Spectral Forms Research Articles

Identification of spectral forms of protochlorophyllide in the region 670-730 nm.

Dark-grown leaves of three different species, maize, wheat, pea and a pea mutant (lip1) have been used to study protochlorophyllide (Pchlide) spectral forms. As a comparison also pea epicotyls were used. Different native forms of Pchlide were identified using the variation in the spectral properties of the plant material and the second derivatives of the 77 K fluorescence excitation and emission spectra. The spectral forms were further characterised by Gaussian deconvolution. In addition to short-wavelength and long-wavelength forms the area between 660 and 730 nm was shown to contain, together with some vibrational bands, five far-red Pchlide forms. They had pairs of excitation and emission peaks at 658 and 666 nm, 668 and 680 nm, 677 and 690 nm, 686 and 698 as well as 696 and 728 nm, respectively. The presence of several far-red Pchlide forms in dark-grown leaves gave evidence for additional aggregated states of Pchlide under native conditions.

Modeling whistler wave generation regimes in magnetospheric cyclotron maser

Abstract. Numerical analysis of the model for cyclotron instability in the Earth's magnetosphere is performed. This model, based on the self-consistent set of equations of quasi-linear plasma theory, describes different regimes of wave generation and related energetic particle precipitation. As the source of free energy the injection of energetic electrons with transverse anisotropic distribution function to the interaction region is considered. A parametric study of the model is performed. The main attention is paid to the analysis of generation regimes for different characteristics of energetic electron source, such as the shape of pitch angle distributions and its intensity. Two mechanisms of removal of energetic electrons from a generation region are considered, one is due to the particle precipitation through the loss cone and another one is related to the magnetic drift of energetic particles. It was confirmed that two main regimes occur in this system in the presence of a constant particle source, in the case of precipitation losses. At small source intensity relaxation oscillations were found, whose parameters are in good agreement with simplified analytical theory developed earlier. At a larger source intensity, transition to a periodic generation occurs. In the case of drift losses the regime of self-sustained periodic generation regime is realized for source intensity higher than some threshold. The dependencies of repetition period and dynamic spectrum shape on the source parameters were studied in detail. In addition to simple periodic regimes, those with more complex spectral forms were found. In particular, alteration of spikes with different spectral shape can take place. It was also shown that quasi-stationary generation at the low-frequency band can coexist with periodic modulation at higher frequencies. On the basis of the results obtained, the model for explanation of quasi-periodic whistler wave emissions is verified.

Origin of the 701-nm Fluorescence Emission of the Lhca2 Subunit of Higher Plant Photosystem I

Photosystem I of higher plants is characterized by red-shifted spectral forms deriving from chlorophyll chromophores. Each of the four Lhca1 to -4 subunits exhibits a specific fluorescence emission spectrum, peaking at 688, 701, 725, and 733 nm, respectively. Recent analysis revealed the role of chlorophyll-chlorophyll interactions of the red forms in Lhca3 and Lhca4, whereas the basis for the fluorescence emission at 701 nm in Lhca2 is not yet clear. We report a detailed characterization of the Lhca2 subunit using molecular biology, biochemistry, and spectroscopy and show that the 701-nm emission form originates from a broad absorption band at 690 nm. Spectroscopy on recombinant mutant proteins assesses that this band represents the low energy form of an excitonic interaction involving two chlorophyll a molecules bound to sites A5 and B5, the same protein domains previously identified for Lhca3 and Lhca4. The resulting emission is, however, substantially shifted to higher energies. These results are discussed on the basis of the structural information that recently became available from x-ray crystallography (Ben Shem, A., Frolow, F., and Nelson, N. (2003) Nature 426, 630-635). We suggest that, within the Lhca subfamily, spectroscopic properties of chromophores are modulated by the strength of the excitonic coupling between the chromophores A5 and B5, thus yielding fluorescence emission spanning a large wavelength interval. It is concluded that the interchromophore distance rather than the transition energy of the individual chromophores or the orientation of transition vectors represents the critical factor in determining the excitonic coupling in Lhca pigment-protein complexes.

Molecular organization of the antifungal and anticancer drug 2-(2,4-dihydroxyphenylo)-5,6-dichlorobenzothiazole (dHBBT) in solution and in lipid membranes studied by means of electronic absorption spectroscopy

2-(2,4-Dihydroxyphenylo)-5,6-dichlorobenzthiazole (dHBBT) is a new drug from the group of chemical compounds characterized by documented antifungal, antibacterial, cytostatic as well as antitumour activity. Despite general knowledge regarding pharmacological importance of dHBBT its interaction to biomembranes has not been investigated. In this work, we present the electronic absorption spectroscopic study on molecular organization of dHBBT in organic solvents and on its localization and molecular organization within model lipid membranes formed with dipalmitoylphosphatidylcholine (DPPC). The spectroscopic measurements are interpreted within the framework of the exciton splitting theory. It is concluded that complex absorption spectrum of dHBBT both in the organic solvents and incorporated to DPPC represents superposition of two spectral forms: representing monomers and hypsochromically shifted spectrum representing molecular dimers. Analysis of the temperature dependencies of the absorption spectra of dHBBT incorporated to DPPC liposomes suggests localization of the drug in the polar head-group region of the membrane or in the region of the polar–nonpolar interface. Linear dichroism measurements of dHBBT incorporated to DPPC multibilayers reveal roughly vertical orientation of the drug molecules with respect to the plane of the membrane. A model is presented of molecular organization of dHBBT in lipid membranes. Potential effects of dHBBT on membrane physical properties is briefly discussed.

Protochlorophyllide phototransformation in the bundle sheath cells of Zea mays

The protochlorophyllide transformation process was investigated by using comparative analysis of 77 K fluorescence spectral changes occurring in isolated bundle sheath (BS) cells of etiolated Zea mays leaves after being exposed to a 200 ms saturating flash. Deconvolution analysis of the fluorescence spectra showed essential differences in the ratio of protochlorophyll(ides) and chlorophyll(ides) spectral forms indicating for BS cells to have a characteristic pathway of protochlorophyllide transformation. Bundle sheath cells showed a high ratio between non-photoactive protochlorophyll(ide)-F632 and photoactive protochlorophyllide-F655. In those cells, the 200 ms flash triggered a preferential formation of chlorophyll(ide)-F675 which remained stable in the dark for at least 90 min. Isolated BS cells showed an accumulation of chlorophyll(ide)-F675 resulting in the formation of inactive photosystem II. However for mesophyll cells of intact leaves, it was found to have a high ratio between photoactive and non-photoactive protochlorophyll(ide), showing the succession of chlorophyll(ide) forms usually known in C 3 plants. Protochlorophyllide phototransformation pathway in BS cells related to early stages of plastid differentiation triggered by light may indicate specific conditions for PSII assembly process leading to inactive PSII forms.

Regeneration of protochlorophyllide in green and greening leaves of plants with varying proportions of protochlorophyllide forms in darkness

During illumination of dark‐grown plants protochlorophyllide (Pchlide) is continuously transformed to chlorophyllide (Chlide). Different dark‐grown plants, maize (Zea mays cv. Sundance), wheat (Triticum aestivum cv. Kosack), pea (Pisum sativum cv. Kelwedon wonder), the lip1 mutant of pea, and the aurea mutant of tomato (Solanum lycopersicum), have various ratios of spectral Pchlide forms in darkness. When the plants were illuminated and then returned to darkness Pchlide re‐accumulated. The proportions of different Pchlide forms within the pool of re‐accumulated Pchlide were followed by low temperature fluorescence emission and excitation spectra in green and greening leaves. After 1 h of illumination the spectral characteristics of regenerated Pchlide forms mirrored those of Pchlide in dark‐grown plants and were thus species dependent. After a prolonged illumination period (24 h) as well as in fully green leaves energy transfer to chlorophyll (Chl) masked the presence of long‐wavelength Pchlide in the fluorescence emission spectra. However, excitation spectra showed Pchlide absorption around 650 nm and its flash‐induced disappearance confirmed its nature of phototransformable Pchlide. In fact the excitation spectra showed that the proportions of different Pchlide forms in green leaves highly resembled the proportions of Pchlide forms in dark‐grown leaves and were specific for the plant variety. Thus Chl formation in both dark‐grown and light‐grown leaves can occur in a similar way through the main photoactive long‐wavelength form of Pchlide.

Large Systems of Boolean Functions: Realization by Modular Arithmetic Methods

Modular polynomial and spectral arithmetic-logical forms are introduced for representing Boolean functions so as to determine certain useful properties associated with the restricted number range (solution of the problem of large coefficients of arithmetical polynomials) in parallel logical computations.

Interactions of Copper(I) Phenanthroline Chelate with Polyadenylic-Polyuridylic Acid in Aqueous Dioxane

Acid-base transformations in the system copper(I) phenanthroline chelate [Cu(phen)2]+aq-poly-adenylic-polyuridylic acid in aqueous dioxane were studied by spectrophotometry. Changes in band intensi-ties, positions were revealed in the visible, near UV regions, dependent on the pH of the solution.Factor analysis was used to show that the absorption variance on titration of copper(I) bisphenanthrolinechelate is determined by mutual transformations of three spectral forms of complexes. Concentration profiles were calculated for compounds prevailing in the solution. In the presence of polyadenylic-polyuridylic acid, an additional spectral form appears as a result of a short-wave shift of the d-π* MLCT transition in the copper(I) chelate complex. Analysis of the calculated concentration profiles established that the new complex is formed at pH 5.2-5.6 from the bisphenanthroline chelate and the double-helix rod-like form of the polymer.

Zebrafish reveals different and conserved features of vertebrate neuroglobin gene structure, expression pattern, and ligand binding.

Neuroglobin has been identified as a respiratory protein that is primarily expressed in the mammalian nervous system. Here we present the first detailed analysis of neuroglobin from a non-mammalian vertebrate, the zebrafish Danio rerio. The zebrafish neuroglobin gene reveals a mammalian-type exon-intron pattern in the coding region (B12.2, E11.0, and G7.0), plus an additional 5'-non-coding exon. Similar to the mammalian neuroglobin, the zebrafish protein displays a hexacoordinate deoxy-binding scheme. Flash photolysis kinetics show the competitive binding on the millisecond timescale of external ligands and the distal histidine, resulting in an oxygen affinity of 1 torr. Western blotting, immune staining, and mRNA in situ hybridization demonstrate neuroglobin expression in the fish central nervous system and the retina but also in the gills. Neurons containing neuroglobin have a widespread distribution in the brain but are also present in the olfactory system. In the fish retina, neuroglobin is mainly present in the inner segments of the photoreceptor cells. In the gills, the chloride cells were identified to express neuroglobin. Neuroglobin appears to be associated with mitochondria-rich cell types and thus oxygen consumption rates, suggesting a myoglobin-like function of this protein in facilitated oxygen diffusion.

Narrow‐scale flow and a weak field by the top of Earth's core: Evidence from Ørsted, Magsat, and secular variation

To test two hypotheses against seismology, the Ørsted initial field model is used to estimate the radius of Earth's core by spectral methods. The model coefficients are used to compute the mean‐square magnetic flux density in spherical harmonics of degree n on the reference sphere of radius a = 6371.2 km, which is an observational spectrum Rn. The theoretical spectrum tested, {Rnc} = K(n + 1/2)[(n(n + 1)]−1(c/a)2n+4, is obtained from the hypotheses of narrow‐scale flow and a dynamically weak magnetic field near the top of Earth's core; it describes a low‐degree, core source magnetic energy range. Core radius c and amplitude K are estimated by fitting log theoretical to log observational spectra at low degrees. Estimates of c from Rn of degrees 1 through N vary between 3441 and 3542 km as N increases from 4 to 12. None of these estimates differ significantly from the seismologic core radius of 3480 km. Significant differences do occur if N exceeds 12, which is consistent with appreciable noncore, crustal source fields at degrees 13 and above, or if other spectral forms are assumed. Similar results are obtained from the 1980 epoch Magsat model CM3. One way to deduce {Rnc} uses an expectation spectrum for low‐degree secular variation (SV) induced by narrow‐scale flow near the top of Earth's core, {Fnc} = Cn(n + 1/2)(n + 1)(c/a)2n+4. The value of c obtained by fitting this form to the mean observational SV spectrum from model GSFC 9/80 is 3470 ± 91 km, also in accord with seismologic estimates. This test of the narrow‐scale flow hypothesis is independent of the weak field hypothesis. The agreement between SV, Magsat, Ørsted, and seismologic estimates of core radius means the hypotheses pass these tests. Additional tests are described.

04/00969 Effect of water vapor on tritium release from ceramic breeder material: Munakata, K. et al. Fusion Engineering and Design, 2003, 69, (1–4), 27–31

Pb(PO3)2-TeO2 glasses in the whole range of glass composition were first obtained and their properties (refractive index, density, Tg and light scattering losses) were determined. Based on the vibrational spectroscopy data a new approach was applied to investigate the interactions of initial oxides in melts resulted in so-called constant stoichiometry groupings (CSGs) formation symbolizing intermediate range order in glasses. Vibrational spectra of glasses are interpreted as a superposition of unchangeable spectral forms (principal spectral components (PSCs)) belonging to CSGs: PbO · P2O5, TeO2 · 2PbO · 2P2O5, TeO2 · PbO · P2O5, TeO2, and possibly 2TeO2 · PbO · P2O5 and 6TeO2 · PbO · P2O5. In this work Multivariate Data Analysis has been applied as the independent mathematical tool to decompose Raman spectra of glasses and reveal the number of PSCs. It is shown that application of factor analysis results in the same five PSCs that confirms our data obtained from the CSG concept. This concept allows also the prediction of the existence of unknown compounds, and correspondingly some crystals (TeO2⋅ 2PbO⋅2P2O5 and others) were revealed by XRPD of the crystallized glasses. The CSG concept opens the way for elaboration of low scattering glasses as candidates for Raman amplifiers. It is shown that Pb(PO3)2-TeO2 glasses with small content of TeO2 are of interest to photonic technology.

Modulation and acceleration of anomalous protons in the outer heliosphere

A comprehensive time-dependent modulation model including particle drifts, enhanced perpendicular diffusion, a solar wind termination shock (TS), and a heliosheath is used to study the acceleration and modulation of anomalous protons in the outer heliosphere. It is shown how the spectral forms of the accelerated anomalous protons at 90 AU change for the two heliospheric magnetic field polarity configurations during solar minimum conditions. Further, it is shown how these shocked spectra are modified and modulated in the outer heliosphere if the compression ratio of the TS was changed. The compression ratio is found to be by far the most dominant modulation factor.

Optical reflectance spectroscopy of ancient papers with discoloration or foxing

Our purpose is to study the effect of degradation processes on the optical response of ancient paper specimens. The paper samples under study originate from several European countries, date back to the XV and XVI centuries and show different states of degradation. Paper optical response is checked by reflectance spectroscopy in the wavelength range of 250–1100 nm. Similar spectral forms are shown by paper specimens displaying a broad range of widespread discoloration, of different manufacture, geographical origins and ages. A similar form is also observed by measuring foxing spots of several intensities on a single foxed sheet. Moreover, the entire spectra set shows a clear connection between the paper’s state of degradation and a monotonic transformation of the spectral curves, suggesting the existence of uniform degradation effects implied in the optical response of both foxed as well widespread discoloured papers. These results suggest for usage of optical reflectance as a general and non-destructive method for degradation calibration.

Universal R operator with Jordanian deformation of conformal symmetry

The Jordanian deformation of sl(2) bialgebra structure is studied in view of physical applications to breaking of conformal symmetry in the high energy asymptotics of scattering. Representations are formulated in terms of polynomials, generators in terms of differential operators. The deformed R operator with generic representations is analyzed in spectral and integral forms.

The Nature of a Chlorophyll Ligand in Lhca Proteins Determines the Far Red Fluorescence Emission Typical of Photosystem I

Photosystem I of higher plants is characterized by a typically long wavelength fluorescence emission associated to its light-harvesting complex I moiety. The origin of these low energy chlorophyll spectral forms was investigated by using site-directed mutagenesis of Lhca1-4 genes and in vitro reconstitution into recombinant pigment-protein complexes. We showed that the red-shifted absorption originates from chlorophyll-chlorophyll (Chl) excitonic interactions involving Chl A5 in each of the four Lhca antenna complexes. An essential requirement for the presence of the red-shifted absorption/fluorescence spectral forms was the presence of asparagine as a ligand for the Chl a chromophore in the binding site A5 of Lhca complexes. In Lhca3 and Lhca4, which exhibit the most red-shifted red forms, its substitution by histidine maintains the pigment binding and, yet, the red spectral forms are abolished. Conversely, in Lhca1, having very low amplitude of red forms, the substitution of Asn for His produces a red shift of the fluorescence emission, thus confirming that the nature of the Chl A5 ligand determines the correct organization of chromophores leading to the excitonic interaction responsible for the red-most forms. The red-shifted fluorescence emission at 730 nm is here proposed to originate from an absorption band at approximately 700 nm, which represents the low energy contribution of an excitonic interaction having the high energy band at 683 nm. Because the mutation does not affect Chl A5 orientation, we suggest that coordination by Asn of Chl A5 holds it at the correct distance with Chl B5.

Excited State Trapping and the Stepanov Relation with Reference to Photosystem I

It has been previously demonstrated that the Stepanov equation provides a rather good description of the absorption/fluorescence spectra in Photosystem I, even though excited state equilibration is not rapid with respect to the excited state decay. In the present article this apparent contradiction is examined analytically for two-state systems and numerically for many-state systems. It is demonstrated that, in the special case of the trapping process being associated with the initially populated state, neither very rapid excited state equilibration nor a transfer equilibrium, which approximates a true Boltzmann distribution, are prerequisites to obtaining a very close approximation to a correct Stepanov result. This interesting conclusion is discussed in terms of plant Photosystem I (PSI-200). It is concluded that whereas, in compartmental modeling, photochemical trapping may be formally associated with the bulk antenna pigments due to the strong energy coupling between them and the trap pigments, this is not the case for the red spectral forms.

Turbulence and fossil turbulence in oceans and lakes

Turbulence is defined as an eddy-like state of fluid motion where the intertial-vortex forces of the eddies are larger than any of the other forces that tend to damp the eddies out. Energy cascades of irrotational flows from large scales to small are non-turbulent, even if they supply energy to turbulence. Turbulent flows are rotational and cascade from small scales to large, with feedback. Viscous forces limit the smallest turbulent eddy size to the Kolmogorov scale. In stratified fluids, buoyancy forces limit large vertical overturns to the Ozmidov scale and convert the largest turbulent eddies into a unique class of saturated, non-propagating, internal waves, termed fossil-vorticity-turbulence. These waves have the same energy but different properties and spectral forms than the original turbulence patch. The Gibson (1980, 1986) theory of fossil turbulence applies universal similarity theories of turbulence and turbulent mixing to the vertical evolution of an isolated patch of turbulence in a stratified fluid as its growth is constrained and fossilized by buoyancy forces. Quantitative hydrodynamic-phase-diagrams (HPDs) from the theory are used to classify microstructure patches according to their hydrodynamic states. When analyzed in HPD space, previously published oceanic datasets showed their dominant microstructure patches are fossilized at large scales in all layers. Laboratory and field measurements suggested phytoplankton species with different swimming abilities adjust their growth strategies by pattern recognition of turbulence-fossil-turbulence dissipation and persistence times that predict survival-relevant surface layer sea changes. New data collected near a Honolulu waste-water outfall showed the small-to-large evolution of oceanic turbulence microstructure from active to fossil states, and revealed the ability of fossil-density-tubulence patches to absorb, and vertically radiate, internal wave energy, information, and enhanced turbulent-mixing-rates toward the sea surface so that the submerged waste-field could be detected from a space satellite (Bondur and Filatov, 2003).

Two redox-active beta-carotene molecules in photosystem II.

Photosystem II (PS II) contains secondary electron-transfer paths involving cytochrome b(559) (Cyt b(559)), chlorophyll (Chl), and beta-carotene (Car) that are active under conditions when oxygen evolution is blocked such as in inhibited samples or at low temperature. Intermediates of the secondary electron-transfer pathways of PS II core complexes from Synechocystis PCC 6803 and Synechococcus sp. and spinach PS II membranes have been investigated using low temperature near-IR spectroscopy and electron paramagnetic resonance (EPR) spectroscopy. We present evidence that two spectroscopically distinct redox-active carotenoids are formed upon low-temperature illumination. The Car(+) near-IR absorption peak varies in wavelength and width as a function of illumination temperature. Also, the rate of decay during dark incubation of the Car(+) peak varies as a function of wavelength. Factor analysis indicates that there are two spectral forms of Car(+) (Car(A)(+) has an absorbance maximum of 982 nm, and Car(B)(+) has an absorbance maximum of 1027 nm) that decay at different rates. In Synechocystis PS II, we observe a shift of the Car(+) peak to shorter wavelength when oxidized tyrosine D (Y(D)*) is present in the sample that is explained by an electrostatic interaction between Y(D)* and a nearby beta-carotene that disfavors oxidation of Car(B). The sequence of electron-transfer reactions in the secondary electron-transfer pathways of PS II is discussed in terms of a hole-hopping mechanism to attain the equilibrated state of the charge separation at low temperatures.

A structural model for the assembly of the reaction centre and the B808-866 complex in the membranes of Chloroflexus aurantiacus based on the calculation of the triplet minus singlet spectrum of the primary donor

A well resolved triplet minus singlet spectrum of the primary donor P870 of the green bacterium Chloroflexus aurantiacus, detected by optically detected magnetic resonance (ODMR), in intact membranes, was reported in our previous work [Photosynth. Res. 71 (2002) 45]. The spectrum is now interpreted and reconstructed by calculating the electronic interactions between the primary donor and the BChl a molecules belonging to the 866 absorption component of the B808-866 light-harvesting complex. The good agreement between the calculation and the experimental data strongly supports a topological model for the B808-866 complex which consists in a circular aggregate structure of a number of polypeptide units binding BChl a molecules assembled as in the LH2 peripheral antenna complex of purple bacteria, giving rise to two spectral forms. The aggregate surrounds the reaction centre (RC) resembling in this respect the LH1 core antenna complex of purple bacteria.

42 Diversity of phycoerythrin‐containing picocyanobacteria that share the same spectral phenotype

Phycoerythrin (PE) is an important light‐harvesting pigment for many marine picocyanobacteria. There are numerous spectral forms of PE, which differ in their ability to absorb blue and green wavelengths of light, depending on the precise chromophore composition. It remains unclear how the evolutionary history of this family of proteins relates to the diversity of the marine picocyanobacteria. In order to ascertain the level of diversity present in marine picocyanobacterial communities and to determine if specific spectral phenotypes are homologous or convergent, we have begun to examine the genetic diversity found in marine picocyanobacterial strains that share the same or similar spectral signatures for PE fluorescence. The strains we examined are all clonal cultures isolated from a range of environments, including the Arabian Sea and Black Sea. We report results from sequence data obtained using degenerate primers for 16S rRNA, rpoC1, and PE genes; we also examine the utility of taxonomically grouping these organisms by using physiological characteristics such as size and PE signature.