Analyses of structure of photoreceptor organelle and blepharismin-associated protein in unicellular eukaryote Blepharisma

In the ciliated protozoan Blepharisma, step-up photophobic response is believed to be mediated by a novel type of photosensory pigment known as "blepharismins" (BL) that are contained in the pigment granules located just beneath the plasma membrane. We examined the ultrastructure of the pigment granules by freeze-fracture and thin-section electron microscopy and proposed a schematic diagram showing the granules' three-dimensional inner membranous structure. Some of the BL are suggested to be associated with 200 kDa membrane protein. High-pressure liquid chromatography analysis of pigment species associated with 200 kDa protein obtained from blue forms of Blepharisma (oxyblepharisma) revealed that the 200 kDa protein was associated with five types of oxyblepharismin. The fluorescence intensity was increased when the pigments were dissociated from the 200 kDa protein. The result supports the hypothesis that the pigment-200 kDa complex is able to transduce light energy into signals mediating the photobehavior of Blepharisma.     

Immunochemical analysis of a photoreceptor protein using anti-IP3 receptor antibody in the unicellular organism, Blepharisma

The blepharismin-200 kD protein complex of the ciliated protozoan Blepharisma is a novel type of photosensor responsible for the step-up photophobic response of the cell. In immunoblotting assays, the 200 kD protein is weakly cross-reacted with anti-inositol triphosphate receptor antibody (anti-IP3 R antibody). Indirect immunofluorescence assays show that the pigment granules in which the blepharismin-200 kD protein complex is localized are labelled by anti-IP3 R antibody. When the anti-IP3 R antibody or antisense oligonucleotide for IP3 receptor is introduced into the living cells of Blepharisma, both the photosensitivity of the cells and content of blepharismin-200 kD protein are reduced. The results suggest that the photoreceptor 200 kD protein is possibly an IP3 receptor-like protein.     

Distinguishing Activities in the Photodynamic Arsenals of the Pigmented Ciliates Blepharisma sinuosum Sawaya, 1940 and Blepharisma japonicum Suzuki, 1954 (Ciliophora: Heterotrichea)

Blepharismins are photodynamic hypericin-like dianthrones produced as a variable pigment blend in Blepharisma ciliates and mostly studied in the Afro-Asiatic Blepharisma japonicum. The present work describes the bioactivity of pigments from the Brazilian Blepharisma sinuosum. Comparative analyses showed that the pigments from both species can trigger photo-induced modifications in phospholipids, but different redox properties and biological activities were assigned for each pigment blend. Stronger activities were detected for B. sinuosum pigments, with the lethal concentration LC₅₀ 10 × lower than B. japonicum pigments in light-irradiated tests against Bacillus cereus and less than half for treatments on the human HeLa tumor cells. HPLC showed B. sinuosum producing a simpler pigment blend, mostly with the blepharismin-C (~ 70%) and blepharismin-E (~ 30%) types. Each blepharismin engaged a specific dose–response profile on sensitive cells. The blepharismin-B and blepharismin-C were the most toxic pigments, showing LC₅₀ ~ 2.5–3.0 µm and ~ 100 µm on B. cereus and HeLa cells, respectively, after illumination. Similarity clustering analysis compiling the bioactivity data revealed two groups of blepharismins: the most active, B and C, and the less active, A, D and E. The B. sinuosum pigment blend includes one representative of each clade. Functional and medical implications are discussed.     

Immobilized cells of a unicellular green alga and a photosynthetic bacterium for use in a biophotolysis system

Applied Biochemistry and Biotechnology - Immobilization of algal and bacterial cells was investigated, and found applicable to our hydrogen production system. Both a unicellular green alga,...     

Photophysics and multifunctionality of hypericin-like pigments in heterotrich ciliates: a phylogenetic perspective

In this paper, we review the literature and present some new data to examine the occurrence and photophysics of the diverse hypericin-like chromophores in heterotrichs, the photoresponses of the cells, the various roles of the pigments and the taxa that might be studied to advance our understanding of these pigments. Hypericin-like chromophores are known chemically and spectrally so far only from the stentorids and Fabrea, the latter now seen to be sister to stentorids in the phylogenetic tree. For three hypericin-like pigments, the structures are known but these probably do not account for all the colors seen in stentorids. At least eight physiological groups of Stentor exist depending on pigment color and presence/absence of zoochlorellae, and some species can be bleached, leading to many opportunities for comparison of pigment chemistry and cell behavior. Several different responses to light are exhibited among heterotrichs, sometimes by the same cell; in particular, cells with algal symbionts are photophilic in contrast to the well-studied sciaphilous (shade-loving) species. Hypericin-like pigments are involved in some well-known photophobic reactions but other pigments (rhodopsin and flavins) are also involved in photoresponses in heterotrichs and other protists. The best characterized role of hypericin-like pigments in heterotrichs is in photoresponses and they have at least twice evolved a role as photoreceptors. However, hypericin and hypericin-like pigments in diverse organisms more commonly serve as predator defense and the pigments are multifunctional in heterotrichs. A direct role for the pigments in UV protection is possible but evidence is equivocal. New observations are presented on a folliculinid from deep water, including physical characterization of its hypericin-like pigment and its phylogenetic position based on SSU rRNA sequences. The photophysics of hypericin and hypericin-like pigments is reviewed. Particular attention is given to how their excited-state properties are modified by the environment. Dramatic changes in excited-state behavior are observed as hypericin is moved from the homogeneous environment of organic solvents to the much more structured surroundings provided by the complexes it forms with proteins. Among these complexes, it is useful to consider the differences between environments where hypericin is not found naturally and those where it is, notably, for example, in heterotrichs. It is clear that interaction with a protein modifies the photophysics of hypericin and understanding the molecular basis of this interaction is one of the outstanding problems in elucidating the function of hypericin and hypericin-like chromophores.     

Link between allosteric signal transduction and functional dynamics in a multisubunit enzyme: S-adenosylhomocysteine hydrolase

S-adenosylhomocysteine hydrolase (SAHH), a cellular enzyme that plays a key role in methylation reactions including those required for maturation of viral mRNA, is an important drug target in the discovery of antiviral agents. While targeting the active site is a straightforward strategy of enzyme inhibition, evidence of allosteric modulation of active site in many enzymes underscores the molecular origin of signal transduction. Information of co-evolving sequences in SAHH family and the key residues for functional dynamics that can be identified using native topology of the enzyme provide glimpses into how the allosteric signaling network, dispersed over the molecular structure, coordinates intra- and intersubunit conformational dynamics. To study the link between the allosteric communication and functional dynamics of SAHHs, we performed Brownian dynamics simulations by building a coarse-grained model based on the holo and ligand-bound structures. The simulations of ligand-induced transition revealed that the signal of intrasubunit closure dynamics is transmitted to form intersubunit contacts, which in turn invoke a precise alignment of active site, followed by the dimer-dimer rotation that compacts the whole tetrameric structure. Further analyses of SAHH dynamics associated with ligand binding provided evidence of both induced fit and population shift mechanisms and also showed that the transition-state ensemble is akin to the ligand-bound state. Besides the formation of enzyme-ligand contacts at the active site, the allosteric couplings from the residues distal to the active site are vital to the enzymatic function.     

Enantioselective ketoester reductions in water: a comparison between microorganism- and ruthenium-catalyzed reactions

In the search for green chemistry methods for the enantioselective reduction of ketoesters Saccharomyces cerevisiae- and ruthenium-catalyzed reactions in water have been investigated. The highest enantiomeric excesses for the reduction of α- and β-ketoesters have been obtained by S. cerevisiae. Chiral ruthenium catalysts are active for the reduction of all ketoesters with low to moderate enantioselectivities depending on the nature of the substrate and ligand. Interestingly, for several substrates both enantiomers of the hydroxyesters have been obtained according either to the catalytic method or to the structure of the ligand.     

Energy transport in peptide helices: a comparison between high- and low-energy excitations

Energy transport in a short helical peptide in chloroform solution is studied by time-resolved femtosecond spectroscopy and accompanying nonequilibrium molecular dynamics (MD) simulations. In particular, the heat transport after excitation of an azobenzene chromophore attached to one terminus of the helix with 3 eV (UV) photons is compared to the excitation of a peptide C=O oscillator with 0.2 eV (IR) photons. The heat in the helix is detected at various distances from the heat source as a function of time by employing vibrational pump-probe spectroscopy. As a result, the carbonyl oscillators at different positions along the helix act as local thermometers. The experiments show that heat transport through the peptide after excitation with low-energy photons is at least 4 times faster than after UV excitation. On the other hand, the heat transport obtained by nonequilibrium MD simulations is largely insensitive to the kind of excitation. The calculations agree well with the experimental results for the low-frequency case; however, they give a factor of 5 too fast energy transport for the high-energy case. Employing instantaneous normal mode calculations of the MD trajectories, a simple harmonic model of heat transport is adopted, which shows that the heat diffusivity decreases significantly at temperatures initially reached by high-energy excitation. This finding suggests that the photoinduced energy gets trapped, if it is deposited in high amounts. The various competing mechanisms, such as vibrational T(1) relaxation, resonant transfer between excitonic states, cascading down relaxation, and low-frequency mode transfer, are discussed in detail.     

A characterization of the Raman modes in a J-aggregate-forming dye: a comparison between theory and experiment

J-Aggregates are a class of organic molecules that possess several interesting characteristics that make them attractive for a range of organic-based optoelectronic devices. We present experimental and computer-simulation studies of the Raman-active vibrational modes in the J-aggregate-forming dye 5,6-dichloro-2-[[5,6-dichloro-1-ethyl-3-(4-sulfobutyl)benzimidazol-2-ylidene]propenyl]-1-ethyl-3-(4-sulfobutyl)benzimidazolium hydroxide, sodium salt, inner salt. The molecular monomer and dimer are analyzed computationally and the Raman mode energies extracted. There is a good agreement between the energies of the theoretical and experimental Raman modes. Experimentally, an enhancement is seen in the intensity of two low frequency modes upon aggregation of the dye. This is attributed to aggregation-enhanced Raman scattering. An enhancement is also observed in certain modes of the calculated spectra upon changing from a monomer to dimeric arrangement. A link is suggested between the Raman-active vibrational modes of the molecule, and a time-dependent electronic coupling present over several molecules.     

Surface forces in polymer fluids: a comparison between simulations and density functional theory

A polymer density functional theory is evaluated in terms of its ability to predict interactions between large surfaces in a polymer fluid. Comparisons are made with results from simulations in an expanded isotension ensemble. The variation of the net surface-surface interaction with adsorption strength is examined. Cases where the monomers interact via a pure hard sphere potential are investigated, but we have also studied the effect of attractions between the monomers. In all cases, we obtain an almost quantitative agreement between the simulated results and the predictions from the polymer density functional theory.     

Reversible addition-fragmentation chain transfer polymerization of N-isopropylacrylamide: a comparison between a conventional and a fast initiator

The reversible addition-fragmentation chain transfer (RAFT) polymerization of N-isopropylacrylamide (NIPAM) was studied to determine the reasons for deviation of experimental molecular weights to lower molecular weight at high monomer conversion when S-1-dodecyl-S-(alpha,alpha'-dimethyl-alpha' '-acetic acid)trithiocarbonate (CTAm) and S,S-bis(alpha,alpha'-dimethyl-alpha' '-acetic acid)trithiocarbonate (CTAd) were used as RAFT agents at 65 degrees C. For this purpose, experiments were performed in N,N'-dimethylformamide (DMF) at the NIPAM/CTA ratio of 200 with initiators capable of yielding fast and slow initiation, respectively by photochemical and thermal process, either at ambient temperature or at 65 degrees C. When the polymerization of NIPAM was conducted under these conditions with Irgacure-2959 (IRGC) as photoinitiator, a continuing supply of primary radicals by incremental initiator addition was required to achieve reasonably high conversion. This effect was also apparent by the loss of linearity of the first-order kinetic plot with a conventional initiator (4,4-azobis(4-cyanovaleric acid) (ACVA) as azo-initiator, 10h (t1/2) decomposition at 65 degrees C) indicating that steady-state concentration of the macroradical decreases significantly with the initiator consumption. Nevertheless, polymers with predictable number-average molecular weight Mn (i.e., based on [monomer]/([CTA] + [initiator]) ratio) and narrow polydispersities were obtained (PDIs < 1.2) with CTAm indicating that the process of chain growth was controlled. When CTAd was used, instead of CTAm, the polymers obtained were characterized by a larger polydispersity (1.2 < PDIs < 1.3). The so-called "living steady-state concentration" in chain equilibration together with the linear dependence of Mn vs conversion was observed only when the 200/1 NIPAM/CTA mixture in DMF was subjected to a permanent photoirradiation at 65 degrees C. With ACVA, the deviation of the experimentally measured molecular weights at high conversion was accounted for by the simultaneous self-initiated polymerization of NIPAM with the controlled process in the presence of CTA at 65 degrees C. Similar drift from the linear dependence Mn vs conversion was also observed at 65 degrees C when a significant number of low molecular weight polymer chains were generated intentionally by photodecomposition of IRGC.     

Static properties of end-tethered polymers in good solution: a comparison between different models

We present a comparison between results, obtained from different simulation models, for the static properties of end-tethered polymer layers in good solvent. Our analysis includes data from two previous studies--the bond fluctuation model of Wittmer et al. [J. Chem. Phys. 101, 4379 (1994)] and the off-lattice bead-spring model of Grest and Murat [Macromolecules 26, 3108 (1993)]. Additionally, we explore the properties of a similar off-lattice model simulated close to the Theta temperature. We show that the data for the bond fluctuation and the Grest-Murat model can be analyzed in terms of scaling theory because chains are swollen inside the Pincus blob. In the vicinity of the Theta point the structure of the chains is essentially Gaussian in the Pincus blob. Therefore, the data for the second off-lattice model can be compared quantitatively to the self-consistent field theory. Different ways to determine the parameters of the self-consistent field theory are discussed.     

Synthesis of polyester from renewable feedstock: a comparison between microwave and conventional heating

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Charge delocalization of 1,4-benzenedicyclometalated ruthenium: a comparison between tris-bidentate and bis-tridentate complexes

A dimetallic biscyclometalated ruthenium complex, [(bpy)(2)Ru(dpb)Ru(bpy)(2)](2+) (bpy = 2,2'-bipyridine; dpb = 1,4-di-2-pyridylbenzene), with a tris-bidentate coordination mode has been prepared. The electronic properties of this complex were studied by electrochemical and spectroscopic analysis and DFT/TDDFT calculations on both rac and meso isomers. Complex [(bpy)(2)Ru(dpb)Ru(bpy)(2)](2+) has a similar 1,4-benzenedicyclometalated ruthenium (Ru-phenyl-Ru) structural component with a previously reported bis-tridentate complex, [(tpy)Ru(tpb)Ru(tpy)](2+) (tpy = 2,2';6',2″-terpyridine; tpb = 1,2,4,5-tetra-2-pyridylbenzene). The charge delocalizations of these complexes across the Ru-phenyl-Ru array were investigated and compared by studying the corresponding one-electron-oxidized species, generated by chemical oxidation or electrochemical electrolysis, with DFT/TDDFT calculations and spectroscopic and EPR analysis. These studies indicate that both [(bpy)(2)Ru(dpb)Ru(bpy)(2)](3+) and [(tpy)Ru(tpb)Ru(tpy)](3+) are fully delocalized systems. However, the coordination mode of the metal component plays an important role in influencing their electronic properties.     

Mode coupling behavior of a Lennard-Jones binary mixture: a comparison between bulk and confined phases

We present a quantitative comparison at equivalent thermodynamical conditions of bulk and confined dynamical properties of a Lennard-Jones binary mixture upon supercooling. Both systems had been previously found to display a behavior in agreement with the mode coupling theory of the evolution of glassy dynamics. Differences and analogies of behavior are discussed focusing, in particular, on the role of hopping in reducing spatially correlated dynamics in the confined system with respect to the bulk.     

Chemical interactions between silver nanoparticles and thiols: a comparison of mercaptohexanol against cysteine

The interaction between citrate capped silver nanoparticles and two different thiols, mercaptohexanol(MH) and cysteine, was investigated. The thiols interacted with silver nanoparticles in a significantly contrasting manner. With MH, a sparingly soluble silver(I) thiolate complex AgSRm(Rm = –(CH2)6OH) was formed on the silver nanoparticle surface. Cyclic voltammograms and UV-vis spectra were used to infer that the AgSRm complex on the nanoparticle surface undergoes a phase transition to give a mixture of AgSRm and Ag2S-like complexes. In contrast, when silver nanoparticles were exposed to cysteine, the citrate capping agent on the silver nanoparticles was replaced by cysteine to give cysteine capped nanoparticles. As cysteine capped nanoparticles form, the electrochemical data displayed a decrease in oxidative peak charge but the UV-vis spectra showed a constant signal. Therefore, cysteine capped nanoparticles were suggested to have either inactivated the silver surface or else promoted detachment from the electrode surface.     

Quality assurance and quality control in forest soil analyses: a comparison between European soil laboratories

In transnational monitoring programmes, a balance between international reference methods, which improve spatial comparability, and national analysis methods that favour temporal comparability, by their use and testing over many years, needs to be sought. Prior to the next Pan-European Forest Soil Survey, a third interlaboratory comparison of soil analysis methods was organised. All participating laboratories were requested to use the same reference methods. Fifty-two soil laboratories from 27 European countries analysed a total of 48 soil parameters on three soil samples which were typical for European forest soils. The results of the statistical analysis showed a high interlaboratory and intralaboratory variability, especially for the acid oxalate extractions, particle size distribution, exchangeable elements and total carbonates. The intercomparability of the test results did not improve compared to the previous ring test. As the exercise aimed primarily at comparing the performance of the laboratories, it was not powerful enough to find cause–effect relationships between the meta information provided by the laboratories and the variability of the test results.

     

Raman scattering in crystalline oligothiophenes: a comparison between density functional theory and bond polarizability model

Raman intensity of intramolecular and lattice modes of crystalline alpha-bithiophene (alpha-2T) are investigated within density functional theory using a nonlinear response formalism. First, comparison between the calculated Raman spectrum and the experimental data allows the assignment of the main Raman lines over the whole frequency range. Then, a bond polarizability (BP) model, limited to first neighbors, is built. We show that, although the BP model cannot reproduce the changes of dielectric susceptibility under individual atomic displacements, it is accurate enough to reproduce the profile of the unpolarized nonresonant Raman spectrum of alpha-2T powder. Finally, the BP model, fitted on our first-principles results on alpha-2T, is applied with success to the alpha-quaterthiophene polymorph phases and alpha-sexithiophene, demonstrating on practical examples that first-principles and BP approaches are powerful complementary tools to calculate the nonresonant Raman spectrum of alpha-2T and make reasonable predictions on larger oligothiophenes.     

Theory of vibronic interactions in D2 and H2: a comparison between multichannel-quantum-defect and coupled-equation approaches

New experimental energy levels for the 2pπC(1)Π(u)(-) state of D(2) are reported extending up to the dissociation limit and including rotational quantum numbers up to N = 10. These data are extracted from recent high resolution optical emission spectra, and they are used for a detailed comparison of two theoretical approaches, both of which are fully ab initio and are based on the same state-of-the-art clamped-nuclei potential energy curves. These are the coupled differential equations (CE) and the multichannel quantum defect theory (MQDT) approaches, each of which accounts for adiabatic corrections and non-adiabatic couplings. Both theoretical approaches reproduce the experimental levels to within a fraction of a wavenumber unit (cm(-1)) for the lower vibrational quantum numbers, with the MQDT surpassing the CE method. As the dissociation limit is approached, the residuals observed-calculated increase up to several cm(-1) and the MQDT method is up to a factor of two less accurate than the CE method. The same analysis is carried out with existing data for the H(2) isotopomer and yields similar results. An analogous comparison is also made for the 3pπD(1)Π(u)(-) and 4pπD('1)Π(u)(-) states for both isotopomers, where the MQDT is found to be superior to the CE approach.