bluuebunny/crossref_metadata_2025 huggingface dataset:
Accumulation of Palmitate in Arabidopsis Mediated by the Acyl-Acyl Carrier Protein Thioesterase FATB1
Authors: Dörmann Peter , Voelker Toni A. , Ohlrogge John B.
Published: July 2002

The acyl-acyl carrier protein thioesterase B1 from Arabidopsis (AtFATB1) was previously shown to exhibit in vitro hydrolytic activity for long chain acyl-acyl carrier proteins (P. Dörmann, T.A. Voelker, J.B. Ohlrogge [1995] Arch Biochem Biophys 316: 612–618). In this study, we address the question of which role in fatty acid biosynthesis this enzyme plays within the plant. Over-expression of the AtFATB1 cDNA under a seed-specific promoter resulted in accumulation of high amounts of palmitate (16:0) in seeds. RNA and protein-blot analysis in Arabidopsis and rapeseed (Brassica napus) showed that the endogenous AtFATB1 expression was highest in flowers and lower in leaves. All floral tissues of wild-type plants contained elevated amounts of 16:0, and in the polar lipid fraction of flowers close to 50 mol % of the fatty acids were 16:0. Therefore, flowers contain polar lipids with an unusually high amount of saturated fatty acids as compared to all other plant tissues. Antisense expression of theAtFATB1 cDNA under the cauliflower mosaic virus 35S promoter resulted in a reduction of seed and flower 16:0 content, but no changes in leaf fatty acids. We conclude that the AtFATB1 thioesterase contributes to 16:0 production particularly in flowers, but that additional factors are involved in leaves.
Antisense Suppression of 2-Cysteine Peroxiredoxin in Arabidopsis Specifically Enhances the Activities and Expression of Enzymes Associated with Ascorbate Metabolism But Not Glutathione Metabolism
Authors: Baier Margarete , Noctor Graham , Foyer Christine H. , Dietz Karl-Josef
Published: July 2002

The aim of this study was to characterize the effect of decreased 2-cysteine peroxiredoxin (2-CP) on the leaf anti-oxidative system in Arabidopsis. At three stages of leaf development, two lines of transgenic Arabidopsis mutants with decreased contents of chloroplast 2-CP were compared with wild type and a control line transformed with an empty vector. Glutathione contents and redox state were similar in all plants, and no changes in transcript levels for enzymes involved in glutathione metabolism were observed. Transcript levels for chloroplastic glutathione peroxidase were much lower than those for 2-CP, and both cytosolic and chloroplastic glutathione peroxidase were not increased in the mutants. In contrast, the foliar ascorbate pool was more oxidized in the mutants, although the difference decreased with plant age. The activities of thylakoid and stromal ascorbate peroxidase and particularly monodehydroascorbate reductase were increased as were transcripts for these enzymes. No change in dehydroascorbate reductase activity was observed, and effects on transcript abundance for glutathione reductase, catalase, and superoxide dismutase were slight or absent. The results demonstrate that 2-CP forms an integral part of the anti-oxidant network of chloroplasts and is functionally interconnected with other defense systems. Suppression of 2-CP leads to increased expression of other anti-oxidative genes possibly mediated by increased oxidation state of the leaf ascorbate pool.
Production of Recombinant Proteins in Tobacco Guttation Fluid
Authors: Komarnytsky Slavko , Borisjuk Nikolai V. , Borisjuk Ljudmila G. , Alam Muhammad Z. , Raskin Ilya
Published: July 2002

Guttation, the loss of water and dissolved materials from uninjured plant organs, is a common phenomenon in higher plants. By using endoplasmic reticulum signal peptides fused to the recombinant protein sequences, we have generated transgenic tobacco (Nicotiana tabacum L. cv Wisconsin) plants that secrete three heterologous proteins of different genetic backgrounds (bacterial xylanase, green fluorescent protein of jellyfish [Aequorea victoria], and human placental alkaline phosphatase) through the leaf intercellular space into tobacco guttation fluid. Production rates of 1.1 μg/g of leaf dry weight per day were achieved for alkaline phosphatase with this protein comprising almost 3% of total soluble protein in the guttation fluid. Guttation fluid can be collected throughout a plant's life, thus providing a continuous and nondestructive system for recombinant protein production. Guttation fluid has the potential of increasing the efficiency of recombinant protein production technology by increasing yield, abolishing extraction, and simplifying its downstream processing.
Brassinosteroid Levels Increase Drastically Prior to Morphogenesis of Tracheary Elements
Authors: Yamamoto Ryo , Fujioka Shozo , Demura Taku , Takatsuto Suguru , Yoshida Shigeo , Fukuda Hiroo
Published: July 2002

As the first step toward understanding the involvement of endogenous brassinosteroids (BRs) in cytodifferentiation, we analyzed biosynthetic activities of BRs in zinnia (Zinnia elegansL. cv Canary Bird) cells differentiating into tracheary elements. The results of feeding experiments suggested that both the early and late C6-oxidation pathways occur during tracheary element differentiation. Gas chromatography-mass spectrometry analysis revealed that five BRs, castasterone, typhasterol, 6-deoxocastasterone, 6-deoxotyphasterol, and 6-deoxoteasterone, actually existed in cultured zinnia cells and culture medium. Quantification of endogenous BRs in each stage of tracheary element differentiation by gas chromatography-mass spectrometry exhibited that they increased dramatically prior to the morphogenesis, which was consistent with the idea that BRs are necessary for the initiation of the final stage of tracheary element differentiation. Moreover, the proportion of each BR in culture medium was quite different from that in cells, suggesting that specific BRs are selectively secreted into medium and may function outside the cells.
Salinity-Induced Inhibition of Leaf Elongation in Maize Is Not Mediated by Changes in Cell Wall Acidification Capacity
Authors: Neves-Piestun Beatriz G. , Bernstein Nirit
Published: July 2002

The physiological mechanisms underlying leaf growth inhibition under salt stress are not fully understood. Apoplastic pH is considered to play an important role in cell wall loosening and tissue growth and was demonstrated to be altered by several growth-limiting environmental conditions. In this study we have evaluated the possibility that inhibition of maize (Zea mays) leaf elongation by salinity is mediated by changes in growing cell wall acidification capacity. The kinetics of extended apoplast pH changes by leaf tissue of known expansion rates and extent of growth reduction under stress was investigated (in vivo) and was found similar for non-stressed and salt-stressed tissues at all examined apoplast salinity levels (0.1, 5, 10, or 25 mm NaCl). A similar rate of spontaneous acidification for the salt and control treatments was demonstrated also in in situ experiments. Unlike growing cells that acidified the external medium, mature nongrowing cells caused medium alkalinization. The kinetics of pH changes by mature tissue was also unchanged by salt stress. Fusicoccin, an enhancer of plasmalemma H+-ATPase activity level, greatly stimulated elongation growth and acidification rate to a similar extent in the control and salt treatments. That the ability of the growing tissue to acidify the apoplast did not change under same salt stress conditions that induced inhibition of tissue elongation rate suggests that salinity does not inhibit cell growth by impairing the acidification process or reducing the inherent capacity for cell wall acidification.
Iron Stress-Induced Changes in Root Epidermal Cell Fate Are Regulated Independently from Physiological Responses to Low Iron Availability
Authors: Schikora Adam , Schmidt Wolfgang
Published: July 2002

Iron-overaccumulating mutants were investigated with respect to changes in epidermal cell patterning and root reductase activity in response to iron starvation. In all mutants under investigation, ferric chelate reductase activity was up-regulated both in the presence and absence of iron in the growth medium. The induction of transfer cells in the rhizodermis appeared to be iron regulated in the pea (Pisum sativum L. cv Dippes Gelbe Viktoria and cv Sparkle) mutants bronze and degenerated leaflets, but not in roots of the tomato (Lycopersicon esculentum Mill. cv Bonner Beste) mutantchloronerva, suggesting that inchloronerva iron cannot be recognized by putative sensor proteins. Experiments with split-root plants supports the hypothesis that Fe(III) chelate reductase is regulated by a shoot-borne signal molecule, communicating the iron status of the shoot to the roots. In contrast, the formation of transfer cells was dependent on the local concentration of iron, implying that this shoot signal does not affect their formation. Different repression curves of the two responses imply that the induction of transfer cells occurs after the enhancement of electron transfer across the plasma membrane rather than being causally linked. Similar to transfer cells, the formation of extra root hairs in the Arabidopsis mutant man1 was regulated by the iron concentration of the growth medium and was unaffected by interorgan signaling.
Analysis and Expression of the α-Expansin and β-Expansin Gene Families in Maize
Authors: Wu Yajun , Meeley Robert B. , Cosgrove Daniel J.
Published: July 2002

Expansins comprise a multigene family of proteins in maize (Zea mays). We isolated and characterized 13 different maize expansin cDNAs, five of which are α-expansins and eight of which are β-expansins. This paper presents an analysis of these 13 expansins, as well as an expression analysis by northern blotting with materials from young and mature maize plants. Some expansins were expressed in restricted regions, such as the β-expansins ExpB1 (specifically expressed in maize pollen) and ExpB4 (expressed principally in young husks). Other expansins such as α-expansin Exp1 and β-expansin ExpB2 were expressed in several organs. The expression of yet a third group was not detected in the selected organs and tissues. An analysis of expansin sequences from the maize expressed sequence tag collection is also presented. Our results indicate that expansin genes may have general, overlapping expression in some instances, whereas in other cases the expression may be highly specific and limited to a single organ or cell type. In contrast to the situation in Arabidopsis, β-expansins in maize seem to be more numerous and more highly expressed than are α-expansins. The results support the concept that β-expansins multiplied and evolved special functions in the grasses.
Aluminum Activates a Citrate-Permeable Anion Channel in the Aluminum-Sensitive Zone of the Maize Root Apex. A Comparison Between an Aluminum- Sensitive and an Aluminum-Resistant Cultivar
Authors: Kollmeier Malte , Dietrich Petra , Bauer Claudia S. , Horst Walter J. , Hedrich Rainer
Published: July 2002

In search for the cellular and molecular basis for differences in aluminum (Al) resistance between maize (Zea mays) cultivars we applied the patch-clamp technique to protoplasts isolated from the apical root cortex of two maize cultivars differing in Al resistance. Measurements were performed on protoplasts from two apical root zones: The 1- to 2-mm zone (DTZ), described as most Al-sensitive, and the main elongation zone (3–5 mm), the site of Al-induced inhibition of cell elongation. Al stimulated citrate and malate efflux from intact root apices, revealing cultivar differences. In the elongation zone, anion channels were not observed in the absence and presence of Al. Preincubation of intact roots with 90 μmAl for 1 h induced a citrate- and malate-permeable, large conductance anion channel in 80% of the DTZ protoplasts from the resistant cultivar, but only 30% from the sensitive cultivar. When Al was applied to the protoplasts in the whole-cell configuration, anion currents were elicited within 10 min in the resistant cultivar only. La3+ was not able to replace or counteract with Al3+ in the activation of this channel. In the presence of the anion-channel blockers, niflumic acid and 4, 4′-dinitrostilbene-2, 2′disulfonic acid, anion currents as well as exudation rates were strongly inhibited. Application of cycloheximide did not affect the Al response, suggesting that the channel is activated through post-translational modifications. We propose that the Al-activated large anion channel described here contributes to enhanced genotypical Al resistance by facilitating the exudation of organic acid anions from the DTZ of the maize root apex.
The Phenylalanine Ammonia-Lyase Gene Family in Raspberry. Structure, Expression, and Evolution
Authors: Kumar Amrita , Ellis Brian E.
Published: July 2002

In raspberry (Rubus idaeus), development of fruit color and flavor are critically dependent on products of the phenylpropanoid pathway. To determine how these metabolic functions are integrated with the fruit ripening program, we are examining the properties and expression of key genes in the pathway. Here, we report that l- phenylalanine ammonia-lyase (PAL) is encoded in raspberry by a family of two genes (RiPAL1 andRiPAL2). RiPAL1 shares 88% amino acid sequence similarity to RiPAL2, but phylogenetic analysis places RiPAL1 and RiPAL2 in different clusters within the plant PAL gene family. The spatial and temporal expression patterns of the two genes were investigated in various vegetative and floral tissues using the reverse transcriptase competitor polymerase chain reaction assay. Although expression of both genes was detected in all tissues examined, RiPAL1 was associated with early fruit ripening events, whereas expression ofRiPAL2 correlated more with later stages of flower and fruit development. Determination of the absolute levels of the two transcripts in various tissues showed that RiPAL1transcripts were 3- to 10-fold more abundant than those ofRiPAL2 in leaves, shoots, roots, young fruits, and ripe fruits. The two RiPAL genes therefore appear to be controlled by different regulatory mechanisms.
Three-Dimensional Analysis of Syncytial-Type Cell Plates during Endosperm Cellularization Visualized by High Resolution Electron Tomography[W]
Authors: Otegui Marisa S. , Mastronarde David N. , Kang Byung-Ho , Bednarek Sebastian Y. , Staehelin L. Andrew
Published: July 2002

The three-dimensional architecture of syncytial-type cell plates in the endosperm of Arabidopsis has been analyzed at ∼6-nm resolution by means of dual-axis high-voltage electron tomography of high-pressure frozen/freeze-substituted samples. Mini-phragmoplasts consisting of microtubule clusters assemble between sister and nonsister nuclei. Most Golgi-derived vesicles appear connected to these microtubules by two molecules that resemble kinesin-like motor proteins. These vesicles fuse with each other to form hourglass-shaped intermediates, which become wide (∼45 nm in diameter) tubules, the building blocks of wide tubular networks. New mini-phragmoplasts also are generated de novo around the margins of expanding wide tubular networks, giving rise to new foci of cell plate growth, which later become integrated into the main cell plate. Spiral-shaped rings of the dynamin-like protein ADL1A constrict but do not fission the wide tubules at irregular intervals. These rings appear to maintain the tubular geometry of the network. The wide tubular network matures into a convoluted fenestrated sheet in a process that involves increases of 45 and 130% in relative membrane surface area and volume, respectively. The proportionally larger increase in volume appears to reflect callose synthesis. Upon fusion with the parental plasma membrane, the convoluted fenestrated sheet is transformed into a planar fenestrated sheet. This transformation involves clathrin-coated vesicles that reduce the relative membrane surface area and volume by ∼70%. A ribosome-excluding matrix encompasses the cell plate membranes from the fusion of the first vesicles until the onset of the planar fenestrated sheet formation. We postulate that this matrix contains the molecules that mediate cell plate assembly.
Measurement of the fine structure factors and extinction distance by convergent-beam electron diffraction in Co3Ti with and without B doping
Authors: Wu M.-Y. , Zhu Jing , Li S.-Y. , Du Z.-H. , Li S.-L.
Published: July 2002

Using convergent-beam electron diffraction (CBED), the fine structure factors of Co3Ti alloys have been measured and the effects of boron microalloying on the fine structure factors have been studied. The extinction distances of Co3Ti have been obtained by both Kelly's method (making use of the positions of the maximum and minimum intensities in the CBED pattern) and the CBED simulation method.
Optimization of the energy constant of the methionine Sδ—C∊bond forX-PLORrefinement of protein structure
Authors: Odoko Mamiko , Yao Min , Yamashita Eiki , Nakashima Ryosuke , Hirata Kunio , Aoyama Hiroshi , Muramoto Kazumasa , Shinzawa-Itoh Kyoko , Yoshikawa Shinya , Tsukihara Tomitake
Published: July 2002

The bond energy constant of methionine Sδ—C∊, 170.066 kcal mol−1 Å−2, is given as a default value in X-ray protein structure refinement withX-PLOR[Brünger (1992).X-PLOR Version 3.1. A system for X-ray Crystallography and NMR. New York University Press]. When the atomic parameters of 3564 amino acid residues of bovine heart cytochromecoxidase were refined at 2.0 Å resolution by usingX-PLORwith default restraining parameters, 36 bond lengths deviated by over 0.06 Å from their ideal values. Out of the 36 bonds, 25 were methionine Sδ—C∊bonds. Refinement with an energy parameter of 500.0 kcal mol−1 Å−2for the methionine Sδ—C∊bond resulted in convergence of the Sδ—C∊bond lengths to within 0.06 Å from their ideal values and reduced the crystallographicRand free-Rfactors by 0.6 and 0.3%, respectively. Consequently, a strong bond energy constant for Sδ—C∊of 500.0 kcal mol−1 Å−2is recommended instead of the default value of 170.066 kcal mol−1 Å−2.
Small-angle neutron scattering of aggregated whey protein colloids with an exocellular polysaccharide
Authors: Tuinier R. , Holt C. , Timmins P.A. , de Kruif K.
Published: July 2002

We have investigated the scattering properties of mixtures of aggregated-whey-protein colloid (AWC) particles and an exocellular polysaccharide (EPS) from a lactic acid bacterium. Exceeding a certain concentration leads to a phase separation, which can be explained by an effective depletion attraction between the AWCs due to non-adsorbing EPS. The measured scattering intensity of a AWC/EPS mixture shows that the structure factor of the AWC particles increases at low wave vectors with increasing EPS concentration. The measurements can be described qualitatively in terms of the structure factor, calculated using integral theory including an expression for the depletion interaction potential.
The reliability indexR2as a versatile tool in structure analysis of inorganic and small molecular compounds
Authors: Beurskens Paul T. , Israël Randy , de Gelder René , Beurskens Gezina , de Graaff Rudolf A. G.
Published: July 2002

Applications of R_2 in small-molecule crystallography are described. Ways of using R_2 to evaluate initial models of a structure are discussed. These models, obtained from Patterson methods, are usually small. They may include one or more heavy atoms and pseudosymmetry is sometimes present in the model. The R_2 criterion is used also to identify misplaced atoms prior to the start of the expansion process. Finally, R_2 is used during structure expansion by the application of phase refinement or Fourier methods. Details of the procedures of extension, as well as the role of R_2 therein, are presented and evaluated. Results obtained with various test structures are discussed.
Rietveld quantitative amorphous content analysis
Authors: De La Torre A. G. , Bruque S. , Aranda M. A. G.
Published: July 2002

A procedure for Rietveld quantitative amorphous content analysis (RQACA) is outlined, in which the effects of systematic errors in the powder patterns are studied. The method derives the amorphous content from the small overestimation of an internal crystalline standard in a Rietveld refinement of an appropriate mixture. Of several standards studied, Al2O3gave the best results. The statistical analysis of standard mixtures with a known amount of amorphous content indicated that this is a precise and accurate tool. It enables the measurement of the amorphous content with an accuracy close to 1%. Sample preparation and Rietveld analysis need to be optimized in order to minimize the systematic errors. The analysis of samples with phases displaying strong preferred orientation effects gives very high errors in the amorphous content. Samples with different absorption coefficients have also been studied in order to evaluate the importance of microabsorption. This plays an important role but it can be adequately corrected if the absorption coefficients of the standard and the sample are not very different. RQACA has been applied to tricalcium silicate, C3S, which is the main component of Portland cement. The average amorphous content of C3S, after microabsorption correction using two standards of higher and lower absorption coefficients, was found to be 19%.
A 1000°C furnace forin situX-ray diffraction
Authors: Puig-Molina Anna , Gorges Bernard , Graafsma Heinz
Published: July 2002

A furnace covering the temperature range from 25 to 1000°C has been designed and constructed to studyin situsolid-state reactions and melting and crystallization processes, with X-ray diffraction in transmission geometry using a two-dimensional-detector system. The oven can work in low vacuum and under a controlled atmosphere.
Anisotropic diffraction peak broadening and dislocation substructure in hydrogen-cycled LaNi5and substitutional derivatives. Erratum
Authors: Černý R. , Joubert J.-M. , Latroche M. , Percheron-Guégan A. , Yvon K.
Published: July 2002

An erroneous equation and some consequently underestimated values of dislocation densities in the paper by Černýet al.[J. Appl. Cryst.(2000),33, 997–1005] are corrected.
Crystal data for anhydrous theophylline
Authors: Naqvi A. A. , Bhattacharyya G. C.
Published: July 2002

The powder data for anhydrous theophylline (1,3-dimethylxanthine), C7H8N4O2, are reported. It is orthorhombic, Pna21, with a = 24.628 (4), b = 3.833 (2), c = 8.501 (5) Å; U = 802.49 Å3; Z = 4; Dm
= 1.478, Dc
= 1.489 Mg m−3.
Etude microstructurale de carbures M
7C3
Authors: Morniroli J. P. , Gantois M.
Published: July 2002

Three cells with trigonal, orthorhombic or hexagonal symmetry have been proposed to describe M
7
C
3 carbides. Examinations of heavily faulted chromium, iron, vanadium mixed carbides present in white cast irons and in chromium steels have been performed by means of electron microscopy and diffraction. Electron diffraction patterns of the first-order Laue zone have been obtained with crystals having their c axis nearly parallel to the electron beam. They contain reflections which are typical of the symmetry and streaks which are typical of the faults. This original method of examination has systematically been applied to numerous carbides and comparisons of these experimental patterns with theoretical patterns expected from models which view the three structures of M
7
C
3 carbides as three different superlattices of a hypothetical disordered lattice lead to the following two main results: the structure of these carbides is well described with the orthorhombic cell previously given by Fruchart, Senateur, Bouchard & Michel [C.R. Acad. Sci. (1965), 260, 913]; the planar faults, which are often periodic, are antiphase boundaries or twins with fault planes {10{\bar 1}0} and fault vectors R = a, b or a + b.
Defect structure analysis of polycrystalline materials by computer-controlled double-crystal diffractometer with position-sensitive detector
Authors: Yazici R. , Mayo W. , Takemoto T. , Weissmann S.
Published: July 2002

The method represents an extension of a previously developed X-ray double-crystal diffractometer method when a film was used to record the crystallite reflections, each reflecting crystallite being regarded as the second crystal of a double-crystal diffractometer. By utilizing a position-sensitive detector (PSD) with interactive computer controls, the tedious and limiting task of data acquisition and analysis is greatly simplified. The specimen is irradiated with crystal-monochromated radiation and the numerous microscopic spots emanating from the reflecting crystallites are recorded separately by the position-sensitive detector and its associated multichannel analyzer at each increment of specimen rotation. An on-line minicomputer simultaneously collects these data and applies the necessary corrections. This process is then automatically repeated through the full rocking-curve range. The computer carries out the rocking-curve analysis of the individual crystallite reflections as well as that of the entire reflecting crystallite population. The instrument is provided with a specimen translation device which permits analysis of large sections of solid specimens. Thus, sites of local lattice defects induced either mechanically, chemically or by radiation can rapidly be established and quantitatively determined in terms of rocking-curve parameters as well as imaged by X-ray topography, by inserting a film in front of the PSD. The versatility and usefulness of the method is demonstrated by examples given from studies of fracture, fatigue and stress-corrosion cracking of commercial alloys.
Thermal expansion coefficients of a binary alloy Ni80Zr20 at elevated temperatures
Authors: Shadangi S. K. , Shadangi U. K. , Panda S. C.
Published: July 2002

The Debye–Scherrer pattern of the alloy Ni80Zr20 clearly shows the presence of a nickel solid-solution phase along with a new intermetallic phase Ni23Zr6, which seems to be isostructural with the Co23Zr6 phase. The thermal expansion coefficient of the Ni23Zr6 phase has been investigated in the temperature range 1003–1493 K. Linear variation of lattice parameter with temperature has been observed. The thermal expansion coefficient remains almost constant throughout this temperature interval.
Some aspects of the X-ray structural characterization of (Ga1−x
Al
x
As)n1(GaAs)n2/GaAs(001) superlattices: erratum
Authors: Kervarec J. , Baudet M. , Caulet J. , Auvrey P. , Emery J. Y. , Regreny A.
Published: July 2002

In the paper by Kervarec, Baudet, Caulet, Auvrey, Emery & Regreny [J. Appl. Cryst. (1984). 17, 196–205], an error has been introduced. On page 202, right-hand column, the second paragraph should read: The uneven surfaces of the interfaces can be taken into account by assuming that the SL is made of a juxtaposition of perfect crystallites of the same composition x whose period varies between the extreme values of 2n
1
d
1 + 2n
2
d
2. In this hypothesis, the experimental diagram is the sum of the X-ray diagrams given by each crystallite; the value of n
1 + n
2 deduced from such a diagram is an average value in the sample zone analyzed, therefore most of the time not integer.
X-ray powder diffraction data for diaminoacetyl urea, N,N'-bis(aminoacetyl)urea
Authors: Sen Gupta A. , Aravindakshan C.
Published: July 2002

Indexing of the powder diffraction data and refinement of the unit-cell parameters for N,N'-bis(aminoacetyl)urea (NH2CH2CO)2(NH)2CO are reported. The refined crystallographic data are: C5H10N403, P21/n (probable) a = 5.5436 (6) Å, b = 12.0338 (8) Å, c = 5.1243 (4) Å, β = 111.696 (6)°, V = 317.63, Z = 2, Dm
= 1.84, Dx
= 1.82 g cm-3 Cu Kα. The quantitative figure of merit (FN
) is F
20 = 22(0.014556, 64). The JCPDS Diffraction File No. for C5H10N403 is 36-1999.
Rietveld refinement of 3CaO.Al2O3.6H2O
Authors: Smrčok Ľ.
Published: July 2002

The lattice parameter of the title compound was found from X-ray Rietveld refinement to be 12.5755(1) Å; in addition to the diffractometer zero point, the specimen surface displacement was also varied. The estimated atomic positions of O and H atoms obtained from several refinements are in agreement with the values reported previously either from neutron or X-ray data. The degree of serial correlation in residuals was evaluated using the Durbin–Watson d statistic.
An efficient algorithm for incommensurate structure refinement
Authors: Paciorek W. A. , Uszynski I.
Published: July 2002

A least-squares algorithm to refine incommensurate structures in the framework of (3 + 1)-dimensional crystallographic symmetry is described in some detail. It is applicable to the cases of occupational and/or harmonic displacive modulation. Compact analytical expressions for the structure factor and its partial derivatives well suited for structure refinement by the least-squares method have been obtained. The efficiency of the algorithm is discussed.
The heavy-atom method without Patterson. A symmetry sum function
Authors: Pavelčík F.
Published: July 2002

The Fourier representation of the symmetry sum function is derived. This function represents an effective and direct way for the localization of one heavy atom in crystal structure determination.
Polarized neutron scattering by polarized protons of bovine serum albumin in deuterated solvent
Authors: Knop W. , Schink H.-J. , Stuhrmann H. B. , Wagner R. , Wenkow-Es-Souni M. , Schärpf O. , Krumpolc M. , Niinikoski T. O. , Rieubland M. , Rijllart A.
Published: July 2002

Bovine serum albumin (BSA) was dissolved in a mixture of deuterated glycerol and heavy water. The clusters formed by the 3300 proton spins in each BSA molecule were dynamically polarized up to P = 40%. Spin-contrast variation in small-angle neutron scattering was studied at several target polarizations. Zero contrast, and hence minimum polarized neutron small-angle scattering, is expected at P
H = 60% from extrapolation of present data. The three basic scattering functions of spin-contrast variation look very similar because the shape of the BSA molecule and its proton distribution are congruent. Neutron small-angle scattering of BSA is similar to X-ray small-angle scattering at room temperature, indicating no deterioration of the molecular structure of BSA on solidification.
Non-crystallographic symmetry invariant phases
Authors: Harrison R. W.
Published: July 2002

There is a simple way to apply non-crystallographic symmetry during the course of crystallographic coordinate refinement or structure determination by molecular replacement. A phase set is generated from the molecular coordinates which is invariant with respect to the non-crystallographic symmetry.
Study of thermal behaviour of 30Li2O·70TeO2glass by X-ray dynamic observation
Authors: Taniguchi Taketoshi , Inoue Satoru , Mitsuhashi Takefumi , Nukui Akihiko
Published: July 2002

The thermal behaviour of a 30Li2O·70TeO2glass was studied by use of anin situhigh-temperature X-ray diffractometer equipped with a position-sensitive detector (PSD). The dynamical structural changes were also observed by differential thermal analysis (DTA) and differential scanning calorimetry (DSC) measurements. Differences and contradictions exist in previous studies related to the phase relation at high temperature, including the process of phase change. It is found that in the exothermic process after a glass transition between 553 and 623 K, an unknown phase of lithium tellurite (LT-X) crystallizes at first. At almost the same temperature, a minor component of vitreous TeO2appears during decomposition of vitreous 30Li2O·70TeO2of the initial phase. After that, the thermal changes of the lithium tellurite and the TeO2components proceed independently. The LT-Xphase converts to α-Li2Te2O5, and the vitreous TeO2phase is followed by crystallization of an α-TeO2phase. In the endothermic process between 673 and 793 K, the α-Li2Te2O5phase transforms into a β-Li2Te2O5phase and the minor crystalline α-TeO2phase melts. Then, β-Li2Te2O5incongruently melts to form Li2TeO3and a molten TeO2phase. Li2TeO3continuously melts at around 763 K. The results show a possibility of reversible change between the α-Li2Te2O5and the β-Li2Te2O5phases.
Fractal structure of basic silica gels with low Ca content
Authors: Gaboriaud F. , Chaumont D. , Nonat A. , Craievich A.
Published: July 2002

Several gels were produced by addition of low amounts of calcium ions to strongly basic silico-alkaline sols. These gels, previously studied by small-angle x-ray scattering (SAXS), small-angle neutron scattering (SANS) and elastic light scattering (ELS), were analysed over a wide range of scattering vectors extending from 8 x 10−4 Å−1 up to 2 x 10−4 Å. The joint use of various scattering techniques allowed us the simultaneous characterisation of coarse, medium and fine structural features of the studied gels. Clear discrepancies between SANS and earlier ELS results were attributed to effects of multiple scattering on light scattering experiments. The experimental results demonstrate that the studied gels are composed of aggregates exhibiting a fractal structure within a scale range extending from less than 10 to more than 1000 Å, with the same fractal dimension over the whole scale range. The fractal dimension and so the mechanism of aggregation depend on the initial sol composition and Ca content. The mechanism responsible for gel formation in precursor sols with low calcium concentration ([Ca2+] = 0.3 mol.L−1) is reaction limited cluster-cluster aggregation (RLCA).
R factors in X-ray fiber diffraction. III. Asymptotic approximations to largest likely R factors
Authors: Millane R. P.
Published: July 2002

The largest likely R factor is useful for evaluating the significance of R factors obtained in structure determinations, and is smaller in fiber diffraction than in traditional crystallography. Very simple approximations to functions used to calculate the largest likely R factor in fiber diffraction are derived. For example, the largest R factor (R
m) for m overlapping terms is very well approximated by Rm
≃ (2/π)1/2
m
-1/2. These are a useful alternative to the exact, but quite complicated, expressions derived previously. More significantly, they provide insight into the behavior of R factors in fiber diffraction and may be useful in further analysis.
A new relation between bond valence and bond distance
Authors: Mohri Fumihito
Published: July 2002

A new empirical relationship s = s
0(R
0 − λ)3/(R − λ)3 between bond distances and bond valences is proposed, where s is the bond valence for the bond distance R, s
0 is the reference bond valence for the reference system with the reference bond distance R
0 and λ is the sum of the cation radii of bonding atoms defined by Pauling. Since λ is the size of the inner electron region, R − λ represents the valence electron region between bonding atoms. The new relationship was derived based on the following three hypotheses. (i) The number of electrons (p) in the volumes of (R − λ)3 in a coordination polyhedron are equal, even if the bond distances are not equal to each other. (ii) The average electron density p/(R − λ)3 is a measure of covalent bond strength. (iii) The sum of the average electron densities around the central atom is conserved, even if the coordination number changes. The new relationship is applicable not only to polyhedra with one type of ligand atom, but also to polyhedra with two or more types of ligand atoms and explains why the Brown–Shannon formula [Brown & Shannon (1973). Acta Cryst. A29, 266–282] and the Brown–Altermatt formula [Brown & Altermatt (1985). Acta Cryst. B41, 244–247] work well. The new relationship was applied to a penta-coordinated silicon compound, strong hydrogen-bond systems and some organic compounds with carbon–carbon bonds.
Fast estimation of crystal densities
Authors: Hofmann Detlef Walter Maria
Published: July 2002

A simple, efficient and accurate method for the estimation of crystal densities is of interest for different applications. By analysis of the Cambridge Structural Database (CSD) we derived an average atom volume method to estimate the cell volume for a given formula and Z value. This method extends the work of Mighell et al. (1987) by inclusion of the thermal expansion and error estimation.
The ab initio crystal structure determination of vapour-deposited methyl fluoride by high-resolution neutron powder diffraction
Authors: Ibberson R. M. , Prager M.
Published: July 2002

The crystal structure of methyl fluoride (m.p. = 131 K, b.p. = 195 K) at 5 K has been solved ab initio from high-resolution neutron powder diffraction data. A good quality powder sample was produced using a vapour deposition technique and enabled an accurate and precise structure refinement to be carried out; the C—F bond length is 1.399 (4) Å, and the average C—D bond length is 1.070 (4) Å. The monoclinic structure may be described in terms of dipole-dipole intermolecular interactions and is distinct from the structures of the other methyl halides.
Room-Temperatrue Structure and Geometrical Analysis of the Cubic–Tetragonal Phase Transition in Dodecasil 3C-THF
Authors: Knorr K. , Depmeier W.
Published: July 2002

The structure of dodecasil 3C-tetrahydrofuran [Si68O136]·4M, M = (CH2)4O, at room temperature was determined from a merohedrally twinned crystal in the tetragonal space group I41/a. The deformation of the ideal framework at the cubic tetragonal phase transition at T

c
≃ 365 K could be explained mainly by two different symmetry-breaking processes. (i) A tetragonal tetrahedron distortion of the Si(5) tetrahedra and (ii) a hitherto unknown local one-dimensional tilt mechanism, localized in the tetrahedral network. The location of the axes of this tilt system coincides with the positions of the fourfold inversion axes in the space group I41/a. At room temperature the tilt angle is = 24°. The symmetry properties of the tilt system can explain the reduction of space-group symmetry from the space group of the ideal structure Fd\overline 3m to the space group at ambient conditions I41/a. The guest molecule tetrahydrofuran does not fit the cage symmetry and has been found to be dynamically disordered. The average structure shows an off-center location in the [51264] cage and follows the local \overline 4symmetry of the cage.
Crystal morphology prediction and morphology variation in NaIO4 and NaIO4.3H2O
Authors: Soltzberg L. J. , Madden Erin
Published: July 2002

Attachment energies computed with only Coulomb potentials have been utilized to predict crystal morphologies for NaIO4, sodium iodate, and the hydrate NaIO4.3H2O, sodium iodate trihydrate [actually Na(H3O)(IO3)(OH)3]. As with other previously studied water-soluble ionic compounds, these two systems exhibit a systematic relationship between the early growth morphology and that of mature crystals; this relationship can in each case be reproduced by adjusting one attachment energy value. Morphology prediction for these two substances is of particular interest because NaIO4.3H2O is a polar crystal and involves extensive hydrogen bonding, and because obtaining the observed morphology for NaIO4 involved consideration of solvent desorption at the growing faces.
Refinement of large structures by simultaneous minimization of energy and R factor
Authors: Jack A. , Levitt M.
Published: July 2002

An improved method of crystallographic structure refinement, especially suitable for large molecules, is described, it is based on simultaneous minimization of a realistic potential-energy function and a crystallographic residual. The method has already proved its worth in the final stages of refinement of two structures; an application to crude wiremodel coordinates of a small protein is described and evaluated.
Crystallization and preliminary X-ray analysis of porcine muscle prolyl oligopeptidase
Authors: Böcskei Zsolt , Fuxreiter Mónika , Náray-Szabó Gábor , Szabó Erika , Polgár László
Published: July 2002

Prolyl oligopeptidase from pig muscle has been crystallized in complex with an inhibitor, using PEG 8000 and calcium acetate as precipitants. The crystals are orthorombic and the space group is P212121 with cell dimensions a = 111.8, b = 101.8, c = 72.4 Å. The asymmetric unit contains a single chain of prolyl oligopeptidase, corresponding to a specific volume of 2.55 Å3 Da−1 and a solvent content of 52%. The observed diffraction pattern extends to 2.3 Å resolution and the native crystals are well suited for structural analysis by X-ray diffraction methods.
Meaningful refinement of polyalanine models using rigid-body simulated annealing: application to the structure determination of the A31P Rop mutant
Authors: Glykos Nicholas M. , Kokkinidis Michael
Published: July 2002

Conventional refinement methods, when applied to even correctly positioned polyalanine models of a target structure, result in a systematic distortion of the molecular geometry and to a concomitant increase in the mean phase difference from the correct phase set. Here, it is shown that iterative rigid-body simulated-annealing refinement of polyalanine models employing successively fewer residues per rigid body (down to one alanine residue per body) at a very high initial temperature (of the order of T
0 = 10000 K) and with the geometric energy terms switched on, not only preserves the geometry of the model but can also converge to an essentially correct polyalanine trace of the target structure, even when the starting model deviates systematically and significantly from the sought structure. As an example of the application of the method, details are presented of the structure determination of the Ala31Pro mutant of the Rop protein, where an initial roughly positioned polyalanine model (giving an average phase difference of 78.2° from the final phase set) was successfully refined against a 1.8 Å resolution native data set, leading to an essentially correct model of the main chain with an average displacement of its atomic positions from the final model of 0.275 Å. The phases calculated from this refined polyalanine model had an average difference of 43.8° from the final phase set (corresponding to a mean figure of merit of 0.72) and gave a readily interpretable electron-density map.
Packing of aromatic rings against tryptophan residues in proteins
Authors: Samanta Uttamkumar , Pal Debnath , Chakrabarti Pinak
Published: July 2002

The geometry of the interaction of the aromatic side chains of phenylalanine (Phe), tyrosine (Tyr), tryptophan (Trp) and histidine (His) with the indole ring of Trp has been analyzed using the structures in the Protein Data Bank in order to understand the dependence of the packing behaviour on the size and chemical nature of the aromatic rings. The Phe ring prefers to interact either perpendicularly, with its edge pointing towards the Trp face, or in an offset-stacked arrangement. The edge-to-face motif is typical of a Trp–Trp pair. While parallel stacking is the dominant feature of Trp–His interaction, Tyr packs in a more uniform manner around Trp with a higher than expected occurrence at the edge and a few cases of possible OH–π interaction.
Combination of methods used in the structure solution of pyruvate:ferredoxin oxidoreductase from two crystal forms
Authors: Chabrière E. , Volbeda A. , Fontecilla-Camps J. C. , Roth M. , Charon M.-H.
Published: July 2002

The structure of the homodimeric 267 kDa pyruvate:ferredoxin oxidoreductase (PFOR) of Desulfovibrio africanus was solved with data from two crystals forms, both containing two monomers per asymmetric unit. Phases were obtained from multiwavelength anomalous dispersion (MAD), solvent flattening (SF), molecular replacement (MR) using a 5 Å resolution electron-density search model, multiple isomorphous replacement (MIR) and, finally, electron-density averaging (DA) procedures. It is shown how the combination of all these techniques was used to overcome problems arising from incompleteness of MAD data and weak phasing power of MIR data. A real-space refinement (RSR) procedure is described to improve MR solutions and obtain very accurate protein envelopes and non-crystallographic symmetry (NCS) transformations from 5 Å resolution phase information. These were crucial for the phase extension to high resolution by DA methods.
Crystallization and preliminary X-ray analysis of Thermotoga maritima ribosome recycling factor
Authors: Selmer Maria , Al-Karadaghi Salam , Hirokawa Go , Kaji Akira , Liljas Anders
Published: July 2002

Thermotoga maritima ribosome recycling factor (RRF) is one of the proteins catalyzing the fourth step in prokaryotic protein synthesis, ribosome recycling. The RRF protein was crystallized with ammonium sulfate. Native diffraction data to 2.55 Å resolution were obtained at the MAX II synchrotron from a flash-frozen crystal at 100 K. The crystals belong to space group P41212 or P43212, with unit-cell parameters a = b = 47, c = 298 Å, and probably contain one monomer per asymmetric unit.
A study of the coordination environment in aqueous cadmium–thiol complexes by EXAFS spectroscopy: experimental vs theoretical standards
Authors: Frenkel Anatoly I. , Vairavamurthy A. , Newville M.
Published: July 2002

Using EXAFS, we investigated the changes in the local structure of Cd(II) complexes formed with a series of low-molecular-weight thiols at different thiol/cadmium stoichiometries. For dilute solutions, a comparison of theoretical and experimental standards proved the latter approach superior. The number of bound oxygen atoms decreased while the number of sulfur atoms increased as the thiol/cadmium ratios increased, indicating that up to four thiol compounds can bind to cadmium in aqueous solutions. The computer code FEFFIT was modified to employ experimental and theoretical standards with equal facility.
Local structures of mechanically alloyed Fe100−x
Cu
x
solid solutions studied by X-ray absorption fine structure
Authors: Wei Shiqiang , Yan Wensheng , Fan Jiangwei , Li Yuzhi , Liu Wenhan , Wang Xiaoguang
Published: July 2002

The local structures of the immiscible Fe100-xCux alloys (x= 0, 10, 20, 40, 60, 80 and 100) produced by mechanical alloying have been investigated by XAFS. For the Fe100-xCux (x ≥ 40) solid solutions, the local structures around Fe atoms change from bcc structure to fcc one and the Cu atoms maintain the original coordination geometry after milling for 160 hours. On the contrary, the local structures around Cu atoms in both of Fe80Cu20 and Fe90Cu10 alloys appear a transition from fcc to bcc structure. We found that the Debye-waller factor σ of fcc Fe-Cu phase is larger than that of bcc Fe-Cu phase, and the σ (0.099 Å) around Fe atoms is larger than that (0.089 Å) of Cu in the Fe100-xCux (x ≥ 40) solid solutions. This suggests that the mechanically alloyed Fe100-xCux supersaturated solid solution is not a homogeneous alloy, and consists of Fe-rich and Cu-rich regions for various compositions. A possible mechanism for bcc-to-fcc and fcc-to-bcc changes in Fe100-xCux solid solutions is discussed in relation to the interdiffusion and transition induced by the ball milling.
Application of synchrotron X-ray imaging to phase objects in orthopedics
Authors: Mori K. , Sekine N. , Sato H. , Shimao D. , Shiwaku H. , Hyodo K. , Sugiyama H. , Ando M. , Ohashi K. , Koyama M. , Nakajima Y.
Published: July 2002

Novel imaging of the fine structures of the ribs of a pig and a specimen of human osteosarcoma utilizing the spatial coherence of X-rays was successfully performed with an incident X-ray energy of 30 keV at SPring-8, Japan. The image contrast appearing at the periphery of trabecular bone, small calcifications and small fractures is caused by the phase shift of the X-rays at the boundary of these objects that have different X-ray refractive indices. The image is recorded on mammography film without an intensifying screen. Comparison of the image contrast using different sample-to-film distances, Z, such as Z = 5 m and Z ≃ 0 m, showed that the former images were always more informative, i.e. better in resolution and/or image contrast when imaging trabecular bone, bone marrow and small fractures in compact bone, and for imaging cartilage. Radiography using synchrotron X-rays for phase objects should be a powerful tool for diagnosis in orthopedics, especially for bone disease.
N-(8-Quinolylamino)phthalimide
Authors: Lynch Daniel E. , McClenaghan Ian
Published: July 2002

The structure of the title compound, C17H11N3O2, (I), comprises twisted molecules that associateviaa single N—H...O intermolecular interaction, forming a linear one-dimensional hydrogen-bonded chain. The dihedral angle between the two ring systems is 89.9 (1)°.