bluuebunny/crossref_metadata_2025 huggingface dataset:
The Involvement of Hydrogen Peroxide in the Differentiation of Secondary Walls in Cotton Fibers1
Authors: Potikha Tamara S. , Collins Cheryl C. , Johnson Douglas I. , Delmer Deborah P. , Levine Alex
Published: July 2002

H2O2 is a widespread molecule in many biological systems. It is created enzymatically in living cells during various oxidation reactions and by leakage of electrons from the electron transport chains. Depending on the concentration H2O2 can induce cell protective responses, programmed cell death, or necrosis. Here we provide evidence that H2O2 may function as a developmental signal in the differentiation of secondary walls in cotton (Gossypium hirsutum) fibers. Three lines of evidence support this conclusion: (a) the period of H2O2 generation coincided with the onset of secondary wall deposition, (b) inhibition of H2O2 production or scavenging the available H2O2 from the system prevented the wall differentiation process, and (c) exogenous addition of H2O2 prematurely promoted secondary wall formation in young fibers. Furthermore, we provide support for the concept that H2O2 generation could be mediated by the expression of the small GTPase Rac, the accumulation of which was shown previously to be strongly induced during the onset of secondary wall differentiation. In support of Rac's role in the activation of NADPH oxidase and the generation of reactive oxygen species, we transformed soybean (Glycine max) and Arabidopsis cells with mutated Rac genes. Transformation with a dominantly activated cotton Rac13 gene resulted in constitutively higher levels of H2O2, whereas transformation with the antisense and especially with dominant-negative Rac constructs decreased the levels of H2O2.
Characterization of Ethylene Biosynthesis Associated with Ripening in Banana Fruit
Authors: Liu Xuejun , Shiomi Shinjiro , Nakatsuka Akira , Kubo Yasutaka , Nakamura Reinosuke , Inaba Akitsugu
Published: July 2002

We investigated the characteristics of ethylene biosynthesis associated with ripening in banana (Musa sp. [AAA group, Cavendish subgroup] cv Grand Nain) fruit.MA-ACS1 encoding 1-aminocyclopropane-1-carboxylic acid (ACC) synthase in banana fruit was the gene related to the ripening process and was inducible by exogenous ethylene. At the onset of the climacteric period in naturally ripened fruit, ethylene production increased greatly, with a sharp peak concomitant with an increase in the accumulation of MA-ACS1 mRNA, and then decreased rapidly. At the onset of ripening, the in vivo ACC oxidase activity was enhanced greatly, followed by an immediate and rapid decrease. Expression of the MA-ACO1 gene encoding banana ACC oxidase was detectable at the preclimacteric stage, increased when ripening commenced, and then remained high throughout the later ripening stage despite of a rapid reduction in the ACC oxidase activity. This discrepancy between enzyme activity and gene expression of ACC oxidase could be, at least in part, due to reduced contents of ascorbate and iron, cofactors for the enzyme, during ripening. Addition of these cofactors to the incubation medium greatly stimulated the in vivo ACC oxidase activity during late ripening stages. The results suggest that ethylene production in banana fruit is regulated by transcription of MA-ACS1 until climacteric rise and by reduction of ACC oxidase activity possibly through limited in situ availability of its cofactors once ripening has commenced, which in turn characterizes the sharp peak of ethylene production.
Villin-Like Actin-Binding Proteins Are Expressed Ubiquitously in Arabidopsis
Authors: Klahre Ulrich , Friederich Evelyne , Kost Benedikt , Louvard Daniel , Chua Nam-Hai
Published: July 2002

In an attempt to elucidate the biological function of villin-like actin-binding proteins in plants we have cloned several genes encoding Arabidopsis proteins with high homology to animal villin. We found that Arabidopsis contains at least four villin-like genes (AtVLNs) encoding four different VLN isoforms. Two AtVLN isoforms are more closely related to mammalian villin in their primary structure and are also antigenically related, whereas the other two contain significant changes in the C-terminal headpiece domain. RNA and promoter/β-glucuronidase expression studies demonstrated that AtVLN genes are expressed in all organs, with elevated expression levels in certain types of cells. These results suggest that AtVLNs have less-specialized functions than mammalian villin, which is found only in the microvilli of brush border cells. Immunoblot experiments using a monoclonal antibody against pig villin showed that AtVLNs are widely distributed in a variety of plant tissues. Green fluorescent protein fused to full-length AtVLN and individual AtVLN headpiece domains can bind to both animal and plant actin filaments in vivo.
Auxin-Regulated Genes Encoding Cell Wall-Modifying Proteins Are Expressed during Early Tomato Fruit Growth
Authors: Catalá Carmen , Rose Jocelyn K.C. , Bennett Alan B.
Published: July 2002

An expansin gene,LeExp2, was isolated from auxin-treated, etiolated tomato (Lycopersicon esculentum cv T5) hypocotyls.LeExp2 mRNA expression was restricted to the growing regions of the tomato hypocotyl and was up-regulated during incubation of hypocotyl segments with auxin. The pattern of expression ofLeExp2 was also studied during tomato fruit growth, a developmental process involving rapid cell enlargement. The expression of genes encoding a xyloglucan endotransglycosylase (LeEXT1) and an endo-1,4-β-glucanase (Cel7), which, like LeExp2, are auxin-regulated in etiolated hypocotyls (C. Catalá, J.K.C. Rose, A.B. Bennett [1997] Plant J 12: 417–426), was also studied to examine the potential for synergistic action with expansins.LeExp2 and LeEXT1 genes were coordinately regulated, with their mRNA accumulation peaking during the stages of highest growth, while Cel7 mRNA abundance increased and remained constant during later stages of fruit growth. The expression of LeExp2, LeEXT1, andCel7 was undetectable or negligible at the onset of and during fruit ripening, which is consistent with a specific role of these genes in regulating cell wall loosening during fruit growth, not in ripening-associated cell wall disassembly.
Acquired Thermotolerance and Expression of the HSP100/ClpB Genes of Lima Bean
Authors: Keeler Sharon J. , Boettger Cynthia M. , Haynes Janine G. , Kuches Kelly Ann , Johnson Marisia M. , Thureen Dean L. , Keeler Calvin L. , Kitto Sherry L.
Published: July 2002

Acquired thermotolerance (AT) is the ability of cells to survive a normally lethal temperature treatment as a consequence of pretreatment at an elevated but sublethal temperature. In yeast and cyanobacteria, the expression of the HSP100/ClpB protein is required for the AT response. To determine whether the HSP100/ClpB protein is associated with this response in lima bean (Phaseolus lunatus), we have cloned an HSP100/ClpB homolog and assessed expression of the two gene copies under heat stress conditions, which induce AT. Transcription of the cytoplasmically localized HSP100/ClpB protein genes is stringently controlled by heat stress in both of the laboratory and field heat stress conditions. From a heat-induced cDNA library, we identified a clone of a putative chloroplast-targeted (cp) HSP100/ClpB protein gene sequence. The cp HSP100/ClpB protein genes are constitutively expressed, but transcript levels increase post-heat stress in laboratory heat stress experiments. In field conditions the genes for the cp HSP100/ClpB are constitutively expressed. Although we were unable to correlate differences in the timing of AT response with the expression or genetic structure of the HSP100/ClpB genes in heat-tolerant or -sensitive varieties of lima bean, we clearly demonstrate the association of expression of HSP100/ClpB proteins with heat response in this species.
Identification of Phloem Involved in Assimilate Loading in Leaves by the Activity of the Galactinol Synthase Promoter
Authors: Haritatos Edith , Ayre Brian G. , Turgeon Robert
Published: July 2002

The definition of “minor” veins in leaves is arbitrary and of uncertain biological significance. Generally, the term refers to the smallest vein classes in the leaf, believed to function in phloem loading. We found that a galactinol synthase promoter, cloned from melon (Cucumis melo), directs expression of thegusA gene to the smallest veins of mature Arabidopsis and cultivated tobacco (Nicotiana tabacum) leaves. This expression pattern is consistent with the role of galactinol synthase in sugar synthesis and phloem loading in cucurbits. The expression pattern in tobacco is especially noteworthy since galactinol is not synthesized in the leaves of this plant. Also, we unexpectedly found that expression in tobacco is limited to two of three companion cells in class-V veins, which are the most extensive in the leaf. Thus, the “minor” vein system is defined and regulated at the genetic level, and there is heterogeneity of response to this system by different companion cells of the same vein.
Zinc Deficiency Up-Regulates Expression of High-Affinity Phosphate Transporter Genes in Both Phosphate-Sufficient and -Deficient Barley Roots
Authors: Huang Chunyuan , Barker Susan Jane , Langridge Peter , Smith Frank W. , Graham Robin David
Published: July 2002

Phosphate (P) is taken up by plants through high-affinity P transporter proteins embedded in the plasma membrane of certain cell types in plant roots. Expression of the genes that encode these transporters responds to the P status of the plants, and their transcription is normally tightly controlled. However, this tight control of P uptake is lost under Zn deficiency, leading to very high accumulation of P in plants. We examined the effect of plant Zn status on the expression of the genes encoding the HVPT1 and HVPT2 high-affinity P transporters in barley (Hordeum vulgareL. cv Weeah) roots. The results show that the expression of these genes is intimately linked to the Zn status of the plants. Zn deficiency induced the expression of genes encoding these P transporters in plants grown in either P-sufficient or -deficient conditions. Moreover, the role of Zn in the regulation of these genes is specific in that it cannot be replaced by manganese (a divalent cation similar to Zn). It appears that Zn plays a specific role in the signal transduction pathway responsible for the regulation of genes encoding high-affinity P transporters in plant roots. The significance of Zn involvement in the regulation of genes involved in P uptake is discussed.
Production of the Isoflavones Genistein and Daidzein in Non-Legume Dicot and Monocot Tissues
Authors: Yu Oliver , Jung Woosuk , Shi June , Croes Robert A. , Fader Gary M. , McGonigle Brian , Odell Joan T.
Published: July 2002

Metabolic engineering for production of isoflavones in non-legume plants may provide the health benefits of these phytoestrogens from consumption of more widely used grains. In legumes, isoflavones function in both the symbiotic relationship with rhizobial bacteria and the plant defense response. Expression of a soybean isoflavone synthase (IFS) gene in Arabidopsis plants was previously shown to result in the synthesis and accumulation of the isoflavone genistein in leaf and stem tissue (Jung et al., 2000). Here we further investigate the ability of the heterologous IFS enzyme to interact with the endogenous phenylpropanoid pathway, which provides the substrate for IFS, and produces genistein in several plant tissue systems. In tobacco (Nicotiana tabacum) floral tissue that synthesizes anthocyanins, genistein production was increased relative to leaves. Induction of the flavonoid/anthocyanin branch of the phenylpropanoid pathway through UV-B treatment also enhanced genistein production in Arabidopsis. In a monocot cell system, introduced expression of a transcription factor regulating genes of the anthocyanin pathway was effective in conferring the ability to produce genistein in the presence of the IFS gene. Introduction of a third gene, chalcone reductase, provided the ability to synthesize an additional substrate of IFS resulting in production of the isoflavone daidzein in this system. The genistein produced in tobacco, Arabidopsis, and maize (Zea mays) cells was present in conjugated forms, indicating that endogenous enzymes were capable of recognizing genistein as a substrate. This study provides insight into requirements for metabolic engineering for isoflavone production in non-legume dicot and monocot tissues.
Chloroplast Division and Morphology Are Differentially Affected by Overexpression of FtsZ1 and FtsZ2 Genes in Arabidopsis,
Authors: Stokes Kevin D. , McAndrew Rosemary S. , Figueroa Rubi , Vitha Stanislav , Osteryoung Katherine W.
Published: July 2002

In higher plants, two nuclear gene families, FtsZ1and FtsZ2, encode homologs of the bacterial protein FtsZ, a key component of the prokaryotic cell division machinery. We previously demonstrated that members of both gene families are essential for plastid division, but are functionally distinct. To further explore differences between FtsZ1 and FtsZ2 proteins we investigated the phenotypes of transgenic plants overexpressingAtFtsZ1-1 or AtFtsZ2-1, Arabidopsis members of the FtsZ1 and FtsZ2 families, respectively. Increasing the level of AtFtsZ1-1 protein as little as 3-fold inhibited chloroplast division. Plants with the most severe plastid division defects had 13- to 26-fold increases in AtFtsZ1-1 levels over wild type, and some of these also exhibited a novel chloroplast morphology. Quantitative immunoblotting revealed a correlation between the degree of plastid division inhibition and the extent to which the AtFtsZ1-1 protein level was elevated. In contrast, expression of an AtFtsZ2-1 sense transgene had no obvious effect on plastid division or morphology, though AtFtsZ2-1 protein levels were elevated only slightly over wild-type levels. This may indicate that AtFtsZ2-1 accumulation is more tightly regulated than that of AtFtsZ1-1. Plants expressing the AtFtsZ2-1transgene did accumulate a form of the protein smaller than those detected in wild-type plants. AtFtsZ2-1 levels were unaffected by increased or decreased accumulation of AtFtsZ1-1 and vice versa, suggesting that the levels of these two plastid division proteins are regulated independently. Taken together, our results provide additional evidence for the functional divergence of the FtsZ1 andFtsZ2 plant gene families.
Sugar Coordinately and Differentially Regulates Growth- and Stress-Related Gene Expression via a Complex Signal Transduction Network and Multiple Control Mechanisms
Authors: Ho Shin-Lon , Chao Yu-Chan , Tong Wu-Fu , Yu Su-May
Published: July 2002

In plants, sugars are required to sustain growth and regulate gene expression. A large set of genes are either up- or down-regulated by sugars; however, whether there is a common mechanism and signal transduction pathway for differential and coordinated sugar regulation remain unclear. In the present study, the rice (Oryza sativa cv Tainan 5) cell culture was used as a model system to address this question. Sucrose and glucose both played dual functions in gene regulation as exemplified by the up-regulation of growth-related genes and down-regulation of stress-related genes. Sugar coordinately but differentially activated or repressed gene expression, and nuclear run-on transcription and mRNA half-life analyses revealed regulation of both the transcription rate and mRNA stability. Although coordinately regulated by sugars, these growth- and stress-related genes were up-regulated or down-regulated through hexokinase-dependent and/or hexokinase-independent pathways. We also found that the sugar signal transduction pathway may overlap the glycolytic pathway for gene repression. α-Amylase and the stress-related genes identified in this study were coordinately expressed under sugar starvation, suggesting a convergence of the nutritional and environmental stress signal transduction pathways. Together, our studies provide a new insight into the complex signal transduction network and mechanisms of sugar regulation of growth and stress-related genes in plants.
Inventory of the Superfamily of P-Type Ion Pumps in Arabidopsis
Authors: Axelsen Kristian B. , Palmgren Michael G.
Published: July 2002

A total of 45 genes encoding for P-type ATPases have been identified in the complete genome sequence of Arabidopsis. Thus, this plant harbors a primary transport capability not seen in any other eukaryotic organism sequenced so far. The sequences group in all five subfamilies of P-type ATPases. The most prominent subfamilies are P1B ATPases (heavy metal pumps; seven members), P2A and P2B ATPases (Ca2+ pumps; 14 in total), P3A ATPases (plasma membrane H+pumps; 12 members including a truncated pump, which might represent a pseudogene or an ATPase-like protein with an alternative function), and P4 ATPases (12 members). P4 ATPases have been implicated in aminophosholipid flipping but it is not known whether this is a direct or an indirect effect of pump activity. Despite this apparent plethora of pumps, Arabidopsis appears to be lacking Na+ pumps and secretory pathway (PMR1-like) Ca2+-ATPases. A cluster of Arabidopsis heavy metal pumps resembles bacterial Zn2+/Co2+/Cd2+/Pb2+transporters. Two members of the cluster have extended C termini containing putative heavy metal binding motifs. The complete inventory of P-type ATPases in Arabidopsis is an important starting point for reverse genetic and physiological approaches aiming at elucidating the biological significance of these pumps.
Comprehensive Expression Profile Analysis of the Arabidopsis Hsp70 Gene Family
Authors: Sung Dong Yul , Vierling Elizabeth , Guy Charles L.
Published: July 2002

We isolated cDNA clones for two nuclear-encoded, organellar members of the Arabidopsis hsp70 gene family, mtHsc70-2(AF217458) and cpHsc70-2 (AF217459). Together with the completion of the genome sequence, the hsp70 family in Arabidopsis consists of 14 members unequally distributed among the five chromosomes. To establish detailed expression data of this gene family, a comprehensive reverse transcriptase-polymerase chain reaction analysis for 11 hsp70s was conducted including analysis of organ-specific and developmental expression and expression in response to temperature extremes. All hsp70s showed 2- to 20-fold induction by heat shock treatment except cpHsc70-1 andmtHsc70-1, which were unchanged or repressed. The expression profiles in response to low temperature treatment were more diverse than those evoked by heat shock treatment. Both mitochondrial and all cytosolic members of the family except Hsp70bwere strongly induced by low temperature, whereas endoplasmic reticulum and chloroplast members were not induced or were slightly repressed. Developmentally regulated expression of the heat-inducibleHsp70 in mature dry seed and roots in the absence of temperature stress suggests prominent roles in seed maturation and root growth for this member of the hsp70 family. This reverse transcriptase-polymerase chain reaction analysis establishes the complex differential expression pattern for the hsp70s in Arabidopsis that portends specialized functions even among members localized to the same subcellular compartment.
Enhanced Accumulation of BiP in Transgenic Plants Confers Tolerance to Water Stress
Authors: Alvim Fátima C. , Carolino Sônia M.B. , Cascardo Júlio C.M. , Nunes Cristiano C. , Martinez Carlos A. , Otoni Wagner C. , Fontes Elizabeth P.B.
Published: July 2002

The binding protein (BiP) is an important component of endoplasmic reticulum stress response of cells. Despite extensive studies in cultured cells, a protective function of BiP against stress has not yet been demonstrated in whole multicellular organisms. Here, we have obtained transgenic tobacco (Nicotiana tabacum L. cv Havana) plants constitutively expressing elevated levels of BiP or its antisense cDNA to analyze the protective role of this endoplasmic reticulum lumenal stress protein at the whole plant level. Elevated levels of BiP in transgenic sense lines conferred tolerance to the glycosylation inhibitor tunicamycin during germination and tolerance to water deficit during plant growth. Under progressive drought, the leaf BiP levels correlated with the maintenance of the shoot turgidity and water content. The protective effect of BiP overexpression against water stress was disrupted by expression of an antisense BiP cDNA construct. Although overexpression of BiP prevented cellular dehydration, the stomatal conductance and transpiration rate in droughted sense leaves were higher than in control and antisense leaves. The rate of photosynthesis under water deficit might have caused a degree of greater osmotic adjustment in sense leaves because it remained unaffected during water deprivation, which was in marked contrast with the severe drought-induced decrease in the CO2 assimilation in control and antisense leaves. In antisense plants, the water stress stimulation of the antioxidative defenses was higher than in control plants, whereas in droughted sense leaves an induction of superoxide dismutase activity was not observed. These results suggest that overexpression of BiP in plants may prevent endogenous oxidative stress.
Estimation of the background in powder diffraction patterns through a robust smoothing procedure
Authors: Brückner Sergio
Published: July 2002

A procedure is described for estimating the background outline in powder diffraction patterns. It essentially consists of an extension of traditional smoothing procedures to include Bragg peaks in addition to profile random fluctuations. This approach is particularly suited for dealing with diffraction patterns obtained from semicrystalline polymer samples; some applications to this kind of experimental data are presented.
Effect of a crystallite size distribution on X-ray diffraction line profiles and whole-powder-pattern fitting
Authors: Langford J. I. , Louër D. , Scardi P.
Published: July 2002

A distribution of crystallite size reduces the width of a powder diffraction line profile, relative to that for a single crystallite, and lengthens its tails. It is shown that estimates of size from the integral breadth or Fourier methods differ from the arithmetic mean of the distribution by an amount which depends on its dispersion. It is also shown that the form of `size' line profiles for a unimodal distribution is generally not Lorentzian. A powder pattern can be simulated for a given distribution of sizes, if it is assumed that on average the crystallites have a regular shape, and this can then be compared with experimental data to give refined parameters defining the distribution. Unlike `traditional' methods of line-profile analysis, this entirely physical approach can be applied to powder patterns with severe overlap of reflections, as is demonstrated by using data for nanocrystalline ceria. The procedure is compared with alternative powder-pattern fitting methods, by using pseudo-Voigt and Pearson VII functions to model individual line profiles, and with transmission electron microscopy (TEM) data.
Determination of lattice-transform density profiles for multilayered three-dimensional microcrystals in electron crystallography
Authors: Dimmeler Eva , Vossen Oliver , Schröder Rasmus R.
Published: July 2002

Electron crystallography on multilayered three-dimensional microcrystals has been limited in application by the need to define precisely the three-dimensional shape of the diffraction density profiles. A new method is presented here to obtain this profile from experimental spot positions which are shifted in a characteristic way from the expected Bragg positions. While the Bragg positions are defined by the diffraction geometry, the characteristic shift additionally depends on the density profile in Fourier space. In general, these two effects are intermingled. A new correlation approach is presented which uses characteristic shift patterns to separate these effects. This technique also allows the determination of all three crystallographic unit-cell dimensions from a single tilted electron diffraction pattern. It was tested on simulated diffraction patterns and applied to experimental data of frozen hydrated crystals of the protein catalase. Since multilayered catalase crystals with different numbers of crystallographic layers were studied, an inhomogeneous data set had to be evaluated. Processing of such data is now possible using the new correlation approach.
Data smoothing and distortion of X-ray diffraction peaks. II. Application
Authors: Wang Hejing , Zhou Jian
Published: July 2002

Based on the analysis of geometric relations, it is found that the amplitude of the distortion of the full width at half-maximum (FWHM) of a peak after smoothing is the largest among the distortions of the seven parameters of a peak: maximum intensity, FWHM, shape, asymmetry, integral intensity, peak position and integral width. Hence the FWHM distortion is used as a criterion of smoothing. The 1% and 5% error limits of smoothing are calculated. Quadratic and quartic polynomial Savitzky–Golay filters are compared. Aberrations of an X-ray diffraction (XRD) peak caused by using double, matched, 1.5 and 0.7 FWHM filters are described in more detail by means of the analyses of internal and external factors. It is found that the smoothing-induced distortions of an actual XRD peak trend towards those of ideal curves. The distortions are classified according to three types of peak. A possible method to obtain the actual peak parameters, called `system smoothing refinement', is presented.
The disordered structure of tetraferrocenyl-[3]-cumulene, (Fc)2C=C=C=C(Fc)2, by simulated annealing using synchrotron powder diffraction data
Authors: Dinnebier Robert E. , Schweiger Manuela , Bildstein Benno , Shankland Kenneth , David William I. F. , Jobst Andreas , van Smaalen Sander
Published: July 2002

In the molecular structure of tetraferrocenyl-[3]-cumulene, (Fc)2C=C=C=C(Fc)2, four ferrocene molecules are connectedviaa linear bridge consisting of four carbon atoms. At room temperature, the crystal structure has space groupP21/a(Z= 1) witha= 13.104 (5),b= 6.121 (2),c= 11.194 (4) Å, β = 114.922 (1)° andV= 814.3 (8) Å3. A phase transition during cooling was not observed from room temperature to 75 K. From high-resolution X-ray powder diffraction data, the structure of the room-temperature phase was solved by the method of simulated annealing and refined by the Rietveld method using rigid bodies and restraints. The crystal structure was found to be highly disordered with the molecules occupying two orientations with equal probability and a 50% occupancy of the carbon atoms in the cumulene bridge. The disorder could be modelled by stacking faults in ordered structures. In contrast to other compounds of this class, the ferrocenyl groups are in asynrather than in an up–down conformation with respect to the cumulene bridge.
Identification of an Al–Ni–O precipitate in combustion-synthesized NiAl
Authors: Biswas A. , Madangopal K.  , Singh J. B. , Roy S. K. , Banerjee S.
Published: July 2002

The complete identity of a second-phase precipitate detected by transmission electron microscopy in combustion-synthesized NiAl was established. The crystal structure, including the point group, the space group and the lattice parameters, was determined by convergent and selected-area electron diffraction techniques. Energy dispersive X-ray spectroscopy was used for the determination of the chemical composition. Analysis established the phase to be the solid solution of NiO in Al2O3and presented evidence of the hitherto unreported room-temperature solubility.
Kα1–Kα2characteristic of a parabolic graded multilayer
Authors: Toraya H. , Hibino H.
Published: July 2002

Line shapes of theKα1–Kα2doublet beam reflected from a parabolic graded multilayer (PGM) were analysed by ray tracing and rocking-curve measurements using an Si(400) flat single crystal. The integrated intensity and the intensity ratio ofKα2toKα1of the reflected beam vary with the angle of incidence at the PGM. The rates of these variations are considered to increase with increasing spectral resolution of the PGM. TheKα1andKα2beams are reflected from the PGM in slightly different directions. Therefore, the angular separation between theKα1andKα2peaks of the observed diffraction profile of a sample becomes smaller than that calculated from the two wavelengths forKα1andKα2when the PGM and the sample are arranged in the (+−) setting, andvice versawhen they are in the (++) setting. The magnitude of the shift of the angular separation is close to the experimental uncertainty in the determination of the peak positions when the PGM consists of W/Si bilayers, whereas it is estimated to be three times as large when a PGM of high spectral resolution is used.
Water calibration at DLL verified with polymer samples
Authors: Lindner P.
Published: July 2002

The effective differential scattering cross section of a 0.1cm standard water sample at ambient temperature (T = 298 K), used for absolute calibration of SANS-data, has been determined at D11 with its BF3-gas detector. Systematic calibrations against primary standards were done in the wavelength range 4.5 ≤ [Å] ≤ 20. The standard samples are well-characterised polymer solutions and blends with known differential scattering cross sections. Data are compared to previous measurements at D11 and to recent results obtained at D22, equipped with a 3He gas-detector.
GISAXS study of Cu–Ni alloy clusters obtained by double ion implantation in silicate glasses
Authors: Cattaruzza E. , d'Acapito F. , Gonella F. , Longo A. , Martorana A. , Mattei G. , Maurizio C. , Thiaudière D.
Published: July 2002

Sequential double ion implantation in silicate glasses has been used to realize copper-nickel alloy nanoclusters embedded in the host dielectric matrix. A grazing incidence small-angle X-ray scattering experiment has been performed on copper+nickel implanted silicate glasses, to obtain information on the cluster size and size distribution, as well as on the volume fraction. The potential of the technique in the study of these composite glasses is discussed.
Neutron transmission through pyrolytic graphite monochromators
Authors: Mildner D. F. R , Arif M. , Werner S. A.
Published: July 2002

Thermal neutron transmission measurements have been made as a function of wavelength on a pyrolytic graphite monochromator crystal that has been set to diffract a horizontal beam at different take-off angles. The major dips in the transmission caused by the various reflections have been identified. These results can be used for the design of a beamline on which more than one instrument is placed. The transmission data show that it is best for the monochromator with the greatest (horizontal) take-off angle to be placed upstream, with monochromators with decreasing take-off angles progressively further downstream. The order of instruments for which the wavelength is greater than 0.43 nm is unimportant.
On planarity and similarity restraints
Authors: Blanc Eric , Paciorek Włodzimierz
Published: July 2002

Planarity and similarity restraints are described using a unified framework for the computation layout. In both cases, the gradient and Hessian of the restraint residual with respect to atomic coordinates are derived. All computed quantities (residual, gradient, Hessian, normal and distance to the plane for planarity restraints, rotation and translation in the case of similarity) can be obtained directly, without iterative procedure.
WinXPRO: a program for calculating crystal and molecular properties using multipole parameters of the electron density
Authors: Stash Adam , Tsirelson Vladimir
Published: July 2002

The computer programWinXPROenables the calculation of crystal and molecular properties using the multipole parameters of the electron density. The list of properties includes the electron density and its topological and electric field characteristics, the local kinetic and potential energies, the electron localization function, and the effective crystal potential.WinXPROworks under the Windows operating system and can utilize any existing graphics program to display output.
Determination of small alterations in the radius of gyration by small-angle X-ray scattering
Authors: Simon I.
Published: July 2002

A differential method is presented for the evaluation of small-angle X-ray scattering data. The direct determination of slight changes in the radius of gyration of colloid particles is rendered possible by the method proposed.
A device for in situ α-irradiation of diffractometer mounted single crystals
Authors: Denne W. A. , Janky S. , Venn R.
Published: July 2002

A diffractometer-mounted device for the controlled α-irradiation of the single crystals is described.
The effect of diffuse scattering on the dark-field contrast from precipitates
Authors: Gjønnes J. , Solberg J. K.
Published: July 2002

Precipitate contrast due to Bragg interactions in the diffuse scattering has been studied. Both ordinary dark-field contrast and moiré contrast were found to be preserved at quite large distances from the Bragg spots, especially along the direction normal to the reciprocal lattice vector. The effects, which are similar to those seen in thickness fringe contrast from perfect crystals, may be disturbing in the search for faint precipitate reflections with the dark-field technique, especially in thicker parts of the crystal.
Crystal data for the dihydrate and anhydrate of 11-aminoundecanoic acid
Authors: Rigotti G. , Rivero B. E. , Macchi E. M. , Giorgi A. A.
Published: July 2002

X-ray and electron diffraction studies were made on the two phases of 11-aminoundecanoic acid, C11H21NO2. Phase I: dihydrate, monoclinic, C2/c, z = 8, a = 15.96±0.03, b = 4.71±0.01, c = 35.48±0.08 Å, β = 82.1±0.3°. Phase II: anhydrate, orthorhombic, P212121, z = 4, a = 7.526±0.003, b = 4.623±0.003, c = 32.42±0.01 Å.
Application of the maximum entropy method to electron density determination
Authors: Wei W.
Published: July 2002

The principle of maximum entropy is adopted to derive a procedure for obtaining the electron density distribution in crystals from incomplete X-ray diffraction data. This method was applied to cementite and the result proved to be better than the conventional Fourier inversion in resolution as well as in the absence of ripples. The potential advantages of this method are: (1) the amount of subjective judgment imposed on unavailable data is significantly limited, and (2) the result of this method is consistent with the known information and maximally noncommittal with regard to the unknowns. It is shown that the method is especially well suited to the problem of the determination of a high-resolution electron density map from insufficient experimental data.
SHAMGAR's OXGOAD: A new approach to the problem of resolution corrections for triple-axis neutron inelastic scattering data using parallel processors
Authors: Mitchell P. W. , Dove M. T.
Published: July 2002

One problem in the analysis of triple-axis neutron inelastic scattering data is the large numerical computations involved in applying full resolution corrections, which in one extreme involves an often-repeated four-dimensional numerical integral. A program called SHAMGAR has been written for an ICL Distributed Array Processor that will both calculate the full convolution of a model scattering function with the resolution function and allow refinement of the model simultaneously to many sets of experimental data by a non-linear least-squares fit. Sample results and performance figures are given.
Correction of integrated X-ray intensities for preferred orientation in quantitative phase analysis
Authors: Valvoda V.
Published: July 2002

A method is presented for the correction of integrated X-ray intensities for preferred orientation of crystallites in a powder specimen. It is based on knowledge of the relative intensities of reflections of a random specimen on an arbitrary scale; these are supposed to be known in quantitative phase analysis. The orientation distribution of crystallites is represented by a harmonic expansion of which the coefficients can be determined from the intensities of reflections measured in the standard diffraction geometry of a powder diffractometer. The method was tested on a specimen of cubic titanium carbide by comparison with the texture correction obtained from direct examination of the pole-density distribution measured on a texture goniometer. The results of both methods are in agreement to within 1%.
A simple method of absorption and decay correction in intensities measured by area-detector X-ray diffractometer
Authors: Takusagawa F.
Published: July 2002

A simple numerical method has been developed to correct for absorption and decay effects in the intensities measured by area-detector X-ray diffractometers. Application of this method improves not only the internal consistency of symmetry-equivalent reflections, but also the agreement between the two independent data sets.
Sensitivity of X-ray diffractometry for strain depth profiling in III–V heterostructures
Authors: Bensoussan S. , Malgrange C. , Sauvage-Simkin M.
Published: July 2002

The use of the fine structure of X-ray rocking curves for the characterization of the abruptness of heterointerfaces is presented for the particular example of Ga1−x
Al
x
As/GaAs heterojunctions. The sensitivity of the method is discussed in detail for the 400 reflection with two different wavelengths (1.2378 and 1.5410 Å). It is shown that the conclusions can be extended to other reflections and wavelengths provided that the ratio χ
hi
/χ
hr
depending on both the absorption and the strength of the reflection is kept below 10−1.
Resolution corrections in diffuse scattering experiments
Authors: Boysen H. , Adlhart W.
Published: July 2002

The variation of diffuse scattered intensities with scattering angle due to resolution effects is described by different Lorentz factors depending on the dimensionality of the disorder (e.g. diffuse streaks or planes) and the type of scan. Intensities are calculated by folding the cross section of the diffuse scattering with the resolution function of the instrument. For the most general results existing calculations of the resolution function are extended to include (i) a characteristic line spectrum used together with a monochromator, (ii) a possible mis-set of the monochromator (e.g. between Kα
1 and Kα
2) and (iii) a perpendicular arrangement of the scattering planes at the monochromator and at the sample. Both a Gaussian and a slightly simplified rectangular approximation have been applied. Explicit formulae are derived for sharp diffuse streaks and planes for a point measurement as well as integrated intensities. Since the evaluation of point measurements requires exact knowledge of the instrumental divergences and, moreover, there are differences between the two approximations, it is strongly recommended that integrated intensities be used, preferably from scans perpendicular to the streak or plane.
SWATAB, a program to obtain required tables for publication from SHELX76 final output
Authors: Swaminathan K.
Published: July 2002

SWATAB is a Fortran IV computer program which helps in obtaining most of the required tables for crystal structure publication from the widely used SHELX76 program output. The strategy, installation, required local modifications, merits and limitations are discussed.
Localizing adsorption sites in zeolitic materials by X-ray powder diffraction: pyridine sorbed in B.ZSM-5
Authors: Mentzen B. F.
Published: July 2002

Interpretation of X-ray powder diffraction spectra shows that it is possible to determine the locations of at least three distinct pyridine species in a saturated B.ZSM-5 zeolitic material (space group Pnma). Refinement of site occupancy factors leads to a total of ten pyridine molecules/unit cell distributed in the channel system of the MFI topology: four pyr1 molecules at the channel intersections (centred on 4cl sites), two pyr2 species in the sinusoidal channels (centred on 4c2 sites), and four pyr3 guests in the straight channels (centred on 4b inversion centres). Possible hydrogen-bond formation between pyridine molecules and framework oxygen atoms through silanol groups and/or charge-compensating protons is discussed. This work represents the first successful localization of more than eight aromatic molecules sorbed in an MFI topology.
A method of equilibrating protein crystals with heavy-atom reagents
Authors: David P. R. , Burley S. K.
Published: July 2002

A novel method of heavy-atom equilibration with protein crystals is presented. This method utilizes a central drop of mother liquor containing the crystal surrounded by a locus of small drops containing the heavy-atom reagent.
The determination of crystal size and disorder from the X-ray diffraction photograph of polymer fibres. 2. Modelling intensity profiles
Authors: Hall I. H. , Somashekar R.
Published: July 2002

The intensity profile of the X-ray reflection from a crystalline material is related to the lattice disorder and the distribution of crystal sizes through its Fourier cosine coefficients. However, existing methods of obtaining these structural parameters from the coefficients require more than one order of reflection and this is seldom available with polymer fibres. They also rely heavily on the low-order harmonics which are those determined with least accuracy. The development and testing of a method which overcomes this weakness and which is suitable for use with a single order is described. The coefficients are calculated for a model with paracrystalline disorder and an assumed distribution of crystal sizes and the parameters describing this model are refined to minimize the discrepancy between the calculated and experimental values of the coefficients. Provided the distribution of lengths is asymmetric this discrepancy is no greater than would be expected from experimental error and so the assumed model cannot be rejected on the evidence available. Since a range of model parameters all gave equally good agreement with experiment, it was not possible with a single order to obtain a well defined set of values. Diffraction patterns displaying two orders had been chosen and results from the second order were consistent with the first, only a narrow range satisfying both simultaneously. The method was further developed by calculating the intensity profile from the harmonics and using this in the refinement. There was no advantage over using harmonics; indeed, on occasions the refinement algorithm was unstable producing unreliable results.
Multiple small-angle scattering from a statistical medium
Authors: Mazumder S. , Sequeira A.
Published: July 2002

A generalized formalism on multiple small-angle scattering is proposed to investigate the nature of the extractable structural information on inhomogeneities from the multiple-scattering profile. It is found that the statistical nature of the medium can broaden as well as narrow the scattering profile depending upon the characteristics of the medium. The nature and the extent of the effect of the various approximations on analysing the multiple-scattering data are discussed.
Scaling functions for the finite-size effect in fractal aggregates
Authors: Zang Y. , Meriani S.
Published: July 2002

An exact scaling function for the finite-sized fractal aggregates sharply bounded by a sphere of radius R has been established by using the convolution square of the shape function of aggregates and the inhomogeneity function, which is introduced to take into account the presence of inhomogeneity in fractal aggregates. The scaling function for an inhomogeneous aggregate is mainly determined by the geometric shape of the aggregate but is also dependent upon the degree of inhomogeneity present in the aggregate. The differences between the scaling function reported in this paper and the commonly used ones, exp (−r/ξ) and exp [−(r/ξ)2], are discussed. The simulating calculations have shown that the use of different scaling functions will not only influence the cross-over behavior between the Guinier regime and the fractal regime, but also make the low-q scattering intensity converge to different values.
CIF Applications. VI. CIFLIB: an application program interface to CIF dictionaries and data files
Authors: Westbrook J. D. , Hsieh S.-H. , Fitzgerald P. M. D.
Published: July 2002

A software library is described that provides simple and convenient access to information in Crystallographic Information File (CIF) dictionaries and data files. This library gives the application programmer a collection of high-level functions that can be used to process and check data stored in the CIF format using the full detail of the CIF dictionary of crystallographic terminology. Two applications are presented that demonstrate the features of the library: a CIF browser and a CIF dictionary-to-HTML converter.
Small-Angle Scattering of Interacting Particles. I. Basic Principles of a Global Evaluation Technique
Authors: Brunner-Popela J. , Glatter O.
Published: July 2002

Indirect Fourier transformation is a well established method for the evaluation of small-angle scattering data. This technique, however, is restricted to dilute solutions, as for higher concentrations particle interactions can no longer be neglected. As the scattering intensity contains intra- and interparticle scattering contributions, the evaluation of scattering data is no longer just the solution of a linear weighted least-squares problem because the scattering intensity can, under certain conditions, be written as the product of the particle form factor and the so-called structure factor, which leads to a highly non-linear problem. In this paper a global evaluation technique including the structure factor is presented so that it is possible to determine the form factor and the structure factor simultaneously. This technique can be understood as a generalized version of the indirect Fourier transformation method. Like in the indirect Fourier transformation, there are no models or no analytical restrictions used for the form factor, and the structure factor is parameterized with up to four parameters for a given interaction model. A simultaneous determination of these two functions is possible due to the different analytical behavior of these functions, which also leads in most cases to the existence of a global minimum in the parameter surface. An algorithm to solve this nonlinear least-squares problem has been developed and applied to simulated data for a variety of different uncharged systems.
X-ray Standing Waves in X-ray Specular Reflection and Fluorescence Study of Nano-Films
Authors: Zheludeva S. I. , Kovalchuk M. V. , Novikova N. N. , Sosphenov A. N. , Salaschenko N. N. , Shamov E. A. , Prokhorov K. A. , Burattini E. , Cappuccio G.
Published: July 2002

The analysis of the wavefield intensity distribution connected with X-ray standing wave (XRSW) generation above the mirror surface at total reflection (TR) is presented for a vacuum/film/substrate sample along with experimental examples for organic and inorganic films for cases where the refractive index of the film is greater than that of the substrate. The thickness of an ultra-thin film may be estimated from the value of the XRSW period formed above the film/substrate interface at TR. In some cases, the thickness of an ultra-thin film may be roughly obtained just from the form of the X-ray reflection curve at incident angles smaller than the critical angle of the substrate. It is demonstrated that interference phenomena at TR, leading to waveguide mode formation inside the layered structure and responsible for a modulation of the X-ray reflection and fluorescence angular dependence, can be used for characterization of nano-films.
Small-Angle Neutron Scattering Investigation of Precipitation in Single-Crystal Nickel-Based Superalloy ZS26
Authors: Strunz P. , Wiedenmann A. , Zrník J. , Lukás P.
Published: July 2002

The influence of different heat treatments on the microstructure of ordered cuboidal γ′ precipitates in the ZS26 superalloy (wt%: Ni 64, W 11, Co 9, Al 6, Cr 5, Nb 1.5, Ti 1, Mo 1, V 1) was studied by small-angle neutron scattering. The average shape and size of the precipitates were determined by modelling the scattering curves and by fitting them to the measured 2D data. The volume fraction of the precipitates was deduced from the fitted parameters under the assumption of a homogeneous distribution of particles inside the sample.