disease states. Using the technique, we have been able to achieve a throughput of about 1000 cells per second. We demonstrate the proof-of-principle by detecting malaria in a given blood sample. The presented technique is capable of detecting very lower levels of parasitemia within time scales comparable to antigen-based rapid diagnostic tests.

Origin of the blueshift in the infrared absorbance of intersubband transitions in AlxGa1-x/GaN multiple quantum wells

A self-consistent calculation of the subband energy levels of n-doped quantum wells is studied. A comparison is made between theoretical results and experimental data. In order to account for the deviations between them, the ground-state electron-electron exchange interactions, the ground-state direct Coulomb interactions, the depolarization effect, and the exciton-like effect are considered in the simulations. The agreement between theory and experiment is greatly improved when all these aspects are taken into account. The ground-to-excited-state energy difference increases by 8 meV from its self-consistent value if one considers the depolarization effect and the exciton-like effect only. It appears that the electron-electron exchange interactions account for most of the observed residual blueshift for the infrared intersubband absorbance in AlxGa1-xN/GaN multiple quantum wells. It seems that electrons on the surface of the k-space Fermi gas make the main contribution to the electron-electron exchange interactions, while for electrons further inside the Fermi gas it is difficult to exchange their positions. (C) 2004 Elsevier B.V. All rights reserved.

Absorbance kinetics of dye-doped systems with photochemical first order kinetics

Often it is assumed that absorbance decays in photochromic materials with the time dependence of the photochemical kinetics, i.e. exponentially for first order kinetics. Although this may hold in the limiting case of vanishing absorbance, deviations are to be expected for realistic samples, because the local photochemical kinetics slows down with increasing initial absorption and penetration depth of the radiation. We discuss the theory of the kinetics of initially homogeneous photochromic samples and derive analytical solutions. In extension of Tomlinson's theory we find an analytical solution that holds with good approximation even for samples that exhibit a small residual absorption in the saturation limit. The theoretical time dependence of the absorbance originating from photochemical first order kinetics of dye-doped systems is compared with experimental data published by Lafond et al. for fulgides doped in different polymer matrices. (c) 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Surface charge influence on the surface plasmon absorbance of electroactive thiol-protected gold nanoparticles

Gold nanoparticles (3.1-5.0 nm in size) surface-derivatized with both electroactive and nonelectroactive self-assembled monolayers were synthesized. The surface-derivatized electroactive particles can be easily oxidized/reduced at an electrode surface based on the diffusion-controlled current-voltage curve observed in cyclic voltammetry measurements. Spectroelectrochemical investigation demonstrated that the maximum absorbance of the nanoparticles in their oxidized state red-shifted compared with their reduced state to a different extent according to their size distribution. In the case of the particles surface-derivatized with nonelectroactive monolayers, much less shift was observed. This study showed that surface plasmon absorbance of gold nanoparticles was not only related to core charge states but was also influenced by surface charge states as well.

Detection of carbohydrates using new labeling reagent 1-(2-naphthyl)-3-methyl-5-pyrazolone by capillary zone electrophoresis with absorbance (UV)

A novel labeling reagent 1-(2-naphthyl)-3-methyl-5-pyrazolone (NMP) coupled with capillary electrophoresis (CE) with DAD detection for the determination of carbohydrates has been developed. The chromophore in the 1-phenyl-3-methyl-5-pyrazolone (PMP) reagent is replaced by naphthyl functional group, which results in a reagent with very high molar absorptivity (epsilon(251nm) = 5.58 x 10(4) L mol(-1) cm(-1)). This pen-nits NMP-labeled carbohydrates to be detected with UV absorbance in standard 50-mu m-i.d. fused silica capillaries by zone electrophoresis. in this mode, nanomolar concentrations of detection limits are obtained. The method for the derivatization. of carbohydrates with NMP is simplified. The derivatization reaction is rapid and mild in the presence of ammonia catalyst without further transfer steps. Nine monosaccharide derivatives such as mannose, galacturonic acid, glucuronic acid, rhamnose, glucose, galactose, xylose, arabinose and fucose can successfully be detected in CE mode. Good reproducibility can be obtained with relative standard deviation (R.S.D.) values of the migration times and peak area, respectively, from 0.44 to 0.48 and from 3.2 to 4.8. Furthermore, the developed method has been successfully applied to the analysis of carbohydrates in the hydrolyzed rape bee pollen samples. (C) 2008 Published by Elsevier B.V.

Absorbance enhancement in microplate wells for improved-sensitivity biosensors

A generic optical biosensing strategy was developed that relies on the absorbance enhancement phenomenon occurring in a multiple scattering matrix. Experimentally, inserts made of glass fiber membrane were placed into microplate wells in order to significantly lengthen the trajectory of the incident light through the sample and therefore increase the corresponding absorbance. Enhancement factor was calculated by comparing the absorbance values measured for a given amount of dye with and without the absorbance-enhancing inserts in the wells. Moreover, the dilution of dye in solutions with different refractive indices (RI) clearly revealed that the enhancement factor increased with the ΔRI between the membrane and the surrounding medium, reaching a maximum value (EF>25) when the membranes were dried. On this basis, two H2O2-biosensing systems were developed based on the biofunctionalization of the glass fiber inserts either with cytochrome c or horseradish peroxidase (HRP) and the analytical performances were systematically compared with the corresponding bioassay in solution. The efficiency of the absorbance-enhancement approach was particularly clear in the case of the cytochrome c-based biosensor with a sensitivity gain of 40 folds and wider dynamic range. Therefore, the developed strategy represents a promising way to convert standard colorimetric bioassays into optical biosensors with improved sensitivity.

Electron Transfer Involving the Phylloquinone (A1) Cofactor of Photosystem I Examined with Time Resolved Absorbance and Electron Paramagnetic Resonance Spectroscopy

The dependence of the electron transfer (ET) rate on the Photosystem I (PSI) cofactor phylloquinone (A1) is studied by time-resolved absorbance and electron paramagnetic resonance (EPR) spectroscopy. Two active branches (A and B) of electron transfer converge to the FX cofactor from the A1A and A1B quinone. The work described in Chapter 5 investigates the single hydrogen bond from the amino acid residue PsaA-L722 backbone nitrogen to A1A for its effect on the electron transfer rate to FX. Room temperature transient EPR measurements show an increase in the rate for the A1A- to FX for the PsaA-L722T mutant and an increased hyperfine coupling to the 2-methyl group of A1A when compared to wild type. The Arrhenius plot of the A1A- to FX ET in the PsaA-L722T mutant suggests that the increased rate is probably the result of a slight change in the electronic coupling between A1A- and FX. The reasons for the non-Arrhenius behavior are discussed. The work discussed in Chapter 6 investigates the directionality of ET at low temperature by blocking ET to the iron-sulfur clusters FX, FA and FB in the menB deletion mutant strain of Synechocyctis sp. PCC 6803, which is unable to synthesize phylloquinone, by incorporating the high midpoint potential (49 mV vs SHE) 2,3-dichloro-1,4-naphthoquinone (Cl2NQ) into the A1A and A1B binding sites. Various EPR spectroscopic techniques were implemented to differentiate between the spectral features created from A and B- branch electron transfer. The implications of this result for the directionality of electron transfer in PS I are discussed. The work discussed in Chapter 7 was done to study the dependence of the heterogeneous ET at low temperature on A1 midpoint potential. The menB PSI mutant contains plastiquinone-9 in the A1 binding site. The solution midpoint potential of the quinone measures 100 mV more positive then wild-type phylloquinone. The irreversible ET to the terminal acceptors FA and FB at low temperature is not controlled by the forward step from A1 to FX as expected due to the thermodynamic differences of the A1 cofactor in the two active branches A and B. Alternatives for the ET heterogeneity are discussed.

The analysis of café espresso using two-dimensional reversed phase–reversed phase high performance liquid chromatography with UV-absorbance and chemiluminescence detection

In this study, an activity based screening technique combining two-dimensional liquid chromatography (2DHPLC) with UV-absorbance and chemiluminescence detection was applied to study “Ristretto”, "Decaffeinatto” and “Volluto” espresso coffees. This technique, which coupled the separation power of 2DHPLC with the sensitivity and selectivity of the chemiluminescence detection, offers great potential for screening complex samples for antioxidant compounds. Detailed information regarding the complexity of the sample, and the variation between these three coffees could be obtained using this multidimensional-hyphenated method of analysis.

Absorbance of retinal oil droplets of the budgerigar : sex, spatial and plumage morph-related variation

Intraspecific variation in photoreceptor physiology is known in several vertebrate taxa, but is currently unknown in birds, despite many avian traits varying intraspecifically, and avian visual ecology encompassing a wide range of environments and visual stimuli, which might influence spectral sensitivity. Avian retinal photoreceptors contain light absorbing carotenoid-rich oil droplets that affect vision. Carotenoids are also important plumage components. However, our understanding of the regulation of carotenoids in oil droplets remains rudimentary. Among birds, Melopsittacus undulatus has probably the best-studied colour vision, shows profound intraspecific variation in plumage colour, and increased plasma carotenoids during moult. We used microspectrophotometry to determine whether a relationship exists between oil droplet carotenoid concentration and plumage pigmentation, and tested for sex and spatial variation in droplet absorbance across the retina. Absorbance of one variety of P-type droplets was higher in males. No relationship was found between droplet absorbance and plumage colour. We found a spatial pattern of droplets absorbance across the retina that matched a pattern found in another parrot, and other avian species. Our work provides insights into the development and maintenance of retinal oil droplets and suggests a common mechanism and function for carotenoid deposition in the retina across bird species.