bluuebunny/crossref_metadata_2025 huggingface dataset:
Simultaneous Suppression of Multiple Genes by Single Transgenes. Down-Regulation of Three Unrelated Lignin Biosynthetic Genes in Tobacco
Authors: Abbott James C. , Barakate Abdellah , Pinçon Gaelle , Legrand Michel , Lapierre Catherine , Mila Isabelle , Schuch Wolfgang , Halpin Claire
Published: July 2002

Many reports now describe the manipulation of plant metabolism by suppressing the expression of single genes. The potential of such work could be greatly expanded if multiple genes could be coordinately suppressed. In the work presented here, we test a novel method for achieving this by using single chimeric constructs incorporating partial sense sequences for multiple genes to target suppression of two or three lignin biosynthetic enzymes. We compare this method with a more conventional approach to achieving the same end by crossing plants harboring different antisense transgenes. Our results indicate that crossing antisense plants is less straightforward and predictable in outcome than anticipated. Most progeny had higher levels of target enzyme activity than predicted and had lost the expected modifications to lignin structure. In comparison, plants transformed with the chimeric partial sense constructs had more consistent high level suppression of target enzymes and had significant changes to lignin content, structure, and composition. It was possible to suppress three target genes coordinately using a single chimeric construct. Our results indicate that chimeric silencing constructs offer great potential for the rapid and coordinate suppression of multiple genes on diverse biochemical pathways and that the technique therefore deserves to be adopted by other researchers.
Fruit-Specific Expression of a Defensin-Type Gene Family in Bell Pepper (Upregulation during Ripening and upon Wounding)
Authors: Meyer B. , Houlne G. , Pozueta-Romero J. , Schantz M. L. , Schantz R.
Published: July 2002

We have isolated a 454-bp cDNA that encodes a novel fruit-specific defensin from bell pepper (Capsicum annuum). The encoded 75-amino-acid polypeptide contains an N-terminal domain characteristic of a signal peptide and a 48-amino-acid mature domain named J1. The mature protein, from which the N-terminal amino acid sequence was determined, contains eight cysteines that form four intramolecular disulfide bridges, suggesting a monomeric form for J1. In healthy fruits J1 is undetectable at the green stage but high levels accumulate during ripening. In wound areas of the green fruit the accumulation of J1 dramatically increased, suggesting a role for J1 in the plant's defense response. Moreover, we have demonstrated that J1 possesses an antifungal activity. We have isolated and characterized the corresponding two homologous genes (j1–1 and j1–2) that exist in the bell pepper genome. Both genes are interrupted by the insertion, at the same position, of one intron of 853 bp for j1–1 and 4900 bp for j1–2. Northern blot and reverse transcriptase-polymerase chain reaction and restriction fragment length polymorphism analyses revealed that j1–1 transcripts are present only in fruits, only in trace amounts in mature green fruits, and that they accumulate to high levels in fully ripe fruits, whereas no j1–2 transcripts were detected in the samples monitored.
Isolation and Characterization of Soluble Boron Complexes in Higher Plants (The Mechanism of Phloem Mobility of Boron)
Authors: Hu H. , Penn S. G. , Lebrilla C. B. , Brown P. H.
Published: July 2002

Boron (B) polyol complexes have been isolated and characterized from the phloem sap of celery (Apium graveolens L.) and the extra-floral nectar of peach (Prunus persica L.). In celery the direct analysis of untreated phloem sap by matrix-assisted laser desorption-Fourier transform mass spectrometry, with verification by high-performance liquid chromagraphy and gas chromatography-mass spectrometry, revealed that B is present in the phloem as the mannitol-B-mannitol complex. Molecular modeling further predicted that this complex is present in the 3,4 3[prime],4[prime] bis-mannitol configuration. In the extrafloral nectar of peach, B was present as a mixture of sorbitol-B-sorbitol, fructose-B-fructose, or sorbitol-B-fructose. To our knowledge, these findings represent the first successful isolation and characterization of soluble B complexes from higher plants and provide a mechanistic explanation for the observed phloem B mobility in these species.
Independent Genetic Control of Maize Starch-Branching Enzymes IIa and IIb (Isolation and Characterization of a Sbe2a cDNA)
Authors: Gao M. , Fisher D. K. , Kim K. N. , Shannon J. C. , Guiltinan M. J.
Published: July 2002

In maize (Zea mays L.) three isoforms of starch-branching enzyme (SBEI, SBEIIa, and SBEIIb) are involved in the synthesis of amylopectin, the branched component of starch. To isolate a cDNA encoding SBEIIa, degenerate oligonucleotides based on domains highly conserved in Sbe2 family members were used to amplify Sbe2-family cDNA from tissues lacking SBIIb activity. The predicted amino acid sequence of a Sbe2a cDNA matches the N-terminal sequence of SBIIa protein purified from maize endosperm. The size of the mature protein deduced from the cDNA also matches that of SBEIIa Features of the predicted protein are most similar to members of the SBEII family; however, it differs from maize SBEIIb in having a 49-amino acid N-terminal extension and a region of substantial sequence divergence. Sbe2a mRNA levels are 10-fold higher in embryonic than in endosperm tissue, and are much lower than Sbe2b in both tissues. Unlike Sbe2b, Sbe2a-hybridizing mRNA accumulates in leaf and other vegetative tissues, consistent with the known distribution of SBEIIa and SBEIIb activities.
Membrane Lipid Unsaturation Modulates Processing of the Photosystem II Reaction-Center Protein D1 at Low Temperatures
Authors: Kanervo E. , Tasaka Y. , Murata N. , Aro E. M.
Published: July 2002

The role of membrane lipid unsaturation in the restoration of photosystem II (PSII) function and in the synthesis of the D1 protein at different temperatures after photoinhibition was studied in wild-type cells and a mutant of Synechocystis sp. PCC 6803 with genetically inactivated desaturase genes. We show that posttranslational carboxyl-terminal processing of the precursor form of the D1 protein is an extremely sensitive reaction in the PSII repair cycle and is readily affected by low temperature. Furthermore, the threshold temperature at which perturbations in D1-protein processing start to emerge is specifically dependent on the extent of thylakoid membrane lipid unsaturation, as indicated by comparison of wild-type cells with the mutant defective in desaturation of 18:1 fatty acids of thylakoid membranes. When the temperature was decreased from 33[deg]C (growth temperature) to 18[deg]C, the inability of the fatty acid mutant to recover from photoinhibition was accompanied by a failure to process the newly synthesized D1 protein, which accumulated in considerable amounts as an unprocessed precursor D1 protein. Precursor D1 integrated into PSII monomer and dimer complexes even at low temperatures, but no activation of oxygen evolution occurred in these complexes in mutant cells defective in fatty acid unsaturation.
Construction of a Lotus japonicus Late Nodulin Expressed Sequence Tag Library and Identification of Novel Nodule-Specific Genes
Authors: Szczyglowski K. , Hamburger D. , Kapranov P. , de Bruijn F. J.
Published: July 2002

A range of novel expressed sequence tags (ESTs) associated with late developmental events during nodule organogenesis in the legume Lotus japonicus were identified using mRNA differential display; 110 differentially displayed polymerase chain reaction products were cloned and analyzed. Of 88 unique cDNAs obtained, 22 shared significant homology to DNA/protein sequences in the respective databases. This group comprises, among others, a nodule-specific homolog of protein phosphatase 2C, a peptide transporter protein, and a nodule-specific form of cytochrome P450. RNA gel-blot analysis of 16 differentially displayed ESTs confirmed their nodule-specific expression pattern. The kinetics of mRNA accumulation of the majority of the ESTs analyzed were found to resemble the expression pattern observed for the L. japonicus leghemoglobin gene. These results indicate that the newly isolated molecular markers correspond to genes induced during late developmental stages of L. japonicus nodule organogenesis and provide important, novel tools for the study of nodulation.
Differential Gene Expression in Ripening Banana Fruit
Authors: Clendennen S. K. , May G. D.
Published: July 2002

During banana (Musa acuminata L.) fruit ripening ethylene production triggers a developmental cascade that is accompanied by a massive conversion of starch to sugars, an associated burst of respiratory activity, and an increase in protein synthesis. Differential screening of cDNA libraries representing banana pulp at ripening stages 1 and 3 has led to the isolation of 11 nonredundant groups of differentially expressed mRNAs. Identification of these transcripts by partial sequence analysis indicates that two of the mRNAs encode proteins involved in carbohydrate metabolism, whereas others encode proteins thought to be associated with pathogenesis, senescence, or stress responses in plants. Their relative abundance in the pulp and tissue-specific distribution in greenhouse-grown banana plants were determined by northern-blot analyses. The relative abundance of transcripts encoding starch synthase, granule-bound starch synthase, chitinase, lectin, and a type-2 metallothionein decreased in pulp during ripening. Transcripts encoding endochitinase, β-1,3-glucanase, a thaumatin-like protein, ascorbate peroxidase, metallothionein, and a putative senescence-related protein increased early in ripening. The elucidation of the molecular events associated with banana ripening will facilitate a better understanding and control of these processes, and will allow us to attain our long-term goal of producing candidate oral vaccines in transgenic banana plants.
Accumulation of Salicylic Acid and 4-Hydroxybenzoic Acid in Phloem Fluids of Cucumber during Systemic Acquired Resistance Is Preceded by a Transient Increase in Phenylalanine Ammonia-Lyase Activity in Petioles and Stems1
Authors: Smith-Becker Jennifer , Marois Eric , Huguet Elisabeth J. , Midland Sharon L. , Sims James J. , Keen Noel T.
Published: July 2002

Cucumber (Cucumis sativa) leaves infiltrated withPseudomonas syringae pv. syringae cells produced a mobile signal for systemic acquired resistance between 3 and 6 h after inoculation. The production of a mobile signal by inoculated leaves was followed by a transient increase in phenylalanine ammonia-lyase (PAL) activity in the petioles of inoculated leaves and in stems above inoculated leaves; with peaks in activity at 9 and 12 h, respectively, after inoculation. In contrast, PAL activity in inoculated leaves continued to rise slowly for at least 18 h. No increases in PAL activity were detected in healthy leaves of inoculated plants. Two benzoic acid derivatives, salicylic acid (SA) and 4-hydroxybenzoic acid (4HBA), began to accumulate in phloem fluids at about the time PAL activity began to increase, reaching maximum concentrations 15 h after inoculation. The accumulation of SA and 4HBA in phloem fluids was unaffected by the removal of all leaves 6 h after inoculation, and seedlings excised from roots prior to inoculation still accumulated high levels of SA and 4HBA. These results suggest that SA and 4HBA are synthesized de novo in stems and petioles in response to a mobile signal from the inoculated leaf.
Effects of Xylem pH on Transpiration from Wild-Type andflaccaTomato Leaves1
Authors: Wilkinson Sally , Corlett Janet E. , Oger Ludovic , Davies William J.
Published: July 2002

The pH of xylem sap from tomato (Lycopersicon esculentum) plants increased from pH 5.0 to 8.0 as the soil dried. Detached wild-type but notflacca leaves exhibited reduced transpiration rates when the artificial xylem sap (AS) pH was increased. When a well-watered concentration of abscisic acid (0.03 μm) was provided in the AS, the wild-type transpirational response to pH was restored toflacca leaves. Transpiration from flaccabut not from wild-type leaves actually increased in some cases when the pH of the AS was increased from 6.75 to 7.75, demonstrating an absolute requirement for abscisic acid in preventing stomatal opening and excessive water loss from plants growing in many different environments.
Does a Low Nitrogen Supply Necessarily Lead to Acclimation of Photosynthesis to Elevated CO2?
Authors: Farage Peter K. , McKee Ian F. , Long Steve P.
Published: July 2002

Long-term exposure of plants to elevated partial pressures of CO2 (pCO2) often depresses photosynthetic capacity. The mechanistic basis for this photosynthetic acclimation may involve accumulation of carbohydrate and may be promoted by nutrient limitation. However, our current knowledge is inadequate for making reliable predictions concerning the onset and extent of acclimation. Many studies have sought to investigate the effects of N supply but the methodologies used generally do not allow separation of the direct effects of limited N availability from those caused by a N dilution effect due to accelerated growth at elevated pCO2. To dissociate these interactions, wheat (Triticum aestivum L.) was grown hydroponically and N was added in direct proportion to plant growth. Photosynthesis did not acclimate to elevated pCO2 even when growth was restricted by a low-N relative addition rate. Ribulose-1, 5-bisphosphate carboxylase/oxygenase activity and quantity were maintained, there was no evidence for triose phosphate limitation of photosynthesis, and tissue N content remained within the range recorded for healthy wheat plants. In contrast, wheat grown in sand culture with N supplied at a fixed concentration suffered photosynthetic acclimation at elevated pCO2 in a low-N treatment. This was accompanied by a significant reduction in the quantity of active ribulose-1, 5-bisphosphate carboxylase/oxygenase and leaf N content.
Purification and Characterization of a NADPH-Dependent Aldehyde Reductase from Mung Bean That Detoxifies Eutypine, a Toxin from Eutypa lata1
Authors: Colrat Ségolène , Latché Alain , Guis Monique , Pech Jean-Claude , Bouzayen Mondher , Fallot Jean , Roustan Jean-Paul
Published: July 2002

Eutypine (4-hydroxy-3-[3-methyl-3-butene-1-ynyl] benzaldehyde) is a toxin produced by Eutypa lata, the causal agent of eutypa dieback in the grapevine (Vitis vinifera). Eutypine is enzymatically converted by numerous plant tissues into eutypinol (4-hydroxy-3-[3-methyl-3-butene-1-ynyl] benzyl alcohol), a metabolite that is nontoxic to grapevine. We report a four-step procedure for the purification to apparent electrophoretic homogeneity of a eutypine-reducing enzyme (ERE) from etiolated mung bean (Vigna radiata) hypocotyls. The purified protein is a monomer of 36 kD, uses NADPH as a cofactor, and exhibits aKm value of 6.3 μm for eutypine and a high affinity for 3- and 4-nitro-benzaldehyde. The enzyme failed to catalyze the reverse reaction using eutypinol as a substrate. ERE detoxifies eutypine efficiently over a pH range from 6.2 to 7.5. These data strongly suggest that ERE is an aldehyde reductase that could probably be classified into the aldo-keto reductase superfamily. We discuss the possible role of this enzyme in eutypine detoxification.
Molecular Cloning and Characterization of Apricot Fruit Polyphenol Oxidase
Authors: Chevalier Tony , de Rigal David , Mbéguié-A-Mbéguié Didier , Gauillard Frédéric , Richard-Forget Florence , Fils-Lycaon Bernard R.
Published: July 2002

A reverse transcriptase-polymerase chain reaction experiment was done to synthesize a homologous polyphenol oxidase (PPO) probe from apricot (Prunus armeniaca var Bergeron) fruit. This probe was further used to isolate a full-length PPO cDNA, PA-PPO (accession no.AF020786), from an immature-green fruit cDNA library.PA-PPO is 2070 bp long and contains a single open reading frame encoding a PPO precursor peptide of 597 amino acids with a calculated molecular mass of 67.1 kD and an isoelectric point of 6.84. The mature protein has a predicted molecular mass of 56.2 kD and an isoelectric point of 5.84. PA-PPO belongs to a multigene family. The gene is highly expressed in young, immature-green fruit and is turned off early in the ripening process. The ratio of PPO protein to total proteins per fruit apparently remains stable regardless of the stage of development, whereas PPO specific activity peaks at the breaker stage. These results suggest that, in addition to a transcriptional control of PPO expression, other regulation factors such as translational and posttranslational controls also occur.
Phloem Transport of d,l-Glufosinate and Acetyl-l-Glufosinate in Glufosinate-Resistant and -Susceptible Brassica napus
Authors: Beriault Jennifer N. , Horsman Geoff P. , Devine Malcolm D.
Published: July 2002

Phloem transport of d,l-[14C]glufosinate,d-[14C]glufosinate, and acetyl-l-[14C]glufosinate was examined in the susceptible Brassica napus cv Excel and a glufosinate-resistant genotype (HCN27) derived by transformation of cv Excel with the phosphinothricin-N-acetyltransferase (pat) gene. Considerably more 14C was exported from an expanded leaf in HCN27 than in cv Excel following application of d,l-[14C]glufosinate (25% versus 6.3% of applied, respectively, 72 h after treatment). The inactive isomer, d-glufosinate, was much more phloem mobile in cv Excel than racemicd,l-glufosinate. Foliar or root supplementation with 1 mm glutamine increasedd,l-[14C]glufosinate translocation in cv Excel but only transiently, suggesting that glutamine depletion is not the major cause of the limited phloem transport. Acetyl-l-[14C]glufosinate (applied as such or derived from l-glufosinate in pattransformants) was translocated extensively in the phloem of both genotypes. Acetyl-l-[14C]glufosinate was readily transported into the floral buds and flowers, and accumulated in the anthers in both genotypes. These results suggest that phloem transport of d,l-glufosinate is limited by rapid physiological effects of the l-isomer in source leaf tissue. The accumulation of acetyl-l-glufosinate in the anthers indicates that it is sufficiently phloem mobile to act as a foliar-applied chemical inducer of male sterility in plants expressing a deacetylase gene in the tapetum, generating toxic concentrations ofl-glufosinate in pollen-producing tissues.
Auxin Biosynthesis in Maize Kernels
Authors: Glawischnig Erich , Tomas Adriana , Eisenreich Wolfgang , Spiteller Peter , Bacher Adelbert , Gierl Alfons
Published: July 2002

Auxin biosynthesis was analyzed in a maize (Zea mays) kernel culture system in which the seeds develop under physiological conditions similar to the in vivo situation. This system was modified for precursor feeding experiments. Tryptophan (Trp) is efficiently incorporated into indole-3-acetic acid (IAA) with retention of the 3,3′ bond. Conversion of Trp to IAA is not competed by indole. Labeling with the general precursors [U-13C6]glucose and [1,2-13C2]acetate followed by retrobiosynthetic analysis strongly suggest that Trp-dependent IAA synthesis is the predominant route for auxin biosynthesis in the maize kernel. The synthesis of IAA from indole glycerol phosphate and IAA formation via condensation of indole with an acetyl-coenzyme A or phosphoenolpyruvate derived metabolite can be excluded.
β-Cyanoalanine Synthase Is a Mitochondrial Cysteine Synthase-Like Protein in Spinach and Arabidopsis
Authors: Hatzfeld Yves , Maruyama Akiko , Schmidt Ahlert , Noji Masaaki , Ishizawa Kimiharu , Saito Kazuki
Published: July 2002

β-Cyano-alanine synthase (CAS; EC 4.4.1.9) plays an important role in cyanide metabolism in plants. Although the enzymatic activity of β-cyano-Ala synthase has been detected in a variety of plants, no cDNA or gene has been identified so far. We hypothesized that the mitochondrial cysteine synthase (CS; EC 4.2.99.8) isoform, Bsas3, could actually be identical to CAS in spinach (Spinacia oleracea) and Arabidopsis. An Arabidopsis expressed sequence tag database was searched for putative Bsas3homologs and four new CS-like isoforms, ARAth;Bsas1;1,ARAth;Bsas3;1, ARAth;Bsas4;1, andARAth;Bsas4;2, were identified in the process. ARAth;Bsas3;1 protein was homologous to the mitochondrial SPIol;Bsas3;1 isoform from spinach, whereas ARAth;Bsas4;1 and ARAth;Bsas4;2 proteins defined a new class within the CS-like proteins family. In contrast to spinach SPIol;Bsas1;1 and SPIol;Bsas2;1 recombinant proteins, spinach SPIol;Bsas3;1 and Arabidopsis ARAth;Bsas3;1 recombinant proteins exhibited preferred substrate specificities for the CAS reaction rather than for the CS reaction, which identified these Bsas3 isoforms as CAS. Immunoblot studies supported this conclusion. This is the first report of the identification of CAS synthase-encoding cDNAs in a living organism. A new nomenclature for CS-like proteins in plants is also proposed.
RSF1, an Arabidopsis Locus Implicated in Phytochrome A Signaling
Authors: Fankhauser Christian , Chory Joanne
Published: July 2002

In Arabidopsis, phytochrome A (phyA) is the major photoreceptor both for high irradiance responses to far-red light and broad spectrum very low fluence responses, but little is known of its signaling pathway(s). rsf1 was isolated as a recessive mutant with reduced sensitivity to far-red inhibition of hypocotyl elongation. At the seedling stage rsf1 mutants are affected, to various degrees, in all described phyA-mediated responses. However, in adultrsf1 plants, the photoperiodic flowering response is normal. The rsf1 mutant has wild-type levels of phyA suggesting that RSF1 is required for phyA signaling rather than phyA stability or biosynthesis. RSF1 thus appears to be a major phyA signaling component in seedlings, but not in adult, Arabidopsis plants.
Cloning and Expression Pattern of a Gene Encoding an α-Xylosidase Active against Xyloglucan Oligosaccharides from Arabidopsis
Authors: Sampedro Javier , Sieiro Carmen , Revilla Gloria , González-Villa Tomás , Zarra Ignacio
Published: July 2002

An α-xylosidase active against xyloglucan oligosaccharides was purified from cabbage (Brassica oleracea var. capitata) leaves. Two peptide sequences were obtained from this protein, the N-terminal and an internal one, and these were used to identify an Arabidopsis gene coding for an α-xylosidase that we propose to callAtXYL1. It has been mapped to a region of chromosome I between markers at 100.44 and 107.48 cM. AtXYL1comprised three exons and encoded a peptide that was 915 amino acids long, with a potential signal peptide of 22 amino acids and eight possible N-glycosylation sites. The protein encoded byAtXYL1 showed the signature regions of family 31 glycosyl hydrolases, which comprises not only α-xylosidases, but also α-glucosidases. The α-xylosidase activity is present in apoplastic extractions from Arabidopsis seedlings, as suggested by the deduced signal peptide. The first eight leaves from Arabidopsis plants were harvested to analyze α-xylosidase activity and AtXYL1expression levels. Both increased from older to younger leaves, where xyloglucan turnover is expected to be higher. When this gene was introduced in a suitable expression vector and used to transformSaccharomyces cerevisiae, significantly higher α-xylosidase activity was detected in the yeast cells. α-Glucosidase activity was also increased in the transformed cells, although to a lesser extent. These results show thatAtXYL1 encodes for an apoplastic α-xylosidase active against xyloglucan oligosaccharides that probably also has activity againstp-nitrophenyl-α-d-glucoside.
Determination of γ′ solution temperature in Re-rich Ni-base superalloy by small-angle neutron scattering. Erratum
Authors: Strunz Pavel , Mukherji Debashis , Gilles Ralph , Wiedenmann Albrecht , Fuess Hartmut
Published: July 2002

In the paper by Strunzet al.[J. Appl. Cryst.(2001),34, 541–548], Joachim Rösler is missing from the list of authors. The complete list of authors should be: P. Strunz, D. Mukherji, R. Gilles, A. Wiedenmann, J. Rösler and H. Fuess.
Assessment of preferred orientation with neutron powder diffraction data
Authors: Sitepu H.
Published: July 2002

Crystallographic texture (or preferred orientation) characterization of uniaxially pressed molybdite (MoO3) and calcite (CaCO3) powders has been carried out using the BT-1 high-resolution fixed-wavelength 32-detector powder diffractometer at the NIST Center for Neutron Research. Initially, each pattern was analysed assuming a random orientation of the crystallites. Subsequently, the March model and the generalized spherical harmonic description were used independently to extract the texture description directly from a refinement with neutron diffraction data of molybdite and calcite. The results indicate that the generalized spherical harmonic description provided a better Rietveld fit than the March model for the molybdite sample that had been subjected to the highest pressure.
Real-space technique applied to crystal structure determination from powder data
Authors: Altomare Angela , Cuocci Corrado , Giacovazzo Carmelo , Guagliardi Antonietta , Moliterni Anna Grazia Giuseppina , Rizzi Rosanna
Published: July 2002

Real-space techniques used for phase extension and refinement in the modern direct procedures forab initiocrystal structure solution of proteins have been optimized for application to powder diffraction data. The new process has been implemented in a modified version ofEXPO[Altomareet al.(1999).J.Appl.Cryst.32, 339–340]. The method is able to supply a structural model that is more complete than that provided by the standardEXPOprogram. The model is then refinedviaa diagonal least-squares procedure, but only when the ratio of the number of observations to the number of structure parameters to be refined is larger than a given threshold.
An analytical approximation for a size-broadened profile given by the lognormal and gamma distributions
Authors: Popa N. C. , Balzar D.
Published: July 2002

The size-broadened profile given by the lognormal and gamma size distributions of spherical crystallites is considered. An analytical approximation for the size-broadened profile is derived that can be analytically convolved with the strain-broadened and instrumental-broadened profiles. The method is tested on two CeO2powders; one shows `super-Lorentzian' profiles that were successfully modelled under the assumption of a broad lognormal size distribution. It is shown that the Voigt function, as a common model for a size-broadened profile, fails for both very narrow and broad size distributions. It is argued that the size-broadened line profile is not very sensitive to variations in size distribution and that an apparent domain size or even column-length distribution function can correspond to significantly different size distributions.
Lattice-parameter-difference measurement of heteroepitaxial structures by means of extremely asymmetrical Bragg diffraction
Authors: Pietsch U. , Borchard W.
Published: July 2002

The sensitivity of measurements of the lattice-parameter difference in monocrystalline heterostructures can be enhanced by use of an extremely asymmetrical diffraction geometry. If the angle of incidence is somewhat higher than the critical angle for total external reflection, the Bragg peak is shifted from the position calculated by kinematic theory. The amount of shift depends on the angle of incidence as well as on the mass density of the material used. For heteroepitaxic structures both the layer and the substrate peaks are shifted but by different amounts. Therefore it becomes possible to characterize layers of totally lattice-matched structures also.
AXES1.9: new tools for estimation of crystallite size and shape by Williamson–Hall analysis
Authors: Mändar Hugo , Felsche Jürgen , Mikli Valdek , Vajakas Toivo
Published: July 2002

Dialogues for the estimation of crystallite size, shape and lattice strain are designed and included in an X-ray powder diffraction (XRPD) program, namedAXES. They implement peak fitting and Voigt analysis followed by a Williamson–Hall plot (WHP). Eight different peak-shape functions can be used for individual peak fitting. Volume-weighted crystallite size and effective lattice deformation are calculated from linear interpolation of the WHP. Actual dimensions (diameters of spheres, diameters and heights of cylinders) are calculated, assuming spherical or cylindrical shapes of the crystallites. Results of size–shape analyses can be visualized in the form of a WHP and as an arrow diagram (HPGL format), which shows distribution of observed apparent and true sizes of crystallites with a diffraction vector. The program has been written in Borland Pascal 7.0 for MS-DOS. The executable code is availableviathe World Wide Web.
The contrast factors of dislocations in cubic crystals: the dislocation model of strain anisotropy in practice
Authors: Ungár T. , Dragomir I. , Révész Á. , Borbély A.
Published: July 2002

It has been shown recently that in many cases strain anisotropy in powder diffraction can be well accounted for by the dislocation model of the mean square strain. The practical application assumes knowledge of the individual contrast factorsCof dislocations related to particular Burgers, line and diffraction vectors or to the average contrast factorsC¯. A simple procedure for the experimental determination ofC¯has been worked out, enabling the determination of the character of the dislocations in terms of a simple parameterq. The values of the individualCfactors were determined numerically for a wide range of elastic constants for cubic crystals. TheC¯factors andqparameters were parametrized by simple analytical functions, which can be used in a straightforward manner in numerical analyses, ase.g.in Rietveld structure refinement procedures.
Triplet phase invariants from single isomorphous replacement or one-wavelength anomalous dispersion data, given heavy-atom information
Authors: Karle J.
Published: July 2002

Certain general algebraic formulas for computing triplet phase invariants become accessible when structural information is available concerning the replacement atoms in isomorphous replacement or the predominant type of anomalously scattering atoms in one-wavelength anomalous dispersion experiments. The formulas of interest are presented and subjected to a number of test calculations to obtain insight into their accuracy and to determine the effects of errors in the data. The formulas are simple to calculate and some possible strategies for their use are discussed.
Absolute structure and absolute configuration
Authors: Flack H. D. , Bernardinelli G.
Published: July 2002

Fundamental notions concerning absolute structure and absolute configuration, and their determination from single-crystal diffraction measurements, are presented and reviewed. A glossary of terms with definitions useful in this field is provided. For absolute structure and its determination, the separate but interacting influences of the structure and the inversion-distinguishing power of an X-ray diffraction experiment with dispersive scatterers are examined. Important experimental and algorithmic details of the current methods used for absolute-structure determination are provided. Characterization of crystals for absolute-structure determination and of molecules for absolute-configuration determination are treated. Attention is given to the analysis of absolute structure and absolute configuration in twinned crystals.
Reversible phase transitions in Na2S under pressure: a comparison with the cation array in Na2SO4
Authors: Vegas A. , Grzechnik A. , Syassen K. , Loa I. , Hanfland M. , Jansen M.
Published: July 2002

The structural behavior of the antifluorite Na2S, disodium sulfide, has been studied under pressure up to 22 GPa by in situ synchrotron X-ray diffraction experiments in a diamond anvil cell at room temperature. At approximately 7 GPa, Na2S undergoes a first phase transition to the orthorhombic anticotunnite (PbCl2) structure (Pnma, Z = 4). The lattice parameters at 8.2 GPa are a = 6.707 (5), b = 4.120 (3), c = 8.025 (4) Å. At approximately 16 GPa, Na2S undergoes a second transition adopting the structure of the Ni2In-type (P63/mmc, Z = 2). The lattice parameters at 16.6 GPa are a = 4.376 (18), c = 5.856 (9) Å. Both pressure-induced phases have been confirmed by full Rietveld refinements. An inspection of the cation array of Na2SO4 reveals that its Na2S subarray is also of the Ni2In-type. This feature represents a new example of how the cation arrangements in ternary oxides correspond to the topology of the respective binary compounds. We discuss analogies between the insertion of oxygen and the application of pressure.
Stereochemistry of serotonin receptor ligands from crystallographic data. Crystal structures of NAN-190.HBr, 1-phenylbiguanide, MDL 72222 and mianserin.HCl and selectivity criteria towards 5-HT1, 5-HT2 and 5-HT3 receptor subtypes
Authors: Dalpiaz A. , Ferretti V. , Gilli P. , Bertolasi V.
Published: July 2002

The crystal and molecular structures of the following serotoninergic drugs have been determined: (1) 1-(2-methoxyphenyl)-4-[4-(2-phthalimido)butyl]piperazine hydrobromide hemihydrate (NAN-190.HBr), C23H28N3O3
+.Br−.1/2H2O, Mr
= 483.42, monoclinic, C2/c, a = 21.916 (4), b = 15.207 (2), c = 14.052 (2) Å, β = 101.56 (1)°, V = 4588 (1) Å3, Z = 8, Dx
= 1.40 Mg m−3, λ(Mo Kα) = 0.71069 Å, μ = 1.823 mm−1, F(000) = 2008, T = 295 K, R = 0.035 for 2617 observed reflections; (2) N-phenylimidocarbonimidic diamide (1-phenylbiguanide), C8H11N5, Mr
= 177.21, monoclinic, P21/c, a = 9.781 (2), b = 35.040 (5), c = 11.000 (2) Å, β = 97.72 (1)°, V = 3736 (1) Å3, Z = 16, Dx
= 1.26 Mg m−3, λ(Mo Kα) = 0.71069 Å, μ= 0.084 mm−1, F(000) = 1504, T = 295 K, R = 0.070 for 3407 observed reflections; (3) 8-methyl-8-azabicyclo[3.2.1.]oct-3-yl 3,5-dichlorobenzoate (MDL 72222), C15H17C12NO2, Mr
= 314.21, triclinic, P{\bar 1}, a = 8.480 (3), b = 9.840 (3), c = 10.15 (4) Å, α = 90.04 (3), β = 111.77 (3), γ = 105.07 (3)°, V = 755.6 (5) Å3, Z = 2, Dx
= 1.38 Mg m−3, λ(Mo Kα) = 0.71069 Å, μ = 0.430 mm−1, F(000) = 328, T = 295 K, R = 0.070 for 1685 observed reflections; (4) 1,2,3,4,10,14b-hexahydro-2-methyldibenzo[cf]pyrizino[1,2-a]azepine hydrochloride (mianserin.HCl), C18H21N2
+.Cl−, Mr
= 300.83, monoclinic, P21/a, a = 9.014 (2), b = 14.917 (2), c = 12.412 (2) Å, β = 108.84 (1)°, V = 1579.5 (5) Å3, Z = 4, Dx
= 1.26 Mg m−3, λ(Mo Kα) = 0.71069 Å, μ = 0.237 mm−1, F(000) = 640, T = 295 K, R = 0.063 for 1493 observed reflections. A systematic structural analysis of the present compounds and others known to interact with the 5-HT1, 5-HT2 and 5-HT3 receptors allows to identify their similarities with the endogenous ligand serotonin (5-HT) and the stereochemical differences which determine selectivity for the various receptor subtypes. The pharmacophoric feature for 5-HT receptor binding is identified in a constant-length vector linking an aromatic ring with a protonated nitrogen, while specific affinities for receptorial subtypes and the nature of the effect appear to be modulated by the dimensions of the substituents at nitrogen.
Crystal packing calculations and Rietveld refinement in elucidating the crystal structures of two modifications of 4-amidinoindanone guanylhydrazone
Authors: Karfunkel H. R. , Wu Z. J. , Burkhard A. , Rihs G. , Sinnreich D. , Buerger H. M. , Stanek J.
Published: July 2002

The crystal structures of two modifications (termed A and B) of 4-amidinoindanone guanylhydrazone (AIGH), 2-(4-amidino-1-indanylideneamino)guanidine, have been determined. Modification B, for which single crystals were available, has been treated in the usual manner. The determination of modification A, for which no single crystals were available, was made on the basis of the X-ray powder pattern and ab initio packing calculations. It has been shown that it is possible to determine in a routine manner the crystal structure of a polar and moderately flexible molecule, which can be specified as several tautomeric forms, using a combination of high-precision computational chemistry and Rietveld refinement. The resulting R-factor was ca 10%. Although the resolution of the powder diagram allowed for indexing, it is shown that the structure determination is also possible without indexing the powder diagram. The presented structure determination should be understood as an example of a new and generalized use of the Rietveld refinement where the two main problems, indexing of the powder pattern and making an initial structure guess, could be bypassed.
Structures and photochemistry of dibenzobarrelene monoamides
Authors: Jones R. , Rattray A. G. M. , Rettig S. J. , Scheffer J. R. , Trotter J.
Published: July 2002

The photochemistry of 9,10-ethenoanthracene-11-monoamides has been studied and correlated with the crystal structures determined for two derivatives; photoproduct structures have been established from a crystal structure analysis of one of the products and from NMR correlations. Crystal data are: (1)-Et, N, N-diethyl-9,10-dihydro-9,10-ethenoanthracene-11-carboxamide, C21H21NO, Pbca; (1)-Pr, 9,10-dihydro-N,N-di(isopropyl)-9,10-ethenoanthracene-11-carboxamide, C23H25NO, P21/c; (2 L)-Bz, 9,10-dihydro-9,10-ethenoanthracene-11-spiro-3′-(1-benzyl-4-phenylazetidine)-2′-one, C31H25NO (+ solvent), P21/a (Z = 8). The two dibenzobarrelene molecules have geometries and dimensions similar to those of related materials; the amide group in each molecule is only partially conjugated with the C 11=C 12 double bond. Mechanisms are derived for the formation of three types of photoproduct: (i) the well known di-π-methane reaction [(2M)-type photoproduct]; (ii) a hydrogen abstraction process (2H); (iii) β-lactam formation (2 L).
Conformational Analysis of Macrocyclic Ether Ligands. I. 1,4,7,10-Tetraoxacyclododecane and 1,4,7,10-Tetrathiacyclododecane
Authors: Raithby P. R. , Shields G. P. , Allen F. H.
Published: July 2002

Crystallographic results retrieved from the Cambridge Structural Database (CSD) have been used to perform systematic conformational analyses of both free and metal-coordinated unsaturated 12-membered oxa and thia macrocycles. Conformational classifications established using symmetry-modified Jarvis–Patrick clustering are visualized in conformational space by principal component analysis (PCA) plots. These show that the relationship between cluster populations and relative molecular mechanics energies is modified by the coordination requirements of a metal ion. With oxa donors the [3333] conformer (oxygen in edge positions) predominates for metal-coordinated macrocycles, with the donor atoms in a square-planar arrangement, whilst the [48] conformer occurs bound in a cis-octahedral fashion to metal ions and the [66] conformer does not bind in an endo-dentate manner at all. The [3333] and [66] conformers are both common for free ligands, reflecting their similar molecular mechanics energies; the conformation is often determined by the hydrogen-bonding network. There are few thia examples: it is found that conformers with low molecular mechanics energies are unsuited to metal coordination and substantial reorganization is necessary for chelation. The differences in behaviour of oxa and thia macrocycles may be rationalized in terms of differing torsion-angle preferences for CXCC and XCCX units (X = O, S).
Effects of Crystal Packing on Photoinduced Proton-Transfer Processes of 2,4-Dinitrobenzylpyridine Derivatives
Authors: Khatib S. , Botoshansky M. , Eichen Y.
Published: July 2002

Photoinduced and thermally activated proton-transfer processes taking place in crystals of 2-(2,4-dinitrobenzyl)pyridine and some of its derivatives are highly sensitive to molecular packing. Small differences in the way the molecules are packed in the crystal are found to dominate molecular properties in controlling the photoactivity of the different phototautomers, leading, for example, to photoactive or photoinert systems. Three compounds, 2-(2,4-dinitrobenzyl)-4-methylpyridine, 1-(2,4-dinitrophenyl)-l-(2-pyridine)ethane and 4′-(2,4-dinitrobenzyl)-4-methyl-2,2′-bipyridine, having different photochemical properties, were prepared and their crystal structures characterized by means of X-ray analysis. In the photoinert crystals the 2,4-dinitrophenyl group is π-stacked with other aromatic rings of neighboring molecules. This arrangement may open some deactivation channels to the excited state which are faster than the proton-transfer process, leading to photoinert crystals. The absence of π-stacking between the chromophore and other aromatic rings leads to photoactive systems. An O atom of the o-nitro group is the only basic atom that is systematically found to interact with the abstracted proton. It seems that this atom is responsible for the photoinduced proton abstraction of the benzylic H atom, while the role of the N atom of the pyridine ring in the proton-abstraction process is mainly inductive.
Packing Modes in Nitrobenzene Derivatives. II. The `Pseudo-Herringbone' Mode
Authors: André I. , Foces-Foces C. , Cano F. H. , Martinez-Ripoll M.
Published: July 2002

Nitrobenzene derivatives pack in two main motifs: stacks [see André , Foces-Foces, Cano & Martinez-Ripoll (1997). Acta Cryst. B53, 984–995] and `pseudo- herringbone' together account for some 61.5% of the structures classified as BCLASS = 15 by the Cambridge Structural Database. Several geometrical parameters allow the classification of the `pseudo-herringbone' category into four main motifs. Weak interactions appear to play an important role in this packing mode.
Disorder in cyclodextrin clathrates: X-ray diffuse scattering analysis of α-cyclodextrin cyclopentanone hydrate. Erratum
Authors: Le Bas G. , Doucet J.
Published: July 2002

The captions to Figs. 7 and 8 on p. 677 were transposed [Le Bas & Doucet (1997). Acta Cryst. B53, 673–679]. The correct figures and their corresponding captions are shown here.
The crystal structure of Tm5Re2O12
Authors: Ehrenberg H. , Hartmann T. , Wltschek G. , Fuess H. , Morgenroth W. , Krane H.-G.
Published: July 2002

The crystal structure of Tm5Re2O12, pentathulium dirhenium dodecaoxide, was determined by synchrotron diffraction on a reticular merohedral twin, revealing space group C2/m with a = 12.3717 (7), b = 5.6744 (3), c = 7.4805 (4) Å, β = 107.816 (2)° and Z = 2. Distorted ReO6 octahedra form chains with alternating rhenium–rhenium distances of 2.455 (1) and 3.219 (1) Å. Early reports on Ln2ReO5 compounds are critically reviewed in the light of our results for Tm5Re2O12.
Structure of the defect perovskite Ce1/3NbO3: a redetermination by electron and neutron powder diffraction
Authors: Bridges C. , Greedan J. E. , Barbier J.
Published: July 2002

The crystal structure of the defect perovskite Ce1/3NbO3, cerium niobium oxide, has been re-examined by neutron powder and electron diffraction. The results of a powder neutron Rietveld refinement indicate that the structure is monoclinic: space group P2/m with Z = 4, a = 5.5267 (3), b = 7.8824 (2), c = 5.5245 (3) Å, β = 90.294 (1)°, V = 240.67 (2) Å3 at 298 K with χ2 = 2.570. Previous reports have described the Ce1/3NbO3 structure in a smaller (V/2) orthorhombic cell based solely upon X-ray powder diffraction data. The presence of weak reflections in the electron diffraction pattern provides conclusive evidence for a monoclinic superstructure of the orthorhombic cell. While these superlattice reflections are barely detectable with X-ray radiation, they are clearly visible in the neutron diffraction experiments. The superlattice reflections are shown to arise from a tilting of the NbO6 octahedra which results in the reduction of symmetry from orthorhombic to monoclinic. It is also found that the Ce3+ and Nb5+ cations are displaced from the centres of their respective polyhedra to accommodate the bond-valence requirements of the crystal structure. It is likely that distortions of this type are present in other Ln1/3NbO3 and Ln1/3TaO3 defect perovskites.
Multidimensional molecular replacement
Authors: Glykos Nicholas M. , Kokkinidis Michael
Published: July 2002

A method is described which attempts to simultaneously and independently determine the positional and orientational parameters of all molecules present in the asymmetric unit of a target crystal structure. This is achieved through a reverse Monte Carlo optimization of a suitable statistic (such as the R factor or the linear correlation coefficient between the observed and calculated amplitudes of the structure factors) in the 6n-dimensional space defined by the rotational and translational parameters of the n search models. Results from the application of this stochastic method – obtained with a space-group-general computer program which has been developed for this purpose – indicate that with present-day computing capabilities the method may be applied successfully to molecular-replacement problems for which the target crystal structure contains up to three molecules per asymmetric unit. It is also shown that the method may be useful in cases where the assumption of topological segregation of the self- and cross-vectors in the Patterson function is violated (as may happen, for example, in closely packed crystal structures).
Evaluating the potential of using fold-recognition models for molecular replacement
Authors: Jones David T.
Published: July 2002

Here, the proposal is investigated that protein tertiary structure prediction methods and threading methods in particular might be applied to the problem of solving a protein structure by X-ray crystallography, thus reducing the need for the more traditional experimental intensity methods of data phasing, such as heavy-metal isomorphous replacement and anomalous scattering methods, and without reference to a very closely related protein of known structure. If this kind of approach were to become successful and reliable, this would represent a significant advance in protein structure determination, offering an easy and accessible method for the initial data phasing for proteins' crystal structures, utilizing the vast amount of structural data, deposited in the Brookhaven PDB, that has been accumulated over the past 30 years of crystallographic structural studies. In the light of the ongoing structural genomics initiatives, the successful development of this kind of approach would be of enormous benefit.
Reliability of atomic displacement parameters in protein crystal structures
Authors: Carugo Oliviero , Argos Patrick
Published: July 2002

Mean standard errors in atomic displacement parameters (ADPs) resulting from protein crystal structure determinations are estimated by comparing the ADPs of protein-chain pairs of identical sequence within the same crystal or within different crystals displaying the same or different space groups. The estimated ADP standard errors increase nearly linearly as the resolution decreases – an unexpected result given the nonlinear dependence of the resolution on the amount of diffraction data. The estimated ADP standard errors are larger for side-chain and solvent-exposed atoms than for main-chain and buried atoms and, surprisingly, are also larger for residues in the helical secondary structure relative to other local backbone conformations. The results allow an estimate of the influence of crystallographic refinement restraints on ADP standard errors. Such corrections should be applied when comparing different protein structures.
Crystallization and preliminary X-ray crystallographic analysis of the B800–820 light-harvesting complex from Rhodopseudomonas acidophila strain 7050
Authors: McLuskey Karen , Prince Stephen M. , Cogdell Richard J. , Isaacs Neil W.
Published: July 2002

The B800–820 peripheral light-harvesting complex, an integral membrane protein from Rhodopseudomonas acidophila strain 7050, has been crystallized in a form suitable for X-ray diffraction analysis. The crystals belong to space group R32 with hexagonal cell dimensions a = 117.20, c = 295.14 Å (at 100 K). A complete 2.8 Å resolution data set has been collected and a structure solution obtained using molecular-replacement methods.