bluuebunny/crossref_metadata_2025 huggingface dataset:
A Nitrilase-Like Protein Interacts with GCC Box DNA-Binding Proteins Involved in Ethylene and Defense Responses
Authors: Xu Ping , Narasimhan Meena L. , Samson Teresa , Coca Maria A. , Huh Gyung-Hye , Zhou Jianmin , Martin Gregory B. , Hasegawa Paul M. , Bressan Ray A.
Published: July 2002

Ethylene-responsive element-binding proteins (EREBPs) of tobacco (Nicotiana tabacum L.) bind to the GCC box of many pathogenesis-related (PR) gene promoters, including osmotin (PR-5). The two GCC boxes on the osmotin promoter are known to be required, but not sufficient, for maximal ethylene responsiveness. EREBPs participate in the signal transduction pathway leading from exogenous ethylene application and pathogen infection to PR gene induction. In this study EREBP3 was used as bait in a yeast two-hybrid interaction trap with a tobacco cDNA library as prey to isolate signal transduction pathway intermediates that interact with EREBPs. One of the strongest interactors was found to encode a nitrilase-like protein (NLP). Nitrilase is an enzyme involved in auxin biosynthesis. NLP interacted with other EREBP family members, namely tobacco EREBP2 and tomato (Lycopersicon esculentum L.) Pti4/5/6. The EREBP2-EREBP3 interaction with NLP required part of the DNA-binding domain. The specificity of interaction was further confirmed by protein-binding studies in solution. We propose that the EREBP-NLP interaction serves to regulate PR gene expression by sequestration of EREBPs in the cytoplasm.
Expression Analysis of a Ripening-Specific, Auxin-Repressed Endo-1,4-β-Glucanase Gene in Strawberry
Authors: Harpster Mark H. , Brummell David A. , Dunsmuir Pamela
Published: July 2002

A cDNA (Cel1) encoding an endo-1,4-β-glucanase (EGase) was isolated from ripe fruit of strawberry (Fragaria × ananassa). The deduced protein of 496 amino acids contains a presumptive signal sequence, a common feature of cell wall-localized EGases, and one potential N-glycosylation site. Southern- blot analysis of genomic DNA from F. × ananassa, an octoploid species, and that from the diploid species Fragaria vesca indicated that the Cel1 gene is a member of a divergent multigene family. In fruit, Cel1 mRNA was first detected at the white stage of development, and at the onset of ripening, coincident with anthocyanin accumulation, Cel1mRNA abundance increased dramatically and remained high throughout ripening and subsequent fruit deterioration. In all other tissues examined, Cel1 expression was invariably absent. Antibodies raised to Cel1 protein detected a protein of 62 kD only in ripening fruit. Upon deachenation of young white fruit to remove the source of endogenous auxins, ripening, as visualized by anthocyanin accumulation, and Cel1 mRNA accumulation were both accelerated. Conversely, auxin treatment of white fruit repressed accumulation of both Cel1 mRNA and ripening. These results indicate that strawberry Cel1 is a ripening-specific and auxin-repressed EGase, which is regulated during ripening by a decline in auxin levels originating from the achenes.
Change in Apoplastic Aluminum during the Initial Growth Response to Aluminum by Roots of a Tolerant Maize Variety1
Authors: Vázquez María Dolores , Poschenrieder Charlotte , Corrales Isabel , Barceló Juan
Published: July 2002

Root elongation, hematoxylin staining, and changes in the ultrastructure of root-tip cells of an Al-tolerant maize variety (Zea mays L. C 525 M) exposed to nutrient solutions with 20 μm Al (2.1 μm Al3+ activity) for 0, 4, and 24 h were investigated in relation to the subcellular distribution of Al using scanning transmission electron microscopy and energy-dispersive x-ray microanalysis on samples fixed by different methods. Inhibition of root-elongation rates, hematoxylin staining, cell wall thickening, and disturbance of the distribution of pyroantimoniate-stainable cations, mainly Ca, was observed only after 4 and not after 24 h of exposure to Al. The occurrence of these transient, toxic Al effects on root elongation and in cell walls was accompanied by the presence of solid Al-P deposits in the walls. Whereas no Al was detectable in cell walls after 24 h, an increase of vacuolar Al was observed after 4 h of exposure. After 24 h, a higher amount of electron-dense deposits containing Al and P or Si was observed in the vacuoles. These results indicate that in this tropical maize variety, tolerance mechanisms that cause a change in apoplastic Al must be active. Our data support the hypothesis that in Al-tolerant plants, Al can rapidly cross the plasma membrane; these data clearly contradict the former conclusions that Al mainly accumulates in the apoplast and enters the symplast only after severe cell damage has occurred.
NADH-Glutamate Synthase in Alfalfa Root Nodules. Immunocytochemical Localization1
Authors: Trepp Gian B. , Plank David W. , Stephen Gantt J. , Vance Carroll P.
Published: July 2002

In root nodules of alfalfa (Medicago sativa L.), N2 is reduced to NH4+ in the bacteroid by the nitrogenase enzyme and then released into the plant cytosol. The NH4+ is then assimilated by the combined action of glutamine synthetase (EC 6.3.1.2) and NADH-dependent Glu synthase (NADH-GOGAT; EC 1.4.1.14) into glutamine and Glu. The alfalfa nodule NADH-GOGAT protein has a 101-amino acid presequence, but the subcellular location of the protein is unknown. Using immunocytochemical localization, we determined first that the NADH-GOGAT protein is found throughout the infected cell region of both 19- and 33-d-old nodules. Second, in alfalfa root nodules NADH-GOGAT is localized predominantly to the amyloplast of infected cells. This finding, together with earlier localization and fractionation studies, indicates that in alfalfa the infected cells are the main location for the initial assimilation of fixed N2.
Chloroplast-Targeted ERD1 Protein Declines but Its mRNA Increases during Senescence in Arabidopsis1
Authors: Weaver L. Michael , Froehlich John E. , Amasino Richard M.
Published: July 2002

Arabidopsis ERD1 is a ClpC-like protein that sequence analysis suggests may interact with the chloroplast-localized ClpP protease to facilitate proteolysis. The mRNA encoded by the ERD1 gene has previously been shown to accumulate in response to senescence and to a variety of stresses and hormones. Here we show that the ERD1 protein, in contrast to theERD1 mRNA, strongly declines in abundance with age, becoming undetectable in fully expanded leaves. Sequence analysis also suggests that ERD1 is chloroplast targeted, and we show in an in vitro system that the native protein is properly imported, processed, and present within the soluble fraction of the chloroplast, presumably the stroma. We show that ClpP protein, which is also present in the stroma, declines with age in parallel with ERD1. These results are consistent with the interaction of ERD1 and ClpP, but they suggest that it is unlikely that either plays a major role during senescence. Certain other chloroplast proteins decline with age coordinately with ERD1 and ClpP, suggesting that these declines are markers of an early age-mediated change that occurs within the chloroplast.
Changes in Phosphoinositide Metabolism with Days in Culture Affect Signal Transduction Pathways inGaldieria sulphuraria1
Authors: Heilmann Ingo , Perera Imara Y. , Gross Wolfgang , Boss Wendy F.
Published: July 2002

The metabolism of phosphatidylinositol-4,5-bisphosphate (PIP2) changed during the culture period of the thermoacidophilic red alga Galdieria sulphuraria. Seven days after inoculation, the amount of PIP2 in the cells was 910 ± 100 pmol g−1fresh weight; by 12 d, PIP2 levels increased to 1200 ± 150 pmol g−1 fresh weight. In vitro assays indicated that phosphatidylinositol monophosphate (PIP) kinase specific activity increased from 75 to 230 pmol min−1mg−1 protein between d 7 and 12. When G. sulphuraria cells were osmostimulated, transient increases of up to 4-fold could be observed in inositol-1,4,5-trisphosphate (IP3) levels within 90 s, regardless of the age of the cells. In d-12 cells, the increase in IP3 was preceded by a transient increase of up to 5-fold in specific PIP kinase activity, whereas no such increase was detected after osmostimulation of d-7 cells. The increase in PIP kinase activity before IP3signaling in d-12 cells indicates that there is an additional pathway for regulation of phosphoinositide metabolism after stimulation other than an initial activation of phospholipase C. Also, the rapid activation of PIP2 biosynthesis in cells with already-high PIP2 levels suggests that the PIP2 present was not available for signal transduction. By comparing the response of the cells at d 7 and 12, we have identified two potentially distinct pools of PIP2.
Processing, Targeting, and Antifungal Activity of Stinging Nettle Agglutinin in Transgenic Tobacco
Authors: Does Mirjam P. , Houterman Petra M. , Dekker Henk L. , Cornelissen Ben J.C.
Published: July 2002

The gene encoding the precursor to stinging nettle (Urtica dioica L.) isolectin I was introduced into tobacco (Nicotiana tabacum). In transgenic plants this precursor was processed to mature-sized lectin. The mature isolectin is deposited intracellularly, most likely in the vacuoles. A gene construct lacking the C-terminal 25 amino acids was also introduced in tobacco to study the role of the C terminus in subcellular trafficking. In tobacco plants that expressed this construct, the mutant precursor was correctly processed and the mature isolectin was targeted to the intercellular space. These results indicate the presence of a C-terminal signal for intracellular retention of stinging nettle lectin and most likely for sorting of the lectin to the vacuoles. In addition, correct processing of this lectin did not depend on vacuolar deposition. Isolectin I purified from tobacco displayed identical biological activities as isolectin I isolated from stinging nettle. In vitro antifungal assays on germinated spores of the fungiBotrytis cinerea, Trichoderma viride, andColletotrichum lindemuthianum revealed that growth inhibition by stinging nettle isolectin I occurs at a specific phase of fungal growth and is temporal, suggesting that the fungi had an adaptation mechanism.
Identification of Natural Rubber and Characterization of Rubber Biosynthetic Activity in Fig Tree
Authors: Kang Hunseung , Kang Min Young , Han Kyung-Hwan
Published: July 2002

Natural rubber was extracted from the fig tree (Ficus carica) cultivated in Korea as part of a survey of rubber producing plants. Fourier transform infrared and 13C nuclear magnetic resonance analysis of samples prepared by successive extraction with acetone and benzene confirmed that the benzene-soluble residues are natural rubber, cis-1,4-polyisoprene. The rubber content in the latex of fig tree was about 4%, whereas the rubber content in the bark, leaf, and fruit was 0.3%, 0.1%, and 0.1%, respectively. Gel-permeation chromatography revealed that the molecular size of the natural rubber from fig tree is about 190 kD. Similar to rubber tree (Hevea brasiliensis) and guayule (Parthenium argentatum Gray), rubber biosynthesis in fig tree is tightly associated with rubber particles. The rubber transferase in rubber particles exhibited a higher affinity for farnesyl pyrophosphate than for isopentenyl pyrophosphate, with apparentK  m values of 2.8 and 228 μm, respectively. Examination of latex serum from fig tree by sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed major proteins of 25 and 48 kD in size, and several proteins with molecular mass below 20 and above 100 kD. Partial N-terminal amino acid sequencing and immunochemical analyses revealed that the 25- and 48-kD proteins were novel and not related to any other suggested rubber transferases. The effect of EDTA and Mg2+ ion on in vitro rubber biosynthesis in fig tree and rubber tree suggested that divalent metal ion present in the latex serum is an important factor in determining the different rubber biosynthetic activities in fig tree and rubber tree.
Nod Factors and Chitooligomers Elicit an Increase in Cytosolic Calcium in Aequorin-Expressing Soybean Cells
Authors: Müller Joachim , Staehelin Christian , Xie Zhi-Ping , Neuhaus-Url Gabriele , Boller Thomas
Published: July 2002

Rhizobial Nod factors (NFs) function as nodulation signals that trigger symbiotic responses of leguminous host plants. NFs consist of a chitin oligomer backbone carrying a fatty acid at the non-reducing end. Depending on the rhizobial strain, NFs carry additional substituents, which may determine host specificity. Transgenic suspension-cultured soybean (Glycine max [L.] Merr.) cells expressing aequorin have been used to record cytosolic [Ca2+] changes upon treatment with purified NFs and chitin fragments. Both compounds elicited an increase of cytosolic [Ca2+] at nanomolar concentrations. The shape and amplitude of cytosolic [Ca2+] changes was similar to the response elicited by un-derivatized chitin oligomers. Cells challenged first with NFs did not respond to a subsequent treatment with chitin oligomers and vice versa. Dose-response experiments showed that un-derivatized chitin oligomers were more active compared with NFs. The capacity of NFs to elicit the calcium response depended on their structure. The presence of reducing end substituents in methylfucosylated NFs fromRhizobium sp. NGR234 and the O-acetyl group at the non-reducing end in NFs from Sinorhizobium meliloti attenuated the activity to cause the calcium changes. The sulfate group in NFs from Rhizobium tropici did not affect the elicitor activity. Pentameric S. meliloti NFs were more active than tetrameric molecules, whereas trimeric or dimeric degradation products were inactive. Substituents in NFs may have the function to avoid stimulation of defense reactions mediated by the perception system for chitin oligomers.
Expression and Stress-Dependent Induction of Potassium Channel Transcripts in the Common Ice Plant
Authors: Su Hua , Golldack Dortje , Katsuhara Maki , Zhao Chengsong , Bohnert Hans J.
Published: July 2002

We have characterized transcripts for three potassium channel homologs in the AKT/KAT subfamily (Shaker type) from the common ice plant (Mesembryanthemum crystallinum), with a focus on their expression during salt stress (up to 500 mm NaCl).Mkt1 and 2, Arabidopsis AKT homologs, andKmt1, a KAT homolog, are members of small gene families with two to three isoforms each. Mkt1 is root specific;Mkt2 is found in leaves, flowers, and seed capsules; andKmt1 is expressed in leaves and seed capsules.Mkt1 is present in all cells of the root, and in leaves a highly conserved isoform is detected present in all cells with highest abundance in the vasculature. MKT1 for which antibodies were made is localized to the plasma membrane. Following salt stress, MKT1 (transcripts and protein) is drastically down-regulated,Mkt2 transcripts do not change significantly, andKmt1 is strongly and transiently (maximum at 6 h) up-regulated in leaves and stems. The detection and stress-dependent behavior of abundant transcripts representing subfamilies of potassium channels provides information about tissue specificity and the complex regulation of genes encoding potassium uptake systems in a halophytic plant.
Hydrogen Peroxide Mediates the Induction of Chloroplastic Ndh Complex under Photooxidative Stress in Barley
Authors: Casano Leonardo M. , Martı́n Mercedes , Sabater Bartolomé
Published: July 2002

Chloroplast-encoded NDH polypeptides (components of the plastid Ndh complex) and the NADH dehydrogenase activity of the Ndh complex (NADH-DH) increased under photooxidative stress. The possible involvement of H2O2-mediated signaling in the photooxidative induction of chloroplastic ndh genes was thoroughly studied. We have analyzed the changes in the NADH-DH and steady-state levels of NDH-F polypeptide and ndhB andndhF transcripts in barley (Hordeum vulgare cv Hassan) leaves. Subapical leaf segments were incubated in growing light (GL), photooxidative light (PhL), GL and H2O2 (GL + H2O2), or PhL and 50 nm paraquat in the incubation medium. Treatments with H2O2 under GL mimicked the photooxidative stimulus, causing a dose-dependent increase of NADH-DH and NDH-F polypeptide. The kinetic of Ndh complex induction was further studied in leaves pre-incubated with or without the H2O2-scavenger dimethyltiourea. NADH-DH and NDH-F polypeptide rapidly increased up to 16 h in PhL, GL+ H2O2, and, at higher rate, in PhL and paraquat. The observed increases of NADH-DH and NDH-F after 4 h in PhL and GL + H2O2 were not accompanied by significant changes in ndhB and ndhF transcripts. However, at 16-h incubations NADH-DH and NDH-F changes closely correlated with higher ndhB and ndhFtranscript levels. All these effects were prevented by dimethylthiourea. It is proposed that the induction of chloroplasticndh genes under photooxidative stress is mediated by H2O2 through mechanisms that involve a rapid translation of pre-existing transcripts and the increase of thendh transcript levels.
Simultaneous Down-Regulation of Caffeic/5-Hydroxy Ferulic Acid-O-Methyltransferase I and Cinnamoyl-Coenzyme A Reductase in the Progeny from a Cross between Tobacco Lines Homozygous for Each Transgene. Consequences for Plant Development and Lignin Synthesis
Authors: Pinçon Gaelle , Chabannes Matthieu , Lapierre Catherine , Pollet Brigitte , Ruel Katia , Joseleau Jean-Paul , Boudet Alain M. , Legrand Michel
Published: July 2002

Inhibition of specific lignin biosynthetic steps by antisense strategy has previously been shown to alter lignin content and/or structure. In this work, homozygous tobacco (Nicotiana tabacum) lines transformed with cinnamoyl-coenzyme A reductase (CCR) or caffeic acid/5-hydroxy ferulic acid-O-methyltransferase I (COMT I) antisense sequences have been crossed and enzyme activities, lignin synthesis, and cell wall structure of the progeny have been analyzed. In single transformed parents, CCR inhibition did not affect COMT I expression, whereas marked increases in CCR activity were observed in COMT I antisense plants, suggesting potential cross talk between some genes of the pathway. In the progeny, both CCR and COMT I activities were shown to be markedly decreased due to the simultaneous repression of the two genes. In these double transformants, the lignin profiles were dependent on the relative extent of down-regulation of each individual enzyme. For the siblings issued from a strongly repressed antisense CCR parent, the lignin patterns mimicked the patterns obtained in single transformants with a reduced CCR activity. In contrast, the specific lignin profile of COMT I repression could not be detected in double transformed siblings. By transmission electron microscopy some cell wall loosening was detected in the antisense CCR parent but not in the antisense COMT I parent. In double transformants, immunolabeling of non-condensed guaiacyl-syringyl units was weaker and revealed changes in epitope distribution that specifically affected vessels. Our results more widely highlight the impact of culture conditions on phenotypes and gene expression of transformed plants.
Molecular Characterization of At5PTase1, an Inositol Phosphatase Capable of Terminating Inositol Trisphosphate Signaling,
Authors: Berdy Sara E. , Kudla Joerg , Gruissem Wilhelm , Gillaspy Glenda E.
Published: July 2002

The inositol triphosphate (IP3)-signaling pathway has been associated with several developmental and physiological processes in plants, but we currently know little about the regulation of this pathway. Inositol 5′ phosphatases (5PTases) are enzymes that remove a 5′ phosphate from several potential second messengers, including IP3. In catalyzing the removal of a 5′ phosphate from second messenger substrates, 5PTases can act to terminate signal transduction events. We describe the molecular analysis of At5PTase1, a 5PTase gene from Arabidopsis. When expressed transiently in Arabidopsis leaf tissue or ectopically in transgenic plants, At5PTase1 allowed for the increased hydrolysis of I(1,4,5)P3 and I(1,3,4,5)P4 substrates. At5PTase1 did not hydrolyze I(1)P, I(1,4)P2, or PI(4,5)P2 substrates. This substrate specificity was similar to that of the human Type I 5PTase. We identified 14 other potential At5PTase genes and constructed an unrooted phylogenetic tree containing putative Arabidopsis, human, and yeast 5PTase proteins. This analysis indicated that the Arabidopsis 5PTases were grouped in two separate branches of the tree. The multiplicity of At5PTases indicates that these enzymes may have different substrate specificities and play different roles in signal termination in Arabidopsis.
Systematic errors in the high-accuracy universal polarimeter: application to determining temperature-dependent optical anisotropy of KDC and KDP crystals
Authors: Hernández-Rodríguez C. , Gómez-Garrido P. , Veintemillas S.
Published: July 2002

The problem of removing the characteristic parasitic errors of the high-accuracy universal polarimeter method in a linearly birefringent and optically active crystal section is examined. The use of constant parasitic errors typical of each particular polarimetric system is shown to be inappropriate. The parasitics should preferably be determined in each measurement process, since the instrumental parasitics depend not only on the optical and mechanical elements of the experimental system (polarizers, rotators, detection unitetc.), but on sample quality, alignment of the system, and even in many cases on exactly where the light beam passes through the sample. Thus, measurements with different samples give different values of parasitic errors. Such instrumental parasitics can be held within the same order of magnitude for different samples (∼10−4) if they are of good optical quality. However, the parasitics are increased by an order of magnitude (∼10−3) when the samples are of moderate or bad optical quality. Optical anisotropy properties as coefficients of thermal variation of the birefringence of KDC and KDP single crystals and the optical activity of KDP at 632.8 nm wavelength are obtained, in the ranges from room temperature to 353 K and to 373 K, respectively.
Anisotropic diffraction peak broadening and dislocation substructure in hydrogen-cycled LaNi5and substitutional derivatives
Authors: Černý R. , Joubert J.-M. , Latroche M. , Percheron-Guégan A. , Yvon K.
Published: July 2002

Anisotropic peak broadening in hydrogen-cycled hexagonal LaNi5and substitutional derivatives has been studied by means of synchrotron powder diffraction. The data have been analysed by a local lattice parameter variation method implemented in a Rietveld code and by an individual profile fitting using a dislocation peak broadening model. Two main dislocation systems, both with Burgers vector 1/3〈\bar{2}110〉, are activated by misfit of the lattice parameters between the intermetallic compounds and their hydrides. Two types of diffraction peak broadening effect were observed as a function of the substitution in LaNi5: (i) a decrease or disappearance of the broadening related to the decrease of the total dislocation density and (ii) a change in the anisotropy of the broadening related to the change of the nature of the dislocation system involved. The latter effect was attributed to a change in shape of the hydride precipitates.
Determination of hydrogen ordering within the β-RH2+xphase (R= Ho, Y) using electron diffraction techniques
Authors: Grier Elizabeth J. , Petford-Long Amanda K. , Ward Roger C. C.
Published: July 2002

Computer simulations of the electron diffraction patterns along the [\bar{1}10] zone axes of four ordered structures within the β-RH2+xphase, withR= Ho or Y, and 0 ≤x≤ 0.25, have been performed to establish whether or not the hydrogen ordering could be detected using electron diffraction techniques. Ordered structures within otherRH2+x(R= Ce, Tb) systems have been characterized with neutron scattering experiments; however, for HoH(D)2+x, neutron scattering failed to characterize the superstructure, possibly because of the lowxconcentration or lack of long-range order within the crystal. This paper aims to show that electron diffraction could overcome both of these problems. The structures considered were the stoichiometric face-centred cubic (f.c.c.) fluorite structure (x= 0), theD1 structure (x= 0.125), theD1astructure (x= 0.2) and theD022structure (x= 0.25). In the stoichiometric structure, with all hydrogen atoms located on the tetrahedral (t) sites, only the diffraction pattern from the f.c.c. metal lattice was seen; however, for the superstoichiometric structures, with the excess hydrogen atoms ordered on the octahedral (o) sites, extra reflections were visible. All the superstoichiometric structures showed extra reflections at the (001)f.c.c.and (110)f.c.c.type positions, with structureD1 also showing extra peaks at (½ ½ ½)f.c.c.. These reflections are not seen in the simulations at similar hydrogen concentrations with the hydrogen atoms randomly occupying theovacancies.
Automated matching of high- and low-resolution structural models
Authors: Kozin M. B. , Svergun D. I.
Published: July 2002

A method is presented for automated best-matching alignment of three-dimensional models represented by ensembles of points. A normalized spatial discrepancy (NSD) is introduced as a proximity measure between three-dimensional objects. Starting from an inertia-axes alignment, the algorithm minimizes the NSD; the final value of the NSD provides a quantitative estimate of similarity between the objects. The method is implemented in a computer program. Simulations have been performed to test its performance on model structures with specified numbers of points ranging from a few to a few thousand. The method can be used for comparative analysis of structural models obtained by different methods,e.g.of high-resolution crystallographic atomic structures and low-resolution models from solution scattering or electron microscopy.
Correction for thermal diffuse scattering in single-crystal time-of-flight neutron diffraction: first applications
Authors: Jauch W. , Peters J.
Published: July 2002

The thermal diffuse scattering (TDS) correction developed by Popa & Willis [Acta Cryst.(1997), A53, 537–545] for single-crystal pulsed neutron diffraction is examinedviaa series of experimental data sets collected at the spallation neutron source IPNS. The effect on the derived temperature parameter values is assessed and compared with reference structures obtained from gamma-ray diffraction. The importance of carrying out TDS corrections is emphasized. Suggestions are made regarding the method of evaluation of the TDS in situations where the elastic constants are unknown.
Concepts in spin echo small-angle neutron scattering
Authors: Zhao Jinkui
Published: July 2002

Two-dimensional spin echo small-angle neutron scattering experiments that measure the vector-length distribution function, or pair-distance distribution function, in real space are discussed. The proposed diffractometer uses two cylindrically symmetric magnetic fields with conically shaped front and end faces to enable experiments in two dimensions. It also features a π/2 neutron spin flipper to make the effective analyzing direction of the analyzer perpendicular to the polarizing direction of the polarizer. The theoretical aspect of one-dimensional spin echo small-angle neutron scattering experiments is also explored. The relationship between the correlation function from one-dimensional experiments and the vector-length distribution function is established, and interpretation of this correlation function in real space is presented.
Structure, crystal growth and physical anisotropy of KYb(WO4)2, a new laser matrix
Authors: Pujol M. C. , Mateos X. , Solé R. , Massons J. , Gavaldà Jna. , Solans X. , Díaz F. , Aguiló M.
Published: July 2002

The crystal structure of monoclinic KYb(WO4)2(KYbW) crystals has been refined (in space groupC2/c) at room temperature by using single-crystal X-ray diffraction data. KYbW undoped crystals were grown by the TSSG (top-seeded-solution growth) slow-cooling method. The crystals show {110}, {\bar{1}11}, {010} and {310} faces, which basically define their habit. The linear thermal expansion tensor has been determined and the principal axis with maximum thermal expansion (\alpha ^{\,\prime}_{33} = 16.68 × 10−6 K−1), {\bf X}^{\,\prime}_{3}, was located 12° from thecaxis. Its principal {\bf X}^{\,\prime}_{1}, {\bf X}^{\,\prime}_{2} and {\bf X}^{\,\prime}_{3} axes are [302], [010] and [106] directions, respectively, in the crystallographic system. The optical tensor has been studied at λ = 632.8 nm at room temperature; two principal axes,NgandNm, are located in theacplane, while the other,Np, is parallel to [010]. The principal axis with maximum refractive index (ng= 2.45),Ng, was located 19° from thecaxis.
Interactive motif and fold recognition in protein structures
Authors: Madsen Dennis , Kleywegt Gerard J.
Published: July 2002

Two previously developed software tools for pattern recognition in protein structures at the level of the fold (DEJAVU) and at the level of assemblies of individual residues (SPASM) have been improved in order to increase their specificity significantly. In addition, web-servers have been developed for both tools thereby greatly enhancing the ease with which even non-experts can employ them.
Abinitiomodelling of intermetallics with CuAl2structure type: computed powder patterns from cell-and-type CRYSTMET entries
Authors: Le Page Y. , Rodgers John R. , White Peter S.
Published: July 2002

Searchable calculated powder patterns of crystalline substances are commonly used nowadays to complement experimental patterns for the identification of materials by diffraction methods. Reliable such patterns are often calculable from the known cell, type and chemistry data on types with fixed Wyckoff positions, like NaCl, but not on typeC16 ofAB2compounds, with CuAl2as its representative material, because of the variablexcoordinate of itsBsite.Ab initiocell and coordinate relaxation for four key compounds withC16 type, all started from the samec/a= 1 andx= 1/6 configuration, converged on the correct axial ratios and fractional coordinates. A linear regression on a plot ofxcoordinates optimizedab initioat experimental cell dataversusX-ray coordinates for all 48C16-type compositions for pure-phase compounds with coordinates in the CRYSTMET database gavey= 0.998x,R2= 0.88. Credible calculated powder patterns were then produced for AlHf2, AlZr2, AuTl2, BCr2, GaHf2, IrZr2and TlTh2, all with cell, type and pure-phase composition information but no coordinates in this database, using their X-ray cell data andab initiocoordinates. Those patterns, now inserted in the search system of the database, will help users identify those phases from powder diffraction angle and intensity data. The corresponding entries in a new `X-ray cell-and-type,ab initiocoordinates' category of full structure entries may be helpful for other applications, such as the simulation of EXAFS spectra or of backscattered electron patterns.
Design and performance of a γ-ray diffractometer at 0.12 Å
Authors: Alkire R. W. , Yelon W. B.
Published: July 2002

At the University of Missouri Research Reactor, a γ-ray diffractometer has been constructed which uses 0.12 Å radiation produced from the decay of 153Sm. Use of this source rather than 198Au (λ = 0.03 Å), which is used at several instruments in Europe, has important advantages which are discussed. Details of the design necessary to work with 1000 Ci (37 TBq) sources at this wavelength are presented. In addition, the results of several experiments intended to test the capability of the instrument for measuring extinction-free structure factors at low angles and for measuring to high sin θ/λ (~ 2 Å−1) are reported. These results show that it will be relatively straightforward to make absolute structure-factor determinations for light elements and to determine electron density distributions more accurately than has been done in the past with X-ray diffraction. Furthermore, determination of anharmonic thermal motion and form factors will be possible. Crystal perfection studies on small samples have also been performed and can be done routinely.
Crystal powder data of MoGa5(CuS2)0.0556
Authors: Horyn R. , Andruszkiewicz R.
Published: July 2002

The X-ray powder data have been obtained for a new phase MoGa5(CuS2)0.0556. The powder patterns were indexed on the basis of a tetragonal body-centred unit cell with the lattice constants a = 12.872, c = 5.284 Å, c/a = 0.410, dm
= 6.825(8), dx
= 6.869 Mg m−3, Z = 8.
An X-ray determination of the thermal expansion of the intermetallic compound Ni3Zr
Authors: Shadangi S. K. , Panda S. C. , Bhan S.
Published: July 2002

The lattice spacings of the intermetallic compound Ni3Zr have been measured by X-ray methods in the temperature interval 298–1033 K using a Debye–Scherrer camera. In all the cases the measured lattice spacings have been found to increase non-linearly with temperature and the dependence has been expressed by a polynomial of second degree from the least-squares fitting of the data. The thermal expansion coefficients for both parameters have been found to decrease with increase in temperature.
A fast Fourier transformation algorithm for parallel computers
Authors: Raftery J. , Sawyer L. , Pawley G. S.
Published: July 2002

A new algorithm is presented for using the fast Fourier transform (FFT) in a very efficient mode. This algorithm is ideal for a parallel computer such as the ICL Distributed Array Processor (DAP), though it can be used with benefit on any serial computer. For a two- or three-dimensional electron density Fourier map the Fourier coefficients are arranged in a one-dimensional vector form of the chosen length and the whole map is obtained by a single FFT operation. To obtain a higher density of calculated points in the map a number of FFT operations is required, each entailing a phase modification of the one-dimensional Fourier coefficients. A three-dimensional map using 1429 crystal reflections and giving the density at 32768 points takes roughly 2 s in the ICL DAP.
Characterization of alumina powder using multiple small-angle neutron scattering. I. Theory
Authors: Berk N. F. , Hardman-Rhyne K. A.
Published: July 2002

Microstructural parameters of high-purity alumina powder are determined quantitatively throughout the bulk of the material using small-angle neutron scattering techniques. A unified theoretical and experimental approach for analyzing multiple scattering data is developed to obtain values for particle size, volume fraction and surface area. It is shown how particle size and volume fraction can be measured in a practical way from SANS data totally dominated by incoherent multiple scattering (`beam broadening'). The general phase-shift dependence of single-particle scattering is incorporated into the multiple scattering formalism, and it is also shown that the diffractive limit (small phase shift) applies even for phase shifts as large as unity (particle radii of order 1 μm). The stability of the Porod law against multiple scattering and the phase-shift scale are described, a useful empirical formula for analysis of beam broadening data is exhibited, and the applicability of the formulations to polydispersed systems is discussed.
Determination of beam polarization from integrated Borrmann intensities
Authors: Staudenmann J.-L. , Chapman L. D. , Murphy W. J. , Horning R. D. , Liedl G. L.
Published: July 2002

The beam polarization ratio of a dual graphite monochromator system was studied with the Borrmann polarimeter technique in the wavelength range between 0.7093 and 1.6782 Å. This ratio depends on the polarization of the beam incident on the first `crystal', on the properties of the `crystals' and on geometrical effects, especially those arising from the collimation conditions. All these dependences were studied. Furthermore, the experimental difficulties in using a Borrmann polarimeter were examined with some care and are outlined for the benefit of others who realise the importance of measuring their own beam polarization ratio. In this connection, a number of pictures of scans showing the horizontal and vertical divergences, the background levels arising from Borrmann crystals of inadequate thickness, the effects of crystal settings on χ scans etc. are displayed. In accordance with custom, the results are reported in terms of the exponent n in the expression (beam polarization ratio) K′ = cos 2n
2θ
m
, where the 2 in the exponent arises from using a dual monochromator. As is well known, secondary extinction leads to values of n from near zero to two, even if the incident beam is unpolarized, n values ranging from 0.35 to 1.67 were found and these are discussed in terms of polarization of the incident beam and the collimation conditions.
The N-crystal spectrometer
Authors: Sabine T. M.
Published: July 2002

It is shown that a recurrence relation exists such that the resolution function and luminosity of an optical system consisting of any number of alternate collimators and reflecting crystals can be calculated analytically. Certain cases of practical interest in neutron and X-ray diffraction are evaluated explicitly using a Gaussian approximation for the transmission functions of the collimators, and for the mosaic spread distributions or reflection profiles of the crystals. It is shown that true absorption has a negligible effect on luminosity when the Darwin width of a reflection is of the order of the opening angle of the X-ray beam from a synchrotron source.
Structure refinement of an FeCl3 crystal using a thin plate sample
Authors: Hashimoto S. , Forster K. , Moss S. C.
Published: July 2002

Positional parameters (x, y, z) and anisotropic Debye–Waller factors B
⊥ (normal to the xy plane) and B|| (parallel to the xy plane) have been determined for the Fe and Cl atoms in FeCl3 within the space group R{\bar 3} with a = 6.065, c = 17.42 Å. These are (0, 0, 1/3), B
Fe⊥ = 1.75 and B
Fe|| = 1.2 Å2 for the Fe atoms at 6(c) positions in the hexagonal-axis representation, and (0.358, 0, 0.078), B
Cl⊥ = 1.6 and B
Cl|| = 1.55 Å2 for the Cl atoms at 18(f) positions. In addition to the crystallographic parameters, the observed twinning is discussed using the possible variants of ABC and ACB stacking sequences, each of which has two variants with a 60° rotation of the chlorine lattice. One of the four twin variants is found to be strongly enhanced. The fit for these parameters yields a reliability factor R = \sum_{i} \parallel F^{i}_{\rm cal} \mid - \mid F^{i}_{\rm obs}\parallel / \sum_{i} \mid F^{i}_{\rm obs} \mid = 0.60.
Coefficients of molecular homeomorphism and crystalline isomorphism in the series of 2-R-naphthalene (R = H, F, Cl, CH3, SH, Br)
Authors: Haget Y. , Bonpunt L. , Michaud F. , Negrier P. , Cuevas-Diarte M. A. , Oonk H. A. J.
Published: July 2002

Crystallographic data on the stable and metastable phases of the high-temperature forms of the substances of the series of substituted naphthalenes are given. The data are used to calculate for each pair of substances the coefficient ∊K
of molecular homeomorphism as well as the coefficient ∊m
of crystalline isomorphism, which allow a comparison of the (stable and/or metastable) crystal framework.
Sub-nanosecond X-ray powder diffraction
Authors: Woolsey N. C. , Wark J. S. , Riley D.
Published: July 2002

The X-rays emitted from a laser-produced plasma have been used to obtain powder diffraction patterns with exposures of less than a nanosecond. The X-rays were produced by focusing approximately 50 J of 0.53 μm laser light in a 600 ps (FWHM) pulse to a tight (~100 μm diameter) spot on a solid titanium target. The spectral brightness of the resonance line of the helium-like titanium thus produced was sufficient to record diffraction from LiF powder in a single exposure using the Seemann–Bohlin geometry. These results indicate that time-resolved measurements of the lattice parameters of polycrystalline materials can be made with sub-nanosecond temporal resolution.
Experience with commercial area detectors: a `buyer's' perspective
Authors: Krause K. L. , Phillips G. N.
Published: July 2002

Area detectors have revolutionized data collection in protein crystallography, but unsubstantiated opinion as to the merits of these detectors has sometimes interfered with objective comparisons of area detector quality. Area detectors from four manufacturers were evaluated by collecting data sets on two different protein crystals, carboxypeptidase A and recombinant sperm whale myoglobin. These data sets were first compared by studying their internal consistency using R
sym measurements and as expected these R
sym values were excellent. Next, the data were studied by merging with diffractometer data sets and with each other. Finally, the myoglobin data were used to calculate anomalous difference Pattersons. Area detectors studied in this way included the Mark II from San Diego Multiwire Systems, the FAST from Enraf–Nonius, Inc., the R-AXIS II from Rigaku Corporation and the X-1000A from Siemens Analytical X-ray Instruments, Inc. Wide variations existed in the data-collection parameters chosen by the manufacturers, but all four detectors produced acceptable data as evidenced by mutual agreement and clear interpretability of anomalous difference Patterson maps based on the Fe atom in myoglobin.
Molecular replacement real-space averaging
Authors: Rossmann M. G. , McKenna R. , Tong L. , Xia D. , Dai J. , Wu H. , Choi H. K. , Lynch R. E.
Published: July 2002

Structure determination of macromolecules often depends on phase improvement and phase extension by use of real-space averaging of electron density related by noncrystallographic symmetry. Although techniques for such procedures have been described previously [Bricogne (1976). Acta Cryst. A32, 832–847; Johnson (1978). Acta Cryst. B34, 576–577], modern computer architecture and experience with these methods have suggested changes and improvements. Two unit cells are considered: (1) the p-cell corresponding to the actual crystal structure(s) being determined (there would be more than one of these if the molecule crystallizes in more than one crystal form) and (2) the h-cell corresponding to the molecule in a standard orientation with respect to which the molecular symmetry axes are defined. Averaging can proceed entirely within the p-cell, referring to the h-cell only in as far as knowledge of the molecular symmetry is required. It is also possible to place the averaged molecule back into the h-cell, where it can be used to redefine the molecular envelope or for displaying a suitably chosen asymmetric unit of the molecule. Techniques are discussed for automatically selecting a molecular envelope which is consistent with packing considerations within the p-cell and which retains the symmetry of the molecular point group. The electron density map to be averaged is divided into bricks for storage in virtual memory. Roughly as many bricks as there are noncrystallographic asymmetric units per crystallographic asymmetric unit need to be retained in memory at one time. This procedure minimizes paging problems and avoids double sorting. Use of eight-point interpolation permits storing the map at grid points separated by no more than 1/2.5 of the resolution limit to obtain rapid convergence.
Logiciel de génération et représentation de structures cristallines
Authors: Soyer A. , Rimsky A.
Published: July 2002

Software has been written in Fortran77 for the space-filling representation of crystal structures. It generates atomic positions starting from the asymmetric unit and taking into account the 230 possible space groups. It then computes realistic shaded images in correct perspective with the hidden part removed. The main differences from existing programs are the ability to represent thermal ellipsoids and good portability to commonly used workstations. Details are given about the organization and operation of the program and some applications.
Concentration dependence of Debye temperature in mixed K
x
Rb1−x
Cl
Authors: Bashir J. , Beg M. M. , Butt N. M. , Khan Q. H. , Nasir Khan M.
Published: July 2002

Integrated intensities of Bragg reflections were measured with a triple-axis neutron spectrometer for powder samples of K
x
Rb1−x
Cl for x = 0.5. The temperature factors were corrected for thermal diffuse scattering (TDS) and static contributions. The Debye temperature and the mean temperature factors obtained from these measurements are compared with the values obtained by other techniques and are found to be in good agreement. The Debye temperatures for RbCl (x = 0) and KCl (x = 1) determined by other authors were combined with these results and the concentration dependence of Θ in K
x
Rb1−x
Cl, was found to be non-linear.
Intensity enhancement in asymmetric diffraction with parallel-beam synchrotron radiation
Authors: Toraya H. , Huang T. C. , Wu Y.
Published: July 2002

An intensity enhancement obtained from asymmetric diffraction with a fixed incident angle α has been studied. Parallel-beam synchrotron radiation with λ = 1.54 Å (Stanford Synchrotron Radiation Laboratory) and λ = 1.53 Å (Photon Factory) was used to collect powder diffraction patterns of Si, CeO2 (α = 5 and 10°) and monoclinic ZrO2 (α = 10°). The synchrotron-radiation data were analyzed using single-reflection profile fitting and whole-powder-pattern fitting techniques. The integrated intensities in the asymmetric diffraction were compared with those of symmetric diffraction obtained by the conventional θ–2θ scanning technique. An intensity, after correction for a limited height of counter aperture, was enhanced by factors of 1.8 (α = 5°) and 1.7 (α = 10°) at the maximum in asymmetric diffraction and its magnitudes agreed well with those calculated from theory.
Analysis of diffuse scattering from the mineral mullite
Authors: Butler B. D. , Welberry T. R.
Published: July 2002

A full reciprocal-space volume of diffuse scattering data from a single-crystal of the mineral mullite, Al2(Al2 + 2x
Si2 − 2x
)O10 − x
, x = 0.4, was collected. These data were analysed using least-squares techniques by writing an equation for the diffuse scattering that involves only the local order between vacancies on specific oxygen sites in the material. The effect of the large, but predictable, cation shifts on the diffuse intensity is taken account of in the coefficients of the oxygen-vacancy short-range-order intensities. This analysis shows that the vacancies are negatively correlated at the near-neighbour ½ 〈110〉, [110], 〈001〉 and 〈011〉 interatomic vectors and positively correlated along the 〈010〉, 〈101〉, ½ 〈112〉 and ½ 〈310〉 vectors. Subsequent Monte Carlo modelling of the structure based on these local-order parameters demonstrates that the structure of mullite is dominated by effective near-neighbour vacancy–vacancy repulsive interactions. A real-space model of mullite is presented that is approximately consistent with the measured local-order parameters.
A rapid method to assess X-ray area detectors by oriented protein crystal diffraction
Authors: Phillips J. C.
Published: July 2002

Siemens recently introduced the HI-STAR, a multiwire area detector with new read-out electronics. A performance comparison was made with the previous model, the X-1000. This note presents the method devised, which used X-ray diffraction from an oriented protein crystal and produced repeatable results in a short time with problems of absorption and sample decay eliminated. The method could have general applicability for the comparison of detectors, the rapid evaluation of modifications to a detector, or production line testing, especially because of the short time of each measurement.