bluuebunny/crossref_metadata_2025 huggingface dataset:
A Benzothiadiazole Primes Parsley Cells for Augmented Elicitation of Defense Responses
Authors: Katz Vera A. , Thulke Oliver U. , Conrath Uwe
Published: July 2002

Systemic acquired resistance is an important component of the disease-resistance arsenal of plants, and is associated with an enhanced potency for activating local defense responses upon pathogen attack. Here we demonstrate that pretreatment with benzothiadiazole (BTH), a synthetic activator of acquired resistance in plants, augmented the sensitivity for low-dose elicitation of coumarin phytoalexin secretion by cultured parsley (Petroselinum crispum L.) cells. Enhanced coumarin secretion was associated with potentiated activation of genes encoding Phe ammonia-lyase (PAL). The augmentation of PAL gene induction was proportional to the length of pretreatment with BTH, indicating time-dependent priming of the cells. In contrast to the PAL genes, those for anionic peroxidase were directly induced by BTH in the absence of elicitor, thus confirming a dual role for BTH in the activation of plant defenses. Strikingly, the ability of various chemicals to enhance plant disease resistance correlated with their capability to potentiate parsley PAL gene elicitation, emphasizing an important role for defense response potentiation in acquired plant disease resistance.
Feedback Inhibition of Chlorophyll Synthesis in the Phytochrome Chromophore-Deficientaureaandyellow-green-2Mutants of Tomato
Authors: Terry Matthew J. , Kendrick Richard E.
Published: July 2002

The aurea(au) and yellow-green-2(yg-2) mutants of tomato (Solanum lycopersicum L.) are unable to synthesize the linear tetrapyrrole chromophore of phytochrome, resulting in plants with a yellow-green phenotype. To understand the basis of this phenotype, we investigated the consequences of the au andyg-2 mutations on tetrapyrrole metabolism. Dark-grown seedlings of both mutants have reduced levels of protochlorophyllide (Pchlide) due to an inhibition of Pchlide synthesis. Feeding experiments with the tetrapyrrole precursor 5-aminolevulinic acid (ALA) demonstrate that the pathway between ALA and Pchlide is intact inau and yg-2 and suggest that the reduction in Pchlide is a result of the inhibition of ALA synthesis. This inhibition was independent of any deficiency in seed phytochrome, and experiments using an iron chelator to block heme synthesis demonstrated that both mutations inhibited the degradation of the physiologically active heme pool, suggesting that the reduction in Pchlide synthesis is a consequence of feedback inhibition by heme. We discuss the significance of these results in understanding the chlorophyll-deficient phenotype of the au andyg-2 mutants.
Restrictions to Carbon Dioxide Conductance and Photosynthesis in Spinach Leaves Recovering from Salt Stress
Authors: Delfine Sebastiano , Alvino Arturo , Villani Maria Concetta , Loreto Francesco
Published: July 2002

Salt accumulation in spinach (Spinacia oleracea L.) leaves first inhibits photosynthesis by decreasing stomatal and mesophyll conductances to CO2 diffusion and then impairs ribulose-1,5-bisphosphate carboxylase/oxygenase (S. Delfine, A. Alvino, M. Zacchini, F. Loreto [1998] Aust J Plant Physiol 25: 395–402). We measured gas exchange and fluorescence in spinach recovering from salt accumulation. When a 21-d salt accumulation was reversed by 2 weeks of salt-free irrigation (rewatering), stomatal and mesophyll conductances and photosynthesis partially recovered. For the first time, to our knowledge, it is shown that a reduction of mesophyll conductance can be reversed and that this may influence photosynthesis. Photosynthesis and conductances did not recover when salt drainage was restricted and Na content in the leaves was greater than 3% of the dry matter. Incomplete recovery of photosynthesis in rewatered and control leaves may be attributed to an age-related reduction of conductances. Biochemical properties were not affected by the 21-d salt accumulation. However, ribulose-1,5-bisphosphate carboxylase/oxygenase activity and content were reduced by a 36- to 50-d salt accumulation. Photochemical efficiency was reduced only in 50-d salt-stressed leaves because of a decrease in the fraction of open photosystem II centers. A reduction in chlorophyll content and an increase in the chlorophylla/b ratio were observed in 43- and 50-d salt-stressed leaves. Low chlorophyll affects light absorptance but is unlikely to change light partitioning between photosystems.
Biochemical Characterization of the Suberization-Associated Anionic Peroxidase of Potato
Authors: Bernards Mark A. , Fleming Warren D. , Llewellyn David B. , Priefer Ronny , Yang Xiaolong , Sabatino Anita , Plourde Guy L.
Published: July 2002

The anionic peroxidase associated with the suberization response in potato (Solanum tuberosum L.) tubers during wound healing has been purified and partially characterized at the biochemical level. It is a 45-kD, class III (plant secretory) peroxidase that is localized to suberizing tissues and shows a preference for feruloyl (o-methoxyphenol)-substituted substrates (order of substrate preference: feruloyl > caffeoyl >p-coumaryl ≈ syringyl) such as those that accumulate in tubers during wound healing. There was little influence on oxidation by side chain derivatization, although hydroxycinnamates were preferred over the corresponding hydroxycinnamyl alcohols. The substrate specificity pattern is consistent with the natural substrate incorporation into potato wound suberin. In contrast, the cationic peroxidase(s) induced in response to wound healing in potato tubers is present in both suberizing and nonsuberizing tissues and does not discriminate between hydroxycinnamates and hydroxycinnamyl alcohols. A synthetic polymer prepared usingE-[8-13C]ferulic acid, H2O2, and the purified anionic enzyme contained a significant amount of cross-linking through C-8, albeit with retention of unsaturation.
Carbon Metabolism in Spores of the Arbuscular Mycorrhizal FungusGlomus intraradices as Revealed by Nuclear Magnetic Resonance Spectroscopy
Authors: Bago Berta , Pfeffer Philip E. , Douds David D. , Brouillette Janine , Bécard Guillaume , Shachar-Hill Yair
Published: July 2002

Arbuscular mycorrhizal (AM) fungi are obligate symbionts that colonize the roots of over 80% of plants in all terrestrial environments. Understanding why AM fungi do not complete their life cycle under free-living conditions has significant implications for the management of one of the world's most important symbioses. We used 13C-labeled substrates and nuclear magnetic resonance spectroscopy to study carbon fluxes during spore germination and the metabolic pathways by which these fluxes occur in the AM fungus Glomus intraradices. Our results indicate that during asymbiotic growth: (a) sugars are made from stored lipids; (b) trehalose (but not lipid) is synthesized as well as degraded; (c) glucose and fructose, but not mannitol, can be taken up and utilized; (d) dark fixation of CO2 is substantial; and (e) arginine and other amino acids are synthesized. The labeling patterns are consistent with significant carbon fluxes through gluconeogenesis, the glyoxylate cycle, the tricarboxylic acid cycle, glycolysis, non-photosynthetic one-carbon metabolism, the pentose phosphate pathway, and most or all of the urea cycle. We also report the presence of an unidentified betaine-like compound. Carbon metabolism during asymbiotic growth has features in between those presented by intraradical and extraradical hyphae in the symbiotic state.
Effects of Solar Ultraviolet Radiation on the Potential Efficiency of Photosystem II in Leaves of Tropical Plants
Authors: Krause G. Heinrich , Schmude Claudia , Garden Hermann , Koroleva Olga Y. , Winter Klaus
Published: July 2002

The effects of solar ultraviolet (UV)-B and UV-A radiation on the potential efficiency of photosystem II (PSII) in leaves of tropical plants were investigated in Panama (9°N). Shade-grown tree seedlings or detached sun leaves from the outer crown of mature trees were exposed for short periods (up to 75 min) to direct sunlight filtered through plastic or glass filters that absorbed either UV-B or UV-A+B radiation, or transmitted the complete solar spectrum. Persistent changes in potential PSII efficiency were monitored by means of the dark-adapted ratio of variable to maximum chlorophyll a fluorescence. In leaves of shade-grown tree seedlings, exposure to the complete solar spectrum resulted in a strong decrease in potential PSII efficiency, probably involving protein damage. A substantially smaller decline in the dark-adapted ratio of variable to maximum chlorophylla fluorescence was observed when UV-B irradiation was excluded. The loss in PSII efficiency was further reduced by excluding both UV-B and UV-A light. The photoinactivation of PSII was reversible under shade conditions, but restoration of nearly full activity required at least 10 d. Repeated exposure to direct sunlight induced an increase in the pool size of xanthophyll cycle pigments and in the content of UV-absorbing vacuolar compounds. In sun leaves of mature trees, which contained high levels of UV-absorbing compounds, effects of UV-B on PSII efficiency were observed in several cases and varied with developmental age and acclimation state of the leaves. The results show that natural UV-B and UV-A radiation in the tropics may significantly contribute to photoinhibition of PSII during sun exposure in situ, particularly in shade leaves exposed to full sunlight.
A Weakly Voltage-Dependent, Nonselective Cation Channel Mediates Toxic Sodium Influx in Wheat
Authors: Davenport Romola Jane , Tester Mark
Published: July 2002

To determine the transporters responsible for toxic Na+ influx in wheat (Triticum aestivum), root plasma membrane preparations were screened using the planar lipid bilayer technique as an assay for Na+-permeable ion channel activity. The predominant channel in the bilayer was a 44-pS channel that we called the nonselective cation (NSC) channel, which was nonselective for monovalent cations and weakly voltage dependent. Single channel characteristics of the NSC channel were compared with 22Na+ influx into excised root segments. Na+ influx through the NSC channel resembled 22Na+ influx in its partial sensitivity to inhibition by Ca2+, Mg2+, and Gd3+, and its insensitivity to all other inhibitors tested (tetraethylammonium, quinine, Cs+, tetrodotoxin, verapamil, amiloride, and flufenamate). Na+ influx through the NSC channel also closely resembled an instantaneous current in wheat root protoplasts (S.D. Tyerman, M. Skerrett, A. Garill, G.P. Findlay, R. Leigh [1997] J Exp Bot 48: 459–480) in its permeability sequence, selectivity for K+ over Na+(approximately 1.25), insensitivity to tetraethylammonium, voltage independence, and partial sensitivity to Ca2+. Comparison of tissue, protoplast (S.D. Tyerman, M. Skerrett, A. Garill, G.P. Findlay, R. Leigh [1997] J Exp Bot 48: 459–480), and single- channel data indicate that toxic Na+ influx is catalyzed by a single transporter, and this is likely to be the NSC channel identified in planar lipid bilayers.
Hormonal Interactions in the Control of Arabidopsis Hypocotyl Elongation
Authors: Collett Clare E. , Harberd Nicholas P. , Leyser Ottoline
Published: July 2002

The Arabidopsis hypocotyl, together with hormone mutants and chemical inhibitors, was used to study the role of auxin in cell elongation and its possible interactions with ethylene and gibberellin. When wild-type Arabidopsis seedlings were grown on media containing a range of auxin concentrations, hypocotyl growth was inhibited. However, when axr1-12 and 35S-iaaL(which have reduced auxin response and levels, respectively) were grown in the same conditions, auxin was able to promote hypocotyl growth. In contrast, auxin does not promote hypocotyl growth ofaxr3-1, which has phenotypes that suggest an enhanced auxin response. These results are consistent with the hypothesis that auxin levels in the wild-type hypocotyl are optimal for elongation and that additional auxin is inhibitory. When ethylene responses were reduced using either the ethylene-resistant mutantetr1 or aminoethoxyvinylglycine, an inhibitor of ethylene synthesis, auxin responses were unchanged, indicating that auxin does not inhibit hypocotyl elongation through ethylene. To test for interactions between auxin and gibberellin, auxin mutants were grown on media containing gibberellin and gibberellin mutants were grown on media containing auxin. The responses were found to be the same as wild-type Arabidopsis seedlings in all cases. In addition, 1 μm of the auxin transport inhibitor 1-naphthylphthalmic acid does not alter the response of wild-type seedlings to gibberellin. Double mutants were made between gibberellin and auxin mutants and the phenotypes of these appear additive. These results indicate that auxin and gibberellin are acting independently in hypocotyl elongation. Thus auxin, ethylene, and gibberellin each regulate hypocotyl elongation independently.
Identification of Rice Varieties with High Tolerance or Sensitivity to Lead and Characterization of the Mechanism of Tolerance
Authors: Yang Young-Yell , Jung Ji-Young , Song Won-Yong , Suh Hak-Soo , Lee Youngsook
Published: July 2002

Pb inhibits plant growth. To study Pb tolerance in rice (Oryza sativa), we screened 229 varieties for Pb tolerance or sensitivity. Three-day-old seedlings were treated for 12 d with 20 μm Pb solution. Based on the dry weight of the root, three Pb-tolerant (var CH-55, var KH-2J, var Kumnung) and three Pb-sensitive (var Aixueru, var C-9491, var Milyang23) rice varieties were selected. The root biomasses of the tolerant varieties were approximately 10-fold higher than those of the sensitive ones. The greatest morphological difference between the two groups was in the growth of the adventitious roots, as tolerant lines were able to develop adventitious roots after 6 d of Pb treatment, whereas sensitive ones did not develop any even after 15 d. The growth of adventitious roots in the tolerant varieties was dependent on a mechanism, whereby Pb was altered to a form that cannot be taken up by the tissue, because (a) the solution in which the tolerant varieties of rice had grown still contained Pb but nevertheless did not affect the root growth of new rice seedlings, and (b) the adventitious roots of tolerant seedlings developed in Pb solution contained little Pb. The oxalate content in the root and root exudate increased upon Pb treatment in the tolerant varieties, whereas the opposite was observed for the sensitive ones. Oxalate added to the growth solution ameliorated the inhibition of root growth by Pb. These results suggest that compounds such as oxalate secreted from the root may reduce the bio-availability of Pb, and that this may constitute an important Pb tolerance mechanism in the tolerant rice varieties studied here.
The Arabidopsis eer1 Mutant Has Enhanced Ethylene Responses in the Hypocotyl and Stem
Authors: Larsen Paul B. , Chang Caren
Published: July 2002

By screening for enhanced ethylene-response(eer) mutants in Arabidopsis, we isolated a novel recessive mutant, eer1, which displays increased ethylene sensitivity in the hypocotyl and stem. Dark-growneer1 seedlings have short and thick hypocotyls even in the absence of added ethylene. This phenotype is suppressed, however, by the ethylene biosynthesis inhibitor 1-aminoethoxyvinyl-glycine. Following ethylene treatment, the dark-grown eer1hypocotyl response is greatly exaggerated in comparison with the wild type, indicating that the eer1 phenotype is not simply due to ethylene overproduction. eer1 seedlings have significantly elevated levels of basic-chitinaseexpression, suggesting that eer1 may be highly sensitive to low levels of endogenous ethylene. Adult eer1 plants display exaggerated ethylene-dependent stem thickening, which is an ethylene response previously unreported in Arabidopsis.eer1 also has enhanced responsiveness to the ethylene agonists propylene and 2,5-norbornadiene. The eer1phenotype is completely suppressed by the ethylene-insensitive mutationetr1-1, and is additive with the constitutive ethylene-response mutation ctr1-3. Our findings suggest that the wild-type EER1 product acts to oppose ethylene responses in the hypocotyl and stem.
Investigation of bone and cartilage by synchrotron scanning-SAXS and -WAXD with micrometer spatial resolution
Authors: Žižak I. , Paris O. , Roschger P. , Bernstorff S. , Amenitsch H. , Klaushofer K. , Fratzl P.
Published: July 2002

Biological materials such as bone or wood are hierarchically structured to optimize mechanical and other properties. Several methods and experimental techniques are usually needed to study these materials on different length scales. We developed a device for small angle X-ray scattering (SAXS) and wide-angle X-ray diffraction (WAXD), optimized for position resolved investigations of bone sections using synchrotron radiation. Thin samples can be scanned with 20 µm steps, acquiring two-dimensional SAXS or WAXD patterns at every point. The system was tested by performing one-dimensional scans across bone cartilage interfaces, revealing information about size, shape and orientation of nanometer sized mineral particles as well as about crystal type and texture of these particles.
Design and performance of a ASAXS instrument at the Advanced Photon Source
Authors: Seifert S. , Winans R.E. , Tiede D.M. , Thiyagarajan P.
Published: July 2002

The SAXS instrument on the high brilliance undulator beam line (ID12, BESSRC-CAT) at APS has been designed to produce high-resolution scattering patterns in the millisecond time domain. This instrument is equipped with a 18 cm x 18 cm position sensitive gas detector and a 15 cm x 15 cm high-resolution position sensitive CCD mosaic detector. A photodiode detector mounted on a 3.7 mm diameter beam stop permits quick alignment of the instrument as well as precise measurement of the transmitted beam intensity. The exposure time with the CCD detector varies from 0.1 to 10 seconds depending on the scattering cross-section of the samples. Techniques to interface ancillary equipment for time-resolved studies and software for faster online analysis of the data have also been developed. We have obtained data on the unfolding of proteins in the millisecond time domain and ASAXS of metallic alloys using this instrument.
The crystal neutron diffractometer resolution function, spatial effects included
Authors: Ionita I. , Stoica A. D.
Published: July 2002

A procedure for computing the resolution function for a crystal neutron diffractometer, taking into account the spatial configuration of the experimental setup and the monochromator curvature, is presented. A brief general description of the matrix computation technique is given. The programDAX, which employs this technique, is presented.
Computing in macromolecular crystallography using a parallel architecture
Authors: Diederichs Kay
Published: July 2002

Despite advances in computer technology, computing in macromolecular crystallography keeps pace in its demand for CPU power. Improvements in CPU speed, together with advances in computing methods that depend on it, often translate into the possibility to solve structures that would otherwise require additional experiments. Programs for data reduction, molecular-replacement programs employing multidimensional searches on a grid in real, Patterson or reciprocal space, and phasing and refinement programs, currently have, among others, the highest requirements for CPU power. For these and other programs, speed-up of calculations as a result of parallel execution on multiprocessor computers is possible. This paper outlines the use of the OpenMP programming interface and reports its successful application for parallelization ofESSENS[Kleywegt & Jones (1997).Acta Cryst.D53, 179–185] andSHELXL[Schneider & Sheldrick (1997).Methods Enzymol.277, 319–343]. Parallel computing, which is possible as a result of the inherent parallelism of crystallographic algorithms, extends the range of problems in macromolecular crystallography that programs can be applied to and can significantly reduce the time required for progressing from a data set to a refined model.
Solving the generalized indirect Fourier transformation (GIFT) by Boltzmann simplex simulated annealing (BSSA)
Authors: Bergmann A. , Fritz G. , Glatter O.
Published: July 2002

The structure of colloidal particles can be studied with small-angle X-ray and neutron scattering (SAXS and SANS). In the case of randomly oriented systems, the indirect Fourier transformation (IFT) is a well established technique for the calculation of model-free real-space information. Interaction leads to an overlap of inter- and intraparticle scattering effects, preventing most detailed interpretations. The recently developed generalized indirect Fourier transformation (GIFT) technique allows these effects to be separated by assuming various models for the interaction,i.e.the so-called structure factors. The different analytical behaviour of these structure factors from that of the form factors, describing the intraparticle scattering, allows this separation. The mean-deviation surface is defined by the quality of the fit for different parameter sets of the structure factor. Its global minimum represents the solution. The former non-linear least-squares approach has proved to be inefficient and not very reliable. In this paper, the incorporation of the completely different Boltzmann simplex simulated annealing (BSSA) algorithm for finding the global minimum of the hypersurface is presented. This new method increases not only the calculation speed but also the reliability of the evaluation.
Evolution structurale de la nacrite en fonction de la nature des molécules organiques intercalees
Authors: Ben Haj Amara A. , Ben Rhaiem H. , Plançon A.
Published: July 2002

Nacrite has been intercalated with two polar organic molecules: dimethyl sulfoxide (DMSO) andN-methylacetamide (NMA). The homogeneous nacrite complexes have been studied by X-ray diffraction (XRD) and infrared (IR) spectroscopy. The XRD study is based on a comparison between experimental and calculated patterns. The structures of the intercalated compounds have been determined, including the mutual positions of the layers after intercalation and the positions of the intercalated molecules in the interlayer space. It has been shown that the intercalation process causes not only a swelling of the interlayer space but also a shift in the mutual in-plane positions of the layers. This shift depends on the nature of the intercalated molecules and is related to their shape and the hydrogen bonds which are established with the surrounding surfaces. For a given molecule, the intercalation process is the same for the different polytypes of the kaolinite family. These XRD results are consistent with those of IR spectroscopy.
Resolution calculations for novel neutron beam elements
Authors: Cussen Leo D.
Published: July 2002

It is now possible to build new types of optical elements for neutron beams. These include monochromating crystals with rectangular mosaic profiles, `gradient' monochromating crystals with varying lattice spacing, and collimators with rectangular profiles. Phase-space methods are used to describe the resolution of a combination of two collimators and a monochromating crystal for various combinations of novel beam elements. The description of rectangular-profile elements in this formalism considerably simplifies the normal description of resolution effects and should thus prove useful as a teaching tool.
A small-angle neutron scattering model for polydisperse spherical particles with diffusion zones and application to soft magnetic metallic glass
Authors: Heinemann André , Hermann Helmut , Wiedenmann Albrecht , Mattern Norbert , Wetzig Klaus
Published: July 2002

An analytical expression for the small-angle neutron scattering intensity of diluted systems of polydisperse spherical particles, with diffusion zones, embedded in a matrix is presented. It is used within a nonlinear regression procedure to analyse small-angle neutron scattering experiments with polarized neutrons on an Fe73.5Si15.5B7CuNb3alloy. The results for the nuclear and magnetic scattering length densities allow verification of the inhibitor concept introduced for the explanation of the limited sizes of precipitates developing during nanocrystallization. In the case of amorphous Fe73.5Si15.5B7CuNb3alloy, the observed nanocrystals of the Fe3Si type are surrounded by an Nb-enriched shell, which stops the growth of the precipitates. With the results of polarized neutron scattering experiments, it is shown that magnetic and nuclear small-angle neutron scattering signals have the same origin. Additionally, the precision of the fits is improved by complementary use of polarized neutrons.
Refinement of modulated structures against X-ray powder diffraction data withJANA2000
Authors: Dušek M. , Petříček V. , Wunschel M. , Dinnebier R. E. , van Smaalen S.
Published: July 2002

JANAis a computer program for the refinement and analysis of periodic and aperiodic (incommensurately modulated structures and composite crystals) crystal structures. Here a new module is introduced that allows Rietveld refinements against powder diffraction data. It is shown thatJANA2000 provides a state-of-the-art description of the peak profiles. A re-analysis of the low-temperature structure of (CO)xC60showed that the application of icosahedral symmetry restrictions to the C60molecule leads to a better description of the electron density and to a corrected position of the CO molecule as compared with a rigid-body refinement. The incommensurately modulated structure of NbTe4has been successfully refined against X-ray powder diffraction data. The structural parameters are equal to, but less accurate, than the parameters obtained from a single-crystal study.
Monte Carlo simulation of a reactor-based neutron strain scanning diffractometer
Authors: Borlado C. R. , Mompean F. J. , Peng Ru Lin
Published: July 2002

A Monte Carlo code for the simulation of neutron strain scanning experiments on a reactor-based two-axis diffractometer is described. In order to validate this code, several experiments have been performed. A comparison is made between experimental and simulated results for instrumental resolution, primary beam divergence and wavelength distribution in the incident neutron beam. Finally, the application of the simulation results to the analysis of a real neutron strain scanning experiment is outlined.
UsingSitusfor the registration of protein structures with low-resolution bead models from X-ray solution scattering
Authors: Wriggers Willy , Chacón Pablo
Published: July 2002

Three-dimensional bead models of proteins in solution are routinely determined from one-dimensional small-angle X-ray scattering (SAXS) data. TheSitussoftware provides a novel set of visualization and registration procedures to facilitate the localization of protein structures in low-resolution SAXS bead models. The docking algorithm takes advantage of a reduced representation of the input data sets by means of topology-representing neural networks to expedite the rigid-body search. The precision of the docking was tested on ten different simulated bead models: for >100 beads typically arising in SAXS models, a docking precision of the order of an ångström can be achieved. The shape-matching score captured the correct solutions in all ten trial cases and was sufficiently stringent to yield unique matches in seven systems. A size-invariant shape descriptor of `sphericity' is proposed to assess the onset of ambiguity in the matching of globular molecules. The software, a tutorial and supplementary data are available at http://situs.scripps.edu/saxs.
NADA– a computer program for the simultaneous refinement of orientation matrix and modulation vector(s)
Authors: Schönleber Andreas , Meyer Mathias , Chapuis Gervais
Published: July 2002

NADAis a computer program for the simultaneous refinement of the components of the orientation matrix and the components of up to three modulation vectors by the method of least squares. Using the spatial peak positions and the orientation matrix of the main reflections from a single-crystal diffraction experiment and rough estimates of the modulation vector(s) components,NADAre-indexes the peaks (main and satellite reflections) with integers in higher dimensions (hklm1,hklm1m2orhklm1m2m3, respectively) and refines the orientation matrix and modulation vector(s) components from the observed peak positions. Standard uncertainties on all refined parameters are calculated analytically.
MCGRtof: Monte CarloG(r) with resolution corrections for time-of-flight neutron diffractometers
Authors: Tucker Matthew G. , Dove Martin T. , Keen David A.
Published: July 2002

A new implementation of the programMCGR[Pusztai & McGreevy (1997).Physica B,234–236, 357–358] for the calculation of pair distribution functions from neutron total scattering data using an inverse Monte Carlo algorithm is presented. The new implementation, calledMCGRtof, incorporates the resolution functions for time-of-flight neutron diffractometers, and is suitable for analysis of data from instruments such as GEM at the ISIS spallation neutron source. The effect of including resolution correctly is to increase the magnitude of the pair distribution function at larger distances. The working program is illustrated with total scattering measurements from crystalline AlPO4.
Performance of a confocal multilayer X-ray optic
Authors: Kusz J. , Böhm H.
Published: July 2002

In recent years, several companies have developed the technique of arranging two multilayer mirrors in confocal optics for monochromatizing X-rays. In this study, a focusing device of Osmic Inc., with a source-to-focus distance of 1005 mm, has been used. The goal was to measure the homogeneity of the beam, the cross section at various distances from the focus and the efficiency of the optic when it is operated with vacuum and with air in the beam path. A small crystal sphere set at various distances is used to compare the intensities and the widths of reflections with those of a flat graphite monochromator. In a standard diffraction experiment (crystal size 0.25 mm), the gain factor with respect to graphite is roughly ten at a position where the beam plateau is 0.5 mm. The suppression of the CuKβ radiation and of higher harmonics ofKα is very good.
ENIGMA: maximum-entropy method program package for huge systems
Authors: Tanaka Hiroshi , Takata Masaki , Nishibori Eiji , Kato Kenichi , Iishi Takashi , Sakata Makoto
Published: July 2002

ENIGMA(Electron and Nuclear Image Generator by Max-ent Analysis) is a program package to evaluate three-dimensional electron and nuclear density from X-ray and neutron diffraction data by using the maximum-entropy method (MEM). Compared with the previous program packageMEED,ENIGMAsaves computing time and frees memory space at the same time by employing parallel data processing. The fast Fourier transformation (FFT) technique is also implemented. As a consequence of these improvements, the MEM analysis byENIGMAbecomes applicable to huge systems, such as proteins and polymers, when the phased structure factors are provided. The package is transferable to a wide variety of parallel computers, because it is written in Fortran 90 and a standard message-passing interface (MPI).
Automatic indexing of area-detector data of periodic and aperiodic crystals
Authors: Pilz Katrin , Estermann Michael , van Smaalen Sander
Published: July 2002

An autoindexing procedure is described that produces the indexing of diffraction data of aperiodic crystals. The procedure has been designed for indexing the data obtained with an area detector, but it can also be applied to data obtained with a single-point detector. The essential step in the indexing process is the ability to discriminate between reflections that fit to a reciprocal lattice, the satellite reflections and possible reflections that do not belong to this indexing. To achieve this goal, the refinement of the orientation matrix and the diffractometer parameters is made an intrinsic part of the process of indexing. The proposed autoindexing procedure has been implemented in a computer program calledBAYINDEX. Successful application to data sets of three different one-dimensionally modulated structures, one two-dimensionally modulated structure and a periodic crystal is presented. Very good agreement between experimental and theoretical reflection positions is found. The indexing produced byBAYINDEXcan serve as the basis for integration routines.
Propagation of X-ray coherence for diffraction of perfect crystals
Authors: Yamazaki Hiroshi , Ishikawa Tetsuya
Published: July 2002

Propagation of X-ray coherence through dynamical diffraction of a perfect crystal is discussed theoretically. A rigorous and general relation between coherence functions before and after diffraction is found by using time-dependent field solutions of Takagi–Taupin equations for a temporally and spatially inhomogeneous incident X-ray pulse. Asymmetry of the diffraction, together with the finite penetration depth, is shown to modify the coherence function in the direction of the diffraction vector.
A high-temperature X-ray diffraction study of the NiO–Li2O system
Authors: Toussaint C. J.
Published: July 2002

A crystallographic study of the system Ni2+
1−2x
Ni3+

x
Li+

x
O has been carried out. The crystal structure of the material in the range 0≤x≤0.4 at room temperature and up to 1000°C has been studied. The principal coefficients of thermal expansion and the phase diagram are given. The structural rhombohedral → face-centred cubic transition temperature of NiO has been determined.
Dimensions de micelles mixtes de p-alkylbenzènesulfonates par diffusion central des rayons X
Authors: Cabos C. , Delord P. , Rouviere J.
Published: July 2002

The structure of micellar solutions is determined from X-ray small-angle scattering measurements on an absolute scale. The most probable structure is chosen by comparison with spherical cylindrical and lamellar models. This method is applied to two-component micelles and it is possible to follow the variation of micellar dimensions when the concentration of each component is varying.
The crystal structure of high-pressure americium, phase III
Authors: Roof R. B.
Published: July 2002

The structure of high-pressure americium, phase III, which occurs at room temperature in the pressure range 10–15 GPa, has been determined. The material has a monoclinic lattice with a = 3.025±0.005, b = 11.887±0.019, c = 2.830±0.005 Å, and β = 106.11±0.14° at 12.5 GPa. The space group is P21/m with Z = 4. Intensity data were obtained from powder-pattern films taken at pressure with Mo Kα radiation, λ = 0.7107 Å. The structure, which can be described as a layer stacking intermediate between the lower-pressure f.c.c. and higher-pressure α-U structure types, was refined by least-squares calculations to R
1 = 0.07 with 12 observed reflections. Am–Am distances of nearest neighbors range from 2.83 to 3.21 Å.
Crystal data for two cis-o,o'-azodioxytoluene modifications
Authors: Azoulay M. , Trysberg L.
Published: July 2002

The title compound, C14H14N2O2, crystallizes from solutions in two different forms, α and β. The α form belongs to the orthorhombic system with cell dimensions a = 15.554(7), b = 15.451(8), c = 10.629(6) Å, V = 2.554(2) Å3 and Z = 8. Possible space groups are I m m a or I m 2 a. The β modification is monoclinic. P21/c, with a = 14.939(14), b = 9.587(5), c = 18.512(8) Å, β = 91.75(4)°, V = 2.598(3) Å3 and Z = 8. Indexed powder data are given for the two crystal forms. Within the temperature range investigated (255–298 K) the β form seems to be metastable.
Crystal data for C.I. Pigment Yellow 4, α-(1 -hydroxyethylidene)acetanilide-α-azo-(4'-nitrobenzine)
Authors: Whitaker A.
Published: July 2002

The single-crystal data and powder pattern are reported for C.I. Pigment Yellow 4, α-(1-hydroxyethylidene)acetanilide-α-azo-(4′-nitrobenzene), C16H14N4O4 (C.I. No 11665). The powder pattern has been indexed from the single-crystal dimensions; the problems of multiple indexing have been reduced by comparison with single-crystal intensities. Crystal is triclinic, P1 or P\bar 1, a = 7.691(2), b = 10.247(2), c = 11.195(2) Å, α = 109.00(2), β = 73.80(2), γ = 112.21(2)°, Z = 2, Dx
= 1.426 Mg m−3. The JCPDS Diffraction File No. for C.I. Pigment Yellow 4 is 33-1985.
Reply to Comments on The accuracy of experimental radial distribution functions for metallic glasses by B.J. Thijsse (1984) by F. Hajdu and G. Herms
Authors: Thijsse B. J.
Published: July 2002

Comments made by Hajdu & Herms [J. Appl. Cryst. (1986). 19, 198–199] on the original paper by Thijsse [J. Appl. Cryst. (1984). 17, 61–76] are replied to.
A fixture for X-ray crystallographic studies of biomolecules under high gas pressure
Authors: Tilton R. F.
Published: July 2002

A fixture is described for collecting X-ray diffraction data from biomolecule crystals under gas pressures up to 300 atm (30 MPa). The fixture is completely portable and can be used on conventional diffractometers. Normal procedures for crystal mounting, alignment and data collection require only slight modification. A test data set of the protein sperm whale metmyoglobin under a gas pressure of 145 atm of N2 gas has been collected to a nominal resolution of 2.0 Å using Cu Kα radiation and refined to an R-factor of 16.2%. Data collection beyond 2.0 Å resolution is hampered by the presence of strong powder diffraction from the beryllium shroud.
Automatic indexing of rotation diffraction patterns
Authors: Kabsch W.
Published: July 2002

A method is described which assigns indices to a set of single-crystal reflections recorded by the rotation-oscillation technique using a fixed X-ray wavelength. It is assumed that the space group and approximate unit-cell parameters are known. The unknown crystal orientation is determined directly from the observed diffraction pattern of one or several oscillation data records. A local indexing procedure is described which tolerates large initial errors in the parameters controlling the diffraction pattern. These parameters are refined subsequently, thereby satisfying the constraints imposed by the space-group symmetry.
On the estimation of the unit-cell volume from powder diffraction data. Erratum
Authors: Paszkowicz W.
Published: July 2002

Table 2 of the paper by Paszkowicz [J. Appl Cryst. (1987). 20, 161–165] is in error; columns N
0 and κ were combined. A revised Table 2 is given.
Quantitative phase analysis from neutron powder diffraction data using the Rietveld method
Authors: Hill R. J. , Howard C. J.
Published: July 2002

The weight of a phase in a mixture is proportional to the product of the scale factor, as derived in a multi-component Rietveld analysis of the powder diffraction pattern, with the mass and volume of the unit cell. If all phases are identified and crystalline, the weight fraction W of phase p is given by W_{p} = S_{p}(ZMV)_{p}/\sum_{i}S_{i}(ZMV)_{i},where S, Z, M and V are, respectively, the Rietveld scale factor, the number of formula units per unit cell, the mass of the formula unit and the unit-cell volume. This is the basis of a method providing accurate phase analyses without the need for standards or for laborious experimental calibration procedures. The method is demonstrated by measurements on binary mixtures of rutile, corundum, silicon and quartz.
A method for analyzing powder patterns of phases of low symmetry
Authors: Bartell L. S. , Caillat J. C.
Published: July 2002

A procedure for determining cell parameters from Debye–Scherrer intensities is described which has been successful in analyses of triclinic phases resisting previous methods of attack. It minimizes the difference between observed and calculated powder pattern profiles, the principal elements of novelty being several new strategies for avoiding entrapment in false local minima while steering the refinement in the proper direction. A preliminary model of the distribution of atoms in the cell is required to enable the computation of intensities. So far the method has been applied only to molecular crystals for which trial molecular coordinates could be generated with the aid of an energy minimization algorithm. Besides its discrimination against false minima, the procedure offers the advantages that provisional assignments of reflections never need to be made, and the overlapping of reflections, even in severe cases, causes no particular trouble.
A computer-based method of measuring the integrated intensities of the reflections on the X-ray diffraction photograph of an oriented crystalline polymer
Authors: Hall I. H. , Neisser J. Z. , Elder M.
Published: July 2002

The method is designed to be used with a batch-processing computer system and will determine the integrated intensities of the spots on an X-ray diffraction photograph of an oriented fibre of a partially crystalline synthetic polymer. It is necessary to assume that the spot boundary is elliptical, that the intensity distribution along any line through the centre of this ellipse is Gaussian, and that the background intensity variation is linear over the region of a spot; these are justified experimentally, although, in the radial direction, the choice of a Gaussian intensity distribution is probably theoretically unsound. The computational procedures correct for minor differences between users in the choice of input parameters and reject bad choices. The method was applied to determine the intensities of the 30 visible spots in the diffraction photograph of oriented poly(trimethyleneterephthalate) which were used in a subsequent structure refinement. successful integrations were obtained for 22 spots, the failures being (1) pairs of similar intensity just resolved by eye, (2) better resolved pairs of which one member is stronger than the other, or (3) very weak. Statistical tests indicated very much better internal consistency of data than is usually obtained with these materials, and enabled a rational weighting scheme to be used in the structure refinement. The R factor of 7.9% obtained is unusually low, indicating much improved accuracy over earlier methods.
An X-ray determination of the thermal expansion of α-phase Cu–Si alloys at high temperature
Authors: Pradhan S. K. , De M.
Published: July 2002

Lattice parameters for four Cu–Si alloys containing 2.2, 4.3, 6.4 and 8.7 at.% Si in the solid-solution range have been calculated in the temperature range 303–928 K. The lattice parameters increase slowly in a nonlinear manner with rise in temperature. The calculated linear thermal-expansion coefficients (α) at room temperature increase with increasing solute concentration (Si) but decrease almost linearly with increasing temperature, the rate of decrease being higher for alloys with higher solute concentration. All the alloys have almost the same average α value (α
av ~ 16.0 × 10−6 K−1), which is the value of α at the temperature interval 615–625 K for all the alloy compositions.
High-pressure single-crystal X-ray diffraction studies of MoO3. I. Lattice parameters up to 7.4 GPa. Erratum
Authors: Åsbrink S. , Kihlborg L. , Malinowski M.
Published: July 2002

Owing to a printer's error, the fourth equation given in the Abstract of the paper by Åsbrink, Kihlborg & Malinowski [J. Appl. Cryst. (1988). 21, 960–962] is incorrect. The correct equation is {\bar \beta}_c(0–7.41 GPa) = −3.35 × 10−4 (GPa)−1.
Electronically focused time-of-flight powder diffractometers at the intense pulsed neutron source
Authors: Jorgensen J. D. , Faber J. , Carpenter J. M. , Crawford R. K. , Haumann J. R. , Hitterman R. L. , Kleb R. , Ostrowski G. E. , Rotella F. J. , Worlton T. G.
Published: July 2002

Two time-of-flight powder diffractometers have operated at the Intense Pulsed Neutron Source (IPNS) since August 1981. These instruments use dedicated microcomputers to focus time-of-flight events so that data from different detectors can be summed into a single histogram. Thus, large multidetector arrays can be employed at any scattering angle from 12 to 157°. This design permits data to be collected over a uniquely wide range of d spacings while maintaining high resolution and count rates. The performance of the two instruments is evaluated by analyzing data from a standard Al2O3 sample by the Rietveld method. These instruments provide the capability for moderate- to high-resolution measurements with the duration of a typical run being a few hours.
An evaluation of selected density-modification methods for protein-structure determination
Authors: Fenderson F. F. , Herriott J. R. , Adman E. T.
Published: July 2002

The effectiveness of density-modification methods in reducing phase errors has been quantitatively analyzed under conditions in which the source and magnitude of phase error could be defined. Progress was gauged by monitoring both the phase errors and electron density. Changes in electron density were monitored in and around the protein density and in the solvent density. The results of this analysis suggest that the improvement possible is more dependent upon the magnitude than on the source of phase error, and that the methods are most effective when the initial phase error is relatively small. As the magnitude of error increases, the improvement gained decreases, and in some cases noise is introduced by the procedure(s).
The importance of, and a method for, optimizing the calculation of rotation functions
Authors: Wilson C. C.
Published: July 2002

A method is described by which a fine-grid rotation function can be calculated efficiently. The importance of optimizing the calculation of this function is discussed and illustrated.
A new method for determining the normals to planar structures and their trace directions in transmission electron microscopy
Authors: Liu Q.
Published: July 2002

With aid of a transmission-electron-microscope (TEM) double-tilt holder, a method for determining the normals to planar structures and their traces in a TEM is developed. This method is considered to be simple and convenient when compared with other methods. The accuracy of the method for the determination of both the normals to planar structures and their traces is within 2°.
DIFFUSE: a procedure to measure diffuse intensity on a CAD-4 diffractometer with CAD-4-EXPRESS software
Authors: Neder R. B.
Published: July 2002

An inaccuracy in the GRIDSCAN procedure, included in version 5.1 of CAD-4-EXPRESS, is pointed out. The program presented allows interactive and batch-type scans on a true grid in reciprocal-lattice units. Two measurement modes are provided: (i) calculation of all points at general Eulerian angles with fixed ψ for all reflections; (ii) two-circle geometry by definition of a zone axis.
Improvements in the Quantitative Evaluation of Three-Dimensional Texture. II. The Pole-Figure-Multiplying Method
Authors: Yu L.-G. , Guo H. , Hendrix B. C. , Xu K.-W. , He J.-W.
Published: July 2002

A new simple method is proposed for determining the orientation distribution function (ODF) for three-dimensional texture analysis in a polycrystal based on the reality that the accuracy of an ODF is dependent on both the accuracy of each measured pole figure and the number of pole figures.