bluuebunny/crossref_metadata_2025 huggingface dataset:
Complementation of the Arabidopsispds1Mutation with the Gene Encodingp-Hydroxyphenylpyruvate Dioxygenase
Authors: Norris Susan R. , Shen Xiaohua , Della Penna Dean
Published: July 2002

Plastoquinone and tocopherols are the two major quinone compounds in higher plant chloroplasts and are synthesized by a common pathway. In previous studies we characterized two loci in Arabidopsis defining key steps of this biosynthetic pathway. Mutation of the PDS1 locus disrupts the activity of p-hydroxyphenylpyruvate dioxygenase (HPPDase), the first committed step in the synthesis of both plastoquinone and tocopherols in plants. Although plants homozygous for the pds1 mutation could be rescued by growth in the presence of homogentisic acid, the product of HPPDase, we were unable to determine if the mutation directly or indirectly disrupted HPPDase activity. This paper reports the isolation of a cDNA, pHPPD, encoding Arabidopsis HPPDase and its functional characterization by expression in both plants and Escherichia coli. pHPPD encodes a 50-kD polypeptide with homology to previously identified HPPDases, including 37 highly conserved amino acid residues clustered in the carboxyl region of the protein. Expression of pHPPD in E. coli catalyzes the accumulation of homogentisic acid, indicating that it encodes a functional HPPDase enzyme. Mapping of pHPPD and co-segregation analysis of the pds1 mutation and the HPPD gene indicate tight linkage. Constitutive expression of pHPPD in a pds1 mutant background complements this mutation. Finally, comparison of the HPPD genomic sequences from wild type and pds1 identified a 17-bp deletion in thepds1 allele that results in deletion of the carboxyterminal 26 amino acids of the HPPDase protein. Together, these data conclusively demonstrate that pds1 is a mutation in the HPPDase structural gene.
Circadian-Regulated Transcription of thepsbD Light-Responsive Promoter in Wheat Chloroplasts
Authors: Nakahira Yoichi , Baba Kyoko , Yoneda Akito , Shiina Takashi , Toyoshima Yoshinori
Published: July 2002

The level of mRNAs derived from the plastid-encoded psbD light-responsive promoter (LRP) is controlled by a circadian clock(s) in wheat (Triticum aestivum). The circadian oscillations in the psbD LRP mRNA level persisted for at least three cycles in continuous light and for one cycle in continuous dark, with maxima in subjective morning and minima in subjective early night. In vitro transcription in chloroplast extracts revealed that the circadian cycles in the psbD LRP mRNA level were dominantly attributed to the circadian-regulated transcription of thepsbD LRP. The effects of various mutations introduced into the promoter region on the psbD LRP activity in vitro suggest the existence of two positive elements located between −54 and −36, which generally enhance the transcription activity, and an anomalous core promoter structure lacking the functional “−35” element, which plays a crucial role in the circadian fluctuation and light dependency of psbD LRP transcription activity.
Induction of Acclimative Proteolysis of the Light-Harvesting Chlorophyll a/b Protein of Photosystem II in Response to Elevated Light Intensities
Authors: Yang Dan-Hui , Webster Jeanette , Adam Zach , Lindahl Marika , Andersson Bertil
Published: July 2002

Most plants have the ability to respond to fluctuations in light to minimize damage to the photosynthetic apparatus. A proteolytic activity has been discovered that is involved in the degradation of the major light-harvesting chlorophyll a/b-binding protein of photosystem II (LHCII) when the antenna size of photosystem II is reduced upon acclimation of plants from low to high light intensities. This ATP-dependent proteolytic activity is of the serine or cysteine type and is associated with the outer membrane surface of the stroma-exposed thylakoid regions. The identity of the protease is not known, but it does not correspond to the recently identified chloroplast ATP-dependent proteases Clp and FtsH, which are homologs to bacterial enzymes. The acclimative response shows a delay of 2 d after transfer of the leaves to high light. This lag period was shown to be attributed to expression or activation of the responsible protease. Furthermore, the LHCII degradation was found to be regulated at the substrate level. The degradation process involves lateral migration of LHCII from the appressed to the nonappressed thylakoid regions, which is the location for the responsible protease. Phosphorylated LHCII was found to be a poor substrate for degradation in comparison with the unphosphorylated form of the protein. The relationship between LHCII degradation and other regulatory proteolytic processes in the thylakoid membrane, such as D1-protein degradation, is discussed.
Root-Growth Behavior of the Arabidopsis Mutantrgr1
Authors: Mullen Jack L. , Turk Ed , Johnson Karin , Wolverton Chris , Ishikawa Hideo , Simmons Carl , Söll Deiter , Evans Michael L.
Published: July 2002

In this study we investigated the kinetics of the gravitropic response of the Arabidopsis mutant rgr1 (reducedroot gravitropism). Although the rate of curvature in rgr1, which is allelic toaxr4, was smaller than in the wild type (ecotype Wassilewskija), curvature was initiated in the same region of the root, the distal elongation zone. The time lag for the response was unaffected in the mutant; however, the gravitropic response ofrgr1 contained a feature not found in the wild type: when roots growing along the surface of an agar plate were gravistimulated, there was often an upward curvature that initiated in the central elongation zone. Because this response was dependent on the tactile environment of the root, it most likely resulted from the superposition of the waving/coiling phenomenon onto the gravitropic response. We found that the frequency of the waving pattern and circumnutation, a cyclic endogenous pattern of root growth, was the same in rgr1 and in the wild type, so the waving/coiling phenomenon is likely governed by circumnutation patterns. The amplitudes of these oscillations may then be selectively amplified by tactile stimulation to provide a directional preference to the slanting.
Benzothiadiazole-Mediated Induced Resistance toFusarium oxysporum f. sp.radicis-lycopersici in Tomato
Authors: Benhamou Nicole , Bélanger Richard R.
Published: July 2002

Benzo-(1,2,3)-thiadiazole-7-carbothioic acid S-methyl ester (BTH), a synthetic chemical, was applied as a foliar spray to tomato (Lycopersicon esculentum) plants and evaluated for its potential to confer increased resistance against the soil-borne pathogen Fusarium oxysporum f. sp. radicis-lycopersici (FORL). In nontreated tomato plants all root tissues were massively colonized by FORL hyphae. Pathogen ingress toward the vascular stele was accompanied by severe host cell alterations, including cell wall breakdown. In BTH-treated plants striking differences in the rate and extent of fungal colonization were observed. Pathogen growth was restricted to the epidermis and the outer cortex, and fungal ingress was apparently halted by the formation of callose-enriched wall appositions at sites of fungal penetration. In addition, aggregated deposits, which frequently established close contact with the invading hyphae, accumulated in densely colonized epidermal cells and filled most intercellular spaces. Upon incubation of sections with gold-complexed laccase for localization of phenolic-like compounds, a slight deposition of gold particles was observed over both the host cell walls and the wall appositions. Labeling was also detected over the walls of fungal cells showing signs of obvious alteration ranging from cytoplasm disorganization to protoplasm retraction. We provide evidence that foliar applications of BTH sensitize susceptible tomato plants to react more rapidly and more efficiently to FORL attack through the formation of protective layers at sites of potential fungal entry.
Dynamics of Cytokinins in Apical Shoot Meristems of a Day-Neutral Tobacco during Floral Transition and Flower Formation1
Authors: Dewitte Walter , Chiappetta Adriana , Azmi Abdelkrim , Witters Erwin , Strnad Miroslav , Rembur Jacques , Noin Michelle , Chriqui Dominique , Van Onckelen Henri
Published: July 2002

This study considered cytokinin distribution in tobacco (Nicotiana tabacum L.) shoot apices in distinct phases of development using immunocytochemistry and quantitative tandem mass spectrometry. In contrast to vegetative apices and flower buds, we detected no free cytokinin bases (zeatin, dihydrozeatin, or isopentenyladenine) in prefloral transition apices. We also observed a 3-fold decrease in the content of cytokinin ribosides (zeatin riboside, dihydrozeatin riboside, and isopentenyladenosine) during this transition phase. The group concluded that organ formation (e.g. leaves and flowers) is characterized by enhanced cytokinin content, in contrast to the very low endogenous cytokinin levels found in prefloral transition apices, which showed no organogenesis. The immunocytochemical analyses revealed a differing intracellular localization of the cytokinin bases. Dihydrozeatin and isopentenyladenine were mainly cytoplasmic and perinuclear, whereas zeatin showed a clear-cut nuclear labeling. To our knowledge, this is the first time that this phenomenon has been reported. Cytokinins do not seem to act as positive effectors in the prefloral transition phase in tobacco shoot apices. Furthermore, the differences in distribution at the cellular level may be indicative of a specific physiological role of zeatin in nuclear processes.
Water Stress Inhibits Hydraulic Conductance and Leaf Growth in Rice Seedlings but Not the Transport of Water via Mercury-Sensitive Water Channels in the Root1
Authors: Lu Zhongjin , Neumann Peter M.
Published: July 2002

The mechanisms by which moderate water stress (adding polyethylene glycol 6000 to the root medium) induces a sustained inhibition of growth in emerging first leaves of intact rice (Oryza sativa) seedlings was investigated under growth-chamber conditions. Early (24 h) inhibition of leaf growth was not related to changes in root size or in osmotic potential gradients and cell wall-yielding characteristics in the leaf-expansion zone of stressed seedlings. However, reductions in root-to-leaf hydraulic conductance (L) were measured in two rice cultivars after 4 or 24 h at various levels of water stress, and these reductions correlated well with the inhibition of leaf growth. We assayed L by a psychrometric method and, in intact seedlings, by a novel osmotic-jump method. The addition of 0.5 mm HgCl2 to the root medium to inhibit water transport through Hg-sensitive water channels in the roots did not inhibit leaf growth in unstressed seedlings. However, both leaf growth and L were additionally reduced (by 49% and 43%, respectively) within minutes of adding HgCl2 to roots of water-stressed seedlings. Water stress therefore appeared to increase the transport of water via Hg-sensitive water channels. Other mechanisms were apparently involved in inhibiting overallL and leaf growth.
Characterization of Photosystem II Activity and Heterogeneity during the Cell Cycle of the Green AlgaScenedesmus quadricauda1
Authors: Kaftan David , Meszaros Tibor , Whitmarsh John , Nedbal Ladislav
Published: July 2002

The photosynthetic activity of the green alga Scenedesmus quadricauda was investigated during synchronous growth in light/dark cycles. The rate of O2 evolution increased 2-fold during the first 3 to 4 h of the light period, remained high for the next 3 to 4 h, and then declined during the last half of the light period. During cell division, which occurred at the beginning of the dark period, the ability of the cells to evolve O2 was at a minimum. To determine if photosystem II (PSII) controls the photosynthetic capacity of the cells during the cell cycle we measured PSII activity and heterogeneity. Measurements of electron-transport activity revealed two populations of PSII, active centers that contribute to carbon reduction and inactive centers that do not. Measurements of PSII antenna sizes also revealed two populations, PSIIα and PSIIβ, which differ from one another by their antenna size. During the early light period the photosynthetic capacity of the cells doubled, the O2-evolving capacity of PSII was nearly constant, the proportion of PSIIβ centers decreased to nearly zero, and the proportion of inactive PSII centers remained constant. During the period of minimum photosynthetic activity 30% of the PSII centers were insensitive to the inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea, which may be related to reorganization of the thylakoid membrane. We conclude from these results that PSII does not limit the photosynthetic activity of the cells during the first half of the light period. However, the decline in photosynthetic activity observed during the last half of the light period can be accounted for by limited PSII activity.
Influence of the Testa on Seed Dormancy, Germination, and Longevity in Arabidopsis
Authors: Debeaujon Isabelle , Léon-Kloosterziel Karen M. , Koornneef Maarten
Published: July 2002

The testa of higher plant seeds protects the embryo against adverse environmental conditions. Its role is assumed mainly by controlling germination through dormancy imposition and by limiting the detrimental activity of physical and biological agents during seed storage. To analyze the function of the testa in the model plant Arabidopsis, we compared mutants affected in testa pigmentation and/or structure for dormancy, germination, and storability. The seeds of most mutants exhibited reduced dormancy. Moreover, unlike wild-type testas, mutant testas were permeable to tetrazolium salts. These altered dormancy and tetrazolium uptake properties were related to defects in the pigmentation of the endothelium and its neighboring crushed parenchymatic layers, as determined by vanillin staining and microscopic observations. Structural aberrations such as missing layers or a modified epidermal layer in specific mutants also affected dormancy levels and permeability to tetrazolium. Both structural and pigmentation mutants deteriorated faster than the wild types during natural aging at room temperature, with structural mutants being the most strongly affected.
Independent Action of ELF3 and phyB to Control Hypocotyl Elongation and Flowering Time
Authors: Reed Jason W. , Nagpal Punita , Bastow Ruth M. , Solomon Keely S. , Dowson-Day Mandy J. , Elumalai Rangasamy P. , Millar Andrew J.
Published: July 2002

Light regulates various aspects of plant growth, and the photoreceptor phytochrome B (phyB) mediates many responses to red light. In a screen for Arabidopsis mutants with phenotypes similar to those ofphyB mutants, we isolated two new elf3mutants. One has weaker morphological phenotypes than previously identified elf3 alleles, but still abolishes circadian rhythms under continuous light. Like phyB mutants,elf3 mutants have elongated hypocotyls and petioles, flower early, and have defects in the red light response. However, we found that elf3 mutations have an additive interaction with a phyB null mutation, with phyA orhy4 null mutations, or with a PHYB overexpression construct, and that an elf3 mutation does not prevent nuclear localization of phyB. These results suggest that either there is substantial redundancy in phyB and elf3 function, or the two genes regulate distinct signaling pathways.
A Germination-Specific Endo-β-Mannanase Gene Is Expressed in the Micropylar Endosperm Cap of Tomato Seeds
Authors: Nonogaki Hiroyuki , Gee Oliver H. , Bradford Kent J.
Published: July 2002

Endo-β-mannanase (EC 3.2.1.78) is involved in hydrolysis of the mannan-rich cell walls of the tomato (Lycopersicon esculentum Mill.) endosperm during germination and post-germinative seedling growth. Different electrophoretic isoforms of endo-β-mannanase are expressed sequentially in different parts of the endosperm, initially in the micropylar endosperm cap covering the radicle tip and subsequently in the remaining lateral endosperm surrounding the rest of the embryo. We have isolated a cDNA from imbibed tomato seeds (LeMAN2) that shares 77% deduced amino acid sequence similarity with a post-germinative tomato mannanase (LeMAN1). When expressed in Escherichia coli, the protein encoded by LeMAN2 cDNA was recognized by anti-mannanase antibody and exhibited endo-β-mannanase activity, confirming the identity of the gene. LeMAN2was expressed exclusively in the endosperm cap tissue of tomato seeds prior to radicle emergence, whereas LeMAN1 was expressed only in the lateral endosperm after radicle emergence.LeMAN2 mRNA accumulation and mannanase activity were induced by gibberellin in gibberellin-deficient gib-1mutant seeds but were not inhibited by abscisic acid in wild-type seeds. Distinct mannanases are involved in germination and post-germinative growth, with LeMAN2 being associated with endosperm cap weakening prior to radicle emergence, whereasLeMAN1 mobilizes galactomannan reserves in the lateral endosperm.
A Comparative Analysis of the Plant Cellulose Synthase (CesA) Gene Family
Authors: Holland Neta , Holland Doron , Helentjaris Tim , Dhugga Kanwarpal S. , Xoconostle-Cazares Beatriz , Delmer Deborah P.
Published: July 2002

CesA genes are believed to encode the catalytic subunit of cellulose synthase. Identification of nine distinctCesA cDNAs from maize (Zea mays) has allowed us to initiate comparative studies with homologs from Arabidopsis and other plant species. Mapping studies show that closely related CesA genes are not clustered but are found at different chromosomal locations in both Arabidopsis and maize. Furthermore, sequence comparisons among the CesA-deduced proteins show that these cluster in groups wherein orthologs are often more similar than paralogs, indicating that different subclasses evolved prior to the divergence of the monocot and dicot lineages. Studies using reverse transcriptase polymerase chain reaction with gene-specific primers for six of the nine maize genes indicate that all genes are expressed to at least some level in all of the organs examined. However, when expression patterns for a few selected genes from maize and Arabidopsis were analyzed in more detail, they were found to be expressed in unique cell types engaged in either primary or secondary wall synthesis. These studies also indicate that amino acid sequence comparisons, at least in some cases, may have value for prediction of such patterns of gene expression. Such analyses begin to provide insights useful for future genetic engineering of cellulose deposition, in that identification of close orthologs across species may prove useful for prediction of patterns of gene expression and may also aid in prediction of mutant combinations that may be necessary to generate severe phenotypes.
Chitinase Genes Responsive to Cold Encode Antifreeze Proteins in Winter Cereals
Authors: Yeh Sansun , Moffatt Barbara A. , Griffith Marilyn , Xiong Fei , Yang Daniel S.C. , Wiseman Steven B. , Sarhan Fathey , Danyluk Jean , Xue Yi Qi , Hew Choy L. , Doherty-Kirby Amanda , Lajoie Gilles
Published: July 2002

Antifreeze proteins similar to two different chitinases accumulate during cold acclimation in winter rye (Secale cereale). To determine whether these cold-responsive chitinases require post-translational modification to bind to ice, cDNAs coding for two different full-length chitinases were isolated from a cDNA library produced from cold-acclimated winter rye leaves. CHT9 is a 1,193-bp clone that encodes a 31.7-kD class I chitinase andCHT46 is a 998-bp clone that codes for a 24.8-kD class II chitinase. Chitinase-antifreeze proteins purified from the plant were similar in mass to the predicted mature products ofCHT9 and CHT46, thus indicating that there was little chemical modification of the amino acid sequences in planta. To confirm these results, the mature sequences ofCHT9 and CHT46 were expressed inEscherichia coli and the products of both cDNAs modified the growth of ice. Transcripts of both genes accumulated late in cold acclimation in winter rye. Southern analysis of winter rye genomic DNA indicated the presence of a small gene family homologous toCHT46. In hexaploid wheat, CHT46 homologs mapped to the homeologous group 1 chromosomes and were expressed in response to cold and drought. We conclude that two novel cold-responsive genes encoding chitinases with ice-binding activity may have arisen in winter rye and other cereals through gene duplication.
Pericycle Cell Proliferation and Lateral Root Initiation in Arabidopsis
Authors: Dubrovsky Joseph G. , Doerner Peter W. , Colón-Carmona Adán , Rost Thomas L.
Published: July 2002

In contrast with other cells generated by the root apical meristem in Arabidopsis, pericycle cells adjacent to the protoxylem poles of the vascular cylinder continue to cycle without interruption during passage through the elongation and differentiation zones. However, only some of the dividing pericycle cells are committed to the asymmetric, formative divisions that give rise to lateral root primordia (LRPs). This was demonstrated by direct observation and mapping of mitotic figures, cell-length measurements, and the histochemical analysis of a cyclin-GUS fusion protein in pericycle cells. The estimated duration of a pericycle cell cycle in the root apical meristem was similar to the interval between cell displacement from the meristem and the initiation of LRP formation. Developmentally controlled LRP initiation occurs early, 3 to 8 mm from the root tip. Thus the first growth control point in lateral root formation is defined by the initiation of primordia in stochastic patterns by cells passing through the elongation and young differentiation zones, up to where lateral roots begin to emerge from the primary root. Therefore, the first growth control point is not restricted to a narrow developmental window. We propose that late LRP initiation is developmentally unrelated to the root apical meristem and is operated by a second growth control point that can be activated by environmental cues. The observation that pericycle cells divide and lateral root primordia form without intervening mitotic quiescence suggests that lateral organ formation in roots and shoots might not be as fundamentally different as previously thought.
Transposon-Mediated Single-Copy Gene Delivery Leads to Increased Transgene Expression Stability in Barley
Authors: Koprek Thomas , Rangel Sergio , McElroy David , Louwerse Jeanine D. , Williams-Carrier Rosalind E. , Lemaux Peggy G.
Published: July 2002

Instability of transgene expression in plants is often associated with complex multicopy patterns of transgene integration at the same locus, as well as position effects due to random integration. Based on maize transposable elements Activator(Ac) and Dissociation(Ds), we developed a method to generate large numbers of transgenic barley (Hordeum vulgare var Golden Promise) plants, each carrying a single transgene copy at different locations. Plants expressing Ac transposase (AcTPase) were crossed with plants containing one or more copies of bar, a selectable herbicide (Basta) resistance gene, located between inverted-repeatDs ends (Ds-bar). F1 plants were self-pollinated and the F2 generation was analyzed to identify plants segregating for transposed Ds-barelements. Of Ds-bar transpositions, 25% were in unlinked sites that segregated from vector sequences, otherDs-bar copies, and the AcTPase gene, resulting in numerous single-copy Ds-bar plants carrying the transgene at different locations. Transgene expression in F2 plants with transposed Ds-bar was 100% stable, whereas only 23% of F2 plants carryingDs-bar at the original site expressed the transgene product stably. In F3 and F4 populations, transgene expression in 81.5% of plants from progeny of F2plants with single-copy, transposed Ds-bar remained completely stable. Analysis of the integration site in single-copy plants showed that transposed Ds-bar inserted into single- or low-copy regions of the genome, whereas silencedDs-bar elements at their original location were inserted into redundant or highly repetitive genomic regions. Methylation of the non-transposed transgene and its promoter, as well as a higher condensation of the chromatin around the original integration site, was associated with plants exhibiting transgene silencing.
Expression of a Gibberellin 2-Oxidase Gene around the Shoot Apex Is Related to Phase Transition in Rice
Authors: Sakamoto Tomoaki , Kobayashi Masatomo , Itoh Hironori , Tagiri Akemi , Kayano Toshiaki , Tanaka Hiroshi , Iwahori Shuichi , Matsuoka Makoto
Published: July 2002

A major catabolic pathway for gibberellin (GA) is initiated by 2β-hydroxylation, a reaction catalyzed by GA 2-oxidase. We have isolated and characterized a cDNA, designated Oryza sativa GA 2-oxidase 1 (OsGA2ox1) from rice (Oryza sativa L. cv Nipponbare) that encodes a GA 2-oxidase. The encoded protein, produced by heterologous expression inEscherichia coli, converted GA1, GA4, GA9, GA20, and GA44 to the corresponding 2β-hydroxylated products GA8, GA34, GA51, GA29, and GA98, respectively. Ectopic expression of theOsGA2ox1 cDNA in transgenic rice inhibited stem elongation and the development of reproductive organs. These transgenic plants were deficient in endogenous GA1. These results indicate that OsGA2ox1 encodes a GA 2-oxidase, which is functional not only in vitro but also in vivo. OsGA2ox1was expressed in shoot apex and roots but not in leaves and stems. In situ hybridization analysis revealed that OsGA2ox1 mRNA was localized in a ring at the basal region of leaf primordia and young leaves. This ring-shaped expression around the shoot apex was drastically decreased after the phase transition from vegetative to reproductive growth. It was absent in the floral meristem, but it was still present in the lateral meristem that remained in the vegetative phase. These observations suggest that OsGA2ox1 controls the level of bioactive GAs in the shoot apical meristem; therefore, reduction in its expression may contribute to the early development of the inflorescence meristem.
Expression of a Pseudomonas aeruginosa Citrate Synthase Gene in Tobacco Is Not Associated with Either Enhanced Citrate Accumulation or Efflux
Authors: Delhaize Emmanuel , Hebb Diane M. , Ryan Peter R.
Published: July 2002

Aluminum (Al) toxicity and poor phosphorus (P) availability are factors that limit plant growth on many agricultural soils. Previous work reported that expression of a Pseudomonas aeruginosa citrate synthase gene in tobacco (Nicotiana tabacum; CSb lines) resulted in improved Al tolerance (J.M. de la Fuente, V. Ramı́rez-Rodrı́guez, J.L. Cabrera-Ponce, L. Herrera-Estrella [1997] Science 276: 1566–1568) and an enhanced ability to acquire P from alkaline soils (J. López-Bucio, O. Martı́nez de la Vega, A. Guevara-Garcı́a, L. Herrera-Estrella [2000] Nat Biotechnol 18: 450–453). These effects were attributed to the P. aeruginosa citrate synthase increasing the biosynthesis and efflux of citrate from roots. To verify these findings we: (a) characterized citrate efflux from roots of wild-type tobacco; (b) generated tobacco lines expressing the citrate synthase gene from P. aeruginosa; and (c) analyzed selected CSb lines described above. Al stimulated citrate efflux from intact roots of wild-type tobacco and root apices were found to be responsible for most of the efflux. Despite generating transgenic tobacco lines that expressed the citrate synthase protein at up to a 100-fold greater level than the previously described CSb lines, these lines did not show increased accumulation of citrate in roots or increased Al-activated efflux of citrate from roots. Selected CSb lines, similarly, failed to show differences compared with controls in either citrate accumulation or efflux. We conclude that expression of the P. aeruginosa citrate synthase gene in plants is unlikely to be a robust and easily reproducible strategy for enhancing the Al tolerance and P-nutrition of crop and pasture species.
Approximate calculation of multiple-diffraction patterns based on Renninger's kinematical `simplest approach'
Authors: Rossmanith Elisabeth
Published: July 2002

Analytical expressions for the absolute change of the primary reflection intensity due to multiple diffraction are given in the kinematical approach. It is shown that satisfactory agreement between experiment and theory can be obtained for a mosaic crystal (diamond) as well as for a perfect crystal (silicon) even in the case of strong reflections.
GraphEnt: a maximum-entropy program with graphics capabilities
Authors: Glykos Nicholas M. , Kokkinidis Michael
Published: July 2002

A maximum-entropy formalism aimed at the production of a `maximally noncommittal' map is a standard method in fields of science like radioastronomy, but a rare exception in both X-ray crystallography and electron microscopy (or crystallography). This is rather unfortunate, given the wealth of information that a maximum-entropy map can reveal, especially when the map itself is the end product (for example, low-resolution electron or potential density maps, Patterson functions, deformation maps). The programGraphEntattempts to automate the procedure of calculating maximum-entropy maps, with emphasis on the calculation of difference Patterson functions for macromolecular crystallographic problems, while providing a useful graphical output of the current stage of the calculation.
A novel free-mounting system for protein crystals: transformation and improvement of diffraction power by accurately controlled humidity changes
Authors: Kiefersauer Reiner , Than Manuel E. , Dobbek Holger , Gremer Lothar , Melero Marcos , Strobl Stefan , Dias João M. , Soulimane Tewfik , Huber Robert
Published: July 2002

A novel device for capillary-free mounting of protein crystals is described. A controlled stream of air allows an accurate adjustment of the humidity at the crystal. The crystal is held on the tip of a micropipette. With a video system (CCD camera), the two-dimensional shadow projections of crystals can be recorded for optical analysis. Instead of the micropipette, a standard loop can also be used. Experiments and results for different crystal systems demonstrate the use of this method, also in combination with shock-freezing, to improve crystal order. Working with oxygen-free gases offers the possibility of crystal measurements under anaerobic conditions. Furthermore, the controlled application of arbitrary volatile substances with the gas stream is practicable.
Preferred orientation in Debye–Scherrer geometry: interpretation of the March coefficient
Authors: Howard C. J. , Kisi E. H.
Published: July 2002

The March function is a widely used preferred-orientation correction function that, in flat-plate geometry, often closely approximates the pole-density profile of axially symmetric textures. It is shown that in Debye–Scherrer geometry, the assumption that the pole-density profile of a powder specimen can be described by a March function with coefficientR, leads to an intensity correction factor that can be approximated quite well by another March function, with coefficientR−1/2. This result validates the use of the March function correction in Debye–Scherrer geometry, facilitates the comparison of results obtained in the different geometries and should prove useful in some studies of axially symmetric textures and in residual-stress analysis.
Kinematical two-dimensional multiple-diffraction intensity profiles. Application to ω–ψ scans obtained with CuKα radiation
Authors: Rossmanith Elisabeth
Published: July 2002

Expressions for the calculation of multiple-diffraction patterns observed in ω–ψ scans of Bragg reflections are derived within the framework of the kinematical theory, taking into account the divergence and wavelength-spread of the incident beam as well as the mosaicity of the crystal sample. The theoretical results can be applied to X-ray tube radiation as well as synchrotron radiation experiments. A 189.9° experimental CuKα \bar2\bar2\bar2 ω–ψ scan of diamond is compared with the corresponding theoretical multiple-diffraction pattern.
Treatment of grazing-incidence small-angle X-ray scattering data taken above the critical angle
Authors: Martorana A. , Longo A , d'Acapito F. , Maurizio C. , Cattaruzza E. , Gonella F.
Published: July 2002

The equations taking into account refraction at the sample surface in grazing-incidence small-angle X-ray scattering (GISAXS) when the angle between the incoming beam and the sample surface is slightly larger than the critical angle are derived and discussed. It is demonstrated that the refraction of both the incoming and the scattered beam at the sample surface affects the GISAXS pattern and that, when a planar bidimensional detector perpendicular to the incoming beam is used, the effect depends on the azimuthal detector angle. The smearing of the pattern depending on the size of the illuminated sample area in grazing incidence is estimated by simulations with Cauchy functions of different widths. The possibility of integrating the recorded intensities over a suitable azimuthal angular range and then of making the correction for refraction is also analysed, employing simulations involving the intensity function of monodisperse interacting hard spheres. As a case study, the refraction correction is applied to the investigation of a Cu–Ni implant on silica glass.
The SAXS/WAXS software system of the DUBBLE CRG beamline at the ESRF
Authors: Homan E. , Konijnenburg M. , Ferrero C. , Ghosh R. E. , Dolbnya I. P. , Bras W.
Published: July 2002

The small/wide-angle X-ray scattering (SAXS/WAXS) system on the DUBBLE CRG beamline at the ESRF is used for both static and time-resolved measurements. The integrated system developed for control and data reduction deals effectively with the high rates of incoming data from the different detector systems, as well as the presentation of results for the user. To ensure that the data may be used directly by a wide range of packages, they may be recorded in a number of output formats, thus serving as a practical test bed where developing standards may be compared and contrasted. The software system implements proposals raised at the canSAS meetings to promote a limited set of standard data formats for small-angle scattering studies. The system presented can cope with a volume of results in excess of 10 Gbytes of data per experiment and shows the advantages achieved by minimizing the dependence on raw-data formats.
SIR2000-N, a program for large and small crystal structures
Authors: Burla Maria Cristina , Camalli Mercedes , Carrozzini Benedetta , Cascarano Giovanni Luca , Giacovazzo Carmelo , Polidori Giampiero , Spagna Riccardo
Published: July 2002

The programSIR2000[Burlaet al.(2000).Acta Cryst.A56, 451–457] was designed for theab initiosolution of macromolecular crystal structures, provided that the data resolution is no lower than 1.2 Å. As the phasing procedure ofSIR2000is rather time consuming, modifications have been introduced to improve its efficiency and to make it additionally suitable for small molecules (new versionSIR2000-N). The role of the tangent refinement in modern phasing procedures is enlightened.
Teaching diffraction using computer simulations over the Internet
Authors: Proffen Th. , Neder R. B. , Billinge S. J. L.
Published: July 2002

Computer simulations are a versatile tool to enhance the teaching of diffraction physics and related crystallographic topics to students of chemistry, materials science, physics and crystallography. Interactive computer simulations are presented, which have been added to a World Wide Web (WWW) based tutorial. A simple WWW interface is used to choose appropriate values for selected simulation parameters. The resulting structure and diffraction pattern are then plotted on the screen. Simulated structures range from a single atom to complex disordered or modulated structures. The simple interface requires no special computing knowledge and allows students to explore systematically the relationship between a real-space structure and the corresponding diffraction pattern. The large function set of the underlying simulation program (DISCUS) makes it easy to tailor the tutorial to a given syllabus by modifying or extending the current interactive examples.
High-resolution diffraction using Larmor precession of polarized neutrons
Authors: Rekveldt M. Theo , Kraan Wicher , Keller Thomas
Published: July 2002

A new Larmor precession device, consisting of two separate precession modules, is introduced. It operates as a high-resolution neutron diffractometer, without the need for a highly collimated beam, necessary in conventional high-resolution neutron diffraction. The same instrument operates in different modes as an effective small-angle scattering device or accurately determines the line profile, the lattice plane orientation or the angular spread in crystal orientations. A dramatic intensity gain can be obtained in all applications discussed, compared with the conventional analogues, owing to the possibility to use a relaxed wavelength and angular resolution. Experiments in the high-resolution diffraction mode on Si and Al are discussed.
Application of normal probability plot analysis to lutetium orthoborate factors and parameters
Authors: Abrahams S. C. , Bernstein J. L. , Keve E. T.
Published: July 2002

The methods of normal probability plot analysis have been applied to two nearly complete sets of structure factors (F
meas) and the corresponding objectively assigned standard deviations (σF
meas) obtained by diffractometer measurement with two different crystals of lutetium orthoborate. The least-squares derived positional and thermal vibration parameters are shown to be too small by a factor of 1.8, and the σF
meas to be overestimated by a factor of 1.55. The two sets of F
meas are found to contain a small but parallel bias. The lattice constants of rhombohedral calcite-type LuBO3 are measured as a

H
= 4.91538±0.00002 Å and cH
= 16.21200±0.00003 Å at 298°K, with six formulas in the unit cell, space group R\overline 3c. The Lu–O distance in this six-coordinated Lu compound is 2.240±0.002 Å (corrected standard deviation). The B–O distance in the BO3 triangular groups is 1.370±0.005 Å. The characteristic Θ temperature is estimated as 446±19°K.
Stacking disorder in martensite with 3R close-packed structure
Authors: Kajiwara S.
Published: July 2002

The shift and diffuseness of electron diffraction spots due to stacking faults were observed in martensite crystals with 3R close-packed structure. The analysis of these shifted and diffused spots by the Kakinoki–Komura theory shows that 3R structure martensite is faulted in such a way that its stacking sequence changes to that of the 9R close-packed structure.
Crystal data for some tetraethylammonium salt hydrates
Authors: Lam Y.-S. , Mak T. C. W.
Published: July 2002

Stoichiometries and crystal data are reported for the hydrates of tetraethylammonium fluoride, chloride, acetate, and sulfate.
The small-angle neutron scattering spectrometer at the University of Missouri research reactor
Authors: Mildner D. F. R. , Berliner R. , Pringle O. A. , King J. S.
Published: July 2002

A small-angle neutron scattering (SANS) spectrometer has been constructed at the University of Missouri Research Reactor Facility (MURR). The design of the MURR–SANS is unusual in that the size of the reactor containment building constrains the flight path to be vertical. This is achieved by Bragg scattering upward through 90° from a set of slightly misaligned pyrolytic graphite crystals to provide a neutron beam at 4.75 Å with a wavelength spread of approximately 4.1%. The beam incident on the sample is defined by two matched variable apertures located either 3.0 or 4.5 m apart. The evacuated scattered flight path is designed with removable extensions to match the primary flight path in length. The instrument has an automatic sample handling capability provided by its own dedicated PDP 11/03 computer. The detector is a large assembly of commercially available linear 3He detectors as an economic alternative to a crossed-wire two-dimensional multi-detector. An array of 43 position-sensitive proportional counters, 24 in (609.6 mm) long and 0.5 in (12.7 mm) in diameter, using charge division gives a spatial resolution of 5 x 12.7 mm. The area-averaged detector efficiency is about 84% at a wavelength of 4.75 Å. The range of scattering vectors that can be measured is 0.005 < Q< 0.15 Å−1. The instrument is well suited to a wide variety of experiments on specimens having characteristic dimensions between 20 and 500 Å. MURR–SANS is designed as a user-oriented facility which provides both reasonable resolution and intensity on sample at a modest cost, and forms part of a neutron scattering center.
Deconvolution analysis in membrane diffraction using the modulus of the continuous Fourier transform
Authors: Worthington C. R.
Published: July 2002

A method of deconvolution using the modulus of the continuous Fourier transform of the unit cell is described. This method differs from previous deconvolution methods in membrane diffraction in that calculations are carried out in reciprocal space. The modulus profile is obtained from the continuous intensity transform which is itself the Fourier transform of the autocorrelation function. Sampling theorem methods are used to reconstruct the continuous Fourier transform of the unit cell. The various phase choices are examined and compared. In membrane diffraction, the autocorrelation function is derived in two distinct situations: when the interference function is broad as in the case of a few unit cells and when the membrane systems contain wide regions of constant electron density. It is concluded that, in the first situation, the derived autocorrelation function contains missing information and is incorrect. On the other hand, in the second situation, the derived autocorrelation function is a good representation of the true autocorrelation function.
Application of the method of moments to X-ray diffraction line profiles from paracrystals: Native cellulose fibres
Authors: Mitra G. B. , Mukherjee P. S.
Published: July 2002

The `microparacrystallite size' and `distortion parameter' of delignified ramie, hemp and jute have been determined – with the assumption that these materials are paracrystalline in nature – with the second and fourth central moments of X-ray diffraction line profiles. A new method of curvature correction has been developed. Background as well as non-additivity corrections have also been accounted for. Theories of determining the `microparacrystallite size' and the `distortion parameter' from single reflections independently from each of these two central moments have been developed, and described. Determination of these two parameters for several directions in the samples studied have been based on the above work. It has been shown that, in conformity with the recent findings of Hosemann & Balta Calleja [Ber. Bunsenges. Phys. Chem. (1980), 84, 91], the larger the paracrystalline distortion the smaller is the `microparacrystallite size'.
Application of in situ synchrotron X-ray topography to the study of a solid-phase transformation: crystallography of the transition in pure titanium
Authors: Jourdan C. , Gastaldi J.
Published: July 2002

With a high-temperature camera, designed for in situ synchrotron radiation X-ray topography, the crystallography of the α → β transition in titanium has been studied.
Profile refinement of powder diffraction patterns using the Voigt function
Authors: David W. I. F. , Matthewman J. C.
Published: July 2002

The Voigt function has been incorporated as a peak-shape description into a program for the refinement of constant-wavelength X-ray and neutron diffraction patterns. The results obtained for neutron diffraction are encouraging and indicate that the Voigt function describes the symmetrical component of the profile peak shape to high accuracy even in the presence of substantial line broadening from particle-size effects. In contrast with approximations to the Voigt function, such as the pseudo-Voigt and Pearson VII functions, the present treatment allows the angular dependences of line-broadening effects resulting from particle-size and instrumental contributions to be coded independently from each other in the Rietveld technique. The present treatment, which details improvements to the symmetrical component of the peak shape, does not offer a fully rigorous description of the peak shape as asymmetry corrections such as those given by Howard [J. Appl. Cryst. (1982), 15, 615–620] are not included.
Anomalous small-angle-X-ray scattering on Al–Zn and Al–Zn–Ag alloys
Authors: Lyon O. , Hoyt J. J. , Pro R. , Davis B. E. C. , Clark B. , de Fontaine D. , Simon J. P.
Published: July 2002

Anomalous small-angle scattering (ASAXS) spectra from Al–Zn and Al–Zn–Ag alloys have been recorded at the Stanford Synchrotron Radiation Laboratory (SSRL). The data were obtained at different energies close to the Zn absorption edge. For the binary alloy, the ASAXS intensities follow quantitatively the variation in the atomic scattering factor of zinc. For the ternary alloys, the anomalous effect decreases when the Zn content decreases. Although only weighted sums of the partial structure functions could be determined, it is shown that the results are consistent with the `two-phase' unmixing model and the direction of tie lines of the metastable miscibility gap has been determined. A new method for analyzing ASAXS data for two absorption edges is proposed.
Universal crystal cooling device for precession cameras, rotation cameras and diffractometers
Authors: Hajdu J. , McLaughlin P. J. , Helliwell J. R. , Sheldon J. , Thompson A. W.
Published: July 2002

A versatile crystal cooling device is described for macromolecular crystallographic applications in the 290 to 80 K temperature range. It utilizes a fluctuation-free cold-nitrogen-gas supply, an insulated Mylar crystal cooling chamber and a universal ball joint, which connects the cooling chamber to the goniometer head and the crystal. The ball joint is a novel feature over all previous designs. As a result, the device can be used on various rotation cameras, precession cameras and diffractometers. The lubrication of the interconnecting parts with graphite allows the cooling chamber to remain stationary while the crystal and goniometer rotate. The construction allows for 360° rotation of the crystal around the goniometer axis and permits any settings on the arcs and slides of the goniometer head (even if working at 80 K). There are no blind regions associated with the frame holding the chamber. Alternatively, the interconnecting ball joint can be tightened and fixed. This results in a set up similar to the construction described by Bartunik & Schubert [J. Appl. Cryst. (1982), 15, 277–231], where the cooling chamber rotates with the crystal. The flexibility of the systems allows for the use of the device on most cameras or diffractometers. This device has been installed at the protein crystallographic stations of the Synchrotron Radiation Source at Daresbury Laboratory and in the Laboratory of Molecular Biophysics, Oxford. Several data sets have been collected with processing statistics typical of data collected without a cooling chamber. Tests using the full white beam of the synchrotron also look promising.
Crystal orientation and X-ray pattern prediction routines for area-detector diffractometer systems in macromolecular crystallography
Authors: Messerschmidt A. , Pflugrath J. W.
Published: July 2002

Routines for crystal orientation and the prediction of expected reflections which are part of the data collection software package MADNES for area-detector diffractometer systems in macromolecular crystallography are described. This package is designed to be area-detector-system independent. In addition to refining crystal cell lengths and angles, crystal orientation, crystal-to-detector distance, position of the primary beam on the detector, and rotation of the detector around the primary beam, the orientation routine also refines the effective mosaic spread of the crystal, the beam inclination angle μand the detector tilt angle τ. A prealignment procedure is described for rapid rough orientation of the crystal. The routines are written in Fortran 77 in a modular way, so that they may be used independently of MADNES and each other.