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Sample records for 6-4 photolyase crystal

  1. Flavin adenine dinucleotide as a chromophore of the Xenopus (6-4)photolyase.

    PubMed Central

    Todo, T; Kim, S T; Hitomi, K; Otoshi, E; Inui, T; Morioka, H; Kobayashi, H; Ohtsuka, E; Toh, H; Ikenaga, M

    1997-01-01

    Two types of enzyme utilizing light from the blue and near-UV spectral range (320-520 nm) are known to have related primary structures: DNA photolyase, which repairs UV-induced DNA damage in a light-dependent manner, and the blue light photoreceptor of plants, which mediates light-dependent regulation of seedling development. Cyclobutane pyrimidine dimers (CPDs) and pyrimidine (6-4) pyrimidone photoproducts [(6-4)photoproducts] are the two major photoproducts produced in DNA by UV irradiation. Two types of photolyases have been identified, one specific for CPDs (CPD photolyase) and another specific for (6-4)photoproducts [(6-4)photolyase]. (6-4)Photolyase activity was first found in Drosophila melanogaster and to date this gene has been cloned only from this organism. The deduced amino acid sequence of the cloned gene shows that (6-4)photolyase is a member of the CPD photolyase/blue light photoreceptor family. Both CPD photolyase and blue light photoreceptor are flavoproteins and bound flavin adenine dinucleotides (FADs) are essential for their catalytic activity. Here we report isolation of a Xenopus laevis(6-4)photolyase gene and show that the (6-4)photolyase binds non- covalently to stoichiometric amounts of FAD. This is the first indication of FAD as the chromophore of (6-4)photolyase. PMID:9016626

  2. On binding specificity of (6-4) photolyase to a T(6-4)T DNA photoproduct*

    NASA Astrophysics Data System (ADS)

    Jepsen, Katrine Aalbæk; Solov'yov, Ilia A.

    2017-06-01

    Different factors lead to DNA damage and if it is not repaired in due time, the damaged DNA could initiate mutagenesis and cancer. To avoid this deadly scenario, specific enzymes can scavenge and repair the DNA, but the enzymes have to bind first to the damaged sites. We have investigated this binding for a specific enzyme called (6-4) photolyase, which is capable of repairing certain UV-induced damage in DNA. Through molecular dynamics simulations we describe the binding between photolyase and the DNA and reveal that several charged amino acid residues in the enzyme, such as arginines and lysines turn out to be important. Especially R421 is crucial, as it keeps the DNA strands at the damaged site inside the repair pocket of the enzyme separated. DNA photolyase is structurally highly homologous to a protein called cryptochrome. Both proteins are biologically activated similarly, namely through flavin co-factor photoexcitation. It is, however, striking that cryptochrome cannot repair UV-damaged DNA. The present investigation allowed us to conclude on the small but, apparently, critical differences between photolyase and cryptochrome. The performed analysis gives insight into important factors that govern the binding of UV-damaged DNA and reveal why cryptochrome cannot have this functionality.

  3. Energetics of Photoinduced Charge Migration within the Tryptophan Tetrad of an Animal (6-4) Photolyase.

    PubMed

    Cailliez, Fabien; Müller, Pavel; Firmino, Thiago; Pernot, Pascal; de la Lande, Aurélien

    2016-02-17

    Cryptochromes and photolyases are flavoproteins that undergo cascades of electron/hole transfers after excitation of the flavin cofactor. It was recently discovered that animal (6-4) photolyases, as well as animal cryptochromes, feature a chain of four tryptophan residues, while other members of the family contain merely a tryptophan triad. Transient absorption spectroscopy measurements on Xenopus laevis (6-4) photolyase have shown that the fourth residue is effectively involved in photoreduction but at the same time could not unequivocally ascertain the final redox state of this residue. In this article, polarizable molecular dynamics simulations and constrained density functional theory calculations are carried out to reveal the energetics of charge migration along the tryptophan tetrad. Migration toward the fourth tryptophan is found to be thermodynamically favorable. Electron transfer mechanisms are sought either through an incoherent hopping mechanism or through a multiple sites tunneling process. The Jortner-Bixon formulation of electron transfer (ET) theory is employed to characterize the hopping mechanism. The interplay between electron transfer and relaxation of protein and solvent is analyzed in detail. Our simulations confirm that ET in (6-4) photolyase proceeds out of equilibrium. Multiple site tunneling is modeled with the recently proposed flickering resonance mechanism. Given the position of energy levels and the distribution of electronic coupling values, tunneling over three tryptophan residues may become competitive in some cases, although a hopping mechanism is likely to be the dominant channel. For both reactive channels, computed rates are very sensitive to the starting protein configuration, suggesting that both can take place and eventually be mixed, depending on the state of the system when photoexcitation takes place.

  4. Physicochemical Mechanism of Light-Driven DNA Repair by (6-4) Photolyases

    NASA Astrophysics Data System (ADS)

    Faraji, Shirin; Dreuw, Andreas

    2014-04-01

    DNA photolyases are light-activated enzymes that repair DNA damage induced by ultraviolet (UV) radiation. UV radiation causes two of the most abundant mutagenic and cytotoxic DNA lesions: cyclobutane pyrimidine dimers and 6-4 photolesions. Photolyases selectively bind to DNA and initiate the splitting of mutagenic pyrimidine dimers via photoinduced electron transfer from a flavin adenine dinucleotide anion (FADH-) to the lesion triggering its repair. This review discusses the consecutive steps of the repair process, from both experimental and theoretical points of view. It covers the following issues: the process of how photolyases accommodate the lesion into their binding pockets, excitation energy transfer between two involved catalytic cofactors, photoinduced electron transfer to the lesion, the splitting of the pyrimidine dimer radical anion, and the fate of the unstable radical species created after the splitting of the thymine dimer. In particular, mechanisms of the splitting and restoration of the original bases are described in detail, and the most probable repair pathways are outlined.

  5. A quantum chemical perspective on (6-4) photolesion repair by photolyases.

    PubMed

    Dreuw, Andreas; Faraji, Shirin

    2013-12-14

    (6-4)-Photolyases are fascinating enzymes which repair (6-4)-DNA photolesions utilizing light themselves. It is well known that upon initial photo-excitation of an antenna pigment an electron is transferred from an adjacent FADH(-) cofactor to the photolesion initiating repair, i.e. restoration of the original undamaged DNA bases. Concerning the molecular details of this amazing repair mechanism, the early steps of energy transfer and catalytic electron generation are well understood, the terminal repair mechanism, however, is still a matter of ongoing debate. In this perspective article, recent results of quantum chemical investigations are presented, and their meaning for the repair mechanism under natural conditions is outlined. Consequences of natural light conditions, temperature and thermal equilibration are highlighted when issues like the initial protonation state of the relevant histidines and the lesion, or the direction of electron transfer are discussed.

  6. Characterization and differential expression of CPD and 6-4 DNA photolyases in Xiphophorus species and interspecies hybrids.

    PubMed

    Walter, Dylan J; Boswell, Mikki; Volk de García, Sara M; Walter, Sean M; Breitenfeldt, Erik W; Boswell, William; Walter, Ronald B

    2014-06-01

    Among the many Xiphophorus interspecies hybrid tumor models are those that exhibit ultraviolet light (UVB) induced melanoma. In previous studies, assessment of UVB induced DNA damage and nucleotide excision DNA repair has been performed in parental lines and interspecies hybrids. Species and hybrid specific differences in the levels of DNA damage induced and the dark repair rates for cyclobutane pyrimidine dimers (CPDs) and 6-4 pyrimidine pyrimidine photoproducts (6-4PPs) have been reported. However, UVB induced DNA lesions in Xiphophorus fishes are thought to primarily be repaired via light dependent CPD and 6-4PP specific photolyases. Photolyases are of evolutionary interest since they are ancient and presumably function solely to ameliorate the deleterious effects of UVB exposure. Herein, we report results from detailed studies of CPD and 6-4PP photolyase gene expression within several Xiphophorus tissues. We determined photolyase gene expression patterns before and after exposure to fluorescent light in X. maculatus, X. couchianus, and for F1 interspecies hybrids produced from crossing these two parental lines (X. maculatus Jp 163 B×X. couchianus). We present novel results showing these two photolyase genes exhibit species, tissue, and hybrid-specific differences in basal and light induced gene expression.

  7. Structural role of two histidines in the (6-4) photolyase reaction

    PubMed Central

    Yamada, Daichi; Iwata, Tatsuya; Yamamoto, Junpei; Hitomi, Kenichi; Todo, Takeshi; Iwai, Shigenori; Getzoff, Elizabeth D.; Kandori, Hideki

    2015-01-01

    Photolyases (PHRs) are DNA repair enzymes that revert UV-induced photoproducts, either cyclobutane pyrimidine dimers (CPD) or (6-4) photoproducts (PPs), into normal bases to maintain genetic integrity. (6-4) PHR must catalyze not only covalent bond cleavage, but also hydroxyl or amino group transfer, yielding a more complex mechanism than that postulated for CPD PHR. Previous mutation analysis revealed the importance of two histidines in the active center, H354 and H358 for Xenopus (6-4) PHR, whose mutations significantly lowered the enzymatic activity. Based upon highly sensitive FTIR analysis of the repair function, here we report that both H354A and H358A mutants of Xenopus (6-4) PHR still maintain their repair activity, although the efficiency is much lower than that of the wild type. Similar difference FTIR spectra between the wild type and mutant proteins suggest a common mechanism of repair in which (6-4) PP binds to the active center of each mutant, and is released after repair, as occurs in the wild type. Similar FTIR spectra also suggest that a decrease in volume by the H-to-A mutation is possibly compensated by the addition of water molecule( s). Such a modified environment is sufficient for the repair function that is probably controlled by proton-coupled electron transfer between the enzyme and substrate. On the other hand, two histidines must work in a concerted manner in the active center of the wild-type enzyme, which significantly raises the repair efficiency. PMID:27493863

  8. Similarities and differences between cyclobutane pyrimidine dimer photolyase and (6-4) photolyase as revealed by resonance Raman spectroscopy: Electron transfer from the FAD cofactor to ultraviolet-damaged DNA.

    PubMed

    Li, Jiang; Uchida, Takeshi; Todo, Takeshi; Kitagawa, Teizo

    2006-09-01

    The cyclobutane pyrimidine dimer (CPD) and (6-4) photoproduct, two major types of DNA damage caused by UV light, are repaired under illumination with near UV-visible light by CPD and (6-4) photolyases, respectively. To understand the mechanism of DNA repair, we examined the resonance Raman spectra of complexes between damaged DNA and the neutral semiquinoid and oxidized forms of (6-4) and CPD photolyases. The marker band for a neutral semiquinoid flavin and band I of the oxidized flavin, which are derived from the vibrations of the benzene ring of FAD, were shifted to lower frequencies upon binding of damaged DNA by CPD photolyase but not by (6-4) photolyase, indicating that CPD interacts with the benzene ring of FAD directly but that the (6-4) photoproduct does not. Bands II and VII of the oxidized flavin and the 1398/1391 cm(-1) bands of the neutral semiquinoid flavin, which may reflect the bending of U-shaped FAD, were altered upon substrate binding, suggesting that CPD and the (6-4) photoproduct interact with the adenine ring of FAD. When substrate was bound, there was an upshifted 1528 cm(-1) band of the neutral semiquinoid flavin in CPD photolyase, indicating a weakened hydrogen bond at N5-H of FAD, and band X seemed to be downshifted in (6-4) photolyase, indicating a weakened hydrogen bond at N3-H of FAD. These Raman spectra led us to conclude that the two photolyases have different electron transfer mechanisms as well as different hydrogen bonding environments, which account for the higher redox potential of CPD photolyase.

  9. Crystal structure of thermostable DNA photolyase: Pyrimidine-dimer recognition mechanism

    PubMed Central

    Komori, Hirofumi; Masui, Ryoji; Kuramitsu, Seiki; Yokoyama, Shigeyuki; Shibata, Takehiko; Inoue, Yorinao; Miki, Kunio

    2001-01-01

    DNA photolyase is a pyrimidine-dimer repair enzyme that uses visible light. Photolyase generally contains two chromophore cofactors. One is a catalytic cofactor directly contributing to the repair of a pyrimidine-dimer. The other is a light-harvesting cofactor, which absorbs visible light and transfers energy to the catalytic cofactor. Photolyases are classified according to their second cofactor into either a folate- or deazaflavin-type. The native structures of both types of photolyases have already been determined, but the mechanism of substrate recognition remains largely unclear because of the lack of structural information regarding the photolyase-substrate complex. Photolyase from Thermus thermophilus, the first thermostable class I photolyase found, is favorable for function analysis, but even the type of the second cofactor has not been identified. Here, we report the crystal structures of T. thermophilus photolyase in both forms of the native enzyme and the complex along with a part of its substrate, thymine. A structural comparison with other photolyases suggests that T. thermophilus photolyase has structural features allowing for thermostability and that its light-harvesting cofactor binding site bears a close resemblance to a deazaflavin-type photolyase. One thymine base is found at the hole, a putative substrate-binding site near the catalytic cofactor in the complex form. This structural data for the photolyase-thymine complex allow us to propose a detailed model for the pyrimidine-dimer recognition mechanism. PMID:11707580

  10. Crystal structure of thermostable DNA photolyase: pyrimidine-dimer recognition mechanism.

    PubMed

    Komori, H; Masui, R; Kuramitsu, S; Yokoyama, S; Shibata, T; Inoue, Y; Miki, K

    2001-11-20

    DNA photolyase is a pyrimidine-dimer repair enzyme that uses visible light. Photolyase generally contains two chromophore cofactors. One is a catalytic cofactor directly contributing to the repair of a pyrimidine-dimer. The other is a light-harvesting cofactor, which absorbs visible light and transfers energy to the catalytic cofactor. Photolyases are classified according to their second cofactor into either a folate- or deazaflavin-type. The native structures of both types of photolyases have already been determined, but the mechanism of substrate recognition remains largely unclear because of the lack of structural information regarding the photolyase-substrate complex. Photolyase from Thermus thermophilus, the first thermostable class I photolyase found, is favorable for function analysis, but even the type of the second cofactor has not been identified. Here, we report the crystal structures of T. thermophilus photolyase in both forms of the native enzyme and the complex along with a part of its substrate, thymine. A structural comparison with other photolyases suggests that T. thermophilus photolyase has structural features allowing for thermostability and that its light-harvesting cofactor binding site bears a close resemblance to a deazaflavin-type photolyase. One thymine base is found at the hole, a putative substrate-binding site near the catalytic cofactor in the complex form. This structural data for the photolyase-thymine complex allow us to propose a detailed model for the pyrimidine-dimer recognition mechanism.

  11. Synthesis of oligonucleotides containing the Dewar valence isomer of the (6-4) photoproduct and their application to (6-4) photolyase studies.

    PubMed

    Yamamoto, Junpei; Hitomi, Kenichi; Todo, Takeshi; Iwai, Shigenori

    2006-01-01

    The (6-4) photoproduct, which is a major UV light-induced lesion formed between adjacent pyrimidine bases, is isomerized to its Dewar valence isomer by exposure to longer wavelengths. We have synthesized a phosphoramidite building block of the Dewar photoproduct formed at the thymidylyl(3'-5')thymidine site, and incorporated it into oligonucleotides on a DNA synthesizer, aiming to use them for biological studies. An alternative activator, benzimidazolium triflate, gave better results, while by-products were detected at longer retention time in the ordinary synthesis. We characterized the synthetic oligonucleotides by UV conversion, nuclease digestion and mass spectrometry. Their use in the study of the (6-4) photolyase, a DNA repair enzyme, revealed its different recognition modes between the (6-4) photoproduct and the Dewar isomer.

  12. Crystal structure of archaeal photolyase from Sulfolobus tokodaii with two FAD molecules: implication of a novel light-harvesting cofactor.

    PubMed

    Fujihashi, Masahiro; Numoto, Nobutaka; Kobayashi, Yukiko; Mizushima, Akira; Tsujimura, Masanari; Nakamura, Akira; Kawarabayasi, Yutaka; Miki, Kunio

    2007-01-26

    UV exposure of DNA molecules induces serious DNA lesions. The cyclobutane pyrimidine dimer (CPD) photolyase repairs CPD-type - lesions by using the energy of visible light. Two chromophores for different roles have been found in this enzyme family; one catalyzes the CPD repair reaction and the other works as an antenna pigment that harvests photon energy. The catalytic cofactor of all known photolyases is FAD, whereas several light-harvesting cofactors are found. Currently, 5,10-methenyltetrahydrofolate (MTHF), 8-hydroxy-5-deaza-riboflavin (8-HDF) and FMN are the known light-harvesting cofactors, and some photolyases lack the chromophore. Three crystal structures of photolyases from Escherichia coli (Ec-photolyase), Anacystis nidulans (An-photolyase), and Thermus thermophilus (Tt-photolyase) have been determined; however, no archaeal photolyase structure is available. A similarity search of archaeal genomic data indicated the presence of a homologous gene, ST0889, on Sulfolobus tokodaii strain7. An enzymatic assay reveals that ST0889 encodes photolyase from S. tokodaii (St-photolyase). We have determined the crystal structure of the St-photolyase protein to confirm its structural features and to investigate the mechanism of the archaeal DNA repair system with light energy. The crystal structure of the St-photolyase is superimposed very well on the three known photolyases including the catalytic cofactor FAD. Surprisingly, another FAD molecule is found at the position of the light-harvesting cofactor. This second FAD molecule is well accommodated in the crystal structure, suggesting that FAD works as a novel light-harvesting cofactor of photolyase. In addition, two of the four CPD recognition residues in the crystal structure of An-photolyase are not found in St-photolyase, which might utilize a different mechanism to recognize the CPD from that of An-photolyase.

  13. Photoactivation of the flavin cofactor in Xenopus laevis (6 - 4) photolyase: Observation of a transient tyrosyl radical by time-resolved electron paramagnetic resonance

    NASA Astrophysics Data System (ADS)

    Weber, Stefan; Kay, Christopher W. M.; Mögling, Heike; Möbius, Klaus; Hitomi, Kenichi; Todo, Takeshi

    2002-02-01

    The light-induced electron transfer reaction of flavin cofactor photoactivation in Xenopus laevis (6-4) photolyase has been studied by continuous-wave and time-resolved electron paramagnetic resonance spectroscopy. When the photoactivation is initiated from the fully oxidized form of the flavin, a neutral flavin radical is observed as a long-lived paramagnetic intermediate of two consecutive single-electron reductions under participation of redox-active amino acid residues. By time-resolved electron paramagnetic resonance, a spin-polarized transient radical-pair signal was detected that shows remarkable differences to the signals observed in the related cyclobutane pyrimidine dimer photolyase enzyme. In (6-4) photolyase, a neutral tyrosine radical has been identified as the final electron donor, on the basis of the characteristic line width, hyperfine splitting pattern, and resonance magnetic field position of the tyrosine resonances of the transient radical pair.

  14. The g-tensor of the flavin cofactor in (6-4) photolyase: a 360 GHz/12.8 T electron paramagnetic resonance study

    NASA Astrophysics Data System (ADS)

    Schnegg, A.; Kay, C. W. M.; Schleicher, E.; Hitomi, K.; Todo, T.; Möbius, K.; Weber, S.

    2006-05-01

    The g-tensor of the neutral radical form of the flavin adenine dinucleotide cofactor FADH• of (6-4) photolyase from Xenopus laevis has been determined by very high-magnetic-field/high-microwave-frequency electron-paramagnetic resonance (EPR) performed at 360 GHz/12.8 T. Due to the high spectral resolution the anisotropy of the g-tensor could be fully resolved in the frozen-solution continuous-wave EPR spectrum. By least square fittings of spectral simulations to experimental data, the principal values of the g-tensor have been established: gX = 2.00433(5), gY = 2.00368(5), gZ = 2.00218(7). A comparison of very high-field EPR data and proton and deuteron electron-nuclear double resonance measurements yielded precise information concerning the orientation of the g-tensor with respect to the molecular frame. This data allowed a comparison to be made between the principal values of the g-tensors of the FADH• cofactors of photolyases involved in the repair of two different DNA lesions: the cyclobutane pyrimidine dimer (CPD) and the (6-4) photoproduct. It was found that gX and gZ are similar in both enzymes, whereas the gY component is slightly larger in (6-4) photolyase. This result clearly shows the sensitivity of the g-tensor to subtle differences in the protein environment experienced by the flavin.

  15. Crystal structure of DNA photolyase from Escherichia coli

    SciTech Connect

    Park, H.W.; Kim, S.T.; Sancar, A.

    1995-06-30

    Photolyase repairs ultraviolet (UV) damage to DNA by splitting the cyclobutane ring of the major UV photoproduct, the cis,syn-cyclobutane pyrimidine dimer (Pyr<>Pyr). The reaction is initiated by blue light and proceeds through long-range energy transfer, single electron transfer, and enzyme catalysis by a radical mechanism. The three-dimensional crystallographic structure of DNA photolyase from Escherichia coli is presented and the atomic model was refined to an R value of 0.172 at 2.3 {angstrom} resolution. The polypeptide chain of 471 amino acids is folded into an amino-terminal {alpha}/{beta} domain resembling dinucleotide binding domains and a carboxyl-terminal helical domain; a loop of 72 residues connects the domains. The light-harvesting cofactor 5,10-methenyltetrahydrofolylpolyglutamate (MTHF) binds in a cleft between the two domains. Energy transfer from MTHF to the catalytic cofactor flavin adenine dinucleotide (FAD) occurs over a distance of 16.8 {angstrom}. The FAD adopts a U-shaped conformation between two helix clusters in the center of the helical domain and is accessible through a hole in the surface of this domain. Dimensions and polarity of the hole match those of a Pyr<>Pyr dinucleotide, suggesting that the Pyr<>Pyr {open_quotes}flips out{close_quotes} of the helix to fit into this hole, and that electron transfer between the flavin and the Pyr<>Pyr occurs over van der Waals contact distance. 56 refs., 5 figs., 2 tabs.

  16. Searching for novel photolyases in UVC-resistant Antarctic bacteria.

    PubMed

    Marizcurrena, Juan José; Morel, María A; Braña, Victoria; Morales, Danilo; Martinez-López, Wilner; Castro-Sowinski, Susana

    2017-03-01

    Ultraviolet (UV) light irradiation has serious consequences for cell survival, including DNA damage by formation of cyclobutane pyrimidine dimers (CPD) and pyrimidine (6,4) pyrimidone photoproducts. In general, the Nucleotide Excision Repair pathway repairs these lesions; however, all living forms, except placental mammals and some marsupials, produce a flavoprotein known as photolyase that directly reverses these lesions. The aim of this work was the isolation and identification of Antarctic UVC-resistant bacteria, and the search for novel photolyases. Two Antarctic water samples were UVC-irradiated (254 nm; 50-200 J m(- 2)) and 12 UVC-resistant bacteria were isolated and identified by 16S rDNA amplification/analysis as members of the genera Pseudomonas, Janthinobacterium, Flavobacterium, Hymenobacter and Sphingomonas. The UVC 50% lethal dose and the photo-repair ability of isolates were analyzed. The occurrence of photolyase coding sequences in Pseudomonas, Hymenobacter and Sphingomonas isolates were searched by PCR or by searching in the draft DNA genome. Results suggest that Pseudomonas and Hymenobacter isolates produce CDP-photolyases, and Sphingomonas produces two CPD-photolyases and a 6,4-photolyase. Results suggest that the Antarctic environment is an important source of genetic material for the identification of novel photolyase genes with potential biotechnological applications.

  17. Photolyase: Dynamics and electron-transfer mechanisms of DNA repair.

    PubMed

    Zhang, Meng; Wang, Lijuan; Zhong, Dongping

    2017-08-09

    Photolyase, a flavoenzyme containing flavin adenine dinucleotide (FAD) molecule as a catalytic cofactor, repairs UV-induced DNA damage of cyclobutane pyrimidine dimer (CPD) and pyrimidine-pyrimidone (6-4) photoproduct using blue light. The FAD cofactor, conserved in the whole protein superfamily of photolyase/cryptochromes, adopts a unique folded configuration at the active site that plays a critical functional role in DNA repair. Here, we review our comprehensive characterization of the dynamics of flavin cofactor and its repair photocycles by different classes of photolyases on the most fundamental level. Using femtosecond spectroscopy and molecular biology, significant advances have recently been made to map out the entire dynamical evolution and determine actual timescales of all the catalytic processes in photolyases. The repair of CPD reveals seven electron-transfer (ET) reactions among ten elementary steps by a cyclic ET radical mechanism through bifurcating ET pathways, a direct tunneling route mediated by the intervening adenine and a two-step hopping path bridged by the intermediate adenine from the cofactor to damaged DNA, through the conserved folded flavin at the active site. The unified, bifurcated ET mechanism elucidates the molecular origin of various repair quantum yields of different photolyases from three life kingdoms. For 6-4 photoproduct repair, a similar cyclic ET mechanism operates and a new cyclic proton transfer with a conserved histidine residue at the active site of (6-4) photolyases is revealed. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Optical properties of the (3.4.6.4) hexagonal Archimedean photonic crystal

    NASA Astrophysics Data System (ADS)

    Jovanović, Djordje; Gajić, Radoš

    2011-01-01

    We theoretically investigated the optical properties of the lesser known (3.4.6.4) Archimedean photonic crystal. The structure is two dimensional and made of dielectric GaAs rods in air. The calculations of the band structures, equifrequency contours, and simulations of the wave propagation through the structure were performed by the plane wave expansion and finite-difference time-domain methods. With analysis of the gap map and equifrequency contours we obtained frequency ranges for best performance for wave guiding. For those frequency ranges, we designed a new type of waveguide for possible applications in integrated optics. In addition, negative refraction was exhibited by the structure.

  19. Targeted Inactivation of DNA Photolyase Genes in Medaka Fish (Oryzias latipes).

    PubMed

    Ishikawa-Fujiwara, Tomoko; Shiraishi, Eri; Fujikawa, Yoshihiro; Mori, Toshio; Tsujimura, Tohru; Todo, Takeshi

    2017-01-01

    Proteins of the cryptochrome/photolyase family (CPF) exhibit sequence and structural conservation, but their functions are divergent. Photolyase is a DNA repair enzyme that catalyzes the light-dependent repair of ultraviolet (UV)-induced photoproducts, whereas cryptochrome acts as a photoreceptor or circadian clock protein. Two types of DNA photolyase exist: CPD photolyase, which repairs cyclobutane pyrimidine dimers (CPDs), and 6-4 photolyase, which repairs 6-4 pyrimidine-pyrimidone photoproducts (6-4PPs). Although the Cry-DASH protein is classified as a cryptochrome, it also has light-dependent DNA repair activity. To determine the significance of the three light-dependent repair enzymes in recovering from solar UV-induced DNA damage at the organismal level, we generated mutants in each gene in medaka using the CRISPR genome editing technique. The light-dependent repair activity of the mutants was examined in vitro in cultured cells and in vivo in skin tissue. Light-dependent repair of CPD was lost in the CPD photolyase-deficient mutant, whereas weak repair activity against 6-4PPs persisted in the 6-4 photolyase-deficient mutant. These results suggest the existence of a heretofore unknown 6-4PP repair pathway and thus improve our understanding of the mechanisms of defense against solar UV in vertebrates.

  20. Dynamics and mechanisms of DNA repair by photolyase.

    PubMed

    Liu, Zheyun; Wang, Lijuan; Zhong, Dongping

    2015-05-14

    Photolyases, a class of flavoproteins, use blue light to repair two types of ultraviolet-induced DNA damage, a cyclobutane pyrimidine dimer (CPD) and a pyrimidine-pyrimidone (6-4) photoproduct (6-4PP). In this perspective, we review the recent progress in the repair dynamics and mechanisms of both types of DNA restoration by photolyases. We first report the spectroscopic characterization of flavin in various redox states and the active-site solvation dynamics in photolyases. We then systematically summarize the detailed repair dynamics of damaged DNA by photolyases and a biomimetic system through resolving all elementary steps on ultrafast timescales, including multiple intermolecular electron- and proton-transfer reactions and bond-breaking and -making processes. We determined the unique electron tunneling pathways, identified the key functional residues and revealed the molecular origin of high repair efficiency, and thus elucidate the molecular mechanisms and repair photocycles at the most fundamental level. We finally conclude that the active sites of photolyases, unlike the aqueous solution for the biomimetic system, provide a unique electrostatic environment and local flexibility and thus a dedicated synergy for all elementary dynamics to maximize the repair efficiency. This repair photomachine is the first enzyme that the entire functional evolution is completely mapped out in real time.

  1. Purification, cDNA cloning, and expression profiles of the cyclobutane pyrimidine dimer photolyase of Xenopus laevis.

    PubMed

    Tanida, Hiroaki; Tahara, Eiji; Mochizuki, Miwa; Yamane, Yukiko; Ryoji, Masaru

    2005-12-01

    Photolyase is a light-dependent enzyme that repairs pyrimidine dimers in DNA. Two types of photolyases have been found in frog Xenopus laevis, one for repairing cyclobutane pyrimidine dimers (CPD photolyase) and the other for pyrimidine-pyrimidone (6-4)photoproduct [(6-4)photolyase]. However, little is known about the former type of the Xenopus photolyases. To characterize this enzyme and its expression profiles, we isolated the entire coding region of a putative CPD photolyase cDNA by extending an EST (expressed sequence tag) sequence obtained from the Xenopus database. Nucleotide sequence analysis of the cDNA revealed a protein of 557 amino acids with close similarity to CPD photolyase of rat kangaroo. The identity of this cDNA was further established by the molecular mass (65 kDa) and the partial amino acid sequences of the major CPD photolyase that we purified from Xenopus ovaries. The gene of this enzyme is expressed in various tissues of Xenopus. Even internal organs like heart express relatively high levels of mRNA. A much smaller amount was found in skin, although UV damage is thought to occur most frequently in this tissue. Such expression profiles suggest that CPD photolyase may have roles in addition to the photorepair function.

  2. Light-induced activation of class II cyclobutane pyrimidine dimer photolyases.

    PubMed

    Okafuji, Asako; Biskup, Till; Hitomi, Kenichi; Getzoff, Elizabeth D; Kaiser, Gebhard; Batschauer, Alfred; Bacher, Adelbert; Hidema, Jun; Teranishi, Mika; Yamamoto, Kazuo; Schleicher, Erik; Weber, Stefan

    2010-05-04

    Light-induced activation of class II cyclobutane pyrimidine dimer (CPD) photolyases of Arabidopsis thaliana and Oryza sativa has been examined by UV/Vis and pulsed Davies-type electron-nuclear double resonance (ENDOR) spectroscopy, and the results compared with structure-known class I enzymes, CPD photolyase and (6-4) photolyase. By ENDOR spectroscopy, the local environment of the flavin adenine dinucleotide (FAD) cofactor is probed by virtue of proton hyperfine couplings that report on the electron-spin density at the positions of magnetic nuclei. Despite the amino-acid sequence dissimilarity as compared to class I enzymes, the results indicate similar binding motifs for FAD in the class II photolyases. Furthermore, the photoreduction kinetics starting from the FAD cofactor in the fully oxidized redox state, FAD(ox), have been probed by UV/Vis spectroscopy. In Escherichia coli (class I) CPD photolyase, light-induced generation of FADH from FAD(ox), and subsequently FADH(-) from FADH, proceeds in a step-wise fashion via a chain of tryptophan residues. These tryptophans are well conserved among the sequences and within all known structures of class I photolyases, but completely lacking from the equivalent positions of class II photolyase sequences. Nevertheless, class II photolyases show photoreduction kinetics similar to those of the class I enzymes. We propose that a different, but also effective, electron-transfer cascade is conserved among the class II photolyases. The existence of such electron transfer pathways is supported by the observation that the catalytically active fully reduced flavin state obtained by photoreduction is maintained even under oxidative conditions in all three classes of enzymes studied in this contribution. (c) 2010 Elsevier B.V. All rights reserved.

  3. PHL1 of Cercospora Zeae-Maydis Encodes a Member of the Photolyase/Cryptochrome Family Involved in UV Protection and Fungal Development

    USDA-ARS?s Scientific Manuscript database

    DNA photolyases harvest light energy to repair genomic lesions induced by UV light, whereas cryptochromes, paralogs of 6-4 DNA photolyases, have evolved in plants and animals as blue-light photoreceptors that function exclusively in signal transduction. Although members of the cryptochrome/photolyas...

  4. PHL1 of Cercospora zeae-maydis encodes a member of the photolyase/cryptochrome family involved in UV protection and fungal development.

    PubMed

    Bluhm, B H; Dunkle, L D

    2008-10-01

    DNA photolyases harvest light energy to repair genomic lesions induced by UV irradiation, whereas cryptochromes, presumptive descendants of 6-4 DNA photolyases, have evolved in plants and animals as blue-light photoreceptors that function exclusively in signal transduction. Orthologs of 6-4 photolyases are predicted to exist in the genomes of some filamentous fungi, but their function is unknown. In this study, we identified two putative photolyase-encoding genes in the maize foliar pathogen Cercospora zeae-maydis: CPD1, an ortholog of cyclobutane pyrimidine dimer (CPD) photolyases described in other filamentous fungi, and PHL1, a cryptochrome/6-4 photolyase-like gene. Strains disrupted in PHL1 (Deltaphl1) displayed abnormalities in development and secondary metabolism but were unaffected in their ability to infect maize leaves. After exposure to lethal doses of UV light, conidia of Deltaphl1 strains were abolished in photoreactivation and displayed reduced expression of CPD1, as well as RAD2 and RVB2, orthologs of genes involved in nucleotide excision and chromatin remodeling during DNA damage repair. This study presents the first characterization of a 6-4 photolyase ortholog in a filamentous fungus and provides evidence that PHL1 regulates responses to UV irradiation.

  5. Cloning and characterization of a gene (UVR3) required for photorepair of 6-4 photoproducts in Arabidopsis thaliana.

    PubMed Central

    Nakajima, S; Sugiyama, M; Iwai, S; Hitomi, K; Otoshi, E; Kim, S T; Jiang, C Z; Todo, T; Britt, A B; Yamamoto, K

    1998-01-01

    UV radiation induces two major classes of pyrimidine dimers: the pyrimidine [6-4] pyrimidone photoproduct (6-4 product) and the cyclobutane pyrimidine dimer (CPD). Many organisms produce enzymes, termed photolyases, that specifically bind to these damage products and split them via a UV-A/blue light-dependent mechanism, thereby reversing the damage. These photolyases are specific for either CPDs or 6-4 products. A gene that expresses a protein with 6-4 photolyase activity in vitro was recently cloned from Drosophila melanogaster and Xenopus laevis. We report here the isolation of a homolog of this gene, cloned on the basis of sequence similarity, from the higher plant Arabidopsis thaliana. This cloned gene produces a protein with 6-4 photolyase activity when expressed in Escherichia coli. We also find that a previously described mutant of Arabidopsis (uvr3) that is defective in photoreactivation of 6-4 products carries a nonsense mutation in this 6-4 photolyase homolog. We have therefore termed this gene UVR3. Although homologs of this gene have previously been shown to produce a functional 6-4 photolyase when expressed in heterologous systems, this is the first demonstration of a requirement for this gene for photoreactivation of 6-4 products in vivo. PMID:9421527

  6. Identification and Purification of the CPD Photolyase in Vibrio parahaemolyticus RIMD2210633.

    PubMed

    Su, Zehong; Lian, Gaojian; Mawatari, Kazuaki; Tang, Ping; He, Shuya; Shimohata, Takaaki; Wu, Yimou; Yin, Weidong; Takahashi, Akira

    2015-01-01

    Photoreactivation is an error-free mechanism of DNA repair, utilized by prokaryotes and most eukaryotes and is catalyzed by specific enzymes called DNA photolyases. Photoreactivation has been reported in Vibrio parahaemolyticus WP28; however, information on photolyases in V. parahaemolyticus (V.p) strains has not been reported. This study examined the photoreactivation in V.p RIMD2210633. The photolyase responsible for repairing cyclobutane pyrimidine dimer (CPD) in DNA was identified, and the corresponding gene was determined as VPA1471. The protein was overexpressed in Escherichia coli and was purified for functional assessment in vitro. The mRNA level and protein expression level of this gene increased after ultraviolet A (UVA) illumination following ultraviolet C (UVC) irradiation. In vitro experiments confirmed that the protein encoded by VPA1471 could reduce the quantity of CPD in DNA. We designated the corresponding gene and protein of VPA1471 phr and Phr, respectively, although the function of two other photolyase/cryptochrome family members, VPA0203 and VPA0204, remains unclear. UV (ultraviolet) irradiation experiments suggest that these two genes possess some photorepairing ability. Therefore, we hypothesize that VPA0203 and VPA0204 encode (6-4) photolyase in V. parahaemolyticus RIMD2210633.

  7. Light-driven enzymatic catalysis of DNA repair: a review of recent biophysical studies on photolyase.

    PubMed

    Weber, Stefan

    2005-02-25

    More than 50 years ago, initial experiments on enzymatic photorepair of ultraviolet (UV)-damaged DNA were reported [Proc. Natl. Acad. Sci. U. S. A. 35 (1949) 73]. Soon after this discovery, it was recognized that one enzyme, photolyase, is able to repair UV-induced DNA lesions by effectively reversing their formation using blue light. The enzymatic process named DNA photoreactivation depends on a non-covalently bound cofactor, flavin adenine dinucleotide (FAD). Flavins are ubiquitous redox-active catalysts in one- and two-electron transfer reactions of numerous biological processes. However, in the case of photolyase, not only the ground-state redox properties of the FAD cofactor are exploited but also, and perhaps more importantly, its excited-state properties. In the catalytically active, fully reduced redox form, the FAD absorbs in the blue and near-UV ranges of visible light. Although there is no direct experimental evidence, it appears generally accepted that starting from the excited singlet state, the chromophore initiates a reductive cleavage of the two major DNA photodamages, cyclobutane pyrimidine dimers and (6-4) photoproducts, by short-distance electron transfer to the DNA lesion. Back electron transfer from the repaired DNA segment is believed to eventually restore the initial redox states of the cofactor and the DNA nucleobases, resulting in an overall reaction with net-zero exchanged electrons. Thus, the entire process represents a true catalytic cycle. Many biochemical and biophysical studies have been carried out to unravel the fundamentals of this unique mode of action. The work has culminated in the elucidation of the three-dimensional structure of the enzyme in 1995 that revealed remarkable details, such as the FAD-cofactor arrangement in an unusual U-shaped configuration. With the crystal structure of the enzyme at hand, research on photolyases did not come to an end but, for good reason, intensified: the geometrical structure of the enzyme

  8. Eukaryotic class II cyclobutane pyrimidine dimer photolyase structure reveals basis for improved ultraviolet tolerance in plants.

    PubMed

    Hitomi, Kenichi; Arvai, Andrew S; Yamamoto, Junpei; Hitomi, Chiharu; Teranishi, Mika; Hirouchi, Tokuhisa; Yamamoto, Kazuo; Iwai, Shigenori; Tainer, John A; Hidema, Jun; Getzoff, Elizabeth D

    2012-04-06

    Ozone depletion increases terrestrial solar ultraviolet B (UV-B; 280-315 nm) radiation, intensifying the risks plants face from DNA damage, especially covalent cyclobutane pyrimidine dimers (CPD). Without efficient repair, UV-B destroys genetic integrity, but plant breeding creates rice cultivars with more robust photolyase (PHR) DNA repair activity as an environmental adaptation. So improved strains of Oryza sativa (rice), the staple food for Asia, have expanded rice cultivation worldwide. Efficient light-driven PHR enzymes restore normal pyrimidines to UV-damaged DNA by using blue light via flavin adenine dinucleotide to break pyrimidine dimers. Eukaryotes duplicated the photolyase gene, producing PHRs that gained functions and adopted activities that are distinct from those of prokaryotic PHRs yet are incompletely understood. Many multicellular organisms have two types of PHR: (6-4) PHR, which structurally resembles bacterial CPD PHRs but recognizes different substrates, and Class II CPD PHR, which is remarkably dissimilar in sequence from bacterial PHRs despite their common substrate. To understand the enigmatic DNA repair mechanisms of PHRs in eukaryotic cells, we determined the first crystal structure of a eukaryotic Class II CPD PHR from the rice cultivar Sasanishiki. Our 1.7 Å resolution PHR structure reveals structure-activity relationships in Class II PHRs and tuning for enhanced UV tolerance in plants. Structural comparisons with prokaryotic Class I CPD PHRs identified differences in the binding site for UV-damaged DNA substrate. Convergent evolution of both flavin hydrogen bonding and a Trp electron transfer pathway establish these as critical functional features for PHRs. These results provide a paradigm for light-dependent DNA repair in higher organisms.

  9. Crystal structures of ethyl 6-(4-methyl-phen-yl)-4-oxo-4H-chromene-2-carboxyl-ate and ethyl 6-(4-fluoro-phen-yl)-4-oxo-4H-chromene-2-carboxyl-ate.

    PubMed

    Gomes, Ligia R; Low, John Nicolson; Fernandes, Carlos; Gaspar, Alexandra; Borges, Fernanda

    2016-01-01

    The crystal structures of two chromone derivatives, viz. ethyl 6-(4-methyl-phen-yl)-4-oxo-4H-chromene-2-carboxyl-ate, C19H16O4, (1), and ethyl 6-(4-fluoro-phen-yl)-4-oxo-4H-chromene-2-carboxyl-ate C18H13FO4, (2), have been determined: (1) crystallizes with two mol-ecules in the asymmetric unit. A comparison of the dihedral angles beween the mean planes of the central chromone core with those of the substituents, an ethyl ester moiety at the 2-position and a para-substituted phenyl ring at the 6-position shows that each mol-ecule differs significantly from the others, even the two independent mol-ecules (a and b) of (1). In all three mol-ecules, the carbonyl groups of the chromone and the carboxyl-ate are trans-related. The supra-molecular structure of (1) involves only weak C-H⋯π inter-actions between H atoms of the substituent phenyl group and the phenyl group, which link mol-ecules into a chain of alternating mol-ecules a and b, and weak π-π stacking inter-actions between the chromone units. The packing in (2) involves C-H⋯O inter-actions, which form a network of two inter-secting ladders involving the carbonyl atom of the carboxyl-ate group as the acceptor for H atoms at the 7-position of the chromone ring and from an ortho-H atom of the exocyclic benzene ring. The carbonyl atom of the chromone acts as an acceptor from a meta-H atom of the exocyclic benzene ring. π-π inter-actions stack the mol-ecules by unit translation along the a axis.

  10. Enhanced UV Resistance and Improved Killing of Malaria Mosquitoes by Photolyase Transgenic Entomopathogenic Fungi

    PubMed Central

    Fang, Weiguo; St. Leger, Raymond J.

    2012-01-01

    The low survival of microbial pest control agents exposed to UV is the major environmental factor limiting their effectiveness. Using gene disruption we demonstrated that the insect pathogenic fungus Metarhizium robertsii uses photolyases to remove UV-induced cyclobutane pyrimidine dimers (CPD) and pyrimidine (6-4) photoproducts [(6-4)PPs] from its DNA. However, this photorepair is insufficient to fix CPD lesions and prevent the loss of viability caused by seven hours of solar radiation. Expression of a highly efficient archaeal (Halobacterium salinarum) CPD photolyase increased photorepair >30-fold in both M. robertsii and Beauveria bassiana. Consequently, transgenic strains were much more resistant to sunlight and retained virulence against the malaria vector Anopheles gambiae. In the field this will translate into much more efficient pest control over a longer time period. Conversely, our data shows that deleting native photolyase genes will strictly contain M. robertsii to areas protected from sunlight, alleviating safety concerns that transgenic hypervirulent Metarhizium spp will spread from mosquito traps or houses. The precision and malleability of the native and transgenic photolyases allows design of multiple pathogens with different strategies based on the environments in which they will be used. PMID:22912789

  11. A gene for a Class II DNA photolyase from Oryza sativa: cloning of the cDNA by dilution-amplification.

    PubMed

    Hirouchi, T; Nakajima, S; Najrana, T; Tanaka, M; Matsunaga, T; Hidema, J; Teranishi, M; Fujino, T; Kumagai, T; Yamamoto, K

    2003-07-01

    Ultraviolet radiation induces the formation of two classes of photoproducts in DNA-the cyclobutane pyrimidine dimer (CPD) and the pyrimidine [6-4] pyrimidone photoproduct (6-4 product). Many organisms produce enzymes, termed photolyases, which specifically bind to these lesions and split them via a UV-A/blue light-dependent mechanism, thereby reversing the damage. These photolyases are specific for either CPDs or 6-4 products. Two classes of photolyases (class I and class II) repair CPDs. A gene that encodes a protein with class II CPD photolyase activity in vitro has been cloned from several plants including Arabidopsis thaliana, Cucumis sativus and Chlamydomonas reinhardtii. We report here the isolation of a homolog of this gene from rice (Oryza sativa), which was cloned on the basis of sequence similarity and PCR-based dilution-amplification. The cDNA comprises a very GC-rich (75%) 5; region, while the 3; portion has a GC content of 50%. This gene encodes a protein with CPD photolyase activity when expressed in E. coli. The CPD photolyase gene encodes at least two types of mRNA, formed by alternative splicing of exon 5. One of the mRNAs encodes an ORF for 506 amino acid residues, while the other is predicted to code for 364 amino acid residues. The two RNAs occur in about equal amounts in O. sativa cells.

  12. Residues at a Single Site Differentiate Animal Cryptochromes from Cyclobutane Pyrimidine Dimer Photolyases by Affecting the Proteins' Preferences for Reduced FAD.

    PubMed

    Xu, Lei; Wen, Bin; Wang, Yuan; Tian, Changqing; Wu, Mingcai; Zhu, Guoping

    2017-06-19

    Cryptochromes (CRYs) and photolyases belong to the cryptochrome/photolyase family (CPF). Reduced FAD is essential for photolyases to photorepair UV-induced cyclobutane pyrimidine dimers (CPDs) or 6-4 photoproducts in DNA. In Drosophila CRY (dCRY, a type I animal CRY), FAD is converted to the anionic radical but not to the reduced state upon illumination, which might induce a conformational change in the protein to relay the light signal downstream. To explore the foundation of these differences, multiple sequence alignment of 650 CPF protein sequences was performed. We identified a site facing FAD (Ala377 in Escherichia coli CPD photolyase and Val415 in dCRY), hereafter referred to as "site 377", that was distinctly conserved across these sequences: CPD photolyases often had Ala, Ser, or Asn at this site, whereas animal CRYs had Ile, Leu, or Val. The binding affinity for reduced FAD, but not the photorepair activity of E. coli photolyase, was dramatically impaired when replacing Ala377 with any of the three CRY residues. Conversely, in V415S and V415N mutants of dCRY, FAD was photoreduced to its fully reduced state after prolonged illumination, and light-dependent conformational changes of these mutants were severely inhibited. We speculate that the residues at site 377 play a key role in the different preferences of CPF proteins for reduced FAD, which differentiate animal CRYs from CPD photolyases. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Photoactivated excited states of DNA repair photolyase: Dynamical and semiempircal identification

    NASA Astrophysics Data System (ADS)

    Zheng, Xuehe; Ly, Ngan M.; Stuchebrukhov, Alexei A.

    DNA damage caused by UV light radiation is often naturally repaired in a process initiated by excited state electron transfer from the photoactivated photolyase enzyme to the DNA cyclobutane pyrimidine dimer lesion. The active cofactor in the excited state electron transfer in the photolyase is the two-electron fully reduced form of the flavin adenine dinucleotide (FADH-). To calculate electron tunneling matrix element and model the DNA binding with photolyase, the LUMO of the FADH- calculated using extended Huckel method was previously chosen from the SCF wavefunctions. Recently, the DNA-photolyase complex was crystallized in its bound form, in good agreement with our previous model in even minute details at the active site. Here we carry out molecular dynamics simulation of the entire complex using the new experimental structure of Anacystis nidulans and identify the low-lying photoactivated states of the enzyme for the dynamical confirmations. Our results from ZINDO/S CIS calculations are compared with experimental UV spectra, and their implications for excited state electron transfer and energy transfer are discussed.0

  14. The Class III Cyclobutane Pyrimidine Dimer Photolyase Structure Reveals a New Antenna Chromophore Binding Site and Alternative Photoreduction Pathways*

    PubMed Central

    Scheerer, Patrick; Zhang, Fan; Kalms, Jacqueline; von Stetten, David; Krauß, Norbert; Oberpichler, Inga; Lamparter, Tilman

    2015-01-01

    Photolyases are proteins with an FAD chromophore that repair UV-induced pyrimidine dimers on the DNA in a light-dependent manner. The cyclobutane pyrimidine dimer class III photolyases are structurally unknown but closely related to plant cryptochromes, which serve as blue-light photoreceptors. Here we present the crystal structure of a class III photolyase termed photolyase-related protein A (PhrA) of Agrobacterium tumefaciens at 1.67-Å resolution. PhrA contains 5,10-methenyltetrahydrofolate (MTHF) as an antenna chromophore with a unique binding site and mode. Two Trp residues play pivotal roles for stabilizing MTHF by a double π-stacking sandwich. Plant cryptochrome I forms a pocket at the same site that could accommodate MTHF or a similar molecule. The PhrA structure and mutant studies showed that electrons flow during FAD photoreduction proceeds via two Trp triads. The structural studies on PhrA give a clearer picture on the evolutionary transition from photolyase to photoreceptor. PMID:25784552

  15. The class III cyclobutane pyrimidine dimer photolyase structure reveals a new antenna chromophore binding site and alternative photoreduction pathways.

    PubMed

    Scheerer, Patrick; Zhang, Fan; Kalms, Jacqueline; von Stetten, David; Krauß, Norbert; Oberpichler, Inga; Lamparter, Tilman

    2015-05-01

    Photolyases are proteins with an FAD chromophore that repair UV-induced pyrimidine dimers on the DNA in a light-dependent manner. The cyclobutane pyrimidine dimer class III photolyases are structurally unknown but closely related to plant cryptochromes, which serve as blue-light photoreceptors. Here we present the crystal structure of a class III photolyase termed photolyase-related protein A (PhrA) of Agrobacterium tumefaciens at 1.67-Å resolution. PhrA contains 5,10-methenyltetrahydrofolate (MTHF) as an antenna chromophore with a unique binding site and mode. Two Trp residues play pivotal roles for stabilizing MTHF by a double π-stacking sandwich. Plant cryptochrome I forms a pocket at the same site that could accommodate MTHF or a similar molecule. The PhrA structure and mutant studies showed that electrons flow during FAD photoreduction proceeds via two Trp triads. The structural studies on PhrA give a clearer picture on the evolutionary transition from photolyase to photoreceptor. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  16. Electrically monitoring DNA repair by photolyase

    NASA Astrophysics Data System (ADS)

    DeRosa, Maria C.; Sancar, Aziz; Barton, Jacqueline K.

    2005-08-01

    Cyclobutane pyrimidine dimers are the major DNA photoproducts produced upon exposure to UV radiation. If left unrepaired, these lesions can lead to replication errors, mutation, and cell death. Photolyase is a light-activated flavoenzyme that binds to pyrimidine dimers in DNA and repairs them in a reaction triggered by electron transfer from the photoexcited flavin cofactor to the dimer. Using gold electrodes modified with DNA duplexes containing a cyclobutane thymine dimer (T<>T), here we probe the electrochemistry of the flavin cofactor in Escherichia coli photolyase. Cyclic and square-wave voltammograms of photolyase deposited on these electrodes show a redox signal at 40 mV versus normal hydrogen electrode, consistent with electron transfer to and from the flavin in the DNA-bound protein. This signal is dramatically attenuated on surfaces where the π-stacking of the DNA bases is perturbed by the presence of an abasic site below the T<>T, an indication that the redox pathway is DNA-mediated. DNA repair can, moreover, be monitored electrically. Exposure of photolyase on T<>T-damaged DNA films to near-UV/blue light leads to changes in the flavin signal consistent with repair, as confirmed by parallel HPLC experiments. These results demonstrate the exquisite sensitivity of DNA electrochemistry to perturbations in base pair stacking and the applicability of this chemistry to probe reactions of proteins with DNA. Author contributions: M.C.D. and J.K.B. designed research; M.C.D. performed research; A.S. contributed new reagents/analytic tools; M.C.D. analyzed data; and M.C.D. and J.K.B. wrote the paper.This paper was submitted directly (Track II) to the PNAS office.Abbreviations: T<>T, thymine dimer; CT, charge transport.

  17. CPD photolyase gene from Spinacia oleracea: repair of UV-damaged DNA and expression in plant organs.

    PubMed

    Yoshihara, Ryouhei; Imaki, Toshiyuki; Hori, Manabu; Watanabe, Chihiro; Yamamoto, Kazuo; Takimoto, Koichi

    2005-06-01

    The UV-B radiation contained in solar radiation has deleterious effects on plant growth, development and physiology. Specific damage to DNA caused by UV radiation involves the cyclobutyl pyrimidine dimers (CPD) and the pyrimidine (6-4) pyrimidone photoproducts. CPDs are repaired by CPD photolyase via a UV-A/blue light-dependent mechanism. The gene for the class II CPD photolyase has been cloned from higher plants such as Arabidopsis, cucumbers and rice. We isolated and characterized the cDNA and a genomic clone encoding the spinach class II CPD photolyase. The gene consisted of 3777 bases and 9 exons. The sequence of amino acids predicted from the nucleotide sequence of the cDNA of the gene was highly homologous to that of the higher plants listed above. When a photolyase-deficient Escherichia coli strain was transformed with the cDNA, photoreactivation activity was partially restored, by the illumination with photoreactivating light, resulting in an increased survival and decreased content of CPDs in the Escherichia coli genome. In both the male and female plants, the gene was highly expressed in leaves and flowers under the condition of 14-h light and 10-h dark cycle. The expression in the roots was quite low compared with the other organs.

  18. The Trichoderma reesei Cry1 Protein Is a Member of the Cryptochrome/Photolyase Family with 6–4 Photoproduct Repair Activity

    PubMed Central

    Guzmán-Moreno, Jesús; Flores-Martínez, Alberto; Brieba, Luis G.; Herrera-Estrella, Alfredo

    2014-01-01

    DNA-photolyases use UV-visible light to repair DNA damage caused by UV radiation. The two major types of DNA damage are cyclobutane pyrimidine dimers (CPD) and 6–4 photoproducts (6-4PP), which are repaired under illumination by CPD and 6–4 photolyases, respectively. Cryptochromes are proteins related to DNA photolyases with strongly reduced or lost DNA repair activity, and have been shown to function as blue-light photoreceptors and to play important roles in circadian rhythms in plants and animals. Both photolyases and cryptochromes belong to the cryptochrome/photolyase family, and are widely distributed in all organisms. Here we describe the characterization of cry1, a member of the cryptochrome/photolyase protein family of the filamentous fungus Trichoderma reesei. We determined that cry1 transcript accumulates when the fungus is exposed to light, and that such accumulation depends on the photoreceptor Blr1 and is modulated by Envoy. Conidia of cry1 mutants show decreased photorepair capacity of DNA damage caused by UV light. In contrast, strains over-expressing Cry1 show increased repair, as compared to the parental strain even in the dark. These observations suggest that Cry1 may be stimulating other systems involved in DNA repair, such as the nucleotide excision repair system. We show that Cry1, heterologously expressed and purified from E. coli, is capable of binding to undamaged and 6-4PP damaged DNA. Photorepair assays in vitro clearly show that Cry1 repairs 6-4PP, but not CPD and Dewar DNA lesions. PMID:24964051

  19. Electron Transfer Mechanisms of DNA Repair by Photolyase

    NASA Astrophysics Data System (ADS)

    Zhong, Dongping

    2015-04-01

    Photolyase is a flavin photoenzyme that repairs two DNA base damage products induced by ultraviolet (UV) light: cyclobutane pyrimidine dimers and 6-4 photoproducts. With femtosecond spectroscopy and site-directed mutagenesis, investigators have recently made significant advances in our understanding of UV-damaged DNA repair, and the entire enzymatic dynamics can now be mapped out in real time. For dimer repair, six elementary steps have been characterized, including three electron transfer reactions and two bond-breaking processes, and their reaction times have been determined. A unique electron-tunneling pathway was identified, and the critical residues in modulating the repair function at the active site were determined. The dynamic synergy between the elementary reactions for maintaining high repair efficiency was elucidated, and the biological nature of the flavin active state was uncovered. For 6-4 photoproduct repair, a proton-coupled electron transfer repair mechanism has been revealed. The elucidation of electron transfer mechanisms and two repair photocycles is significant and provides a molecular basis for future practical applications, such as in rational drug design for curing skin cancer.

  20. Electron transfer mechanisms of DNA repair by photolyase.

    PubMed

    Zhong, Dongping

    2015-04-01

    Photolyase is a flavin photoenzyme that repairs two DNA base damage products induced by ultraviolet (UV) light: cyclobutane pyrimidine dimers and 6-4 photoproducts. With femtosecond spectroscopy and site-directed mutagenesis, investigators have recently made significant advances in our understanding of UV-damaged DNA repair, and the entire enzymatic dynamics can now be mapped out in real time. For dimer repair, six elementary steps have been characterized, including three electron transfer reactions and two bond-breaking processes, and their reaction times have been determined. A unique electron-tunneling pathway was identified, and the critical residues in modulating the repair function at the active site were determined. The dynamic synergy between the elementary reactions for maintaining high repair efficiency was elucidated, and the biological nature of the flavin active state was uncovered. For 6-4 photoproduct repair, a proton-coupled electron transfer repair mechanism has been revealed. The elucidation of electron transfer mechanisms and two repair photocycles is significant and provides a molecular basis for future practical applications, such as in rational drug design for curing skin cancer.

  1. A new mineral species ferricoronadite, Pb[Mn6 4+(Fe3+, Mn3+)2]O16: mineralogical characterization, crystal chemistry and physical properties

    NASA Astrophysics Data System (ADS)

    Chukanov, Nikita V.; Aksenov, Sergey M.; Jančev, Simeon; Pekov, Igor V.; Göttlicher, Jörg; Polekhovsky, Yury S.; Rusakov, Vyacheslav S.; Nelyubina, Yuliya V.; Van, Konstantin V.

    2016-07-01

    A new mineral ferricoronadite with the simplified formula Pb(Mn6 4+Fe2 3+)O16 was discovered in the orogenetic zone related to the "Mixed Series" metamorphic complex near the Nežilovo village, Pelagonian massif, Republic of Macedonia. Associated minerals are franklinite, gahnite, hetaerolite, roméite, almeidaite, Mn-analogue of plumboferrite, zincohögbomite analogue with Fe3+ > Al, zincochromite, Zn-bearing talc, Zn-bearing muscovite, baryte, quartz and zircon. Ferricoronadite is a late hydrothermal mineral forming veinlets up to 8 mm thick in granular aggregate predominantly composed by zinc-dominant spinels. The new mineral is opaque, black, with brownish black streak. The luster is strong submetallic to metallic. The micro-indentation hardness is 819 kg/mm2. Distinct cleavage is observed on (100). Ferricoronadite is brittle, with uneven fracture. The density calculated from the empirical formula is 5.538 g/cm3. In reflected light, ferricoronadite is light gray. The reflectance values [ R max/ R min, % ( λ, nm)] are: 28.7/27.8 (470), 27.6/26.6 (546), 27.2/26.1 (589), 26.5/25.5 (650). The IR spectrum shows the absence of H2O and OH groups. According to the Mössbauer spectrum, all iron is trivalent. The Mn K-edge XANES spectroscopy shows that Mn is predominantly tetravalent, with subordinate Mn3+. The chemical composition is (wt%; electron microprobe, Mn apportioned between MnO2 and Mn2O3 based on the charge-balance requirement): BaO 5.16, PbO 24.50, ZnO 0.33, Al2O3 0.50, Mn2O3 9.90, Fe2O3 11.45, TiO2 4.19, MnO2 44.81, total 100.84. The empirical formula based on 8 cations Mn + Fe + Ti + Al + Zn pfu is Pb1.03Ba0.32(Mn 4.85 4+ Fe 1.35 3+ Mn 1.18 3+ Ti0.49Al0.09Zn0.04)Σ8.00O16. The crystal structure was determined using single-crystal X-ray diffraction data. The new mineral is tetragonal, space group I4/ m, a = 9.9043(7), c = 2.8986(9) Å, V = 284.34(9) Å3, Z = 1. In ferricoronadite, double chains of edge-sharing (Mn, Fe, Ti)-centered octahedra are connected

  2. Human white blood cells contain cyclobutyl pyrimidine dimer photolyase

    SciTech Connect

    Sutherland, B.M.; Bennett, P.V.

    1995-10-10

    Although enzymatic photoreactivation of cyclobutyl pyrimidine dimers in DNA is present in almost all organisms, its presence in placental mammals is controversial. We tested human white blood cells for photolyase by using three defined DNAs (suprecoiled pET-2, nonsupercoiled bacteriphage {lambda}, and a defined-sequence 287-bp oligonucleotide), two dimer-specific endonucleases (T4 endonuclease V and UV endonuclease from Micrococcus luteus), and three assay methods. We show that human white blood cells contain photolyase that can photorepair pyrimidine dimers in defined supercoiled and linear DNAs and in a 287-bp oligonucleotide and that human photolyase is active on genomic DNA in intact human cells. 44 refs., 3 figs.

  3. Evolutionary History of the Photolyase/Cryptochrome Superfamily in Eukaryotes

    PubMed Central

    Mei, Qiming; Dvornyk, Volodymyr

    2015-01-01

    Background Photolyases and cryptochromes are evolutionarily related flavoproteins, which however perform distinct physiological functions. Photolyases (PHR) are evolutionarily ancient enzymes. They are activated by light and repair DNA damage caused by UV radiation. Although cryptochromes share structural similarity with DNA photolyases, they lack DNA repair activity. Cryptochrome (CRY) is one of the key elements of the circadian system in animals. In plants, CRY acts as a blue light receptor to entrain circadian rhythms, and mediates a variety of light responses, such as the regulation of flowering and seedling growth. Results We performed a comprehensive evolutionary analysis of the CRY/PHR superfamily. The superfamily consists of 7 major subfamilies: CPD class I and CPD class II photolyases, (6–4) photolyases, CRY-DASH, plant PHR2, plant CRY and animal CRY. Although the whole superfamily evolved primarily under strong purifying selection (average ω = 0.0168), some subfamilies did experience strong episodic positive selection during their evolution. Photolyases were lost in higher animals that suggests natural selection apparently became weaker in the late stage of evolutionary history. The evolutionary time estimates suggested that plant and animal CRYs evolved in the Neoproterozoic Era (~1000–541 Mya), which might be a result of adaptation to the major climate and global light regime changes occurred in that period of the Earth’s geological history. PMID:26352435

  4. Supramolecular hydrogen-bonded 1D arrangement in the crystals of 2,4-diamino-6-benzyl-1,3,5-triazine and 2,4-diamino-6-(4‧-methylbenzyl)-1,3,5-triazine

    NASA Astrophysics Data System (ADS)

    Janczak, Jan; Kubiak, Ryszard

    2009-02-01

    Two crystals of triazine derivatives, 2,4-diamino-6-benzyl-1,3,5-triazine ( 1) and 2,4-diamino-6-(4'-methylbenzyl)-1,3,5-triazine ( 2), are synthesised by a direct reaction of cyanoguanidine with the respective cyanocompounds. The IR spectra of the compounds are very similar. In the crystals the molecules are interconnected by N sbnd H⋯N hydrogen bonds forming one-dimensional hydrogen bonded polymer in 1 and three-dimensional hydrogen bonded network in 2. The arrangement of molecules in the crystal of 1 is denser than in 2 due to the π-π interactions between the π-clouds of the aromatic triazine rings that are absent in the crystal of 2. The geometries of the molecules in the crystals have been compared with those obtained by ab-initio molecular orbital calculated results that represent the geometries of molecules in the gas-phase.

  5. Molecular Understanding of Efficient DNA Repair Machinery of Photolyase

    NASA Astrophysics Data System (ADS)

    Tan, Chuang; Liu, Zheyun; Li, Jiang; Guo, Xunmin; Wang, Lijuan; Zhong, Dongping

    2012-06-01

    Photolyases repair the UV-induced pyrimidine dimers in damage DNA with high efficiency, through a cylic light-driven electron transfer radical mechanism. We report here our systematic studies of the repair dynamics in E. coli photolyase with mutation of five active-site residues. The significant loss of repair efficiency by the mutation indicates that those active-site residues play an important role in the DNA repair by photolyase. To understand how the active-site residues modulate the efficiency, we mapped out the entire evolution of each elementary step during the repair in those photolyase mutants with femtosecond resolution. We completely analyzed the electron transfer dynamics using the Sumi-Marcus model. The results suggest that photolyase controls the critical electron transfer and the ring-splitting of pyrimidine dimer through modulation of the redox potentials and reorganization energies, and stabilization of the anionic intermediates, maintaining the dedicated balance of all the reaction steps and achieving the maximum function activity.

  6. Study of Proton Transfer in E. Coli Photolyase

    NASA Astrophysics Data System (ADS)

    Zhang, Meng; Liu, Zheyun; Li, Jiang; Wang, Lijuan; Zhong, Dongping

    2013-06-01

    Photolyase is a flavoprotein which utilizes blue-light energy to repair UV-light damaged DNA. The catalytic cofactor of photolyase, flavin adenine dinucleotide (FAD), has five redox states. Conversions between these redox states involve intraprotein electron transfer and proton transfer, which play important role in protein function. Here we systematically studied proton transfer in E. coli photolyase in vitro by site-directed mutagenesis and steady-state UV-vis spectroscopy, and proposed the proton channel in photolyase. We found that in the mutant N378C/E363L, proton channel was completely eliminated when DNA substrate was bound to the protein. Proton is suggested to be transported from protein surface to FAD by two pathways: the proton relay pathway through E363 and surface water to N378 and then to FAD; and the proton diffusion pathway through the substrate binding pocket. In addition, reaction kinetics of conversions between the redox states was then solved and redox potentials of the redox states were determined. These results described a complete picture of FAD redox changes, which are fundamental to the functions of all flavoenzymes.

  7. MD studies on conformational behavior of a DNA photolyase enzyme

    NASA Astrophysics Data System (ADS)

    Dushanov, E.; Kholmurodov, Kh.; Yasuoka, K.; Krasavin, E.

    2013-11-01

    In this work, molecular dynamics (MD) simulations were performed on a DNA photolyase protein with two cofactors, FAD (flavin adenine dinucleotide) and MTHF (methenyltetrahydrofolate), inside the enzyme pocket. A DNA photolyase is a highly efficient light-driven enzyme that repairs the UV-induced cyclobutane-pyrimidine dimer in damaged DNA. We were aimed to compare the conformational changes of the FAD cofactor and other constituent fragments of the molecular system under consideration. The conformational behavior of the FAD molecule is very important for understanding the functional and structural properties of the DNA repair protein photolyase. The photoactive FAD is an essential cofactor both for specificial binding to damaged DNA and for catalysis. The second chromophore (MTHF or 8-HDF) is not necessary for catalysis and has no effect on specific enzyme—substrate binding. The obtained results were discussed to gain insight into the light-driven mechanism of DNA repair by a DNA photolyase enzyme—based on the enzyme structure, the FAD mobility, and conformation shape.

  8. A new class of DNA photolyases present in various organisms including aplacental mammals.

    PubMed Central

    Yasui, A; Eker, A P; Yasuhira, S; Yajima, H; Kobayashi, T; Takao, M; Oikawa, A

    1994-01-01

    DNA photolyase specifically repairs UV light-induced cyclobutane-type pyrimidine dimers in DNA through a light-dependent reaction mechanism. We have obtained photolyase genes from Drosophila melanogaster (fruit fly), Oryzias latipes (killifish) and the marsupial Potorous tridactylis (rat kangaroo), the first photolyase gene cloned from a mammalian species. The deduced amino acid sequences of these higher eukaryote genes show only limited homology with microbial photolyase genes. Together with the previously cloned Carassius auratus (goldfish) gene they form a separate group of photolyase genes. A new classification for photolyases comprising two distantly related groups is proposed. For functional analysis P.tridactylis photolyase was expressed and purified as glutathione S-transferase fusion protein from Escherichia coli cells. The biologically active protein contained FAD as light-absorbing cofactor, a property in common with the microbial class photolyases. Furthermore, we found in the archaebacterium Methanobacterium thermoautotrophicum a gene similar to the higher eukaryote photolyase genes, but we could not obtain evidence for the presence of a homologous gene in the human genome. Our results suggest a divergence of photolyase genes in early evolution. Images PMID:7813451

  9. Identification of a phosphorylation site in cyclobutane pyrimidine dimer photolyase of rice.

    PubMed

    Teranishi, Mika; Nakamura, Kentaro; Furukawa, Haruya; Hidema, Jun

    2013-02-01

    Cyclobutane pyrimidine dimer (CPD) photolyase monomerises ultraviolet (UV) radiation-induced CPDs present in DNA, using energy from UVA and visible light. In plants, CPD photolyase activity is a crucial factor for determining UVB sensitivity. We previously demonstrated that native rice CPD photolyase is phosphorylated. To determine the phosphorylation site(s), the phosphorylation status of CPD photolyase was analyzed in rice varieties that have amino acid alterations at the potential phosphorylation sites. In wild-rice species, CPD photolyase was phosphorylated. In Poaceae species, CPD photolyase was phosphorylated in wheat but not in maize. Mutant CPD photolyase proteins, in which these putative phosphorylated residues were replaced with alanine residues, were synthesized using an insect cell-free translation system. A slow-migrating band disappeared when the serine residue at position 7 was mutated. A phospho-specific antibody was generated to determine whether this residue is phosphorylated in CPD photolyase. Only the slow-migrating band of native rice CPD photolyase was detected using this antibody, indicating that the serine residue at position 7 is a phosphorylation site in native rice CPD photolyase. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

  10. Flavin Charge Transfer Transitions Assist DNA Photolyase Electron Transfer

    NASA Astrophysics Data System (ADS)

    Skourtis, Spiros S.; Prytkova, Tatiana; Beratan, David N.

    2007-12-01

    This contribution describes molecular dynamics, semi-empirical and ab-initio studies of the primary photo-induced electron transfer reaction in DNA photolyase. DNA photolyases are FADH--containing proteins that repair UV-damaged DNA by photo-induced electron transfer. A DNA photolyase recognizes and binds to cyclobutatne pyrimidine dimer lesions of DNA. The protein repairs a bound lesion by transferring an electron to the lesion from FADH-, upon photo-excitation of FADH- with 350-450 nm light. We compute the lowest singlet excited states of FADH- in DNA photolyase using INDO/S configuration interaction, time-dependent density-functional, and time-dependent Hartree-Fock methods. The calculations identify the lowest singlet excited state of FADH- that is populated after photo-excitation and that acts as the electron donor. For this donor state we compute conformationally-averaged tunneling matrix elements to empty electron-acceptor states of a thymine dimer bound to photolyase. The conformational averaging involves different FADH--thymine dimer confromations obtained from molecular dynamics simulations of the solvated protein with a thymine dimer docked in its active site. The tunneling matrix element computations use INDO/S-level Green's function, energy splitting, and Generalized Mulliken-Hush methods. These calculations indicate that photo-excitation of FADH- causes a π→π* charge-transfer transition that shifts electron density to the side of the flavin isoalloxazine ring that is adjacent to the docked thymine dimer. This shift in electron density enhances the FADH--to-dimer electronic coupling, thus inducing rapid electron transfer.

  11. Detection of distinct α-helical rearrangements of cyclobutane pyrimidine dimer photolyase upon substrate binding by Fourier transform infrared spectroscopy.

    PubMed

    Wijaya, I M Mahaputra; Zhang, Yu; Iwata, Tatsuya; Yamamoto, Junpei; Hitomi, Kenichi; Iwai, Shigenori; Getzoff, Elizabeth D; Kandori, Hideki

    2013-02-12

    Photolyases (PHRs) utilize near-ultraviolet (UV)-blue light to specifically repair the major photoproducts (PPs) of UV-induced damaged DNA. The cyclobutane pyrimidine dimer PHR (CPD-PHR) from Escherichia coli binds flavin adenine dinucleotide (FAD) as a cofactor and 5,10-methenyltetrahydrofolate as a light-harvesting pigment and specifically repairs CPD lesions. By comparison, a second photolyase known as (6-4) PHR, present in a range of higher organisms, uniquely repairs (6-4) PPs. To understand the repair mechanism and the substrate specificity that distinguish CPD-PHR from (6-4) PHR, we applied Fourier transform infrared (FTIR) spectroscopy to bacterial CPD-PHR in the presence or absence of a well-defined DNA substrate, as we have studied previously for vertebrate (6-4) PHR. PHRs show light-induced reduction of FAD, and photorepair by CPD-PHR involves the transfer of an electron from the photoexcited reduced FAD to the damaged DNA for cleaving the dimers to maintain the DNA's integrity. Here, we measured and analyzed difference FTIR spectra for the photoactivation and DNA photorepair processes of CPD-PHR. We identified light-dependent signals only in the presence of substrate. The signals, presumably arising from a protonated carboxylic acid or the DNA substrate, implicate conformational rearrangements of the protein and substrate during the repair process. Deuterium exchange FTIR measurements of CPD-PHR highlight potential differences in the photoactivation and photorepair mechanisms in comparison to those of (6-4) PHR. Although CPD-PHR and (6-4) PHR appear to exhibit similar overall structures, our studies indicate that distinct conformational rearrangements, especially in the α-helices, are initiated within these enzymes upon binding of their respective DNA substrates.

  12. UVB sensitivity and cyclobutane pyrimidine dimer (CPD) photolyase genotypes in cultivated and wild rice species.

    PubMed

    Iwamatsu, Yutaka; Aoki, Chizuru; Takahashi, Masaaki; Teranishi, Mika; Ding, Yuanying; Sun, Chuanqing; Kumagai, Tadashi; Hidema, Jun

    2008-03-01

    We investigated the UVB-sensitivity in 12 rice strains belonging to two cultivated species (O. sativa and O. glaberrima) and three wild species (O. barthii, O. meridionalis and O. rufipogon) of rice possessing the AA genome, while focusing on the CPD photolyase activity and the genotypes of CPD photolyase. Although the UVB sensitivity, CPD photolyase activity, and CPD photolyase genotype varied widely among these rice species, the sensitivity to UVB radiation depended on the activity of the CPD photolyase, regardless of grass shape, habitat, or species. The rice strains examined here clearly divided into three groups based on the CPD photolyase activity, and the activity of the strains greatly depended on amino acid residues at positions 126 and 296, with the exception of the W1299 strain (O. meridionalis). The amino acid residues 126 and 296 of CPD photolyase in Sasanishiki strain (O. sativa), which showed higher enzymatic activity and more resistance to UVB, were glutamine (Gln) and Gln, respectively. An amino acid change at position 126 from Gln to arginine ("Nori"-type) in the photolyase led to a reduction of enzymatic activity. Additionally, an amino acid change at position 296 from Gln to histidine led to a further reduction in activity. The activity of the W1299 strain, which possesses a "Nori"-type CPD photolyase, was the highest among the strains examined here, and was similar to that of the Sasanishiki. The CPD photolyase of the W1299 contains ten amino acid substitutions, compared to Sasanishiki. The alterations in amino acid residues in the W1299 CPD photolyase compensated for the reduction in activity caused by the amino acid substitutions at positions 126. Knowledge of the activity of different CPD photolyase genotypes will be useful in developing improved rice cultivars.

  13. Codon usage analysis of photolyase encoding genes of cyanobacteria inhabiting diverse habitats.

    PubMed

    Rajneesh; Pathak, Jainendra; Kannaujiya, Vinod K; Singh, Shailendra P; Sinha, Rajeshwar P

    2017-07-01

    Nucleotide and amino acid compositions were studied to determine the genomic and structural relationship of photolyase gene in freshwater, marine and hot spring cyanobacteria. Among three habitats, photolyase encoding genes from hot spring cyanobacteria were found to have highest GC content. The genomic GC content was found to influence the codon usage and amino acid variability in photolyases. The third position of codon was found to have more effect on amino acid variability in photolyases than the first and second positions of codon. The variation of amino acids Ala, Asp, Glu, Gly, His, Leu, Pro, Gln, Arg and Val in photolyases of three different habitats was found to be controlled by first position of codon (G1C1). However, second position (G2C2) of codon regulates variation of Ala, Cys, Gly, Pro, Arg, Ser, Thr and Tyr contents in photolyases. Third position (G3C3) of codon controls incorporation of amino acids such as Ala, Phe, Gly, Leu, Gln, Pro, Arg, Ser, Thr and Tyr in photolyases from three habitats. Photolyase encoding genes of hot spring cyanobacteria have 85% codons with G or C at third position, whereas marine and freshwater cyanobacteria showed 82 and 60% codons, respectively, with G or C at third position. Principal component analysis (PCA) showed that GC content has a profound effect in separating the genes along the first major axis according to their RSCU (relative synonymous codon usage) values, and neutrality analysis indicated that mutational pressure has resulted in codon bias in photolyase genes of cyanobacteria.

  14. Crystal structures of ethyl 6-(4-methyl­phen­yl)-4-oxo-4H-chromene-2-carboxyl­ate and ethyl 6-(4-fluoro­phen­yl)-4-oxo-4H-chromene-2-carboxyl­ate

    PubMed Central

    Gomes, Ligia R.; Low, John Nicolson; Fernandes, Carlos; Gaspar, Alexandra; Borges, Fernanda

    2016-01-01

    The crystal structures of two chromone derivatives, viz. ethyl 6-(4-methyl­phen­yl)-4-oxo-4H-chromene-2-carboxyl­ate, C19H16O4, (1), and ethyl 6-(4-fluoro­phen­yl)-4-oxo-4H-chromene-2-carboxyl­ate C18H13FO4, (2), have been determined: (1) crystallizes with two mol­ecules in the asymmetric unit. A comparison of the dihedral angles beween the mean planes of the central chromone core with those of the substituents, an ethyl ester moiety at the 2-position and a para-substituted phenyl ring at the 6-position shows that each mol­ecule differs significantly from the others, even the two independent mol­ecules (a and b) of (1). In all three mol­ecules, the carbonyl groups of the chromone and the carboxyl­ate are trans-related. The supra­molecular structure of (1) involves only weak C—H⋯π inter­actions between H atoms of the substituent phenyl group and the phenyl group, which link mol­ecules into a chain of alternating mol­ecules a and b, and weak π–π stacking inter­actions between the chromone units. The packing in (2) involves C—H⋯O inter­actions, which form a network of two inter­secting ladders involving the carbonyl atom of the carboxyl­ate group as the acceptor for H atoms at the 7-position of the chromone ring and from an ortho-H atom of the exocyclic benzene ring. The carbonyl atom of the chromone acts as an acceptor from a meta-H atom of the exocyclic benzene ring. π–π inter­actions stack the mol­ecules by unit translation along the a axis. PMID:26870574

  15. Direct Observation of Thymine Dimer Repair in DNA by Photolyase

    NASA Astrophysics Data System (ADS)

    Zhong, Dongping

    2006-03-01

    Departments of Physics, Chemistry, and Biochemistry, Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, 191 West Woodruff Avenue, OH 43210. Photolyase uses light energy to split ultraviolet-induced cyclobutane pyrimidine dimers in damaged DNA, but its molecular mechanism has never been directly revealed. We report here the direct mapping of catalytic processes through femtosecond synchronization of the enzymatic dynamics with the repair function. We observed direct electron transfer from the excited flavin cofactor to the dimer in 170 ps and back electron transfer from the repaired thymines in 560 ps. Both reactions are strongly modulated by active-site solvation to achieve maximum repair efficiency. These results show that the photocycle of DNA repair by photolyase is through a radical mechanism and completed on subnanosecond time scale at the dynamic active site with no net electron change in redox states of the flavin cofactor.

  16. Investigation of the cyclobutane pyrimidine dimer (CPD) photolyase DNA recognition mechanism by NMR analyses.

    PubMed

    Torizawa, Takuya; Ueda, Takumi; Kuramitsu, Seiki; Hitomi, Kenichi; Todo, Takeshi; Iwai, Shigenori; Morikawa, Kosuke; Shimada, Ichio

    2004-07-30

    The cyclobutane pyrimidine dimer (CPD) is one of the major forms of DNA damage caused by irradiation with ultraviolet (UV) light. CPD photolyases recognize and repair UV-damaged DNA. The DNA recognition mechanism of the CPD photolyase has remained obscure because of a lack of structural information about DNA-CPD photolyase complexes. In order to elucidate the CPD photolyase DNA binding mode, we performed NMR analyses of the DNA-CPD photolyase complex. Based upon results from (31)P NMR measurements, in combination with site-directed mutagenesis, we have demonstrated the orientation of CPD-containing single-stranded DNA (ssDNA) on the CPD photolyase. In addition, chemical shift perturbation analyses, using stable isotope-labeled DNA, revealed that the CPD is buried in a cavity within CPD photolyase. Finally, NMR analyses of a double-stranded DNA (dsDNA)-CPD photolyase complex indicated that the CPD is flipped out of the dsDNA by the enzyme, to gain access to the active site.

  17. Spectroscopic and thermodynamic comparisons of Escherichia coli DNA photolyase and Vibrio cholerae cryptochrome 1.

    PubMed

    Sokolowsky, Kathleen; Newton, Maire; Lucero, Carlos; Wertheim, Bradley; Freedman, Jaryd; Cortazar, Frank; Czochor, Jennifer; Schelvis, Johannes P M; Gindt, Yvonne M

    2010-05-27

    Escherichia coli DNA photolyase and cryptochrome 1 isolated from Vibrio cholerae, a member of the CRY-DASH family, are directly compared using a variety of experimental methods including UV-vis and Raman spectroscopy, reduction potential measurements, and isothermal titration calorimetry. The semiquinone form of the cryptochrome has an absorption spectrum that is red-shifted from that of the photolyase, but the Raman spectrum indicates that the FAD binding pocket is similar to that of photolyase. The FADH(-)/FADH* reduction potential of the cryptochrome is significantly higher than that of the photolyase at 164 mV vs NHE, but it also increases upon substrate binding (to 195 mV vs NHE), an increase similar to what is observed in photolyase. The FADH(-)/FADH* reduction potential for both proteins was found to be insensitive to ATP binding. Isothermal titration calorimetry found that photolyase binds tighter to substrate (K(A) approximately 10(5) M(-1) for photolyase and approximately 10(4) M(-1) for cryptochrome 1), and the binding constants for both proteins were slightly sensitive to oxidation state. Based upon this work, it appears that this cryptochrome has significant spectroscopic and electrochemical similarities to CPD photolyase. The thermodynamic cycle of the enzymatic repair in the context of this work is discussed.

  18. A pseudo-tetragonal tungsten bronze superstructure: a combined solution of the crystal structure of K6.4(Nb,Ta)(36.3)O94 with advanced transmission electron microscopy and neutron diffraction.

    PubMed

    Paria Sena, Robert; Babaryk, Artem A; Khainakov, Sergiy; Garcia-Granda, Santiago; Slobodyanik, Nikolay S; Van Tendeloo, Gustaaf; Abakumov, Artem M; Hadermann, Joke

    2016-01-21

    The crystal structure of the K6.4Nb28.2Ta8.1O94 pseudo-tetragonal tungsten bronze-type oxide was determined using a combination of X-ray powder diffraction, neutron diffraction and transmission electron microscopy techniques, including electron diffraction, high angle annular dark field scanning transmission electron microscopy (HAADF-STEM), annular bright field STEM (ABF-STEM) and energy-dispersive X-ray compositional mapping (STEM-EDX). The compound crystallizes in the space group Pbam with unit cell parameters a = 37.468(9) Å, b = 12.493(3) Å, c = 3.95333(15) Å. The structure consists of corner sharing (Nb,Ta)O6 octahedra forming trigonal, tetragonal and pentagonal tunnels. All tetragonal tunnels are occupied by K(+) ions, while 1/3 of the pentagonal tunnels are preferentially occupied by Nb(5+)/Ta(5+) and 2/3 are occupied by K(+) in a regular pattern. A fractional substitution of K(+) in the pentagonal tunnels by Nb(5+)/Ta(5+) is suggested by the analysis of the HAADF-STEM images. In contrast to similar structures, such as K2Nb8O21, also parts of the trigonal tunnels are fractionally occupied by K(+) cations.

  19. A Review of Spectroscopic and Biophysical-Chemical Studies of the Complex of Cyclobutane Pyrimidine Dimer Photolyase and Cryptochrome DASH with Substrate DNA.

    PubMed

    Schelvis, Johannes P M; Gindt, Yvonne M

    2017-01-01

    Cyclobutane pyrimidine dimer (CPD) photolyase (PL) is a structure-specific DNA repair enzyme that uses blue light to repair CPD on DNA. Cryptochrome (CRY) DASH enzymes use blue light for the repair of CPD lesions on single-stranded (ss) DNA, although some may also repair these lesions on double-stranded (ds) DNA. In addition, CRY DASH may be involved in blue light signaling, similar to cryptochromes. The focus of this review is on spectroscopic and biophysical-chemical experiments of the enzyme-substrate complex that have contributed to a more detailed understanding of all the aspects of the CPD repair mechanism of CPD photolyase and CRY DASH. This will be performed in the backdrop of the available X-ray crystal structures of these enzymes bound to a CPD-like lesion. These structures helped to confirm conclusions that were drawn earlier from spectroscopic and biophysical-chemical experiments, and they have a critical function as a framework to design new experiments and to interpret new experimental data. This review will show the important synergy between X-ray crystallography and spectroscopic/biophysical-chemical investigations that is essential to obtain a sufficiently detailed picture of the overall mechanism of CPD photolyases and CRY DASH proteins. © 2016 The American Society of Photobiology.

  20. Toward an artificial oxidative DNA photolyase.

    PubMed

    Pauvert, Mickaël; Laine, Patrick; Jonas, Marco; Wiest, Olaf

    2004-01-23

    The design, synthesis, structure, and binding affinity of two dioptic receptors for the selective molecular recognition of the cis,syn cyclobutane pyrimidine dimer are reported. The design is based on two 2,6-di(acetamino)pyridine recognition units that are covalently linked via triple bonds to an anthraquinone functional spacer unit. The convergent synthesis uses a modified Sonogashira reaction involving a zinc transmetalation as the key step. The crystal structure of one of the receptors reveals a supramolecular 1D polymer with strong interactions mediated by shape self-complementarity, pi-stacking, and hydrogen bonding between adjacent molecules. Hydrogen bonding between adjacent strands enforces a parallel orientation, which leads to a noncentrosymmetric crystal structure of the highly polar compound. The receptor has an association constant of K(a) = 1.0 x 10(3) M(-1) with the cis,syn pyrimidine dimer, whereas binding of the trans,syn isomer is approximately 1 order of magnitude weaker.

  1. Crystal structure of (1S,3R,8R,9R)-2,2-di-chloro-3,7,7-tri-methyl-10-methylenetri-cyclo-[6.4.0.0(1,3)]dodecan-9-ol.

    PubMed

    Benzalim, Ahmed; Auhmani, Aziz; Bimoussa, Abdoullah; Ait Itto, My Youssef; Daran, Jean-Claude; Auhmani, Abdelwahed

    2016-08-01

    The title compound, C16H24Cl2O, was synthesized by treating (1S,3R,8S,9R,10S)-2,2-di-chloro-3,7,7,10-tetra-methyl-9,10-ep-oxy-tri-cyclo-[6.4.0.0(1,3)]dodecane with a concentrated solution of hydro-bromic acid. It is built up from three fused rings: a cyclo-heptane ring, a cyclo-hexyl ring bearing alkene and hy-droxy substituents, and a cyclo-propane ring bearing two chlorine atoms. The asymmetric unit contains two mol-ecules linked by an O-H⋯O hydrogen bond. In the crystal, further O-H⋯O hydrogen bonds build up an R 4 (4)(8) cyclic tetra-mer. One of the mol-ecules presents disorder that affects the seven-membered ring. In both mol-ecules, the six-membered rings display a chair conformation, whereas the seven-membered rings display conformations inter-mediate between boat and twist-boat for the non-disordered mol-ecule and either a chair or boat and twist-boat for the disordered mol-ecule owing to the disorder. The absolute configuration for both mol-ecules is 1S,3R,8R,9R and was deduced from the chemical pathway and further confirmed by the X-ray structural analysis.

  2. Discrimination of class I cyclobutane pyrimidine dimer photolyase from blue light photoreceptors by single methionine residue.

    PubMed

    Miyazawa, Yuji; Nishioka, Hirotaka; Yura, Kei; Yamato, Takahisa

    2008-03-15

    DNA photolyase recognizes ultraviolet-damaged DNA and breaks improperly formed covalent bonds within the cyclobutane pyrimidine dimer by a light-activated electron transfer reaction between the flavin adenine dinucleotide, the electron donor, and cyclobutane pyrimidine dimer, the electron acceptor. Theoretical analysis of the electron-tunneling pathways of the DNA photolyase derived from Anacystis nidulans can reveal the active role of the protein environment in the electron transfer reaction. Here, we report the unexpectedly important role of the single methionine residue, Met-353, where busy trafficking of electron-tunneling currents is observed. The amino acid conservation pattern of Met-353 in the homologous sequences perfectly correlates with experimentally verified annotation as photolyases. The bioinformatics sequence analysis also suggests that the residue plays a pivotal role in biological function. Consistent findings from different disciplines of computational biology strongly suggest the pivotal role of Met-353 in the biological function of DNA photolyase.

  3. Magnetic-field effect on the photoactivation reaction of Escherichia coli DNA photolyase.

    PubMed

    Henbest, Kevin B; Maeda, Kiminori; Hore, P J; Joshi, Monika; Bacher, Adelbert; Bittl, Robert; Weber, Stefan; Timmel, Christiane R; Schleicher, Erik

    2008-09-23

    One of the two principal hypotheses put forward to explain the primary magnetoreception event underlying the magnetic compass sense of migratory birds is based on a magnetically sensitive chemical reaction. It has been proposed that a spin-correlated radical pair is produced photochemically in a cryptochrome and that the rates and yields of the subsequent chemical reactions depend on the orientation of the protein in the Earth's magnetic field. The suitability of cryptochrome for this purpose has been argued, in part, by analogy with DNA photolyase, although no effects of applied magnetic fields have yet been reported for any member of the cryptochrome/photolyase family. Here, we demonstrate a magnetic-field effect on the photochemical yield of a flavin-tryptophan radical pair in Escherichia coli photolyase. This result provides a proof of principle that photolyases, and most likely by extension also cryptochromes, have the fundamental properties needed to form the basis of a magnetic compass.

  4. Magnetic-field effect on the photoactivation reaction of Escherichia coli DNA photolyase

    PubMed Central

    Henbest, Kevin B.; Maeda, Kiminori; Hore, P. J.; Joshi, Monika; Bacher, Adelbert; Bittl, Robert; Weber, Stefan; Timmel, Christiane R.; Schleicher, Erik

    2008-01-01

    One of the two principal hypotheses put forward to explain the primary magnetoreception event underlying the magnetic compass sense of migratory birds is based on a magnetically sensitive chemical reaction. It has been proposed that a spin-correlated radical pair is produced photochemically in a cryptochrome and that the rates and yields of the subsequent chemical reactions depend on the orientation of the protein in the Earth's magnetic field. The suitability of cryptochrome for this purpose has been argued, in part, by analogy with DNA photolyase, although no effects of applied magnetic fields have yet been reported for any member of the cryptochrome/photolyase family. Here, we demonstrate a magnetic-field effect on the photochemical yield of a flavin–tryptophan radical pair in Escherichia coli photolyase. This result provides a proof of principle that photolyases, and most likely by extension also cryptochromes, have the fundamental properties needed to form the basis of a magnetic compass. PMID:18799743

  5. A Photolyase-Like Protein from Agrobacterium tumefaciens with an Iron-Sulfur Cluster

    PubMed Central

    Oberpichler, Inga; Pierik, Antonio J.; Wesslowski, Janine; Pokorny, Richard; Rosen, Ran; Vugman, Michal; Zhang, Fan; Neubauer, Olivia; Ron, Eliora Z.; Batschauer, Alfred; Lamparter, Tilman

    2011-01-01

    Photolyases and cryptochromes are evolutionarily related flavoproteins with distinct functions. While photolyases can repair UV-induced DNA lesions in a light-dependent manner, cryptochromes regulate growth, development and the circadian clock in plants and animals. Here we report about two photolyase-related proteins, named PhrA and PhrB, found in the phytopathogen Agrobacterium tumefaciens. PhrA belongs to the class III cyclobutane pyrimidine dimer (CPD) photolyases, the sister class of plant cryptochromes, while PhrB belongs to a new class represented in at least 350 bacterial organisms. Both proteins contain flavin adenine dinucleotide (FAD) as a primary catalytic cofactor, which is photoreduceable by blue light. Spectral analysis of PhrA confirmed the presence of 5,10-methenyltetrahydrofolate (MTHF) as antenna cofactor. PhrB comprises also an additional chromophore, absorbing in the short wavelength region but its spectrum is distinct from known antenna cofactors in other photolyases. Homology modeling suggests that PhrB contains an Fe-S cluster as cofactor which was confirmed by elemental analysis and EPR spectroscopy. According to protein sequence alignments the classical tryptophan photoreduction pathway is present in PhrA but absent in PhrB. Although PhrB is clearly distinguished from other photolyases including PhrA it is, like PhrA, required for in vivo photoreactivation. Moreover, PhrA can repair UV-induced DNA lesions in vitro. Thus, A. tumefaciens contains two photolyase homologs of which PhrB represents the first member of the cryptochrome/photolyase family (CPF) that contains an iron-sulfur cluster. PMID:22066008

  6. UV Radiation–Sensitive Norin 1 Rice Contains Defective Cyclobutane Pyrimidine Dimer Photolyase

    PubMed Central

    Hidema, Jun; Kumagai, Tadashi; Sutherland, Betsy M.

    2000-01-01

    Norin 1, a progenitor of many economically important Japanese rice strains, is highly sensitive to the damaging effects of UVB radiation (wavelengths 290 to 320 nm). Norin 1 seedlings are deficient in photorepair of cyclobutane pyrimidine dimers. However, the molecular origin of this deficiency was not known and, because rice photolyase genes have not been cloned and sequenced, could not be determined by examining photolyase structural genes or upstream regulatory elements for mutations. We therefore used a photoflash approach, which showed that the deficiency in photorepair in vivo resulted from a functionally altered photolyase. These results were confirmed by studies with extracts, which showed that the Norin 1 photolyase–dimer complex was highly thermolabile relative to the wild-type Sasanishiki photolyase. This deficiency results from a structure/function alteration of photolyase rather than of nonspecific repair, photolytic, or regulatory elements. Thus, the molecular origin of this plant DNA repair deficiency, resulting from a spontaneously occurring mutation to UV radiation sensitivity, is defective photolyase. PMID:11006332

  7. Mapping Thymine Dimer Splitting in Damaged DNA by Photolyase

    NASA Astrophysics Data System (ADS)

    Liu, Zheyun; Tan, Chuang; Li, Jiang; Guo, Xunmin; Wang, Lijuan; Zhong, Dongping

    2010-06-01

    Photolyases uses light energy to convert UV-damaged cyclobutane pyrimidine dimer (CPD) to normal bases. We observed the formation and decay of semiquinone flavin and CPD anion intermediate, the recovery of hydroquinone flavin in ground state, and the formation of normal thymine bases in real time with femtosecond time resolution. By monitoring the decay and formation of all reactants, intermediates and products, the functional dynamics of the elementary steps during CPD repair have been mapped out. All elementary reaction steps, namely forward electron transfer, back electron transfer, bond breakage and electron return occur in sub-nanosecond scale. These dynamics are synergistically correlated for maximum of repair efficiency through a redox photocycle with no net change of electrons.

  8. Structural and evolutionary aspects of antenna chromophore usage by class II photolyases.

    PubMed

    Kiontke, Stephan; Gnau, Petra; Haselsberger, Reinhard; Batschauer, Alfred; Essen, Lars-Oliver

    2014-07-11

    Light-harvesting and resonance energy transfer to the catalytic FAD cofactor are key roles for the antenna chromophores of light-driven DNA photolyases, which remove UV-induced DNA lesions. So far, five chemically diverse chromophores have been described for several photolyases and related cryptochromes, but no correlation between phylogeny and used antenna has been found. Despite a common protein topology, structural analysis of the distantly related class II photolyase from the archaeon Methanosarcina mazei (MmCPDII) as well as plantal orthologues indicated several differences in terms of DNA and FAD binding and electron transfer pathways. For MmCPDII we identify 8-hydroxydeazaflavin (8-HDF) as cognate antenna by in vitro and in vivo reconstitution, whereas the higher plant class II photolyase from Arabidopsis thaliana fails to bind any of the known chromophores. According to the 1.9 Å structure of the MmCPDII·8-HDF complex, its antenna binding site differs from other members of the photolyase-cryptochrome superfamily by an antenna loop that changes its conformation by 12 Å upon 8-HDF binding. Additionally, so-called N- and C-motifs contribute as conserved elements to the binding of deprotonated 8-HDF and allow predicting 8-HDF binding for most of the class II photolyases in the whole phylome. The 8-HDF antenna is used throughout the viridiplantae ranging from green microalgae to bryophyta and pteridophyta, i.e. mosses and ferns, but interestingly not in higher plants. Overall, we suggest that 8-hydroxydeazaflavin is a crucial factor for the survival of most higher eukaryotes which depend on class II photolyases to struggle with the genotoxic effects of solar UV exposure.

  9. Structural and Evolutionary Aspects of Antenna Chromophore Usage by Class II Photolyases*

    PubMed Central

    Kiontke, Stephan; Gnau, Petra; Haselsberger, Reinhard; Batschauer, Alfred; Essen, Lars-Oliver

    2014-01-01

    Light-harvesting and resonance energy transfer to the catalytic FAD cofactor are key roles for the antenna chromophores of light-driven DNA photolyases, which remove UV-induced DNA lesions. So far, five chemically diverse chromophores have been described for several photolyases and related cryptochromes, but no correlation between phylogeny and used antenna has been found. Despite a common protein topology, structural analysis of the distantly related class II photolyase from the archaeon Methanosarcina mazei (MmCPDII) as well as plantal orthologues indicated several differences in terms of DNA and FAD binding and electron transfer pathways. For MmCPDII we identify 8-hydroxydeazaflavin (8-HDF) as cognate antenna by in vitro and in vivo reconstitution, whereas the higher plant class II photolyase from Arabidopsis thaliana fails to bind any of the known chromophores. According to the 1.9 Å structure of the MmCPDII·8-HDF complex, its antenna binding site differs from other members of the photolyase-cryptochrome superfamily by an antenna loop that changes its conformation by 12 Å upon 8-HDF binding. Additionally, so-called N- and C-motifs contribute as conserved elements to the binding of deprotonated 8-HDF and allow predicting 8-HDF binding for most of the class II photolyases in the whole phylome. The 8-HDF antenna is used throughout the viridiplantae ranging from green microalgae to bryophyta and pteridophyta, i.e. mosses and ferns, but interestingly not in higher plants. Overall, we suggest that 8-hydroxydeazaflavin is a crucial factor for the survival of most higher eukaryotes which depend on class II photolyases to struggle with the genotoxic effects of solar UV exposure. PMID:24849603

  10. Conservation of DNA photolyase genes in group II nucleopolyhedroviruses infecting plusiine insects.

    PubMed

    Xu, Fang; Vlak, Just M; van Oers, Monique M

    2008-09-01

    DNA photolyase genes (phr) encode photoreactive enzymes, which are involved in the repair of UV-damaged DNA. Cyclobutane pyrimidine dimer (CPD) specific photolyase genes are present in nucleopolyhedroviruses isolated from Chrysodeixis chalcites (ChchNPV) and Trichoplusia ni (TnSNPV), insects belonging to the Plusiinae (Noctuidae). To better understand the occurrence and evolution of these genes in baculoviruses, we investigated their possible conservation in other group II NPVs, which infect plusiine insects. A PCR based strategy using degenerate phr-specific primers was designed to detect and analyze possible photolyase genes. Six additional Plusiinae-infecting NPVs were analyzed and all, except Thysanoplusia oricalcea NPV A28-1, which is a group I NPV, contained one or more phr-like sequences. Phylogenetic analysis revealed that all photolyase genes of the tested Plusiinae-infecting baculoviruses group in a single clade, separated into three subgroups. The phylogeny of the polyhedrin sequences of these viruses confirmed that the analyzed viruses also formed a single clade in group II NPVs. We hypothesize that all plusiine group II NPVs contain one or more photolyase genes and that these have a common ancestor.

  11. Escherichia coli DNA photolyase stimulates uvrABC excision nuclease in vitro.

    PubMed Central

    Sancar, A; Franklin, K A; Sancar, G B

    1984-01-01

    Pyrimidine dimers are the major photoproducts produced in cellular DNA upon UV irradiation. In Escherichia coli there are dark and photorepair mechanisms that eliminate the dimers from DNA and prevent their lethal and mutagenic effects. To determine whether these repair mechanisms act cooperatively or competitively in repairing DNA, we investigated the effects upon one another of DNA photolyase, which mediates photorepair, and uvrABC excision nuclease, an enzyme complex of the uvrABC gene products, which catalyzes nucleotide excision repair. We found that photolyase stimulates the removal of pyrimidine dimers but not other DNA adducts by uvrABC excision nuclease. The two subunits of uvrABC excision nuclease, the uvrA and uvrB proteins which together bind to the dimer region of DNA, had no effect on the activity of photolyase. T4 endonuclease V, which like photolyase is specific for pyrimidine dimers, was inhibited by photolyase, suggesting that these two proteins recognize the same or similar chemical structures in UV-irradiated DNA that are different from those recognized by uvrABC excision nuclease. Images PMID:6390436

  12. The molecular origin of high DNA-repair efficiency by photolyase

    NASA Astrophysics Data System (ADS)

    Tan, Chuang; Liu, Zheyun; Li, Jiang; Guo, Xunmin; Wang, Lijuan; Sancar, Aziz; Zhong, Dongping

    2015-06-01

    The primary dynamics in photomachinery such as charge separation in photosynthesis and bond isomerization in sensory photoreceptor are typically ultrafast to accelerate functional dynamics and avoid energy dissipation. The same is also true for the DNA repair enzyme, photolyase. However, it is not known how the photoinduced step is optimized in photolyase to attain maximum efficiency. Here, we analyse the primary reaction steps of repair of ultraviolet-damaged DNA by photolyase using femtosecond spectroscopy. With systematic mutations of the amino acids involved in binding of the flavin cofactor and the cyclobutane pyrimidine dimer substrate, we report our direct deconvolution of the catalytic dynamics with three electron-transfer and two bond-breaking elementary steps and thus the fine tuning of the biological repair function for optimal efficiency. We found that the maximum repair efficiency is not enhanced by the ultrafast photoinduced process but achieved by the synergistic optimization of all steps in the complex repair reaction.

  13. Baculovirus cyclobutane pyrimidine dimer photolyases show a close relationship with lepidopteran host homologues.

    PubMed

    Biernat, M A; Ros, V I D; Vlak, J M; van Oers, M M

    2011-08-01

    Cyclobutane pyrimidine dimer (CPD) photolyases repair ultraviolet (UV)-induced DNA damage using blue light. To get insight in the origin of baculovirus CPD photolyase (phr) genes, homologues in the lepidopteran insects Chrysodeixis chalcites, Spodoptera exigua and Trichoplusia ni were identified and characterized. Lepidopteran and baculovirus phr genes each form a monophyletic group, and together form a well-supported clade within the insect photolyases. This suggests that baculoviruses obtained their phr genes from an ancestral lepidopteran insect host. A likely evolutionary scenario is that a granulovirus, Spodoptera litura GV or a direct ancestor, obtained a phr gene. Subsequently, it was horizontally transferred from this granulovirus to several group II nucleopolyhedroviruses (NPVs), including those that infect noctuids of the Plusiinae subfamily. © 2011 The Authors. Insect Molecular Biology © 2011 The Royal Entomological Society.

  14. An Arabidopsis photolyase mutant is hypersensitive to ultraviolet-B radiation

    PubMed Central

    Landry, Laurie G.; Stapleton, Ann E.; Lim, Jackie; Hoffman, Peter; Hays, John B.; Walbot, Virginia; Last, Robert L.

    1997-01-01

    Photolyases are DNA repair enzymes that use energy from blue light to repair pyrimidine dimers. We report the isolation of an Arabidopsis thaliana mutant (uvr2-1) that is defective in photorepair of cyclobutylpyrimidine dimers (CPDs). Whereas uvr2-1 is indistinguishable from wild type in the absence of UV light, low UV-B levels inhibit growth and cause leaf necrosis. uvr2-1 is more sensitive to UV-B than wild type when placed under white light after UV-B treatment. In contrast, recovery in darkness or in light lacking photoreactivating blue light results in equal injury in uvr2-1 and wild type. The uvr2-1 mutant is unable to remove CPDs in vivo, and plant extracts lack detectable photolyase activity. This recessive mutation segregates as a single gene located near the top of chromosome 1, and is a structural gene mutation in the type II CPD photolyase PHR1. This mutant provides evidence that CPD photolyase is required for plant survival in the presence of UV-B light. PMID:8990208

  15. 7 CFR 6.4 - Investigations.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 1 2011-01-01 2011-01-01 false Investigations. 6.4 Section 6.4 Agriculture Office of the Secretary of Agriculture IMPORT QUOTAS AND FEES General Provisions § 6.4 Investigations. (a) Section 22. The Administrator shall cause an investigation to be made whenever, based upon a...

  16. 7 CFR 6.4 - Investigations.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 1 2012-01-01 2012-01-01 false Investigations. 6.4 Section 6.4 Agriculture Office of the Secretary of Agriculture IMPORT QUOTAS AND FEES General Provisions § 6.4 Investigations. (a) Section 22. The Administrator shall cause an investigation to be made whenever, based upon a...

  17. 7 CFR 6.4 - Investigations.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 1 2014-01-01 2014-01-01 false Investigations. 6.4 Section 6.4 Agriculture Office of the Secretary of Agriculture IMPORT QUOTAS AND FEES General Provisions § 6.4 Investigations. (a) Section 22. The Administrator shall cause an investigation to be made whenever, based upon a...

  18. 7 CFR 6.4 - Investigations.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 1 2013-01-01 2013-01-01 false Investigations. 6.4 Section 6.4 Agriculture Office of the Secretary of Agriculture IMPORT QUOTAS AND FEES General Provisions § 6.4 Investigations. (a) Section 22. The Administrator shall cause an investigation to be made whenever, based upon a...

  19. 27 CFR 6.4 - Jurisdictional limits.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Jurisdictional limits. 6.4 Section 6.4 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY LIQUORS âTIED-HOUSEâ Scope of Regulations § 6.4 Jurisdictional limits. (a) General. The...

  20. Crystal structure of (1R,3S,8R,11R)-11-acetyl-3,7,7-trimethyl-10-oxatri­cyclo­[6.4.0.01,3]dodecan-9-one

    PubMed Central

    Bismoussa, Abdoullah; Ait Itto, My Youssef; Daran, Jean-Claude; Auhmani, Abdelwahed; Auhmani, Aziz

    2015-01-01

    The title compound, C16H24O3, is built up from three fused rings, a six-membered, a seven-membered and a three-membered ring. The absolute configuration of the title compound was determined as (1R,3S,8R,11R) based on the synthetic pathway. The six-membered ring has an half-chair conformation whereas the seven-membered ring displays a boat conformation. In the cyrstal, C—H⋯O hydrogen bonds build up a two-dimensional network parallel to (0 0 1). The crystal studied was an inversion twin with a minor twin component of 34%. PMID:26870471

  1. Role of CPI-17 in restoring skin homoeostasis in cutaneous field of cancerization: effects of topical application of a film-forming medical device containing photolyase and UV filters.

    PubMed

    Puig-Butillé, Joan Anton; Malvehy, Josep; Potrony, Miriam; Trullas, Carles; Garcia-García, Francisco; Dopazo, Joaquin; Puig, Susana

    2013-07-01

    Cutaneous field of cancerization (CFC) is caused in part by the carcinogenic effect of the cyclobutane pyrimidine dimers CPD and 6-4 photoproducts (6-4PPs). Photoreactivation is carried out by photolyases which specifically recognize and repair both photoproducts. The study evaluates the molecular effects of topical application of a film-forming medical device containing photolyase and UV filters on the precancerous field in AK from seven patients. Skin improvement after treatment was confirmed in all patients by histopathological and molecular assessment. A gene set analysis showed that skin recovery was associated with biological processes involved in tissue homoeostasis and cell maintenance. The CFC response was associated with over-expression of the CPI-17 gene, and a dependence on the initial expression level was observed (P = 0.001). Low CPI-17 levels were directly associated with pro-inflammatory genes such as TNF (P = 0.012) and IL-1B (P = 0.07). Our results suggest a role for CPI-17 in restoring skin homoeostasis in CFC lesions. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  2. The crystal structure of 6-(4-chloro­phen­yl)-2-(4-methyl­benz­yl)imidazo[2,1-b][1,3,4]thia­diazole-5-carbaldehyde

    PubMed Central

    Sowmya, A.; Anil Kumar, G. N.; Kumar, Sujeet; Karki, Subhas S.

    2016-01-01

    In the title imidazo[2,1-b][1,3,4]thia­diazole derivative, C19H14ClN3OS, the 4-methyl­benzyl and chloro­phenyl rings are inclined to the planar imidazo[2,1-b][1,3,4]thia­diazole moiety (r.m.s. deviation = 0.012 Å) by 64.5 (1) and 3.7 (1)°, respectively. The mol­ecular structure is primarily stabilized by a strong intra­molecular C—H⋯O hydrogen bond, leading to the formation of a pseudo-seven-membered S(7) ring motif, and a short intra­molecular C—H⋯N contact forming an S(5) ring motif. In the crystal, mol­ecules are linked by pairs of C—H⋯S hydrogen bonds, forming inversion dimers. The dimers are linked by C—H⋯O and C—H⋯π inter­actions, forming chains propagating along [110]. PMID:27746941

  3. Crystal and molecular structure of the antimalarial agent 4-(tert-butyl)-2-(tert-butylaminomethyl)-6-(4-chlorophenyl)phenol dihydrogen phosphate (WR 194,965 phosphate).

    PubMed Central

    Karle, J M; Karle, I L

    1988-01-01

    WR 194,965 phosphate, a new antimalarial agent containing a biphenyl ring structure active against chloroquine-resistant Plasmodium falciparum, crystallized in ionic form with a positive charge on the quaternary nitrogen atom. The oxygen and nitrogen atoms of WR 194,965 were hydrogen bonded to the same phosphate group. The nitrogen atom was also hydrogen bonded to a second phosphate group. The phosphate ions formed discrete clusters of four phosphate moieties. The phosphate clusters contained fourfold inversion symmetry. The intramolecular N-O distance in WR 194,965 of 3.073 A (1 A = 0.1 nm) was close to the reported values for N-O distances in the active cinchona alkaloids and may be important for activity. A comparison of the crystalline structure of WR 194,965 with those of mefloquine and quinidine sulfate demonstrated that the regions of the three molecules in the vicinity of the aliphatic nitrogen atom and the oxygen atom superimpose. Much of the remainder of the WR 194,965 molecule spatially overlapped with the combined three-dimensional space defined by quinidine and mefloquine. The crystallographic parameters were: C21H29ClNO+.H2PO4-; Mr = 443.9; symmetry of unit cell, tetragonal; space group, I41/a; parameters of unit cell, a = b = 24.305 +/- 0.002 A, c = 17.556 +/- 0.003 A; V (volume of unit cell) = 10370.9 A3; Z (number of molecules per unit cell) = 16; Dx (calculated density) = 1.137 g cm-3; source of radiation, CuK alpha (lambda = 1.54178 A); mu (absorption coefficient) = 21.3 cm-1; F(000) (sum of atomic scattering factors at zero scattering angle) = 3,440; room temperature; final R = 8.2% for 2,508 reflections with [F0] greater than 3 sigma. PMID:3288114

  4. 27 CFR 6.4 - Jurisdictional limits.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2011-04-01 2011-04-01 false Jurisdictional limits. 6.4 Section 6.4 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF... transactions in interstate or foreign commerce in any such products; or (iii) The direct effect of the...

  5. 27 CFR 6.4 - Jurisdictional limits.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2012-04-01 2012-04-01 false Jurisdictional limits. 6.4 Section 6.4 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF... transactions in interstate or foreign commerce in any such products; or (iii) The direct effect of the...

  6. 24 CFR 6.4 - Discrimination prohibited.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 24 Housing and Urban Development 1 2012-04-01 2012-04-01 false Discrimination prohibited. 6.4... COMMUNITY DEVELOPMENT ACT OF 1974 General Provisions § 6.4 Discrimination prohibited. (a) Section 109... benefits of, or be subjected to discrimination under any program or activity funded in whole or in part...

  7. 24 CFR 6.4 - Discrimination prohibited.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 24 Housing and Urban Development 1 2013-04-01 2013-04-01 false Discrimination prohibited. 6.4... COMMUNITY DEVELOPMENT ACT OF 1974 General Provisions § 6.4 Discrimination prohibited. (a) Section 109... benefits of, or be subjected to discrimination under any program or activity funded in whole or in part...

  8. 24 CFR 6.4 - Discrimination prohibited.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 24 Housing and Urban Development 1 2014-04-01 2014-04-01 false Discrimination prohibited. 6.4... COMMUNITY DEVELOPMENT ACT OF 1974 General Provisions § 6.4 Discrimination prohibited. (a) Section 109... benefits of, or be subjected to discrimination under any program or activity funded in whole or in part...

  9. 24 CFR 6.4 - Discrimination prohibited.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 24 Housing and Urban Development 1 2011-04-01 2011-04-01 false Discrimination prohibited. 6.4... COMMUNITY DEVELOPMENT ACT OF 1974 General Provisions § 6.4 Discrimination prohibited. (a) Section 109... benefits of, or be subjected to discrimination under any program or activity funded in whole or in part...

  10. 24 CFR 6.4 - Discrimination prohibited.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 24 Housing and Urban Development 1 2010-04-01 2010-04-01 false Discrimination prohibited. 6.4... COMMUNITY DEVELOPMENT ACT OF 1974 General Provisions § 6.4 Discrimination prohibited. (a) Section 109... benefits of, or be subjected to discrimination under any program or activity funded in whole or in...

  11. Effect of the cyclobutane cytidine dimer on the properties of Escherichia coli DNA photolyase.

    PubMed

    Murphy, Anar K; Tammaro, Margaret; Cortazar, Frank; Gindt, Yvonne M; Schelvis, Johannes P M

    2008-11-27

    Cyclobutane pyrimidine dimer (CPD) photolyases are structure specific DNA-repair enzymes that specialize in the repair of CPDs, the major photoproducts that are formed upon irradiation of DNA with ultraviolet light. The purified enzyme binds a flavin adenine dinucleotide (FAD), which is in the neutral radical semiquinone (FADH(*)) form. The CPDs are repaired by a light-driven, electron transfer from the anionic hydroquinone (FADH(-)) singlet excited state to the CPD, which is followed by reductive cleavage of the cyclobutane ring and subsequent monomerization of the pyrimidine bases. CPDs formed between two adjacent thymidine bases (T< >T) are repaired with greater efficiency than those formed between two adjacent cytidine bases (C< >C). In this paper, we investigate the changes in Escherichia coli photolyase that are induced upon binding to DNA containing C< >C lesions using resonance Raman, UV-vis absorption, and transient absorption spectroscopies, spectroelectrochemistry, and computational chemistry. The binding of photolyase to a C< >C lesion modifies the energy levels of FADH(*), the rate of charge recombination between FADH(-) and Trp(306)(*), and protein-FADH(*) interactions differently than binding to a T< >T lesion. However, the reduction potential of the FADH(-)/FADH(*) couple is modified in the same way with both substrates. Our calculations show that the permanent electric dipole moment of C< >C is stronger (12.1 D) and oriented differently than that of T< >T (8.7 D). The possible role of the electric dipole moment of the CPD in modifying the physicochemical properties of photolyase as well as in affecting CPD repair will be discussed.

  12. Characterization of photolyase/blue-light receptor homologs in mouse and human cells.

    PubMed

    Kobayashi, K; Kanno, S; Smit, B; van der Horst, G T; Takao, M; Yasui, A

    1998-11-15

    We isolated and characterized mouse photolyase-like genes, mCRY1 (mPHLL1) and mCRY2 (mPHLL2), which belong to the photolyase family including plant blue-light receptors. The mCRY1 and mCRY2 genes are located on chromosome 10C and 2E, respectively, and are expressed in all mouse organs examined. We raised antibodies specific against each gene product using its C-terminal sequence, which differs completely between the genes. Immunofluorescent staining of cultured mouse cells revealed that mCRY1 is localized in mitochondria whereas mCRY2 was found mainly in the nucleus. The subcellular distribution of CRY proteins was confirmed by immunoblot analysis of fractionated mouse liver cell extracts. Using green fluorescent protein fused peptides we showed that the C-terminal region of the mouse CRY2 protein contains a unique nuclear localization signal, which is absent in the CRY1 protein. The N-terminal region of CRY1 was shown to contain the mitochondrial transport signal. Recombinant as well as native CRY1 proteins from mouse and human cells showed a tight binding activity to DNA Sepharose, while CRY2 protein did not bind to DNA Sepharose at all under the same condition as CRY1. The different cellular localization and DNA binding properties of the mammalian photolyase homologs suggest that despite the similarity in the sequence the two proteins have distinct function(s).

  13. Direct determination of resonance energy transfer in photolyase: structural alignment for the functional state.

    PubMed

    Tan, Chuang; Guo, Lijun; Ai, Yuejie; Li, Jiang; Wang, Lijuan; Sancar, Aziz; Luo, Yi; Zhong, Dongping

    2014-11-13

    Photoantenna is essential to energy transduction in photoinduced biological machinery. A photoenzyme, photolyase, has a light-harvesting pigment of methenyltetrahydrofolate (MTHF) that transfers its excitation energy to the catalytic flavin cofactor FADH¯ to enhance DNA-repair efficiency. Here we report our systematic characterization and direct determination of the ultrafast dynamics of resonance energy transfer from excited MTHF to three flavin redox states in E. coli photolyase by capturing the intermediates formed through the energy transfer and thus excluding the electron-transfer quenching pathway. We observed 170 ps for excitation energy transferring to the fully reduced hydroquinone FADH¯, 20 ps to the fully oxidized FAD, and 18 ps to the neutral semiquinone FADH(•), and the corresponding orientation factors (κ(2)) were determined to be 2.84, 1.53 and 1.26, respectively, perfectly matching with our calculated theoretical values. Thus, under physiological conditions and over the course of evolution, photolyase has adopted the optimized orientation of its photopigment to efficiently convert solar energy for repair of damaged DNA.

  14. FTIR Study of the Photoactivation Process of Xenopus (6-4) Photolyase†

    PubMed Central

    Yamada, Daichi; Zhang, Yu; Iwata, Tatsuya; Hitomi, Kenichi; Getzoff, Elizabeth D.; Kandori, Hideki

    2012-01-01

    Photolyases (PHRs) are blue-light activated DNA repair enzymes that maintain genetic integrity by reverting UV-induced photoproducts into normal bases. The FAD chromophore of PHRs has four different redox states: oxidized (FADox), anion radical (FAD•−), neutral radical (FADH•) and fully reduced (FADH−). We combined difference Fourier-transform infrared (FTIR) spectroscopy with UV-visible spectroscopy to study the detailed photoactivation process of Xenopus (6-4) PHR. Two photons produce the enzymatically active, fully reduced PHR from oxidized FAD: FADox is converted to semiquinone via light-induced one-electron and one-proton transfers, and then to FADH− by light-induced one-electron transfer. We successfully trapped FAD•− at 200 K, where electron transfer occurs, but proton transfer does not. UV-visible spectroscopy following 450-nm illumination of FADox at 277 K defined the FADH•/FADH− mixture and allowed calculation of difference FTIR spectra among the four redox states. The absence of a characteristic C=O stretching vibration indicated that the proton donor is not a protonated carboxylic acid. Structural changes in Trp and Tyr are suggested from UV-visible and FTIR analysis of FAD•− at 200 K. Spectral analysis of amide-I vibrations revealed structural perturbation of the protein’s β-sheet during initial electron transfer (FAD•− formation), transient increase in α-helicity during proton transfer (FADH• formation) and reversion to the initial amide-I signal following subsequent electron transfer (FADH− formation). Consequently, in (6-4) PHR, unlike cryptochrome-DASH, formation of enzymatically active FADH− did not perturb α-helicity. Protein structural changes in the photoactivation of (6-4) PHR are discussed on the basis of the present FTIR observations. PMID:22747528

  15. 43 CFR 3141.6-4 - Qualifications.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ..., DEPARTMENT OF THE INTERIOR MINERALS MANAGEMENT (3000) LEASING IN SPECIAL TAR SAND AREAS Leasing in Special Tar Sand Areas § 3141.6-4 Qualifications. Each bidder shall submit with the bid a statement over the...

  16. 43 CFR 3141.6-4 - Qualifications.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ..., DEPARTMENT OF THE INTERIOR MINERALS MANAGEMENT (3000) LEASING IN SPECIAL TAR SAND AREAS Leasing in Special Tar Sand Areas § 3141.6-4 Qualifications. Each bidder shall submit with the bid a statement over the...

  17. 43 CFR 3141.6-4 - Qualifications.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ..., DEPARTMENT OF THE INTERIOR MINERALS MANAGEMENT (3000) LEASING IN SPECIAL TAR SAND AREAS Leasing in Special Tar Sand Areas § 3141.6-4 Qualifications. Each bidder shall submit with the bid a statement over the...

  18. 43 CFR 3141.6-4 - Qualifications.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ..., DEPARTMENT OF THE INTERIOR MINERALS MANAGEMENT (3000) LEASING IN SPECIAL TAR SAND AREAS Leasing in Special Tar Sand Areas § 3141.6-4 Qualifications. Each bidder shall submit with the bid a statement over the...

  19. Crystal structure of poly[di-chlorido-(μ-2,5-di-carb-oxy-benzene-1,4-di-carboxyl-ato-κ(2)O(1):O(4))bis-[μ-4'-(pyridin-3-yl)-4,2':6',4''-terpyridine-κ(2)N(1):N(4')]dizinc].

    PubMed

    Tian, Yue; Xu, Sha-Sha; Su, Jian; Zhang, Yang; Zhao, Shao-Shuai; Tian, Yu-Peng

    2016-11-01

    In the title polymeric Zn(II) complex, [Zn2(C10H4O8)Cl2(C20H14N4)2] n , the Zn(II) cations are bridged by both 2,5-di-carb-oxy-benzene-1,4-di-carboxyl-ate dianions and 4'-(pyridin-3-yl)-4,2':6',4''-terpyridine ligands, forming ladder-like polymeric chains propagating along [1-10]. The Cl(-) anion further coordinates the Zn(II) cation to complete a distorted tetra-hedral environment. In the 4'-(pyridin-3-yl)-4,2':6',4''-terpyridine ligand, the three sideward pyridine rings are twisted with respect to the central pyridine ring by 39.27 (12), 14.89 (13) and 3.36 (13)°, respectively. In the crystal, classical O-H⋯N hydrogen bonds and weak C-H⋯O and C-H⋯Cl hydrogen bonds link the chains into a three-dimensional supra-molecular architecture. π-π stacking is observed between the pyridine and benzene rings of neighbouring polymeric chains, with a centroid-to-centroid distance of 3.7280 (14) Å.

  20. Transient induction of photolyase activity in arrested frog cells in response to a short-wave ultraviolet segment of simulated ''sunlight''

    SciTech Connect

    Chao, C.C.; Lin-Chao, S.

    1987-05-29

    Induction of photolyase activity was studied in cultured frog cells using clonogenic assays. Exposure of arrested cells to a pre-irradiation (90% survival) of 254 nm ultraviolet light resulted in a transient enhancement of photolyase activity. Cells expressed a decreased level of photolyase activity in response to an equitoxic fluence of simulated sunlight wavelengths 280-310 nm. However, no significant increase of enzyme activity was detected in cells following treatment with sunlight wavelengths 310-330 nm. In addition, this process depends on newly biosynthesized protein(s).

  1. Dynamics and mechanism of cyclobutane pyrimidine dimer repair by DNA photolyase.

    PubMed

    Liu, Zheyun; Tan, Chuang; Guo, Xunmin; Kao, Ya-Ting; Li, Jiang; Wang, Lijuan; Sancar, Aziz; Zhong, Dongping

    2011-09-06

    Photolyase uses blue light to restore the major ultraviolet (UV)-induced DNA damage, the cyclobutane pyrimidine dimer (CPD), to two normal bases by splitting the cyclobutane ring. Our earlier studies showed that the overall repair is completed in 700 ps through a cyclic electron-transfer radical mechanism. However, the two fundamental processes, electron-tunneling pathways and cyclobutane ring splitting, were not resolved. Here, we use ultrafast UV absorption spectroscopy to show that the CPD splits in two sequential steps within 90 ps and the electron tunnels between the cofactor and substrate through a remarkable route with an intervening adenine. Site-directed mutagenesis reveals that the active-site residues are critical to achieving high repair efficiency, a unique electrostatic environment to optimize the redox potentials and local flexibility, and thus balance all catalytic reactions to maximize enzyme activity. These key findings reveal the complete spatio-temporal molecular picture of CPD repair by photolyase and elucidate the underlying molecular mechanism of the enzyme's high repair efficiency.

  2. Dissection of the triple tryptophan electron transfer chain in Escherichia coli DNA photolyase: Trp382 is the primary donor in photoactivation.

    PubMed

    Byrdin, Martin; Eker, André P M; Vos, Marten H; Brettel, Klaus

    2003-07-22

    In Escherichia coli photolyase, excitation of the FAD cofactor in its semireduced radical state (FADH*) induces an electron transfer over approximately 15 A from tryptophan W306 to the flavin. It has been suggested that two additional tryptophans are involved in an electron transfer chain FADH* <-- W382 <-- W359 <-- W306. To test this hypothesis, we have mutated W382 into redox inert phenylalanine. Ultrafast transient absorption studies showed that, in WT photolyase, excited FADH* decayed with a time constant tau approximately 26 ps to fully reduced flavin and a tryptophan cation radical. In W382F mutant photolyase, the excited flavin was much longer lived (tau approximately 80 ps), and no significant amount of product was detected. We conclude that, in WT photolyase, excited FADH* is quenched by electron transfer from W382. On a millisecond scale, a product state with extremely low yield ( approximately 0.5% of WT) was detected in W382F mutant photolyase. Its spectral and kinetic features were similar to the fully reduced flavin/neutral tryptophan radical state in WT photolyase. We suggest that, in W382F mutant photolyase, excited FADH* is reduced by W359 at a rate that competes only poorly with the intrinsic decay of excited FADH* (tau approximately 80 ps), explaining the low product yield. Subsequently, the W359 cation radical is reduced by W306. The rate constants of electron transfer from W382 to excited FADH* in WT and from W359 to excited FADH* in W382F mutant photolyase were estimated and related to the donor-acceptor distances.

  3. Intraprotein electron transfer between tyrosine and tryptophan in DNA photolyase from Anacystis nidulans.

    PubMed

    Aubert, C; Mathis, P; Eker, A P; Brettel, K

    1999-05-11

    Light-induced electron transfer reactions leading to the fully reduced, catalytically competent state of the flavin adenine dinucleotide (FAD) cofactor have been studied by flash absorption spectroscopy in DNA photolyase from Anacystis nidulans. The protein, overproduced in Escherichia coli, was devoid of the antenna cofactor, and the FAD chromophore was present in the semireduced form, FADH., which is inactive for DNA repair. We show that after selective excitation of FADH. by a 7-ns laser flash, fully reduced FAD (FADH-) is formed in less than 500 ns by electron abstraction from a tryptophan residue. Subsequently, a tyrosine residue is oxidized by the tryptophanyl radical with t(1)/(2) = 50 microseconds. The amino acid radicals were identified by their characteristic absorption spectra, with maxima at 520 nm for Trp. and 410 nm for TyrO. The newly discovered electron transfer between tyrosine and tryptophan occurred for approximately 40% of the tryptophanyl radicals, whereas 60% decayed by charge recombination with FADH- (t(1)/(2) = 1 ms). The tyrosyl radical can also recombine with FADH- but at a much slower rate (t(1)/(2) = 76 ms) than Trp. In the presence of an external electron donor, however, TyrO. is rereduced efficiently in a bimolecular reaction that leaves FAD in the fully reduced state FADH-. These results show that electron transfer from tyrosine to Trp. is an essential step in the process leading to the active form of photolyase. They provide direct evidence that electron transfer between tyrosine and tryptophan occurs in a native biological reaction.

  4. Crystal structure of (1S,3R,8R,9R)-2,2-di­chloro-3,7,7-tri­methyl-10-methylenetri­cyclo­[6.4.0.01,3]dodecan-9-ol

    PubMed Central

    Benzalim, Ahmed; Auhmani, Aziz; Bimoussa, Abdoullah; Ait Itto, My Youssef; Daran, Jean-Claude; Auhmani, Abdelwahed

    2016-01-01

    The title compound, C16H24Cl2O, was synthesized by treating (1S,3R,8S,9R,10S)-2,2-di­chloro-3,7,7,10-tetra­methyl-9,10-ep­oxy­tri­cyclo­[6.4.0.01,3]dodecane with a concentrated solution of hydro­bromic acid. It is built up from three fused rings: a cyclo­heptane ring, a cyclo­hexyl ring bearing alkene and hy­droxy substituents, and a cyclo­propane ring bearing two chlorine atoms. The asymmetric unit contains two mol­ecules linked by an O—H⋯O hydrogen bond. In the crystal, further O—H⋯O hydrogen bonds build up an R 4 4(8) cyclic tetra­mer. One of the mol­ecules presents disorder that affects the seven-membered ring. In both mol­ecules, the six-membered rings display a chair conformation, whereas the seven-membered rings display conformations inter­mediate between boat and twist-boat for the non-disordered mol­ecule and either a chair or boat and twist-boat for the disordered mol­ecule owing to the disorder. The absolute configuration for both mol­ecules is 1S,3R,8R,9R and was deduced from the chemical pathway and further confirmed by the X-ray structural analysis. PMID:27536404

  5. Cyclobutane pyrimidine dimer (CPD) photolyase repairs ultraviolet-B-induced CPDs in rice chloroplast and mitochondrial DNA.

    PubMed

    Takahashi, Masaaki; Teranishi, Mika; Ishida, Hiroyuki; Kawasaki, Junji; Takeuchi, Atsuko; Yamaya, Tomoyuki; Watanabe, Masao; Makino, Amane; Hidema, Jun

    2011-05-01

    Plants use sunlight as energy for photosynthesis; however, plant DNA is exposed to the harmful effects of ultraviolet-B (UV-B) radiation (280-320 nm) in the process. UV-B radiation damages nuclear, chloroplast and mitochondrial DNA by the formation of cyclobutane pyrimidine dimers (CPDs), which are the primary UV-B-induced DNA lesions, and are a principal cause of UV-B-induced growth inhibition in plants. Repair of CPDs is therefore essential for plant survival while exposed to UV-B-containing sunlight. Nuclear repair of the UV-B-induced CPDs involves the photoreversal of CPDs, photoreactivation, which is mediated by CPD photolyase that monomerizes the CPDs in DNA by using the energy of near-UV and visible light (300-500 nm). To date, the CPD repair processes in plant chloroplasts and mitochondria remain poorly understood. Here, we report the photoreactivation of CPDs in chloroplast and mitochondrial DNA in rice. Biochemical and subcellular localization analyses using rice strains with different levels of CPD photolyase activity and transgenic rice strains showed that full-length CPD photolyase is encoded by a single gene, not a splice variant, and is expressed and targeted not only to nuclei but also to chloroplasts and mitochondria. The results indicate that rice may have evolved a CPD photolyase that functions in chloroplasts, mitochondria and nuclei, and that contains DNA to protect cells from the harmful effects of UV-B radiation. © 2011 The Authors. The Plant Journal © 2011 Blackwell Publishing Ltd.

  6. Transport of rice cyclobutane pyrimidine dimer photolyase into mitochondria relies on a targeting sequence located in its C-terminal internal region.

    PubMed

    Takahashi, Sayaka; Teranishi, Mika; Izumi, Masanori; Takahashi, Masaaki; Takahashi, Fumio; Hidema, Jun

    2014-09-01

    The cyclobutane pyrimidine dimer (CPD), which represents a major type of DNA damage induced by ultraviolet-B (UVB) radiation, is a principal cause of UVB-induced growth inhibition in plants. CPD photolyase is the primary enzyme for repairing CPDs and is crucial for determining the sensitivity of Oryza sativa (rice) to UVB radiation. CPD photolyase is widely distributed among species ranging from eubacteria to eukaryotes, and is classified into class I or II based on its primary structure. We previously demonstrated that rice CPD photolyase (OsPHR), which belongs to class II and is encoded by a single-copy gene, is a unique nuclear/mitochondrial/chloroplast triple-targeting protein; however, the location and nature of the organellar targeting information contained within OsPHR are unknown. Here, the nuclear and mitochondrial targeting signal sequences of OsPHR were identified by systematic deletion analysis. The nuclear and mitochondrial targeting sequences are harbored within residues 487-489 and 391-401 in the C-terminal region of OsPHR (506 amino acid residues), respectively. The mitochondrial targeting signal represents a distinct topogenic sequence that differs structurally and functionally from classical N-terminal pre-sequences, and this region, in addition to its role in localization to the mitochondria, is essential for the proper functioning of the CPD photolyase. Furthermore, the mitochondrial targeting sequence, which is characteristic of class-II CPD photolyases, was acquired before the divergence of class-II CPD photolyases in eukaryotes. These results indicate that rice plants have evolved a CPD photolyase that functions in mitochondria to protect cells from the harmful effects of UVB radiation. © 2014 The Authors. The Plant Journal © 2014 John Wiley & Sons Ltd.

  7. Substrate overlap and functional competition between human nucleotide excision repair and Escherichia coli photolyase and (A)BC excision nuclease

    SciTech Connect

    Sibghat-Ullah; Sancar, Z. )

    1990-06-19

    Human cell free extract prepared by the method of Manley et al. carries out repair synthesis on UV-irradiated DNA. Removal of pyrimidine dimers by photoreactivation with DNA photolyase reduces repair synthesis by about 50%. With excess enzyme in the reaction mixture photolyase reduced the repair signal by the same amount even in the absence of photoreactivating light, presumably by binding to pyrimidine dimers and interfering with the binding of human damage recognition protein. Similarly, the UvrB subunit of Escherichia coli (A)BC excinuclease when loaded onto UV-irradiated or psoralen-adducted DNA inhibited repair synthesis by cell-free extract by 75-80%. The opposite was true also as HeLa cell free extract specifically inhibited the photorepair of a thymine dimer by DNA photolyase and its removal by (A)BC excinuclease. Cell-free extracts from xeroderma pigmentosum (XP) complementation groups A and C were equally effective in blocking the E. coli repair proteins, while extracts from complementation groups D and E were ineffective in blocking the E. coli enzyme. These results suggest that XP-D and XP-E cells are defective in the damage recognition subunits(s) of human excision nuclease.

  8. An unidentified ultraviolet-B-specific photoreceptor mediates transcriptional activation of the cyclobutane pyrimidine dimer photolyase gene in plants.

    PubMed

    Ioki, Motohide; Takahashi, Shinya; Nakajima, Nobuyoshi; Fujikura, Kohei; Tamaoki, Masanori; Saji, Hikaru; Kubo, Akihiro; Aono, Mitsuko; Kanna, Machi; Ogawa, Daisuke; Fukazawa, Jutarou; Oda, Yoshihisa; Yoshida, Seiji; Watanabe, Masakatsu; Hasezawa, Seiichiro; Kondo, Noriaki

    2008-12-01

    Cyclobutane pyrimidine dimers (CPDs) constitute a majority of DNA lesions caused by ultraviolet-B (UVB). CPD photolyase, which rapidly repairs CPDs, is essential for plant survival under sunlight containing UVB. Our earlier results that the transcription of the cucumber CPD photolyase gene (CsPHR) was activated by light have prompted us to propose that this light-driven transcriptional activation would allow plants to meet the need of the photolyase activity upon challenges of UVB from sunlight. However, molecular mechanisms underlying the light-dependent transcriptional activation of CsPHR were unknown. In order to understand spectroscopic aspects of the plant response, we investigated the wavelength-dependence (action spectra) of the light-dependent transcriptional activation of CsPHR. In both cucumber seedlings and transgenic Arabidopsis seedlings expressing reporter genes under the control of the CsPHR promoter, the action spectra exhibited the most predominant peak in the long-wavelength UVB waveband (around 310 nm). In addition, a 95-bp cis-acting region in the CsPHR promoter was identified to be essential for the UVB-driven transcriptional activation of CsPHR. Thus, we concluded that the photoperception of long-wavelength UVB by UVB photoreceptor(s) led to the induction of the CsPHR transcription via a conserved cis-acting element.

  9. Reduced ultraviolet-induced DNA damage and apoptosis in human skin with topical application of a photolyase-containing DNA repair enzyme cream: clues to skin cancer prevention.

    PubMed

    Berardesca, Enzo; Bertona, Marco; Altabas, Karmela; Altabas, Velimir; Emanuele, Enzo

    2012-02-01

    The exposure of human skin to ultraviolet radiation (UVR) results in the formation of DNA photolesions that give rise to photoaging, mutations, cell death and the onset of carcinogenic events. Photolyase (EC 4.1.99.3) is a DNA repair enzyme that reverses damage caused by exposure to UVR. We sought to investigate whether addition of photolyase enhances the protection provided by a traditional sunscreen (SS), by reducing the in vivo formation of cyclobutane-type pyrimidine dimers (CPDs) and UVR-induced apoptosis in human skin. Ten volunteers (Fitzpatrick skin type II) were exposed to solar-simulated (ss) UVR at a three times minimal erythema dose for 4 consecutive days. Thirty minutes prior to each exposure, the test materials [vehicle, SS (sun protection factor 50) alone, and SS plus photolyase from Anacystis nidulans] were applied topically to three different sites. One additional site was left untreated and one received ssUVR only. Biopsy specimens were taken 72 h after the last irradiation. The amount of CPDs and the extent of apoptosis were measured by ELISA. Photolyase plus SS was superior to SS alone in reducing both the formation of CPDs and apoptotic cell death (both P<0.001). In conclusion, the addition of photolyase to a traditional SS contributes significantly to the prevention of UVR-induced DNA damage and apoptosis when applied topically to human skin.

  10. 1 CFR 6.4 - Monthly list of sections affected.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 1 General Provisions 1 2011-01-01 2011-01-01 false Monthly list of sections affected. 6.4 Section 6.4 General Provisions ADMINISTRATIVE COMMITTEE OF THE FEDERAL REGISTER THE FEDERAL REGISTER INDEXES AND ANCILLARIES § 6.4 Monthly list of sections affected. A monthly list of sections of the Code...

  11. 1 CFR 6.4 - Monthly list of sections affected.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 1 General Provisions 1 2010-01-01 2010-01-01 false Monthly list of sections affected. 6.4 Section 6.4 General Provisions ADMINISTRATIVE COMMITTEE OF THE FEDERAL REGISTER THE FEDERAL REGISTER INDEXES AND ANCILLARIES § 6.4 Monthly list of sections affected. A monthly list of sections of the Code...

  12. 39 CFR 6.4 - Attendance by conference telephone call.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 39 Postal Service 1 2010-07-01 2010-07-01 false Attendance by conference telephone call. 6.4 Section 6.4 Postal Service UNITED STATES POSTAL SERVICE THE BOARD OF GOVERNORS OF THE U.S. POSTAL SERVICE MEETINGS (ARTICLE VI) § 6.4 Attendance by conference telephone call. For regularly scheduled meetings...

  13. Dynamics and pathway of electron tunneling in repair of damaged DNA by photolyase

    NASA Astrophysics Data System (ADS)

    Liu, Zheyun; Guo, Xunmin; Tan, Chuang; Li, Jiang; Kao, Ya-Ting; Wang, Lijuan; Sancar, Aziz; Zhong, Dongping

    2013-03-01

    Through electron tunneling, photolyase, a photoenzyme, restores damaged DNA into normal bases. Here, we report our systematic characterization and analyses of three electron transfer processes in thymine dimer restoration by following the entire dynamical evolution during enzymatic repair with femtosecond resolution. Using (deoxy)uracil and thymine as dimer substrates, we unambiguously determined the electron tunneling pathways for the forward electron transfer to initiate repairing and for the final electron return to restore the active cofactor and complete the repair photocycle. Significantly, we found that the adenine moiety of the unusual bent cofactor is essential to mediating all electron-transfer dynamics through a super-exchange mechanism, leading to a delicate balance of time scales. The active-site structural integrity, unique electron tunneling pathways and the critical role of adenine assure these elementary dynamics in synergy in this complex photorepair machinery to achieve the maximum repair efficiency close to unity. The authors thank Drs. Chaitanya Sexana, Yi Yang, and Chen Zang for the initial help with experiment, and Prof. Sherwin Singer and Dr. Ali Hassanali for discussion.

  14. Electron Tunneling Pathway and Role of Adenine in Repair of Damaged DNA by Photolyase

    NASA Astrophysics Data System (ADS)

    Liu, Zheyun; Tan, Chuang; Guo, Xunmin; Kao, Ya-Ting; Li, Jiang; Wang, Lijuan; Zhong, Dongping

    2012-06-01

    Through electron tunneling, photolyase, a photoenzyme, restores damaged DNA into normal bases. Here, we report our systematic characterization and analyses of three electron transfer processes in thymine dimer restoration by following the entire dynamical evolution during enzymatic repair with femtosecond resolution. We observed the complete dynamics of the reactants, all intermediates and final products, and determined their reaction time scales. Using (deoxy)uracil and thymine as dimer substrates, we unambiguously determined the electron tunneling pathways for the forward electron transfer to initiate repairing and for the final electron return to restore the active cofactor and complete the repair photocycle. Significantly, we found that the adenine moiety of the unusual bent cofactor is essential to mediating all electron transfer dynamics through a super-exchange mechanism, leading to a delicate balance of time scales. The active-site structural integrity, unique electron tunneling pathways and the critical role of adenine assure these elementary dynamics in synergy in this complex photorepair machinery to achieve the maximum repair efficiency close to unity. Z. Liu, C. Tan, X. Guo, Y.-T. Kao, J. Li, L. Wang, A. Sancar, and D. Zhong, Proc. Natl. Acad. Sci. USA 108, 14831 (2011) J. Li, Z. Liu, C. Tan, X. Guo, L. Wang, A. Sancar, and D. Zhong, Nature 466, 887 (2010)

  15. Atypical E2F activity coordinates PHR1 photolyase gene transcription with endoreduplication onset.

    PubMed

    Radziejwoski, Amandine; Vlieghe, Kobe; Lammens, Tim; Berckmans, Barbara; Maes, Sara; Jansen, Marcel A K; Knappe, Claudia; Albert, Andreas; Seidlitz, Harald K; Bahnweg, Günther; Inzé, Dirk; De Veylder, Lieven

    2011-01-19

    Because of their sessile life style, plants have evolved the ability to adjust to environmentally harsh conditions. An important aspect of stress adaptation involves the reprogramming of the cell cycle to ensure optimal growth. The atypical E2F transcription factor DP-E2F-like 1 (E2Fe/DEL1) had been found previously to be an important regulator of the endocycle onset. Here, a novel role for E2Fe/DEL1 was identified as a transcriptional repressor of the type-II cyclobutane pyrimidine dimer-photolyase DNA repair gene PHR1. Upon ultraviolet-B (UV-B) treatment, plants knocked out for E2Fe/DEL1 had improved DNA repair abilities when compared with control plants, whereas those overexpressing it performed less well. Better DNA repair allowed E2Fe/DEL1 knockout plants to resume endoreduplication faster than control plants, contributing in this manner to UV-B radiation resistance by compensating the stress-induced reduction in cell number by ploidy-dependent cell growth. As E2Fe/DEL1 levels decreased upon UV-B treatment, we hypothesize that the coordinated transcriptional induction of PHR1 with the endoreduplication onset contributes to the adaptation of plants exposed to UV-B stress.

  16. Atypical E2F activity coordinates PHR1 photolyase gene transcription with endoreduplication onset

    PubMed Central

    Radziejwoski, Amandine; Vlieghe, Kobe; Lammens, Tim; Berckmans, Barbara; Maes, Sara; Jansen, Marcel A K; Knappe, Claudia; Albert, Andreas; Seidlitz, Harald K; Bahnweg, Günther; Inzé, Dirk; De Veylder, Lieven

    2011-01-01

    Because of their sessile life style, plants have evolved the ability to adjust to environmentally harsh conditions. An important aspect of stress adaptation involves the reprogramming of the cell cycle to ensure optimal growth. The atypical E2F transcription factor DP-E2F-like 1 (E2Fe/DEL1) had been found previously to be an important regulator of the endocycle onset. Here, a novel role for E2Fe/DEL1 was identified as a transcriptional repressor of the type-II cyclobutane pyrimidine dimer-photolyase DNA repair gene PHR1. Upon ultraviolet-B (UV-B) treatment, plants knocked out for E2Fe/DEL1 had improved DNA repair abilities when compared with control plants, whereas those overexpressing it performed less well. Better DNA repair allowed E2Fe/DEL1 knockout plants to resume endoreduplication faster than control plants, contributing in this manner to UV-B radiation resistance by compensating the stress-induced reduction in cell number by ploidy-dependent cell growth. As E2Fe/DEL1 levels decreased upon UV-B treatment, we hypothesize that the coordinated transcriptional induction of PHR1 with the endoreduplication onset contributes to the adaptation of plants exposed to UV-B stress. PMID:21131907

  17. Do photolyases need to provide considerable activation energy for the splitting of cyclobutane pyrimidine dimer radical anions?

    PubMed

    Song, Qin-Hua; Tang, Wen-Jian; Ji, Xue-Bao; Wang, Hong-Bo; Guo, Qing-Xiang

    2007-01-01

    cis-syn Cyclobutane pyrimidine dimers, major UV-induced DNA lesions, are efficiently repaired by DNA photolyases. The key step of the repair reaction is a light-driven electron transfer from the FADH(-) cofactor to the dimer; the resulting radical anion splits spontaneously. Whether the splitting reaction requires considerable activation energy is still under dispute. Recent reports show that the splitting reaction of a dimer radical anion has a significant activation barrier (0.45 eV), and so photolyases have to provide considerable energy. However, these results contradict observations that cis-syn dimer radical anions split into monomers at -196 degrees C, and that the full process of DNA photoreactivation was fast (1.5-2 ns). To investigate the activation energies of dimer radical anions, three model compounds 1-3 were prepared. These include a covalently linked cyclobutane thymine dimer and a tryptophan residue (1) or a flavin unit (3), and the covalently linked uracil dimer and tryptophan (2). Their properties of photosensitised splitting of the dimer units by tryptophan or flavin unit were investigated over a large temperature range, -196 to 70 degrees C. The activation energies were obtained from the temperature dependency of splitting reactions for 1 and 2, 1.9 kJ mol(-1) and 0.9 kJ mol(-1) for the thymine and uracil dimer radical anions, respectively. These values are much lower than that obtained for E. coli photolyase (0.45 eV), and are surmountable at -196 degrees C. The activation energies provide support for previous observations that repair efficiencies for uracil dimers are higher than thymine dimers, both in enzymatic and model systems. The mechanisms of highly efficient enzymatic DNA repair are discussed.

  18. Electron Tunneling Pathways and Role of Adenine in Repair of Cyclobutane Pyrimidine Dimer by DNA Photolyase

    PubMed Central

    Liu, Zheyun; Guo, Xunmin; Tan, Chuang; Li, Jiang; Kao, Ya-Ting; Wang, Lijuan; Sancar, Aziz; Zhong, Dongping

    2012-01-01

    Electron tunneling pathways in enzymes are critical to their catalytic efficiency. Through electron tunneling, photolyase, a photoenzyme, splits UV-induced cyclobutane pyrimidine dimer into two normal bases. Here, we report our systematic characterization and analyses of photo-initiated three electron transfer processes and cyclobutane ring splitting by following the entire dynamical evolution during enzymatic repair with femtosecond resolution. We observed the complete dynamics of the reactants, all intermediates and final products, and determined their reaction time scales. Using (deoxy)uracil and thymine as dimer substrates, we unambiguously determined the electron tunneling pathways for the forward electron transfer to initiate repair and for the final electron return to restore the active cofactor and complete the catalytic photocycle. Significantly, we found that the adenine moiety of the unusual bent flavin cofactor is essential to mediating all electron-transfer dynamics through a super-exchange mechanism, leading to a delicate balance of time scales. The cyclobutane ring splitting takes tens of picoseconds while electron-transfer dynamics all occur on a longer time scale. The active-site structural integrity, unique electron tunneling pathways and the critical role of adenine assure the synergy of these elementary steps in this complex photorepair machinery to achieve maximum repair efficiency which is close to unity. Finally, we used the Marcus electron-transfer theory to evaluate all three electron transfer processes and thus obtained their reaction driving forces (free energies), reorganization energies, and electronic coupling constants, concluding the forward and futile back electron transfer in the normal region and that the final electron return of the catalytic cycle is in the inverted region. PMID:22533849

  19. Electron tunneling pathways and role of adenine in repair of cyclobutane pyrimidine dimer by DNA photolyase.

    PubMed

    Liu, Zheyun; Guo, Xunmin; Tan, Chuang; Li, Jiang; Kao, Ya-Ting; Wang, Lijuan; Sancar, Aziz; Zhong, Dongping

    2012-05-16

    Electron tunneling pathways in enzymes are critical to their catalytic efficiency. Through electron tunneling, photolyase, a photoenzyme, splits UV-induced cyclobutane pyrimidine dimer into two normal bases. Here, we report our systematic characterization and analyses of photoinitiated three electron transfer processes and cyclobutane ring splitting by following the entire dynamical evolution during enzymatic repair with femtosecond resolution. We observed the complete dynamics of the reactants, all intermediates and final products, and determined their reaction time scales. Using (deoxy)uracil and thymine as dimer substrates, we unambiguously determined the electron tunneling pathways for the forward electron transfer to initiate repair and for the final electron return to restore the active cofactor and complete the catalytic photocycle. Significantly, we found that the adenine moiety of the unusual bent flavin cofactor is essential to mediating all electron-transfer dynamics through a superexchange mechanism, leading to a delicate balance of time scales. The cyclobutane ring splitting takes tens of picoseconds, while electron-transfer dynamics all occur on a longer time scale. The active-site structural integrity, unique electron tunneling pathways, and the critical role of adenine ensure the synergy of these elementary steps in this complex photorepair machinery to achieve maximum repair efficiency which is close to unity. Finally, we used the Marcus electron-transfer theory to evaluate all three electron-transfer processes and thus obtained their reaction driving forces (free energies), reorganization energies, and electronic coupling constants, concluding that the forward and futile back-electron transfer is in the normal region and that the final electron return of the catalytic cycle is in the inverted region.

  20. Kinetics of cyclobutane thymine dimer splitting by DNA photolyase directly monitored in the UV.

    PubMed

    Thiagarajan, Viruthachalam; Byrdin, Martin; Eker, André P M; Müller, Pavel; Brettel, Klaus

    2011-06-07

    CPD photolyase uses light to repair cyclobutane pyrimidine dimers (CPDs) formed between adjacent pyrimidines in UV-irradiated DNA. The enzyme harbors an FAD cofactor in fully reduced state (FADH(-)). The CPD repair mechanism involves electron transfer from photoexcited FADH(-) to the CPD, splitting of its intradimer bonds, and electron return to restore catalytically active FADH(-). The two electron transfer processes occur on time scales of 10(-10) and 10(-9) s, respectively. Until now, CPD splitting itself has only been poorly characterized by experiments. Using a previously unreported transient absorption setup, we succeeded in monitoring cyclobutane thymine dimer repair in the main UV absorption band of intact thymine at 266 nm. Flavin transitions that overlay DNA-based absorption changes at 266 nm were monitored independently in the visible and subtracted to obtain the true repair kinetics. Restoration of intact thymine showed a short lag and a biexponential rise with time constants of 0.2 and 1.5 ns. We assign these two time constants to splitting of the intradimer bonds (creating one intact thymine and one thymine anion radical T(∘-)) and electron return from T(∘-) to the FAD cofactor with recovery of the second thymine, respectively. Previous model studies and computer simulations yielded various CPD splitting times between < 1 ps and < 100 ns. Our experimental results should serve as a benchmark for future efforts to model enzymatic photorepair. The technique and methods developed here may be applied to monitor other photoreactions involving DNA.

  1. Flavin adenine dinucleotide chromophore charge controls the conformation of cyclobutane pyrimidine dimer photolyase α-helices.

    PubMed

    Wijaya, I M Mahaputra; Iwata, Tatsuya; Yamamoto, Junpei; Hitomi, Kenichi; Iwai, Shigenori; Getzoff, Elizabeth D; Kennis, John T M; Mathes, Tilo; Kandori, Hideki

    2014-09-23

    Observations of light-receptive enzyme complexes are usually complicated by simultaneous overlapping signals from the chromophore, apoprotein, and substrate, so that only the initial, ultrafast, photon-chromophore reaction and the final, slow, protein conformational change provide separate, nonoverlapping signals. Each provides its own advantages, whereas sometimes the overlapping signals from the intervening time scales still cannot be fully deconvoluted. We overcome the problem by using a novel method to selectively isotope-label the apoprotein but not the flavin adenine dinucleotide (FAD) cofactor. This allowed the Fourier transform infrared (FTIR) signals to be separated from the apoprotein, FAD cofactor, and DNA substrate. Consequently, a comprehensive structure-function study by FTIR spectroscopy of the Escherichia coli cyclobutane pyrimidine dimer photolyase (CPD-PHR) DNA repair enzyme was possible. FTIR signals could be identified and assigned upon FAD photoactivation and DNA repair, which revealed protein dynamics for both processes beyond simple one-electron reduction and ejection, respectively. The FTIR data suggest that the synergistic cofactor-protein partnership in CPD-PHR linked to changes in the shape of FAD upon one-electron reduction may be coordinated with conformational changes in the apoprotein, allowing it to fit the DNA substrate. Activation of the CPD-PHR chromophore primes the apoprotein for subsequent DNA repair, suggesting that CPD-PHR is not simply an electron-ejecting structure. When FAD is activated, changes in its structure may trigger coordinated conformational changes in the apoprotein and thymine carbonyl of the substrate, highlighting the role of Glu275. In contrast, during DNA repair and release processes, primary conformational changes occur in the enzyme and DNA substrate, with little contribution from the FAD cofactor and surrounding amino acid residues.

  2. 31 CFR 6.4 - Eligibility of applicants.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... public or private organization with a net worth of not more than $5 million and not more than 500... 31 Money and Finance: Treasury 1 2011-07-01 2011-07-01 false Eligibility of applicants. 6.4 Section 6.4 Money and Finance: Treasury Office of the Secretary of the Treasury APPLICATIONS FOR...

  3. 31 CFR 6.4 - Eligibility of applicants.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... public or private organization with a net worth of not more than $5 million and not more than 500... 31 Money and Finance: Treasury 1 2010-07-01 2010-07-01 false Eligibility of applicants. 6.4 Section 6.4 Money and Finance: Treasury Office of the Secretary of the Treasury APPLICATIONS FOR...

  4. 1 CFR 6.4 - Monthly list of sections affected.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 1 General Provisions 1 2012-01-01 2012-01-01 false Monthly list of sections affected. 6.4 Section... AND ANCILLARIES § 6.4 Monthly list of sections affected. A monthly list of sections of the Code of Federal Regulations affected shall be separately published on a cumulative basis during each calendar year...

  5. 1 CFR 6.4 - Monthly list of sections affected.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 1 General Provisions 1 2013-01-01 2012-01-01 true Monthly list of sections affected. 6.4 Section 6... AND ANCILLARIES § 6.4 Monthly list of sections affected. A monthly list of sections of the Code of Federal Regulations affected shall be separately published on a cumulative basis during each calendar year...

  6. 1 CFR 6.4 - Monthly list of sections affected.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 1 General Provisions 1 2014-01-01 2012-01-01 true Monthly list of sections affected. 6.4 Section 6... AND ANCILLARIES § 6.4 Monthly list of sections affected. A monthly list of sections of the Code of Federal Regulations affected shall be separately published on a cumulative basis during each calendar year...

  7. 15 CFR 6.4 - Adjustments to penalties.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 6.4 Commerce and Foreign Trade Office of the Secretary of Commerce CIVIL MONETARY PENALTY INFLATION ADJUSTMENTS § 6.4 Adjustments to penalties. The civil monetary penalties provided by law within the... Sensing Policy Act of 1992, from $11,000 to $11,000. (2) 15 U.S.C. 5658(c), Land Remote Sensing Policy Act...

  8. Sequence analysis of the complete genome of Trichoplusia ni single nucleopolyhedrovirus and the identification of a baculoviral photolyase gene

    SciTech Connect

    Willis, Leslie G.; Siepp, Robyn; Stewart, Taryn M.; Erlandson, Martin A.; Theilmann, David A. . E-mail: TheilmannD@agr.gc.ca

    2005-08-01

    The genome of the Trichoplusia ni single nucleopolyhedrovirus (TnSNPV), a group II NPV which infects the cabbage looper (T. ni), has been completely sequenced and analyzed. The TnSNPV DNA genome consists of 134,394 bp and has an overall G + C content of 39%. Gene analysis predicted 144 open reading frames (ORFs) of 150 nucleotides or greater that showed minimal overlap. Comparisons with previously sequenced baculoviruses indicate that 119 TnSNPV ORFs were homologues of previously reported viral gene sequences. Ninety-four TnSNPV ORFs returned an Autographa californica multiple NPV (AcMNPV) homologue while 25 ORFs returned poor or no sequence matches with the current databases. A putative photolyase gene was also identified that had highest amino acid identity to the photolyase genes of Chrysodeixis chalcites NPV (ChchNPV) (47%) and Danio rerio (zebrafish) (40%). In addition unlike all other baculoviruses no obvious homologous repeat (hr) sequences were identified. Comparison of the TnSNPV and AcMNPV genomes provides a unique opportunity to examine two baculoviruses that are highly virulent for a common insect host (T. ni) yet belong to diverse baculovirus taxonomic groups and possess distinct biological features. In vitro fusion assays demonstrated that the TnSNPV F protein induces membrane fusion and syncytia formation and were compared to syncytia formed by AcMNPV GP64.

  9. The thermodynamics of charge transfer in DNA photolyase: using thermodynamic integration calculations to analyse the kinetics of electron transfer reactions.

    PubMed

    Krapf, Sebastian; Koslowski, Thorsten; Steinbrecher, Thomas

    2010-08-28

    DNA Photolyases are light sensitive oxidoreductases present in many organisms that participate in the repair of photodamaged DNA. They are capable of electron transfer between a bound cofactor and a chain of tryptophan amino acid residues. Due to their unique mechanism and important function, photolyases have been subject to intense study in recent times, with both experimental and computational efforts. In this work, we present a novel application of classical molecular dynamics based free energy calculations, combined with quantum mechanical computations, to biomolecular charge transfer. Our approach allows for the determination of all reaction parameters in Marcus' theory of charge transport. We were able to calculate the free energy profile for the movement of a positive charge along protein sidechains involved in the biomolecule's function as well as charge-transfer rates that are in good agreement with experimental results. Our approach to simulate charge-transfer reactions explicitly includes the influence of protein flexibility and solvent dynamics on charge-transfer energetics. As applied here to a biomolecular system of considerable scientific interest, we believe the method to be easily adaptable to the study of charge-transfer phenomena in biochemistry and other fields.

  10. Charge transfer in E. coli DNA photolyase: understanding polarization and stabilization effects via QM/MM simulations.

    PubMed

    Lüdemann, Gesa; Woiczikowski, P Benjamin; Kubař, Tomáš; Elstner, Marcus; Steinbrecher, Thomas B

    2013-09-19

    We study fast hole transfer events in E. coli DNA photolyase, a key step in the photoactivation process, using a multiscale computational method that combines nonadiabatic propagation schemes and linear-scaling quantum chemical methods with molecular mechanics force fields. This scheme allows us to follow the time-dependent evolution of the electron hole in an unbiased fashion; that is, no assumptions about hole wave function localization, time scale separation, or adiabaticity of the process have to be made beforehand. DNA photolyase facilitates an efficient long-range charge transport between its flavin adenine dinucleotide (FAD) cofactor and the protein surface via a chain of evolutionary conserved Trp residues on the sub-nanosecond time scale despite the existence of multiple potential trap states. By including a large number of aromatic residues along the charge transfer pathway into the quantum description, we are able to identify the main pathway among alternative possible routes. The simulations show that charge transfer, which is extremely fast in this protein, occurs on the same time scale as the protein response to the electrostatic changes; that is, time-scale separation as often presupposed in charge transfer studies seems to be inappropriate for this system. Therefore, coupled equations of motion, which propagate electrons and nuclei simultaneously, appear to be necessary. The applied computational model is shown to capture the essentials of the reaction kinetics and thermodynamics while allowing direct simulations of charge transfer events on their natural time scale.

  11. PHH1, a novel gene from Arabidopsis thaliana that encodes a protein similar to plant blue-light photoreceptors and microbial photolyases.

    PubMed

    Hoffman, P D; Batschauer, A; Hays, J B

    1996-11-27

    A cDNA from Arabidopsis thaliana similar to microbial photolyase genes, and designated AT-PHH1, was isolated using a photolyase-like cDNA from Sinapsis alba (SA-PHR1) as a probe. Multiple isolations yielded only PHH1 cDNAs, and a few blue-light-receptor CRY1 (HY4) cDNAs (also similar to microbial photolyase genes), suggesting the absence of any other highly similar Arabidopsis genes. The AT-PHH1 and SA-PHR1 cDNA sequences predict 89% identity at the protein level, except for an AT-PHH1 C-terminal extension (111 amino acids), also not seen in microbial photolyases. AT-PHH1 and CRY1 show less similarity (54% p4erein identity), including respective C-terminal extensions that are themselves mostly dissimilar. Analysis of fifteen AT-PHH1 genomic isolates reveals a single gene, with three introns in the coding sequence and one in the 5'-untranslated leader. Full-length AT-PHH1, and both AT-PHH1 and AT-PHH1 delta C-513 (truncated to be approximately the size of microbial photolyase genes) cDNAs, were overexpressed, respectively, in yeast and Escherichia coli mutants hypersensitive to ultraviolet light. The absence of significant effects on resistance suggests either that any putative AT-PHH1 DNA repair activity requires cofactors/chromophores not present in yeast or E. coli, or that AT-PHH1 encodes a blue-light/ultraviolet-A receptor rather than a DNA repair protein.

  12. Resonance Raman spectroscopic investigation of the light-harvesting chromophore in escherichia coli photolyase and Vibrio cholerae cryptochrome-1.

    PubMed

    Sokolova, Olga; Cecala, Christine; Gopal, Anand; Cortazar, Frank; McDowell-Buchanan, Carla; Sancar, Aziz; Gindt, Yvonne M; Schelvis, Johannes P M

    2007-03-27

    Photolyases and cryptochromes are flavoproteins that belong to the class of blue-light photoreceptors. They usually bind two chromophores: flavin adenine dinucleotide (FAD), which forms the active site, and a light-harvesting pigment, which is a 5,10-methenyltetrahydrofolate polyglutamate (MTHF) in most cases. In Escherichia coli photolyase (EcPhr), the MTHF cofactor is present in substoichiometric amounts after purification, while in Vibrio cholerae cryptochrome-1 (VcCry1) the MTHF cofactor is bound more strongly and is present at stoichiometric levels after purification. In this paper, we have used resonance Raman spectroscopy to monitor the effect of loss of MTHF on the protein-FAD interactions in EcPhr and to probe the protein-MTHF interactions in both EcPhr and VcCry1. We find that removal of MTHF does not perturb protein-FAD interactions, suggesting that it may not affect the physicochemical properties of FAD in EcPhr. Our data demonstrate that the pteridine ring of MTHF in EcPhr has different interactions with the protein matrix than that of MTHF in VcCry1. Comparison to solution resonance Raman spectra of MTHF suggests that the carbonyl of its pteridine ring in EcPhr experiences stronger hydrogen bonding and a more polar environment than in VcCry1, but that hydrogen bonding to the pteridine ring amine hydrogens is stronger in VcCry-1. These differences in hydrogen bonding may account for the higher binding affinity of MTHF in VcCry1 compared to EcPhr.

  13. Crystal structure of poly[[μ3-4,4'-(4,4'-bipyridine-2,6-diyl)dibenzoato]{μ2-4-[6-(4-carboxyphenyl)-4,4'-bipyridin-4'-ium-2-yl]benzoato}manganese(II)] hemi-hydrate].

    PubMed

    Li, Yaping; Sun, Dajun; Ming, Julia; Han, Liying; Su, Guanfang

    2014-11-01

    The title compound, {[Mn(C24H14N2O4)(C24H16N2O4)]·0.5H2O} n , was obtained by the reaction of manganese nitrate with the ligand 4,4'-(4,4'-bi-pyridine-2,6-di-yl) di-benzoic acid under hydro-thermal conditions. The water O atom is located on a twofold rotation axis. The Mn(2+) ion is hepta-coordinated by six O atoms and one N atom from the ligands. In this structure, the ligands adopts two different forms, one completely deprotonated and one with a protonated N atom (pyridinium) and a carboxylic acid function. In the crystal, N-H⋯O and O-H⋯O hydrogen bonds consolidate the packing, forming a three-dimensional framework.

  14. 34 CFR 6.4 - Central records; confidentiality.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Education Office of the Secretary, Department of Education INVENTIONS AND PATENTS (GENERAL) § 6.4 Central records; confidentiality. Central files and records shall be maintained of all inventions, patents, and... Department under such patents. Invention reports required from employees or others for the purpose of...

  15. 41 CFR 51-6.4 - Military resale commodities.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 41 Public Contracts and Property Management 1 2013-07-01 2013-07-01 false Military resale... PROCEDURES § 51-6.4 Military resale commodities. (a) Purchase procedures for ordering military resale commodities are available from the central nonprofit agencies. Authorized resale outlets (military...

  16. 41 CFR 51-6.4 - Military resale commodities.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 41 Public Contracts and Property Management 1 2012-07-01 2009-07-01 true Military resale... PROCEDURES § 51-6.4 Military resale commodities. (a) Purchase procedures for ordering military resale commodities are available from the central nonprofit agencies. Authorized resale outlets (military...

  17. 41 CFR 51-6.4 - Military resale commodities.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 41 Public Contracts and Property Management 1 2014-07-01 2014-07-01 false Military resale... PROCEDURES § 51-6.4 Military resale commodities. (a) Purchase procedures for ordering military resale commodities are available from the central nonprofit agencies. Authorized resale outlets (military...

  18. 34 CFR 6.4 - Central records; confidentiality.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... Education Office of the Secretary, Department of Education INVENTIONS AND PATENTS (GENERAL) § 6.4 Central records; confidentiality. Central files and records shall be maintained of all inventions, patents, and... Department under such patents. Invention reports required from employees or others for the purpose of...

  19. 34 CFR 6.4 - Central records; confidentiality.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... Education Office of the Secretary, Department of Education INVENTIONS AND PATENTS (GENERAL) § 6.4 Central records; confidentiality. Central files and records shall be maintained of all inventions, patents, and... Department under such patents. Invention reports required from employees or others for the purpose of...

  20. 34 CFR 6.4 - Central records; confidentiality.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Education Office of the Secretary, Department of Education INVENTIONS AND PATENTS (GENERAL) § 6.4 Central records; confidentiality. Central files and records shall be maintained of all inventions, patents, and... Department under such patents. Invention reports required from employees or others for the purpose of...

  1. 34 CFR 6.4 - Central records; confidentiality.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... Education Office of the Secretary, Department of Education INVENTIONS AND PATENTS (GENERAL) § 6.4 Central records; confidentiality. Central files and records shall be maintained of all inventions, patents, and... Department under such patents. Invention reports required from employees or others for the purpose of...

  2. 41 CFR 51-6.4 - Military resale commodities.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 41 Public Contracts and Property Management 1 2010-07-01 2010-07-01 true Military resale... PROCEDURES § 51-6.4 Military resale commodities. (a) Purchase procedures for ordering military resale commodities are available from the central nonprofit agencies. Authorized resale outlets (military commissary...

  3. 41 CFR 51-6.4 - Military resale commodities.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 41 Public Contracts and Property Management 1 2011-07-01 2009-07-01 true Military resale... PROCEDURES § 51-6.4 Military resale commodities. (a) Purchase procedures for ordering military resale commodities are available from the central nonprofit agencies. Authorized resale outlets (military commissary...

  4. Crystal structure of (1S,3R,8R,9R,10S)-2,4,6-tris-(2,2-di-chloro-3,7,7,10-tetra-methyl-tri-cyclo-[6.4.0.0(1,3)]dodec-9-yl)cyclo-triboroxane.

    PubMed

    Benharref, Ahmed; El Ammari, Lahcen; Saadi, Mohamed; Mazoir, Noureddine; Berraho, Moha

    2015-08-01

    The title compound, C48H75B3Cl6O3, was synthesized in two steps from β-himachalene (3,5,5,9-tetra-methyl-2,4a,5,6,7,8-hexa-hydro-1H-benzo-cyclo-hept-ene), which was isolated from the essential oil of the Atlas cedar (Cedrus Atlantica). The mol-ecule consists of an almost planar cyclo-triboroxane ring [maximum deviation = 0.036 (2) Å] linked to three identical fused ring systems with different conformations. Each of the three attached ring systems is built up from a seven-membered ring to which a six- and a three-membered ring are fused. The three six-membered rings have a twist-boat conformation, whereas the seven-membered rings display boat, chair and twist-boat conformations. The dihedral angles between the central boroxane ring and the mean planes of the attached six-membered rings are 63.67 (18), 54.89 (2) and 56.57 (19)°. The crystal packing is governed only by van der Waals inter-actions.

  5. Crystal structure of 5-amino-5'-chloro-6-(4-chloro-benzo-yl)-8-nitro-2,3-di-hydro-1H-spiro-[imidazo[1,2-a]pyridine-7,3'-indolin]-2'-one including an unknown solvent mol-ecule.

    PubMed

    Nagalakshmi, R A; Suresh, J; Sivakumar, S; Kumar, R Ranjith; Lakshman, P L Nilantha

    2014-09-01

    The asymmetric unit of the title compound, C21H15Cl2N5O4, contains two independent mol-ecules (A and B) having similar conformations. The amine (NH2) group forms an intra-molecular hydrogen bond with the benzoyl group, giving an S(6) ring motif in both mol-ecules. The central six-membered rings adopt sofa conformations and the imidazole rings are planar (r.m.s deviations = 0.0150 and 0.0166 Å). The pyridine and imidazole rings are inclined to one another by 3.54 (1) and 3.03 (1)° in mol-ecules A and B, respectively. In the crystal, mol-ecules are linked by N-H⋯O hydrogen bonds, forming chains along the a axis which enclose R 2 (2)(16) ring motifs. The rings are linked by weak N-H⋯O and C-H⋯O hydrogen bonds and C-H⋯π inter-actions forming sheets lying parallel to (001). A region of disordered electron density, most probably disordered solvent mol-ecules, occupying voids of ca 753 Å(3) for an electron count of 260, was treated using the SQUEEZE routine in PLATON [Spek (2009 ▶). Acta Cryst. D65, 148-155]. Their formula mass and unit-cell characteristics were not taken into account during refinement.

  6. Crystal structure of (1S,3R,8R,9R,10S)-2,4,6-tris­(2,2-di­chloro-3,7,7,10-tetra­methyl­tri­cyclo­[6.4.0.01,3]dodec-9-yl)cyclo­triboroxane

    PubMed Central

    Benharref, Ahmed; El Ammari, Lahcen; Saadi, Mohamed; Mazoir, Noureddine; Berraho, Moha

    2015-01-01

    The title compound, C48H75B3Cl6O3, was synthesized in two steps from β-himachalene (3,5,5,9-tetra­methyl-2,4a,5,6,7,8-hexa­hydro-1H-benzo­cyclo­hept­ene), which was isolated from the essential oil of the Atlas cedar (Cedrus Atlantica). The mol­ecule consists of an almost planar cyclo­triboroxane ring [maximum deviation = 0.036 (2) Å] linked to three identical fused ring systems with different conformations. Each of the three attached ring systems is built up from a seven-membered ring to which a six- and a three-membered ring are fused. The three six-membered rings have a twist-boat conformation, whereas the seven-membered rings display boat, chair and twist-boat conformations. The dihedral angles between the central boroxane ring and the mean planes of the attached six-membered rings are 63.67 (18), 54.89 (2) and 56.57 (19)°. The crystal packing is governed only by van der Waals inter­actions. PMID:26396761

  7. Crystal structure of (1S,3R,8R,10S)-2,2-di­chloro-10-hy­droxy-3,7,7,10-tetra­methyl­tri­cyclo­[6.4.0.01,3]dodecan-9-one

    PubMed Central

    Benzalim, Ahmed; Auhmani, Aziz; Ait Itto, My Youssef; Daran, Jean-Claude; Abdelwahed, Auhmani

    2016-01-01

    The asymmetric unit of the title compound, C16H24Cl2O2, contains two independent mol­ecules (A and B) which are built from three fused rings, viz. a seven-membered heptane ring, a six-membered cyclo­hexyl ring bearing a ketone and an alcohol group, and a cyclo­propane ring bearing two Cl atoms. In the crystal, the two mol­ecules are linked via two O—H⋯O hydrogen bonds, forming an A–B dimer with an R 2 2(10) ring motif. The A mol­ecules of these dimers are linked via a C—H⋯O hydrogen bond, forming chains propagating along the a-axis direction. Both mol­ecules have the same absolute configuration, i.e. 1S,3R,8R,10S, which is based on the synthetic pathway and further confirmed by resonant scattering [Flack parameter = 0.03 (5)]. PMID:27308024

  8. Identification of Cyclobutane Pyrimidine Dimer-Responsive Genes Using UVB-Irradiated Human Keratinocytes Transfected with In Vitro-Synthesized Photolyase mRNA.

    PubMed

    Boros, Gábor; Miko, Edit; Muramatsu, Hiromi; Weissman, Drew; Emri, Eszter; van der Horst, Gijsbertus T J; Szegedi, Andrea; Horkay, Irén; Emri, Gabriella; Karikó, Katalin; Remenyik, Éva

    2015-01-01

    Major biological effects of UVB are attributed to cyclobutane pyrimidine dimers (CPDs), the most common photolesions formed on DNA. To investigate the contribution of CPDs to UVB-induced changes of gene expression, a model system was established by transfecting keratinocytes with pseudouridine-modified mRNA (Ψ-mRNA) encoding CPD-photolyase. Microarray analyses of this model system demonstrated that more than 50% of the gene expression altered by UVB was mediated by CPD photolesions. Functional classification of the gene targets revealed strong effects of CPDs on the regulation of the cell cycle and transcriptional machineries. To confirm the microarray data, cell cycle-regulatory genes, CCNE1 and CDKN2B that were induced exclusively by CPDs were selected for further investigation. Following UVB irradiation, expression of these genes increased significantly at both mRNA and protein levels, but not in cells transfected with CPD-photolyase Ψ-mRNA and exposed to photoreactivating light. Treatment of cells with inhibitors of c-Jun N-terminal kinase (JNK) blocked the UVB-dependent upregulation of both genes suggesting a role for JNK in relaying the signal of UVB-induced CPDs into transcriptional responses. Thus, photolyase mRNA-based experimental platform demonstrates CPD-dependent and -independent events of UVB-induced cellular responses, and, as such, has the potential to identify novel molecular targets for treatment of UVB-mediated skin diseases.

  9. Laser shock peening of titanium 6-4 alloy

    NASA Astrophysics Data System (ADS)

    Brar, N. S.; Hopkins, A.; Laber, M. W.

    2000-04-01

    Laser shock peening of titanium 6-4 has been shown to improve its high cycle fatigue life. Residual compressive stresses generated on the surface of titanium 6-4, as a result of laser shocking, have shown dramatic improvement in the performance of aircraft turbine blades. Laser shocking of titanium was carried out with a 20 ns pulse width, 50 joule pulsed laser, operated by LSP Technologies, Columbus, OH. Titanium disks, 20-mm in diameter, and ranging in thicknesses from zero (bare LiF) to 3-mm were subjected to laser shock to monitor amplitude and temporal stress profiles of the pulsed laser. Laser shock stress amplitudes on the back of titanium disks were monitored with VISAR using LiF as the window material. The peak shock stress produced in LiF (titanium thickness zero) was measured to be 16±1 GPa. The laser shock amplitude decays to about 2.7 GPa while propagating through 3-mm thick disk of titanium 6-4.

  10. Laser Shock Peening of Titanium 6-4 Alloy

    NASA Astrophysics Data System (ADS)

    Hopkins, Alan; Laber, Mark; Brar, Nachhatter S.

    1999-06-01

    shock 99 Laser shock peening of titanium 6-4 has been shown to improve its high cycle fatigue life. Residual compressive stresses generated on the surface of titanium 6-4, as a result of laser shocking, have shown dramatic improvement in the performance of aircraft turbine blades. Laser shocking of titanium was carried out with a 20 ns pulse width, 50 joule pulsed laser, operated by LSP Technologies, Columbus, OH. Disks of titanium, 0 to 3-mm thick and 20-mm in diameter, were subjected to the pulsed laser to monitor amplitude and temporal stress profiles of laser shock. Laser shock stress amplitudes on the back of titanium disks were monitored with VISAR using LiF as the window material. The peak shock stress produced in LiF (titanium thickness zero) was measured to be 16±1 GPa. The laser shock amplitude decays to about 2.6 GPa while propagating through 3-mm thick disk of titanium 6-4. *Supported by the U.S. Air Force Research Laboratory

  11. Structural basis of pyrimidine-pyrimidone (6-4) photoproduct recognition by UV-DDB in the nucleosome.

    PubMed

    Osakabe, Akihisa; Tachiwana, Hiroaki; Kagawa, Wataru; Horikoshi, Naoki; Matsumoto, Syota; Hasegawa, Mayu; Matsumoto, Naoyuki; Toga, Tatsuya; Yamamoto, Junpei; Hanaoka, Fumio; Thomä, Nicolas H; Sugasawa, Kaoru; Iwai, Shigenori; Kurumizaka, Hitoshi

    2015-11-17

    UV-DDB, an initiation factor for the nucleotide excision repair pathway, recognizes 6-4PP lesions through a base flipping mechanism. As genomic DNA is almost entirely accommodated within nucleosomes, the flipping of the 6-4PP bases is supposed to be extremely difficult if the lesion occurs in a nucleosome, especially on the strand directly contacting the histone surface. Here we report that UV-DDB binds efficiently to nucleosomal 6-4PPs that are rotationally positioned on the solvent accessible or occluded surface. We determined the crystal structures of nucleosomes containing 6-4PPs in these rotational positions, and found that the 6-4PP DNA regions were flexibly disordered, especially in the strand exposed to the solvent. This characteristic of 6-4PP may facilitate UV-DDB binding to the damaged nucleosome. We present the first atomic-resolution pictures of the detrimental DNA cross-links of neighboring pyrimidine bases within the nucleosome, and provide the mechanistic framework for lesion recognition by UV-DDB in chromatin.

  12. First characterisation of a CPD-class I photolyase from a UV-resistant extremophile isolated from High-Altitude Andean Lakes.

    PubMed

    Albarracín, Virginia Helena; Simon, Julian; Pathak, Gopal P; Valle, Lorena; Douki, Thierry; Cadet, Jean; Borsarelli, Claudio Darío; Farias, María Eugenia; Gärtner, Wolfgang

    2014-05-01

    UV-resistant Acinetobacter sp. Ver3 isolated from High-Altitude Andean Lakes (HAAL) in Argentinean Puna, one of the highest UV exposed ecosystems on Earth, showed efficient DNA photorepairing ability, coupled to highly efficient antioxidant enzyme activities in response to UV-B stress. We herein present the cloning, expression, and functional characterization of a cyclobutane pyrimidine dimer (CPD)-class I photolyase (Ver3Phr) from this extremophile to prove its involvement in the previously noted survival capability. Spectroscopy of the overexpressed and purified protein identified flavin adenine dinucleotide (FAD) and 5,10-methenyltetrahydrofolate (MTHF) as chromophore and antenna molecules, respectively. All functional analyses were performed in parallel with the ortholog E. coli photolyase. Whereas the E. coli enzyme showed the FAD chromophore as a mixture of oxidised and reduced states, the Ver3 chromophore always remained partly (including the semiquinone state) or fully reduced under all experimental conditions tested. Functional complementation of Ver3Phr in Phr(-)-RecA E. coli strains was assessed by traditional UFC counting and measurement of DNA bipyrimidine photoproducts by HPLC coupled with electrospray ionisation-tandem mass spectrometry (ESI-MS/MS) detection. The results identified strong photoreactivation ability in vivo of Ver3Phr while its nonphotoreactivation function, probably related with the stimulation of nucleotide excision repair (NER), was not as manifest as for EcPhr. Whether this is a question of the approach using an exogenous photolyase incorporated in a non-genuine host or a fundamental different behaviour of a novel enzyme from an exotic environment will need further studies.

  13. Efficacy of a photolyase-based device in the treatment of cancerization field in patients with actinic keratosis and non-melanoma skin cancer.

    PubMed

    Puviani, M; Barcella, A; Milani, M

    2013-12-01

    Eryfotona AK-NMSC (ISDIN Spain) is a film-forming medical device in cream or fluid formulation containing the DNA-repair enzyme photolyase and high-protection UV filters in liposomes (repairsomes) indicated in the treatment of cancerization field in patients with actinic keratosis (AK) or non-melanoma skin cancer (NMSC). Photolyase is an enzyme that recognizes and directly repairs UV-induced DNA damage. The most common UV-induced DNA damage is the formation of cyclobutane pyrimidine dimers (CPD). Clinical studies evaluating the histological and cellular effects of Eryfotona AK-NMSC have shown a potential benefit in the treatment of the cancerization field in AK patients. In particular the use of Eryfotona AK-NMSC improves the confocal microscopic appearance of skin at the cancerization field level. In addition, Eryfotona AK-NMSC improves the p53 gene expression at keratinocyte level. In this study we reported a series of 6 cases of patients with AK or NMSC lesions treated with Eryfotona AK-NMSC fluid, both as coadjuvant and as single treatment, applied twice daily in the affected area with photograph documentation. Clinical photographs of the skin lesions at baseline and after Eryfotona AK-NMSC treatment were taken in all cases using a high-definition digital camera. Six patients with multiple AK lesions of the scalp or face with or without NMSC were treated for a mean of 1-3 months with Eryfotona AK-NMSC fluid formulation. Image documentations before and after treatment of this clinical series show a great improvement in AK lesions count and of cancerization field. This clinical series supports the clinical efficacy of the use of photolyase and high-protection UV filters in the treatment of cancerization field and AK lesions in patients with actinic damage.

  14. The efficiency of photolyase and indole complexes to repair DNA containing dimers of pyrimidine: A theoretical analysis of the electron transfer reactions

    NASA Astrophysics Data System (ADS)

    Volcov, Flávia; Goldman, Carla

    2004-02-01

    We analyze the effects of competing reactions to the efficiency of enzymatic splitting of pyrimidine dimers formed in DNA by the incidence of ultraviolet radiation. This is accomplished with the aid of a formula that expresses the efficiency of the repair in terms of parameters that regulate the reaction rates for primary and for back long-range electron transfers taking place in the process. Comparison of experimental data with estimations on account of this formula supports early conjectures in the literature that attribute the relative high performance of the enzymatic complexes of photolyase to its ability to suppress the back reaction.

  15. The Two Cryptochrome/Photolyase Family Proteins Fulfill Distinct Roles in DNA Photorepair and Regulation of Conidiation in the Gray Mold Fungus Botrytis cinerea.

    PubMed

    Cohrs, Kim C; Schumacher, Julia

    2017-09-01

    The plant-pathogenic leotiomycete Botrytis cinerea is known for the strict regulation of its asexual differentiation programs by environmental light conditions. Sclerotia are formed in constant darkness; black/near-UV (NUV) light induces conidiation; and blue light represses both differentiation programs. Sensing of black/NUV light is attributed to proteins of the cryptochrome/photolyase family (CPF). To elucidate the molecular basis of the photoinduction of conidiation, we functionally characterized the two CPF proteins encoded in the genome of B. cinerea as putative positive-acting components. B. cinerea CRY1 (BcCRY1), a cyclobutane pyrimidine dimer (CPD) photolyase, acts as the major enzyme of light-driven DNA repair (photoreactivation) and has no obvious role in signaling. In contrast, BcCRY2, belonging to the cry-DASH proteins, is dispensable for photorepair but performs regulatory functions by repressing conidiation in white and especially black/NUV light. The transcription of bccry1 and bccry2 is induced by light in a White Collar complex (WCC)-dependent manner, but neither light nor the WCC is essential for the repression of conidiation through BcCRY2 when bccry2 is constitutively expressed. Further, BcCRY2 affects the transcript levels of both WCC-induced and WCC-repressed genes, suggesting a signaling function downstream of the WCC. Since both CPF proteins are dispensable for photoinduction by black/NUV light, the origin of this effect remains elusive and may be connected to a yet unknown UV-light-responsive system.IMPORTANCEBotrytis cinerea is an economically important plant pathogen that causes gray mold diseases in a wide variety of plant species, including high-value crops and ornamental flowers. The spread of disease in the field relies on the formation of conidia, a process that is regulated by different light qualities. While this feature has been known for a long time, we are just starting to understand the underlying molecular mechanisms

  16. Evidence for a singlet intermediate in catalysis by Escherichia coli DNA photolyase and evaluation of substrate binding determinants

    SciTech Connect

    Jordan, S.P.; Jorns, M.S.

    1988-12-13

    Escherichia coli DNA photolyase contains 1,5-dihydro-FAD (FADH2) plus 5,10-methenyl-tetrahydrofolate (5,10-CH+-H4folate). Both chromophores are fluorescent, and either can function as a sensitizer in catalysis. At 77 K separate fluorescence emission bands are observed for FADH2 (lambda max = 505 nm, shoulder at 540 nm) and 5,10-CH+-H4folate (lambda max = 465, 440 nm) whereas at 5 degrees C only a shoulder at 505 nm is attributable to FADH2. Formation of an enzyme-substrate complex with various dimer-containing oligothymidylates (UV-oligo(dT)n) quenches the fluorescence due to FADH2 at 5 degrees C or 77 K and also stabilizes FADH2 against air oxidation. The fluorescence of 5,10-CH+-H4folate is unaffected by substrate. Reduction of the pterin chromophore eliminates the chromophore's fluorescence but does not affect catalytic activity or the ability of substrate to quench FADH2 fluorescence. Quenching of FADH2 fluorescence is fully reversible upon dimer repair. The results are consistent with the proposal that the singlet state of FADH2 functions as an intermediate in catalysis. Fluorometric titrations indicate that the enzyme has a similar affinity for dimers in UV-oligo(dT)4 (KD = 2.5 X 10(-7) M, delta G = 8.4 kcal/mol at 5 degrees C) or UV-oligo(dT)6, except for dimers located at the unphosphorylated 3' end of the oligomers where binding is considerably weaker.

  17. Impact of the N5-proximal Asn on the Thermodynamic and Kinetic Stability of the Semiquinone Radical in Photolyase*

    PubMed Central

    Damiani, Michael J.; Nostedt, Jordan J.; O'Neill, Melanie A.

    2011-01-01

    Flavoproteins can dramatically adjust the thermodynamics and kinetics of electron transfer at their flavin cofactor. A versatile regulatory tool is proton transfer. Here, we demonstrate the significance of proton-coupled electron transfer to redox tuning and semiquinone (sq) stability in photolyases (PLs) and cryptochromes (CRYs). These light-responsive proteins share homologous overall architectures and FAD-binding pockets, yet they have evolved divergent functions that include DNA repair, photomorphogenesis, regulation of circadian rhythm, and magnetoreception. We report the first measurement of both FAD redox potentials for cyclobutane pyrimidine dimer PL (CPD-PL, Anacystis nidulans). These values, E1(hq/sq) = −140 mV and E2(sq/ox) = −219 mV, where hq is FAD hydroquinone and ox is oxidized FAD, establish that the sq is not thermodynamically stabilized (ΔE = E2 − E1 = −79 mV). Results with N386D CPD-PL support our earlier hypothesis of a kinetic barrier to sq oxidation associated with proton transfer. Both E1 and E2 are upshifted by ∼100 mV in this mutant; replacing the N5-proximal Asn with Asp decreases the driving force for sq oxidation. However, this Asp alleviates the kinetic barrier, presumably by acting as a proton shuttle, because the sq in N386D CPD-PL oxidizes orders of magnitude more rapidly than wild type. These data clearly reveal, as suggested for plant CRYs, that an N5-proximal Asp can switch on proton transfer and modulate sq reactivity. However, the effect is context-dependent. More generally, we propose that PLs and CRYs tune the properties of their N5-proximal residue to adjust the extent of proton transfer, H-bonding patterns, and changes in protein conformation associated with electron transfer at the flavin. PMID:21131361

  18. Enzymatic Reaction with Unnatural Substrates: DNA Photolyase (Escherichia coli) Recognizes and Reverses Thymine [2+2] Dimers in the DNA Strand of a DNA/PNA Hybrid Duplex

    NASA Astrophysics Data System (ADS)

    Ramaiah, Danaboyina; Kan, Yongzhi; Koch, Troels; Orum, Henrik; Schuster, Gary B.

    1998-10-01

    Peptide nucleic acids (PNA) are mimics with normal bases connected to a pseudopeptide chain that obey Watson--Crick rules to form stable duplexes with itself and natural nucleic acids. This has focused attention on PNA as therapeutic or diagnostic reagents. Duplexes formed with PNA mirror some but not all properties of DNA. One fascinating aspect of PNA biochemistry is their reaction with enzymes. Here we show an enzyme reaction that operates effectively on a PNA/DNA hybrid duplex. A DNA oligonucleotide containing a cis, syn-thymine [2+2] dimer forms a stable duplex with PNA. The hybrid duplex is recognized by photolyase, and irradiation of the complex leads to the repair of the thymine dimer. This finding provides insight into the enzyme mechanism and provides a means for the selective repair of thymine photodimers.

  19. UV hyper-resistance in Prochlorococcus MED4 results from a single base pair deletion just upstream of an operon encoding nudix hydrolase and photolyase

    PubMed Central

    Osburne, Marcia S; Holmbeck, Brianne M; Frias-Lopez, Jorge; Steen, Robert; Huang, Katherine; Kelly, Libusha; Coe, Allison; Waraska, Kristin; Gagne, Andrew; Chisholm, Sallie W

    2010-01-01

    Exposure to solar radiation can cause mortality in natural communities of pico-phytoplankton, both at the surface and to a depth of at least 30 m. DNA damage is a significant cause of death, mainly due to cyclobutane pyrimidine dimer formation, which can be lethal if not repaired. While developing a UV mutagenesis protocol for the marine cyanobacterium Prochlorococcus, we isolated a UV-hyper-resistant variant of high light-adapted strain MED4. The hyper-resistant strain was constitutively upregulated for expression of the mutT-phrB operon, encoding nudix hydrolase and photolyase, both of which are involved in repair of DNA damage that can be caused by UV light. Photolyase (PhrB) breaks pyrimidine dimers typically caused by UV exposure, using energy from visible light in the process known as photoreactivation. Nudix hydrolase (MutT) hydrolyses 8-oxo-dGTP, an aberrant form of GTP that results from oxidizing conditions, including UV radiation, thus impeding mispairing and mutagenesis by preventing incorporation of the aberrant form into DNA. These processes are error-free, in contrast to error-prone SOS dark repair systems that are widespread in bacteria. The UV-hyper-resistant strain contained only a single mutation: a 1 bp deletion in the intergenic region directly upstream of the mutT-phrB operon. Two subsequent enrichments for MED4 UV-hyper-resistant strains from MED4 wild-type cultures gave rise to strains containing this same 1 bp deletion, affirming its connection to the hyper-resistant phenotype. These results have implications for Prochlorococcus DNA repair mechanisms, genome stability and possibly lysogeny. PMID:20345942

  20. Monophyly of class I aminoacyl tRNA synthetase, USPA, ETFP, photolyase, and PP-ATPase nucleotide-binding domains: implications for protein evolution in the RNA.

    PubMed

    Aravind, L; Anantharaman, Vivek; Koonin, Eugene V

    2002-07-01

    Protein sequence and structure comparisons show that the catalytic domains of Class I aminoacyl-tRNA synthetases, a related family of nucleotidyltransferases involved primarily in coenzyme biosynthesis, nucleotide-binding domains related to the UspA protein (USPA domains), photolyases, electron transport flavoproteins, and PP-loop-containing ATPases together comprise a distinct class of alpha/beta domains designated the HUP domain after HIGH-signature proteins, UspA, and PP-ATPase. Several lines of evidence are presented to support the monophyly of the HUP domains, to the exclusion of other three-layered alpha/beta folds with the generic "Rossmann-like" topology. Cladistic analysis, with patterns of structural and sequence similarity used as discrete characters, identified three major evolutionary lineages within the HUP domain class: the PP-ATPases; the HIGH superfamily, which includes class I aaRS and related nucleotidyltransferases containing the HIGH signature in their nucleotide-binding loop; and a previously unrecognized USPA-like group, which includes USPA domains, electron transport flavoproteins, and photolyases. Examination of the patterns of phyletic distribution of distinct families within these three major lineages suggests that the Last Universal Common Ancestor of all modern life forms encoded 15-18 distinct alpha/beta ATPases and nucleotide-binding proteins of the HUP class. This points to an extensive radiation of HUP domains before the last universal common ancestor (LUCA), during which the multiple class I aminoacyl-tRNA synthetases emerged only at a late stage. Thus, substantial evolutionary diversification of protein domains occurred well before the modern version of the protein-dependent translation machinery was established, i.e., still in the RNA world.

  1. Synthesis, spectral, thermal, optical and theoretical studies of (2E,6E)-2-benzylidene-6-(4-methoxybenzylidene)cyclohexanone.

    PubMed

    Meenatchi, V; Muthu, K; Rajasekar, M; Meenakshisundaram, Sp

    2014-01-01

    Single crystals of (2E,6E)-2-benzylidine-6-(4-methoxybenzylidine)cyclohexanone are grown by slow evaporation of ethanolic solution at room temperature. The characteristic functional groups present in the molecule are confirmed by Fourier transform infrared and Fourier transform Raman analyses. The scanning electron microscopy study reveals the surface morphology of the material. Thermogravimetric/differential thermal analysis study reveals the purity of the material and the crystal is transparent in the visible region having a lower optical cut-off at ∼487nm. The second harmonic generation efficiency of as-grown material is estimated by Kurtz and Perry technique. Optimized geometry has been derived using Hartree-Fock calculations performed at the level 6-31G (d,p) and the first-order molecular hyperpolarizability (β) is estimated. The specimen is further characterized by nuclear magnetic resonance spectroscopy.

  2. Physical water scarcity metrics for monitoring progress towards SDG target 6.4: An evaluation of indicator 6.4.2 "Level of water stress".

    PubMed

    Vanham, D; Hoekstra, A Y; Wada, Y; Bouraoui, F; de Roo, A; Mekonnen, M M; van de Bund, W J; Batelaan, O; Pavelic, P; Bastiaanssen, W G M; Kummu, M; Rockström, J; Liu, J; Bisselink, B; Ronco, P; Pistocchi, A; Bidoglio, G

    2017-09-12

    Target 6.4 of the recently adopted Sustainable Development Goals (SDGs) deals with the reduction of water scarcity. To monitor progress towards this target, two indicators are used: Indicator 6.4.1 measuring water use efficiency and 6.4.2 measuring the level of water stress (WS). This paper aims to identify whether the currently proposed indicator 6.4.2 considers the different elements that need to be accounted for in a WS indicator. WS indicators compare water use with water availability. We identify seven essential elements: 1) both gross and net water abstraction (or withdrawal) provide important information to understand WS; 2) WS indicators need to incorporate environmental flow requirements (EFR); 3) temporal and 4) spatial disaggregation is required in a WS assessment; 5) both renewable surface water and groundwater resources, including their interaction, need to be accounted for as renewable water availability; 6) alternative available water resources need to be accounted for as well, like fossil groundwater and desalinated water; 7) WS indicators need to account for water storage in reservoirs, water recycling and managed aquifer recharge. Indicator 6.4.2 considers many of these elements, but there is need for improvement. It is recommended that WS is measured based on net abstraction as well, in addition to currently only measuring WS based on gross abstraction. It does incorporate EFR. Temporal and spatial disaggregation is indeed defined as a goal in more advanced monitoring levels, in which it is also called for a differentiation between surface and groundwater resources. However, regarding element 6 and 7 there are some shortcomings for which we provide recommendations. In addition, indicator 6.4.2 is only one indicator, which monitors blue WS, but does not give information on green or green-blue water scarcity or on water quality. Within the SDG indicator framework, some of these topics are covered with other indicators. Copyright © 2017 The Authors

  3. [Fe(CN)6]4- decorated mesoporous gelatin thin films for colorimetric detection and as sorbents of heavy metal ions.

    PubMed

    Shi, Li; Huang, Hubiao; Sun, Luwei; Lu, Yanping; Du, Binyang; Mao, Yiyin; Li, Junwei; Ye, Zhizhen; Peng, Xinsheng

    2013-09-28

    [Fe(CN)6](4-) decorated mesoporous gelatin films, acting as colorimetric sensors and sorbents for heavy metal ions, were prepared by incorporating [Fe(CN)6](4-) ions into the mesoporous gelatin films through electrostatic interaction. Gelatin-Prussian blue (PB) and gelatin-PB analogue composite films were successfully synthesized by immersing the [Fe(CN)6](4-) decorated gelatin films into aqueous solutions of metal ions, such as Fe(3+), Cu(2+), Co(2+), Pb(2+) and Cd(2+) (all as nitrates). The in situ formation process of PB or its analogues in the films was investigated using quartz crystal microbalance (QCM) measurements. According to the different colors of the PB nanoparticles and its analogues, the [Fe(CN)6](4-) decorated mesoporous gelatin films demonstrated colorimetric sensor abilities for detecting the corresponding metal ions by the naked eye with sufficient sensitivity at 1 ppm level and a quite short response time of 5 minutes. Moreover, due to the [Fe(CN)6](4-) functionality and other functional groups of gelatin itself, this [Fe(CN)6](4-) decorated mesoporous gelatin film shows a tens times higher adsorption ability for heavy metal ions in water than that of activated carbon. Due to both the efficient detection and high adsorption ability for heavy metal ions, this film has wide potential applications for the detection and purification of heavy metal ions from polluted water.

  4. 38 CFR 6.4 - Proof of age, relationship and marriage.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ..., relationship and marriage. 6.4 Section 6.4 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS....4 Proof of age, relationship and marriage. Whenever it is necessary for a claimant to prove age, relationship or marriage, the provisions of 38 U.S.C. 103(c) and Part 3 this chapter will be followed....

  5. 38 CFR 6.4 - Proof of age, relationship and marriage.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ..., relationship and marriage. 6.4 Section 6.4 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS....4 Proof of age, relationship and marriage. Whenever it is necessary for a claimant to prove age, relationship or marriage, the provisions of 38 U.S.C. 103(c) and Part 3 this chapter will be followed....

  6. 38 CFR 6.4 - Proof of age, relationship and marriage.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2012-07-01 2012-07-01 false Proof of age, relationship and marriage. 6.4 Section 6.4 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS....4 Proof of age, relationship and marriage. Whenever it is necessary for a claimant to prove...

  7. 38 CFR 6.4 - Proof of age, relationship and marriage.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2014-07-01 2014-07-01 false Proof of age, relationship and marriage. 6.4 Section 6.4 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS....4 Proof of age, relationship and marriage. Whenever it is necessary for a claimant to prove...

  8. 38 CFR 6.4 - Proof of age, relationship and marriage.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2013-07-01 2013-07-01 false Proof of age, relationship and marriage. 6.4 Section 6.4 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS....4 Proof of age, relationship and marriage. Whenever it is necessary for a claimant to prove...

  9. A temperature-induced order-disorder phase transition in a 4-substituted 4,2':6',4''-terpyridine.

    PubMed

    Granifo, Juan; Westermeyer, Marleen; Riquelme, Maricel; Gaviño, Rubén; Suárez, Sebastián; Halac, Emilia B; Baggio, Ricardo

    2015-12-01

    Crystals of 4'-(isoquinolin-4-yl)-4,2':6',4''-terpyridine (iqtp), C24H16N4, grown from an ethanol solution, undergo a reversible first-order single-crystal to single-crystal phase transition at Tc in the range 273-275 K, from a disordered higher-temperature phase [form (I)] in the space group P21/c, with one single molecule in the asymmetric unit, to an ordered lower-temperature one [form (II)] in the space group P21/n, with two independent molecules in the asymmetric unit. There is a group-subgroup relationship linking (I)-(II), due to cell doubling and the disappearance of a number of symmetry operations. In addition to X-ray diffraction, the transition has been monitored by Raman spectroscopy and differential scanning calorimetry, the latter disclosing an enthalpy change of 0.72 (6) kJ mol(-1). Variations of the unit-cell parameters with temperature between 170 and 293 K are presented. The evolution of diffraction spots in the vicinity of the transition temperature shows the coexistence of both phases, confirming the first-order character of the transition. Structural details of both phases are analyzed and intermolecular interactions compared in order to investigate the mechanism of the phase transition. A three-dimensional Hirshfeld surface analysis was performed to corroborate the significant changes in the intermolecular features.

  10. Vulgarisin A, a new diterpenoid with a rare 5/6/4/5 ring skeleton from the Chinese medicinal plant Prunella vulgaris.

    PubMed

    Lou, Huayong; Zheng, Shan; Li, Tianlei; Zhang, Jianxin; Fei, Yue; Hao, Xiaojiang; Liang, Guangyi; Pan, Weidong

    2014-05-16

    Vulgarisin A (1), a new diterpenoid with an unprecedented 5/6/4/5 fused tetracyclic ring skeleton, has been isolated from the medicinal plant Prunella vulgaris Linn. Its structure was characterized by extensive spectroscopic methods, and the absolute configuration was secured by single crystal X-ray diffraction analysis. Compound 1 showed weak cytotoxicity against human lung carcinoma A549 cells with an IC50 value of 57.0 μM.

  11. An Unexpected Deamination Reaction after Hydrolysis of the Pyrimidine (6-4) Pyrimidone Photoproduct

    PubMed Central

    2015-01-01

    Pyrimidine (6-4) pyrimidone photoproduct (6-4PP), a common DNA photolesion formed under solar irradiation, was indicated to hydrolyze under strong basic conditions, breaking the N3–C4 bond at the 5′-thymine. The reanalysis of this reaction revealed that the resulting water adduct may not be stable as previously proposed; it readily undergoes an esterification reaction induced by the 5-OH group at 6-4PP to form a five-membered ring, eliminating a molecule of ammonia. PMID:25250878

  12. Nucleotide excision repair and photolyase repair of UV photoproducts in nucleosomes: assessing the existence of nucleosome and non-nucleosome rDNA chromatin in vivo.

    PubMed

    Tremblay, Maxime; Toussaint, Martin; D'Amours, Annie; Conconi, Antonio

    2009-02-01

    The genome is organized into nuclear domains, which create microenvironments that favor distinct chromatin structures and functions (e.g., highly repetitive sequences, centromeres, telomeres, noncoding sequences, inactive genes, RNA polymerase II and III transcribed genes, and the nucleolus). Correlations have been drawn between gene silencing and proximity to a heterochromatic compartment. At the other end of the scale are ribosomal genes, which are transcribed at a very high rate by RNA polymerase I (~60% of total transcription), have a loose chromatin structure, and are clustered in the nucleolus. The rDNA sequences have 2 distinct structures: active rRNA genes, which have no nucleosomes; and inactive rRNA genes, which have nucleosomes. Like DNA transcription and replication, DNA repair is modulated by the structure of chromatin, and the kinetics of DNA repair vary among the nuclear domains. Although research on DNA repair in all chromosomal contexts is important to understand the mechanisms of genome maintenance, this review focuses on nucleotide excision repair and photolyase repair of UV photoproducts in the first-order packing of DNA in chromatin: the nucleosome. In addition, it summarizes the studies that have demonstrated the existence of the 2 rDNA chromatins, and the way this feature of the rDNA locus allows for direct comparison of DNA repair in 2 very different structures: nucleosome and non-nucleosome DNA.

  13. Molecular analysis of plasmid DNA repair within ultraviolet-irradiated Escherichia coli. II. UvrABC-initiated excision repair and photolyase-catalyzed dimer monomerization

    SciTech Connect

    Gruskin, E.A.; Lloyd, R.S.

    1988-09-05

    In this study, a novel approach to the analysis of DNA repair in Escherichia coli was employed which allowed the first direct determination of the mechanisms by which endogenous DNA repair enzymes encounter target sites in vivo. An in vivo plasmid DNA repair analysis was employed to discriminate between two possible mechanisms of target site location: a processive DNA scanning mechanism or a distributive random diffusion mechanism. The results demonstrate that photolyase acts by a distributive mechanism within E. coli. In contrast, UvrABC-initiated excision repair occurs by a limited processive DNA scanning mechanism. A majority of the dimer sites on a given plasmid molecule were repaired prior to the dissociation of the UvrABC complex. Furthermore, plasmid DNA repair catalyzed by the UvrABC complex occurs without a detectable accumulation of nicked plasmid intermediates despite the fact that the UvrABC complex generates dual incisions in the DNA at the site of a pyrimidine dimer. Therefore, the binding or assembly of the UvrABC complex on DNA at the site of a pyrimidine dimer represents the rate-limiting step in the overall process of UvrABC-initiated excision repair in vivo.

  14. Genome sequence of Corynebacterium nuruki S6-4 T, isolated from alcohol fermentation starter.

    PubMed

    Shin, Na-Ri; Whon, Tae Woong; Roh, Seong Woon; Kim, Min-Soo; Jung, Mi-Ja; Lee, Jina; Bae, Jin-Woo

    2011-08-01

    Corynebacterium nuruki S6-4(T), isolated from Korean alcohol fermentation starter, is a strictly aerobic, nonmotile, Gram-positive, and rod-shaped bacterium belonging to the genus Corynebacterium and the actinomycete group. We report here the draft genome sequence of C. nuruki strain S6-4(T) (3,106,595 bp, with a G+C content of 69.5%).

  15. Genome Sequence of Corynebacterium nuruki S6-4T, Isolated from Alcohol Fermentation Starter▿

    PubMed Central

    Shin, Na-Ri; Whon, Tae Woong; Roh, Seong Woon; Kim, Min-Soo; Jung, Mi-Ja; Lee, Jina; Bae, Jin-Woo

    2011-01-01

    Corynebacterium nuruki S6-4T, isolated from Korean alcohol fermentation starter, is a strictly aerobic, nonmotile, Gram-positive, and rod-shaped bacterium belonging to the genus Corynebacterium and the actinomycete group. We report here the draft genome sequence of C. nuruki strain S6-4T (3,106,595 bp, with a G+C content of 69.5%). PMID:21685278

  16. Mechanism of the alkali degradation of (6-4) photoproduct-containing DNA.

    PubMed

    Arichi, Norihito; Inase, Aki; Eto, Sachise; Mizukoshi, Toshimi; Yamamoto, Junpei; Iwai, Shigenori

    2012-03-21

    The (6-4) photoproduct is one of the major damaged bases produced by ultraviolet light in DNA. This lesion is known to be alkali-labile, and strand breaks occur at its sites when UV-irradiated DNA is treated with hot alkali. We have analyzed the product obtained by the alkali treatment of a dinucleoside monophosphate containing the (6-4) photoproduct, by HPLC, NMR spectroscopy, and mass spectrometry. We previously found that the N3-C4 bond of the 5' component was hydrolyzed by a mild alkali treatment, and the present study revealed that the following reaction was the hydrolysis of the glycosidic bond at the 3' component. The sugar moiety of this component was lost, even when a 3'-flanking nucleotide was not present. Glycosidic bond hydrolysis was also observed for a dimer and a trimer containing 5-methyl-2-pyrimidinone, which was used as an analog of the 3' component of the (6-4) photoproduct, and its mechanism was elucidated. Finally, the alkali treatment of a tetramer, d(GT(6-4)TC), yielded 2'-deoxycytidine 5'-monophosphate, while 2'-deoxyguanosine 3'-monophosphate was not detected. This result demonstrated the hydrolysis of the glycosidic bond at the 3' component of the (6-4) photoproduct and the subsequent strand break by β-elimination. It was also shown that the glycosidic bond at the 3' component of the Dewar valence isomer was more alkali-labile than that of the (6-4) photoproduct.

  17. The allele frequency of CYP2A6*4 in four ethnic groups of China.

    PubMed

    Pang, Cong; Liu, Jin-Hui; Xu, Yi-Song; Chen, Chao; Dai, Peng-Gao

    2015-06-01

    The CYP2A6*4 allele, characterized as the whole deletion of this gene, is closely associated with nicotine dependence, cancer susceptibility, and drug responsiveness. The frequency of this molecular variant differs across populations. Although genetic polymorphisms of CYP2A6*4 and its functional results have been reported in Chinese Han population, the allele frequency of CYP2A6*4 was largely unknown in other Chinese ethnic population. In this study, we investigated the allele frequency of CYP2A6*4 in four main ethnic groups of China based on our newly developed quantitative real-time PCR assay. The frequencies of the CYP2A6*4 allele were 7.9%, 15%, 0% and 2% in Han (N=120), Uighur (N=100), Bouyei (N=100) and Tibetan (N=100) (P<0.0001), respectively. This work greatly expanded our understanding of the distribution of CYP2A6*4 in Chinese population and provided more information of different ethnic population's smoking behavior and also in disease susceptibility and drug response. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. Independent movement of the voltage sensors in KV2.1/KV6.4 heterotetramers

    PubMed Central

    Bocksteins, Elke; Snyders, Dirk J.; Holmgren, Miguel

    2017-01-01

    Heterotetramer voltage-gated K+ (KV) channels KV2.1/KV6.4 display a gating charge-voltage (QV) distribution composed by two separate components. We use state dependent chemical accessibility to cysteines substituted in either KV2.1 or KV6.4 to assess the voltage sensor movements of each subunit. By comparing the voltage dependences of chemical modification and gating charge displacement, here we show that each gating charge component corresponds to a specific subunit forming the heterotetramer. The voltage sensors from KV6.4 subunits move at more negative potentials than the voltage sensors belonging to KV2.1 subunits. These results indicate that the voltage sensors from the tetrameric channels move independently. In addition, our data shows that 75% of the total charge is attributed to KV2.1, while 25% to KV6.4. Thus, the most parsimonious model for KV2.1/KV6.4 channels’ stoichiometry is 3:1. PMID:28139741

  19. Blockage of RNA polymerase II at a cyclobutane pyrimidine dimer and 6-4 photoproduct.

    PubMed

    Mei Kwei, Joan Seah; Kuraoka, Isao; Horibata, Katsuyoshi; Ubukata, Manabu; Kobatake, Eiry; Iwai, Shigenori; Handa, Hiroshi; Tanaka, Kiyoji

    2004-08-06

    The blockage of transcription elongation by RNA polymerase II (pol II) at a DNA damage site on the transcribed strand triggers a transcription-coupled DNA repair (TCR), which rapidly removes DNA damage on the transcribed strand of the expressed gene and allows the resumption of transcription. To analyze the effect of UV-induced DNA damage on transcription elongation, an in vitro transcription elongation system using pol II and oligo(dC)-tailed templates containing a cyclobutane pyrimidine dimer (CPD) or 6-4 photoproduct (6-4PP) at a specific site was employed. The results showed that pol II incorporated nucleotides opposite the CPD and 6-4PP and then stalled. Pol II formed a stable ternary complex consisting of pol II, the DNA damage template, and the nascent transcript. Furthermore, atomic force microscopy imaging revealed that pol II stalled at the damaged region. These findings may provide the basis for analysis of the initiation step of TCR.

  20. 43 CFR 4130.6-4 - Special grazing permits or leases.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 43 Public Lands: Interior 2 2011-10-01 2011-10-01 false Special grazing permits or leases. 4130.6... LAND MANAGEMENT, DEPARTMENT OF THE INTERIOR RANGE MANAGEMENT (4000) GRAZING ADMINISTRATION-EXCLUSIVE OF ALASKA Authorizing Grazing Use § 4130.6-4 Special grazing permits or leases. Special grazing permits...

  1. Dynamically Complex [6+4] and [4+2] Cycloadditions in the Biosynthesis of Spinosyn A

    PubMed Central

    Patel, Ashay; Chen, Zhuo; Yang, Zhongyue; Gutiérrez, Osvaldo; Liu, Hung-wen; Houk, K. N.; Singleton, Daniel A.

    2017-01-01

    SpnF, an enzyme involved in the biosynthesis of spinosyn A, catalyzes a transannular Diels–Alder reaction. Quantum mechanical computations and dynamic simulations now show that this cycloaddition is not well described as either a concerted or stepwise process, and dynamical effects influence the identity and timing of bond formation. The transition state for the reaction is ambimodal and leads directly to both the observed Diels–Alder and an unobserved [6+4] cycloadduct. The potential energy surface bifurcates and the cycloadditions occur by dynamically stepwise modes featuring an “entropic intermediate”. A rapid Cope rearrangement converts the [6+4] adduct into the observed [4+2] adduct. Control of nonstatistical dynamical effects may serve as another way by which enzymes control reactions. PMID:26909570

  2. DNA photochemistry: geometrically unconstrained pyrimidine (6-4) pyrimidone photoproducts do photoisomerize.

    PubMed

    Douki, Thierry; Rebelo-Moreira, Silvestre; Hamon, Nadège; Bayle, Pierre-Alain

    2015-01-16

    Structural features are of major importance for the formation of mutagenic photoproducts in DNA. It was recently reported that lack of constraints between two adjacent nucleosidic units prevents the conversion of pyrimidine (6-4) pyrimidone photoproducts into their Dewar valence isomers. We here report that this is not the case for the thymidine photoproducts which, although unconstrained, are quantitatively converted into photolysis products identified as Dewar valence isomers by mass spectrometry and NMR and infrared spectroscopies.

  3. In situ dynamic observations of perovskite crystallisation and microstructure evolution intermediated from [PbI6](4-) cage nanoparticles.

    PubMed

    Hu, Qin; Zhao, Lichen; Wu, Jiang; Gao, Ke; Luo, Deying; Jiang, Yufeng; Zhang, Ziyi; Zhu, Chenhui; Schaible, Eric; Hexemer, Alexander; Wang, Cheng; Liu, Yi; Zhang, Wei; Grätzel, Michael; Liu, Feng; Russell, Thomas P; Zhu, Rui; Gong, Qihuang

    2017-06-21

    Hybrid lead halide perovskites have emerged as high-performance photovoltaic materials with their extraordinary optoelectronic properties. In particular, the remarkable device efficiency is strongly influenced by the perovskite crystallinity and the film morphology. Here, we investigate the perovskites crystallisation kinetics and growth mechanism in real time from liquid precursor continually to the final uniform film. We utilize some advanced in situ characterisation techniques including synchrotron-based grazing incident X-ray diffraction to observe crystal structure and chemical transition of perovskites. The nano-assemble model from perovskite intermediated [PbI6](4-) cage nanoparticles to bulk polycrystals is proposed to understand perovskites formation at a molecular- or nano-level. A crystallisation-depletion mechanism is developed to elucidate the periodic crystallisation and the kinetically trapped morphology at a mesoscopic level. Based on these in situ dynamics studies, the whole process of the perovskites formation and transformation from the molecular to the microstructure over relevant temperature and time scales is successfully demonstrated.

  4. In situ dynamic observations of perovskite crystallisation and microstructure evolution intermediated from [PbI6]4- cage nanoparticles

    NASA Astrophysics Data System (ADS)

    Hu, Qin; Zhao, Lichen; Wu, Jiang; Gao, Ke; Luo, Deying; Jiang, Yufeng; Zhang, Ziyi; Zhu, Chenhui; Schaible, Eric; Hexemer, Alexander; Wang, Cheng; Liu, Yi; Zhang, Wei; Grätzel, Michael; Liu, Feng; Russell, Thomas P.; Zhu, Rui; Gong, Qihuang

    2017-06-01

    Hybrid lead halide perovskites have emerged as high-performance photovoltaic materials with their extraordinary optoelectronic properties. In particular, the remarkable device efficiency is strongly influenced by the perovskite crystallinity and the film morphology. Here, we investigate the perovskites crystallisation kinetics and growth mechanism in real time from liquid precursor continually to the final uniform film. We utilize some advanced in situ characterisation techniques including synchrotron-based grazing incident X-ray diffraction to observe crystal structure and chemical transition of perovskites. The nano-assemble model from perovskite intermediated [PbI6]4- cage nanoparticles to bulk polycrystals is proposed to understand perovskites formation at a molecular- or nano-level. A crystallisation-depletion mechanism is developed to elucidate the periodic crystallisation and the kinetically trapped morphology at a mesoscopic level. Based on these in situ dynamics studies, the whole process of the perovskites formation and transformation from the molecular to the microstructure over relevant temperature and time scales is successfully demonstrated.

  5. Thymine photodimer formation in DNA hairpins. Unusual conformations favor (6 - 4) vs. (2 + 2) adducts.

    PubMed

    Hariharan, Mahesh; Siegmund, Karsten; Saurel, Clifton; McCullagh, Martin; Schatz, George C; Lewis, Frederick D

    2014-02-01

    The photochemical reactions of eleven synthetic DNA hairpins possessing a single TT step either in a base-paired stem or in a hexanucleotide linker have been investigated. The major reaction products have been identified as the cis-syn (2 + 2) adduct and the (6 - 4) adduct on the basis of their spectroscopic properties including 1D and 2D NMR spectra, UV spectra and stability or instability to photochemical cleavage. Product quantum yields and ratios determined by HPLC analysis allow the behaviour of the eleven hairpins to be placed into three groups: Group I in which the (2 + 2) adduct is the major product, as is usually the case for DNA, Group II in which comparable amounts of (2 + 2) and (6 - 4) adducts are formed, and Group III in which the major product is the (6 - 4) adduct. The latter behaviour is without precedent in natural or synthetic DNA and appears to be related to the highly fluxional structures of the hairpin reactants. Molecular dynamics simulation of ground state conformations provides quantum yields and product ratios calculated using a single parameter model that are in reasonable agreement with most of the experimental results. Factors which may influence the observed product ratios are discussed.

  6. Single Chirality (6,4) Single-Walled Carbon Nanotubes for Fluorescence Imaging with Silicon Detectors.

    PubMed

    Antaris, Alexander L; Yaghi, Omar K; Hong, Guosong; Diao, Shuo; Zhang, Bo; Yang, Jiang; Chew, Leila; Dai, Hongjie

    2015-12-16

    Postsynthetic single-walled carbon nanotube (SWCNT) sorting methods such as density gradient ultracentrifugation, gel chromatography, and electrophoresis have all been inspired by established biochemistry separation techniques designed to separate subcellular components. Biochemistry separation techniques have been refined to the degree that parameters such as pH, salt concentration, and temperature are necessary for a successful separation, yet these conditions are only now being applied to SWCNT separation methodologies. Slight changes in pH produce radically different behaviors of SWCNTs inside a density gradient, allowing for the facile separation of ultrahigh purity (6,4) SWCNTs from as-synthesized carbon nanotubes. The (6,4) SWCNTs are novel fluorophores emitting below ≈900 nm and can be easily detected with conventional silicon-based charge-coupled device detectors without the need for specialized InGaAs cameras. The (6,4) SWCNTs are used to demonstrate their potential as a clinically relevant NIR-I fluorescence stain for the immunohistochemical staining of cells and cancer tissue sections displaying high endothelial growth factor receptor levels.

  7. Structural determination of the ultraviolet light-induced thymine-cytosine pyrimidine-pyrimidone (6-4) photoproduct.

    PubMed Central

    Franklin, W A; Doetsch, P W; Haseltine, W A

    1985-01-01

    Ultraviolet light induces damage to DNA, with the majority of the damage expressed as the formation of cyclobutane dimers and pyrimidine-pyrimidone (6-4) photoproducts. The (6-4) photoproducts have been implicated as important UV light-induced premutagenic DNA lesions. The most abundant of the (6-4) products is the thymine-cytosine pyrimidine-pyrimidone (6-4) photoproduct, or TC (6-4) product. The structure of the TC (6-4) product was deduced by proton NMR, IR, and fast atom bombardment mass spectroscopy, and the product was found to differ from the previously described photoadduct, Thy(6-4)Pyo, by the presence of an amino group at the 5 position of the 5' pyrimidine. The implications of this structure on DNA base pairing and the induction of ultraviolet light-induced mutations are discussed. PMID:4022781

  8. Enhancement of the catalytic activity of ferulic acid decarboxylase from Enterobacter sp. Px6-4 through random and site-directed mutagenesis.

    PubMed

    Lee, Hyunji; Park, Jiyoung; Jung, Chaewon; Han, Dongfei; Seo, Jiyoung; Ahn, Joong-Hoon; Chong, Youhoon; Hur, Hor-Gil

    2015-11-01

    The enzyme ferulic acid decarboxylase (FADase) from Enterobacter sp. Px6-4 catalyzes the decarboxylation reaction of lignin monomers and phenolic compounds such as p-coumaric acid, caffeic acid, and ferulic acid into their corresponding 4-vinyl derivatives, that is, 4-vinylphenol, 4-vinylcatechol, and 4-vinylguaiacol, respectively. Among various ferulic acid decarboxylase enzymes, we chose the FADase from Enterobacter sp. Px6-4, whose crystal structure is known, and produced mutants to enhance its catalytic activity by random and site-directed mutagenesis. After three rounds of sequential mutations, FADase(F95L/D112N/V151I) showed approximately 34-fold higher catalytic activity than wild-type for the production of 4-vinylguaiacol from ferulic acid. Docking analyses suggested that the increased activity of FADase(F95L/D112N/V151I) could be due to formation of compact active site compared with that of the wild-type FADase. Considering the amount of phenolic compounds such as lignin monomers in the biomass components, successfully bioengineered FADase(F95L/D112N/V151I) from Enterobacter sp. Px6-4 could provide an ecofriendly biocatalytic tool for producing diverse styrene derivatives from biomass.

  9. Tactical Miniature Crystal Oscillator.

    DTIC Science & Technology

    1981-04-01

    87 6.2 Outgassing experiments o......... 88 6.3 Electropolishing ......... 95 6.4 Leaks in the TMXO package...machinable and sealing properties. After considering the thermal and mech- anical characteristics of many materials, nickel was selected. Table 7 gives...and the nickel type used in this program. TABLE 7. CHARACTERISTICS OF CRYSTAL ENCLOSURES Old copper Alumina* Nickel enclosures enclosures enclosure

  10. CFL3D Version 6.4-General Usage and Aeroelastic Analysis

    NASA Technical Reports Server (NTRS)

    Bartels, Robert E.; Rumsey, Christopher L.; Biedron, Robert T.

    2006-01-01

    This document contains the course notes on the computational fluid dynamics code CFL3D version 6.4. It is intended to provide from basic to advanced users the information necessary to successfully use the code for a broad range of cases. Much of the course covers capability that has been a part of previous versions of the code, with material compiled from a CFL3D v5.0 manual and from the CFL3D v6 web site prior to the current release. This part of the material is presented to users of the code not familiar with computational fluid dynamics. There is new capability in CFL3D version 6.4 presented here that has not previously been published. There are also outdated features no longer used or recommended in recent releases of the code. The information offered here supersedes earlier manuals and updates outdated usage. Where current usage supersedes older versions, notation of that is made. These course notes also provides hints for usage, code installation and examples not found elsewhere.

  11. Computation of Estonian CORS data using Bernese 5.2 and Gipsy 6.4 softwares

    NASA Astrophysics Data System (ADS)

    Kollo, Karin; Kall, Tarmo; Liibusk, Aive

    2017-04-01

    GNSS permanent station network in Estonia (ESTREF) was established already in 2007. In 2014-15 extensive reconstruction of ESTREF was carried out, including the establishment of 18 new stations, change of the hardware in CORS stations as well as establishing GNSS-RTK service for the whole Estonia. For GNSS-RTK service one needs precise coordinates in well-defined reference frame, i.e., ETRS89. For long time stability of stations and time-series analysis the re-processing of Estonian CORS data is ongoing. We re-process data from 2007 until 2015 with program Bernese GNSS 5.2 (Dach, 2015). For the set of ESTREF stations established in 2007, we perform as well computations with GIPSY 6.4 software (Ries et al., 2015). In the computations daily GPS-only solution was used. For precise orbits, final products from CODE (CODE analysis centre at the Astronomical Institute of the University of Bern) and JPL (Jet Propulsion Laboratory) for Bernese and GIPSY solutions were used, respectively. The cut-off angle was set to 10 degrees in order to avoid near-field multipath influence. In GIPSY, precise point positioning method with fixing ambiguities was used. Bernese calculations were performed based on double difference processing. Antenna phase centers were modelled based on igs08.atx and epnc_08.atx files. Vienna mapping function was used for mapping tropospheric delays. For the GIPSY solution, the higher order ionospheric term was modelled based on IRI-2012b model. For the Bernese solution higher order ionospheric term was neglected. FES2004 ocean tide loading model was used for the both computation strategies. As a result, two solutions using different scientific GNSS computation programs were obtained. The results from Bernese and GIPSY solutions were compared, using station repeatability values, RMS and coordinate differences. KEYWORDS: GNSS reference station network, Bernese GNSS 5.2, Gipsy 6.4, Estonia. References: Dach, R., S. Lutz, P. Walser, P. Fridez (Eds); 2015

  12. Antioxidant properties of flavone-6(4')-carboxaldehyde oxime ether derivatives.

    PubMed

    Ayhan-Kilcigil, Gülgün; Coban, Tülay; Tunçbilek, Meral; Can-Eke, Benay; Bozdağ-Dündar, Oya; Ertan, Rahmiye; Iscan, Mümtaz

    2004-06-01

    The in vitro antioxidant properties of some flavone-6(4)-carboxaldehyde oxime ether derivatives (Ia-f, IIa-f) were determined by their effects on the rat liver microsomal NADPH-dependent lipid peroxidation (LP) levels by measuring the formation of 2-thiobarbituric acid reactive substances. The free radical scavenging properties of the compounds were also examined in vitro by determining their capacity to scavenge superoxide anions and interact with the stable free radical 2, 2-diphenyl-1-picrylhydrazyl (DPPH). The most active compounds, IIb (Flavone-4'-carboxaldehyde-O-ethyl oxime) and Id (Flavone-6-carboxaldehyde-O-[2-(1-pyrolidino) ethyl] oxime), caused 98 and 79% inhibition of superoxide anion production and DPPH stable free radical at 10(-3) M, respectively.

  13. Results of a new OCTOPUS'' ECR ion source at 6. 4 GHz

    SciTech Connect

    Dupont, C.; Jongen, Y. ); Arakawa, K.; Yokota, W. ); Satoh, T.; Tachikawa, T. )

    1990-01-01

    The first OCTOPUS electron cyclstron resonance (ECR) multicharged heavy ion source was built in 1985 at the Centre de Recherches du Cyclotron of the University of Louvain (Belgium). This first source used an ECR frequency of 14.3 GHz in the injector stage and 8.5 GHz in the main confinement stage. A new OCTOPUS source has now been built for a new cyclotron to be installed at the Japan Atomic Energy Research Institute (JAERI). The design of this new OCTOPUS source is identical to the first OCTOPUS source, but uses an ECR frequency of 6.4 GHz in the main confinement stage. The experimental results are described, and a comparison is made between the two sources. However, the available data does not allow any clear conclusion to be drawn on frequency scaling.

  14. High-power MIXSEL: an integrated ultrafast semiconductor laser with 6.4 W average power.

    PubMed

    Rudin, B; Wittwer, V J; Maas, D J H C; Hoffmann, M; Sieber, O D; Barbarin, Y; Golling, M; Südmeyer, T; Keller, U

    2010-12-20

    High-power ultrafast lasers are important for numerous industrial and scientific applications. Current multi-watt systems, however, are based on relatively complex laser concepts, for example using additional intracavity elements for pulse formation. Moving towards a higher level of integration would reduce complexity, packaging, and manufacturing cost, which are important requirements for mass production. Semiconductor lasers are well established for such applications, and optically-pumped vertical external cavity surface emitting lasers (VECSELs) are most promising for higher power applications, generating the highest power in fundamental transverse mode (>20 W) to date. Ultrashort pulses have been demonstrated using passive modelocking with a semiconductor saturable absorber mirror (SESAM), achieving for example 2.1-W average power, sub-100-fs pulse duration, and 50-GHz pulse repetition rate. Previously the integration of both the gain and absorber elements into a single wafer was demonstrated with the MIXSEL (modelocked integrated external-cavity surface emitting laser) but with limited average output power (<200 mW). We have demonstrated the power scaling concept of the MIXSEL using optimized quantum dot saturable absorbers in an antiresonant structure design combined with an improved thermal management by wafer removal and mounting of the 8-µm thick MIXSEL structure directly onto a CVD-diamond heat spreader. The simple straight cavity with only two components has generated 28-ps pulses at 2.5-GHz repetition rate and an average output power of 6.4 W, which is higher than for any other modelocked semiconductor laser.

  15. 6-(4-Amino-phen-yl)-2-meth-oxy-4-phenyl-nicotino-nitrile.

    PubMed

    Suwunwong, Thitipone; Chantrapromma, Suchada; Quah, Ching Kheng; Fun, Hoong-Kun

    2013-11-23

    In the structure of the title nicotino-nitrile derivative, C19H15N3O, the pyridine ring makes dihedral angles of 11.50 (7) and 43.36 (8)° with the 4-amino-phenyl and phenyl rings, respectively, and the dihedral angle between the phenyl rings is 36.28°. In the crystal, mol-ecules are linked by N-H⋯N hydrogen bonds into wave-like sheets parallel to (10-2). These sheets are stacked by π-π inter-actions between the 4-amino-phenyl rings of adjacent sheets, with centroid-centroid distances of 3.7499 (9) Å. C-H⋯π inter-actions are also present.

  16. Discovery of a 6.4 h black hole binary in NGC 4490

    NASA Astrophysics Data System (ADS)

    Esposito, P.; Israel, G. L.; Sidoli, L.; Mapelli, M.; Zampieri, L.; Motta, S. E.

    2013-12-01

    We report on the discovery with Chandra of a strong modulation (˜90 per cent pulsed fraction) at ˜6.4 h from the source CXOU J123030.3+413853 in the star-forming, low-metallicity spiral galaxy NGC 4490, which is interacting with the irregular companion NGC 4485. This modulation, confirmed also by XMM-Newton observations, is interpreted as the orbital period of a binary system. The spectra from the Chandra and XMM-Newton observations can be described by a power-law model with photon index Γ ˜ 1.5. During these observations, which span from 2000 November to 2008 May, the source showed a long-term luminosity variability by a factor of ˜5, between ˜2 × 1038 and 1.1 × 1039 erg s-1 (for a distance of 8 Mpc). The maximum X-ray luminosity, exceeding by far the Eddington limit of a neutron star, indicates that the accretor is a black hole. Given the high X-ray luminosity, the short orbital period and the morphology of the orbital light curve, we favour an interpretation of CXOU J123030.3+413853 as a rare high-mass X-ray binary system with a Wolf-Rayet star as a donor, similar to Cyg X-3. This would be the fourth system of this kind known in the local Universe. CXOU J123030.3+413853 can also be considered as a transitional object between high-mass X-ray binaries and ultraluminous X-ray sources (ULXs), the study of which may reveal how the properties of persistent black hole binaries evolve entering the ULX regime.

  17. The Influence of Precipitation of Alpha2 on Properties and Microstructure in TIMETAL 6-4

    NASA Astrophysics Data System (ADS)

    Wu, Zhiwei; Qiu, Chunlei; Venkatesh, V.; Fraser, Hamish L.; Williams, R. E. A.; Viswanathan, G. B.; Thomas, Matthew; Nag, S.; Banerjee, Rajarshi; Loretto, Michael H.

    2013-04-01

    Samples of Hot Isostatically Pressed (HIPped) powder of TIMETAL 6-4 (Ti-6Al-4V, compositions in wt pct unless indicated), which was HIPped at 1203 K (930 °C), and of forged bar stock, which was slowly cooled from above the beta transus, were both subsequently held at 773 K (500 °C) for times up to 5 weeks and analyzed using scanning and transmission electron microscopy and atom probe analysis. It has been shown that in the samples aged for 5 weeks at 773 K (500 °C), there is a high density of alpha2 (α2, an ordered phase based on the composition Ti3Al) precipitates, which are typically 5 nm in size, and a significantly smaller density was present in the slowly cooled samples. The fatigue and tensile properties of samples aged for 5 weeks at 773 K (500 °C) have been compared with those of the HIPped powder and of the forged samples which were slowly cooled from just above the transus, and although no significant difference was found between the fatigue properties, the tensile strength of the aged samples was 5 pct higher than that of the as-HIPped and slowly cooled forged samples. The ductility of the forged samples did not decrease after aging at 773 K (500 °C) despite the strength increase. Transmission electron microscopy has been used to assess the nature of dislocations generated during tensile and fatigue deformation and it has been found that not just is planar slip observed, but dislocation pairs are not uncommon in samples aged at 773 K (500 °C) and some are seen in slowly cooled Ti6Al4V.

  18. X-ray spectroscopy of the z = 6.4 quasar SDSS J1148+5251

    NASA Astrophysics Data System (ADS)

    Gallerani, S.; Zappacosta, L.; Orofino, M. C.; Piconcelli, E.; Vignali, C.; Ferrara, A.; Maiolino, R.; Fiore, F.; Gilli, R.; Pallottini, A.; Neri, R.; Feruglio, C.

    2017-05-01

    We present the 78 ks Chandra observations of the z = 6.4 quasar SDSS J1148+5251. The source is clearly detected in the energy range 0.3-7 keV with 42 counts (with a significance ≳9σ). The X-ray spectrum is best fitted by a power law with photon index Γ = 1.9 absorbed by a gas column density of N_H=2.0^{+2.0}_{-1.5}× {10}^{23} cm^{-2}. We measure an intrinsic luminosity at 2-10 and 10-40 keV equal to ˜ 1.5 × 1045 erg s- 1, comparable with luminous local and intermediate-redshift quasar properties. Moreover, the X-ray to optical power-law slope value (αOX = -1.76 ± 0.14) of J1148 is consistent with the one found in quasars with similar rest-frame 2500 Å luminosity (L2500 ˜ 1032 erg s- 1 Å- 1). Then we use Chandra data to test a physically motivated model that computes the intrinsic X-ray flux emitted by a quasar starting from the properties of the powering black hole and assuming that X-ray emission is attenuated by intervening, metal-rich (Z ≥ Z⊙) molecular clouds (MC) distributed on ˜kpc scales in the host galaxy. Our analysis favours a black hole mass MBH ˜ 3 × 109 M⊙ and a molecular hydrogen mass M_H_2˜ 2× {10}^{10} {M_{\\odot }}, in good agreement with estimates obtained from previous studies. We finally discuss strengths and limits of our analysis.

  19. A High-Resolution Study of the IGM at 5 < z < 6.4

    NASA Astrophysics Data System (ADS)

    Becker, G. D.; Sargent, W. L. W.; Rauch, M.; Simcoe, R. A.

    2005-12-01

    The complete Lyman-alpha absorption seen in the spectra of z > 6 quasars suggest that the reionization of the IGM may have completed as late as z = 6.2. However, this late reionization scenario remains controversial due in part to studies of galaxy luminosity functions, which favor a highly-ionized IGM out to z > 6.5. In order to improve our understanding of the IGM at these redshifts, we have acquired Keck/HIRES spectra of nine quasars at 4.8 < z < 6.4. These are the first high-resolution spectra ever taken at z > 4.6, and are providing the first detailed look at the very high-redshift IGM. We will present the first results from this data set, highlighting the evolution of the Lyman-alpha forest and the quasar proximity regions. The high-resolution data also reveal an overabundance of O I systems at z > 6 towards SDSS J1148+5251. These O I absorbers may represent the last pockets of neutral gas to be reionized at z ˜ 6. Alternatively, they may be caused by enriched galaxy halos physically similar to those observed at lower redshift. For these systems we are able to measure accurate column densities of O I, C II, and Si II. The relative abundances are consistent with the yields of ordinary Type II supernovae, with at most ˜ 30% of the silicon contributed by very massive stars. GDB and WLWS have been supported by the NSF through grants AST 99-00733 and AST 02-06067. MR has been supported by the NSF under grant AST 00-98492. RAS has been supported by the MIT Pappalardo Fellowship program.

  20. Crystal Creations.

    ERIC Educational Resources Information Center

    Whipple, Nona; Whitmore, Sherry

    1989-01-01

    Presents a many-faceted learning approach to the study of crystals. Provides instructions for performing activities including crystal growth and patterns, creating miniature simulations of crystal-containing rock formations, charcoal and sponge gardens, and snowflakes. (RT)

  1. Crystal Creations.

    ERIC Educational Resources Information Center

    Whipple, Nona; Whitmore, Sherry

    1989-01-01

    Presents a many-faceted learning approach to the study of crystals. Provides instructions for performing activities including crystal growth and patterns, creating miniature simulations of crystal-containing rock formations, charcoal and sponge gardens, and snowflakes. (RT)

  2. Crystal Meth

    MedlinePlus

    ... from Other Parents Stories of Hope Crystal meth Crystal meth Story of Hope by giovanni January 3, ... about my drug addiction having to deal with Crystal meth. I am now in recovery and fighting ...

  3. Crystal Meth

    MedlinePlus

    ... Navigation Home / Stories of Hope / Crystal meth Crystal meth Story Of Hope By giovanni January 3rd, 2013 ... my drug addiction having to deal with Crystal meth. I am now in recovery and fighting my ...

  4. Preparation of oligodeoxyribonucleotides containing the pyrimidine(6-4)pyrimidone photoproduct by using a dinucleotide building block.

    PubMed

    Iwai, Shigenori

    2013-06-01

    This unit describes procedures for the synthesis of a dinucleotide-type building block of the pyrimidine(6-4)pyrimidone photoproduct [(6-4) photoproduct], which is one of the major DNA lesions induced by ultraviolet (UV) light, and its incorporation into oligodeoxyribonucleotides. Although this type of lesion is frequently found at thymine-cytosine sites, the building block of the (6-4) photoproduct formed at thymine-thymine sites can be synthesized much more easily. The problem in the oligonucleotide synthesis is that the (6-4) photoproduct is labile under alkaline conditions. Therefore, building blocks with an amino-protecting group that can be removed by a brief treatment with ammonia water at room temperature must be used for the incorporation of the normal bases. Byproduct formation by the coupling of phosphoramidites with the N3 of the 5' component should also be considered. This side reaction can be avoided by using benzimidazolium triflate as an activator.

  5. Fluorescence of poly[2,6-(4-phenylquinoline)] and its blends

    NASA Astrophysics Data System (ADS)

    Lin, Hung-Sheng

    Optical absorption measurements and photoluminescence spectroscopy have been carried out on a class of nitrogen-containing pi-conjugated polymers which can be used as active materials in light emitting diodes. In this dissertation, Poly [2,6-(4-phenylquinoline)] (PPQ) was used as a model system to demonstrate that optical properties could be manipulated by inducing morphology changes in various PPQ-blends as well as by solvent interactions with the pi-conjugated backbone of the PPQ. It is shown that by controlling the preparation conditions, adding small molecules, and/or blending with other interactive polymers, the of the absorption and/or emission could be altered. Furthermore, it was found that both doping and chain packing may have important effects on the energy gap between the ground state and the excited state. There are two major peaks in the UV absorption spectrum of the PPQ. One peak is assigned to the phenyl group side chain, whereas the other one reflects the PPQ backbone, whose absorption has been illustrated to be dependent on experimental conditions. The position of the major photoluminescence emission peak was found to be influenced by (1) the nature of the solvent and the doping agents used, (2) different processing methods, and (3) blending with photo-inactive polymers such as Poly(vinyl alcohol) (PVA), Poly(ethylene oxide) (PEO), Poly(acrylic acid)(PAA), Sulfonic polystyrene (SPS), etc. These factors singly or in combination contribute to the shifting of the emission peak. In a polymer blend, the strength of the enthalpic interaction between its components determines the spatial separation of the polymers, which results in different morphologies in the blend, and in turn, different optical properties of the blend. Since the emission from a blend depends on its morphological dispersion, optical studies of polymer blends first involve control of morphologies in these blends. The morphologies of polymer blends have been studied by using Scanning

  6. A novel extended architecture with 4 6·6 4 topology based on mixed-valence Wells-Dawson arsenotungstate and mixed-ligand Cu(I) units

    NASA Astrophysics Data System (ADS)

    Tong, Ruizhan; Ren, Xiaoyu; Li, Zuoxi; Liu, Bin; Hu, Huaiming; Xue, Ganglin; Fu, Feng; Wang, Jiwu

    2010-09-01

    A novel inorganic-organic hybrid compound based on mixed-valence Wells-Dawson arsenotungstate and mixed-ligand Cu(I) units, Cu 8I(imi) 4(bpy) 6(H 2O)[As 2VW 2VW 16VlO 62]·2H 2O ( 1) (bpy=4,4'-bipydine; imi=imidazole), has been hydrothermally synthesized and characterized by elemental analysis, IR spectroscopy, thermal gravimetric analysis, luminescent spectrum and single crystal X-ray diffraction. Single-crystal X-ray diffraction revealed that four terminal and three bridging oxygen atoms of the Wells-Dawson cluster are coordinated to Cu(I) ions and form an unprecedented hepta-supporting polyoxometalate. The functionalized arsenotungstates are further connected by two kinds of tridentate linkers, Imi-Cu-(bpy)-Cu-(bpy)-Cu-(bpy)-Cu-Imi and Imi-Cu-(bpy)-Cu-(bpy)-Cu-H 2O, to construct a 3D framework with 4 6·6 4 topology. The hybrid material has an intense emission at about 397 nm.

  7. The Al Hoceima Mw 6.4 earthquake of 24 February 2004 and its aftershocks sequence

    NASA Astrophysics Data System (ADS)

    van der Woerd, Jérôme; Dorbath, Catherine; Ousadou, Farida; Dorbath, Louis; Delouis, Bertrand; Jacques, Eric; Tapponnier, Paul; Hahou, Youssef; Menzhi, Mohammed; Frogneux, Michel; Haessler, Henri

    2014-07-01

    The Al Hoceima Mw 6.4 earthquake of 24 February 2004 that occurred in the eastern Rif region of Morocco already hit by a large event in May 1994 (Mw 5.9) has been followed by numerous aftershocks in the months following the event. The aftershock sequence has been monitored by a temporary network of 17 autonomous seismic stations during 15 days (28 March-10 April) in addition to 5 permanent stations of the Moroccan seismic network (CNRST, SPG, Rabat). This network allowed locating accurately about 650 aftershocks that are aligned in two directions, about N10-20E and N110-120E, in rough agreement with the two nodal planes of the focal mechanism (Harvard). The aftershock alignments are long enough, about 20 km or more, to correspond both to the main rupture plane. To further constrain the source of the earthquake main shock and aftershocks (mb > 3.5) have been relocated thanks to regional seismic data from Morocco and Spain. While the main shock is located at the intersection of the aftershock clouds, most of the aftershocks are aligned along the N10-20E direction. This direction together with normal sinistral slip implied by the focal mechanism is similar with the direction and mechanisms of active faults in the region, particularly the N10E Trougout oblique normal fault. Indeed, the Al Hoceima region is dominated by an approximate ENE-SSW direction of extension, with oblique normal faults. Three major 10-30 km-long faults, oriented NNE-SSW to NW-SE are particularly clear in the morphology, the Ajdir and Trougout faults, west and east of the Al Hoceima basin, respectively, and the NS Rouadi fault 20 km to the west. These faults show clear evidence of recent vertical displacements during the late Quaternary such as uplifted alluvial terraces along Oued Rihs, offset fan surfaces by the Rouadi fault and also uplifted and tilted abandoned marine terraces on both sides of the Al Hoceima bay. However, the N20E direction is in contrast with seismic sources identified from

  8. Axion crystals

    NASA Astrophysics Data System (ADS)

    Ozaki, Sho; Yamamoto, Naoki

    2017-08-01

    The low-energy effective theories for gapped insulators are classified by three parameters: permittivity ɛ, permeability μ, and theta angle θ. Crystals with periodic ɛ are known as photonic crystals. We here study the band structure of photons in a new type of crystals with periodic θ (modulo 2 π) in space, which we call the axion crystals. We find that the axion crystals have a number of new properties that the usual photonic crystals do not possess, such as the helicity-dependent mass gap and nonrelativistic gapless dispersion relation at small momentum. We briefly discuss possible realizations of axion crystals in condensed matter systems and high-energy physics.

  9. A TeGM6-4r antigen-based immunochromatographic test (ICT) for animal trypanosomosis.

    PubMed

    Nguyen, Thu-Thuy; Ruttayaporn, Ngasaman; Goto, Yasuyuki; Kawazu, Shin-ichiro; Sakurai, Tatsuya; Inoue, Noboru

    2015-11-01

    Animal trypanosomosis is a disease that is distributed worldwide which results in huge economic losses due to reduced animal productivity. Endemic regions are often located in the countryside where laboratory diagnosis is costly or inaccessible. The establishment of simple, effective, and accurate field tests is therefore of great interest to the farming and veterinary sectors. Our study aimed to develop a simple, rapid, and sensitive immunochromatographic test (ICT) for animal trypanosomosis utilizing the recombinant tandem repeat antigen TeGM6-4r, which is conserved amongst salivarian trypanosome species. In the specificity analysis, TeGM6-4r/ICT detected all of Trypanosoma evansi-positive controls from experimentally infected water buffaloes. As expected, uninfected controls tested negative. All sera samples collected from Tanzanian and Ugandan cattle that were Trypanosoma congolense- and/or Trypanosoma vivax-positive by microscopic examination of the buffy coat were found to be positive by the newly developed TeGM6-4r/ICT, which was comparable to results from TeGM6-4r/ELISA (kappa coefficient [κ] = 0.78). TeGM6/ICT also showed substantial agreement with ELISA using Trypanosoma brucei brucei (κ = 0.64) and T. congolense (κ = 0.72) crude antigen, suggesting the high potential of TeGM6-4r/ICT as a field diagnostic test, both for research purposes and on-site diagnosis of animal trypanosomosis.

  10. Origin of the 6.4-keV line of the Galactic Ridge X-ray Emission - First Report -

    NASA Astrophysics Data System (ADS)

    Tsuru, T. G.; Uchiyama, H.; Nobukawa, K. K.; Nobukawa, M.; Nakashima, S.; Koyama, K.; Torii, K.; Fukui, Y.

    2014-09-01

    We report the first results from high-statistics observation of the 6.4-keV line in the region of $l= +1.5^\\circ$ to $+3.5^\\circ$ (hereafter referred to as GC East), with the goal to uncover the origin of the Galactic ridge X-ray emission (GRXE). By comparing this data with that from the previous observations in the region $l=-1.5^\\circ$ to $-3.5^\\circ$ (hereafter referred to as GC West), we discovered that the 6.4-keV line is asymmetrically distributed with respect to the Galactic center, whereas the 6.7-keV line is symmetrically distributed. The distribution of the 6.4-keV line follows that of $^{13}$CO and its flux is proportional to the column density of the molecular gas. This correlation agrees with that seen between the 6.4-keV line and the cold interstellar medium (ISM) (H$_{\\rm I}$ $+$ H$_2$) in the region $|l|>4^\\circ$. This result suggests that the 6.4-keV emission is diffuse fluorescence from the cold ISM not only in GC East and West but also in the entire Galactic plane. This observational result suggests that the surface brightness of the 6.4-keV line is proportional to the column density of the cold ISM in the entire Galactic plane. For the ionizing particles, we consider X-rays and low energy cosmic-ray protons and electrons .

  11. DNA sequence context greatly affects the accuracy of bypass across an ultraviolet light 6-4 photoproduct in mammalian cells.

    PubMed

    Shriber, Pola; Leitner-Dagan, Yael; Geacintov, Nicholas; Paz-Elizur, Tamar; Livneh, Zvi

    2015-10-01

    Translesion DNA synthesis (TLS) is a DNA damage tolerance mechanism carried out by low-fidelity DNA polymerases that bypass DNA lesions, which overcomes replication stalling. Despite the miscoding nature of most common DNA lesions, several of them are bypassed in mammalian cells in a relatively accurate manner, which plays a key role maintaining a low mutation load. Whereas it is generally agreed that TLS across the major UV and sunlight induced DNA lesion, the cyclobutane pyrimidine dimer (CPD), is accurate, there were conflicting reports on whether the same is true for the thymine-thymine pyrimidine-pyrimidone(6-4) ultraviolet light photoproduct (TT6-4PP), which represents the second most common class of UV lesions. Using a TLS assay system based on gapped plasmids carrying site-specific TT6-4PP lesions in defined sequence contexts we show that the DNA sequence context markedly affected both the extent and accuracy of TLS. The sequence exhibiting higher TLS exhibited also higher error-frequency, caused primarily by semi-targeted mutations, at the nearest nucleotides flanking the lesion. Our results resolve the discrepancy reported on TLS across TT6-4PP, and suggest that TLS is more accurate in human cells than in mouse cells.

  12. Virtual Crystallizer

    SciTech Connect

    Land, T A; Dylla-Spears, R; Thorsness, C B

    2006-08-29

    Large dihydrogen phosphate (KDP) crystals are grown in large crystallizers to provide raw material for the manufacture of optical components for large laser systems. It is a challenge to grow crystal with sufficient mass and geometric properties to allow large optical plates to be cut from them. In addition, KDP has long been the canonical solution crystal for study of growth processes. To assist in the production of the crystals and the understanding of crystal growth phenomena, analysis of growth habits of large KDP crystals has been studied, small scale kinetic experiments have been performed, mass transfer rates in model systems have been measured, and computational-fluid-mechanics tools have been used to develop an engineering model of the crystal growth process. The model has been tested by looking at its ability to simulate the growth of nine KDP boules that all weighed more than 200 kg.

  13. Crystal growing

    NASA Technical Reports Server (NTRS)

    Neville, J. P.

    1990-01-01

    One objective is to demonstrate the way crystals grow and how they affect the behavior of material. Another objective is to compare the growth of crystals in metals and nonmetals. The procedures, which involve a supersaturated solution of a salt that will separate into crystals on cooling and the pouring off of an eutectic solution to expose the crystals formed by a solid solution when an alloy of two metals forms a solid and eutectic solution on cooling, are described.

  14. Crystallization and preliminary X-ray analysis of cryptochrome 3 from Arabidopsis thaliana

    SciTech Connect

    Pokorny, Richard; Klar, Tobias; Essen, Lars-Oliver; Batschauer, Alfred

    2005-10-01

    Recombinant cryptochrome 3 from A. thaliana with FAD and MTHF cofactors has been crystallized using the hanging-drop vapour-diffusion technique in the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1} and X-ray diffraction data were collected to 1.9 Å resolution. Cryptochromes are flavoproteins which serve as blue-light receptors in plants, animals, fungi and prokaryotes and belong to the same protein family as the catalytically active DNA photolyases. Cryptochrome 3 from the plant Arabidopsis thaliana (cry3; 525 amino acids, 60.7 kDa) is a representative of the novel cryDASH subfamily of UV-A/blue-light receptors and has been expressed as a mature FAD-containing protein in Escherichia coli without the signal sequence that directs the protein into plant organelles. The purified cryptochrome was found to be complexed to methenyltetrahydrofolate as an antenna pigment. Crystals of the cryptochrome–antenna pigment complex were obtained by vapour diffusion and display orthorhombic symmetry, with unit-cell parameters a = 76.298, b = 116.782, c = 135.024 Å. X-ray diffraction data were collected to 1.9 Å resolution using synchrotron radiation. The asymmetric unit comprises a cry3 dimer, the physiological role of which remains to be elucidated.

  15. Diagnostic value of the recombinant tandem repeat antigen TeGM6-4r for surra in water buffaloes.

    PubMed

    Nguyen, Thu-Thuy; Zhou, Mo; Ruttayaporn, Ngasaman; Nguyen, Quoc Doanh; Nguyen, Viet Khong; Goto, Yasuyuki; Suzuki, Yasuhiko; Kawazu, Shin-ichiro; Inoue, Noboru

    2014-03-17

    Trypanosoma evansi infection, or surra, is currently affecting various species of animals, especially water buffaloes. Since diagnosis is an important aspect of surra control, development of novel diagnostic antigens is of interest to implement and improve the currently utilized methods. Our study evaluated the tandem repeat antigen TeGM6-4r in T. evansi antibody detection in water buffaloes. TeGM6-4r-based ELISA was performed with 20 positive and 8 negative controls and 484 field samples from water buffaloes in Northern Vietnam. To examine cross-reactivity, sera from Japanese cattle that had been experimentally infected with Theileria orientalis (n=10), Babesia bovis (n=3), Babesia bigemina (n=7) and Trypanosoma theileri (n=59) were included in the study. The sensitivity of the test was 80%. TeGM6-4r did not react with Theileria or Babesia infected sera, however it showed cross reactivity with 11/59 T. theileri infected samples. The reference test, CATT/T. evansi also reacted with 3/59 T. theileri infected sera. The lysate antigen-based ELISA reacted with 4/59 T. theileri, 9/10 Theileria and 3/10 Babesia infected sera. In contrast, TeGM6-4r-based ELISA was 86.3% sensitive and 58.3% specific in the screening of field samples. The average seroprevalence of T. evansi infection among water buffaloes in Northern Vietnam was 27.1% by CATT/T. evansi and 53.7% by TeGM6-4r. Seroprevalence in the five surveyed provinces ranged from 17.4% to 39.8% in the reference test, and 47.3% to 67.3% in the recombinant antigen based test. The finding indicated that the disease is still widely endemic in the area and that surveillance programs need to be carried out regularly to better control surra. We proposed TeGM6-4r as a useful serodiagnostic antigen for the detection and epidemiological surveillance of T. evansi infection among water buffaloes. Copyright © 2014 Elsevier B.V. All rights reserved.

  16. Apoferritin crystals

    NASA Technical Reports Server (NTRS)

    2001-01-01

    Dr. Alexander Chernov, of the Universities Space Research Association (USRA) and based at Marshall Space Flight Center, is investigating why protein crystals grown in space are, in about 20 percent of cases, better-ordered than those grown on the ground. They are testing the idea that the amount of impurities trapped by space-grown crystals may be different than the amount trapped by crystals grown on Earth because convection is negligible in microgravity. The concentrations or impurities in many space-grown crystals turned out to be several times lower than that in the terrestrial ones, sometimes below the detection limit. The ground-based experiment also showed that the amount of impurities per unit volume of the crystals was usually higher than the amount per unit volume of the solution. This means that a growing crystal actually purifies the solution in its immediate vicinity. Here, an impurity depletion zone is created around apoferritin crystals grown in gel, imitating microgravity conditions.

  17. Apoferritin crystals

    NASA Technical Reports Server (NTRS)

    2001-01-01

    Dr. Alexander Chernov, of the Universities Space Research Association (USRA) and based at Marshall Space Flight Center, is investigating why protein crystals grown in space are, in about 20 percent of cases, better-ordered than those grown on the ground. They are testing the idea that the amount of impurities trapped by space-grown crystals may be different than the amount trapped by crystals grown on Earth because convection is negligible in microgravity. The concentrations or impurities in many space-grown crystals turned out to be several times lower than that in the terrestrial ones, sometimes below the detection limit. The ground-based experiment also showed that the amount of impurities per unit volume of the crystals was usually higher than the amount per unit volume of the solution. This means that a growing crystal actually purifies the solution in its immediate vicinity. Here, an impurity depletion zone is created around apoferritin crystals grown in gel, imitating microgravity conditions.

  18. CYP2D6*4 polymorphism: A new marker of response to hormonotherapy in male breast cancer?

    PubMed

    Abreu, M H; Gomes, M; Menezes, F; Afonso, N; Abreu, P H; Medeiros, R; Pereira, D; Lopes, C

    2015-08-01

    Tamoxifen remains the standard hormonotherapy for Male breast cancer patients (MBC). Previous studies, in women, tried to evaluate the impact of CYP2D6 polymorphisms in tamoxifen efficacy with conflicting results. Herein we analyze the relation between CYP2D6*4 polymorphism and survival in MBC patients. Fifty-three patients, proposed to tamoxifen in adjuvant setting, were enrolled. Clinical information was collected from records and histological revision with additional immunochemistry analysis was done to better characterize the tumors. Comprehensive CYP2D6*4 genotyping from blood or tumor tissue was performed and translated into two predicted metabolic activity groups. Patients included in the two CYP2D6*4 groups did not differ concerning to age, histological characteristics, and primary treatments performed. Median age at diagnosis was 63 years-old and patients were submitted at least to mastectomy and adjuvant hormonotherapy. Recurrence was observed in 7 patients (13.2%) and 13 patients (25.5%) died with a 5-year disease-free survival of 86.2%. The poorer metabolizer group had a high risk for recurrence (p = 0.034) and this outcome effect remains in different subgroups: in tumors larger than 2 cm (p < 0.001), nodal status, N0 vs N+ (p = 0.04) and in advanced stage, stage III (p < 0.001). Poorer metabolizer patients had also a worse overall survival when tumors were larger than 2 cm (p = 0.03). In our series, there was an association between CYP2D6*4 polymorphism and a probability of recurrence, with a consistent effect in risk groups defined by classic prognostic factors. Multicentric studies with larger samples are needed to validate these results. Copyright © 2015 Elsevier Ltd. All rights reserved.

  19. 41 CFR 304-6.4 - What form must we use to report payments received by the agency from non-Federal sources?

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... report payments received by the agency from non-Federal sources? 304-6.4 Section 304-6.4 Public Contracts and Property Management Federal Travel Regulation System PAYMENT OF TRAVEL EXPENSES FROM A NON-FEDERAL SOURCE AGENCY REQUIREMENTS 6-PAYMENT GUIDELINES Reports § 304-6.4 What form must we use to...

  20. 41 CFR 304-6.4 - What form must we use to report payments received by the agency from non-Federal sources?

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... report payments received by the agency from non-Federal sources? 304-6.4 Section 304-6.4 Public Contracts and Property Management Federal Travel Regulation System PAYMENT OF TRAVEL EXPENSES FROM A NON-FEDERAL SOURCE AGENCY REQUIREMENTS 6-PAYMENT GUIDELINES Reports § 304-6.4 What form must we use to...

  1. 41 CFR 304-6.4 - What form must we use to report payments received by the agency from non-Federal sources?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... report payments received by the agency from non-Federal sources? 304-6.4 Section 304-6.4 Public Contracts and Property Management Federal Travel Regulation System PAYMENT OF TRAVEL EXPENSES FROM A NON-FEDERAL SOURCE AGENCY REQUIREMENTS 6-PAYMENT GUIDELINES Reports § 304-6.4 What form must we use to...

  2. 41 CFR 304-6.4 - What form must we use to report payments received by the agency from non-Federal sources?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... report payments received by the agency from non-Federal sources? 304-6.4 Section 304-6.4 Public Contracts and Property Management Federal Travel Regulation System PAYMENT OF TRAVEL EXPENSES FROM A NON-FEDERAL SOURCE AGENCY REQUIREMENTS 6-PAYMENT GUIDELINES Reports § 304-6.4 What form must we use to...

  3. 41 CFR 304-6.4 - What form must we use to report payments received by the agency from non-Federal sources?

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... report payments received by the agency from non-Federal sources? 304-6.4 Section 304-6.4 Public Contracts and Property Management Federal Travel Regulation System PAYMENT OF TRAVEL EXPENSES FROM A NON-FEDERAL SOURCE AGENCY REQUIREMENTS 6-PAYMENT GUIDELINES Reports § 304-6.4 What form must we use to...

  4. In situ dynamic observations of perovskite crystallisation and microstructure evolution intermediated from [PbI6]4− cage nanoparticles

    PubMed Central

    Hu, Qin; Zhao, Lichen; Wu, Jiang; Gao, Ke; Luo, Deying; Jiang, Yufeng; Zhang, Ziyi; Zhu, Chenhui; Schaible, Eric; Hexemer, Alexander; Wang, Cheng; Liu, Yi; Zhang, Wei; Grätzel, Michael; Liu, Feng; Russell, Thomas P.; Zhu, Rui; Gong, Qihuang

    2017-01-01

    Hybrid lead halide perovskites have emerged as high-performance photovoltaic materials with their extraordinary optoelectronic properties. In particular, the remarkable device efficiency is strongly influenced by the perovskite crystallinity and the film morphology. Here, we investigate the perovskites crystallisation kinetics and growth mechanism in real time from liquid precursor continually to the final uniform film. We utilize some advanced in situ characterisation techniques including synchrotron-based grazing incident X-ray diffraction to observe crystal structure and chemical transition of perovskites. The nano-assemble model from perovskite intermediated [PbI6]4− cage nanoparticles to bulk polycrystals is proposed to understand perovskites formation at a molecular- or nano-level. A crystallisation-depletion mechanism is developed to elucidate the periodic crystallisation and the kinetically trapped morphology at a mesoscopic level. Based on these in situ dynamics studies, the whole process of the perovskites formation and transformation from the molecular to the microstructure over relevant temperature and time scales is successfully demonstrated. PMID:28635947

  5. In situ dynamic observations of perovskite crystallisation and microstructure evolution intermediated from [PbI6]4– cage nanoparticles

    DOE PAGES

    Hu, Qin; Zhao, Lichen; Wu, Jiang; ...

    2017-06-21

    Hybrid lead halide perovskites have emerged as high-performance photovoltaic materials with their extraordinary optoelectronic properties. In particular, the remarkable device efficiency is strongly influenced by the perovskite crystallinity and the film morphology. Here, we investigate the perovskites crystallisation kinetics and growth mechanism in real time from liquid precursor continually to the final uniform film. We utilize some advanced in situ characterisation techniques including synchrotron-based grazing incident X-ray diffraction to observe crystal structure and chemical transition of perovskites. The nano-assemble model from perovskite intermediated [PbI6]4– cage nanoparticles to bulk polycrystals is proposed to understand perovskites formation at a molecular- or nano-level.more » A crystallisation-depletion mechanism is developed to elucidate the periodic crystallisation and the kinetically trapped morphology at a mesoscopic level. Based on these in situ dynamics studies, the whole process of the perovskites formation and transformation from the molecular to the microstructure over relevant temperature and time scales is successfully demonstrated.« less

  6. Synthesis, molecular docking and biological evaluation of novel 6-(4-(4-aminophenylsulfonyl)phenylamino)-5H-benzo[a]phenothiazin-5-one derivatives

    NASA Astrophysics Data System (ADS)

    Ravichandiran, Palanisamy; Athinarayanan, Jegan; Premnath, Dhanaraj; Periasamy, Vaiyapuri Subbarayan; Alshatwi, Ali A.; Vasanthkumar, Samuel

    2015-03-01

    A novel series of 6-(4-(4-aminophenylsulfonyl)phenylamino)-5H-benzo[a]phenothiazin-5-one derivatives have been synthesized and examined for their in vitro antibacterial activity against a panel of Gram-positive and Gram-negative bacteria. Among these, N-(4-(4-(5-oxo-5H-benzo[a]phenothiazin-6-ylamino)phenylsulfonyl)phenyl)-3,5-bis(trifluoromethyl)benzamide (3n) (0.4 μg/mL) and 4-ethyl-N-(4-(4-(5-oxo-5H-benzo[a]phenothiazin-6-ylamino)phenylsulfonyl)phenyl)benzamide (3l) (0.6 μg/mL) systems exhibited a potent inhibitory activity against Gram-positive organism Bacillus subtilis, when compare to the other synthesized compounds. Sparfloxacin (9.76 μg/mL), Norfloxacin (no activity) were employed as the standard drugs. An evaluation of the cytotoxicity of the title compounds (1, 2, 3a-n) revealed that they displayed low toxicity (26-115 mg/L) against cervical cancer cell line (SiHa). The results of these studies suggest that, phenothiazin-5-one derivatives are interesting binding agents for the development of new Gram-positive and Gram-negative antibacterial agents. To understand the interactions with protein receptors, docking simulation was done with crystal structures of B.subtilis (YmaH) and histone deacetylase (HDAC8) to determine the probable binding conformation.

  7. Adipic acid-2,4-diamino-6-(4-meth-oxy-phen-yl)-1,3,5-triazine (1/2).

    PubMed

    Thanigaimani, Kaliyaperumal; Razak, Ibrahim Abdul; Arshad, Suhana; Jagatheesan, Rathinavel; Santhanaraj, Kulandaisamy Joseph

    2012-10-01

    The asymmetric unit of the title compound, 2C(10)H(11)N(5)O·C(6)H(10)O(4), consists of a 2,4-diamino-6-(4-meth-oxy-phen-yl)-1,3,5-triazine mol-ecule and one-half mol-ecule of adipic acid which lies about an inversion center. The triazine ring makes a dihedral angle of 12.89 (4)° with the adjacent benzene ring. In the crystal, the components are linked by N-H⋯O and O-H⋯N hydrogen bonds, thus generating a centrosymmetric 2 + 1 unit of triazine and adipic acid mol-ecules with R(2) (2)(8) motifs. The triazine mol-ecules are connected to each other by N-H⋯N hydrogen bonds, forming an R(2) (2)(8) motif and a supra-molecular ribbon along the c axis. The 2 + 1 units and the supra-molecular ribbons are further inter-linked by weak N-H⋯O, C-H⋯O and C-H⋯π inter-actions, resulting in a three-dimensional network.

  8. Crystal and Molecular Structure of the Antimalarial Agent 4-(tert-Butyl- 2-(tert-Butylaminomethyl)-6-(4-Chlorophenyl)Phenol Dihydrogen Phosphate (WR 194, 965 Phosphate)

    DTIC Science & Technology

    1988-04-01

    became defined. The WR 194,%5 molecule fitted more (Fig. 6C. In her review, Oleksyn (13) points out that in the closely to the three-dimensional space...molecule and the possible importance of 11. Oleksyn , B., L. Lebioda, and M. Ciechanowicz-Rutkowska. 1979. hydrogen bonding with a receptor. Although the...closely into the 12. Oleksyn , B., K. M. Stadnicka, and S. A. Hodorowicz. 1978. The ., -’ three-dimensional space defined by a combination of meflo

  9. Lysozyme Crystal

    NASA Technical Reports Server (NTRS)

    2004-01-01

    To the crystallographer, this may not be a diamond but it is just as priceless. A Lysozyme crystal grown in orbit looks great under a microscope, but the real test is X-ray crystallography. The colors are caused by polarizing filters. Proteins can form crystals generated by rows and columns of molecules that form up like soldiers on a parade ground. Shining X-rays through a crystal will produce a pattern of dots that can be decoded to reveal the arrangement of the atoms in the molecules making up the crystal. Like the troops in formation, uniformity and order are everything in X-ray crystallography. X-rays have much shorter wavelengths than visible light, so the best looking crystals under the microscope won't necessarily pass muster under the X-rays. In order to have crystals to use for X-ray diffraction studies, crystals need to be fairly large and well ordered. Scientists also need lots of crystals since exposure to air, the process of X-raying them, and other factors destroy them. Growing protein crystals in space has yielded striking results. Lysozyme's structure is well known and it has become a standard in many crystallization studies on Earth and in space.

  10. RNA Crystallization

    NASA Technical Reports Server (NTRS)

    Golden, Barbara L.; Kundrot, Craig E.

    2003-01-01

    RNA molecules may be crystallized using variations of the methods developed for protein crystallography. As the technology has become available to syntheisize and purify RNA molecules in the quantities and with the quality that is required for crystallography, the field of RNA structure has exploded. The first consideration when crystallizing an RNA is the sequence, which may be varied in a rational way to enhance crystallizability or prevent formation of alternate structures. Once a sequence has been designed, the RNA may be synthesized chemically by solid-state synthesis, or it may be produced enzymatically using RNA polymerase and an appropriate DNA template. Purification of milligram quantities of RNA can be accomplished by HPLC or gel electrophoresis. As with proteins, crystallization of RNA is usually accomplished by vapor diffusion techniques. There are several considerations that are either unique to RNA crystallization or more important for RNA crystallization. Techniques for design, synthesis, purification, and crystallization of RNAs will be reviewed here.

  11. RNA Crystallization

    NASA Technical Reports Server (NTRS)

    Golden, Barbara L.; Kundrot, Craig E.

    2003-01-01

    RNA molecules may be crystallized using variations of the methods developed for protein crystallography. As the technology has become available to syntheisize and purify RNA molecules in the quantities and with the quality that is required for crystallography, the field of RNA structure has exploded. The first consideration when crystallizing an RNA is the sequence, which may be varied in a rational way to enhance crystallizability or prevent formation of alternate structures. Once a sequence has been designed, the RNA may be synthesized chemically by solid-state synthesis, or it may be produced enzymatically using RNA polymerase and an appropriate DNA template. Purification of milligram quantities of RNA can be accomplished by HPLC or gel electrophoresis. As with proteins, crystallization of RNA is usually accomplished by vapor diffusion techniques. There are several considerations that are either unique to RNA crystallization or more important for RNA crystallization. Techniques for design, synthesis, purification, and crystallization of RNAs will be reviewed here.

  12. Protein Crystallization

    NASA Technical Reports Server (NTRS)

    Chernov, Alexander A.

    2005-01-01

    Nucleation, growth and perfection of protein crystals will be overviewed along with crystal mechanical properties. The knowledge is based on experiments using optical and force crystals behave similar to inorganic crystals, though with a difference in orders of magnitude in growing parameters. For example, the low incorporation rate of large biomolecules requires up to 100 times larger supersaturation to grow protein, rather than inorganic crystals. Nucleation is often poorly reproducible, partly because of turbulence accompanying the mixing of precipitant with protein solution. Light scattering reveals fluctuations of molecular cluster size, its growth, surface energies and increased clustering as protein ages. Growth most often occurs layer-by-layer resulting in faceted crystals. New molecular layer on crystal face is terminated by a step where molecular incorporation occurs. Quantitative data on the incorporation rate will be discussed. Rounded crystals with molecularly disordered interfaces will be explained. Defects in crystals compromise the x-ray diffraction resolution crucially needed to find the 3D atomic structure of biomolecules. The defects are immobile so that birth defects stay forever. All lattice defects known for inorganics are revealed in protein crystals. Contribution of molecular conformations to lattice disorder is important, but not studied. This contribution may be enhanced by stress field from other defects. Homologous impurities (e.g., dimers, acetylated molecules) are trapped more willingly by a growing crystal than foreign protein impurities. The trapped impurities induce internal stress eliminated in crystals exceeding a critical size (part of mni for ferritin, lysozyme). Lesser impurities are trapped from stagnant, as compared to the flowing, solution. Freezing may induce much more defects unless quickly amorphysizing intracrystalline water.

  13. Computational crystallization

    PubMed Central

    Altan, Irem; Charbonneau, Patrick; Snell, Edward H.

    2016-01-01

    Crystallization is a key step in macromolecular structure determination by crystallography. While a robust theoretical treatment of the process is available, due to the complexity of the system, the experimental process is still largely one of trial and error. In this article, efforts in the field are discussed together with a theoretical underpinning using a solubility phase diagram. Prior knowledge has been used to develop tools that computationally predict the crystallization outcome and define mutational approaches that enhance the likelihood of crystallization. For the most part these tools are based on binary outcomes (crystal or no crystal), and the full information contained in an assembly of crystallization screening experiments is lost. The potential of this additional information is illustrated by examples where new biological knowledge can be obtained and where a target can be sub-categorized to predict which class of reagents provides the crystallization driving force. Computational analysis of crystallization requires complete and correctly formatted data. While massive crystallization screening efforts are under way, the data available from many of these studies are sparse. The potential for this data and the steps needed to realize this potential are discussed. PMID:26792536

  14. Computational crystallization.

    PubMed

    Altan, Irem; Charbonneau, Patrick; Snell, Edward H

    2016-07-15

    Crystallization is a key step in macromolecular structure determination by crystallography. While a robust theoretical treatment of the process is available, due to the complexity of the system, the experimental process is still largely one of trial and error. In this article, efforts in the field are discussed together with a theoretical underpinning using a solubility phase diagram. Prior knowledge has been used to develop tools that computationally predict the crystallization outcome and define mutational approaches that enhance the likelihood of crystallization. For the most part these tools are based on binary outcomes (crystal or no crystal), and the full information contained in an assembly of crystallization screening experiments is lost. The potential of this additional information is illustrated by examples where new biological knowledge can be obtained and where a target can be sub-categorized to predict which class of reagents provides the crystallization driving force. Computational analysis of crystallization requires complete and correctly formatted data. While massive crystallization screening efforts are under way, the data available from many of these studies are sparse. The potential for this data and the steps needed to realize this potential are discussed.

  15. Crystallization mechanisms of acicular crystals

    NASA Astrophysics Data System (ADS)

    Puel, François; Verdurand, Elodie; Taulelle, Pascal; Bebon, Christine; Colson, Didier; Klein, Jean-Paul; Veesler, Stéphane

    2008-01-01

    In this contribution, we present an experimental investigation of the growth of four different organic molecules produced at industrial scale with a view to understand the crystallization mechanism of acicular or needle-like crystals. For all organic crystals studied in this article, layer-by-layer growth of the lateral faces is very slow and clear, as soon as the supersaturation is high enough, there is competition between growth and surface-activated secondary nucleation. This gives rise to pseudo-twinned crystals composed of several needle individuals aligned along a crystallographic axis; this is explained by regular over- and inter-growths as in the case of twinning. And when supersaturation is even higher, nucleation is fast and random. In an industrial continuous crystallization, the rapid growth of needle-like crystals is to be avoided as it leads to fragile crystals or needles, which can be partly broken or totally detached from the parent crystals especially along structural anisotropic axis corresponding to weaker chemical bonds, thus leading to slower growing faces. When an activated mechanism is involved such as a secondary surface nucleation, it is no longer possible to obtain a steady state. Therefore, the crystal number, size and habit vary significantly with time, leading to troubles in the downstream processing operations and to modifications of the final solid-specific properties. These results provide valuable information on the unique crystallization mechanisms of acicular crystals, and show that it is important to know these threshold and critical values when running a crystallizer in order to obtain easy-to-handle crystals.

  16. Crystal Data

    National Institute of Standards and Technology Data Gateway

    SRD 3 NIST Crystal Data (PC database for purchase)   NIST Crystal Data contains chemical, physical, and crystallographic information useful to characterize more than 237,671 inorganic and organic crystalline materials. The data include the standard cell parameters, cell volume, space group number and symbol, calculated density, chemical formula, chemical name, and classification by chemical type.

  17. No Ly α emitters detected around a QSO at z = 6.4: Suppressed by the QSO?★

    NASA Astrophysics Data System (ADS)

    Goto, Tomotsugu; Utsumi, Yousuke; Kikuta, Satoshi; Miyazaki, Satoshi; Shiki, Kensei; Hashimoto, Tetsuya

    2017-09-01

    Understanding how quasars' (QSOs') ultraviolet (UV) radiation affects galaxy formation is vital to our understanding of the reionization era. Using a custom-made narrow-band filter, NB906, on Subaru/Suprime-Cam, we investigated the number density of Ly α emitters (LAEs) around a QSO at z = 6.4. To date, this is the highest redshift narrow-band observation, where LAEs around a luminous QSO are investigated. Due to the large field of view of Suprime-Cam, our survey area is ∼5400 cMpc2, much larger than previous studies at z = 5.7 (∼200 cMpc2). In this field, we previously found a factor of 7 overdensity of Lyman break galaxies. Based on this, we expected to detect ∼100 LAEs down to NB906 = 25 ABmag. However, our 6.4 h exposure found none. The obtained upper limit on the number density of LAEs is more than an order lower than the blank fields. Furthermore, this lower density of LAEs spans a large scale of 10 pMpc across. A simple argument suggests that a strong UV radiation from the QSO can suppress star formation in haloes with Mvir < 1010 M⊙ within a pMpc from the QSO, but the deficit at the edge of the field (5 pMpc) remains to be explained.

  18. Parameterization of Highly Charged Metal Ions Using the 12-6-4 LJ-Type Nonbonded Model in Explicit Water

    PubMed Central

    2015-01-01

    Highly charged metal ions act as catalytic centers and structural elements in a broad range of chemical complexes. The nonbonded model for metal ions is extensively used in molecular simulations due to its simple form, computational speed, and transferability. We have proposed and parametrized a 12-6-4 LJ (Lennard-Jones)-type nonbonded model for divalent metal ions in previous work, which showed a marked improvement over the 12-6 LJ nonbonded model. In the present study, by treating the experimental hydration free energies and ion–oxygen distances of the first solvation shell as targets for our parametrization, we evaluated 12-6 LJ parameters for 18 M(III) and 6 M(IV) metal ions for three widely used water models (TIP3P, SPC/E, and TIP4PEW). As expected, the interaction energy underestimation of the 12-6 LJ nonbonded model increases dramatically for the highly charged metal ions. We then parametrized the 12-6-4 LJ-type nonbonded model for these metal ions with the three water models. The final parameters reproduced the target values with good accuracy, which is consistent with our previous experience using this potential. Finally, tests were performed on a protein system, and the obtained results validate the transferability of these nonbonded model parameters. PMID:25145273

  19. Preferential synthesis of (6,4) single-walled carbon nanotubes by controlling oxidation degree of Co catalyst.

    PubMed

    Xu, Bin; Kaneko, Toshiro; Shibuta, Yasushi; Kato, Toshiaki

    2017-09-11

    Chirality-selective synthesis of single-walled carbon nanotubes (SWNTs) has been a research goal for the last two decades and is still challenging due to the difficulty in controlling the atomic structure in the one-dimensional material. Here, we develop an optimized approach for controlling the chirality of species by tuning the oxidation degree of Co catalyst. Predominant synthesis of (6,4) SWNTs is realized for the first time. The detailed mechanism is investigated through a systematic experimental study combined with first-principles calculations, revealing that the independent control of tube diameter and chiral angle achieved by changing the binding energy between SWNTs (cap and tube edge) and catalyst causes a drastic transition of chirality of SWNTs from (6,5) to (6,4). Since our approach of independently controlling the diameter and chiral angle can be applied to other chirality species, our results can be useful in achieving the on-demand synthesis of specific-chirality SWNTs.

  20. Parameterization of highly charged metal ions using the 12-6-4 LJ-type nonbonded model in explicit water.

    PubMed

    Li, Pengfei; Song, Lin Frank; Merz, Kenneth M

    2015-01-22

    Highly charged metal ions act as catalytic centers and structural elements in a broad range of chemical complexes. The nonbonded model for metal ions is extensively used in molecular simulations due to its simple form, computational speed, and transferability. We have proposed and parametrized a 12-6-4 LJ (Lennard-Jones)-type nonbonded model for divalent metal ions in previous work, which showed a marked improvement over the 12-6 LJ nonbonded model. In the present study, by treating the experimental hydration free energies and ion-oxygen distances of the first solvation shell as targets for our parametrization, we evaluated 12-6 LJ parameters for 18 M(III) and 6 M(IV) metal ions for three widely used water models (TIP3P, SPC/E, and TIP4PEW). As expected, the interaction energy underestimation of the 12-6 LJ nonbonded model increases dramatically for the highly charged metal ions. We then parametrized the 12-6-4 LJ-type nonbonded model for these metal ions with the three water models. The final parameters reproduced the target values with good accuracy, which is consistent with our previous experience using this potential. Finally, tests were performed on a protein system, and the obtained results validate the transferability of these nonbonded model parameters.

  1. Effect of Electron Beam Freeform Fabrication (EBF3) Processing Parameters on Composition of Ti-6-4

    NASA Technical Reports Server (NTRS)

    Lach, Cynthia L.; Taminger, Karen; Schuszler, A. Bud, II; Sankaran, Sankara; Ehlers, Helen; Nasserrafi, Rahbar; Woods, Bryan

    2007-01-01

    The Electron Beam Freeform Fabrication (EBF3) process developed at NASA Langley Research Center was evaluated using a design of experiments approach to determine the effect of processing parameters on the composition and geometry of Ti-6-4 deposits. The effects of three processing parameters: beam power, translation speed, and wire feed rate, were investigated by varying one while keeping the remaining parameters constant. A three-factorial, three-level, fully balanced mutually orthogonal array (L27) design of experiments approach was used to examine the effects of low, medium, and high settings for the processing parameters on the chemistry, geometry, and quality of the resulting deposits. Single bead high deposits were fabricated and evaluated for 27 experimental conditions. Loss of aluminum in Ti-6-4 was observed in EBF3 processing due to selective vaporization of the aluminum from the sustained molten pool in the vacuum environment; therefore, the chemistries of the deposits were measured and compared with the composition of the initial wire and base plate to determine if the loss of aluminum could be minimized through careful selection of processing parameters. The influence of processing parameters and coupling between these parameters on bulk composition, measured by Direct Current Plasma (DCP), local microchemistries determined by Wavelength Dispersive Spectrometry (WDS), and deposit geometry will also be discussed.

  2. 3-(4-Chloro-benzo-yl)-6-(4-chloro-phen-yl)-2,4-dimethyl-benzonitrile.

    PubMed

    Wang, Xin; Zhang, Yi-Min; Jia, Xue-Fei

    2012-09-01

    In the title compound, C(22)H(15)Cl(2)NO, the terminal chloro-benzene rings are oriented at 44.51 (15) and 86.06 (17)° with respect to the central polysubstituted benzene ring, and make a dihedral angle of 49.48 (17)°with each other. In the crystal, mol-ecules are linked by weak C-H⋯O and C-H⋯N inter-actions.

  3. Molecular Crystals

    NASA Astrophysics Data System (ADS)

    Wright, John D.

    1995-02-01

    This book describes the chemical and physical structure of molecular crystals, their optical and electronic properties, and the reactions between neighboring molecules in crystals. In the second edition, the author has taken into account research that has undergone extremely rapid development since the first edition was published in 1987. For instance, he gives extensive coverage to the applications of molecular materials in high-technology devices (e.g. optical communications, laser printers, photocopiers, liquid crystal displays, solar cells, and more). There is also an entirely new chapter on the recently discovered Buckminsterfullerene carbon molecule (C60) and organic non-linear optic materials.

  4. Hydrogen film cooling with incident and swept-shock interactions in a Mach 6.4 nitrogen free stream

    NASA Technical Reports Server (NTRS)

    Olsen, George C.; Nowak, Robert J.

    1995-01-01

    The effectiveness of slot film cooling of a flat plate in a Mach 6.4 flow with and without incident and swept oblique shock interactions was experimentally investigated. Hydrogen was the primary coolant gas, although some tests were conducted using helium as the coolant. Tests were conducted in the Calspan 48-Inch Shock Tunnel with a nitrogen flow field to preclude combustion of the hydrogen coolant gas. A two-dimensional highly instrumented model developed in a previous test series was used. Parameters investigated included coolant mass flow rate, coolant gas, local free-stream Reynolds number, incident oblique shock strength, and a swept oblique shock. Both gases were highly effective coolants in undisturbed flow; however, both incident and swept shocks degraded that effectiveness.

  5. Multiple fault slip triggered above the 2016 Mw 6.4 MeiNong earthquake in Taiwan

    NASA Astrophysics Data System (ADS)

    Huang, Mong-Han; Tung, Hsin; Fielding, Eric J.; Huang, Hsin-Hua; Liang, Cunren; Huang, Chung; Hu, Jyr-Ching

    2016-07-01

    Rapid shortening in convergent mountain belts is often accommodated by slip on faults at multiple levels in upper crust, but no geodetic observation of slip at multiple levels within hours of a moderate earthquake has been shown before. Here we show clear evidence of fault slip within a shallower thrust at 5-10 km depth in SW Taiwan triggered by the 2016 Mw 6.4 MeiNong earthquake at 15-20 km depth. We constrain the primary coseismic fault slip with kinematic modeling of seismic and geodetic measurements and constrain the triggered slip and fault geometry using synthetic aperture radar interferometry. The shallower thrust coincides with a proposed duplex located in a region of high fluid pressure and high interseismic uplift rate, and may be sensitive to stress perturbations. Our results imply that under tectonic conditions such as high-background stress level and high fluid pressure, a moderate lower crustal earthquake can trigger faults at shallower depth.

  6. 30/20 GHz and 6/4 GHz band transponder development for communications satellite CS-3

    NASA Astrophysics Data System (ADS)

    Tanaka, Masayoshi; Nakamura, Makoto; Okamoto, Teruki; Kumazawa, Hiroyuki

    The next phase communications satellite CS-3 will be launched in 1988 as a successor to CS-2. The CS-3 is composed of two 6/4 GHz band and ten 30/20 GHz band transponders and its mission life is seven years. This paper describes the newly developed CS-3 transponder, especially a 4 GHz band 7 watt GaAs FET amplifier, Ka-band frequency single-conversion, a 30 GHz band low noise amplifier, and a 20 GHz band 10 watt TWTA. The introduction of these new technologies contributes significantly to reducing the CS-3 transponder weight and size, and to improving performance characteristics and insuring a long life.

  7. Infrared collision-induced absorption by O2 near 6.4 microm for atmospheric applications: measurements and empirical modeling.

    PubMed

    Thibault, F; Menoux, V; Le Doucen, R; Rosenmann, L; Hartmann, J M; Boulet, C

    1997-01-20

    Accurate measurements of collision-induced absorption by O(2) and O(2)-N(2) mixtures in the fundamental band near 6.4 microm have been made. A Fourier-transform spectrometer was used with a resolution of 0.5 cm(-1). Absorption has been investigated in the 0-20-atm and 193-293 K pressure and temperature ranges, respectively. The current measurements confirm that the broad O(2) continuum carries small features whose attribution is not yet clear. Available experimental data in the 190-360 K temperature range have been used to build a simple, low cost computer, empirical model that is well adapted for computation of atmospheric O(2) absorption. Tests show that it is accurate, contrary to predictions of widely used atmospheric transmission codes.

  8. Crystallization and preliminary X-ray analysis of cryptochrome 3 from Arabidopsis thaliana.

    PubMed

    Pokorny, Richard; Klar, Tobias; Essen, Lars-Oliver; Batschauer, Alfred

    2005-10-01

    Cryptochromes are flavoproteins which serve as blue-light receptors in plants, animals, fungi and prokaryotes and belong to the same protein family as the catalytically active DNA photolyases. Cryptochrome 3 from the plant Arabidopsis thaliana (cry3; 525 amino acids, 60.7 kDa) is a representative of the novel cryDASH subfamily of UV-A/blue-light receptors and has been expressed as a mature FAD-containing protein in Escherichia coli without the signal sequence that directs the protein into plant organelles. The purified cryptochrome was found to be complexed to methenyltetrahydrofolate as an antenna pigment. Crystals of the cryptochrome-antenna pigment complex were obtained by vapour diffusion and display orthorhombic symmetry, with unit-cell parameters a = 76.298, b = 116.782, c = 135.024 A. X-ray diffraction data were collected to 1.9 A resolution using synchrotron radiation. The asymmetric unit comprises a cry3 dimer, the physiological role of which remains to be elucidated.

  9. Crystal clear

    NASA Astrophysics Data System (ADS)

    2012-02-01

    A semiconductor is usually opaque to any light whose photon energy is larger than the semiconductor bandgap. Nature Photonics spoke to Stephen Durbin about how to render GaAs semiconductor crystals transparent using intense X-ray pulses.

  10. 40 CFR 180.437 - Methyl 2-(4-isopropyl-4-methyl-5-oxo-2-imidazolin-2-yl)-p-toluate and methyl 6-(4-isopropyl-4...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...-imidazolin-2-yl)-p-toluate and methyl 6-(4-isopropyl-4-methyl-5-oxo-2-imidazolin-2-yl)-m-toluate; tolerances... Tolerances § 180.437 Methyl 2-(4-isopropyl-4-methyl-5-oxo-2-imidazolin-2-yl)-p-toluate and methyl 6-(4... for the combined residues of the herbicide methyl...

  11. 6-[(4′-Ethoxycarbonyl-[1,1′-biphenyl]-4-yl)oxy]hexanoic acid

    PubMed Central

    López-Velázquez, Delia; Mendoza, Angel

    2013-01-01

    In the title compound, C21H24O5, the dihedral angle between the benzene rings is 19.57 (15)°. In the crystal, the mol­ecular arrangement makes up head-to-head centrosymmetric dimers assembled by pairs of O—H⋯O bonds; this arrangement builds a graph-set ring motif of R 2 2(8). The dimers are linked into a tape running along the b-axis direction through C—H⋯O inter­actions. The packing is further consolidated by C—H⋯π inter­actions, forming layers parallel to (10-2). PMID:24098263

  12. High energy resolution, high angular acceptance crystal monochromator

    DOEpatents

    Alp, E.E.; Mooney, T.M.; Toellner, T.

    1996-06-04

    A 4-bounce dispersive crystal monochromator reduces the bandpass of synchrotron radiation to a 10-50 meV range without sacrificing angular acceptance. The monochromator includes the combination of an asymmetrical channel-cut single crystal of lower order reflection and a symmetrical channel-cut single crystal of higher order reflection in a nested geometric configuration. In the disclosed embodiment, a highly asymmetrically cut ({alpha}=20) outer silicon crystal (4 2 2) with low order reflection is combined with a symmetrically cut inner silicon crystal (10 6 4) with high order reflection to condition a hard x-ray component (5--30 keV) of synchrotron radiation down to the {micro}eV-neV level. Each of the crystals is coupled to the combination of a positioning inchworm and angle encoder via a respective rotation stage for accurate relative positioning of the crystals and precise energy tuning of the monochromator. 7 figs.

  13. High energy resolution, high angular acceptance crystal monochromator

    DOEpatents

    Alp, Ercan E.; Mooney, Timothy M.; Toellner, Thomas

    1996-06-04

    A 4-bounce dispersive crystal monochromator reduces the bandpass of synchrotron radiation to a 10-50 meV range without sacrificing angular acceptance. The monochromator includes the combination of an asymmetrical channel-cut single crystal of lower order reflection and a symmetrical channel-cut single crystal of higher order reflection in a nested geometric configuration. In the disclosed embodiment, a highly asymmetrically cut (.alpha.=20) outer silicon crystal (4 2 2) with low order reflection is combined with a symmetrically cut inner silicon crystal (10 6 4) with high order reflection to condition a hard x-ray component (5-30 keV) of synchrotron radiation down to the .mu.eV-neV level. Each of the crystals is coupled to the combination of a positioning inchworm and angle encoder via a respective rotation stage for accurate relative positioning of the crystals and precise energy tuning of the monochromator.

  14. Assembly and performance of a 6.4 T cryogen-free dynamic nuclear polarization system.

    PubMed

    Kiswandhi, Andhika; Niedbalski, Peter; Parish, Christopher; Wang, Qing; Lumata, Lloyd

    2017-09-01

    We report on the assembly and performance evaluation of a 180-GHz/6.4 T dynamic nuclear polarization (DNP) system based on a cryogen-free superconducting magnet. The DNP system utilizes a variable-field superconducting magnet that can be ramped up to 9 T and equipped with cryocoolers that can cool the sample space with the DNP assembly down to 1.8 K via the Joule-Thomson effect. A homebuilt DNP probe insert with top-tuned nuclear magnetic resonance coil and microwave port was incorporated into the sample space in which the effective sample temperature is approximately 1.9 K when a 180-GHz microwave source is on during DNP operation. (13) C DNP of [1-(13) C] acetate samples doped with trityl OX063 and 4-oxo-TEMPO in this system have resulted in solid-state (13) C polarization levels of 58 ± 3% and 18 ± 2%, respectively. The relatively high (13) C polarization levels achieved in this work have demonstrated that the use of a cryogen-free superconducting magnet for (13) C DNP is feasible and in fact, relatively efficient-a major leap to offset the high cost of liquid helium consumption in DNP experiments. Copyright © 2017 John Wiley & Sons, Ltd.

  15. The 29 July 2014 (Mw 6.4) Southern Veracruz, Mexico Earthquake: Scenary Previous to Its Occurrence.

    NASA Astrophysics Data System (ADS)

    Yamamoto, J.

    2014-12-01

    On 29 July 2014 (10:46 UTC) a magnitude 6.4 (Mw) earthquake occurred at the southern Veracruz, Mexico region. The epicenter was preliminary located at 17.70° N and 95.63° W. It was a normal fault event with the slip on a fault that trend NNW and a focus approximately 117 km below the surface of the Gulf of Mexico costal plane. The earthquake was widely felt through centro and southern Mexico. In Oaxaca City 133 km to the south a person die of a hearth attack. No damages were reported. Most prominent moderate-sized earthquakes occurring in the southern Veracruz region since 1959 has been concentrated along two well defined seismic belts. One belt runs off the coast following nearly its contour. Here the earthquakes are shallow depth and mostly show a reverse fault mechanism. This belt of seismicity begins at the Los Tuxtlas volcanic field. Another seismic belt is located inland 70 km to the west. Here most earthquakes are of intermediate-depth (108-154 km) focus and normal faulting mechanism. The July 2014 earthquake is located near to this second seismic belt. In the present paper we discuss, within the regional geotectonic framework, the location and some aspects of the rupture process of the July 2014 earthquake.

  16. [Active management of labor with cesarean index 6.4% and very good materno-fetal outcome].

    PubMed

    Crespo Ruiz, Eliodoro; Rodríguez Fernández, Jesús Javier

    2002-11-01

    The objective of this study is to reduce the incidence of cesarean section and to evaluate the impact on fetal-maternal morbidity and mortality by strictly following the guidelines of the National Health Office (Secretaria de Salud) at the Hospital of Gynecology and Obstetrics of Garza Garcia in Nuevo Leon, Mexico. A prospective and observational study was made. All the patients who culminated their pregnancy on Saturdays and Sundays between 7:00 and 19:00 hrs, in the period June 2000 to June 2001, were included in this study. The incidence of Cesarean sections and its impact on maternal-fetal morbidity and mortality were observed. A total of 798 patients were included in the study. The total number of newborns was 801. The age average was of 23.4 years (14 years-40 years). Of the 798 patients, 280 (35.1%) presented dystocia at vaginal delivery, 467 patients (58.5%) had an eutocic vaginal delivery and 51 patients (6.4%) went through a Caesarean section. The Apgar scores were: 8 at the first minute and 9 at the fifth minute for 681 neonates (85.01%); and 7/9 for 53 (6.6%). According to the results obtained in the present study we can conclude that the incidence of Cesarean section can be reduced by strictly following the guidelines of the National Health Office without affecting the maternal-fetal morbidity and mortality.

  17. ENHANCEMENT OF THE 6.4 keV LINE IN THE INNER GALACTIC RIDGE: PROTON-INDUCED FLUORESCENCE?

    SciTech Connect

    Nobukawa, K. K.; Nobukawa, M.; Tsuru, T. G.; Tanaka, T.; Koyama, K.; Uchiyama, H.; Torii, K.; Fukui, Y.; Chernyshov, D. O.; Dogiel, V. A.

    2015-07-01

    A common idea for the origin of the Galactic diffuse X-ray emission, particularly that of the iron lines from neutral and highly ionized atoms, is a superposition of many cataclysmic variables and coronally active binaries. In this scenario, the flux should symmetrically distribute between the east and west on the plane with respect to Sagittarius A* because the stellar mass distribution determined by infrared observations is nearly symmetric. This symmetry is confirmed for the highly ionized iron line as well as the continuum emission. However, a clear excess of the neutral iron line in the near east of the Galactic center compared to the near-west side is found. The flux distribution of the excess emission well correlates with the molecular column density. The X-ray spectrum of the excess emission is described by a power-law continuum plus a 6.4 keV line with a large equivalent width of ∼1.3 keV, which is hardly explained by the low-energy electron bombardment scenario. The longitudinal and latitudinal distribution of the excess emission disfavors the X-ray irradiation, either by Sagittarius A* or by nearby X-ray binaries. Then, the low-energy proton bombardment is the most probable origin, although the high-energy density ∼80 eV cm{sup −3} in 0.1–1000 MeV is required and there is no conventional proton source in the vicinity.

  18. Monofunctional angular furocoumarins: sequence specificity in DNA photobinding of 6,4,4'-trimethylangelicin and other angelicins.

    PubMed

    Miolo, G; Dall'Acqua, F; Moustacchi, E; Sage, E

    1989-07-01

    The sequence specificity in the photoreaction (365 nm) of 6,4,4'-trimethylangelicin (TMA) with DNA fragments of the lac I gene of Escherichia coli was studied by using DNA sequencing methodology. In order to map the sites of TMA photoaddition, we took advantage of the (3'-5') exonuclease activity associated with T4 DNA polymerase, which is blocked by bulky adducts, such as furocoumarin photoadducts. A quantitative analysis of the sites of photoaddition is reported. TMA was demonstrated to photoreact with thymine and, to a lower extent, to cytosine. AT-rich sequences and TTT sites in a GC context are the most reactive sites towards TMA whereas TA, AT, CA, AC sites are weaker sites with similar reactivity. Cytosines in alternated CG sequences are also targets of TMA photobinding. We observed a less pronounced sequence specificity of TMA than that of other psoralen derivatives already studied (Sage and Moustacchi, 1987; Boyer et al., 1988). A comparison with other furocoumarins 4,4'-dimethylangelicin (4,4'-DMA), 4'-methylangelicin (4'-MA), angelicin, 4,5',8-trimethylpsoralen (TMP) and 8-methoxypsoralen (8-MOP) is also reported. The role of flanking sequence and consequently of the local conformation at the various sites of photoaddition is discussed. A preferential orientation of the TMA molecule during the intercalation in the dark is suggested. Hot alkali treatment of TMA-modified DNA did not reveal any DNA strand breakage due to photooxidized bases.

  19. Enhancement of the 6.4 keV Line in the Inner Galactic Ridge: Proton-induced Fluorescence?

    NASA Astrophysics Data System (ADS)

    Nobukawa, K. K.; Nobukawa, M.; Uchiyama, H.; Tsuru, T. G.; Torii, K.; Tanaka, T.; Chernyshov, D. O.; Fukui, Y.; Dogiel, V. A.; Koyama, K.

    2015-07-01

    A common idea for the origin of the Galactic diffuse X-ray emission, particularly that of the iron lines from neutral and highly ionized atoms, is a superposition of many cataclysmic variables and coronally active binaries. In this scenario, the flux should symmetrically distribute between the east and west on the plane with respect to Sagittarius A* because the stellar mass distribution determined by infrared observations is nearly symmetric. This symmetry is confirmed for the highly ionized iron line as well as the continuum emission. However, a clear excess of the neutral iron line in the near east of the Galactic center compared to the near-west side is found. The flux distribution of the excess emission well correlates with the molecular column density. The X-ray spectrum of the excess emission is described by a power-law continuum plus a 6.4 keV line with a large equivalent width of ˜1.3 keV, which is hardly explained by the low-energy electron bombardment scenario. The longitudinal and latitudinal distribution of the excess emission disfavors the X-ray irradiation, either by Sagittarius A* or by nearby X-ray binaries. Then, the low-energy proton bombardment is the most probable origin, although the high-energy density ˜80 eV cm-3 in 0.1-1000 MeV is required and there is no conventional proton source in the vicinity.

  20. Post-seismic deformation of the Mw 6.4 Shonbeh earthquake (south western Iran) of April 9th, 2013

    NASA Astrophysics Data System (ADS)

    Fathian Baneh, Aram; Tolomei, Cristiano; Lugari, Alessandro; Trasatti, Elisa; Salvi, Stefano

    2016-04-01

    The study of post-seismic deformation within a region is of high significance to have a better understanding of the kinematic behavior of a seismogenic fault. We perform the Small Baseline Subset (SBAS) method to process a large number of X-Band, COSMO-SkyMed images to measure the post-seismic deformation due to the Shonbeh earthquake (Iran) of 9th April 2013 (Mw 6.4). The meizoseismal zone of the earthquake and following aftershocks' epicenters cover an area in the frontal edge of the Zagros Simply Folded Zone, in the southwest of Iran, between Kaki and Kangan anticlines. Exploiting the available dataset of images from the beginning of 2013 to mid 2014, we observe the concentration of the deformation along at least two NW- striking, southwest-dipping fault segments arranged in right-step pattern and parallel to the trend of the folds. The preliminary InSAR results illustrate the migration of the post-seismic deformation and stress relaxation from the southeastern toward the northwestern fault segments.

  1. Liquid Crystals

    NASA Technical Reports Server (NTRS)

    1990-01-01

    Thermochromic liquid crystals, or TLCs, are a type of liquid crystals that react to changes in temperature by changing color. The Hallcrest/NASA collaboration involved development of a new way to visualize boundary layer transition in flight and in wind tunnel testing of aircraft wing and body surfaces. TLCs offered a new and potentially better method of visualizing the boundary layer transition in flight. Hallcrest provided a liquid crystal formulation technique that afforded great control over the sensitivity of the liquid crystals to varying conditions. Method is of great use to industry, government and universities for aerodynamic and hydrodynamic testing. Company's principal line is temperature indicating devices for industrial use, such as non-destructive testing and flaw detection in electric/electronic systems, medical application, such as diagnostic systems, for retail sale, such as room, refrigerator, baby bath and aquarium thermometers, and for advertising and promotion specials. Additionally, Hallcrest manufactures TLC mixtures for cosmetic applications, and liquid crystal battery tester for Duracell batteries.

  2. 6-(4-Amino-phen-yl)-4-(4-eth-oxy-phen-yl)-2-meth-oxy-nicotinonitrile.

    PubMed

    Suwunwong, Thitipone; Chantrapromma, Suchada; Fun, Hoong-Kun

    2012-09-01

    In the title mol-ecule, C(21)H(19)N(3)O(2), the central pyridine ring makes dihedral angles of 14.46 (9) and 34.67 (8)° with the 4-amino- and 4-eth-oxy-substituted benzene rings, respectively. The eth-oxy group is essentially coplanar with the attached benzene ring [C-O-C-C torsion angle = 178.70 (16)°] as is the meth-oxy group with the pyridine ring [C-O-C-N torsion angle = -3.0 (3)°]. In the crystal, mol-ecules are linked by N-H⋯N hydrogen bonds into chains along [201]. Weak C-H⋯O hydrogen bonds and C-H⋯π inter-actions are also present.

  3. (η5-Penta­methyl­cyclo­penta­dien­yl)(η6-4-phenyl­butan-2-one)ruthenium(II) tetra­phenyl­borate

    PubMed Central

    Loughrey, Bradley T.; Williams, Michael L.; Healy, Peter C.

    2010-01-01

    The title compound, [Ru(C10H15)(C10H12O)][B(C6H5)4], crystallizes as discrete (η5-penta­methyl­cyclo­penta­dien­yl)Ru(η6-4-phenyl­butan-2-one)]+ cations and [BPh4]− anions. In the cation, the non-H atoms of the butan-2-one group are approximately planar (r.m.s. deviation = 0.056 Å) and lie nearly perpendicular to the plane of the phenyl ring with a dihedral angle between the two planes of 69.3 (1)°. No significant C—H⋯O inter­actions are observed between the methyl and phenyl H atoms and the carbonyl O atom. PMID:21589253

  4. A fundamental approach to adhesion: Synthesis, surface analysis, thermodynamics and mechanics. [acid-base properties of titanium 6-4 surfaces

    NASA Technical Reports Server (NTRS)

    Siriwardane, R.; Wightman, J. P.

    1980-01-01

    The acid-base properties of titanium 6-4 plates (low surface area) were investigated after three different pretreatments, namely Turco, phosphate-fluoride and Pasa-Jell. A series of indicators was used and color changes were detected using diffuse reflectance visible spectroscopy. Electron spectroscopy for chemical analysis was used to examine the indicator on the Ti 6-4 surface. Specular reflectance infra-red spectroscopy was used to study the adsorption of stearic acid from cyclohexane solutions on the Ti 6-4 surface.

  5. SYMMETRICAL LASER CRYSTALS.

    DTIC Science & Technology

    CRYSTAL GROWTH , SYMMETRY(CRYSTALLOGRAPHY), LASERS, SYNTHESIS, FERROELECTRIC CRYSTALS , FLUORESCENCE, IMPURITIES, BARIUM COMPOUNDS, ZIRCONATES...STRONTIUM COMPOUNDS, TITANATES, STANNATES, SAMARIUM, MANGANESE, REFRACTORY MATERIALS, OXIDES, SINGLE CRYSTALS .

  6. The 2016 south Alboran earthquake (Mw = 6.4): A reactivation of the Ibero-Maghrebian region?

    NASA Astrophysics Data System (ADS)

    Buforn, E.; Pro, C.; Sanz de Galdeano, C.; Cantavella, J. V.; Cesca, S.; Caldeira, B.; Udías, A.; Mattesini, M.

    2017-08-01

    On 25 January 2016, an earthquake of magnitude Mw = 6.4 occurred at the southern part of the Alboran Sea, between southern Spain and northern Morocco. This shock was preceded by a foreshock (Mw = 5.1) and followed by a long aftershock sequence. Focal mechanism of main shock has been estimated from slip inversion of body waves at teleseismic distances. Solution corresponds to left-lateral strike-slip motion, showing a complex bilateral rupture, formed by two sub-events, with most energy propagating along a plane oriented N30°E plane dipping to the NW. Relocation of larger events of the aftershock series, show two alignments of epicentres in NE-SW and NNE-SSW direction that intersect at the epicentre of the main shock. We have estimated the focal mechanisms of the largest aftershocks from moment tensor inversion at regional distances. We have obtained two families of focal mechanisms corresponding to strike slip for the NNE-SSW alignment and thrusting motion for the NE-SW alignment. Among the faults present in the area the Al Idrisi fault (or fault zone) may be a good candidate for the source of this earthquake. The study of Coulomb Failure Stress shows that it is possible that the 2016 earthquake was triggered by the previous nearby earthquakes of 1994 (Mw = 5.8) and 2004 (Mw = 6.3). The possible seismic reactivation of the central part of the Ibero-Maghrebian region is an open question, but it is clear that the occurrence of the 2016 earthquake confirms that from 1994 the seismicity of central part of IMR is increasing and that focal mechanism of largest earthquakes in this central part correspond to complex ruptures (or zone of fault).

  7. Therapeutic Crystals

    ERIC Educational Resources Information Center

    Bond, Charles S.

    2014-01-01

    Some readers might not fully know what the difference is between crystallography, and the "new age" practice of dangling crystals around the body to capitalise on their healing energy. The latter is often considered to be superstition, while ironically, the former has actually resulted in real rationally-based healing of human diseases…

  8. Optical Crystals

    ERIC Educational Resources Information Center

    Bergsten, Ronald

    1974-01-01

    Discusses the production and structure of a sequence of optical crystals which can serve as one-, two-, and three-dimensional diffraction plates to illustrate diffraction patterns by using light rather than x-rays or particles. Applications to qualitative presentations of Laue theory at the secondary and college levels are recommended. (CC)

  9. Therapeutic Crystals

    ERIC Educational Resources Information Center

    Bond, Charles S.

    2014-01-01

    Some readers might not fully know what the difference is between crystallography, and the "new age" practice of dangling crystals around the body to capitalise on their healing energy. The latter is often considered to be superstition, while ironically, the former has actually resulted in real rationally-based healing of human diseases…

  10. Comparing Crystals

    ERIC Educational Resources Information Center

    Sharp, Janet; Hoiberg, Karen; Chumbley, Scott

    2003-01-01

    This standard lesson on identifying salt and sugar crystals expands into an opportunity for students to develop their observation, questioning, and modeling skills. Although sugar and salt may look similar, students discovered that they looked very different under a magnifying glass and behaved differently when dissolved in water. In addition,…

  11. Optical Crystals

    ERIC Educational Resources Information Center

    Bergsten, Ronald

    1974-01-01

    Discusses the production and structure of a sequence of optical crystals which can serve as one-, two-, and three-dimensional diffraction plates to illustrate diffraction patterns by using light rather than x-rays or particles. Applications to qualitative presentations of Laue theory at the secondary and college levels are recommended. (CC)

  12. Translesion synthesis across the (6-4) photoproduct and its Dewar valence isomer by the Y-family and engineered DNA polymerases.

    PubMed

    Yamamoto, Junpei; Loakes, David; Masutani, Chikahide; Simmyo, Shizu; Urabe, Kumiko; Hanaoka, Fumio; Holliger, Philipp; Iwai, Shigenori

    2008-01-01

    We analyzed the translesion synthesis across the UV-induced lesions, the (6-4) photoproduct and its Dewar valence isomer, by using human DNA polymerases eta and iota in vitro. The primer extension experiments revealed that pol eta tended to incorporate dG opposite the 3' component of both lesions, but the incorporation efficiency for the Dewar isomer was higher than that for the (6-4) photoproduct. On the other hand, pol iota was likely to incorporate dA opposite the 3' components of the (6-4) photoproduct and its Dewar isomer with a similar efficiency. Elongation after the incorporation opposite the UV lesions was not observed for these Y-family polymerases. We further analyzed the bypass ability of an engineered polymerase developed from Thermus DNA polymerase for the amplification of ancient DNA. This polymerase could bypass the Dewar isomer more efficiently than the (6-4) photoproduct.

  13. Measurements of the ultraviolet background at 4.6 < z < 6.4 using the quasar proximity effect

    NASA Astrophysics Data System (ADS)

    Calverley, Alexander P.; Becker, George D.; Haehnelt, Martin G.; Bolton, James S.

    2011-04-01

    We present measurements of the ionizing ultraviolet background (UVB) at z˜ 5-6 using the quasar proximity effect. The 15 quasars in our sample cover the range 4.6 < zq < 6.4, enabling the first proximity-effect measurements of the UVB at z > 5. The metagalactic hydrogen ionization rate, Γbkg, was determined by modelling the combined ionization field from the quasar and the UVB in the proximity zone on a pixel-by-pixel basis. The optical depths in the spectra were corrected for the expected effect of the quasar until the mean flux in the proximity region equalled that in the average Lyα forest, and from this we make a measurement of Γbkg. A number of systematic effects were tested using synthetic spectra. Noise in the flux was found to be the largest source of bias at z˜ 5, while uncertainties in the mean transmitted Lyα flux are responsible for the largest bias at z˜ 6. The impacts of large-scale overdensities and Lyman limit systems on Γbkgwere also investigated, but found to be small at z > 5. We find a decline in Γbkg with redshift, from log(Γbkg) =-12.15 ± 0.16 at z˜ 5 to log(Γbkg) =-12.84 ± 0.18 at z˜ 6 (1σ errors). Compared to UVB measurements at lower redshifts, our measurements suggest a drop of a factor of 5 in the H I photoionization rate between z˜ 4 and 6. The decline of Γbkg appears to be gradual, and we find no evidence for a sudden change in the UVB at any redshift that would indicate a rapid change in the attenuation length of ionizing photons. Combined with recent measurements of the evolution of the mean free path of ionizing photons, our results imply a decline in the emissivity of ionizing photons by roughly a factor of 2 from z˜ 5 to 6, albeit with significant uncertainty due to the measurement errors in both Γbkg and the mean free path. A part of the observations were made at the W. M. Keck Observatory which is operated as a scientific partnership between the California Institute of Technology and the University of

  14. Differential recognition of ultraviolet lesions by RecA protein. Possible mechanism for preferential targeting of SOS mutagenesis to (6-4) dipyrimidine sites

    SciTech Connect

    Rosenberg, M.; Echols, H. )

    1990-11-25

    A knowledge of the biochemical basis for UV-induced mutagenesis requires an understanding of the interaction of SOS-activated proteins with DNA polymerase at the replication-blocking dipyrimidine lesions. We have suggested previously that the presence of RecA in this multiprotein complex might be an important feature of induced mutagenesis because RecA associates preferentially with UV-irradiated double-stranded DNA compared to nonirradiated DNA. Previous work by others has indicated that (6-4) dipyrimidine lesions might be more mutagenic than the more common cyclobutane dimer. We have explored the possibility that RecA associates more efficiently with (6-4) lesions than with cyclobutane lesions. We have found that RecA binds DNA with (6-4) lesions much more efficiently than DNA with solely cyclobutane lesions. The distinction between substrates is probably achieved by differential nucleation of the RecA nucleoprotein filament. To investigate the structural basis for differential binding of RecA, we have estimated the unwinding of duplex DNA introduced by (6-4) and cyclobutane lesions. Our data indicate that (6-4) lesions introduce much greater distortion than cyclobutane dimers. We conclude that RecA probably binds preferentially at sites of (6-4) lesions in DNA and that this localization of RecA might target the mutagenic response more frequently to those sites.

  15. Self-assembly in solvates of 2,4-diamino-6-(4-methyl- phenyl)-1,3,5-triazine and in its molecular adducts with some aliphatic dicarboxylic acids

    NASA Astrophysics Data System (ADS)

    Nandy, Purnendu; Nayak, Amrita; Biswas, Sharmita Nandy; Pedireddi, V. R.

    2016-03-01

    Solid state structures of 2,4-diamino-6-(4-methylphenyl)-1,3,5-triazine, 1, in the form of methanol and dimethylsulfoxide (DMSO) solvates, as well as supramolecular assemblies of 1 with various aliphatic dicarboxylic acids, oxalic (a), malonic (b), succinic (c), glutaric (d) and adipic (e) have been reported. Analysis of the assemblies has been carried out by single crystal X-ray diffraction and thermal methods. Triazine 1 yields anhydrous molecular adducts with acids a-d, upon co-crystallization either from CH3OH and DMSO solvents. However acid e gives anhydrous adduct from DMSO solvent, while it gives a methanol adduct from CH3OH. Structure determination reveals that molecular adducts 1a, 1d and 1e are in a 2:1 ratio of 1 and the corresponding acid. However the ratio is 1:1, in 1b, perhaps due to the involvement of one of the acid groups in the intramolecular hydrogen bonding and in adduct 1c the ratio observed is 3:2. Structural features in all these assemblies have been rationalised in terms of various recognition patterns formed between the acceptor and donor groups. A noteworthy feature is that -COOH groups in acid a establish interaction with 1 through amino groups, while such interactions are observed to be through hetero -N atoms in case of the acids b-e.

  16. Experimental and theoretical studies of (E)-2-(2-hydroxystyryl)-6-(4-methoxybenzoyl)-5-(4-methoxyphenyl)-1,2,4-triazin-3(2H)-one.

    PubMed

    Ceylan, Ümit; Hacıyusufoğlu, Mehmet Emin; Sönmez, Mehmet; Yalçın, Şerife Pınar; Özdemir, Namık

    2015-04-15

    Crystal structure of the title compound, C26H21N3O5, has been synthesized and characterized by FT-IR, (1)H NMR, (13)C NMR and X-ray single crystal determination. The molecular geometry was also calculated by using Gaussian 03 software and structure was optimized by using HF and DFT/B3LYP method with the 6-31G(d) basis sets in ground state. The comparison of the theoretical and experimental geometries of the title compound indicated that the X-ray parameters agree with the theoretically obtained values. It was seen that R(2) value changes from 0.015 to 0.021 Å for bond length and angle. The calculated vibrational frequencies are also in good agreement with the experimental results. The (1)H and (13)C NMR chemical shifts values of (E)-2-(2-hydroxystyryl)-6-(4-methoxybenzoyl)-5-(4-methoxyphenyl)-1,2,4-triazin-3(2H)-one molecule have been calculated by the GIAO method. Besides, molecular electrostatic potential maps (MEP), Mulliken charges and Nonlinear Optical effects (NLO) analysis of the compound have been calculated by the HF and B3LYP/6-31G(d) methods. Copyright © 2015 Elsevier B.V. All rights reserved.

  17. Ionic crystals

    SciTech Connect

    Mahan, G.D.

    1985-03-01

    The theme of the second Petra School of Physics was the optical properties of solids. The author's lectures will discuss the theory of ionic crystals such as the alkali halides. The general topics will include a discussion of: the local electric fields, multipole polarizability, core level spectra, and electron energy levels. The subject of alkali halides is today regarded as unfashionable. They were quite popular years ago, but fashions and fancies in science have moved elsewhere. One should not think they are well understood. The author's impression of this field is that activity stopped, not because the problems were solved, but rather because the workers got tired of not being able to solve them. For example, we still do not have a good theory of crystal structure, since microscopic forces are not well characterized. One concludes that other quantities which depend upon forces, such as the elastic constants, are also not well understood, although theories of them are published all of the time. As another example, we still do not have a good theory of bonding. Here there are two camps: one which regards the bonding as ionic, while the other advocates significant amounts of covalency. Recently we have shown that both the elastic constants, and the amount of covalent bonding, depend significantly upon the higher multipole polarizabilities. In summary, the subject of ionic crystals is a field where there are still many unresolved issues awaiting good research. 21 refs., 5 figs., 4 tabs.

  18. Repair of 254 nm ultraviolet-induced (6-4) photoproducts: monoclonal antibody recognition and differential defects in xeroderma pigmentosum complementation groups A, D, and variant

    SciTech Connect

    Hiramoto, T.; Matsunaga, T.; Ichihashi, M.; Nikaido, O.; Fujiwara, Y.; Mishima, Y. )

    1989-11-01

    Repair kinetics of ultraviolet (UV) light-induced (6-4) photoproducts in xeroderma pigmentosum complementation group A, D, and variant cells were studied by the enzyme-linked immunosorbent assay (ELISA) using a specific monoclonal antibody raised against (6-4) photoproducts, together with unscheduled DNA synthesis (UDS) and loss of T4 endonuclease V-susceptible sites (ESS). Group AXP35KO cells completely failed to repair both ESS (cyclobutane pyrimidine dimers) and antibody-recognizing (6-4) photoproducts until tested 24 h after irradiation, and had 2% early-time UDS. Group DXP43KO cells showed about 10% removal of both (6-4) photoproducts and ESS in 24 h, despite showing a residually higher level of 40% early-time and cumulative UDS. Thus, the results substantiated the extreme UV hypersensitivity of XP group A and D cells. However, XP52KO variant cells exhibited the normal level of UDS and ESS loss, but a slightly reduced repair of antibody-recognizing (6-4) photoproducts at 6 and 12 h after irradiation, which may account for a small UV hypersensitivity of the XP variant cells.

  19. EFFECT OF CYP2A6*4 GENETIC POLYMORPHISMS ON SMOKING BEHAVIORS AND NICOTINE DEPENDENCE IN A GENERAL POPULATION OF JAPANESE MEN.

    PubMed

    Ito, Teruna; Tsuji, Masayoshi; Mori, Yayoi; Kanda, Hideyuki; Hidaka, Tomoo; Kakamu, Takeyasu; Kumagai, Tomohiro; Hayakawa, Takehito; Osaki, Yoneatsu; Fukushima, And Tetsuhito

    2015-01-01

    Nicotine in cigarettes is metabolized primarily by CYP2A6-catalyzed oxidation. The CYP2A6*4 allele, in which CYP2A6 is a homozygous whole-deletion variant, completely lacks enzyme activity. The aim of this study was to examine the effects of CYP2A6*4 genetic polymorphism on smoking behavior and nicotine dependence in a general population of Japanese men. The subjects were 124 healthy Japanese men who gave informed consent to give saliva samples. The survey items included general information, smoking behaviors and nicotine dependence. The polymerase chain reaction restriction fragment length polymorphism method was used to analyze the genetic polymorphisms of CYP2A6. The subjects were classified into two groups: Group W (CYP2A6*4 absence: *1A/*1A, *1A/*1B and *1B/*1B) and Group D (CYP2A6*4 presence: *1B/*4A, *4A/*4A, *1A/*4A or *1B/*4D, and *1A/*4D). We analyzed the differences in the survey items between the two groups. There were no significant differences in smoking behaviors between the two groups. However, Group D tended to have less difficulty in refraining from smoking after waking in the morning compared to Group W (p=0.051). CYP2A6*4 genetic polymorphisms may not strongly affect smoking behavior but may possibly have an effect on nicotine dependence.

  20. Biological Macromolecule Crystallization Database

    National Institute of Standards and Technology Data Gateway

    SRD 21 Biological Macromolecule Crystallization Database (Web, free access)   The Biological Macromolecule Crystallization Database and NASA Archive for Protein Crystal Growth Data (BMCD) contains the conditions reported for the crystallization of proteins and nucleic acids used in X-ray structure determinations and archives the results of microgravity macromolecule crystallization studies.

  1. Temporal and spatial expression of homeotic genes is important for segment-specific neuroblast 6-4 lineage formation in Drosophila.

    PubMed

    Kang, Sun-Young; Kim, Su-Na; Kim, Sang Hee; Jeon, Sang-Hak

    2006-06-30

    Different proliferation of neuroblast 6-4 (NB6-4) in the thorax and abdomen produces segmental specific expression pattern of several neuroblast marker genes. NB6-4 is divided to form four medialmost cell body glia (MM-CBG) per segment in thorax and two MM-CBG per segment in abdomen. As homeotic genes determine the identities of embryonic segments along theA/P axis, we investigated if temporal and specific expression of homeotic genes affects MM-CBG patterns in thorax and abdomen. A Ubx loss-of-function mutation was found to hardly affect MM-CBG formation, whereas abd-A and Abd-B caused the transformation of abdominal MM-CBG to their thoracic counterparts. On the other hand, gain-of-function mutants of Ubx, abd-A and Abd-B genes reduced the number of thoracic MM-CBG, indicating that thoracic MM-CBG resembled abdominal MM-CBG. However, mutations in Polycomb group (PcG) genes, which are negative transregulators of homeotic genes, did not cause the thoracic to abdominal MM-CBG pattern transformation although the number of MM-CBG in a few per-cent of embryos were partially reduced or abnormally patterned. Our results indicate that temporal and spa-tial expression of the homeotic genes is important to determine segmental-specificity of NB6-4 daughter cells along the anterior-posterior (A/P) axis.

  2. Immunological detection of UV induced cyclobutane pyrimidine dimers and (6-4) photoproducts in DNA from reference bacteria and natural aquatic populations.

    PubMed

    Kraft, Stephanie; Stephanie, Kraft; Obst, Ursula; Ursula, Obst; Schwartz, Thomas; Thomas, Schwartz

    2011-03-01

    UV light-caused DNA damage is a widespread field of study. As UV light has the biological effect of inactivating or killing bacteria, it is used for water disinfection. Due to this application, it is important to study the DNA damage efficiencies and regeneration capacities in bacteria after UV irradiation. Two monoclonal antibodies, anti-CPD and anti-(6-4) PP, were applied for an immunoassay of UV-induced DNA modifications. Cyclobutane pyrimidine dimer (CPD) and 6-4 photoproduct (6-4 PP) were detected in the reference bacteria Pseudomonas aeruginosa and Enterococcus faecium, and in natural water communities. The antibody-mediated detection signals increased with the UV doses from 100-400J/m(2). Here, the CPD-specific signals were stronger than the (6-4) PP-specific signals. These immunological results were in accordance with parallel cultivation experiments. All UV-irradiated bacteria showed a reduction of their growth rate depending on UV application by several orders of magnitudes. The immunoassay was also applied to three types of natural aquatic habitats with different cell densities. Besides artificial UV irradiation, it was possible to visualize natural sunlight effects on these natural bacterial communities. Light-dependent and dark repair processes were distinguished using the established immunological assays. The antibody-mediated analyses presented are fast methods to detect UV-induced DNA lesions and repair capacities in selected bacterial species as well as in entire natural mixed populations.

  3. Solid-like and liquid-like behaviour in small benzene clusters. A molecular dynamics simulation of (C 6H 6) 4

    NASA Astrophysics Data System (ADS)

    Del Mistro, G.; Stace, A. J.

    1990-08-01

    Molecular dynamics simulations have been performed on the cluster (C 6H 6) 4 with the individual molecules being treated as rigid rotors. Behaviour characteristic of melting is observed at internal temperatures as low as 80 K. It is concluded that the clusters begin to exhibit liquid-like properties when individual molecules acquire sufficient kinetic energy to execute large-ampli- tude motion.

  4. Crystallization process

    DOEpatents

    Adler, Robert J.; Brown, William R.; Auyang, Lun; Liu, Yin-Chang; Cook, W. Jeffrey

    1986-01-01

    An improved crystallization process is disclosed for separating a crystallizable material and an excluded material which is at least partially excluded from the solid phase of the crystallizable material obtained upon freezing a liquid phase of the materials. The solid phase is more dense than the liquid phase, and it is separated therefrom by relative movement with the formation of a packed bed of solid phase. The packed bed is continuously formed adjacent its lower end and passed from the liquid phase into a countercurrent flow of backwash liquid. The packed bed extends through the level of the backwash liquid to provide a drained bed of solid phase adjacent its upper end which is melted by a condensing vapor.

  5. Modulation of Closed-State Inactivation in Kv2.1/Kv6.4 Heterotetramers as Mechanism for 4-AP Induced Potentiation.

    PubMed

    Stas, Jeroen I; Bocksteins, Elke; Labro, Alain J; Snyders, Dirk J

    2015-01-01

    The voltage-gated K+ (Kv) channel subunits Kv2.1 and Kv2.2 are expressed in almost every tissue. The diversity of Kv2 current is increased by interacting with the electrically silent Kv (KvS) subunits Kv5-Kv6 and Kv8-Kv9, into functional heterotetrameric Kv2/KvS channels. These Kv2/KvS channels possess unique biophysical properties and display a more tissue-specific expression pattern, making them more desirable pharmacological and therapeutic targets. However, little is known about the pharmacological properties of these heterotetrameric complexes. We demonstrate that Kv5.1, Kv8.1 and Kv9.3 currents were inhibited differently by the channel blocker 4-aminopyridine (4-AP) compared to Kv2.1 homotetramers. In contrast, Kv6.4 currents were potentiated by 4-AP while displaying moderately increased affinities for the channel pore blockers quinidine and flecainide. We found that the 4-AP induced potentiation of Kv6.4 currents was caused by modulation of the Kv6.4-mediated closed-state inactivation: suppression by 4-AP of the Kv2.1/Kv6.4 closed-state inactivation recovered a population of Kv2.1/Kv6.4 channels that was inactivated at resting conditions, i.e. at a holding potential of -80 mV. This modulation also resulted in a slower initiation and faster recovery from closed-state inactivation. Using chimeric substitutions between Kv6.4 and Kv9.3 subunits, we demonstrated that the lower half of the S6 domain (S6c) plays a crucial role in the 4-AP induced potentiation. These results demonstrate that KvS subunits modify the pharmacological response of Kv2 subunits when assembled in heterotetramers and illustrate the potential of KvS subunits to provide unique pharmacological properties to the heterotetramers, as is the case for 4-AP on Kv2.1/Kv6.4 channels.

  6. Liquid Crystal Devices.

    ERIC Educational Resources Information Center

    Bradshaw, Madeline J.

    1983-01-01

    The nature of liquid crystals and several important liquid crystal devices are described. Ideas for practical experiments to illustrate the properties of liquid crystals and their operation in devices are also described. (Author/JN)

  7. Liquid Crystal Inquiries.

    ERIC Educational Resources Information Center

    Marroum, Renata-Maria

    1996-01-01

    Discusses the properties and classification of liquid crystals. Presents a simple experiment that illustrates the structure of liquid crystals and the differences between the various phases liquid crystals can assume. (JRH)

  8. EFFECT OF CYP2A6*4 GENETIC POLYMORPHISMS ON SMOKING BEHAVIORS AND NICOTINE DEPENDENCE IN A GENERAL POPULATION OF JAPANESE MEN

    PubMed Central

    ITO, TERUNA; TSUJI, MASAYOSHI; MORI, YAYOI; KANDA, HIDEYUKI; HIDAKA, TOMOO; KAKAMU, TAKEYASU; KUMAGAI, TOMOHIRO; HAYAKAWA, TAKEHITO; OSAKI, YONEATSU; FUKUSHIMA, TETSUHITO

    2015-01-01

    ABSTRACT Objectives: Nicotine in cigarettes is metabolized primarily by CYP2A6-catalyzed oxidation. The CYP2A6*4 allele, in which CYP2A6 is a homozygous whole-deletion variant, completely lacks enzyme activity. The aim of this study was to examine the effects of CYP2A6*4 genetic polymorphism on smoking behavior and nicotine dependence in a general population of Japanese men. Methods: The subjects were 124 healthy Japanese men who gave informed consent to give saliva samples. The survey items included general information, smoking behaviors and nicotine dependence. The polymerase chain reaction restriction fragment length polymorphism method was used to analyze the genetic polymorphisms of CYP2A6. The subjects were classified into two groups: Group W (CYP2A6*4 absence: *1A/*1A, *1A/*1B and *1B/*1B) and Group D (CYP2A6*4 presence: *1B/*4A, *4A/*4A, *1A/*4A or *1B/*4D, and *1A/*4D). We analyzed the differences in the survey items between the two groups. Results: There were no significant differences in smoking behaviors between the two groups. However, Group D tended to have less difficulty in refraining from smoking after waking in the morning compared to Group W (p=0.051). Conclusions: CYP2A6*4 genetic polymorphisms may not strongly affect smoking behavior but may possibly have an effect on nicotine dependence. PMID:26370685

  9. The binuclear dual emitter [Br(CO)3Re(PN)(NP)Re(CO)3Br] (PN): 3-chloro-6-(4-diphenylphosphinyl)butoxypyridazine, a new bridging P,N-bidentate ligand resulting from the ring opening of tetrahydrofuran.

    PubMed

    Saldías, Marianela; Manzur, Jorge; Palacios, Rodrigo E; Gómez, María L; Fuente, Julio De La; Günther, Germán; Pizarro, Nancy; Vega, Andrés

    2017-01-31

    Lithium diphenylphosphide unexpectedly provokes the ring-opening of tetrahydrofuran (THF) and by reaction with 3,6-dichloropyridazine leads to the formation of the ligand 3-chloro-6-(4-diphenylphosphinyl)butoxypyridazine (P⋯N), which was isolated. The reaction of this ligand with the (Re(CO)3(THF)Br)2 dimer yields the novel complex [Br(CO)3Re(μ-3-chloro-6-(4-diphenylphosphinyl)butoxypyridazine)2Re(CO)3Br] (BrRe(P⋯N)(N⋯P)ReBr), which was crystallized in the form of a chloroform solvate, (C46H40Br2Cl2N4O8P2Re2)·(CHCl3). The monoclinic crystal (P21/n) displays a bimetallic cage structure with a symmetry inversion centre in the middle of the rhenium to rhenium line. The molecule shows two oxidation signals occurring at +1.50 V and +1.76 V which were assigned to the Re(I)/Re(II) and Re(II)/Re(III) metal-centered couples, respectively, while signals observed at -1.38 V and -1.68 V were assigned to ligand centered reductions. Experimental and DFT/TDDFT results indicate that the UV-Vis absorption maximum of BrRe(P⋯N)(N⋯P)ReBr occurring near 380 nm displays a metal to ligand charge transfer (MLCT) character, which is consistent with CV results. Upon excitation at this wavelength, a weak emission (Φem < 1 × 10(-3)) is observed around 580 nm (in dichloromethane) which decays with two distinct lifetimes τ1 and τ2 of 24 and 4.7 ns, respectively. The prevalence of non-radiative deactivation pathways is consistent with efficient internal conversion induced by the high conformational flexibility of the P⋯N ligand's long carbon chain. Measurements in a frozen solvent at 77 K, where vibrational deactivation is hindered, show intense emission associated with the (3)MLCT state. These results demonstrate that BrRe(P⋯N)(N⋯P)ReBr preserves the dual emitting nature previously reported for the mononuclear complex RePNBr, with emission associated with and states.

  10. PARAMAGNETIC RELAXATION IN CRYSTALS.

    DTIC Science & Technology

    CRYSTALS, PARAMAGNETIC RESONANCE, RELAXATION TIME , CRYSTAL DEFECTS, QUARTZ, GLASS, STRAIN(MECHANICS), TEMPERATURE, NUCLEAR SPINS, HYDROGEN, CALCIUM COMPOUNDS, FLUORIDES, COLOR CENTERS, PHONONS, OXYGEN.

  11. Using Inorganic Crystals To Grow Protein Crystals

    NASA Technical Reports Server (NTRS)

    Shlichta, Paul J.; Mcpherson, Alexander A.

    1989-01-01

    Solid materials serve as nucleating agents. Protein crystals induced by heterogeneous nucleation and in some cases by epitaxy to grow at lower supersaturations than needed for spontaneous nucleation. Heterogeneous nucleation makes possible to grow large, defect-free single crystals of protein more readily. Such protein crystals benefits research in biochemistry and pharmacology.

  12. Using Inorganic Crystals To Grow Protein Crystals

    NASA Technical Reports Server (NTRS)

    Shlichta, Paul J.; Mcpherson, Alexander A.

    1989-01-01

    Solid materials serve as nucleating agents. Protein crystals induced by heterogeneous nucleation and in some cases by epitaxy to grow at lower supersaturations than needed for spontaneous nucleation. Heterogeneous nucleation makes possible to grow large, defect-free single crystals of protein more readily. Such protein crystals benefits research in biochemistry and pharmacology.

  13. Laser-induced crystallization and crystal growth.

    PubMed

    Sugiyama, Teruki; Masuhara, Hiroshi

    2011-11-04

    Recent streams of laser studies on crystallization and crystal growth are summarized and reviewed. Femtosecond multiphoton excitation of solutions leads to their ablation at the focal point, inducing local bubble formation, shockwave propagation, and convection flow. This phenomenon, called "laser micro tsunami" makes it possible to trigger crystallization of molecules and proteins from their supersaturated solutions. Femtosecond laser ablation of a urea crystal in solution triggers the additional growth of a single daughter crystal. Intense continuous wave (CW) near infrared laser irradiation at the air/solution interface of heavy-water amino acid solutions results in trapping of the clusters and evolves to crystallization. A single crystal is always prepared in a spatially and temporally controlled manner, and the crystal polymorph of glycine depends on laser power, polarization, and solution concentration. Upon irradiation at the glass/solution interface, a millimeter-sized droplet is formed, and a single crystal is formed by shifting the irradiation position to the surface. Directional and selective crystal growth is also possible with laser trapping. Finally, characteristics of laser-induced crystallization and crystal growth are summarized.

  14. [Allelic variants of the CYP2D6: *4, *6 and *10 in a sample of resident from the Aragua state, Venezuela].

    PubMed

    Flores-Angulo, Carlos; Villegas, Cecilia; Mora, Yuselin; Martínez, José Antonio; Oropeza, Teresa; Moreno, Nancy

    2015-10-01

    The aim of this study was to determine the CYP2D6: * 4, * 6 and * 10 gene variants frequency and to predict the metabolizer phenotype in a sample of 145 unrelated apparently healthy individuals residing in the state of Aragua, Venezuela. Genotypes were determined by Polymerase chain reaction assays followed by restriction endonucleases digestion. The metabolizer phenotype prediction was made based on the activity score system. The frequencies of CYP2D6 * 4, * 6 and * 10 allelic variants were 14.5%, 0.3% and 1%. A significant percentage of individuals were categorized as heterozygote-extensive/intermediate (23.5%) and poor metabolizers (4.1%), this information has potential clinical impact, because the CYP2D6 protein is involved in the metabolism of drugs frequently prescribed as: carvedilol, captopril, chloroquine, codeine, fluoxetine, fluvastatin, haloperidol, idarubicin, indinavir, imatinib, loperamide, nifedipine, ondansetron and tamoxifen.

  15. The SAURON project - XX. The Spitzer [3.6] - [4.5] colour in early-type galaxies: colours, colour gradients and inverted scaling relations

    NASA Astrophysics Data System (ADS)

    Peletier, Reynier F.; Kutdemir, Elif; van der Wolk, Guido; Falcón-Barroso, Jesús; Bacon, Roland; Bureau, Martin; Cappellari, Michele; Davies, Roger L.; de Zeeuw, P. Tim; Emsellem, Eric; Krajnović, Davor; Kuntschner, Harald; McDermid, Richard M.; Sarzi, Marc; Scott, Nicholas; Shapiro, Kristen L.; van den Bosch, Remco C. E.; van de Ven, Glenn

    2012-01-01

    We investigate the [3.6]-[4.5] Spitzer-IRAC colour behaviour of the early-type galaxies of the SAURON survey, a representative sample of 48 nearby ellipticals and lenticulars. We investigate how this colour, which is unaffected by dust extinction, can be used to constrain the stellar populations in these galaxies. We find a tight relation between the [3.6]-[4.5] colour and effective velocity dispersion, a good mass indicator in early-type galaxies: ([3.6]-[4.5])e = (-0.109 ? 0.007)?+ (0.154 ? 0.016). Contrary to other colours in the optical and near-infrared, we find that the colours become bluer for larger galaxies. The relations are tighter when using the colour inside re (scatter 0.013 mag), rather than the much smaller re/8 aperture (scatter 0.023 mag), due to the presence of young populations in the central regions. We also obtain strong correlations between the [3.6]-[4.5] colour and three strong absorption lines (H?, Mgb and Fe 5015). Comparing our data with the models of Marigo et al., which show that more metal rich galaxies are bluer, we can explain our results in a way consistent with results from the optical, by stating that larger galaxies are more metal rich. The blueing is caused by a strong CO absorption band, whose line strength increases strongly with decreasing temperature and which covers a considerable fraction of the 4.5-?m filter. In galaxies that contain a compact radio source, the [3.6]-[4.5] colour is generally slightly redder (by 0.015 ? 0.007 mag using the re/8 aperture) than in the other galaxies, indicating small amounts of either hot dust, non-thermal emission, or young stars near the centre. We find that the large majority of the galaxies show redder colours with increasing radius. Removing the regions with evidence for young stellar populations (from the H? absorption line) and interpreting the colour gradients as metallicity gradients, we find that our galaxies are more metal poor going outwards. The radial [3.6]-[4.5] gradients

  16. Molecular tectonics: from crystals to crystals of crystals.

    PubMed

    Marinescu, Gabriela; Ferlay, Sylvie; Kyritsakas, Nathalie; Hosseini, Mir Wais

    2013-12-11

    The in situ combination of M(II) cations (Co, Ni, Cu or Zn) with 2,4,6-pyridinetricarboxylic acid as a ligand, a bisamidinium dication as a H-bond donor tecton and NaOH leads to the formation of anionic metal complexes ML2(2-) and their interconnection into isomorphous 3D H-bonded networks displaying different colours which were used as preformed seed crystals for the formation of crystals of crystals by 3D epitaxial growth.

  17. Strand breakage of a (6-4) photoproduct-containing DNA at neutral pH and its repair by the ERCC1-XPF protein complex.

    PubMed

    Arichi, Norihito; Yamamoto, Junpei; Takahata, Chiaki; Sano, Emi; Masuda, Yuji; Kuraoka, Isao; Iwai, Shigenori

    2013-06-07

    The (6-4) photoproduct is one of the major UV-induced lesions in DNA. We previously showed that hydrolytic ring opening of the 5' base and subsequent hydrolysis of the glycosidic bond of the 3' component occurred when this photoproduct was treated with aqueous NaOH. In this study, we found that another product was obtained when the (6-4) photoproduct was heated at 90 °C for 6 h, in a 0.1 M solution of N,N'-dimethyl-1,2-ethanediamine adjusted to pH 7.4 with acetic acid. An analysis of the chemical structure of this product revealed that the 5' base was intact, whereas the glycosidic bond at the 3' component was hydrolyzed in the same manner. The strand break was detected for a 30-mer oligonucleotide containing the (6-4) photoproduct upon treatment with the above solution or other pH 7.4 solutions containing biogenic amines, such as spermidine and spermine. In the case of spermidine, the rate constant was calculated to be 1.4 × 10(-8) s(-1) at 37 °C. The strand break occurred even when the oligonucleotide was heated at 90 °C in 0.1 M sodium phosphate (pH 7.0), although this treatment produced several types of 5' fragments. The Dewar valence isomer was inert to this reaction. The product obtained from the (6-4) photoproduct-containing 30-mer was used to investigate the enzymatic processing of the 3' end bearing the damaged base and a phosphate. The ERCC1-XPF complex removed several nucleotides containing the damaged base, in the presence of replication protein A.

  18. Crystal structure of bis-(1-ethyl-pyridinium) dioxonium hexa-cyanidoferrate(II).

    PubMed

    Tanaka, Rikako; Matsushita, Nobuyuki

    2017-02-01

    The title compound, (C7H10N)2(H3O)2[Fe(CN)6] or (Etpy)2(H3O)2[Fe(CN)6] (Etpy(+) is 1-ethyl-pyridinium), crystallizes in the space group Pnnm. The Fe(II) atom of the [Fe(CN)6](4-) anion lies on a site with site symmetry ..2/m, and has an octa-hedral coordination sphere defined by six cyanido ligands. Both the Etpy(+) and the oxonium cations are located on a mirror plane. In the crystal, electron-donor anions of [Fe(CN)6](4-) and electron-acceptor cations of Etpy(+) are each stacked parallel to the b axis, resulting in a columnar structure with segregated moieties. The crystal packing is stabilized by a three-dimensional O-H⋯N hydrogen-bonding network between the oxonium ions and the cyanide ligands of [Fe(CN)6](4-).

  19. Inhibition of RNA and DNA synthesis in UV-irradiated normal human fibroblasts is correlated with pyrimidine (6-4) pyrimidone photoproduct formation.

    PubMed

    Petit Frère, C; Clingen, P H; Arlett, C F; Green, M H

    1996-07-05

    UV-irradiation of living cells results in an inhibition of RNA and DNA synthesis. The purpose of this study was to determine whether specific photoproducts or the total combined yield of lesions were responsible for these effects. Asynchronously dividing human fibroblasts from normal donors were irradiated with UVC (254 nm), broad spectrum UVB (290-320 + nm, Westinghouse FS20 lamp) or narrow spectrum UVB (310-315 nm, Philips TL01 lamp) at fluences which induce known yields of cyclobutane pyrimidine dimers, pyrimidine (6-4) pyrimidone photoproducts or Dewar isomers. DNA synthesis was approximately 3-4 times more sensitive to both UVC and UVB irradiation than RNA synthesis. The immediate inhibition of RNA and DNA synthesis was correlated with (6-4) rather than overall photoproduct formation suggesting that the (6-4) photoproduct is the mediator of these inhibitory effects. In support of this suggestion we found that photoreactivation of cells cultured from the marsupial, mouse Sminthopsis crassicaudata, resulted in removal of 70% of pyrimidine dimers from the overall genome, but had only a slight effect on the recovery of RNA synthesis.

  20. THE ORIGIN OF THE 6.4 keV LINE EMISSION AND H{sub 2} IONIZATION IN THE DIFFUSE MOLECULAR GAS OF THE GALACTIC CENTER REGION

    SciTech Connect

    Dogiel, V. A.; Chernyshov, D. O.; Tatischeff, V.; Terrier, R.

    2013-07-10

    We investigate the origin of the diffuse 6.4 keV line emission recently detected by Suzaku and the source of H{sub 2} ionization in the diffuse molecular gas of the Galactic center (GC) region. We show that Fe atoms and H{sub 2} molecules in the diffuse interstellar medium of the GC are not ionized by the same particles. The Fe atoms are most likely ionized by X-ray photons emitted by Sgr A* during a previous period of flaring activity of the supermassive black hole. The measured longitudinal intensity distribution of the diffuse 6.4 keV line emission is best explained if the past activity of Sgr A* lasted at least several hundred years and released a mean 2-100 keV luminosity {approx}> 10{sup 38} erg s{sup -1}. The H{sub 2} molecules of the diffuse gas cannot be ionized by photons from Sgr A*, because soft photons are strongly absorbed in the interstellar gas around the central black hole. The molecular hydrogen in the GC region is most likely ionized by low-energy cosmic rays, probably protons rather than electrons, whose contribution into the diffuse 6.4 keV line emission is negligible.

  1. Respective roles of pyrimidine dimer and pyrimidine (6-4) pyrimidone photoproducts in UV mutagenesis of simian virus 40 DNA in mammalian cells

    SciTech Connect

    Bourre, F.; Benoit, A.; Sarasin, A. )

    1989-11-01

    UV light induces DNA lesions which are mutagenic in mammalian cells. We used simian virus 40 tsB201 (unable to produce viral capsid at the restrictive temperature of 41{degree}C because of a point mutation in the VP1 gene) to analyze the mutagenic potency of the two major UV-induced lesions, pyrimidine dimers (Py-Py) and pyrimidine (6-4) pyrimidones (Py(6-4)Py), which are formed on the same nucleotide sites. The mutagenesis criterion was the reversion toward a wild-type growth phenotype. After UV irradiation (mainly at 254 nm), part of the DNA was treated with the photoreactivating enzyme of Escherichia coli, which monomerizes Py-Py but does not modify the Py(6-4)Py photoproduct. Higher survival and lower mutation frequency rates for the photoreactivated DNA indicated that the two lesions were lethal and mutagenic. The VP1 gene of some mutants was entirely sequenced. The mutation spectra showed that the two lesions did not induce the same mutation hot spots, although some sites were common to both. The induced mutation hot spots were not only correlated with lesion hot spots but seemed partially directed by local DNA structures.

  2. Drilling technique for crystals

    NASA Technical Reports Server (NTRS)

    Hunter, T.; Miyagawa, I.

    1977-01-01

    Hole-drilling technique uses special crystal driller in which drill bit rotates at fixed position at speed of 30 rpm while crystal slowly advances toward drill. Technique has been successfully applied to crystal of Rochell salt, Triglycine sulfate, and N-acetyglycine. Technique limits heat buildup and reduces strain on crystal.

  3. The archaeal cofactor F0 is a light-harvesting antenna chromophore in eukaryotes.

    PubMed

    Glas, Andreas F; Maul, Melanie J; Cryle, Max; Barends, Thomas R M; Schneider, Sabine; Kaya, Emine; Schlichting, Ilme; Carell, Thomas

    2009-07-14

    Archae possess unique biochemical systems quite distinct from the pathways present in eukaryotes and eubacteria. 7,8-Dimethyl-8-hydroxy-5deazaflavin (F(0)) and F(420) are unique deazaflavin-containing coenzyme and methanogenic signature molecules, essential for a variety of biochemical transformations associated with methane biosynthesis and light-dependent DNA repair. The deazaflavin cofactor system functions during methane biosynthesis as a low-potential hydrid shuttle F(420)/F(420)H(2). In DNA photolyase repair proteins, the deazaflavin cofactor is in the deprotonated state active as a light-collecting energy transfer pigment. As such, it converts blue sunlight into energy used by the proteins to drive an essential repair process. Analysis of a eukaryotic (6-4) DNA photolyase from Drosophila melanogaster revealed a binding pocket, which tightly binds F(0). Residues in the pocket activate the cofactor by deprotonation so that light absorption and energy transfer are switched on. The crystal structure of F(0) in complex with the D. melanogaster protein shows the atomic details of F(0) binding and activation, allowing characterization of the residues involved in F(0) activation. The results show that the F(0)/F(420) coenzyme system, so far believed to be strictly limited to the archael kingdom of life, is far more widespread than anticipated. Analysis of a D. melanogaster extract and of a DNA photolyase from the primitive eukaryote Ostreococcus tauri provided direct proof for the presence of the F(0) cofactor also in higher eukaryotes.

  4. Mixed crystal organic scintillators

    DOEpatents

    Zaitseva, Natalia P; Carman, M Leslie; Glenn, Andrew M; Hamel, Sebastien; Hatarik, Robert; Payne, Stephen A; Stoeffl, Wolfgang

    2014-09-16

    A mixed organic crystal according to one embodiment includes a single mixed crystal having two compounds with different bandgap energies, the organic crystal having a physical property of exhibiting a signal response signature for neutrons from a radioactive source, wherein the signal response signature does not include a significantly-delayed luminescence characteristic of neutrons interacting with the organic crystal relative to a luminescence characteristic of gamma rays interacting with the organic crystal. According to one embodiment, an organic crystal includes bibenzyl and stilbene or a stilbene derivative, the organic crystal having a physical property of exhibiting a signal response signature for neutrons from a radioactive source.

  5. CRYSTAL COLLIMATION AT RHIC.

    SciTech Connect

    FLILLER,R.P.,III.DREES,A.GASSNER,D.HAMMONS,L.MCINTYRE,G.PEGGS,S.TRBOJEVIC,D.BIRYUKOV,V.CHESNOKOV,Y.TEREKHOV,V.

    2003-06-19

    Crystal Channeling occurs when an ion enters a crystal with a small angle with respect to the crystal planes. The electrostatic interaction between the incoming ion and the lattice causes the ion to follow the crystal planes. By mechanically bending a crystal, it is possible to use a crystal to deflect ions. One novel use of a bent crystal is to use it to channel beam halo particles into a collimator downstream. By deflecting the halo particles into a collimator with a crystal it may be possible to improve collimation efficiency as compared to a single collimator. A bent crystal is installed in the yellow ring of the Relativistic Heavy Ion Collider (RHIC). In this paper we discuss our experience with the crystal collimator, and compare our results to previous data, simulation, and theoretical prediction.

  6. Pressure cryocooling protein crystals

    DOEpatents

    Kim, Chae Un [Ithaca, NY; Gruner, Sol M [Ithaca, NY

    2011-10-04

    Preparation of cryocooled protein crystal is provided by use of helium pressurizing and cryocooling to obtain cryocooled protein crystal allowing collection of high resolution data and by heavier noble gas (krypton or xenon) binding followed by helium pressurizing and cryocooling to obtain cryocooled protein crystal for collection of high resolution data and SAD phasing simultaneously. The helium pressurizing is carried out on crystal coated to prevent dehydration or on crystal grown in aqueous solution in a capillary.

  7. Ethyl 3-[7-eth-oxy-6-(4-meth-oxy-benzene-sulfonamido)-2H-indazol-2-yl]propano-ate.

    PubMed

    Abbassi, Najat; Oulemda, Bassou; Rakib, El Mostapha; Geffken, Detlef; Zouihri, Hafid

    2012-04-01

    In the title compound, C(21)H(25)N(3)O(6)S, the dihedral angle between the meth-oxy-benzene and indazole rings is 74.96 (5)°. The crystal packing is stabilized by an N-H⋯O hydrogen bond into a two-dimensional network. In addition, C-H⋯π inter-actions and a π-π contact, with a centroid-centroid distance of 3.5333 (6) Å, are observed. The crystal packing is stabilized by N-H⋯O and C-H⋯O hydrogen bonds.

  8. Fully functional global genome repair of (6-4) photoproducts and compromised transcription-coupled repair of cyclobutane pyrimidine dimers in condensed mitotic chromatin

    SciTech Connect

    Komura, Jun-ichiro; Ikehata, Hironobu; Mori, Toshio; Ono, Tetsuya

    2012-03-10

    During mitosis, chromatin is highly condensed, and activities such as transcription and semiconservative replication do not occur. Consequently, the condensed condition of mitotic chromatin is assumed to inhibit DNA metabolism by impeding the access of DNA-transacting proteins. However, about 40 years ago, several researchers observed unscheduled DNA synthesis in UV-irradiated mitotic chromosomes, suggesting the presence of excision repair. We re-examined this subject by directly measuring the removal of UV-induced DNA lesions by an ELISA and by a Southern-based technique in HeLa cells arrested at mitosis. We observed that the removal of (6-4) photoproducts from the overall genome in mitotic cells was as efficient as in interphase cells. This suggests that global genome repair of (6-4) photoproducts is fully functional during mitosis, and that the DNA in mitotic chromatin is accessible to proteins involved in this mode of DNA repair. Nevertheless, not all modes of DNA repair seem fully functional during mitosis. We also observed that the removal of cyclobutane pyrimidine dimers from the dihydrofolate reductase and c-MYC genes in mitotic cells was very slow. This suggests that transcription-coupled repair of cyclobutane pyrimidine dimers is compromised or non-functional during mitosis, which is probably the consequence of mitotic transcriptional repression. -- Highlights: Black-Right-Pointing-Pointer Global genome repair of (6-4) photoproducts is fully active in mitotic cells. Black-Right-Pointing-Pointer DNA in condensed mitotic chromatin does not seem inaccessible or inert. Black-Right-Pointing-Pointer Mitotic transcriptional repression may impair transcription-coupled repair.

  9. Upgrading the flow path of the K-500-6.4/3000 turbine's low-pressure cylinder to increase the turbine power output

    NASA Astrophysics Data System (ADS)

    Davidenko, N. N.; Solomeev, V. A.; Trukhnii, A. D.; Shvetsov, V. L.

    2010-09-01

    Results obtained from upgrading the flow paths of the low-pressure cylinders of OAO Turboatom K-500-6.4/3000 steam turbines installed at the Kursk, Smolensk, and Leningrad nuclear power stations are presented. With the annular area of steam outlet from the last stages increased from 6.3 to 8.19 m2, it became possible to reduce the loss due to outlet velocity by a factor of 1.8 and increase the turbine power output by 16MW, which is equivalent to increasing the power unit efficiency by 3.2%.

  10. Synthesis of N-(6-(4-(Piperazin-1-yl)phenoxy)pyridin-3-yl)benzenesulfonamide Derivatives for the Treatment of Metabolic Syndrome

    PubMed Central

    Bajare, Swapnil; Anthony, Jessy; Nair, Amrutha; Damre, Anagha; B-Rao, Chandrika; Sivaramakrishnan, H.; Wilankar, Chandan; Marita, Rosalind

    2013-01-01

    Metabolic syndrome is a widely prevalent multifactorial disorder associated with an increased risk of cardiovascular disease and type 2 diabetes mellitus. High plasma levels of insulin and glucose due to insulin resistance are a major component of the metabolic disorder. Thiazolidinediones (TZDs) are potent PPARγ ligand and used as insulin sensitizers in the treatment of type 2 diabetes mellitus. They are potent insulin-sensitizing agents but due to adverse effects like hepatotoxicity, a safer alternative of TZDs is highly demanded. Here we report synthesis of N-(6-(4-(piperazin-1-yl)phenoxy)pyridin-3-yl)benzenesulfonamide derivatives as an alternate remedy for insulin resistance. PMID:25374688

  11. CRYSTALLIZATION IN MULTICOMPONENT GLASSES

    SciTech Connect

    KRUGER AA; HRMA PR

    2009-10-08

    In glass processing situations involving glass crystallization, various crystalline forms nucleate, grow, and dissolve, typically in a nonuniform temperature field of molten glass subjected to convection. Nuclear waste glasses are remarkable examples of multicomponent vitrified mixtures involving partial crystallization. In the glass melter, crystals form and dissolve during batch-to-glass conversion, melter processing, and product cooling. Crystals often agglomerate and sink, and they may settle at the melter bottom. Within the body of cooling glass, multiple phases crystallize in a non-uniform time-dependent temperature field. Self-organizing periodic distribution (the Liesegnang effect) is common. Various crystallization phenomena that occur in glass making are reviewed.

  12. Evaluation of the anticonvulsant activity of 6-(4-chlorophenyoxy)-tetrazolo[5,1-a]phthalazine in various experimental seizure models in mice.

    PubMed

    Sun, Xian-Yu; Wei, Cheng-Xi; Deng, Xian-Qing; Sun, Zhi-Gang; Quan, Zhe-Shan

    2010-01-01

    This study investigated the anticonvulsant activity of a new phthalazine tetrazole derivative, QUAN-0808 (6-(4-chlorophenoxy)-tetrazolo[5,1-a]phthalazine), in the mouse maximal electroshock (MES) seizure model. The neurotoxicity of QUAN-0808 was investigated using the rotarod neurotoxicity test in mice. QUAN-0808 exhibited higher activity (median effective dose, ED(50) = 6.8 mg/kg) and lower neurotoxicity (median toxic dose, TD(50) = 456.4 mg/kg), resulting in a higher protective index (PI = 67.1) compared with carbamazepine (PI = 6.4). In addition, QUAN-0808 exhibited significant oral anticonvulsant activity (ED(50) = 24 mg/kg) against MES-induced seizure with low neurotoxicity (TD(50) > 4500 mg/kg) in mice, resulting in a PI value of more than 187.5. QUAN-0808 was also tested in chemically induced animal models of seizure (pentylenetetrazole [PTZ], isoniazid [ISO], thiosemicarbazide [THIO] and 3-mercaptopropionic acid [3-MP]) to further investigate the anticonvulsant activity; QUAN-0808 produced significant anticonvulsant activity against seizures induced by ISO, THIO and 3-MP.

  13. Corrosion behaviour of Al86.0Co7.6Ce6.4 glass forming alloy with different microstructures

    NASA Astrophysics Data System (ADS)

    Li, C. L.; Wang, P.; Sun, S. Q.; Voisey, K. T.; McCartney, D. G.

    2016-10-01

    It has been extensively reported that Al-TM-RE amorphous alloy has excellent mechanical properties and corrosion resistance. In this paper, the corrosion behaviour of an Al86.0Co7.6Ce6.4 glass forming alloy with different microstructures is investigated through electrochemical experiments and microscopy. Results show the effect of microstructure. Laser and electron beam surface melting processes produce rapidly solidified microstructures with different extents of passivation compared to the as-cast alloy. An amorphous surface layer produced by these surface treatments had superior corrosion resistance compared with the crystalline alloy. As-cast and laser treated Al86.0Co7.6Ce6.4 suffered localised corrosion in the Al/Al11Ce3 eutectic region whereas the amorphous material exhibited uniform corrosion. Compared with the electrochemical behaviour of AA2024 and Alclad 2024, the fully amorphous layer prepared by combined laser-electron beam treatment exhibited advantages such as the more negative corrosion potential, the higher pitting potential and the uniform corrosion mechanism, which indicates that this material is a potential anode candidate in the protection of AA2024.

  14. Fully functional global genome repair of (6-4) photoproducts and compromised transcription-coupled repair of cyclobutane pyrimidine dimers in condensed mitotic chromatin.

    PubMed

    Komura, Jun-ichiro; Ikehata, Hironobu; Mori, Toshio; Ono, Tetsuya

    2012-03-10

    During mitosis, chromatin is highly condensed, and activities such as transcription and semiconservative replication do not occur. Consequently, the condensed condition of mitotic chromatin is assumed to inhibit DNA metabolism by impeding the access of DNA-transacting proteins. However, about 40 years ago, several researchers observed unscheduled DNA synthesis in UV-irradiated mitotic chromosomes, suggesting the presence of excision repair. We re-examined this subject by directly measuring the removal of UV-induced DNA lesions by an ELISA and by a Southern-based technique in HeLa cells arrested at mitosis. We observed that the removal of (6-4) photoproducts from the overall genome in mitotic cells was as efficient as in interphase cells. This suggests that global genome repair of (6-4) photoproducts is fully functional during mitosis, and that the DNA in mitotic chromatin is accessible to proteins involved in this mode of DNA repair. Nevertheless, not all modes of DNA repair seem fully functional during mitosis. We also observed that the removal of cyclobutane pyrimidine dimers from the dihydrofolate reductase and c-MYC genes in mitotic cells was very slow. This suggests that transcription-coupled repair of cyclobutane pyrimidine dimers is compromised or non-functional during mitosis, which is probably the consequence of mitotic transcriptional repression.

  15. Origin of anomalous electronic circular dichroism spectrum of RuPt2(tppz)2Cl2(PF6)4 in acetonitrile.

    PubMed

    Yu, Hua-Gen

    2014-07-24

    We report a theoretical study of the structures, energetics, and electronic spectra of the Pt(II)/Ru(II) mixed-metal complex RuPt2(tppz)2Cl2(PF6)4 (tppz = 2,3,5,6-tetra(2-pyridyl)pyrazine) in acetonitrile. The hybrid B3LYP density functional theory and its TDDFT methods were used with a complete basis set (CBS) extrapolation scheme and a conductor polarizable continuum model (C-PCM) for solvation effects. Results showed that the trinuclear complex has four types of stable conformers and/or enantiomers. They are separated by high barriers owing to the repulsive H/H geometrical constraints in tppz. A strong entropy effect was found for the dissociation of RuPt2(tppz)2Cl2(PF6)n in acetonitrile. The UV-visible and emission spectra of the complex were also simulated. They are in good agreement with experiments. In this work we have largely focused on exploring the origin of anomalous electronic circular dichroism (ECD) spectra of the RuPt2(tppz)2Cl2(PF6)4 complex in acetonitrile. As a result, a new mechanism has been proposed together with a clear illustration by using a physical model.

  16. Growth of dopamine crystals

    SciTech Connect

    Patil, Vidya Patki, Mugdha

    2016-05-06

    Many nonlinear optical (NLO) crystals have been identified as potential candidates in optical and electro-optical devices. Use of NLO organic crystals is expected in photonic applications. Hence organic nonlinear optical materials have been intensely investigated due to their potentially high nonlinearities, and rapid response in electro-optic effect compared to inorganic NLO materials. There are many methods to grow organic crystals such as vapor growth method, melt growth method and solution growth method. Out of these methods, solution growth method is useful in providing constraint free crystal. Single crystals of Dopamine have been grown by evaporating the solvents from aqueous solution. Crystals obtained were of the size of orders of mm. The crystal structure of dopamine was determined using XRD technique. Images of crystals were obtained using FEG SEM Quanta Series under high vacuum and low KV.

  17. Apparatus for growing crystals

    NASA Technical Reports Server (NTRS)

    Jasinski, Thomas J. (Inventor); Witt, August F. (Inventor)

    1986-01-01

    An improved apparatus and method for growing crystals from a melt employing a heat pipe, consisting of one or more sections, each section serving to control temperature and thermal gradients in the crystal as it forms inside the pipe.

  18. Crystallization Pathways in Biomineralization

    NASA Astrophysics Data System (ADS)

    Weiner, Steve; Addadi, Lia

    2011-08-01

    A crystallization pathway describes the movement of ions from their source to the final product. Cells are intimately involved in biological crystallization pathways. In many pathways the cells utilize a unique strategy: They temporarily concentrate ions in intracellular membrane-bound vesicles in the form of a highly disordered solid phase. This phase is then transported to the final mineralization site, where it is destabilized and crystallizes. We present four case studies, each of which demonstrates specific aspects of biological crystallization pathways: seawater uptake by foraminifera, calcite spicule formation by sea urchin larvae, goethite formation in the teeth of limpets, and guanine crystal formation in fish skin and spider cuticles. Three representative crystallization pathways are described, and aspects of the different stages of crystallization are discussed. An in-depth understanding of these complex processes can lead to new ideas for synthetic crystallization processes of interest to materials science.

  19. Crystal structure and prediction.

    PubMed

    Thakur, Tejender S; Dubey, Ritesh; Desiraju, Gautam R

    2015-04-01

    The notion of structure is central to the subject of chemistry. This review traces the development of the idea of crystal structure since the time when a crystal structure could be determined from a three-dimensional diffraction pattern and assesses the feasibility of computationally predicting an unknown crystal structure of a given molecule. Crystal structure prediction is of considerable fundamental and applied importance, and its successful execution is by no means a solved problem. The ease of crystal structure determination today has resulted in the availability of large numbers of crystal structures of higher-energy polymorphs and pseudopolymorphs. These structural libraries lead to the concept of a crystal structure landscape. A crystal structure of a compound may accordingly be taken as a data point in such a landscape.

  20. Growth of dopamine crystals

    NASA Astrophysics Data System (ADS)

    Patil, Vidya; Patki, Mugdha

    2016-05-01

    Many nonlinear optical (NLO) crystals have been identified as potential candidates in optical and electro-optical devices. Use of NLO organic crystals is expected in photonic applications. Hence organic nonlinear optical materials have been intensely investigated due to their potentially high nonlinearities, and rapid response in electro-optic effect compared to inorganic NLO materials. There are many methods to grow organic crystals such as vapor growth method, melt growth method and solution growth method. Out of these methods, solution growth method is useful in providing constraint free crystal. Single crystals of Dopamine have been grown by evaporating the solvents from aqueous solution. Crystals obtained were of the size of orders of mm. The crystal structure of dopamine was determined using XRD technique. Images of crystals were obtained using FEG SEM Quanta Series under high vacuum and low KV.

  1. Crystal Structure and Prediction

    NASA Astrophysics Data System (ADS)

    Thakur, Tejender S.; Dubey, Ritesh; Desiraju, Gautam R.

    2015-04-01

    The notion of structure is central to the subject of chemistry. This review traces the development of the idea of crystal structure since the time when a crystal structure could be determined from a three-dimensional diffraction pattern and assesses the feasibility of computationally predicting an unknown crystal structure of a given molecule. Crystal structure prediction is of considerable fundamental and applied importance, and its successful execution is by no means a solved problem. The ease of crystal structure determination today has resulted in the availability of large numbers of crystal structures of higher-energy polymorphs and pseudopolymorphs. These structural libraries lead to the concept of a crystal structure landscape. A crystal structure of a compound may accordingly be taken as a data point in such a landscape.

  2. Microgravity protein crystallization

    PubMed Central

    McPherson, Alexander; DeLucas, Lawrence James

    2015-01-01

    Over the past 20 years a variety of technological advances in X-ray crystallography have shortened the time required to determine the structures of large macromolecules (i.e., proteins and nucleic acids) from several years to several weeks or days. However, one of the remaining challenges is the ability to produce diffraction-quality crystals suitable for a detailed structural analysis. Although the development of automated crystallization systems combined with protein engineering (site-directed mutagenesis to enhance protein solubility and crystallization) have improved crystallization success rates, there remain hundreds of proteins that either cannot be crystallized or yield crystals of insufficient quality to support X-ray structure determination. In an attempt to address this bottleneck, an international group of scientists has explored use of a microgravity environment to crystallize macromolecules. This paper summarizes the history of this international initiative along with a description of some of the flight hardware systems and crystallization results. PMID:28725714

  3. Photonic Crystal Fibers

    DTIC Science & Technology

    2005-12-01

    passive and active versions of each fiber designed under this task. Crystal Fibre shall provide characteristics of the fiber fabricated to include core...passive version of multicore fiber iteration 2. 15. SUBJECT TERMS EOARD, Laser physics, Fibre Lasers, Photonic Crystal, Multicore, Fiber Laser 16...9 00* 0 " CRYSTAL FIBRE INT ODUCTION This report describes the photonic crystal fibers developed under agreement No FA8655-o5-a- 3046. All

  4. CRYSTAL FILTER TEST SET

    DTIC Science & Technology

    CRYSTAL FILTERS, *HIGH FREQUENCY, *RADIOFREQUENCY FILTERS, AMPLIFIERS, ELECTRIC POTENTIAL, FREQUENCY, IMPEDANCE MATCHING , INSTRUMENTATION, RADIOFREQUENCY, RADIOFREQUENCY AMPLIFIERS, TEST EQUIPMENT, TEST METHODS

  5. Apparatus for mounting crystal

    DOEpatents

    Longeway, Paul A.

    1985-01-01

    A thickness monitor useful in deposition or etching reactor systems comprising a crystal-controlled oscillator in which the crystal is deposited or etched to change the frequency of the oscillator. The crystal rests within a thermally conductive metallic housing and arranged to be temperature controlled. Electrode contacts are made to the surface primarily by gravity force such that the crystal is substantially free of stress otherwise induced by high temperature.

  6. Crystallization from Gels

    NASA Astrophysics Data System (ADS)

    Narayana Kalkura, S.; Natarajan, Subramanian

    Among the various crystallization techniques, crystallization in gels has found wide applications in the fields of biomineralization and macromolecular crystallization in addition to crystallizing materials having nonlinear optical, ferroelectric, ferromagnetic, and other properties. Furthermore, by using this method it is possible to grow single crystals with very high perfection that are difficult to grow by other techniques. The gel method of crystallization provides an ideal technique to study crystal deposition diseases, which could lead to better understanding of their etiology. This chapter focuses on crystallization in gels of compounds that are responsible for crystal deposition diseases. The introduction is followed by a description of the various gels used, the mechanism of gelling, and the fascinating phenomenon of Liesegang ring formation, along with various gel growth techniques. The importance and scope of study on crystal deposition diseases and the need for crystal growth experiments using gel media are stressed. The various crystal deposition diseases, viz. (1) urolithiasis, (2) gout or arthritis, (3) cholelithiasis and atherosclerosis, and (4) pancreatitis and details regarding the constituents of the crystal deposits responsible for the pathological mineralization are discussed. Brief accounts of the theories of the formation of urinary stones and gallstones and the role of trace elements in urinary stone formation are also given. The crystallization in gels of (1) the urinary stone constituents, viz. calcium oxalate, calcium phosphates, uric acid, cystine, etc., (2) the constituents of the gallstones, viz. cholesterol, calcium carbonate, etc., (3) the major constituent of the pancreatic calculi, viz., calcium carbonate, and (4) cholic acid, a steroidal hormone are presented. The effect of various organic and inorganic ions, trace elements, and extracts from cereals, herbs, and fruits on the crystallization of major urinary stone and gallstone

  7. Triangular ice crystals

    NASA Astrophysics Data System (ADS)

    Murray, Benjamin; Salzmann, Christoph; Heymsfield, Andrew; Neely, Ryan

    2014-05-01

    We are all familiar with the hexagonal form of snow crystals and it is well established that this shape is derived from the arrangement of water molecules in the crystal lattice. However, crystals with a triangular form are often found in the Earth's atmosphere and the reason for this non-hexagonal shape has remained elusive. Recent laboratory work has shed light on why ice crystals should take on this triangular or three-fold scalene habit. Studies of the crystal structure of ice have shown that ice which initially crystallises can be made of up of hexagonal layers which are interlaced with cubic layers to produce a 'stacking disordered ice'. The degree of stacking disorder can vary from crystals which are dominantly hexagonal with a few cubic stacking faults, through to ice where the cubic and hexagonal sequences are fully randomised. The introduction of stacking disorder to ice crystals reduces the symmetry of the crystal from 6-fold (hexagonal) to 3-fold (triangular); this offers an explanation for the long standing problem of why some atmospheric ice crystals have a triangular habit. We discuss the implications of triangular crystals for halos, radiative properties, and also discuss the implications for our understanding of the nucleation and early stages of ice crystal growth for ice crystals in the atmosphere.

  8. Artistic Crystal Creations

    ERIC Educational Resources Information Center

    Lange, Catherine

    2008-01-01

    In this inquiry-based, integrative art and science activity, Grade 5-8 students use multicolored Epsom salt (magnesium sulfate) crystallizing solutions to reveal beautiful, cylindrical, 3-dimensional, needle-shaped structures. Through observations of the crystal art, students analyze factors that contribute to crystal size and formation, compare…

  9. Food Crystalization and Eggs

    USDA-ARS?s Scientific Manuscript database

    Food Crystalization and Eggs Deana R. Jones, Ph.D. USDA Agricultural Research Service Egg Safety and Quality Research Unit Athens, Georgia, USA Deana.Jones@ars.usda.gov Sugar, salt, lactose, tartaric acid and ice are examples of constituents than can crystallize in foods. Crystallization in a foo...

  10. Annealing macromolecular crystals.

    PubMed

    Hanson, B Leif; Bunick, Gerard J

    2007-01-01

    The process of crystal annealing has been used to improve the quality of diffraction from crystals that would otherwise be discarded for displaying unsatisfactory diffraction after flash cooling. Although techniques and protocols vary, macromolecular crystals are annealed by warming the flash-cooled crystal, then flash cooling it again. To apply macromolecular crystal annealing, a flash-cooled crystal displaying unacceptably high mosaicity or diffraction from ice is removed from the goniometer and immediately placed in cryoprotectant buffer. The crystal is incubated in the buffer at either room temperature or the temperature at which the crystal was grown. After about 3 min, the crystal is remounted in the loop and flash cooled. In situ annealing techniques, where the cold stream is diverted and the crystal allowed to warm on the loop prior to flash cooling, are variations of annealing that appears to work best when large solvent channels are not present in the crystal lattice or the solvent content of the crystal is relatively low.

  11. Artistic Crystal Creations

    ERIC Educational Resources Information Center

    Lange, Catherine

    2008-01-01

    In this inquiry-based, integrative art and science activity, Grade 5-8 students use multicolored Epsom salt (magnesium sulfate) crystallizing solutions to reveal beautiful, cylindrical, 3-dimensional, needle-shaped structures. Through observations of the crystal art, students analyze factors that contribute to crystal size and formation, compare…

  12. Protein Crystal Based Nanomaterials

    NASA Technical Reports Server (NTRS)

    Bell, Jeffrey A.; VanRoey, Patrick

    2001-01-01

    This is the final report on a NASA Grant. It concerns a description of work done, which includes: (1) Protein crystals cross-linked to form fibers; (2) Engineering of protein to favor crystallization; (3) Better knowledge-based potentials for protein-protein contacts; (4) Simulation of protein crystallization.

  13. A 6.4MB duplication of the alpha-synuclein locus causing fronto-temporal dementia and parkinsonism - phenotype-genotype correlations

    PubMed Central

    Kara, Eleanna; Kiely, Aoife P; Proukakis, Christos; Giffin, Nicola; Love, Seth; Hehir, Jason; Rantell, Khadija; Pandraud, Amelie; Hernandez, Dena G; Nacheva, Elizabeth; Pittman, Alan M; Nalls, Mike A; Singleton, Andrew B; Revesz, Tamas; Bhatia, Kailash P; Quinn, Niall; Hardy, John; Holton, Janice L; Houlden, Henry

    2015-01-01

    Importance SNCA locus duplications are associated with variable clinical features and reduced penetrance but the reasons underlying this variability are unknown. Objective 1) To report a novel family carrying a heterozygous 6.4Mb duplication of the SNCA locus with an atypical clinical presentation strongly reminiscent of frontotemporal dementia (FTD) and late-onset pallidopyramidal syndromes. 2) To study phenotype-genotype correlations in SNCA locus duplications. Design, Setting, Participants and Data sources We report the clinical and neuropathologic features of a family carrying a 6.4Mb duplication of the SNCA locus. To identify candidate disease modifiers, we undertake a genetic analysis in the family and conduct statistical analysis on previously published cases carrying SNCA locus duplication using regression modelling with robust standard errors to account for clustering at the family level. Main outcome measures To assess whether length of the SNCA locus duplication influences disease penetrance and severity, and whether extra-duplication factors have a disease-modifying role. Results We identified a large 6.4Mb duplication of the SNCA locus in this family. Neuropathological analysis showed extensive α-synuclein pathology with minimal phospho-tau pathology. Genetic analysis showed an increased burden of PD-related risk factors and the disease-predisposing H1/H1 MAPT haplotype. Statistical analysis of previously published cases suggested that there is a trend towards increasing disease severity and disease penetrance with increasing duplication size. The corresponding odds ratios (95% CI) from the univariate analyses were 1.17 (0.81 to 1.68) and 1.34 (0.78 to 2.31) respectively. Gender was significantly associated with both disease risk and severity; males compared to females had increased disease risk and severity and the corresponding odds ratios (95% CI) from the univariate analyses were 8.36 (1.97 to 35.42) and 5.55 (1.39 to 22.22) respectively

  14. Protein crystallization with paper

    NASA Astrophysics Data System (ADS)

    Matsuoka, Miki; Kakinouchi, Keisuke; Adachi, Hiroaki; Maruyama, Mihoko; Sugiyama, Shigeru; Sano, Satoshi; Yoshikawa, Hiroshi Y.; Takahashi, Yoshinori; Yoshimura, Masashi; Matsumura, Hiroyoshi; Murakami, Satoshi; Inoue, Tsuyoshi; Mori, Yusuke; Takano, Kazufumi

    2016-05-01

    We developed a new protein crystallization method that incorporates paper. A small piece of paper, such as facial tissue or KimWipes, was added to a drop of protein solution in the traditional sitting drop vapor diffusion technique, and protein crystals grew by incorporating paper. By this method, we achieved the growth of protein crystals with reducing osmotic shock. Because the technique is very simple and the materials are easy to obtain, this method will come into wide use for protein crystallization. In the future, it could be applied to nanoliter-scale crystallization screening on a paper sheet such as in inkjet printing.

  15. Improving marginal crystals.

    PubMed

    Carter, Charles W; Riès-Kautt, Madeleine

    2007-01-01

    The physical chemistry of crystal growth can help to identify directions in which to look for improved crystal properties. In this chapter, we summarize how crystal growth depends on parameters that can be controlled experimentally, and relate them to the tools available for optimizing a particular crystal form for crystal shape, volume, and diffraction quality. Our purpose is to sketch the conceptual basis of optimization and to provide sample protocols derived from those foundations. We hope to assist even those who chose not to use systematic methods by enabling them to carry out rudimentary optimization searches armed with a better understanding of how the underlying physical chemistry operates.

  16. Solvent effects on the oxidation (electron transfer) reaction of [Fe(CN) 6] 4- by [Co(NH 3) 5pz] 3+

    NASA Astrophysics Data System (ADS)

    Muriel, F.; Jiménez, R.; López, M.; Prado-Gotor, R.; Sánchez, F.

    2004-03-01

    Solvent effects on the title reaction were studied in different reaction media constituted by water and organic cosolvents (methanol, tert-butyl alcohol, ethyleneglycol and glucose) at 298.2 K. The results are considered in light of the Marcus-Hush approach for electron transfer reactions. Variations of the electron transfer rate constant are shown to be mainly due to changes in the reaction free energy. On the other hand the energies of the MMCT band, corresponding to the optical electron transfer within the ion pair [Fe(CN) 6] 4-/[Co(NH 3) 5pz] 3+, in the different reaction media, have been obtained. The activation free energies of the thermal electron transfer process have been calculated from the band ( Eop) data, and compared with those obtained from the kinetic study. Quantitative agreement is found between the two series of data. This shows the possibility of estimating activation free energies for electron transfer reactions from static (optical) measurements.

  17. A Chandra Observation of the Luminous Northeastern Rim of the Galactic Supernova Remnant W28 (G6.4-0.1)

    NASA Astrophysics Data System (ADS)

    Pannuti, Thomas

    2016-06-01

    We present an analysis of a pointed observation made of the luminous northeastern rim of the Galactic supernova remnant (SNR) W28 (G6.4-0.1) with the Chandra X-ray Observatory. W28 is the archetype for the class of SNRs known as the mixed-morphology SNRs: sources in this class of objects feature a shell-like morphology with a contrasting center-filled X-ray morphology. Almost unique amongst mixed-morphology SNRs, W28 exhibits a luminous northeastern rim which is detected in the X-ray, optical and radio: this rim is also the site of a vigorous interaction between W28 and adjacent molecular clouds, as evidenced by the high concentration of hydroxyl (OH) masers seen at this rim. Our pointed Chandra observation of this rim is the highest angular X-ray observation made of this feature: initial analysis and results will be presented and discussed.

  18. Combined experimental and ab initio study of the electronic structure of narrow-diameter single-wall carbon nanotubes with predominant (6,4),(6,5) chirality

    NASA Astrophysics Data System (ADS)

    de Blauwe, K.; Mowbray, D. J.; Miyata, Y.; Ayala, P.; Shiozawa, H.; Rubio, A.; Hoffmann, P.; Kataura, H.; Pichler, T.

    2010-09-01

    Narrow diameter tubes and especially (6,5) tubes with a diameter of 0.75 nm are currently one of the most studied carbon nanotubes because their unique optical and especially luminescence response makes them exceptionally suited for biomedical applications. Here we report on a detailed analysis of the electronic structure of nanotubes with (6,5) and (6,4) chiralities using a combined experimental and theoretical approach. From high-energy spectroscopy involving x-ray absorption and photoemission spectroscopy the detailed valence- and conduction-band response of these narrow diameter tubes is studied. The observed electronic structure is in sound agreement with state of the art ab initio calculations using density-functional theory.

  19. Design, synthesis and bioevaluation of novel 6-(4-Hydroxypiperidino)naphthalen-2-ol-based potential Selective Estrogen Receptor Modulators for breast cancer.

    PubMed

    Jha, Amitabh; Yadav, Yogesh; Naidu, Ajay B; Rao, V Kameswara; Kumar, Anil; Parmar, Virinder S; MacDonald, William J; Too, Catherine K L; Balzarini, Jan; Barden, Christopher J; Cameron, T Stanley

    2015-03-06

    In a study directed towards development of novel Selective Estrogen Receptor Modulators (SERMs), 1-(4-(2-(dialkylamino)ethoxy)benzyl)-6-(4-hydroxypiperidin-1-yl)-2-naphthol and corresponding aryl methyl ethers were synthesized and bioevaluated against the estrogen-responsive human MCF-7 breast cancer cell line. The phenolic analogs displayed little or no activity, but aryl methyl ether analogs showed significant cytotoxic potency. Also, representative compounds from the aryl methyl ether series showed significant binding and antagonistic activity against ERα. Two representative compounds were also evaluated for in vitro membrane permeability, plasma stability as well as in-vivo toxicity in mice. The compounds displayed well-acceptable drug-like in vitro membrane permeability as well as plasma stability and were well-tolerated in experimental mice at 300 mg/kg dose. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  20. Viscoelastic Response of the Titanium Alloy Ti-6-4: Experimental Identification of Time- and Rate-Dependent Reversible and Irreversible Deformation Regions

    NASA Technical Reports Server (NTRS)

    Lerch, Bradley A.; Arnold, Steven M.

    2014-01-01

    In support of an effort on damage prognosis, the viscoelastic behavior of Ti-6Al-4V (Ti-6-4) was investigated. This report documents the experimental characterization of this titanium alloy. Various uniaxial tests were conducted to low load levels over the temperature range of 20 to 538 C to define tensile, creep, and relaxation behavior. A range of strain rates (6x10(exp -7) to 0.001/s) were used to document rate effects. All tests were designed to include an unloading portion, followed by a hold time at temperature to allow recovery to occur either at zero stress or strain. The titanium alloy was found to exhibit viscoelastic behavior below the "yield" point and over the entire range of temperatures (although at lower temperatures the magnitude is extremely small). These experimental data will be used for future characterization of a viscoelastic model.

  1. The CYP4502D6 *4 and *6 alleles are the molecular genetic markers for drug response: implications in colchicine non-responder FMF patients.

    PubMed

    Yalcıntepe, Sinem; Ozdemır, Ozturk; Sılan, Coskun; Ozen, Filiz; Uludag, Ahmet; Candan, Ferhan; Sılan, Fatma

    2016-06-01

    The cytochrome P450 2D6 (CYP2D6) is a cytochrome P450 enzyme involved in the oxidative biotransformation of the xenobiotics, carcinogens and various clinically important drugs. Patients are evaluated in three sub-groups of extensive (EM), intermediate (IM) and poor metabolizer (PM) phenotypes due to their drug-metabolising ability for the target CYP2D6 gene. Colchicine non-responsive FMF patients were prospectively genotyped for the major CYP2D6 alleles in the current study. Major CYP2D6 alleles of *1, *3, *4, *5, and *6 were genotyped for 30 responsive and 60 non-responsive FMF patients by multiplex PCR-based reverse-hybridization StripAssay and real-time PCR methods. DNA banks isolated from blood-EDTA were retrospectively used in the current patients and results were compared statistically. Increased CYP2D6 *4 and *6 allele frequencies were highly detected in the colchicine non-responsive FMF patients when compared to the responsive group. Results showed the frequencies of major CYP2D6 *1(wild), *3(2637A > delA), *4(G1934A), *5(total gene deletion) and *6(1707T del) alleles in 0.550, 0.042, 0.158, 0.025 and 0.225 for non-responder and 0.880 and 0.120 (CYP2D6*1 and *4) for the responder groups, respectively. Despite small sample size, this study suggests that there is an association between CYP2D6*4 and CYP2D6*6 alleles and drug intoxicants in colchicine non-responder FMF patients.

  2. Valence photoemission spectra of aqueous Fe(2+/3+) and [Fe(CN)6](4-/3-) and their interpretation by DFT calculations.

    PubMed

    Seidel, Robert; Thürmer, Stephan; Moens, Jan; Geerlings, Paul; Blumberger, Jochen; Winter, Bernd

    2011-10-13

    Aqueous solutions of ferrous and ferric iron (Fe(2+/3+)) and of the iron-hexacyano complexes [Fe(CN)(6)](4-/3-) are studied by photoelectron spectroscopy using a liquid microjet in conjunction with synchrotron soft X-rays for ionization. For Fe(2+)(aq) we observe two well-resolved peaks at 7.09 and 9.16 eV electron binding energy (BE) that can be assigned to the iron-hexaaquo complex. For Fe(3+)(aq) we observe only one peak above the highest valence band of liquid water, at 10.08 eV BE. Interpreting the spectra in terms of the one-electron levels of Kohn-Sham density functional theory, we find that the two peaks for Fe(2+)(aq) originate from the energy splitting between the highest occupied β (= minority) spin level (Fe d(t(2g))) and the five highest occupied α (= majority) spin levels (Fe d(t(2g)) and d(e(g))). The peak for Fe(3+)(aq) arises from d-levels that are strongly mixed with the solvent. The spectra of the aqueous hexacyano complexes show a single strong peak at 6.11 and 7.52 eV BE for [Fe(CN)(6)](4-) and [Fe(CN)(6)](3-), respectively, originating from the highest occupied Fe d(t(2g)) levels, and two further peaks at higher BE originating from the cyano ligands. The PE spectra of the reduced aquo and cyano ions are then used to obtain-solely on experimental grounds-values for the reorganization free energy of the oxidized ions. DFT/continuum calculations of this important parameter in the Marcus theory of oxidation reactions are in fairly good agreement with experiment.

  3. Conserved Negative Charges in the N-terminal Tetramerization Domain Mediate Efficient Assembly of Kv2.1 and Kv2.1/Kv6.4 Channels*

    PubMed Central

    Bocksteins, Elke; Labro, Alain J.; Mayeur, Evy; Bruyns, Tine; Timmermans, Jean-Pierre; Adriaensen, Dirk; Snyders, Dirk J.

    2009-01-01

    Voltage-gated potassium (Kv) channels are transmembrane tetramers of individual α-subunits. Eight different Shaker-related Kv subfamilies have been identified in which the tetramerization domain T1, located on the intracellular N terminus, facilitates and controls the assembly of both homo- and heterotetrameric channels. Only the Kv2 α-subunits are able to form heterotetramers with members of the silent Kv subfamilies (Kv5, Kv6, Kv8, and Kv9). The T1 domain contains two subdomains, A and B box, which presumably determine subfamily specificity by preventing incompatible subunits to assemble. In contrast, little is known about the involvement of the A/B linker sequence. Both Kv2 and silent Kv subfamilies contain a fully conserved and negatively charged sequence (CDD) in this linker that is lacking in the other subfamilies. Neutralizing these aspartates in Kv2.1 by mutating them to alanines did not affect the gating properties, but reduced the current density moderately. However, charge reversal arginine substitutions strongly reduced the current density of these homotetrameric mutant Kv2.1 channels and immunocytochemistry confirmed the reduced expression at the plasma membrane. Förster resonance energy transfer measurements using confocal microscopy showed that the latter was not due to impaired trafficking, but to a failure to assemble the tetramer. This was further confirmed with co-immunoprecipitation experiments. The corresponding arginine substitution in Kv6.4 prevented its heterotetrameric interaction with Kv2.1. These results indicate that these aspartates (especially the first one) in the A/B box linker of the T1 domain are required for efficient assembly of both homotetrameric Kv2.1 and heterotetrameric Kv2.1/silent Kv6.4 channels. PMID:19717558

  4. Photonic crystal light source

    DOEpatents

    Fleming, James G [Albuquerque, NM; Lin, Shawn-Yu [Albuquerque, NM; Bur, James A [Corrales, NM

    2004-07-27

    A light source is provided by a photonic crystal having an enhanced photonic density-of-states over a band of frequencies and wherein at least one of the dielectric materials of the photonic crystal has a complex dielectric constant, thereby producing enhanced light emission at the band of frequencies when the photonic crystal is heated. The dielectric material can be a metal, such as tungsten. The spectral properties of the light source can be easily tuned by modification of the photonic crystal structure and materials. The photonic crystal light source can be heated electrically or other heating means. The light source can further include additional photonic crystals that exhibit enhanced light emission at a different band of frequencies to provide for color mixing. The photonic crystal light source may have applications in optical telecommunications, information displays, energy conversion, sensors, and other optical applications.

  5. Protein Crystal Growth

    NASA Technical Reports Server (NTRS)

    2003-01-01

    In order to rapidly and efficiently grow crystals, tools were needed to automatically identify and analyze the growing process of protein crystals. To meet this need, Diversified Scientific, Inc. (DSI), with the support of a Small Business Innovation Research (SBIR) contract from NASA s Marshall Space Flight Center, developed CrystalScore(trademark), the first automated image acquisition, analysis, and archiving system designed specifically for the macromolecular crystal growing community. It offers automated hardware control, image and data archiving, image processing, a searchable database, and surface plotting of experimental data. CrystalScore is currently being used by numerous pharmaceutical companies and academic and nonprofit research centers. DSI, located in Birmingham, Alabama, was awarded the patent Method for acquiring, storing, and analyzing crystal images on March 4, 2003. Another DSI product made possible by Marshall SBIR funding is VaporPro(trademark), a unique, comprehensive system that allows for the automated control of vapor diffusion for crystallization experiments.

  6. Macromolecular Crystallization in Microgravity

    NASA Technical Reports Server (NTRS)

    Snell, Edward H.; Helliwell, John R.

    2004-01-01

    The key concepts that attracted crystal growers, macromolecular or solid state, to microgravity research is that density difference fluid flows and sedimentation of the growing crystals are greatly reduced. Thus, defects and flaws in the crystals can be reduced, even eliminated, and crystal volume can be increased. Macromolecular crystallography differs from the field of crystalline semiconductors. For the latter, crystals are harnessed for their electrical behaviors. A crystal of a biological macromolecule is used instead for diffraction experiments (X-ray or neutron) to determine the three-dimensional structure of the macromolecule. The better the internal order of the crystal of a biological macromolecule then the more molecular structure detail that can be extracted. This structural information that enables an understanding of how the molecule functions. This knowledge is changing the biological and chemical sciences with major potential in understanding disease pathologies. Macromolecular structural crystallography in general is a remarkable field where physics, biology, chemistry, and mathematics meet to enable insight to the basic fundamentals of life. In this review, we examine the use of microgravity as an environment to grow macromolecular crystals. We describe the crystallization procedures used on the ground, how the resulting crystals are studied and the knowledge obtained from those crystals. We address the features desired in an ordered crystal and the techniques used to evaluate those features in detail. We then introduce the microgravity environment, the techniques to access that environment, and the theory and evidence behind the use of microgravity for crystallization experiments. We describe how ground-based laboratory techniques have been adapted to microgravity flights and look at some of the methods used to analyze the resulting data. Several case studies illustrate the physical crystal quality improvements and the macromolecular structural

  7. Macromolecular Crystallization in Microgravity

    NASA Technical Reports Server (NTRS)

    Snell, Edward H.; Helliwell, John R.

    2004-01-01

    The key concepts that attracted crystal growers, macromolecular or solid state, to microgravity research is that density difference fluid flows and sedimentation of the growing crystals are greatly reduced. Thus, defects and flaws in the crystals can be reduced, even eliminated, and crystal volume can be increased. Macromolecular crystallography differs from the field of crystalline semiconductors. For the latter, crystals are harnessed for their electrical behaviors. A crystal of a biological macromolecule is used instead for diffraction experiments (X-ray or neutron) to determine the three-dimensional structure of the macromolecule. The better the internal order of the crystal of a biological macromolecule then the more molecular structure detail that can be extracted. This structural information that enables an understanding of how the molecule functions. This knowledge is changing the biological and chemical sciences with major potential in understanding disease pathologies. Macromolecular structural crystallography in general is a remarkable field where physics, biology, chemistry, and mathematics meet to enable insight to the basic fundamentals of life. In this review, we examine the use of microgravity as an environment to grow macromolecular crystals. We describe the crystallization procedures used on the ground, how the resulting crystals are studied and the knowledge obtained from those crystals. We address the features desired in an ordered crystal and the techniques used to evaluate those features in detail. We then introduce the microgravity environment, the techniques to access that environment, and the theory and evidence behind the use of microgravity for crystallization experiments. We describe how ground-based laboratory techniques have been adapted to microgravity flights and look at some of the methods used to analyze the resulting data. Several case studies illustrate the physical crystal quality improvements and the macromolecular structural

  8. Crystallization and crystal properties of squid rhodopsin

    SciTech Connect

    Murakami, Midori; Kitahara, Rei; Gotoh, Toshiaki; Kouyama, Tsutomu

    2007-06-01

    Truncated rhodopsin from the retina of the squid Todarodes pacificus was extracted and crystallized by the sitting-drop vapour-diffusion method. Hexagonal crystals grown in the presence of octylglucoside and ammonium sulfate diffracted to 2.8 Å resolution. Rhodopsin, a photoreceptor membrane protein in the retina, is a prototypical member of the G-protein-coupled receptor family. In this study, rhodopsin from the retina of the squid Todarodes pacificus was treated with V8 protease to remove the C-terminal extension. Truncated rhodopsin was selectively extracted from the microvillar membranes using alkyl glucoside in the presence of zinc ions and was then crystallized by the sitting-drop vapour-diffusion method. Of the various crystals obtained, hexagonal crystals grown in the presence of octylglucoside and ammonium sulfate diffracted to 2.8 Å resolution. The diffraction data suggested that the crystal belongs to space group P6{sub 2}, with unit-cell parameters a = b = 122.1, c = 158.6 Å. Preliminary crystallographic analysis, together with linear dichroism results, suggested that the rhodopsin dimers are packed in such a manner that their transmembrane helices are aligned nearly parallel to the c axis.

  9. Protein crystal growth

    NASA Technical Reports Server (NTRS)

    2001-01-01

    Atomic force microscopy uses laser technology to reveal a defect, a double-screw dislocation, on the surface of this crystal of canavalin, a major source of dietary protein for humans and domestic animals. When a crystal grows, attachment kinetics and transport kinetics are competing for control of the molecules. As a molecule gets close to the crystal surface, it has to attach properly for the crystal to be usable. NASA has funded investigators to look at those attachment kinetics from a theoretical standpoint and an experimental standpoint. Dr. Alex McPherson of the University of California, Irvine, is one of those investigators. He uses X-ray diffraction and atomic force microscopy in his laboratory to answer some of the many questions about how protein crystals grow. Atomic force microscopy provides a means of looking at how individual molecules are added to the surface of growing protein crystals. This helps McPherson understand the kinetics of protein crystal growth. McPherson asks, How fast do crystals grow? What are the forces involved? Investigators funded by NASA have clearly shown that such factors as the level of supersaturation and the rate of growth all affect the habit [characteristic arrangement of facets] of the crystal and the defects that occur in the crystal.

  10. Protein crystal growth

    NASA Technical Reports Server (NTRS)

    2001-01-01

    Atomic force microscopy uses laser technology to reveal a defect, a double-screw dislocation, on the surface of this crystal of canavalin, a major source of dietary protein for humans and domestic animals. When a crystal grows, attachment kinetics and transport kinetics are competing for control of the molecules. As a molecule gets close to the crystal surface, it has to attach properly for the crystal to be usable. NASA has funded investigators to look at those attachment kinetics from a theoretical standpoint and an experimental standpoint. Dr. Alex McPherson of the University of California, Irvine, is one of those investigators. He uses X-ray diffraction and atomic force microscopy in his laboratory to answer some of the many questions about how protein crystals grow. Atomic force microscopy provides a means of looking at how individual molecules are added to the surface of growing protein crystals. This helps McPherson understand the kinetics of protein crystal growth. McPherson asks, How fast do crystals grow? What are the forces involved? Investigators funded by NASA have clearly shown that such factors as the level of supersaturation and the rate of growth all affect the habit [characteristic arrangement of facets] of the crystal and the defects that occur in the crystal.

  11. (8aS)-7,8,8a,9-Tetra­hydro­thieno[3,2-f]indolizin-6(4H)-one

    PubMed Central

    Švorc, Ľubomír; Vrábel, Viktor; Kožíšek, Jozef; Marchalín, Štefan; Šafář, Peter

    2009-01-01

    In the mol­ecular structure of the title compound, C10H11NOS, the central six-membered ring of the indolizine unit adopts an envelope conformation, the maximum deviations from the mean plane of the ring being 0.533 (2) Å. The fused thieno ring is nearly coplanar [mean deviation = 0.007 (2) Å]. The conformation of the fused oxopyrrolidine ring is close to that of a flat-envelope, with a maximum deviation of 0.339 (3) Å. The crystal structure is stabilized by C—H⋯O hydrogen bonds. PMID:21582436

  12. 4-{2-Meth­oxy-6-[(4-methyl­phen­yl)imino­meth­yl]phen­oxy}phthalonitrile

    PubMed Central

    Yazıcı, Serap; Akkaya, Abdullah; Ağar, Erbil; Şenel, İsmet; Büyükgüngör, Orhan

    2009-01-01

    In the mol­ecule of the title compound, C23H17N3O2, the methoxy­phenyl ring is oriented at dihedral angles of 13.34 (12) and 88.83 (12)° with respect to the methyl­phenyl and phthalonitrile rings, respectively; the dihedral angle between methyl­phenyl and phthalonitrile rings is 89.67 (10)°. In the crystal structure, weak inter­molecular C—H⋯N inter­actions link mol­ecules into chains. A weak C—H⋯π inter­action is also found.. PMID:21583974

  13. Ethyl 6-(4-meth-oxy-phen-yl)-2-oxo-4-phenyl-cyclo-hex-3-ene-carboxyl-ate.

    PubMed

    Fun, Hoong-Kun; Farhadikoutenaei, Abbas; Sarojini, B K; Mohan, B J; Narayana, B

    2012-09-01

    The asymmetric unit of the title compound, C(22)H(22)O(4), consists of two independent mol-ecules (A and B). The cyclo-hexene rings adopt slightly distorted sofa conformations in both mol-ecules. The dihedral angles between the benzene rings are 74.16 (13) and 71.85 (13)° in mol-ecules A and B, respectively. In the crystal, weak C-H⋯O hydrogen bonds link the mol-ecules into a ribbon-like structure along the b axis. Weak C-H⋯π inter-actions are also observed.

  14. Automated macromolecular crystallization screening

    DOEpatents

    Segelke, Brent W.; Rupp, Bernhard; Krupka, Heike I.

    2005-03-01

    An automated macromolecular crystallization screening system wherein a multiplicity of reagent mixes are produced. A multiplicity of analysis plates is produced utilizing the reagent mixes combined with a sample. The analysis plates are incubated to promote growth of crystals. Images of the crystals are made. The images are analyzed with regard to suitability of the crystals for analysis by x-ray crystallography. A design of reagent mixes is produced based upon the expected suitability of the crystals for analysis by x-ray crystallography. A second multiplicity of mixes of the reagent components is produced utilizing the design and a second multiplicity of reagent mixes is used for a second round of automated macromolecular crystallization screening. In one embodiment the multiplicity of reagent mixes are produced by a random selection of reagent components.

  15. Protein crystallization in microgravity.

    PubMed

    Aibara, S; Shibata, K; Morita, Y

    1997-12-01

    A space experiment involving protein crystallization was conducted in a microgravity environment using the space shuttle "Endeavour" of STS-47, on a 9-day mission from September 12th to 20th in 1992. The crystallization was carried out according to a batch method, and 5 proteins were selected as flight samples for crystallization. Two of these proteins: hen egg-white lysozyme and co-amino acid: pyruvate aminotransferase from Pseudomonas sp. F-126, were obtained as single crystals of good diffraction quality. Since 1992 we have carried out several space experiments for protein crystallization aboard space shuttles and the space station MIR. Our experimental results obtained mainly from hen egg-white lysozyme are described below, focusing on the effects of microgravity on protein crystal growth.

  16. Single Crystal Membranes

    NASA Technical Reports Server (NTRS)

    Stormont, R. W.; Morrison, A.

    1974-01-01

    Single crystal a- and c-axis tubes and ribbons of sodium beta-alumina and sodium magnesium beta-alumina were grown from sodium oxide rich melts. Additional experiments grew ribbon crystals containing sodium magnesium beta, beta double prime, beta triple prime, and beta quadruple prime. A high pressure crystal growth chamber, sodium oxide rich melts, and iridium for all surfaces in contact with the melt were combined with the edge-defined, film-fed growth technique to grow the single crystal beta-alumina tubes and ribbons. The crystals were characterized using metallographic and X-ray diffraction techniques, and wet chemical analysis was used to determine the sodium, magnesium, and aluminum content of the grown crystals.

  17. Antarctic stratospheric ice crystals

    NASA Technical Reports Server (NTRS)

    Goodman, J.; Toon, O. B.; Pueschel, R. F.; Snetsinger, K. G.; Verma, S.

    1989-01-01

    Ice crystals were replicated over the Palmer Peninsula at approximately 72 deg S on six occasions during the 1987 Airboirne Antarctic Ozone Experiment. The sampling altitude was between 12.5 and 18.5 km (45-65 thousand ft pressure altitude) with the temperature between 190 and 201 K. The atmosphere was subsaturated with respect to ice in all cases. The collected crystals were predominantly solid and hollow columns. The largest crystals were sampled at lower altitudes where the potential temperature was below 400 K. While the crystals were larger than anticipated, their low concentration results in a total surface area that is less than one tenth of the total aerosol surface area. The large ice crystals may play an important role in the observed stratospheric dehydration processes through sedimentation. Evidence of scavenging of submicron particles further suggests that the ice crystals may be effective in the removal of stratospheric chemicals.

  18. Crystallization of Macromolecules

    PubMed Central

    Friedmann, David; Messick, Troy; Marmorstein, Ronen

    2014-01-01

    X-ray crystallography has evolved into a very powerful tool to determine the three-dimensional structure of macromolecules and macromolecular complexes. The major bottleneck in structure determination by X-ray crystallography is the preparation of suitable crystalline samples. This unit outlines steps for the crystallization of a macromolecule, starting with a purified, homogeneous sample. The first protocols describe preparation of the macromolecular sample (i.e., proteins, nucleic acids, and macromolecular complexes). The preparation and assessment of crystallization trials is then described, along with a protocol for confirming whether the crystals obtained are composed of macromolecule as opposed to a crystallization reagent. Next, the optimization of crystallization conditions is presented. Finally, protocols that facilitate the growth of larger crystals through seeding are described. PMID:18429252

  19. Crystallization of Macromolecules

    PubMed Central

    Friedmann, David; Messick, Troy; Marmorstein, Ronen

    2014-01-01

    X-ray crystallography has evolved into a very powerful tool to determine the three-dimensional structure of macromolecules and macromolecular complexes. The major bottleneck in structure determination by X-ray crystallography is the preparation of suitable crystalline samples. This unit outlines steps for the crystallization of a macromolecule, starting with a purified, homogeneous sample. The first protocols describe preparation of the macromolecular sample (i.e., proteins, nucleic acids, and macromolecular complexes). The preparation and assessment of crystallization trials is then described, along with a protocol for confirming whether the crystals obtained are composed of macromolecule as opposed to a crystallization reagent . Next, the optimization of crystallization conditions is presented. Finally, protocols that facilitate the growth of larger crystals through seeding are described. PMID:22045560

  20. Polyamine Resistance Is Increased by Mutations in a Nitrate Transporter Gene NRT1.3 (AtNPF6.4) in Arabidopsis thaliana

    PubMed Central

    Tong, Wurina; Imai, Akihiro; Tabata, Ryo; Shigenobu, Shuji; Yamaguchi, Katsushi; Yamada, Masashi; Hasebe, Mitsuyasu; Sawa, Shinichiro; Motose, Hiroyasu; Takahashi, Taku

    2016-01-01

    Polyamines are small basic compounds present in all living organisms and act in a variety of biological processes. However, the mechanism of polyamine sensing, signaling and response in relation to other metabolic pathways remains to be fully addressed in plant cells. As one approach, we isolated Arabidopsis mutants that show increased resistance to spermine in terms of chlorosis. We show here that two of the mutants have a point mutation in a nitrate transporter gene of the NRT1/PTR family (NPF), NRT1.3 (AtNPF6.4). These mutants also exhibit increased resistance to putrescine and spermidine while loss-of-function mutants of the two closest homologs of NRT1.3, root-specific NRT1.1 (AtNPF6.3) and petiole-specific NRT1.4 (AtNPF6.2), were shown to have a normal sensitivity to polyamines. When the GUS reporter gene was expressed under the control of the NRT1.3 promoter, GUS staining was observed in leaf mesophyll cells and stem cortex cells but not in the epidermis, suggesting that NRT1.3 specifically functions in parenchymal tissues. We further found that the aerial part of the mutant seedling has normal levels of polyamines but shows reduced uptake of norspermidine compared with the wild type. These results suggest that polyamine transport or metabolism is associated with nitrate transport in the parenchymal tissue of the shoot. PMID:27379127

  1. Effects of 6-(4-chlorophenoxy)-tetrazolo[5,1-a]phthalazine on anticoagulation in mice and the inhibition of experimental thrombosis in rats.

    PubMed

    Yu, Hai-Ling; Zhang, Feng; Lan, Tian; Quan, Zhe-Shan

    2014-12-01

    : Thrombosis is a major complication that could be fatal in acute or chronic cardio-cerebral-vascular diseases. Therefore, the development of novel agents for anticlotting and the prevention of thrombosis and cardiovascular diseases are clinically significant. This study aimed to evaluate the anticoagulant and antithrombotic effects of 6-(4-chlorophenoxy)-tetrazolo[5,1-a]phthalazine (Q808), a new phthalazine tetrazole derivative. Bleeding time, clotting time, and serum calcium ion (Ca) concentration were assessed in mice, whereas arteriovenous thrombus weight and plasma prothrombin time were evaluated in rats, and platelets Ca influx was determined in rabbit. Daily oral administration of Q808 at 25, 50, or 100 mg/kg for 3 days significantly delayed bleeding time and clotting time in mice compared with controls. Q808 administration at 50 mg/kg significantly reduced experimental thrombus weight by 62.6% and delayed plasma prothrombin time by 58.7% in rats, whereas 50 and 100 mg/kg of Q808 daily significantly increased serum Ca concentration in mice. Q808 at 0.2, 0.4, and 0.8 mg/mL significantly inhibited thrombin-induced Ca influx in rabbit platelets. Our results suggest that Q808 at 25-200 mg/kg daily exerts anticoagulant and antithrombotic effects, and its mechanisms of action may involve both the intrinsic and extrinsic coagulation pathways that inhibit certain coagulation factors and platelet functions.

  2. A Comparative Study of Source Complexity of Two Moderate-Sized Earthquakes in Southern Taiwan: 2016 Mw6.4 and 2010 Mw6.2 Earthquakes

    NASA Astrophysics Data System (ADS)

    Zhao, Xu; Hao, Jinlai; Liu, Jie; Yao, Zhenxing

    2017-07-01

    We study the complex rupture history of the 2016 Mw6.4 Meinong earthquake and the 2010 Mw6.2 Jiaxian earthquake in southern Taiwan by simultaneously inverting near-field strong-motion records, local and teleseismic broadband waveforms along with long-period surface waves. The focal mechanism results reveal that both earthquakes may rupture two different blind faults. The rupture of the 2016 event is dominated by the strike-slip motion with minor thrust faulting, while the 2010 event is a relatively high-angle thrust earthquake. Our preferred finite-fault source models suggest that the coseismic rupture history of the 2016 event should be relatively more complex than the 2010 event. During the 2016 event, two main patches of slip characterize the coseismic slip history. The cumulative seismic moment within 12 s of rupture is about 5.36 × 1018 N m, which is 1.9 times of the moment of the 2010 event. The slip of the 2016 event is associated with relatively larger perk slip of 0.7 m at shallower depth ( 18-19 km), higher average slip of 0.3 m and faster slip rate with the maximum value of 3.4 m/s. Our kinematic models can shed some light on the cause of the difference in seismic hazard between these two earthquakes, and will be further applied to analyze the deep blind fault structure in southern Taiwan.

  3. Conformational flexibility and base-pairing tendency of the tobacco carcinogen O6-[4-oxo-4-(3-pyridyl)butyl]guanine.

    PubMed

    Wilson, Katie A; Szemethy, Kariann G; Wetmore, Stacey D

    2017-09-01

    The present work uses DFT calculations to characterize the conformational and hydrogen-bonding properties of O6-[4-oxo-4-(3-pyridyl)butyl]guanine (POB-G), a DNA adduct caused by tobacco. POB-G is found to adopt many isoenergetic conformations that allow for discrete interactions between the bulky moiety and the adducted G and/or pairing base. The calculated structure and stability of the hydrogen-bonded pairs between the Watson-Crick or Hoogsteen face of POB-G and the canonical DNA nucleobases fully rationalize the previously reported mutational spectra. Specifically, the stable, non-distorted pseudo-Watson-Crick POB-G:T pair explains the predominant G➔A mutations, while the stable, yet marginally distorted pairs between the Watson-Crick face of POB-G and A or C clarify the G➔T mutations and non-mutagenic replication. Finally, the stable, yet highly distorted Hoogsteen POB-G:G pair rationalizes the experimentally-observed insertion but lack of persistence of G opposite POB-G in DNA. Overall, these structural insights are critical for guiding future studies that strive to fully understand the adduct mutagenicity, including the accessible conformations and the replication of POB-G-adducted DNA. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Synthesis of polypyrrole within the cell wall of yeast by redox-cycling of [Fe(CN)6](3-)/[Fe(CN)6](4-).

    PubMed

    Ramanavicius, Arunas; Andriukonis, Eivydas; Stirke, Arunas; Mikoliunaite, Lina; Balevicius, Zigmas; Ramanaviciene, Almira

    2016-02-01

    Yeast cells are often used as a model system in various experiments. Moreover, due to their high metabolic activity, yeast cells have a potential to be applied as elements in the design of biofuel cells and biosensors. However a wider application of yeast cells in electrochemical systems is limited due to high electric resistance of their cell wall. In order to reduce this problem we have polymerized conducting polymer polypyrrole (Ppy) directly in the cell wall and/or within periplasmic membrane. In this research the formation of Ppy was induced by [Fe(CN)6](3-)ions, which were generated from K4[Fe(CN)6], which was initially added to polymerization solution. The redox process was catalyzed by oxido-reductases, which are present in the plasma membrane of yeast cells. The formation of Ppy was confirmed by spectrophotometry and atomic force microscopy. It was confirmed that the conducting polymer polypyrrole was formed within periplasmic space and/or within the cell wall of yeast cells, which were incubated in solution containing pyrrole, glucose and [Fe(CN)6](4-). After 24h drying at room temperature we have observed that Ppy-modified yeast cell walls retained their initial spherical form. In contrast to Ppy-modified cells, the walls of unmodified yeast have wrinkled after 24h drying. The viability of yeast cells in the presence of different pyrrole concentrations has been evaluated. Copyright © 2015 Elsevier Inc. All rights reserved.

  5. The 26 May 2006 magnitude 6.4 Yogyakarta earthquake south of Mt. Merapi volcano: Did lahar deposits amplify ground shaking and thus lead to the disaster?

    NASA Astrophysics Data System (ADS)

    Walter, T. R.; Wang, R.; Luehr, B.-G.; Wassermann, J.; Behr, Y.; Parolai, S.; Anggraini, A.; Günther, E.; Sobiesiak, M.; Grosser, H.; Wetzel, H.-U.; Milkereit, C.; Sri Brotopuspito, P. J. K.; Harjadi, P.; Zschau, J.

    2008-05-01

    Indonesia is repeatedly unsettled by severe volcano- and earthquake-related disasters, which are geologically coupled to the 5-7 cm/a tectonic convergence of the Australian plate beneath the Sunda Plate. On Saturday, 26 May 2006, the southern coast of central Java was struck by an earthquake at 2254 UTC in the Sultanate Yogyakarta. Although the magnitude reached only M w = 6.4, it left more than 6,000 fatalities and up to 1,000,000 homeless. The main disaster area was south of Mt. Merapi Volcano, located within a narrow topographic and structural depression along the Opak River. The earthquake disaster area within the depression is underlain by thick volcaniclastic deposits commonly derived in the form of lahars from Mt. Merapi Volcano, which had a major influence leading to the disaster. In order to more precisely understand this earthquake and its consequences, a 3-month aftershock measurement campaign was performed from May to August 2006. We here present the first location results, which suggest that the Yogyakarta earthquake occurred at 10-20 km distance east of the disaster area, outside of the topographic depression. Using simple model calculations taking material heterogeneity into account we illustrate how soft volcaniclastic deposits may locally amplify ground shaking at distance. As the high degree of observed damage may have been augmented by the seismic response of the volcaniclastic Mt. Merapi deposits, this work implies that the volcano had an indirect effect on the level of earthquake destruction.

  6. 6-(4-Amino-2-butyl-imidazoquinolyl)-norleucine: Toll-like receptor 7 and 8 agonist amino acid for self-adjuvanting peptide vaccine.

    PubMed

    Fujita, Yoshio; Hirai, Kazuyuki; Nishida, Keigo; Taguchi, Hiroaki

    2016-05-01

    Generally, small peptides by themselves are weak to induce antibody responses. Toll-like receptor (TLR) ligands are attractive candidates of vaccine adjuvants to improve their antigenicity. The covalent conjugation of TLR ligands with antigens to produce self-adjuvanting peptide vaccine is a promising approach. Based on the structure of TLR7/8 ligands, a series of synthetic amino acids 6-imidazoquinolyl-norleucines were synthesized, wherein an imidazoquinoline structure as the TLR7/8 agonistic pharmacophores was constructed on the ε-NH2 group of Lys. Of them, 6-(4-amino-2-butyl-imidazoquinolyl)-norleucine showed the most potent TLR7 and TLR8 agonistic activities with EC50 values of 8.55 and 106 μM, respectively. Subsequently, mice were immunized with the influenza A virus M2e antigen mixed with or covalently conjugated to the TLR7/8 agonist amino acid, which led to induction of M2e specific antibody productions in the absence of other adjuvant. We successfully developed a novel efficient tool for self-adjuvanting peptide vaccines targeting TLR7/8.

  7. High-elevation paleoenvironmental change during MIS 6-4 in the central Rockies of Colorado as determined from pollen analysis

    NASA Astrophysics Data System (ADS)

    Anderson, R. Scott; Jiménez-Moreno, Gonzalo; Ager, Thomas; Porinchu, David F.

    2014-11-01

    Paleoecological studies from Rocky Mountain (USA) high elevations encompassing the previous interglacial (MIS 5e) are rare. The ~ 10-m composite profile from the Ziegler Reservoir fossil site (2705 m asl) of central Colorado allows us to determine paleoenvironments from Marine Oxygen Isotope Stages (MIS) 6- 4 using pollen zones that are approximately equivalent to marine oxygen isotope stages. During Pollen Zone (PZ) 6 time, pollen assemblages dominated by Artemisia (sagebrush) suggest that alpine tundra or steppe occurred nearby. The transition to PZ 5e was characterized by a rapid increase in tree pollen, initially Picea (spruce) and Pinus (pine) but also Quercus (oak) and Pseudotsuga menziesii (Douglas-fir). Non-arboreal pollen (NAP) types increased during PZ 5d, while Abies (fir) and Juniperus (juniper) increased during PZ 5c. Pollen evidence suggests that temperatures during PZ 5b were as cold as during PZ 6, with the site again surrounded by alpine tundra. Picea dominated during PZ 5a before the onset of cooler conditions during PZ 4. The MIS 6-MIS 5e transition here was similar to the MIS 2-MIS 1 transition at other Rocky Mountain sites. However, the Ziegler Reservoir pollen record contains evidence suggesting unexpected climatic trends at this site, including a warmer-than-expected MIS 5d and cooler-than-expected MIS 5b.

  8. Two saturable recognition sites for (-) (125I)iodo-N6-(4-hydroxyphenyl-isopropyl)-adenosine binding on purified cardiac sarcolemma

    SciTech Connect

    Hausleithner, V.; Freissmuth, M.; Schuetz, W.

    1986-01-01

    Analysis of (-) (125)iodo-N6-(4-hydroxyphenylisopropyl)-adenosine (( /sup 125/I)HPIA) binding to purified sarcolemmal preparations of guinea pig and bovine hearts revealed two classes of binding sites when unlabeled iodo-HPIA (100 mumol/l) was used as non-specific binding marker. In the presence of 1 mmol/l theophylline, however, only the high affinity component was detected. Adenosine receptor agonists caused biphasic displacement of (/sup 125/I)HPIA binding, with a high affinity potency rank order typical of interaction with A1-adenosine receptors. Biphasic competition curves were also observed with 8-phenyltheophylline and isobutylmethylxanthine, whereas the theophylline curve was monophasic up to 1 mmol/l. In brain membranes, specific binding of (/sup 125/I)HPIA as well as of (/sup 3/H)PIA was further reduced when unlabeled iodo-HPIA replaces theophylline as the non-specific binding marker. These results suggest the presence of two (/sup 125/I)HPIA binding sites on cardiac sarcolemma and brain membranes, but receptor function can only be ascribed to the high affinity sites. The low affinity site probably represents an artefact, which is often observed when non-specific binding is defined with the unlabeled counterpart or a structurally related ligand of the radioligand used.

  9. Formation of cyclobutane dimers and (6-4) photoproducts upon far-UV photolysis of 5-methylcytosine-containing dinucleotide monophosphates.

    PubMed

    Douki, T; Cadet, J

    1994-10-04

    The far-UV photochemistry of 5-methylcytosine, a minor DNA base, was studied in three dinucleoside monophosphates, including m5dCpT, Tpm5dC, and m5dCpdC. The model compounds were exposed to 254-nm radiation, and the resulting photoproducts were isolated by reverse-phase HPLC and characterized as cyclobutane dimers, (6-4) adducts, and the related Dewar valence isomers by UV, mass, and 1H NMR spectroscopies. The rate of formation of the different photoproducts was compared with those obtained by photolysis of TpT and the corresponding cytosine dinucleoside monophosphates, including dCpT, TpdC, and dCpdC. The formation of deaminated m5dC-containing photoproducts was observed in each of the far-UV irradiated solution of m5dCpT, Tpm5dC, and m5dCpdC. They were shown to be generated mainly through a photochemical process since methylation of the C5 atom of the cytosine ring appeared to dramatically decrease the deamination rate of the C5-C6 saturated photoproducts.

  10. Blind thrust rupture of the 2015 Mw 6.4 Pishan earthquake in the Northwest Tibetan Plateau by joint inversion of InSAR and seismic data

    NASA Astrophysics Data System (ADS)

    Zhang, Guohong; Shan, Xinjian; Zhang, Yingfeng; Hetland, Eric; Qu, Chunyan; Feng, Guangcai

    2016-12-01

    The July 3rd, 2015 Pishan, China Mw 6.4 earthquake occurred within the Hetian fold belt, a frontal thrust region between the Northwestern Tibetan Plateau and the Tarim basin. We investigate the fault geometry and the rupture process of the Pishan earthquake based on joint inversion of teleseismic body waves and InSAR measurements. Our results show that the top of the fault that ruptured in the Pishan earthquake is buried 5 ± 2 km beneath the surface and that the earthquake ruptured only a segment of a deeply-seated detachment lying under the Hetian fold belt. Our inferred coseismic slip model shows two slip asperities, located in the depth range of about 7-9 km and 10-11 km. Additionally, we resolve a slip deficit region between the slip asperities, which might indicate friction heterogeneity on the fault plane. The earthquake ruptured for ∼15 s, releasing a total seismic moment of 4.7 × 1018 N m. We also show that the latest Pishan earthquake caused positive Coulomb stress changes on back thrust faults, potentially decreasing the time to the next earthquake on those faults. Based on our Pishan coseismic slip model, along with both the trend of the anticline system and the pattern of coseismic deformation, we envision an ongoing east-west extensional growth of the anticlines in the Western Kunlun frontal thrust region in addition to the northern underthrusting of the Northwestern Tibetan Plateau below the Tarim basin.

  11. Construction and 13C NMR signal-amplification efficiency of a dynamic nuclear polarizer at 6.4 T and 1.4 K

    NASA Astrophysics Data System (ADS)

    Kiswandhi, Andhika; Niedbalski, Peter; Parish, Christopher; Ferguson, Sarah; Taylor, David; McDonald, George; Lumata, Lloyd

    Dissolution dynamic nuclear polarization (DNP) is a rapidly emerging technique in biomedical and metabolic imaging since it amplifies the liquid-state nuclear magnetic resonance (NMR) and imaging (MRI) signals by >10,000-fold. Originally used in nuclear scattering experiments, DNP works by creating a non-Boltzmann nuclear spin distribution by transferring the high electron (γ = 28,000 MHz/T) thermal polarization to the nuclear spins via microwave irradiation of the sample at high magnetic field and low temperature. A dissolution device is used to rapidly dissolve the frozen sample and consequently produces an injectable ``hyperpolarized'' liquid at physiologically-tolerable temperature. Here we report the construction and performance evaluation of a dissolution DNP hyperpolarizer at 6.4 T and 1.4 K using a continuous-flow cryostat. The solid and liquid-state 13C NMR signal enhancement levels of 13C acetate samples doped with trityl OX063 and 4-oxo-TEMPO free radicals will be discussed and compared with the results from the 3.35 T commercial hyperpolarizer. This work is supported by US Dept of Defense Award No. W81XWH-14-1-0048 and Robert A. Welch Foundation Grant No. AT-1877.

  12. The Microstructure Evolution and Processing Map of Ni-18.3Cr-6.4Co-5.9W-4Mo Superalloy During Hot Deformation

    NASA Astrophysics Data System (ADS)

    Qin, Shengxue; Liu, Jie; Zhang, Hongbin; Zhang, Kaifeng

    2016-06-01

    The processing map and microstructure evolution of Ni-18.3Cr-6.4Co-5.9W-4Mo superalloy were investigated in the temperature range of 1010-1160 °C and strain rate range of 0.001-1 s-1 by means of hot compression tests. According to the processing map, the optimum processing parameters were located in the temperature range of 1100-1160 °C and strain rate range of 0.01-0.3 s-1. The carbides in the alloy contributed to form a fine grain microstructure. In addition, four different instability criteria of Prasad, Gegel, Malas, and Murty were used to predict the unstable domains in the processing map. Meanwhile, the microstructure observations revealed that the unstable domain predicted by Murty's instability criterion was very effective at high strain rate, which was the best choice for the studied alloy. Furthermore, the electron backscattered diffraction technique was used to detect the Σ3 boundaries and the adiabatic shear bands in the alloy. The results revealed that the fractions of Σ3 boundaries in the alloy deformed at 1100 °C/0.01 s-1 and 1160 °C/0.1 s-1 reached about 25 and 27%, respectively. Meanwhile, the fraction of low-angle grain boundaries and dislocation density were relatively high in the adiabatic shear band.

  13. Liquid Crystal Optofluidics

    SciTech Connect

    Vasdekis, Andreas E.; Cuennet, J. G.; Psaltis, D.

    2012-10-11

    By employing anisotropic fluids and namely liquid crystals, fluid flow becomes an additional degree of freedom in designing optofluidic devices. In this paper, we demonstrate optofluidic liquid crystal devices based on the direct flow of nematic liquid crystals in microfluidic channels. Contrary to previous reports, in the present embodiment we employ the effective phase delay acquired by light travelling through flowing liquid crystal, without analysing the polarisation state of the transmitted light. With this method, we demonstrate the variation in the diffraction pattern of an array of microfluidic channels acting as a grating. We also discuss our recent activities in integrating mechanical oscillators for on-chip peristaltic pumping.

  14. Liquid crystal optofluidics

    NASA Astrophysics Data System (ADS)

    Vasdekis, A. E.; Cuennet, J. G.; Psaltis, D.

    2012-10-01

    By employing anisotropic fluids and namely liquid crystals, fluid flow becomes an additional degree of freedom in designing optofluidic devices. In this paper, we demonstrate optofluidic liquid crystal devices based on the direct flow of nematic liquid crystals in microfluidic channels. Contrary to previous reports, in the present embodiment we employ the effective phase delay acquired by light travelling through flowing liquid crystal, without analysing the polarisation state of the transmitted light. With this method, we demonstrate the variation in the diffraction pattern of an array of microfluidic channels acting as a grating. We also discuss our recent activities in integrating mechanical oscillators for on-chip peristaltic pumping.

  15. Heroin crystal nephropathy.

    PubMed

    Bautista, Josef Edrik Keith; Merhi, Basma; Gregory, Oliver; Hu, Susie; Henriksen, Kammi; Gohh, Reginald

    2015-06-01

    In this paper we present an interesting case of acute kidney injury and severe metabolic alkalosis in a patient with a history of heavy heroin abuse. Urine microscopy showed numerous broomstick-like crystals. These crystals are also identified in light and electron microscopy. We hypothesize that heroin crystalizes in an alkaline pH, resulting in tubular obstruction and acute kidney injury. Management is mainly supportive as there is no known specific therapy for this condition. This paper highlights the utility of urine microscopy in diagnosing the etiology of acute kidney injury and proposes a novel disease called heroin crystal nephropathy.

  16. Tunable plasmonic crystal

    DOEpatents

    Dyer, Gregory Conrad; Shaner, Eric A.; Reno, John L.; Aizin, Gregory

    2015-08-11

    A tunable plasmonic crystal comprises several periods in a two-dimensional electron or hole gas plasmonic medium that is both extremely subwavelength (.about..lamda./100) and tunable through the application of voltages to metal electrodes. Tuning of the plasmonic crystal band edges can be realized in materials such as semiconductors and graphene to actively control the plasmonic crystal dispersion in the terahertz and infrared spectral regions. The tunable plasmonic crystal provides a useful degree of freedom for applications in slow light devices, voltage-tunable waveguides, filters, ultra-sensitive direct and heterodyne THz detectors, and THz oscillators.

  17. Automation in biological crystallization.

    PubMed

    Stewart, Patrick Shaw; Mueller-Dieckmann, Jochen

    2014-06-01

    Crystallization remains the bottleneck in the crystallographic process leading from a gene to a three-dimensional model of the encoded protein or RNA. Automation of the individual steps of a crystallization experiment, from the preparation of crystallization cocktails for initial or optimization screens to the imaging of the experiments, has been the response to address this issue. Today, large high-throughput crystallization facilities, many of them open to the general user community, are capable of setting up thousands of crystallization trials per day. It is thus possible to test multiple constructs of each target for their ability to form crystals on a production-line basis. This has improved success rates and made crystallization much more convenient. High-throughput crystallization, however, cannot relieve users of the task of producing samples of high quality. Moreover, the time gained from eliminating manual preparations must now be invested in the careful evaluation of the increased number of experiments. The latter requires a sophisticated data and laboratory information-management system. A review of the current state of automation at the individual steps of crystallization with specific attention to the automation of optimization is given.

  18. Automation in biological crystallization

    PubMed Central

    Shaw Stewart, Patrick; Mueller-Dieckmann, Jochen

    2014-01-01

    Crystallization remains the bottleneck in the crystallographic process leading from a gene to a three-dimensional model of the encoded protein or RNA. Automation of the individual steps of a crystallization experiment, from the preparation of crystallization cocktails for initial or optimization screens to the imaging of the experiments, has been the response to address this issue. Today, large high-throughput crystallization facilities, many of them open to the general user community, are capable of setting up thousands of crystallization trials per day. It is thus possible to test multiple constructs of each target for their ability to form crystals on a production-line basis. This has improved success rates and made crystallization much more convenient. High-throughput crystallization, however, cannot relieve users of the task of producing samples of high quality. Moreover, the time gained from eliminating manual preparations must now be invested in the careful evaluation of the increased number of experiments. The latter requires a sophisticated data and laboratory information-management system. A review of the current state of automation at the individual steps of crystallization with specific attention to the automation of optimization is given. PMID:24915074

  19. Heroin crystal nephropathy

    PubMed Central

    Bautista, Josef Edrik Keith; Merhi, Basma; Gregory, Oliver; Hu, Susie; Henriksen, Kammi; Gohh, Reginald

    2015-01-01

    In this paper we present an interesting case of acute kidney injury and severe metabolic alkalosis in a patient with a history of heavy heroin abuse. Urine microscopy showed numerous broomstick-like crystals. These crystals are also identified in light and electron microscopy. We hypothesize that heroin crystalizes in an alkaline pH, resulting in tubular obstruction and acute kidney injury. Management is mainly supportive as there is no known specific therapy for this condition. This paper highlights the utility of urine microscopy in diagnosing the etiology of acute kidney injury and proposes a novel disease called heroin crystal nephropathy. PMID:26034599

  20. Phononic crystal devices

    DOEpatents

    El-Kady, Ihab F [Albuquerque, NM; Olsson, Roy H [Albuquerque, NM

    2012-01-10

    Phononic crystals that have the ability to modify and control the thermal black body phonon distribution and the phonon component of heat transport in a solid. In particular, the thermal conductivity and heat capacity can be modified by altering the phonon density of states in a phononic crystal. The present invention is directed to phononic crystal devices and materials such as radio frequency (RF) tags powered from ambient heat, dielectrics with extremely low thermal conductivity, thermoelectric materials with a higher ratio of electrical-to-thermal conductivity, materials with phononically engineered heat capacity, phononic crystal waveguides that enable accelerated cooling, and a variety of low temperature application devices.

  1. Crystals in magma chambers

    NASA Astrophysics Data System (ADS)

    Higgins, M.

    2011-12-01

    Differentiation processes in igneous systems are one way in which the diversity of igneous rocks is produced. Traditionally, magmatic diversity is considered as variations in the overall chemical composition, such as basalt and rhyolite, but I want to extend this definition to include textural diversity. Such textural variations can be manifested as differences in the amount of crystalline (and immiscible liquid) phases and in the origin and identity of such phases. One important differentiation process is crystal-liquid separation by floatation or decantation, which clearly necessitates crystals in the magma. Hence, it is important to determine if magmas in chambers (sensu lato) have crystals. The following discussion is framed in generalities - many exceptions occur. Diabase (dolerite) dykes are a common, widespread result of regional mafic magmatism. The rims of most diabase dykes have few or no phenocrysts and crystals in the cores are commonly thought to have crystallized in place. Hence, this major mafic magmatic source did not have crystals, although compositional diversity of these dykes is commonly explained by crystal-liquid separation. This can be resolved if crystallisation was on the walls on the magma chamber. Similarly, most flood basalts are low in crystals and separation of those that are present cannot always explain the observed compositional diversity. Crystal-rich flows do occur, for example the 'Giant Plagioclase Basalts' of the Deccan series, but the crystals are thought to form or accumulate in a crystal-rich zone beneath the roof of the chamber - the rest of the chamber probably has few crystals. Some magmas from Hawaii contain significant amounts of olivine crystals, but most of these are deformed and cannot have crystallised in the chamber. In this case the crystals are thought to grow as the magma passes through a decollement zone. They may have grown on the walls or been trapped by filters. Basaltic andesite ignimbrites generally have

  2. Vitrification and crystallization of metallic liquid under pressures.

    PubMed

    Wang, Li; Peng, Chuanxiao; Wang, Yuqing; Zhang, Yanning

    2006-08-16

    Using molecular dynamics simulation with the embedded atom method, the structural properties of liquid NiAl in a pressure range of 0-20 GPa are investigated with a quenching rate of 2 K ps(-1). Not only is vitrification of liquid at low temperature detected, but also crystallization by change of average atomic volume as a function of temperature. Convincing evidence is presented that the applied pressure strongly affects the vitrification and crystallization of metallic liquid. The simulated glass transition temperature T(g) increases with pressure by 38.4 K GPa(-1) within the range 0-10 GPa, while external pressure induces crystallization of metallic liquid within the pressure range 10-20 GPa, and the crystallization temperature T(c) increases with a slope of 6.4 K GPa(-1). Therefore, the critical pressure for the formation of metallic glass at this cooling rate is estimated to be 10 GPa. The competition between the densification and the suppression of atomic diffusion in the liquid by pressure is able to explain the vitrification and crystallization behaviours of the liquid. Our present work provides a possible guidance for an experiment to study the pressure effect on the glass transition and crystallization process in metallic liquid.

  3. Advanced Protein Crystallization Facility (APCF)

    NASA Technical Reports Server (NTRS)

    1998-01-01

    This section of the Life and Microgravity Spacelab (LMS) publication contains articles entitled: (1) Crystallization of EGFR-EGF; (2) Crystallization of Apocrustacyanin C1; (3) Crystallization and X-ray Analysis of 5S rRNA and the 5S rRNA Domain A; (4) Growth of Lysozyme Crystals at Low Nucleation Density; (5) Comparative Analysis of Aspartyl tRNA-synthetase and Thaumatin Crystals Grown on Earth and In Microgravity; (6) Lysosome Crystal Growth in the Advanced Protein Crystallization Facility Monitored via Mach-Zehnder Interferometry and CCD Video; (7) Analysis of Thaumatin Crystals Grown on Earth and in Microgravity; (8) Crystallization of the Nucleosome Core Particle; (9) Crystallization of Photosystem I; (10) Mechanism of Membrane Protein Crystal Growth: Bacteriorhodopsin-mixed Micelle Packing at the Consolution Boundary, Stabilized in Microgravity; (11) Crystallization in a Microgravity Environment of CcdB, a Protein Involved in the Control of Cell Death; and (12) Crystallization of Sulfolobus Solfataricus

  4. Channeling through Bent Crystals

    SciTech Connect

    Mack, Stephanie; /Ottawa U. /SLAC

    2012-09-07

    Bent crystals have demonstrated potential for use in beam collimation. A process called channeling is when accelerated particle beams are trapped by the nuclear potentials in the atomic planes within a crystal lattice. If the crystal is bent then the particles can follow the bending angle of the crystal. There are several different effects that are observed when particles travel through a bent crystal including dechanneling, volume capture, volume reflection and channeling. With a crystal placed at the edge of a particle beam, part of the fringe of the beam can be deflected away towards a detector or beam dump, thus helping collimate the beam. There is currently FORTRAN code by Igor Yazynin that has been used to model the passage of particles through a bent crystal. Using this code, the effects mentioned were explored for beam energy that would be seen at the Facility for Advanced Accelerator Experimental Tests (FACET) at a range of crystal orientations with respect to the incoming beam. After propagating 5 meters in vacuum space past the crystal the channeled particles were observed to separate from most of the beam with some noise due to dechanneled particles. Progressively smaller bending radii, with corresponding shorter crystal lengths, were compared and it was seen that multiple scattering decreases with the length of the crystal therefore allowing for cleaner detection of the channeled particles. The input beam was then modified and only a portion of the beam sent through the crystal. With the majority of the beam not affected by the crystal, most particles were not deflected and after propagation the channeled particles were seen to be deflected approximately 5mm. After a portion of the beam travels through the crystal, the entire beam was then sent through a quadrupole magnet, which increased the separation of the channeled particles from the remainder of the beam to a distance of around 20mm. A different code, which was developed at SLAC, was used to

  5. Protein crystal growth

    NASA Technical Reports Server (NTRS)

    Bugg, Charles E.

    1993-01-01

    Proteins account for 50% or more of the dry weight of most living systems and play a crucial role in virtually all biological processes. Since the specific functions of essentially all biological molecules are determined by their three-dimensional structures, it is obvious that a detailed understanding of the structural makeup of a protein is essential to any systematic research pertaining to it. At the present time, protein crystallography has no substitute, it is the only technique available for elucidating the atomic arrangements within complicated biological molecules. Most macromolecules are extremely difficult to crystallize, and many otherwise exciting and promising projects have terminated at the crystal growth stage. There is a pressing need to better understand protein crystal growth, and to develop new techniques that can be used to enhance the size and quality of protein crystals. There are several aspects of microgravity that might be exploited to enhance protein crystal growth. The major factor that might be expected to alter crystal growth processes in space is the elimination of density-driven convective flow. Another factor that can be readily controlled in the absence of gravity is the sedimentation of growing crystal in a gravitational field. Another potential advantage of microgravity for protein crystal growth is the option of doing containerless crystal growth. One can readily understand why the microgravity environment established by Earth-orbiting vehicles is perceived to offer unique opportunities for the protein crystallographer. The near term objectives of the Protein Crystal Growth in a Microgravity Environment (PCG/ME) project is to continue to improve the techniques, procedures, and hardware systems used to grow protein crystals in Earth orbit.

  6. Fluorescent Applications to Crystallization

    NASA Technical Reports Server (NTRS)

    Pusey, Marc L.; Forsythe, Elizabeth; Achari, Aniruddha

    2006-01-01

    By covalently modifying a subpopulation, less than or equal to 1%, of a macromolecule with a fluorescent probe, the labeled material will add to a growing crystal as a microheterogeneous growth unit. Labeling procedures can be readily incorporated into the final stages of purification, and tests with model proteins have shown that labeling u to 5 percent of the protein molecules does not affect the X-ray data quality obtained . The presence of the trace fluorescent label gives a number of advantages. Since the label is covalently attached to the protein molecules, it "tracks" the protein s response to the crystallization conditions. The covalently attached probe will concentrate in the crystal relative to the solution, and under fluorescent illumination crystals show up as bright objects against a darker background. Non-protein structures, such as salt crystals, do not show up under fluorescent illumination. Crystals have the highest protein concentration and are readily observed against less bright precipitated phases, which under white light illumination may obscure the crystals. Automated image analysis to find crystals should be greatly facilitated, without having to first define crystallization drop boundaries as the protein or protein structures is all that shows up. Fluorescence intensity is a faster search parameter, whether visually or by automated methods, than looking for crystalline features. Preliminary tests, using model proteins, indicates that we can use high fluorescence intensity regions, in the absence of clear crystalline features or "hits", as a means for determining potential lead conditions. A working hypothesis is that more rapid amorphous precipitation kinetics may overwhelm and trap more slowly formed ordered assemblies, which subsequently show up as regions of brighter fluorescence intensity. Experiments are now being carried out to test this approach using a wider range, of proteins. The trace fluorescently labeled crystals will also

  7. Ethyl 3-[6-(4-meth-oxy-benzene-sulfon-amido)-2H-indazol-2-yl]propano-ate monohydrate.

    PubMed

    Abbassi, Najat; Rakib, El Mostapha; Hannioui, Abdellah; Saadi, Mohamed; El Ammari, Lahcen

    2013-02-01

    In the title compound, C(19)H(21)N(3)O(5)S·H(2)O, the central indazole system is essentially planar (r.m.s. deviation = 0.012 Å), while both the benzene ring and the mean plane defined by the non-H atoms of the ethyl propionic ester unit (r.m.s. deviation = 0.087 Å) are nearly perpendicular to the indazole plane, as indicated by the dihedral angles of 82.45 (8) and 75.62 (8)°, respectively. Consequently, the mol-ecule adopts a U-shaped geometry. In the crystal, the water mol-ecule, which is linked to the indazole system by a strong O-H⋯N hydrogen bond, is also involved in two additional N-H⋯O and O-H⋯O inter-actions, which link the organic mol-ecules into chains along the b-axis direction.

  8. Stochastic finite-fault simulation of ground motion from the August 11, 2012, M w 6.4 Ahar earthquake, northwestern Iran

    NASA Astrophysics Data System (ADS)

    Heidari, Reza

    2016-04-01

    In this study, the 11 August 2012 M w 6.4 Ahar earthquake is investigated using the ground motion simulation based on the stochastic finite-fault model. The earthquake occurred in northwestern Iran and causing extensive damage in the city of Ahar and surrounding areas. A network consisting of 58 acceleration stations recorded the earthquake within 8-217 km of the epicenter. Strong ground motion records from six significant well-recorded stations close to the epicenter have been simulated. These stations are installed in areas which experienced significant structural damage and humanity loss during the earthquake. The simulation is carried out using the dynamic corner frequency model of rupture propagation by extended fault simulation program (EXSIM). For this purpose, the propagation features of shear-wave including {Q}_s value, kappa value {k}_0 , and soil amplification coefficients at each site are required. The kappa values are obtained from the slope of smoothed amplitude of Fourier spectra of acceleration at higher frequencies. The determined kappa values for vertical and horizontal components are 0.02 and 0.05 s, respectively. Furthermore, an anelastic attenuation parameter is derived from energy decay of a seismic wave by using continuous wavelet transform (CWT) for each station. The average frequency-dependent relation estimated for the region is Q=(122± 38){f}^{(1.40± 0.16)}. Moreover, the horizontal to vertical spectral ratio H/V is applied to estimate the site effects at stations. Spectral analysis of the data indicates that the best match between the observed and simulated spectra occurs for an average stress drop of 70 bars. Finally, the simulated and observed results are compared with pseudo acceleration spectra and peak ground motions. The comparison of time series spectra shows good agreement between the observed and the simulated waveforms at frequencies of engineering interest.

  9. Thrust faulting and 3D ground deformation of the 3 July 2015 Mw 6.4 Pishan, China earthquake from Sentinel-1A radar interferometry

    NASA Astrophysics Data System (ADS)

    Sun, Jianbao; Shen, Zheng-Kang; Li, Tao; Chen, Jie

    2016-06-01

    Boosted by the launch of Sentinel-1A radar satellite from the European Space Agency (ESA), we now have the opportunity of fast, full and multiple coverage of the land based deformation field of earthquakes. Here we use the data to investigate a strong earthquake struck Pishan, western China on July 3, 2015. The earthquake fault is blind and no ground break features are found on-site, thus Synthetic Aperture Radar (SAR) data give full play to its technical advantage for the recovery of coseismic deformation field. By using the Sentinel-1A radar data in the Interferometric Wide Swath mode, we obtain 3 tracks of InSAR data over the struck region, and resolve the 3D ground deformation generated by the earthquake. Then the Line-of-Sight (LOS) InSAR data are inverted for the slip-distribution of the seismogenic fault. The final model shows that the earthquake is completely blind with pure-thrust motion. The maximum slip is 0.48 m at a depth of 7 km, consistent with the depth estimate from seismic reflection data. In particular, the inverted model is also compatible with a south-dipping fault ramp among a group of fault interfaces detected by the seismic reflection profile over the region. The seismic moment obtained equals to a Mw 6.4 earthquake. The Pishan earthquake ruptured the frontal part of the thrust ramps under the Slik anticline, and unloaded the coulomb stress of them. However, it may have loaded stress to the back-thrust above the thrust ramps by 1-4 bar, and promoted it for future failure. Moreover, the stress loading on the west side of the earthquake fault is much larger than that on the east side, indicating a higher risk for failure to the west of the Zepu fault.

  10. REDSHIFT 6.4 HOST GALAXIES OF 10{sup 8} SOLAR MASS BLACK HOLES: LOW STAR FORMATION RATE AND DYNAMICAL MASS

    SciTech Connect

    Willott, Chris J.; Omont, Alain; Bergeron, Jacqueline

    2013-06-10

    We present Atacama Large Millimeter Array observations of rest-frame far-infrared continuum and [C II] line emission in two z = 6.4 quasars with black hole masses of Almost-Equal-To 10{sup 8} M{sub Sun }. CFHQS J0210-0456 is detected in the continuum with a 1.2 mm flux of 120 {+-} 35 {mu}Jy, whereas CFHQS J2329-0301 is undetected at a similar noise level. J2329-0301 has a star formation rate limit of <40 M{sub Sun} yr{sup -1}, considerably below the typical value at all redshifts for this bolometric luminosity. Through comparison with hydro simulations, we speculate that this quasar is observed at a relatively rare phase where quasar feedback has effectively shut down star formation in the host galaxy. [C II] emission is also detected only in J0210-0456. The ratio of [C II] to far-infrared luminosity is similar to that of low-redshift galaxies of comparable luminosity, suggesting that the previous finding of an offset in the relationships between this ratio and far-infrared luminosity at low and high redshifts may be partially due to a selection effect due to the limited sensitivity of previous continuum data. The [C II] line of J0210-0456 is relatively narrow (FWHM = 189 {+-} 18 km s{sup -1}), indicating a dynamical mass substantially lower than expected from the local black hole-velocity dispersion correlation. The [C II] line is marginally resolved at 0.''7 resolution with the blue and red wings spatially offset by 0.''5 (3 kpc) and a smooth velocity gradient of 100 km s{sup -1} across a scale of 6 kpc, possibly due to the rotation of a galaxy-wide disk. These observations are consistent with the idea that stellar mass growth lags black hole accretion for quasars at this epoch with respect to more recent times.

  11. Rupture geometry and slip distribution of the 2016 January 21st Ms6.4 Menyuan, China earthquake inferred from Sentinel-1A InSAR measurements

    NASA Astrophysics Data System (ADS)

    Zhou, Y.

    2016-12-01

    On 21 January 2016, an Ms6.4 earthquake stroke Menyuan country, Qinghai Province, China. The epicenter of the main shock and locations of its aftershocks indicate that the Menyuan earthquake occurred near the left-lateral Lenglongling fault. However, the focal mechanism suggests that the earthquake should take place on a thrust fault. In addition, field investigation indicates that the earthquake did not rupture the ground surface. Therefore, the rupture geometry is unclear as well as coseismic slip distribution. We processed two pairs of InSAR images acquired by the ESA Sentinel-1A satellite with the ISCE software, and both ascending and descending orbits were included. After subsampling the coseismic InSAR images into about 800 pixels, coseismic displacement data along LOS direction are inverted for earthquake source parameters. We employ an improved mixed linear-nonlinear Bayesian inversion method to infer fault geometric parameters, slip distribution, and the Laplacian smoothing factor simultaneously. This method incorporates a hybrid differential evolution algorithm, which is an efficient global optimization algorithm. The inversion results show that the Menyuan earthquake ruptured a blind thrust fault with a strike of 124°and a dip angle of 41°. This blind fault was never investigated before and intersects with the left-lateral Lenglongling fault, but the strikes of them are nearly parallel. The slip sense is almost pure thrusting, and there is no significant slip within 4km depth. The max slip value is up to 0.3m, and the estimated moment magnitude is Mw5.93, in agreement with the seismic inversion result. The standard error of residuals between InSAR data and model prediction is as small as 0.5cm, verifying the correctness of the inversion results.

  12. 3D Vs ambient noise tomography in the source region of the 2016 Mw6.4 Meinong earthquake in Taiwan

    NASA Astrophysics Data System (ADS)

    Kuo-Chen, Hao; Chen, Kai-Xun; Sun, Wei-Fang; Ho, Chun-Wei; Lee, Yuan-Hsi; Guan, Zhuo-Kang; Kang, Chu-Chun; Chang, Wen-Yen

    2017-04-01

    Mw6.4 Meinong earthquake occurred on 6th February in 2016 in southern Taiwan and resulted in more than one hundred casualties and several building collapsed. The aftershocks mostly occurred at mid-to-lower crustal depths (10-30 km), which is related to a blind fault system. However, at the surface several centimeters of cosesimic uplift within the Liushuang, Erhchungli, and GutingKeng Formations, which is mainly composed of mudstone, have been recorded from the InSAR results. The uplifted pattern is similar to that of GPS and leveling data from 2000 to 2010, which indicates the deformation is accomplished by creeping due to the mudstone of the shallow structure related to mud diapir. Previous studies have shown limited information about the shallow structure in this region due to few seismic stations deployed. In this study, we deployed 36 temporary seismic stations ( 5 km spacing) for around one month after the main shock to obtain a 3-D shear wave shallow crustal velocity structure using ambient noise tomography. The reliable periods of group and phase velocities from Rayleigh wave are 0.6 to 5 seconds, which correspond to around 0-5 km at depths. As a result, the pattern of low S-wave speeds at 0-4 km depths corresponds to the uplift region from both of InSAR data for coseismic period and GPS and leveling data for interseismic period. Also, the results from this study are compatible with the reflected seismic profile. The results show that with dense seismic array deployment we can obtain a high resolution of subsurface image to link the relationship between the surface observations to the subsurface structures.

  13. The 2012 August 11 MW 6.5, 6.4 Ahar-Varzghan earthquakes, NW Iran: aftershock sequence analysis and evidence for activity migration

    NASA Astrophysics Data System (ADS)

    Rezapour, Mehdi

    2016-02-01

    The Ahar-Varzghan doublet earthquakes with magnitudes MW 6.5 and 6.4 occurred on 2012 August 11 in northwest Iran and were followed by many aftershocks. In this paper, we analyse ˜5 months of aftershocks of these events. The Ahar-Varzghan earthquakes occurred along complex faults and provide a new constraint on the earthquake hazard in northwest Iran. The general pattern of relocated aftershocks defines a complex seismic zone covering an area of approximately 25 × 10 km2. The Ahar-Varzghan aftershock sequence shows a secondary activity which started on November 7, approximately 3 months after the main shocks, with a significant increase in activity, regarding both number of events and their magnitude. This stage was characterized by a seismic zone that propagated to the west of the main shocks. The catalogue of aftershocks for the doublet earthquake has a magnitude completeness of Mc 2.0. A below-average b-value for the Ahar-Varzghan sequence indicates a structural heterogeneity in the fault plane and the compressive stress state of the region. Relocated aftershocks occupy a broad zone clustering east-west with near-vertical dip which we interpret as the fault plane of the first of the doublet main shocks (MW 6.5). The dominant depth range of the aftershocks is from 3 to about 20 km, and the focal depths decrease toward the western part of the fault. The aftershock activity has its highest concentration in the eastern and middle parts of the active fault, and tapers off toward the western part of the active fault segment, indicating mainly a unilateral rupture toward west.

  14. Numerical earthquake model of the 20 April 2015 southern Ryukyu subduction zone M6.4 event and its impact on seismic hazard assessment

    NASA Astrophysics Data System (ADS)

    Lee, Shiann-Jong

    2015-10-01

    The M6.4 earthquake that took place on the 20 April 2015 off the shore of eastern Taiwan was the largest event in the vicinity of Taiwan during 2015. The mainshock was located in the southern Ryukyu subduction zone, which is the interface between the Philippine Sea Plate and the Eurasian Plate. People in Taipei experienced strong ground shaking for more than 40 s, even though the epicenter was located more than 150 km away. In order to understand the origin of ground motions from this earthquake and how it caused such strong shaking in Taipei, a numerical earthquake model is analyzed, including models of source rupture and wave propagation. First, a joint source inversion was performed using teleseismic body wave and local ground motion data. Source inversion results show that a large slip occurred near the hypocenter, which rapidly released seismic energy in the first 2 s. Then, the rupture propagated toward the shallow fault plane. A large amount of seismic energy was released during this rupture stage that slipped for more than 8 s before the end of the rupture. The estimated stress drop is 2.48 MPa, which is consistent with values for subduction zone earthquakes. Forward simulation using this inverted source rupture model and a 3D seismic velocity model based on the spectral-element method was then performed. Results indicate that the strong ground motion in Taipei resulted from two factors: (1) the Taipei basin amplification effect and (2) the specific source radiation pattern. The results of this numerical earthquake model imply that future subduction zone events that occur in offshore eastern Taiwan are likely to cause relatively strong ground shaking in northern Taiwan, especially in the Taipei metropolitan area.

  15. Numerical earthquake model of the 20 April 2015 southern Ryukyu subduction zone M6.4 event and its impact on seismic hazard assessment

    NASA Astrophysics Data System (ADS)

    Lee, S. J.

    2015-12-01

    The M6.4 earthquake that took place on the 20th April 2015 off the shore of eastern Taiwan was the largest event that occurred in the vicinity of Taiwan during 2015. The mainshock located in the southern Ryukyu subduction zone, which is the interface between the Philippine Sea Plate and the Eurasian Plate. People in Taipei experienced strong ground shaking for more than 40 s, even though the epicenter was located more than 150 km away. In order to understand the origin of this earthquake and how it caused such strong shaking in Taipei, a numerical earthquake model is analyzed, including models of source rupture and wave propagation. First, a joint source inversion is performed using teleseismic body wave and local ground motion data. Source inversion results show that a large slip occurred near the hypocenter, which rapidly released seismic energy in the first 2 s. Then, the rupture propagated toward the shallow fault plane. A large amount of seismic energy was released during this rupture stage that slipped for more than 8 s before the end of the rupture. The estimated stress drop is 2.48 MPa, which is consistent with values for subduction zone earthquakes. Forward simulation using this inverted source rupture model based on the spectral-element method is then performed. Results indicate that the strong ground motion in Taipei resulted from two factors: (1) the Taipei basin amplification effect and (2) the specific source radiation pattern. The results of this numerical earthquake model imply that future subduction zone events that occur in offshore eastern Taiwan are likely to cause relatively strong ground shaking in northern Taiwan, especially in the Taipei metropolitan area.

  16. CTIO, ROSAT HRI, and Chandra ACIS Observations of the Archetypical Mixed-morphology Supernova Remnant W28 (G6.4-0.1)

    NASA Astrophysics Data System (ADS)

    Pannuti, Thomas G.; Rho, Jeonghee; Kargaltsev, Oleg; Rangelov, Blagoy; Kosakowski, Alekzander R.; Winkler, P. Frank; Keohane, Jonathan W.; Hare, Jeremy; Ernst, Sonny

    2017-04-01

    We present a joint analysis of optical emission-line and X-ray observations of the archetypical Galactic mixed-morphology supernova remnant (MMSNR) W28 (G6.4-0.1). MMSNRs comprise a class of sources whose shell-like radio morphology contrasts with a filled center in X-rays; the origin of these contrasting morphologies remains uncertain. Our CTIO images reveal enhanced [S ii] emission relative to Hα along the northern and eastern rims of W28. Hydroxyl (OH) masers are detected along these same rims, supporting prior studies suggesting that W28 is interacting with molecular clouds at these locations, as observed for several other MMSNRs. Our ROSAT HRI mosaic of W28 provides almost complete coverage of the supernova remnant (SNR). The X-ray and radio emission is generally anti-correlated, except for the luminous northeastern rim, which is prominent in both bands. Our Chandra observation sampled the X-ray-luminous central diffuse emission. Spectra extracted from the bright central peak and from nearby annular regions are best fit with two overionized recombining plasma models. We also find that while the X-ray emission from the central peak is dominated by swept-up material, that from the surrounding regions shows evidence for oxygen-rich ejecta, suggesting that W28 was produced by a massive progenitor. We also analyze the X-ray properties of two X-ray sources (CXOU J175857.55-233400.3 and 3XMM J180058.5-232735) projected into the interior of W28 and conclude that neither is a neutron star associated with the SNR. The former is likely to be a foreground cataclysmic variable or a quiescent low-mass X-ray-binary, while the latter is likely to be a coronally active main-sequence star.

  17. Metabolic effects of newly synthesized phosphodiesterase-3 inhibitor 6-[4-(4-methylpiperidin-1-yl)-4-oxobutoxy]-4-methylquinolin-2(1H)-one on rat adipocytes.

    PubMed

    Alinejad, Bagher; Shafiee-Nick, Reza; Sadeghian, Hamid; Ghorbani, Ahmad

    2015-02-21

    Clinical use of selective PDE3 inhibitors as cardiotonic agents is limited because of their chronotropic and lipolytic side effects. In our previous work, we synthesized a new PDE3 inhibitor named MC2 (6-[4-(4-methylpiperidin-1-yl)-4-oxobutoxy]-4-methylquinolin-2(1H)-one) which produced a high positive inotropic action with a negative chronotropic effect. This work was done to evaluate the effects of MC2 on adipocytes and compare its effects with those of amrinone and cilostamide. Preadipocytes were isolated from rat adipose tissue and differentiated to adipocyte in the presence of cilostamide, amrinone or MC2. Lipolysis and adipogenesis was evaluated by measuring glycerol level and Oil Red O staining, respectively. Adipocyte proliferation and apoptosis were determined with MTT assay and Annexin V/PI staining, respectively. Differentiation to adipocyte was induced by amrinone but not by cilostamide or MC2. Basal and isoproterenol-stimulated lipolysis significantly increased by cilostamide (p<0.05). Similarly, amrinone enhanced the stimulated lipolysis (p<0.01). On the other hand, MC2 significantly decreased both adipogenesis (p<0.05) and stimulated lipolysis (p<0.001). Also, incubation of differentiated adipocytes with MC2 caused the loss of cell viability, which was associated with the elevation in apoptotic rate (p<0.05). Our data indicate that selective PDE3 inhibitors produce differential effects on adipogenesis and lipolysis. MC2 has proapoptotic and antilipolytic effects on adipocytes and does not stimulate adipogenesis. Therefore, in comparison with the clinically available selective PDE3 inhibitors, MC2 has lowest metabolic side effects and might be a good candidate for treatment of congestive heart failure.

  18. Crystals for stellar spectrometers

    NASA Technical Reports Server (NTRS)

    Alexandropoulos, N. G.; Cohen, G. G.

    1974-01-01

    Crystal evaluation as it applies to instrumentation employed in X-ray astronomy is reviewed, and some solutions are offered to problems that are commonly encountered. A general approach for selecting the most appropriate crystals for a given problem is also suggested. The energy dependence of the diffraction properties of (002) PET, (111) Ge, (101) ADP, (101) KAP, and (001) RAP are reported.

  19. Thermotropic Ionic Liquid Crystals

    PubMed Central

    Axenov, Kirill V.; Laschat, Sabine

    2011-01-01

    The last five years’ achievements in the synthesis and investigation of thermotropic ionic liquid crystals are reviewed. The present review describes the mesomorphic properties displayed by organic, as well as metal-containing ionic mesogens. In addition, a short overview on the ionic polymer and self-assembled liquid crystals is given. Potential and actual applications of ionic mesogens are also discussed. PMID:28879986

  20. Crystal Shape Bingo.

    ERIC Educational Resources Information Center

    Rule, Audrey C.

    This document describes a game that provides students with practice in recognizing three dimensional crystal shapes and planar geometric shapes of crystal faces. It contains information on the objective of the game, game preparation, and rules for playing. Play cards are included (four to a page). (ASK)

  1. Crystals for stellar spectrometers

    NASA Technical Reports Server (NTRS)

    Alexandropoulos, N. G.; Cohen, G. G.

    1974-01-01

    Crystal evaluation as it applies to instrumentation employed in X-ray astronomy is reviewed, and some solutions are offered to problems that are commonly encountered. A general approach for selecting the most appropriate crystals for a given problem is also suggested. The energy dependence of the diffraction properties of (002) PET, (111) Ge, (101) ADP, (101) KAP, and (001) RAP are reported.

  2. Crystal growth and crystallography

    NASA Technical Reports Server (NTRS)

    Chernov, A. A.

    1998-01-01

    Selected topics that may be of interest for both crystal-structure and crystal-growth communities are overviewed. The growth of protein crystals, along with that of some other compounds, is one of the topics, and recent insights into related phenomena are considered as examples of applications of general principles. The relationship between crystal growth shape and structure is reviewed and an attempt to introduce semiquantitative characterization of binding for proteins is made. The concept of kinks for complex structures is briefly discussed. Even at sufficiently low supersaturations, the fluctuation of steps may not be sufficient to implement the Gibbs-Thomson law if the kink density is low enough. Subsurface ordering of liquids and growth of rough interfaces from melts is discussed. Crystals growing in microgravity from solution should be more perfect if they preferentially trap stress-inducing impurities, thus creating an impurity-depleted zone around themselves. Evidently, such a zone is developed only around the crystals growing in the absence of convection. Under terrestrial conditions, the self-purified depleted zone is destroyed by convection, the crystal traps more impurity and grows stressed. The stress relief causes mosaicity. In systems containing stress-inducing but poorly trapped impurities, the crystals grown in the absence of convection should be worse than those of their terrestrial counterparts.

  3. Walkout in Crystal City

    ERIC Educational Resources Information Center

    Barrios, Greg

    2009-01-01

    When students take action, they create change that extends far beyond the classroom. In this article, the author, who was a former teacher from Crystal City, Texas, remembers the student walkout that helped launch the Latino civil rights movement 40 years ago. The Crystal City student walkout remains a high point in the history of student activism…

  4. Demonstration of Crystal Structure.

    ERIC Educational Resources Information Center

    Neville, Joseph P.

    1985-01-01

    Describes an experiment where equal parts of copper and aluminum are heated then cooled to show extremely large crystals. Suggestions are given for changing the orientation of crystals by varying cooling rates. Students are more receptive to concepts of microstructure after seeing this experiment. (DH)

  5. Walkout in Crystal City

    ERIC Educational Resources Information Center

    Barrios, Greg

    2009-01-01

    When students take action, they create change that extends far beyond the classroom. In this article, the author, who was a former teacher from Crystal City, Texas, remembers the student walkout that helped launch the Latino civil rights movement 40 years ago. The Crystal City student walkout remains a high point in the history of student activism…

  6. Solvent-dependent 4(4) square grid and 6(4).8(2) NbO frameworks formed by Cu(Pyac)2 (bis[3-(4-pyridyl)pentane-2,4-dionato]copper(II)).

    PubMed

    Chen, Banglin; Fronczek, Frank R; Maverick, Andrew W

    2003-09-07

    The title compound crystallizes from anhydrous solvents in a simple square-grid topology, but when water is present, crystals form with an unusual interpenetrated 3D NbO topology whose pores contain hydrogen-bonded solvent molecules.

  7. Conformal Vortex Crystals.

    PubMed

    Menezes, Raí M; Silva, Clécio C de Souza

    2017-10-06

    We investigate theoretically globally nonuniform configurations of quantized-flux vortices in clean superconductors trapped by an external force field that induces a nonuniform vortex density profile. Using an extensive series of numerical simulations, we demonstrate that, for suitable choices of the force field, and bellow a certain transition temperature, the vortex system self-organizes into highly inhomogeneous conformal crystals in a way as to minimize the total energy. These nonuniform structures are topologically ordered and can be mathematically mapped into a triangular Abrikosov lattice via a conformal transformation. Above the crystallization temperature, the conformal vortex crystal becomes unstable and gives place to a nonuniform polycrystalline structure. We propose a simple method to engineer the potential energy profile necessary for the observation of conformal crystals of vortices, which can also be applied to other 2D particle systems, and suggest possible experiments in which conformal or quasi-conformal vortex crystals could be observed in bulk superconductors and in thin films.

  8. Processing anthracene single crystals

    NASA Astrophysics Data System (ADS)

    Ujhelyi, S.

    1981-11-01

    A mechanical-chemical process for cutting anthracene crystals is described. A thread, soaked in toluene, dissolves a thin layer away from the material. The crystal is fixed to a metal platform placed between the two spools which wind the thread. The thread is not allowed to tighten as it crosses the crystal. For polishing, the slices are bonded with a gelatin solution onto a plexiglass disk, and rubbed with fine silk wetted with toluene. When one side is done the disk is immersed in water (room temperature) and soaks until the crystal can be removed, and the other side can be done. If the crystal splits in two, it can be rejoined using Canada balsam.

  9. Bioengineered magnetic crystals

    NASA Astrophysics Data System (ADS)

    Kasyutich, O.; Sarua, A.; Schwarzacher, W.

    2008-07-01

    In this paper we report on the successful application of a protein crystallization technique to fabricate a three-dimensionally ordered array of magnetic nanoparticles, i.e. a novel type of metamaterial with unique magnetic properties. We utilize ferritin protein cages for the template-constrained growth of superparamagnetic nanoparticles of magnetite/maghemite Fe3O4-γ-Fe2O3 (magnetoferritin), followed by thorough nanoparticle bioprocessing and purification, and finally by protein crystallization. Protein crystallization is driven by the natural response of proteins to the supersaturation of the electrolyte, which leads to spontaneous nucleation and 3D crystal growth. Within a short period of time (hours to days) we were able to grow functional crystals on the meso-scale, with sizes of the order of tens, up to a few hundred micrometres. We present initial magnetic and Raman spectroscopy characterization results for the obtained 3D arrays of magnetic nanoparticles.

  10. Polymer Crystallization under Confinement

    NASA Astrophysics Data System (ADS)

    Floudas, George

    Recent efforts indicated that polymer crystallization under confinement can be substantially different from the bulk. This can have important technological applications for the design of polymeric nanofibers with tunable mechanical strength, processability and optical clarity. However, the question of how, why and when polymers crystallize under confinement is not fully answered. Important studies of polymer crystallization confined to droplets and within the spherical nanodomains of block copolymers emphasized the interplay between heterogeneous and homogeneous nucleation. Herein we report on recent studies1-5 of polymer crystallization under hard confinement provided by model self-ordered AAO nanopores. Important open questions here are on the type of nucleation (homogeneous vs. heterogeneous), the size of critical nucleus, the crystal orientation and the possibility to control the overall crystallinity. Providing answers to these questions is of technological relevance for the understanding of nanocomposites containing semicrystalline polymers. In collaboration with Y. Suzuki, H. Duran, M. Steinhart, H.-J. Butt.

  11. Crystal growth of semiconductor bulk crystals

    SciTech Connect

    Kakimoto, Koichi

    2010-07-22

    This course is aimed at showing how to grow bulk crystals by using several methods. The course involves the following points. The growth methods of Bridgman and Czochralski will be introduced. The course also focuses on the mechanism of some processes with consideration of the basic phenomenon. Experimental and numerical examples of the methods will also be introduced.

  12. Crystallization of macromolecular complexes: combinatorial complex crystallization

    NASA Astrophysics Data System (ADS)

    Stura, Enrico A.; Graille, Marc; Charbonnier, Jean-Baptiste

    2001-11-01

    The usefulness of antibody complexation, as a way of increasing the chances of crystallization needs to be re-evaluated after many antibody complexes have been crystallized and their structure determined. It is somewhat striking that among these, only a small number is a complex with a large protein antigen. The problem is that the effort of raising, cleaving and purifying an Fab is rewarded only by an extra chance of getting crystals; depending on the relative likelihood of crystallization of the complexed and uncomplexed protein. The example of the complex between HIV gp120, CD4 and an Fab fragment from a neutralizing antibody suggests that further complexation of an antigen-antibody complex with a third protein could, by increasing the number of possible combinations, improve the likelihood of crystallization. We propose the use of Ig-binding proteins as a way of extending the method from HIV gp120 to all proteins for which there are monoclonal antibodies. We discuss this technique, combinatorial complex crystallization (CCC), as part of a multi-component system for the enhancement of crystallization of macromolecular complexes. The method makes use of single Ig-binding domains from Staphylococcus aureus protein A (SpA), Peptostreptococcus magnus protein L (PpL) and the streptococcal protein G (SpG). The generality of the method depends on the ability of these domains to interact with a large repertoire of antibodies without affecting antigen binding. There is strong evidence to suggest that these Ig-binding domains bind outside the antigen-combining site of the antibody without perturbing antigen binding. It is clear from the crystal structure of the single SpG domain complexed with an Fab that the interaction involves mainly the immunoglobulin CH1 domain, a region not involved in antigen recognition. We have recently determined the structure of the complex between a human Fab and the domain D from SpA and found that steric hindrance is unlikely even for large

  13. Dispersion in photonic crystals

    NASA Astrophysics Data System (ADS)

    Witzens, Jeremy

    2005-11-01

    Investigations on the dispersive properties of photonic crystals, modified scattering in ring-resonators, monolithic integration of vertical-cavity surface-emitting lasers and advanced data processing techniques for the finite-difference time-domain method are presented. Photonic crystals are periodic mesoscopic arrays of scatterers that modify the propagation properties of electromagnetic waves in a similar way as "natural" crystals modify the properties of electrons in solid-state physics. In this thesis photonic crystals are implemented as planar photonic crystals, i.e., optically thin semiconductor films with periodic arrays of holes etched into them, with a hole-to-hole spacing of the order of the wavelength of light in the dielectric media. Photonic crystals can feature forbidden frequency ranges (the band-gaps) in which light cannot propagate. Even though most work on photonic crystals has focused on these band-gaps for application such as confinement and guiding of light, this thesis focuses on the allowed frequency regions (the photonic bands) and investigates how the propagation of light is modified by the crystal lattice. In particular the guiding of light in bulk photonic crystals in the absence of lattice defects (the self-collimation effect) and the angular steering of light in photonic crystals (the superprism effect) are investigated. The latter is used to design a planar lightwave circuit for frequency domain demultiplexion. Difficulties such as efficient insertion of light into the crystal are resolved and previously predicted limitations on the resolution are circumvented. The demultiplexer is also fabricated and characterized. Monolithic integration of vertical-cavity surface-emitting lasers by means of resonantly enhanced grating couplers is investigated. The grating coupler is designed to bend light through a ninety-degree angle and is characterized with the finite-difference time-domain method. The vertical-cavity surface-emitting lasers are

  14. Shaped Crystal Growth

    NASA Astrophysics Data System (ADS)

    Tatartchenko, Vitali A.

    Crystals of specified shape and size (shaped crystals) with controlled crystal growth (SCG) defect and impurity structure have to be grown for the successful development of modern engineering. Since the 1950s many hundreds of papers and patents concerned with shaped growth have been published. In this chapter, we do not try to enumerate the successful applications of shaped growth to different materials but rather to carry out a fundamental physical and mathematical analysis of shaping as well as the peculiarities of shaped crystal structures. Four main techniques, based on which the lateral surface can be shaped without contact with the container walls, are analyzed: the Czochralski technique (CZT), the Verneuil technique (VT), the floating zone technique (FZT), and technique of pulling from shaper (TPS). Modifications of these techniques are analyzed as well. In all these techniques the shape of the melt meniscus is controlled by surface tension forces, i.e., capillary forces, and here they are classified as capillary shaping techniques (CST). We look for conditions under which the crystal growth process in each CST is dynamically stable. Only in this case are all perturbations attenuated and a crystal of constant cross section shaping technique (CST) grown without any special regulation. The dynamic stability theory of the crystal growth process for all CST is developed on the basis of Lyapunov's dynamic stability theory. Lyapunov's equations for the crystal growth processes follow from fundamental laws. The results of the theory allow the choice of stable regimes for crystal growth by all CST as well as special designs of shapers in TPS. SCG experiments by CZT, VT, and FZT are discussed but the main consideration is given to TPS. Shapers not only allow crystal of very complicated cross section to be grown but provide a special distribution of impurities. A history of TPS is provided later in the chapter, because it can only be described after explanation of the

  15. Protein crystal growth in microgravity

    NASA Technical Reports Server (NTRS)

    Delucas, Lawrence J.; Smith, Craig D.; Smith, H. Wilson; Vijay-Kumar, Senadhi; Senadhi, Shobha E.; Ealick, Steven E.; Carter, Daniel C.; Snyder, Robert S.

    1989-01-01

    The crystals of most proteins or other biological macromolecules are poorly ordered and diffract to lower resolutions than those observed for most crystals of simple organic and inorganic compounds. Crystallization in the microgravity environment of space may improve crystal quality by eliminating convection effects near growing crystal surfaces. A series of 11 different protein crystal growth experiments was performed on U.S. Space Shuttle flight STS-26 in September 1988. The microgravity-grown crystals of gamma-interferon D1, porcine elastase, and isocitrate lyase are larger, display more uniform morphologies, and yield diffraction data to significantly higher resolutions than the best crystals of these proteins grown on earth.

  16. Temporal changes of seismic velocity and anisotropy in the shallow crust induced by the 1999 October 22 M6.4 Chia-Yi, Taiwan earthquake

    NASA Astrophysics Data System (ADS)

    Chao, Kevin; Peng, Zhigang

    2009-12-01

    Observing temporal changes of material properties in the upper crust has been a long-sought goal within the geophysics community for many decades. A better quantification of temporal changes in the near-surface layers associated with nearby large earthquakes is crucial for improved understandings of rock rheology in the shallow crust, better characterization of site response, and accurate predictions of strong ground motions for future large earthquakes. We systematically analyse temporal changes of seismic velocity and anisotropy in the shallow crust in southwest Taiwan using local earthquakes recorded at a 200-m-deep borehole station CHY. This station is located directly above the hypocentre of the 1999 October 22, M6.4 Chia-Yi earthquake. Three-component seismograms recorded at this station show clear direct (upgoing) and surface-reflected (downgoing) P and S waves, and S-wave splitting signals. We use the time delays between the upgoing and downgoing waves in the autocorrelation functions as the proxies for the two-way traveltimes in the top 200 m. The S-wave traveltimes measured in two horizontal components increase by ~1-2 per cent at the time of Chia-Yi main shock, and followed by a logarithmic recovery, while the temporal changes of S-wave splitting and P-wave traveltimes are less than 1 per cent and are not statistically significant. We obtain similar results by grouping earthquakes into clusters according to their locations and waveform similarities. This suggests that the observed temporal changes are not very sensitive to the seismic ray paths below CHY, but are mostly controlled by the variation of material properties in the top 200 m of the crust. We propose that strong ground motions of the Chia-Yi main shock cause transient openings of fluid-filled microcracks and increases the porosity in the near-surface layers, followed by logarithemic recovery processes. No clear change in the delay times of the shear wave anisotropy is found following the main

  17. Analysis of O(6)-[4-(3-Pyridyl)-4-oxobut-1-yl]-2'-deoxyguanosine and Other DNA Adducts in Rats Treated with Enantiomeric or Racemic N'-Nitrosonornicotine.

    PubMed

    Yang, Jing; Villalta, Peter W; Upadhyaya, Pramod; Hecht, Stephen S

    2016-01-19

    (S)-N'-Nitrosonornicotine [(S)-NNN] and racemic NNN are powerful oral and esophageal carcinogens in the F344 rat, whereas (R)-NNN has only weak activity. Tumor formation in these tissues of rats treated with racemic NNN was far greater than the sum of the activities of the individual enantiomers. We hypothesized that metabolites of (R)-NNN enhanced levels of DNA adducts produced by (S)-NNN. A test of that hypothesis necessitated the development of a novel liquid chromatography-nanoelectrospray ionization-high resolution tandem mass spectrometry method for the analysis of O(6)-[4-(3-pyridyl)-4-oxobut-1-yl]-2'-deoxyguanosine (O(6)-POB-dGuo), a highly mutagenic DNA adduct not previously quantified in rats treated with NNN. The new method, with a limit of detection of 6.5 amol for diluted standard and 100 amol for DNA samples, was applied in this study. Groups of nine F344 rats were treated with doses as follows: 7 ppm (R)-NNN, 7 ppm (S)-NNN, and 14 ppm racemic NNN; 14 ppm (R)-NNN, 14 ppm (S)-NNN, and 28 ppm racemic NNN; or 28 ppm (R)-NNN, 28 ppm (S)-NNN, and 56 ppm racemic NNN for 5 weeks, and tissues were analyzed for DNA adducts. We found statistically significant, but modest, synergistic enhancement of levels of O(6)-POB-dGuo in the esophagus but not the oral cavity of rats treated with racemic NNN (low and median doses only) compared to the sum of the amounts formed in these tissues of rats treated with (S)-NNN or (R)-NNN. There was no synergy in the formation of other POB-DNA adducts of NNN in oral cavity and esophagus, nor was there any evidence for synergy in nasal respiratory and olfactory epithelium, lung, or liver. Our results provide the first quantitation of O(6)-POB-dGuo in DNA from tissues of rats treated with NNN and evidence for synergy in DNA adduct formation as one possible mechanism by which (R)-NNN enhances the carcinogenicity of (S)-NNN in rats.

  18. Relocation of the Mw 6.4 July 1, 2009 earthquake to the south of Crete and modeling of its associated small tsunami

    NASA Astrophysics Data System (ADS)

    Bocchini, Gian Maria; Papadopoulos, Gerassimos A.; Novikova, Tatiana; Karastathis, Vassilis K.; Mouzakiotis, Aggelos; Voulgaris, Nikolaos

    2016-04-01

    On July 1, 2009 (09:30 UTC) a Mw6.4 earthquake ruptured south of Crete Island triggering a small tsunami. Eyewitness reported the tsunami from Myrtos and Arvi Port, in the SE coast of Crete, and in Chrisi islet. In Arvi 4 or 5 wave arrivals were reported after a withdrawal of the sea of about 1 m. The sea disturbance lasted for about 1 h. The earthquake occurred as the result of the subduction of the oceanic African Plate beneath the continental Eurasian Plate along the Hellenic Subduction Zone (HSZ). South of Crete the Nubia-Aegean convergence rate (~3.5 cm/yr) is partially accommodated by low-angle (~20-25°) thrust faults at 20-40km depths and by steeper (>30°) reverse-faults at shallower depths. The area of interest has been struck by large magnitude earthquakes in historical times that in some cases triggered damaging tsunamis (e.g AD 1303). Routine earthquake locations performed by NOA do not provide good quality hypocenters for the area under investigation given the poor azimuthal coverage and the low density of the seismic stations. The 2009 earthquake, given its tsunamigenic nature, has been identified as a key event to study the central segment of the HSZ. We performed the relocation of the 2009 mainshock along with the seismicity of the area (ML>=3, period 2008-2015) using the NLLoc algorithm and testing several 1D velocity models available for the area and a 2D velocity model obtained from a published N-S seismic refraction profile across Crete. The hypocenters obtained from NLLoc have been subsequently relocated with HypoDD algorithm using catalog phase data. The results from the various relocation procedures showed a shallow hypocentral depth (12-17km) of the 2009 event and its likely intraplate nature. A set of hypocentral solutions were selected on the basis of minimum RMS and smaller errors with the aim to perform tsunami simulations with varying source parameters. Two different fault dips were used to discriminate between the intraplate (dip 32

  19. Resistance of the genome of Escherichia coli and Listeria monocytogenes to irradiation evaluated by the induction of cyclobutane pyrimidine dimers and 6-4 photoproducts using gamma and UV-C radiations

    NASA Astrophysics Data System (ADS)

    Beauchamp, S.; Lacroix, M.

    2012-08-01

    The effect of gamma and UV-C irradiation on the production of cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts (6-4 PPs) in DNA was investigated to compare the natural resistance of the genome of a Gram-positive bacterium and a Gram-negative bacterium against irradiation. Solution of pure DNA and bacterial strains Listeria monocytogenes and Escherichia coli were irradiated using gamma and UV-C rays. Extracted DNA from bacteria and pure DNA samples were then analysed by ELISA using anti-CPDs and anti-6-4 PPs monoclonal antibodies. The results show that gamma rays, as well as UV-C rays, induce the formation of CPDs and 6-4 PPs in DNA. During UV-C irradiation, the three samples showed a difference in their sensitivity against formation of CPDs (P≤0.05). Pure DNA was the most sensitive while the genome of L. monocytogenes was the most resistant. Also during UV-C irradiation, the genome of L. monocytogenes was the only one to show a significant resistance against formation of 6-4 PPs (P≤0.05). During gamma irradiation, for both types of lesion, pure DNA and the genome of E. coli did not show significant difference in their sensitivity (P>0.05) while the genome of L. monocytogenes showed a resistance against formation of CPDs and 6-4 PPs.

  20. Quartz crystal growth

    DOEpatents

    Baughman, Richard J.

    1992-01-01

    A process for growing single crystals from an amorphous substance that can undergo phase transformation to the crystalline state in an appropriate solvent. The process is carried out in an autoclave having a lower dissolution zone and an upper crystallization zone between which a temperature differential (.DELTA.T) is maintained at all times. The apparatus loaded with the substance, solvent, and seed crystals is heated slowly maintaining a very low .DELTA.T between the warmer lower zone and cooler upper zone until the amorphous substance is transformed to the crystalline state in the lower zone. The heating rate is then increased to maintain a large .DELTA.T sufficient to increase material transport between the zones and rapid crystallization. .alpha.-Quartz single crystal can thus be made from fused quartz in caustic solvent by heating to 350.degree. C. stepwise with a .DELTA.T of 0.25.degree.-3.degree. C., increasing the .DELTA.T to about 50.degree. C. after the fused quartz has crystallized, and maintaining these conditions until crystal growth in the upper zone is completed.

  1. Ethyl 3-[6-(4-meth­oxy­benzene­sulfon­amido)-2H-indazol-2-yl]propano­ate monohydrate

    PubMed Central

    Abbassi, Najat; Rakib, El Mostapha; Hannioui, Abdellah; Saadi, Mohamed; El Ammari, Lahcen

    2013-01-01

    In the title compound, C19H21N3O5S·H2O, the central indazole system is essentially planar (r.m.s. deviation = 0.012 Å), while both the benzene ring and the mean plane defined by the non-H atoms of the ethyl propionic ester unit (r.m.s. deviation = 0.087 Å) are nearly perpendicular to the indazole plane, as indicated by the dihedral angles of 82.45 (8) and 75.62 (8)°, respectively. Consequently, the mol­ecule adopts a U-shaped geometry. In the crystal, the water mol­ecule, which is linked to the indazole system by a strong O—H⋯N hydrogen bond, is also involved in two additional N—H⋯O and O—H⋯O inter­actions, which link the organic mol­ecules into chains along the b-axis direction. PMID:23424475

  2. Crystals in light.

    PubMed

    Kahr, Bart; Freudenthal, John; Gunn, Erica

    2010-05-18

    We have made images of crystals illuminated with polarized light for almost two decades. Early on, we abandoned photosensitive chemicals in favor of digital electrophotometry with all of the attendant advantages of quantitative intensity data. Accurate intensities are a boon because they can be used to analytically discriminate small effects in the presence of larger ones. The change in the form of our data followed camera technology that transformed picture taking the world over. Ironically, exposures in early photographs were presumed to correlate simply with light intensity, raising the hope that photography would replace sensorial interpretation with mechanical objectivity and supplant the art of visual photometry. This was only true in part. Quantitative imaging accurate enough to render the separation of crystalloptical quantities had to await the invention of the solid-state camera. Many pioneers in crystal optics were also major figures in the early history of photography. We draw out the union of optical crystallography and photography because the tree that connects the inventors of photography is a structure unmatched for organizing our work during the past 20 years, not to mention that silver halide crystallites used in chemical photography are among the most consequential "crystals in light", underscoring our title. We emphasize crystals that have acquired optical properties such as linear birefringence, linear dichroism, circular birefringence, and circular dichroism, during growth from solution. Other crystalloptical effects were discovered that are unique to curiously dissymmetric crystals containing embedded oscillators. In the aggregate, dyed crystals constitute a generalization of single crystal matrix isolation. Simple crystals provided kinetic stability to include guests such as proteins or molecules in excited states. Molecular lifetimes were extended for the preparation of laser gain media and for the study of the photodynamics of single

  3. Swimming in a crystal.

    PubMed

    Brown, Aidan T; Vladescu, Ioana D; Dawson, Angela; Vissers, Teun; Schwarz-Linek, Jana; Lintuvuori, Juho S; Poon, Wilson C K

    2016-01-07

    We study catalytic Janus particles and Escherichia coli bacteria swimming in a two-dimensional colloidal crystal. The Janus particles orbit individual colloids and hop between colloids stochastically, with a hopping rate that varies inversely with fuel (hydrogen peroxide) concentration. At high fuel concentration, these orbits are stable for 100s of revolutions, and the orbital speed oscillates periodically as a result of hydrodynamic, and possibly also phoretic, interactions between the swimmer and the six neighbouring colloids. Motile E. coli bacteria behave very differently in the same colloidal crystal: their circular orbits on plain glass are rectified into long, straight runs, because the bacteria are unable to turn corners inside the crystal.

  4. Analysis of Crystallization Kinetics

    NASA Technical Reports Server (NTRS)

    Kelton, Kenneth F.

    1997-01-01

    A realistic computer model for polymorphic crystallization (i.e., initial and final phases with identical compositions), which includes time-dependent nucleation and cluster-size-dependent growth rates, is developed and tested by fits to experimental data. Model calculations are used to assess the validity of two of the more common approaches for the analysis of crystallization data. The effects of particle size on transformation kinetics, important for the crystallization of many systems of limited dimension including thin films, fine powders, and nanoparticles, are examined.

  5. Hypersonic phononic crystals.

    PubMed

    Gorishnyy, T; Ullal, C K; Maldovan, M; Fytas, G; Thomas, E L

    2005-03-25

    In this Letter we propose the use of hypersonic phononic crystals to control the emission and propagation of high frequency phonons. We report the fabrication of high quality, single crystalline hypersonic crystals using interference lithography and show that direct measurement of their phononic band structure is possible with Brillouin light scattering. Numerical calculations are employed to explain the nature of the observed propagation modes. This work lays the foundation for experimental studies of hypersonic crystals and, more generally, phonon-dependent processes in nanostructures.

  6. Aluminum Nitride Crystal Growth

    DTIC Science & Technology

    1979-12-01

    UOSR-TR- 80 - 04 2 4EL4- G LEYEL ALUMINUM NITRIDE CRYSTAL GROWTH G.A. Slack FINAL REPORT Contract F49620-78-C-0021 DTIC Period Covered ELECTE I...Laboratory personnel worked on the problem of Aluminum Nitride Heat Sink Crystal Growth for the U.S. Air Force Office of Scientific Research under Contract...Number F44620-76-C-0039. From November 1, 1977 to the present we have worked on Aluminum Nitride and Boron Phosphide Crystal Growth under Contract NUmber

  7. Molecules in crystals

    NASA Astrophysics Data System (ADS)

    Spackman, Mark A.

    2013-04-01

    Hirshfeld surface analysis has developed from the serendipitous discovery of a novel partitioning of the crystal electron density into discrete molecular fragments, to a suite of computational tools used widely for the identification, analysis and discussion of intermolecular interactions in molecular crystals. The relationship between the Hirshfeld surface and very early ideas on the internal structure of crystals is outlined, and applications of Hirshfeld surface analysis are presented for three molecules of historical importance in the development of modern x-ray crystallography: hexamethylbenzene, hexamethylenetetramine and diketopiperazine.

  8. Crystallization on prestructured seeds.

    PubMed

    Jungblut, Swetlana; Dellago, Christoph

    2013-01-01

    The crystallization transition of an undercooled monodisperse Lennard-Jones fluid in the presence of small prestructured seeds is studied with transition path sampling combined with molecular dynamics simulations. Compared to the homogeneous crystallization, clusters of a few particles arranged into a face- and body-centered cubic structure enhance the crystallization, while icosahedrally ordered seeds do not change the reaction rate. We identify two distinct nucleation regimes-close to the seed and in the bulk. Crystallites form close to the face- and body-centered structures and tend to stay away from the icosahedrally ordered seeds.

  9. Single crystals of chitosan.

    PubMed

    Cartier, N; Domard, A; Chanzy, H

    1990-10-01

    Lamellar single crystals of chitosan were prepared at 125 degrees C by adding ammonia to a low DP fraction of chitosan dissolved in water. The crystals gave sharp electron diffraction diagrams which could be indexed in an orthorhombic P2(1)2(1)2(1) unit cell with a = 8.07 A, b = 8.44 A, c = 10.34 A. The unit cell contained two anti-parallel chitosan chains and no water molecules. It was found that cellulose microfibrils from Valonia ventricosa could act as nuclei for inducing the crystallization of chitosan on cellulose. This produced a shish-kebab morphology.

  10. Shaping Crystal-Crystal Phase Transitions

    NASA Astrophysics Data System (ADS)

    Du, Xiyu; van Anders, Greg; Dshemuchadse, Julia; Glotzer, Sharon

    Previous computational and experimental studies have shown self-assembled structure depends strongly on building block shape. New synthesis techniques have led to building blocks with reconfigurable shape and it has been demonstrated that building block reconfiguration can induce bulk structural reconfiguration. However, we do not understand systematically how this transition happens as a function of building block shape. Using a recently developed ``digital alchemy'' framework, we study the thermodynamics of shape-driven crystal-crystal transitions. We find examples of shape-driven bulk reconfiguration that are accompanied by first-order phase transitions, and bulk reconfiguration that occurs without any thermodynamic phase transition. Our results suggest that for well-chosen shapes and structures, there exist facile means of bulk reconfiguration, and that shape-driven bulk reconfiguration provides a viable mechanism for developing functional materials.

  11. Computer Modeling of Crystallization and Crystal Size distributions

    NASA Astrophysics Data System (ADS)

    Amenta, R. V.

    2002-05-01

    The crystal size distribution of an igneous rock has been shown to be related to the crystallization kinetics. In order to better understand crystallization processes, the nucleation and growth of crystals in a closed system is modeled computationally and graphically. Units of volume analogous to unit cells are systematically attached to stationary crystal nuclei. The number of volume units attached to each crystal per growth stage is proportional to the crystal size insuring that crystal dimensional growth rates are constant regardless of their size. The number of new crystal nuclei per total system volume that form in each growth stage increases exponentially Cumulative crystal size distributions (CCSD) are determined for various stages of crystallization (30 percent, 60 pct, etc) from a database generated by the computer model, and each distribution is fit to an exponential function of the same form. Simulation results show that CCSD functions appear to fit the data reasonably well (R-square) with the greatest misfit at 100 pct crystallization. The crystal size distribution at each pct crystallization can be obtained from the derivative of the respective CCSD function. The log form of each crystal size distribution (CSD) is a linear function with negative slope. Results show that the slopes of the CSD functions at pcts crystallization up to 90 pct are parallel, but the slope at 100 pct crystallization differs from the others although still in approximate alignment. We suggest that real crystallization of igneous rocks may show this pattern. In the early stages of crystallization crystals are far apart and CSD's are ideal as predicted by theory based on growth of crystals in a brine. At advanced stages of crystallization growth collision boundaries develop between crystals. As contiguity increases crystals become blocked and inactive because they can no longer grow. As crystallization approaches 100 pct a significant number of inactive crystals exist resulting in

  12. Ice crystal terminal velocities

    NASA Technical Reports Server (NTRS)

    Heymsfield, A.

    1972-01-01

    Terminal velocities of different ice crystal forms were calculated using the most recent ice crystal drag coefficients, aspect ratios, and densities. The equations derived were primarily for use in calculating precipitation rates by sampling particles with an aircraft in cirrus clouds, and determining particle size in cirrus clouds by Doppler radar. However, the equations are sufficiently general for determining particle terminal velocity at any altitude, and most any crystal type. Two sets of equations were derived. The general equations provide a good estimate of terminal velocities at any altitude. The specific equations are a set of equations for ice crystal terminal velocities at 1000 mb. The calculations are in good agreement with terminal velocity measurements. The results from the present study were also compared to prior calculations by others and seem to give more reasonable results, particularly at higher altitudes.

  13. Ice crystal terminal velocities.

    NASA Technical Reports Server (NTRS)

    Heymsfield, A.

    1972-01-01

    Terminal velocities of different ice crystal forms were calculated, using the most recent ice crystal drag coefficients, aspect ratios, and densities. The equations derived were primarily for use in calculating precipitation rates by sampling particles with an aircraft in cirrus clouds, and determining particle size in cirrus clouds by Doppler radar. However, the equations are sufficiently general for determining particle terminal velocity at any altitude, and almost any crystal type. Two sets of equations were derived. The 'general' equations provide a good estimate of terminal velocities at any altitude. The 'specific' equations are a set of equations for ice crystal terminal velocities at 1000 mb. The calculations are in good agreement with terminal velocity measurements. The results from the present study were also compared to prior calculations by others and seem to give more reasonable results, particularly at higher altitudes.

  14. Crystallization of Silicon Ribbons

    NASA Technical Reports Server (NTRS)

    Leipold, M. H.

    1984-01-01

    Purity constraints for reasonable solar-cell efficiency require that silicon-ribbon growth for photovoltaics occur in a regime in which constitutional supercooling or other compositional effects on the crystallization front are not important. A major consideration in the fundamentals of crystallization is the removal of the latent heat of fusion. The direction of removal, compared with the growth direction, has a major influence on the crystallization rate and the development of localized stresses. The detailed shape of the crystallization front appears to have two forms: that required for dendritic-web growth, and that occurring in all others. After the removal of the latent heat of fusion, the thermal-mechanical behavior of all ribbons appears similar within the constraints of the exothermal gradient. The technological constraints in achieving the required thermal and mechanical conditions vary widely among the growth processes.

  15. Shaping Crystals using Electrophoresis

    NASA Astrophysics Data System (ADS)

    Palacci, Jeremie; Mackiewicz, Kristian

    2016-11-01

    Electrophoresis is size and shape independent as stressed by Morrison in his seminal paper. Here we present an original approach to reshape colloidal crystals using an electric field as a carving tool.

  16. Diffusion in Coulomb crystals.

    PubMed

    Hughto, J; Schneider, A S; Horowitz, C J; Berry, D K

    2011-07-01

    Diffusion in Coulomb crystals can be important for the structure of neutron star crusts. We determine diffusion constants D from molecular dynamics simulations. We find that D for Coulomb crystals with relatively soft-core 1/r interactions may be larger than D for Lennard-Jones or other solids with harder-core interactions. Diffusion, for simulations of nearly perfect body-centered-cubic lattices, involves the exchange of ions in ringlike configurations. Here ions "hop" in unison without the formation of long lived vacancies. Diffusion, for imperfect crystals, involves the motion of defects. Finally, we find that diffusion, for an amorphous system rapidly quenched from Coulomb parameter Γ=175 to Coulomb parameters up to Γ=1750, is fast enough that the system starts to crystalize during long simulation runs. These results strongly suggest that Coulomb solids in cold white dwarf stars, and the crust of neutron stars, will be crystalline and not amorphous.

  17. No warmup crystal oscillator

    NASA Technical Reports Server (NTRS)

    Phillips, D. H.

    1982-01-01

    During warmup, crystal oscillators often show a frequency offset as large as 1 part in 10 to the 5th power. If timing information is transferred to the oscillator and then the oscillator is allowed to warmup, a timing error greater than 1 millisecond will occur. For many applications, it is unsuitable to wait for the oscillator to warmup. For medium accuracy timing requirements where overall accuracies in the order of 1 millisecond are required, a no warmup crystal concept was developed. The concept utilizes two crystal oscillator, used sequentially to avoid using a crystal oscillator for timing much higher frequency accuracy once warmed up. The accuracy achieved with practical TCXOs at initial start over a range of temperatures is discussed. A second design utilizing two oven controlled oscillators is also discussed.

  18. Crystallization of supercooled liquids

    NASA Astrophysics Data System (ADS)

    Odagaki, Takashi; Shikuya, Yuuna

    2014-03-01

    We investigate the crystallization process on the basis of the free energy landscape (FEL) approach to non-equilibrium systems. In this approach, the crystallization time is given by the first passage time of the representative point arriving at the crystalline basin in the FEL. We devise an efficient method to obtain the first passage time exploiting a specific boundary condition. Applying this formalism to a model system, we show that the first passage time is determined by two competing effects; one is the difference in the free energy of the initial and the final basins, and the other is the slow relaxation. As the temperature is reduced, the former accelerates the crystallization and the latter retards it. We show that these competing effects give rise to the typical nose-shape form of the time-temperature transformation curve and that the retardation of the crystallization is related to the mean waiting time of the jump motion.

  19. Crystallization behavior of anorthite

    NASA Technical Reports Server (NTRS)

    Klein, L.; Uhlmann, D. R.

    1974-01-01

    The growth rate of anorthite crystals from the melt is studied as a function of temperature with undercooling in the ranges 52-152 and 402-652 degrees C. The triclinic form is invariably observed as the crystallization product, growth is preferentially in the c direction, and the interface morphology is faceted. Significant growth rate anisotropy is indicated. The maximum growth rate of anorthite from the melt is higher than for anorthite-rich lunar compositions. Recent computer studies are combined with experimental data to estimate the heat of fusion of anorthite as 28000-45000 cal/mol; the corresponding range for entropy of fusion is (7.8-12)R (where R is the gas constant). The observations and kinetic data support Jackson's predictions concerning materials with large entropies of fusion and his suggestion that entropy of fusion is an important parameter for characterizing the crystal-liquid interface and the nature of the crystallization process.

  20. Crystal-Clear Technology.

    ERIC Educational Resources Information Center

    Ondris-Crawford, Renate J.; And Others

    1993-01-01

    Provides diagrams to aid in discussing polymer dispersed liquid crystal (PDLC) technology. Equipped with a knowledge of PDLC, teachers can provide students with insight on how the gap between basic science and technology is bridged. (ZWH)

  1. Diffusion in Coulomb crystals

    SciTech Connect

    Hughto, J.; Schneider, A. S.; Horowitz, C. J.; Berry, D. K.

    2011-07-15

    Diffusion in Coulomb crystals can be important for the structure of neutron star crusts. We determine diffusion constants D from molecular dynamics simulations. We find that D for Coulomb crystals with relatively soft-core 1/r interactions may be larger than D for Lennard-Jones or other solids with harder-core interactions. Diffusion, for simulations of nearly perfect body-centered-cubic lattices, involves the exchange of ions in ringlike configurations. Here ions ''hop'' in unison without the formation of long lived vacancies. Diffusion, for imperfect crystals, involves the motion of defects. Finally, we find that diffusion, for an amorphous system rapidly quenched from Coulomb parameter {Gamma}=175 to Coulomb parameters up to {Gamma}=1750, is fast enough that the system starts to crystalize during long simulation runs. These results strongly suggest that Coulomb solids in cold white dwarf stars, and the crust of neutron stars, will be crystalline and not amorphous.

  2. Study of Geomagnetic Anomalies Related to Earthquakes at Pisco Peru 2007 (M=8.0) and at Taiwan 2009 (M= 6.4) (Invited)

    NASA Astrophysics Data System (ADS)

    Yumoto, K.; Takla, E.; Ishitsuka, J.; Rosales, D.; Dutra, S. L.; Liu, J. G.; Kakinami, Y.; Uozumi, T.; Abe, S.

    2010-12-01

    The Space Environment Research Center (SERC), Kyushu University deployed the MAGnetic Data Acqusition System (MAGDAS) at 53 stations along the 210- and 96-degree magnetic meridians (MM) and the magnetic Dip equator, and three FM-CW radars along the 210-degree MM during the International Heliophysical Year (IHY) period of 2005-2009 (see http://magdas.serc.kyushu-u.ac.jp/ and http://magdas2.serc.kyushu-u.ac.jp/). By analyzing these new MAGDAS data, we can perform a real-time monitoring for understanding the plasma and electromagnetic environment changes in geospace and lithosphere. In the present paper, we will introduce geomagnetic anomalies associated with larger earthquakes (EQs), observed at the MAGDAS stations. The first event is the Pisco earthquake (M=8.0) on August 15, 2007, which was the largest shallow earthquake and affected the coastal area south of Lima for 250 years. This occurred at the boundary between the Nazca and South American tectonic plates. Geomagnetic data from the MAGDAS Ancon (ANC; about 180 km from the epicenter), the INTERMAGNET Huancayo (HUA;about 190 km from the epicenter) and the MAGDAS Eusebio (EUS; about 39°east from ANC) stations were analyzed to clarify if there is a relation between the geomagnetic variations and the tectonic activities at Peru during 2007. Our results indicate both long- (several months) and short-term (daily) anomalous geomagnetic variations (H and Z components) in relation with these seismic activities. In addition, there were anomalous signals of Pc 3 polarization (Z/H) a few months before the onset of seismic activities. The second event is the Taiwan earthquake of M=6.4 on the Richter scale, which occurred at depth ≈ 45 km, on 19th of December 2009. The epicenter was located about 20 Km away from our MAGDAS Hualien (HLN) station. The MAGDAS Amami-ohshima (AMA) station in Japan was used as a remote reference station. The geomagnetic components (H, D and Z) at the HLN station showed baseline fluctuations

  3. Protein Crystal Quality Studies

    NASA Technical Reports Server (NTRS)

    1998-01-01

    Eddie Snell, Post-Doctoral Fellow the National Research Council (NRC) uses a reciprocal space mapping diffractometer for macromolecular crystal quality studies. The diffractometer is used in mapping the structure of macromolecules such as proteins to determine their structure and thus understand how they function with other proteins in the body. This is one of several analytical tools used on proteins crystallized on Earth and in space experiments. Photo credit: NASA/Marshall Space Flight Center (MSFC)

  4. SINGLE CRYSTAL NEUTRON DIFFRACTION.

    SciTech Connect

    KOETZLE,T.F.

    2001-03-13

    Single-crystal neutron diffraction measures the elastic Bragg reflection intensities from crystals of a material, the structure of which is the subject of investigation. A single crystal is placed in a beam of neutrons produced at a nuclear reactor or at a proton accelerator-based spallation source. Single-crystal diffraction measurements are commonly made at thermal neutron beam energies, which correspond to neutron wavelengths in the neighborhood of 1 Angstrom. For high-resolution studies requiring shorter wavelengths (ca. 0.3-0.8 Angstroms), a pulsed spallation source or a high-temperature moderator (a ''hot source'') at a reactor may be used. When complex structures with large unit-cell repeats are under investigation, as is the case in structural biology, a cryogenic-temperature moderator (a ''cold source'') may be employed to obtain longer neutron wavelengths (ca. 4-10 Angstroms). A single-crystal neutron diffraction analysis will determine the crystal structure of the material, typically including its unit cell and space group, the positions of the atomic nuclei and their mean-square displacements, and relevant site occupancies. Because the neutron possesses a magnetic moment, the magnetic structure of the material can be determined as well, from the magnetic contribution to the Bragg intensities. This latter aspect falls beyond the scope of the present unit; for information on magnetic scattering of neutrons see Unit 14.3. Instruments for single-crystal diffraction (single-crystal diffractometers or SCDs) are generally available at the major neutron scattering center facilities. Beam time on many of these instruments is available through a proposal mechanism. A listing of neutron SCD instruments and their corresponding facility contacts is included in an appendix accompanying this unit.

  5. Protein Crystal Quality Studies

    NASA Technical Reports Server (NTRS)

    1998-01-01

    Eddie Snell, Post-Doctoral Fellow the National Research Council (NRC) uses a reciprocal space mapping diffractometer for macromolecular crystal quality studies. The diffractometer is used in mapping the structure of macromolecules such as proteins to determine their structure and thus understand how they function with other proteins in the body. This is one of several analytical tools used on proteins crystallized on Earth and in space experiments. Photo credit: NASA/Marshall Space Flight Center (MSFC)

  6. Ordering in Conformal Crystals

    NASA Astrophysics Data System (ADS)

    Soni, Vishal; Gomez, Leopoldo; Irvine, William

    2014-03-01

    Condensed matter systems commonly undergo ordering processes that are frustrated by geometric constraints. Experiments on interfacial colloidal systems have resulted in several recent insights into the two dimensional ordering of crystalline lattices frustrated by Gaussian curvature. We study the ordering of flat colloidal Wigner crystals immersed in an axially symmetric potential. By relating the resulting inhomogenous structure to a lattice with Gaussian curvature, we investigate the role of topological defects in organizing the conformal crystal-like ground state.

  7. SINGLE CRYSTAL NEUTRON DIFFRACTION.

    SciTech Connect

    KOETZLE,T.F.

    2001-03-13

    Single-crystal neutron diffraction measures the elastic Bragg reflection intensities from crystals of a material, the structure of which is the subject of investigation. A single crystal is placed in a beam of neutrons produced at a nuclear reactor or at a proton accelerator-based spallation source. Single-crystal diffraction measurements are commonly made at thermal neutron beam energies, which correspond to neutron wavelengths in the neighborhood of 1 Angstrom. For high-resolution studies requiring shorter wavelengths (ca. 0.3-0.8 Angstroms), a pulsed spallation source or a high-temperature moderator (a ''hot source'') at a reactor may be used. When complex structures with large unit-cell repeats are under investigation, as is the case in structural biology, a cryogenic-temperature moderator (a ''cold source'') may be employed to obtain longer neutron wavelengths (ca. 4-10 Angstroms). A single-crystal neutron diffraction analysis will determine the crystal structure of the material, typically including its unit cell and space group, the positions of the atomic nuclei and their mean-square displacements, and relevant site occupancies. Because the neutron possesses a magnetic moment, the magnetic structure of the material can be determined as well, from the magnetic contribution to the Bragg intensities. This latter aspect falls beyond the scope of the present unit; for information on magnetic scattering of neutrons see Unit 14.3. Instruments for single-crystal diffraction (single-crystal diffractometers or SCDs) are generally available at the major neutron scattering center facilities. Beam time on many of these instruments is available through a proposal mechanism. A listing of neutron SCD instruments and their corresponding facility contacts is included in an appendix accompanying this unit.

  8. Liquid Crystal Airborne Display

    DTIC Science & Technology

    1977-08-01

    81/2X 11- 10 -9 .8 display using a large advertising alphanimeric ( TCI ) has been added to the front of the optical box used in the F-4 aircraft for HUD...properties over a wide range of tempera - tures, including normal room temperature. What are Liquid Crystals? Liquid crystals have been classified in three...natic fanctions and to present data needed for the semi- automatic and manual control of system functions. Existing aircraft using CRT display

  9. Active cluster crystals

    NASA Astrophysics Data System (ADS)

    Delfau, Jean-Baptiste; López, Cristóbal; Hernández-García, Emilio

    2017-09-01

    We study the appearance and properties of cluster crystals (solids in which the unit cell is occupied by a cluster of particles) in a two-dimensional system of self-propelled active Brownian particles with repulsive interactions. Self-propulsion deforms the clusters by depleting particle density inside, and for large speeds it melts the crystal. Continuous field descriptions at several levels of approximation allow us to identify the relevant physical mechanisms.

  10. Macromolecular Crystal Quality

    NASA Technical Reports Server (NTRS)

    Snell, Edward H.; Borgstahl, Gloria E. O.; Bellamy, Henry D.; Curreri, Peter A. (Technical Monitor)

    2001-01-01

    There are many ways of judging a good crystal. Which we use depends on the qualities we seek. For gemstones size, clarity and impurity levels (color) are paramount. For the semiconductor industry purity is probably the most important quality. For the structural crystallographer the primary desideratum is the somewhat more subtle concept of internal order. In this chapter we discuss the effect of internal order (or the lack of it) on the crystal's diffraction properties.

  11. Crystal growth of drug materials by spherical crystallization

    NASA Astrophysics Data System (ADS)

    Szabó-Révész, P.; Hasznos-Nezdei, M.; Farkas, B.; Göcző, H.; Pintye-Hódi, K.; Erős, I.

    2002-04-01

    One of the crystal growth processes is the production of crystal agglomerates by spherical crystallization. Agglomerates of drug materials were developed by means of non-typical (magnesium aspartate) and typical (acetylsalicylic acid) spherical crystallization techniques. The growth of particle size and the spherical form of the agglomerates resulted in formation of products with good bulk density, flow, compactibility and cohesivity properties. The crystal agglomerates were developed for direct capsule-filling and tablet-making.

  12. Reduced efficiency and increased mutagenicity of translesion DNA synthesis across a TT cyclobutane pyrimidine dimer, but not a TT 6-4 photoproduct, in human cells lacking DNA polymerase eta.

    PubMed

    Hendel, Ayal; Ziv, Omer; Gueranger, Quentin; Geacintov, Nicholas; Livneh, Zvi

    2008-10-01

    Xeroderma pigmentosum variant (XPV) patients carry germ-line mutations in DNA polymerase eta (poleta), a major translesion DNA synthesis (TLS) polymerase, and exhibit severe sunlight sensitivity and high predisposition to skin cancer. Using a quantitative TLS assay system based on gapped plasmids we analyzed TLS across a site-specific TT CPD (thymine-thymine cyclobutane pyrimidine dimer) or TT 6-4 PP (thymine-thymine 6-4 photoproduct) in three pairs of poleta-proficient and deficient human cells. TLS across the TT CPD lesion was reduced by 2.6-4.4-fold in cells lacking poleta, and exhibited a strong 6-17-fold increase in mutation frequency at the TT CPD. All targeted mutations (74%) in poleta-deficient cells were opposite the 3'T of the CPD, however, a significant fraction (23%) were semi-targeted to the nearest nucleotides flanking the CPD. Deletions and insertions were observed at a low frequency, which increased in the absence of poleta, consistent with the formation of double strand breaks due to defective TLS. TLS across TT 6-4 PP was about twofold lower than across CPD, and was marginally reduced in poleta-deficient cells. TLS across TT 6-4 PP was highly mutagenic (27-63%), with multiple mutations types, and no significant difference between cells with or without poleta. Approximately 50% of the mutations formed were semi-targeted, of which 84-93% were due to the insertion of an A opposite the template G 5' to the 6-4 PP. These results, which are consistent with the UV hyper-mutability of XPV cells, highlight the critical role of poleta in error-free TLS across CPD in human cells, and suggest a potential involvement, although minor, of poleta in TLS across 6-4 PP under some conditions.

  13. Engineering Crystal Morphology

    NASA Astrophysics Data System (ADS)

    Dandekar, Preshit; Kuvadia, Zubin B.; Doherty, Michael F.

    2013-07-01

    Crystallization is an important separation and particle formation technique in the manufacture of high-value-added products. During crystallization, many physicochemical characteristics of the substance are established. Such characteristics include crystal polymorph, shape and size, chemical purity and stability, reactivity, and electrical and magnetic properties. However, control over the physical form of crystalline materials has remained poor, due mainly to an inadequate understanding of the basic growth and dissolution mechanisms, as well as of the influence of impurities, additives, and solvents on the growth rate of individual crystal faces. Crystal growth is a surface-controlled phenomenon in which solute molecules are incorporated into surface lattice sites to yield the bulk long-range order that characterizes crystalline materials. In this article, we describe some recent advances in crystal morphology engineering, with a special focus on a new mechanistic model for spiral growth. These mechanistic ideas are simple enough that they can be made to work and accurate enough that they are useful.

  14. Phononic crystal diffraction gratings

    NASA Astrophysics Data System (ADS)

    Moiseyenko, Rayisa P.; Herbison, Sarah; Declercq, Nico F.; Laude, Vincent

    2012-02-01

    When a phononic crystal is interrogated by an external source of acoustic waves, there is necessarily a phenomenon of diffraction occurring on the external enclosing surfaces. Indeed, these external surfaces are periodic and the resulting acoustic diffraction grating has a periodicity that depends on the orientation of the phononic crystal. This work presents a combined experimental and theoretical study on the diffraction of bulk ultrasonic waves on the external surfaces of a 2D phononic crystal that consists of a triangular lattice of steel rods in a water matrix. The results of transmission experiments are compared with theoretical band structures obtained with the finite-element method. Angular spectrograms (showing frequency as a function of angle) determined from diffraction experiments are then compared with finite-element simulations of diffraction occurring on the surfaces of the crystal. The experimental results show that the diffraction that occurs on its external surfaces is highly frequency-dependent and has a definite relation with the Bloch modes of the phononic crystal. In particular, a strong influence of the presence of bandgaps and deaf bands on the diffraction efficiency is found. This observation opens perspectives for the design of efficient phononic crystal diffraction gratings.

  15. The Crystallization of Monosodium Urate

    PubMed Central

    Martillo, Miguel A.; Nazzal, Lama; Crittenden, Daria B.

    2014-01-01

    Gout is a common crystal-induced arthritis, in which monosodium urate (MSU) crystals precipitate within joints and soft tissues and elicit an inflammatory response. The causes of elevated serum urate and the inflammatory pathways activated by MSU crystals have been well studied, but less is known about the processes leading to crystal formation and growth. Uric acid, the final product of purine metabolism, is a weak acid that circulates as the deprotonated urate anion under physiologic conditions, and combines with sodium ions to form MSU. MSU crystals are known to have a triclinic structure, in which stacked sheets of purine rings form the needle-shaped crystals that are observed microscopically. Exposed, charged crystal surfaces are thought to allow for interaction with phospholipid membranes and serum factors, playing a role in the crystal-mediated inflammatory response. While hyperuricemia is a clear risk factor for gout, local factors have been hypothesized to play a role in crystal formation, such as temperature, pH, mechanical stress, cartilage components, and other synovial and serum factors. Interestingly, several studies suggest that MSU crystals may drive the generation of crystal-specific antibodies that facilitate future MSU crystallization. Here, we review MSU crystal biology, including a discussion of crystal structure, effector function, and factors thought to play a role in crystal formation. We also briefly compare MSU biology to that of uric acid stones causing nephrolithasis, and consider the potential treatment implications of MSU crystal biology. PMID:24357445

  16. Crystal growth of artificial snow

    NASA Technical Reports Server (NTRS)

    Kimura, S.; Oka, A.; Taki, M.; Kuwano, R.; Ono, H.; Nagura, R.; Narimatsu, Y.; Tanii, J.; Kamimiytat, Y.

    1984-01-01

    Snow crystals were grown onboard the space shuttle during STS-7 and STS-8 to facilitate the investigation of crystal growth under conditions of weightlessness. The experimental design and hardware are described. Space-grown snow crystals were polyhedrons looking like spheres, which were unlike snow crystals produced in experiments on Earth.

  17. High-throughput crystallization screening.

    PubMed

    Skarina, Tatiana; Xu, Xiaohui; Evdokimova, Elena; Savchenko, Alexei

    2014-01-01

    Protein structure determination by X-ray crystallography is dependent on obtaining a single protein crystal suitable for diffraction data collection. Due to this requirement, protein crystallization represents a key step in protein structure determination. The conditions for protein crystallization have to be determined empirically for each protein, making this step also a bottleneck in the structure determination process. Typical protein crystallization practice involves parallel setup and monitoring of a considerable number of individual protein crystallization experiments (also called crystallization trials). In these trials the aliquots of purified protein are mixed with a range of solutions composed of a precipitating agent, buffer, and sometimes an additive that have been previously successful in prompting protein crystallization. The individual chemical conditions in which a particular protein shows signs of crystallization are used as a starting point for further crystallization experiments. The goal is optimizing the formation of individual protein crystals of sufficient size and quality to make them suitable for diffraction data collection. Thus the composition of the primary crystallization screen is critical for successful crystallization.Systematic analysis of crystallization experiments carried out on several hundred proteins as part of large-scale structural genomics efforts allowed the optimization of the protein crystallization protocol and identification of a minimal set of 96 crystallization solutions (the "TRAP" screen) that, in our experience, led to crystallization of the maximum number of proteins.

  18. Signal enhancement for gene detection based on a redox reaction of [Fe(CN)(6)](4-) mediated by ferrocene at the terminal of a peptide nucleic acid as a probe with hybridization-amenable conformational flexibility.

    PubMed

    Aoki, Hiroshi; Tao, Hiroaki

    2008-07-01

    Electrochemically enhanced DNA detection was demonstrated by utilizing the couple of a synthesized ferrocene-terminated peptide nucleic acid (PNA) with a cysteine anchor and a sacrificial electron donor [Fe(CN)(6)](4-). DNA detection sensors were prepared by modifying a gold electrode surface with a mixed monolayer of the probe PNA and 11-hydroxy-1-undecanethiol (11-HUT), protecting [Fe(CN)(6)](4-) from any unexpected redox reaction. Before hybridization, the terminal ferrocene moiety of the probe was subject to a redox reaction due to the flexible probe structure and, in the presence of [Fe(CN)(6)](4-), the observed current was amplified based on regeneration of the ferrocene moiety. Hybridization decreased the redox current of the ferrocene. This occurred because hybridization rigidified the probe structure: the ferrocene moiety was then removed from the electrode surface, and the redox reaction of [Fe(CN)(6)](4-) was again prevented. The change in the anodic current before and after hybridization was enhanced 1.75-fold by using the electron donor [Fe(CN)(6)](4-). Sequence-specific detection of the complementary target DNA was also demonstrated.

  19. Crystal Ball Functional Model

    NASA Astrophysics Data System (ADS)

    Plotnick, David

    2016-09-01

    The A2 collaboration of the MAinz MIkrotron is dedicated to studying meson production and nucleon structure and behavior via photon scattering. The photons are made via bremsstrahlung process and energy-tagged using the Glasgow Photon tagger. The photon beam then interacts in a variety of targets: cryogenic, polarized or solid state, and scattered particles deposit their energy within the NaI crystals. Scintillators are able to give results on particles energy and time. Events are reconstructed by combining information from the Tagging spectrometer, the Crystal Ball detector, the TAPS forward wall spectrometer, a Cherenkov detector, and multi-wire proportional chambers. To better understand the detector and experimental events, a live display was built to show energies deposited in crystals in real-time. In order to show a range of energies and particles, addressable LEDs that are individually programmable were used. To best replicate the Crystal Ball, 3D printing technology was employed to build a similar highly segmented icosahedron that can hold each LED, creating a 3D representation of what photons see during experiments. The LEDs were controlled via Arduino microcontroller. Finally, we implemented the Experimental Physics and Industrial Control System to grab live event data, and a simple program converts this data in to color and crystal number data that is able to communicate with the Arduino. Using these simple parts, we can better visualize and understand the tools used in nuclear physics. This material is based upon work supported by the National Science Foundation Grant No. IIA-1358175.

  20. Crystal Growth Control

    NASA Technical Reports Server (NTRS)

    Duval, Walter M. B.; Batur, Celal; Bennett, Robert J.

    1997-01-01

    We present an innovative design of a vertical transparent multizone furnace which can operate in the temperature range of 25 C to 750 C and deliver thermal gradients of 2 C/cm to 45 C/cm for the commercial applications to crystal growth. The operation of the eight zone furnace is based on a self-tuning temperature control system with a DC power supply for optimal thermal stability. We show that the desired thermal profile over the entire length of the furnace consists of a functional combination of the fundamental thermal profiles for each individual zone obtained by setting the set-point temperature for that zone. The self-tuning system accounts for the zone to zone thermal interactions. The control system operates such that the thermal profile is maintained under thermal load, thus boundary conditions on crystal growth ampoules can be predetermined prior to crystal growth. Temperature profiles for the growth of crystals via directional solidification, vapor transport techniques, and multiple gradient applications are shown to be easily implemented. The unique feature of its transparency and ease of programming thermal profiles make the furnace useful for scientific and commercial applications for the determination of process parameters to optimize crystal growth conditions.

  1. Introduction to protein crystallization.

    PubMed

    McPherson, Alexander; Gavira, Jose A

    2014-01-01

    Protein crystallization was discovered by chance about 150 years ago and was developed in the late 19th century as a powerful purification tool and as a demonstration of chemical purity. The crystallization of proteins, nucleic acids and large biological complexes, such as viruses, depends on the creation of a solution that is supersaturated in the macromolecule but exhibits conditions that do not significantly perturb its natural state. Supersaturation is produced through the addition of mild precipitating agents such as neutral salts or polymers, and by the manipulation of various parameters that include temperature, ionic strength and pH. Also important in the crystallization process are factors that can affect the structural state of the macromolecule, such as metal ions, inhibitors, cofactors or other conventional small molecules. A variety of approaches have been developed that combine the spectrum of factors that effect and promote crystallization, and among the most widely used are vapor diffusion, dialysis, batch and liquid-liquid diffusion. Successes in macromolecular crystallization have multiplied rapidly in recent years owing to the advent of practical, easy-to-use screening kits and the application of laboratory robotics. A brief review will be given here of the most popular methods, some guiding principles and an overview of current technologies.

  2. Introduction to protein crystallization

    PubMed Central

    McPherson, Alexander; Gavira, Jose A.

    2014-01-01

    Protein crystallization was discovered by chance about 150 years ago and was developed in the late 19th century as a powerful purification tool and as a demonstration of chemical purity. The crystallization of proteins, nucleic acids and large biological complexes, such as viruses, depends on the creation of a solution that is supersaturated in the macromolecule but exhibits conditions that do not significantly perturb its natural state. Supersaturation is produced through the addition of mild precipitating agents such as neutral salts or polymers, and by the manipulation of various parameters that include temperature, ionic strength and pH. Also important in the crystallization process are factors that can affect the structural state of the macromolecule, such as metal ions, inhibitors, cofactors or other conventional small molecules. A variety of approaches have been developed that combine the spectrum of factors that effect and promote crystallization, and among the most widely used are vapor diffusion, dialysis, batch and liquid–liquid diffusion. Successes in macromolecular crystallization have multiplied rapidly in recent years owing to the advent of practical, easy-to-use screening kits and the application of laboratory robotics. A brief review will be given here of the most popular methods, some guiding principles and an overview of current technologies. PMID:24419610

  3. Sound absorption enhancement of nonwoven felt by using coupled membrane - sonic crystal inclusion

    NASA Astrophysics Data System (ADS)

    Fitriani, M. C.; Yahya, I.; Harjana; Ubaidillah; Aditya, F.; Siregar, Y.; Moeliono, M.; Sulaksono, S.

    2016-11-01

    The experimental results from laboratory test on the sound absorption performance of nonwoven felt with an array thin tubes and sonic crystal inclusions reported in this paper. The nonwoven felt sample was produced by a local company with 15 mm in its thickness and 900 gsm. The 6.4 mm diameter plastic straw was used to construct the thin tubes array while the sonic crystal is arranged in a 4 × 4 lattice crystal formation. It made from a PVC cylinder with 17 mm and 50 mm in diameter and length respectively. All cylinders have two holes positioned on 10 mm and 25 mm from the base. The results show that both treatments, array of thin tube and sonic crystal inclusions are effectively increased the sound absorption coefficient of the nonwoven felt significantly especially in the low frequency range starting from 200Hz.

  4. Crystallization of brushite from EDTA-chelated calcium in agar gels

    NASA Astrophysics Data System (ADS)

    Plovnick, Ross H.

    1991-10-01

    Brushite (dicalcium phosphate dihydrate, CaHPO 4·2H 2O, DCPD) has been crystallized from ethylenediaminetetraacetic acid (EDTA)-chelated calcium in agar gels at initial pH 4.5-6.4 and Ca/P molar ratio above about 0.8. White, spherular crystalline DCPD aggregates up to 1 mm in diameter grew in 8-10 weeks. Liesegang ring were occassionally observed at initial gel pH 5 and Ca/P molar ratio near 1. Crystals were characterized by X-ray diffraction analysis, scanning electron microscopy, and infrared absorption spectroscopy. Brushite crystals were also grown in agar gels with either unchelated Ca initially present in the gels and EDTA in overlying solutions, or EDTA initially present in the gels and unchelated Ca in overlying solutions. These crystals grew as 2-3 mm aggregates mainly within 1-3 cm of the gel-solution interface.

  5. Kinetic study of the oxidation of [Fe(CN) 6] 4- by [Co(NH 3) 4pzCO 2] 2+ and SO82- in the presence of the tripodal ligand Tren Aminopropil

    NASA Astrophysics Data System (ADS)

    García-España, E.; Sornosa-Ten, A.; Albelda, M. T.; Sánchez, F.; Marchena, M.

    2011-03-01

    Oxidations (electron transfers) of [Fe(CN) 6] 4- by [Co(NH 3) 4pzCO 2] 2+ and SO82- have been studied in solutions containing the receptor N,N',N″-(aminopropil)-tris (2-aminoetil) amina [Tren Aminopropil, TAL], which can incorporate [Fe(CN) 6] 4- and SO82- but not the cobalt complex. The results can be explained using the Brönsted equation that allows to obtain the binding constant of the transition state, a parameter that the Pseudophase Model cannot provide.

  6. Protein crystals and their growth

    NASA Technical Reports Server (NTRS)

    Chernov, Alexander A.

    2003-01-01

    Recent results on the associations between protein molecules in crystal lattices, crystal-solution surface energy, elastic properties, strength, and spontaneous crystal cracking are reviewed and discussed. In addition, some basic approaches to understanding the solubility of proteins are followed by an overview of crystal nucleation and growth. It is argued that variability of mixing in batch crystallization may be a source of the variation in the number of crystals ultimately appearing in the sample. The frequency at which new molecules join a crystal lattice is measured by the kinetic coefficient and is related to the observed crystal growth rate. Numerical criteria used to discriminate diffusion- and kinetic-limited growth are discussed on this basis. Finally, the creation of defects is discussed with an emphasis on the role of impurities and convection on macromolecular crystal perfection.

  7. Protein Crystals and their Growth

    NASA Technical Reports Server (NTRS)

    Chernov, A. A.

    2004-01-01

    Recent results on binding between protein molecules in crystal lattice, crystal-solution surface energy, elastic properties and strength and spontaneous crystal cracking are reviewed and discussed in the first half of this paper (Sea 2-4). In the second par&, some basic approaches to solubility of proteins are followed by overview on crystal nucleation and growth (Sec 5). It is argued that variability of mixing in batch crystallization may be a source for scattering of crystal number ultimately appearing in the batch. Frequency at which new molecules join crystal lattice is measured by kinetic coefficient and related to the observable crystal growth rate. Numerical criteria to discriminate diffusion and kinetic limited growth are discussed on this basis in Sec 7. In Sec 8, creation of defects is discussed with the emphasis on the role of impurities and convection on macromolecular crystal I;erfection.

  8. Protein crystals and their growth

    NASA Technical Reports Server (NTRS)

    Chernov, Alexander A.

    2003-01-01

    Recent results on the associations between protein molecules in crystal lattices, crystal-solution surface energy, elastic properties, strength, and spontaneous crystal cracking are reviewed and discussed. In addition, some basic approaches to understanding the solubility of proteins are followed by an overview of crystal nucleation and growth. It is argued that variability of mixing in batch crystallization may be a source of the variation in the number of crystals ultimately appearing in the sample. The frequency at which new molecules join a crystal lattice is measured by the kinetic coefficient and is related to the observed crystal growth rate. Numerical criteria used to discriminate diffusion- and kinetic-limited growth are discussed on this basis. Finally, the creation of defects is discussed with an emphasis on the role of impurities and convection on macromolecular crystal perfection.

  9. Protein Crystals and their Growth

    NASA Technical Reports Server (NTRS)

    Chernov, A. A.

    2004-01-01

    Recent results on binding between protein molecules in crystal lattice, crystal-solution surface energy, elastic properties and strength and spontaneous crystal cracking are reviewed and discussed in the first half of this paper (Sea 2-4). In the second par&, some basic approaches to solubility of proteins are followed by overview on crystal nucleation and growth (Sec 5). It is argued that variability of mixing in batch crystallization may be a source for scattering of crystal number ultimately appearing in the batch. Frequency at which new molecules join crystal lattice is measured by kinetic coefficient and related to the observable crystal growth rate. Numerical criteria to discriminate diffusion and kinetic limited growth are discussed on this basis in Sec 7. In Sec 8, creation of defects is discussed with the emphasis on the role of impurities and convection on macromolecular crystal I;erfection.

  10. Flexible ferroelectric organic crystals

    PubMed Central

    Owczarek, Magdalena; Hujsak, Karl A.; Ferris, Daniel P.; Prokofjevs, Aleksandrs; Majerz, Irena; Szklarz, Przemysław; Zhang, Huacheng; Sarjeant, Amy A.; Stern, Charlotte L.; Jakubas, Ryszard; Hong, Seungbum; Dravid, Vinayak P.; Stoddart, J. Fraser

    2016-01-01

    Flexible organic materials possessing useful electrical properties, such as ferroelectricity, are of crucial importance in the engineering of electronic devices. Up until now, however, only ferroelectric polymers have intrinsically met this flexibility requirement, leaving small-molecule organic ferroelectrics with room for improvement. Since both flexibility and ferroelectricity are rare properties on their own, combining them in one crystalline organic material is challenging. Herein, we report that trisubstituted haloimidazoles not only display ferroelectricity and piezoelectricity—the properties that originate from their non-centrosymmetric crystal lattice—but also lend their crystalline mechanical properties to fine-tuning in a controllable manner by disrupting the weak halogen bonds between the molecules. This element of control makes it possible to deliver another unique and highly desirable property, namely crystal flexibility. Moreover, the electrical properties are maintained in the flexible crystals. PMID:27734829

  11. Flexible ferroelectric organic crystals

    SciTech Connect

    Owczarek, Magdalena; Hujsak, Karl A.; Ferris, Daniel P.; Prokofjevs, Aleksandrs; Majerz, Irena; Szklarz, Przemysław; Zhang, Huacheng; Sarjeant, Amy A.; Stern, Charlotte L.; Jakubas, Ryszard; Hong, Seungbum; Dravid, Vinayak P.; Stoddart, J. Fraser

    2016-10-13

    Flexible organic materials possessing useful electrical properties, such as ferroelectricity, are of crucial importance in the engineering of electronic devices. But, until now, only ferroelectric polymers have intrinsically met this flexibility requirement, leaving small-molecule organic ferroelectrics with room for improvement. Since both flexibility and ferroelectricity are rare properties on their own, combining them in one crystalline organic material is challenging. We report that trisubstituted haloimidazoles not only display ferroelectricity and piezoelectricity-the properties that originate from their non-centrosymmetric crystal lattice-but also lend their crystalline mechanical properties to fine-tuning in a controllable manner by disrupting the weak halogen bonds between the molecules. This element of control makes it possible to deliver another unique and highly desirable property, namely crystal flexibility. Moreover, the electrical properties are maintained in the flexible crystals.

  12. Photonic Crystal Microchip Laser

    NASA Astrophysics Data System (ADS)

    Gailevicius, Darius; Koliadenko, Volodymyr; Purlys, Vytautas; Peckus, Martynas; Taranenko, Victor; Staliunas, Kestutis

    2016-09-01

    The microchip lasers, being very compact and efficient sources of coherent light, suffer from one serious drawback: low spatial quality of the beam strongly reducing the brightness of emitted radiation. Attempts to improve the beam quality, such as pump-beam guiding, external feedback, either strongly reduce the emission power, or drastically increase the size and complexity of the lasers. Here it is proposed that specially designed photonic crystal in the cavity of a microchip laser, can significantly improve the beam quality. Experiments show that a microchip laser, due to spatial filtering functionality of intracavity photonic crystal, improves the beam quality factor M2 reducing it by a factor of 2, and increase the brightness of radiation by a factor of 3. This comprises a new kind of laser, the “photonic crystal microchip laser”, a very compact and efficient light source emitting high spatial quality high brightness radiation.

  13. Photonic Crystal Microchip Laser

    PubMed Central

    Gailevicius, Darius; Koliadenko, Volodymyr; Purlys, Vytautas; Peckus, Martynas; Taranenko, Victor; Staliunas, Kestutis

    2016-01-01

    The microchip lasers, being very compact and efficient sources of coherent light, suffer from one serious drawback: low spatial quality of the beam strongly reducing the brightness of emitted radiation. Attempts to improve the beam quality, such as pump-beam guiding, external feedback, either strongly reduce the emission power, or drastically increase the size and complexity of the lasers. Here it is proposed that specially designed photonic crystal in the cavity of a microchip laser, can significantly improve the beam quality. Experiments show that a microchip laser, due to spatial filtering functionality of intracavity photonic crystal, improves the beam quality factor M2 reducing it by a factor of 2, and increase the brightness of radiation by a factor of 3. This comprises a new kind of laser, the “photonic crystal microchip laser”, a very compact and efficient light source emitting high spatial quality high brightness radiation. PMID:27683066

  14. Photonic Crystal Microchip Laser.

    PubMed

    Gailevicius, Darius; Koliadenko, Volodymyr; Purlys, Vytautas; Peckus, Martynas; Taranenko, Victor; Staliunas, Kestutis

    2016-09-29

    The microchip lasers, being very compact and efficient sources of coherent light, suffer from one serious drawback: low spatial quality of the beam strongly reducing the brightness of emitted radiation. Attempts to improve the beam quality, such as pump-beam guiding, external feedback, either strongly reduce the emission power, or drastically increase the size and complexity of the lasers. Here it is proposed that specially designed photonic crystal in the cavity of a microchip laser, can significantly improve the beam quality. Experiments show that a microchip laser, due to spatial filtering functionality of intracavity photonic crystal, improves the beam quality factor M(2) reducing it by a factor of 2, and increase the brightness of radiation by a factor of 3. This comprises a new kind of laser, the "photonic crystal microchip laser", a very compact and efficient light source emitting high spatial quality high brightness radiation.

  15. Photonic crystal microchip laser

    NASA Astrophysics Data System (ADS)

    Gailevicius, D.; Koliadenko, V.; Purlys, V.; Peckus, M.; Taranenko, V.; Staliunas, K.

    2017-02-01

    The microchip lasers, being sources of coherent light, suffer from one serious drawback: low spatial quality of the beam, strongly reducing the brightness of emitted radiation. Attempts to improve the beam quality, such as pump-beam guiding, external feedback, either strongly reduce the emission power, or drastically increase the size and complexity of the lasers. Here we propose that specially designed photonic crystal in the cavity of a microchip laser, can significantly improve the beam quality. We experimentally show that a microchip laser, due to spatial filtering functionality of intracavity photonic crystal, improves the beam quality factor M2 reducing it by factor of 2, and thus increase the brightness of radiation by a factor of 4. This comprises a new kind of laser, the "photonic crystal microchip laser", a very compact and efficient light source emitting high spatial high brightness radiation.

  16. Frequency doubling crystals

    DOEpatents

    Wang, Francis; Velsko, Stephan P.

    1989-01-01

    A systematic approach to the production of frequency conversion crystals is described in which a chiral molecule has attached to it a "harmonic generating unit" which contributes to the noncentrosymmetry of the molecule. Certain preferred embodiments of such harmonic generating units include carboxylate, guanadyly and imidazolyl units. Certain preferred crystals include L-arginine fluoride, deuterated L-arginine fluoride, L-arginine chloride monohydrate, L-arginine acetate, dithallium tartrate, ammonium N-acetyl valine, N-acetyl tyrosine and N-acetyl hydroxyproline. Chemical modifications of the chiral molecule, such as deuteration, halogenation and controlled counterion substitution are available to adapt the dispersive properties of a crystal in a particular wavelength region.

  17. Crystallization under nonuniform conditions

    NASA Astrophysics Data System (ADS)

    Kumar, C.

    1980-03-01

    The tendency of crystals to grow uniformly to maintain their habit is the characteristic feature of such growth. Classical crystal growth theory predicts that this uniform growth should break down when the growth reaches its Wilson-Frenkel limiting value locally. If the local supersaturation is known at the point of breakdown, as determined experimentally, the deposition coefficient can then be calculated directly avoiding the usual multiparameter fitting of growth data. An experimental technique employing an impinging jet was used in this study of crystal growth of MgSO47H2O from water. The radial onset of liquid inclusions about the jet stagnation point is believed to indicate local Wilson-Frenkel growth. The deposition coefficient C is then determined from C=G/ sigma sub 0 min, where G is from transport modelling. The results are encouraging enough to recommend further intensive study.

  18. Time Crystals: a review.

    PubMed

    Sacha, Krzysztof; Zakrzewski, Jakub

    2017-09-08

    Time crystals are time-periodic self-organized structures postulated by Frank Wilczek in 2012. While the original concept was strongly criticized, it stimulated at the same time an intensive research leading to propositions and experimental verifications of discrete (or Floquet) time crystals -- the structures that appear in the time domain due to spontaneous breaking of discrete time translation symmetry. The struggle to observe discrete time crystals is reviewed here together with propositions that generalize this concept introducing condensed matter like physics in the time domain. We shall also revisit the original Wilczek's idea and review strategies aimed at spontaneous breaking of continuous time translation symmetry. . © 2017 IOP Publishing Ltd.

  19. Microgravity crystal growth

    NASA Technical Reports Server (NTRS)

    2001-01-01

    Advanced finite element models are used to study three-dimensional, time-dependent flow and segregation in crystal growth systems. In this image of a prototypical model for melt and crystal growth, pathlines at one instant in time are shown for the flow of heated liquid silicon in a cylindrical container. The container is subjected to g-jitter disturbances along the vertical axis. A transverse magnetic field is applied to control them. Such computations are extremely powerful for understanding melt growth in microgravity where g-jitter drives buoyant flows. The simulation is part of the Theoretical Analysis of 3D, Transient Convection and Segregation in Microgravity Bridgman Crystal Growth investigation by Dr. Jeffrey J. Derby of the University of Mirnesota, Minneapolis.

  20. Microgravity crystal growth

    NASA Technical Reports Server (NTRS)

    2001-01-01

    Advanced finite element models are used to study three-dimensional, time-dependent flow and segregation in crystal growth systems. In this image of a prototypical model for melt and crystal growth, pathlines at one instant in time are shown for the flow of heated liquid silicon in a cylindrical container. The container is subjected to g-jitter disturbances along the vertical axis. A transverse magnetic field is applied to control them. Such computations are extremely powerful for understanding melt growth in microgravity where g-jitter drives buoyant flows. The simulation is part of the Theoretical Analysis of 3D, Transient Convection and Segregation in Microgravity Bridgman Crystal Growth investigation by Dr. Jeffrey J. Derby of the University of Mirnesota, Minneapolis.

  1. Flexible ferroelectric organic crystals

    DOE PAGES

    Owczarek, Magdalena; Hujsak, Karl A.; Ferris, Daniel P.; ...

    2016-10-13

    Flexible organic materials possessing useful electrical properties, such as ferroelectricity, are of crucial importance in the engineering of electronic devices. But, until now, only ferroelectric polymers have intrinsically met this flexibility requirement, leaving small-molecule organic ferroelectrics with room for improvement. Since both flexibility and ferroelectricity are rare properties on their own, combining them in one crystalline organic material is challenging. We report that trisubstituted haloimidazoles not only display ferroelectricity and piezoelectricity-the properties that originate from their non-centrosymmetric crystal lattice-but also lend their crystalline mechanical properties to fine-tuning in a controllable manner by disrupting the weak halogen bonds between the molecules.more » This element of control makes it possible to deliver another unique and highly desirable property, namely crystal flexibility. Moreover, the electrical properties are maintained in the flexible crystals.« less

  2. Flexible ferroelectric organic crystals

    NASA Astrophysics Data System (ADS)

    Owczarek, Magdalena; Hujsak, Karl A.; Ferris, Daniel P.; Prokofjevs, Aleksandrs; Majerz, Irena; Szklarz, Przemysław; Zhang, Huacheng; Sarjeant, Amy A.; Stern, Charlotte L.; Jakubas, Ryszard; Hong, Seungbum; Dravid, Vinayak P.; Stoddart, J. Fraser

    2016-10-01

    Flexible organic materials possessing useful electrical properties, such as ferroelectricity, are of crucial importance in the engineering of electronic devices. Up until now, however, only ferroelectric polymers have intrinsically met this flexibility requirement, leaving small-molecule organic ferroelectrics with room for improvement. Since both flexibility and ferroelectricity are rare properties on their own, combining them in one crystalline organic material is challenging. Herein, we report that trisubstituted haloimidazoles not only display ferroelectricity and piezoelectricity--the properties that originate from their non-centrosymmetric crystal lattice--but also lend their crystalline mechanical properties to fine-tuning in a controllable manner by disrupting the weak halogen bonds between the molecules. This element of control makes it possible to deliver another unique and highly desirable property, namely crystal flexibility. Moreover, the electrical properties are maintained in the flexible crystals.

  3. The effect of the temperature on the bandgaps based on the chiral liquid crystal polymer

    NASA Astrophysics Data System (ADS)

    Wang, Jianhua; Shi, Shuhui; Wang, Bainian

    2015-10-01

    Chiral side-chain liquid crystal polymer is synthesized from polysiloxanes and liqud crystal monomer 4-(Undecenoic-1- yloxybenzoyloxy)-4'-benzonitrile and 6-[4-(4- Undecenoic -1-yloxybenzoyloxy)- hydroxyphenyl] cholesteryl hexanedioate. The optical and thermal property of the monomer and polymer are shown by POM and DSC. As the unique optical property of the polymer, the bandgaps are shifted for heating temperature. The reflection bandgaps is shifted from 546nm to 429nm with temperature increase. As a photonic material, the chiral polymer which sensitive responses under the outfield is widely studied for reflection display, smart switchable reflective windows and defect model CLC laser etc.

  4. Protein Crystal Quality Studies

    NASA Technical Reports Server (NTRS)

    1998-01-01

    Eddie Snell (standing), Post-Doctoral Fellow the National Research Council (NRC),and Marc Pusey of Marshall Space Flight Center (MSFC) use a reciprocal space mapping diffractometer for marcromolecular crystal quality studies. The diffractometer is used in mapping the structure of marcromolecules such as proteins to determine their structure and thus understand how they function with other proteins in the body. This is one of several analytical tools used on proteins crystalized on Earth and in space experiments. Photo credit: NASA/Marshall Space Flight Center (MSFC)

  5. Protein Crystal Quality Studies

    NASA Technical Reports Server (NTRS)

    1998-01-01

    Eddie Snell (standing), Post-Doctoral Fellow the National Research Council (NRC),and Marc Pusey of Marshall Space Flight Center (MSFC) use a reciprocal space mapping diffractometer for marcromolecular crystal quality studies. The diffractometer is used in mapping the structure of marcromolecules such as proteins to determine their structure and thus understand how they function with other proteins in the body. This is one of several analytical tools used on proteins crystalized on Earth and in space experiments. Photo credit: NASA/Marshall Space Flight Center (MSFC)

  6. Protein Crystal Malic Enzyme

    NASA Technical Reports Server (NTRS)

    1992-01-01

    Malic Enzyme is a target protein for drug design because it is a key protein in the life cycle of intestinal parasites. After 2 years of effort on Earth, investigators were unable to produce any crystals that were of high enough quality and for this reason the structure of this important protein could not be determined. Crystals obtained from one STS-50 were of superior quality allowing the structure to be determined. This is just one example why access to space is so vital for these studies. Principal Investigator is Larry DeLucas.

  7. FRACTIONAL CRYSTALLIZATION FEED ENVELOPE

    SciTech Connect

    HERTING DL

    2008-03-19

    Laboratory work was completed on a set of evaporation tests designed to establish a feed envelope for the fractional crystallization process. The feed envelope defines chemical concentration limits within which the process can be operated successfully. All 38 runs in the half-factorial design matrix were completed successfully, based on the qualitative definition of success. There is no feed composition likely to be derived from saltcake dissolution that would cause the fractional crystallization process to not meet acceptable performance requirements. However, some compositions clearly would provide more successful operation than other compositions.

  8. Protein Crystal Malic Enzyme

    NASA Technical Reports Server (NTRS)

    1992-01-01

    Malic Enzyme is a target protein for drug design because it is a key protein in the life cycle of intestinal parasites. After 2 years of effort on Earth, investigators were unable to produce any crystals that were of high enough quality and for this reason the structure of this important protein could not be determined. Crystals obtained from one STS-50 were of superior quality allowing the structure to be determined. This is just one example why access to space is so vital for these studies. Principal Investigator is Larry DeLucas.

  9. Quartz Crystal Clocks

    NASA Technical Reports Server (NTRS)

    1976-01-01

    General Time Corporation, under contract to NASA, developed a quartz crystal for obtaining a stable time base from which all mission times could be derived. This later became basis of consumer clocks and watches with accuracy of one minute a year, watches useful in timing sports events as well as general use. When quartz is electrically stimulated it can vibrate millions of times a second. Since timepieces use a vibrating body to keep up time, incredibly fast vibration of a quartz crystal--up to 4,194,304 beats a second opened a new horizon in accuracy.

  10. Dynamically controlled crystallization method and apparatus and crystals obtained thereby

    NASA Technical Reports Server (NTRS)

    Arnowitz, Leonard (Inventor); Steinberg, Emanuel (Inventor)

    1999-01-01

    A method and apparatus for dynamically controlling the crystallization of proteins including a crystallization chamber or chambers for holding a protein in a salt solution, one or more salt solution chambers, two communication passages respectively coupling the crystallization chamber with each of the salt solution chambers, and transfer mechanisms configured to respectively transfer salt solution between each of the salt solution chambers and the crystallization chamber. The transfer mechanisms are interlocked to maintain the volume of salt solution in the crystallization chamber substantially constant. Salt solution of different concentrations is transferred into and out of the crystallization chamber to adjust the salt concentration in the crystallization chamber to achieve precise control of the crystallization process.

  11. Functionalizing Designer DNA Crystals

    NASA Astrophysics Data System (ADS)

    Chandrasekaran, Arun Richard

    Three-dimensional crystals have been self-assembled from a DNA tensegrity triangle via sticky end interaction. The tensegrity triangle is a rigid DNA motif containing three double helical edges connected pair-wise by three four-arm junctions. The symmetric triangle contains 3 unique strands combined in a 3:3:1 ratio: 3 crossover, 3 helical and 1 central. The length of the sticky end reported previously was two nucleotides (nt) (GA:TC) and the motif with 2-helical turns of DNA per edge diffracted to 4.9 A at beam line NSLS-X25 and to 4 A at beam line ID19 at APS. The purpose of these self-assembled DNA crystals is that they can be used as a framework for hosting external guests for use in crystallographic structure solving or the periodic positioning of molecules for nanoelectronics. This thesis describes strategies to improve the resolution and to incorporate guests into the 3D lattice. The first chapter describes the effect of varying sticky end lengths and the influence of 5'-phosphate addition on crystal formation and resolution. X-ray diffraction data from beam line NSLS-X25 revealed that the crystal resolution for 1-nt (G:C) sticky end was 3.4 A. Motifs with every possible combination of 1-nt and 2-nt sticky-ended phosphorylated strands were crystallized and X-ray data were collected. The position of the 5'-phosphate on either the crossover (strand 1), helical (strand 2), or central strand (3) had an impact on the resolution of the self-assembled crystals with the 1-nt 1P-2-3 system diffracting to 2.62 A at APS and 3.1 A at NSLS-X25. The second chapter describes the sequence-specific recognition of DNA motifs with triplex-forming oligonucleotides (TFOs). This study examined the feasibility of using TFOs to bind to specific locations within a 3-turn DNA tensegrity triangle motif. The TFO 5'-TTCTTTCTTCTCT was used to target the tensegrity motif containing an appropriately embedded oligopurine.oligopyrimidine binding site. As triplex formation involving cytidine

  12. Exotic crystal superstructures of colloidal crystals in confinement.

    PubMed

    Fontecha, Ana Barreira; Schöpe, Hans Joachim

    2008-06-01

    Colloidal model systems have been used for over three decades for investigating liquids, crystals, and glasses. Colloidal crystal superstructures have been observed in binary systems of repulsive spheres as well as oppositely charged sphere systems showing structures well known from atomic solids. In this work we study the structural transition of colloidal crystals under confinement. In addition to the known sequence of crystalline structures, crystal superstructures with dodecagonal and hexagonal symmetry are observed in one component systems. These structures have no atomic counterpart.

  13. The Crystal Hotel: A Microfluidic Approach to Biomimetic Crystallization.

    PubMed

    Gong, Xiuqing; Wang, Yun-Wei; Ihli, Johannes; Kim, Yi-Yeoun; Li, Shunbo; Walshaw, Richard; Chen, Li; Meldrum, Fiona C

    2015-12-02

    A "crystal hotel" microfluidic device that allows crystal growth in confined volumes to be studied in situ is used to produce large calcite single crystals with predefined crystallographic orientation, microstructure, and shape by control of the detailed physical environment, flow, and surface chemistry. This general approach can be extended to form technologically important, nanopatterned single crystals. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. REFINEMENT OF THE CRYSTAL STRUCTURE OF GUANIDINIUM ALUMINUM SULFATE HEXAHYDRATE.

    DTIC Science & Technology

    FERROELECTRIC CRYSTALS, * CRYSTAL STRUCTURE ), (*GUANIDINES, CRYSTAL STRUCTURE ), (*ALUMINUM COMPOUNDS, CRYSTAL STRUCTURE ), SULFATES, HYDRATES, X RAY DIFFRACTION, CHROMIUM COMPOUNDS, CRYSTAL LATTICES, CHEMICAL BONDS

  15. Ultraviolet-reduced reduction and crystallization of indium oxide films

    NASA Astrophysics Data System (ADS)

    Imai, Hiroaki; Tominaga, Atsushi; Hirashima, Hiroshi; Toki, Motoyuki; Asakuma, Naoko

    1999-01-01

    Structural changes stimulated by ultraviolet (UV) irradiations of sol-gel-derived indium oxide thin films were investigated. Illumination of incoherent UV photons (4.9 eV) from a low-pressure mercury lamp resulted in formation of crystalline indium metal. Irradiation of coherent UV beams from an ArF excimer laser (6.4 eV) and from the fourth harmonics of a Nd:YAG laser (4.7 eV) was found to be effective in the crystallization of indium oxide, accompanied by a decrease in the sheet resistance. The lowest resistance without a reduction of transmission in the visible region was achieved with a 6.4 eV laser beam at a fluence over 10-20 mJ cm-2 shot-1. The results of x-ray photoelectron spectroscopy revealed that charge transfer from O2- to In3+ was induced by the incoherent and the coherent UV photons. The partial reduction with the incoherent illumination and the crystallization with the laser irradiation are tentatively assumed to be due to electronic excitations in the amorphous network.

  16. The Crystal Set

    ERIC Educational Resources Information Center

    Greenslade, Thomas B., Jr.

    2014-01-01

    In past issues of this journal, the late H. R. Crane wrote a long series of articles under the running title of "How Things Work." In them, Dick dealt with many questions that physics teachers asked themselves, but did not have the time to answer. This article is my attempt to work through the physics of the crystal set, which I thought…

  17. Thermoelectricity in liquid crystals

    NASA Astrophysics Data System (ADS)

    Mohd Said, Suhana; Nordin, Abdul Rahman; Abdullah, Norbani; Balamurugan, S.

    2015-09-01

    The thermoelectric effect, also known as the Seebeck effect, describes the conversion of a temperature gradient into electricity. A Figure of Merit (ZT) is used to describe the thermoelectric ability of a material. It is directly dependent on its Seebeck coefficient and electrical conductivity, and inversely dependent on its thermal conductivity. There is usually a compromise between these parameters, which limit the performance of thermoelectric materials. The current achievement for ZT~2.2 falls short of the expected threshold of ZT=3 to allow its viability in commercial applications. In recent times, advances in organic thermoelectrics been significant, improving by over 3 orders of magnitude over a period of about 10 years. Liquid crystals are newly investigated as candidate thermoelectric materials, given their low thermal conductivity, inherent ordering, and in some cases, reasonable electrical conductivity. In this work the thermoelectric behaviour of a discotic liquid crystal, is discussed. The DLC was filled into cells coated with a charge injector, and an alignment of the columnar axis perpendicular to the substrate was allowed to form. This thermoelectric behavior can be correlated to the order-disorder transition. A reasonable thermoelectric power in the liquid crystal temperature regime was noted. In summary, thermoelectric liquid crystals may have the potential to be utilised in flexible devices, as a standalone power source.

  18. Crystal Ball Replica

    NASA Astrophysics Data System (ADS)

    Ajamian, John

    2016-09-01

    The A2 collaboration of the Institute for Nuclear Physics of Johannes Gutenberg University performs research on (multiple) meson photoproduction and nucleon structure and dynamics using a high energy polarized photon beam at specific targets. Particles scattered from the target are detected in the Crystal Ball, or CB. The CB is composed of 672 NaI crystals that surround the target and can analyze particle type and energy of ejected particles. Our project was to create a replica of the CB that could display what was happening in real time on a 3 Dimensional scale replica. Our replica was constructed to help explain the physics to the general public, be used as a tool when calibrating each of the 672 NaI crystals, and to better analyze the electron showering of particles coming from the target. This poster will focus on the hardware steps necessary to construct the replica and wire the 672 programmable LEDS in such a way that they can be mapped to correspond to the Crystal Ball elements. George Washington NSF Grant.

  19. Protein Crystal Bovine Insulin

    NASA Technical Reports Server (NTRS)

    1991-01-01

    The comparison of protein crystal, Bovine Insulin space-grown (left) and earth-grown (right). Facilitates the incorporation of glucose into cells. In diabetics, there is either a decrease in or complete lack of insulin, thereby leading to several harmful complications. Principal Investigator is Larry DeLucas.

  20. DIFFRACTION FROM MODEL CRYSTALS

    USDA-ARS?s Scientific Manuscript database

    Although calculating X-ray diffraction patterns from atomic coordinates of a crystal structure is a widely available capability, calculation from non-periodic arrays of atoms has not been widely applied to cellulose. Non-periodic arrays result from modeling studies that, even though started with at...