bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative Analysis of Noncoding Regions of 77 Orthologous Mouse and Human Gene Pairs
Authors: Jareborg Niclas , Birney Ewan , Durbin Richard
Published: July 2002

A data set of 77 genomic mouse/human gene pairs has been compiled from the EMBL nucleotide database, and their corresponding features determined. This set was used to analyze the degree of conservation of noncoding sequences between mouse and human. A new alignment algorithm was developed to cope with the fact that large parts of noncoding sequences are not alignable in a meaningful way because of genetic drift. This new algorithm, DNA Block Aligner (DBA), finds colinear-conserved blocks that are flanked by nonconserved sequences of varying lengths. The noncoding regions of the data set were aligned with DBA. The proportion of the noncoding regions covered by blocks >60% identical was 36% for upstream regions, 50% for 5′ UTRs, 23% for introns, and 56% for 3′ UTRs. These blocks of high identity were more or less evenly distributed across the length of the features, except for upstream regions in which the first 100 bp upstream of the transcription start site was covered in up to 70% of the gene pairs. This data set complements earlier sets on the basis of cDNA sequences and will be useful for further comparative studies.

[This paper contains supplementary data that can be found at http://www.genome.com.]
Tactile Experience Induces c-fos Expression in Rat Barrel Cortex
Authors: Filipkowski Robert K. , Rydz Marek , Berdel Bozena , Morys Janusz , Kaczmarek Leszek
Published: July 2002

Understanding gene expression that is responsive to sensory stimulation is central to elucidate molecular mechanisms underlying neuronal plasticity. In this study we demonstrate two new methods of stimulating whiskers that provide major sensory input to rat neocortex. In the first paradigm, animals were placed on the top of a cylinder and their vibrissae were brushed by hand. In the second paradigm, animals were placed for a brief period of time into a new, wired cage resulting in vibrissae stimulation when they explored the new environment. Both approaches induced c-Fos expression in barrel cortex corresponding to the stimulated vibrissae, especially in layer IV. Layers II/III and V/VI also showed c-Fos induction, but there were no detectable changes in layer VIb. The majority of c-Fos-expressing cells are probably not inhibitory neurons, because they do not show parvalbumin staining. Both paradigms, in contrast to the previous methods, are simple to use and do not require anesthesia, restraint of animals, or elaborate experimental setups.
Phloem Transport of Fructans in the Crassulacean Acid Metabolism Species Agave deserti1
Authors: Wang Ning , Nobel Park S.
Published: July 2002

Four oligofructans (neokestose, 1-kestose, nystose, and an un-identified pentofructan) occurred in the vascular tissues and phloem sap of mature leaves of Agave deserti. Fructosyltransferases (responsible for fructan biosynthesis) also occurred in the vascular tissues. In contrast, oligofructans and fructosyltransferases were virtually absent from the chlorenchyma, suggesting that fructan biosynthesis was restricted to the vascular tissues. On a molar basis, these oligofructans accounted for 46% of the total soluble sugars in the vascular tissues (sucrose [Suc] for 26%) and for 19% in the phloem sap (fructose for 24% and Suc for 53%). The Suc concentration was 1.8 times higher in the cytosol of the chlorenchyma cells than in the phloem sap; the nystose concentration was 4.9 times higher and that of pentofructan was 3.2 times higher in the vascular tissues than in the phloem sap. To our knowledge, these results provide the first evidence that oligofructans are synthesized and transported in the phloem of higher plants. The polymer-trapping mechanism proposed for dicotyledonous C3 species may also be valid for oligofructan transport in monocotyledonous species, such as A. deserti, which may use a symplastic pathway for phloem loading of photosynthates in its mature leaves.
Mapping Intercellular CO2 Mole Fraction (Ci) inRosa rubiginosaLeaves Fed with Abscisic Acid by Using Chlorophyll Fluorescence Imaging1
Authors: Meyer Sylvie , Genty Bernard
Published: July 2002

Imaging of photochemical yield of photosystem II (PSII) computed from leaf chlorophyll fluorescence images and gas-exchange measurements were performed on Rosa rubiginosa leaflets during abscisic acid (ABA) addition. In air ABA induced a decrease of both the net CO2 assimilation (An) and the stomatal water vapor conductance (gs). After ABA treatment, imaging in transient nonphotorespiratory conditions (0.1% O2) revealed a heterogeneous decrease of PSII photochemical yield. This decline was fully reversed by a transient high CO2 concentration (7400 μmol mol−1) in the leaf atmosphere. It was concluded that ABA primarily affected An by decreasing the CO2 supply at ribulose-1,5-bisphosphate carboxylase/oxygenase. Therefore, the An versus intercellular mole fraction (Ci) relationship was assumed not to be affected by ABA, and images ofCi and gs were constructed from images of PSII photochemical yield under nonphotorespiratory conditions. The distribution ofgs remained unimodal following ABA treatment. A comparison of calculations of Ci from images and gas exchange in ABA-treated leaves showed that the overestimation of Ci estimated from gas exchange was only partly due to heterogeneity. This overestimation was also attributed to the cuticular transpiration, which largely affects the calculation of the leaf conductance to CO2, when leaf conductance to water is low.
ΔpH-Dependent Photosystem II Fluorescence Quenching Induced by Saturating, Multiturnover Pulses in Red Algae1
Authors: Delphin Estelle , Duval Jean-Claude , Etienne Anne-Lise , Kirilovsky Diana
Published: July 2002

We have previously shown that in the red alga Rhodella violacea, exposure to continuous low intensities of light 2 (green light) or near-saturating intensities of white light induces a ΔpH-dependent PSII fluorescence quenching. In this article we further characterize this fluorescence quenching by using white, saturating, multiturnover pulses. Even though the pulses are necessary to induce the ΔpH and the quenching, the development of the latter occurred in darkness and required several tens of seconds. In darkness or in the light in the presence of 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone, the dissipation of the quenching was very slow (more than 15 min) due to a low consumption of the ΔpH, which corresponds to an inactive ATP synthase. In contrast, under far-red illumination or in the presence of 3-(3,4-dichlorophenyl)-1,1′-dimethylurea (only in light), the fluorescence quenching relaxed in a few seconds. The presence of N,N′-dicyclohexyl carbodiimide hindered this relaxation. We propose that the quenching relaxation is related to the consumption of ΔpH by ATP synthase, which remains active under conditions favoring pseudolinear and cyclic electron transfer.
Limonene Synthase, the Enzyme Responsible for Monoterpene Biosynthesis in Peppermint, Is Localized to Leucoplasts of Oil Gland Secretory Cells1
Authors: Turner Glenn , Gershenzon Jonathan , Nielson Erik E. , Froehlich John E. , Croteau Rodney
Published: July 2002

Circumstantial evidence based on ultrastructural correlation, specific labeling, and subcellular fractionation studies indicates that at least the early steps of monoterpene biosynthesis occur in plastids. (4S)-Limonene synthase, which is responsible for the first dedicated step of monoterpene biosynthesis in mint species, appears to be translated as a preprotein bearing a long plastidial transit peptide. Immunogold labeling using polyclonal antibodies raised to the native enzyme demonstrated the specific localization of limonene synthase to the leucoplasts of peppermint (Mentha× piperita) oil gland secretory cells during the period of essential oil production. Labeling was shown to be absent from all other plastid types examined, including the basal and stalk cell plastids of the secretory phase glandular trichomes. Furthermore, in vitro translation of the preprotein and import experiments with isolated pea chloroplasts were consistent in demonstrating import of the nascent protein to the plastid stroma and proteolytic processing to the mature enzyme at this site. These experiments confirm that the leucoplastidome of the oil gland secretory cells is the exclusive location of limonene synthase, and almost certainly the preceding steps of monoterpene biosynthesis, in peppermint leaves. However, succeeding steps of monoterpene metabolism in mint appear to occur outside the leucoplasts of oil gland cells.
A Specific β-Glucosidase-Aggregating Factor Is Responsible for the β-Glucosidase Null Phenotype in Maize
Authors: Esen Asim , Blanchard David J.
Published: July 2002

Maize (Zea mays L.) β-glucosidase was extracted from shoots of a wild-type (K55) and a “null” (H95) maize genotype. Enzyme activity assays and electrophoretic data showed that extracts from the null genotype had about 10% of the activity present in the normal genotype. Zymograms of the null genotype were devoid of any activity bands in the resolving gel, but had a smeared zone of activity in the stacking gel after native polyacrylamide gel electrophoresis. When extracts were made with buffers containing 0.5% to 2% sodium dodecyl sulfate, the smeared activity zone entered the resolving gel as a distinct band. These data indicated that the null genotypes have β-glucosidase activity, but the enzyme occurs as insoluble or poorly soluble large quaternary complexes mediated by a β-glucosidase-aggregating factor (BGAF). BGAF is a 35-kD protein and binds specifically to β-glucosidase and renders it insoluble during extraction. BGAF also precipitates β-glucosidase that is added exogenously to supernatant fluids of the null tissue extracts. The specific β-glucosidase-aggregating activity of BGAF is unequivocally demonstrated. These data clearly show that the monogenic inheritance reported for the null alleles at the β-glucosidase gene is actually for the BGAF protein, and BGAF is solely responsible for β-glucosidase aggregation and insolubility and, thus, the apparent null phenotype.
Plasma Membrane Intrinsic Proteins from Maize Cluster in Two Sequence Subgroups with Differential Aquaporin Activity
Authors: Chaumont François , Barrieu François , Jung Rudolf , Chrispeels Maarten J.
Published: July 2002

The transport of water through membranes is regulated in part by aquaporins or water channel proteins. These proteins are members of the larger family of major intrinsic proteins (MIPs). Plant aquaporins are categorized as either tonoplast intrinsic proteins (TIPs) or plasma membrane intrinsic proteins (PIPs). Sequence analysis shows that PIPs form several subclasses. We report on the characterization of three maize (Zea mays) PIPs belonging to the PIP1 and PIP2 subfamilies (ZmPIP1a, ZmPIP1b, and ZmPIP2a). The ZmPIP2a clone has normal aquaporin activity in Xenopus laevisoocytes. ZmPIP1a and ZmPIP1b have no activity, and a review of the literature shows that most PIP1 proteins identified in other plants have no or very low activity in oocytes. Arabidopsis PIP1 proteins are the only exception. Control experiments show that this lack of activity of maize PIP1 proteins is not caused by their failure to arrive at the plasma membrane of the oocytes. ZmPIP1b also does not appear to facilitate the transport of any of the small solutes tried (glycerol, choline, ethanol, urea, and amino acids). These results are discussed in relationship to the function and regulation of the PIP family of aquaporins.
Five Geranylgeranyl Diphosphate Synthases Expressed in Different Organs Are Localized into Three Subcellular Compartments in Arabidopsis
Authors: Okada Kazunori , Saito Takeshi , Nakagawa Tsuyoshi , Kawamukai Makoto , Kamiya Yuji
Published: July 2002

Geranylgeranyl diphosphate (GGPP) is the precursor for the biosynthesis of gibberellins, carotenoids, chlorophylls, isoprenoid quinones, and geranylgeranylated proteins in plants. There is a small gene family for GGPP synthases encoding five isozymes and one related protein in Arabidopsis, and all homologs have a putative localization signal to translocate into specific subcellular compartments. Using a synthetic green fluorescent protein (sGFP), we studied the subcellular localization of these GGPP synthases. When these fusion proteins were expressed by the cauliflower mosaic virus 35S promoter in Arabidopsis, GGPS1-sGFP and GGPS3-sGFP proteins were translocated into the chloroplast, GGPS2-sGFP and GGPS4-sGFP proteins were localized in the endoplasmic reticulum, and the GGPS6-sGFP protein was localized in the mitochondria. Both GGPS1 and GGPS3 proteins synthesized in vitro were taken up into isolated intact pea chloroplasts and processed to the mature form. RNA-blot and promoter-β-glucuronidase (GUS) analysis showed that these GGPP synthases genes are organ-specifically expressed in Arabidopsis.GGR and GGPS1 were ubiquitously expressed, while GGPS2, GGPS3, andGGPS4 were expressed specifically in the flower, root, and flower, respectively. These results suggest that each GGPP synthase gene is expressed in different tissues during plant development and GGPP is synthesized by the organelles themselves rather than being transported into the organelles. Therefore, we predict there will be specific pathways of GGPP production in each organelle.
Deletion of the Nitrate Reductase N-Terminal Domain Still Allows Binding of 14-3-3 Proteins but Affects Their Inhibitory Properties
Authors: Provan Fiona , Aksland Liv-Margareth , Meyer Christian , Lillo Cathrine
Published: July 2002

Nitrate reductase (NR) is post-translationally regulated by phosphorylation and binding of 14-3-3 proteins. Deletion of 56 amino acids in the amino-terminal domain of NR was previously shown to impair this type of regulation in tobacco (Nicotiana plumbaginifolia) (L. Nussaume, M. Vincentez, C. Meyer, J.-P. Boutin, M. Caboche [1995] Plant Cell 7: 611–621), although both full-length NR and deleted NR (ΔNR) appeared to be phosphorylated in darkness (C. Lillo, S. Kazazaic, P. Ruoff, C. Meyer [1997] Plant Physiol 114: 1377–1383). We show here that in the presence of Mg2+ and phosphatase inhibitors, NR and endogenous 14-3-3 proteins copurify through affinity chromatography. Assay of NR activity and western blots showed that endogenous 14-3-3 proteins copurified with both NR and ΔNR. Electron transport in the heme-binding domain of ΔNR was inhibited by Mg2+/14-3-3, whereas this was not the case for NR. This may indicate a different way of binding for 14-3-3 in the ΔNR compared with NR. The ΔNR was more labile than NR, in vitro. Lability was ascribed to the molybdopterin binding domain, and apparently an important function of the 56 amino acids is stabilization of this domain.
Analysis of Gene Promoters for Two Tomato Polygalacturonases Expressed in Abscission Zones and the Stigma
Authors: Hong Seung-Beom , Sexton Roy , Tucker Mark L.
Published: July 2002

The tomato (Lycopersicon esculentum cv Ailsa Craig) polygalacturonase genes TAPG1(LYCes;Pga1;2) and TAPG4(LYCes;Pga1;5) are abundantly expressed in both abscission zones and the pistils of mature flowers. To further investigate the spatial and temporal expression patterns for these genes, the TAPG gene promoters were ligated to β-glucuronidase (GUS) reporter genes and transformed into tomato. GUS expression with both constructs was similar and entirely consistent with the expression patterns of the native gene transcripts. GUS activity was observed in the weakening abscission zones of the leaf petiole, flower and fruit pedicel, flower corolla, and fruit calyx. In leaf petiole and flower pedicel zones this activity was enhanced by ethylene and inhibited by indole-3-acetic acid. On induction of abscission with ethylene, GUS accumulation was much earlier in TAPG4:GUS than in TAPG1:GUS transformants. Moreover, TAPG4:GUS staining appeared to predominate in the vascular bundles relative to surrounding cortex cells whereas TAPG1:GUS was more evenly distributed across the separation layer. Like the native genes, GUS was also expressed in the stigma. Activity was not apparent in pistils until the flowers had opened and was confined to the stigma and style immediately proximal to it. A minimal promoter construct consisting of a 247-bp 5′-upstream element from TAPG1 was found to be sufficient to direct GUS expression in both abscission zones and the stigma.
Analysis of the Expression of CLA1, a Gene That Encodes the 1-Deoxyxylulose 5-Phosphate Synthase of the 2-C-Methyl-d-Erythritol-4-Phosphate Pathway in Arabidopsis
Authors: Estévez Juan M. , Cantero Araceli , Romero Cynthia , Kawaide Hiroshi , Jiménez Luis F. , Kuzuyama Tomohisa , Seto Haruo , Kamiya Yuji , León Patricia
Published: July 2002

The discovery of the 2-C-methyl-d-erythritol-4-phosphate pathway for the biosynthesis of isoprenoids raises the important question of the nature and regulation of the enzymes involved in this pathway.CLA1, a gene previously isolated from Arabidopsis, encodes the first enzyme of the 2-C-methyl-d-erythritol-4-phosphate pathway, 1-deoxy-d-xylulose-5-phosphate synthase. We demonstrate this enzyme activity by complementation of the cla1-1mutant phenotype and by direct enzymatic assays. Based on mRNA and protein expression patterns this enzyme is expressed mainly in developing photosynthetic and non-photosynthetic tissues. The β-glucuronidase expression pattern driven from theCLA1 gene regulatory region supports the northern and protein data while also showing that this gene has some level of expression in most tissues of the plant. A mutation in theCLA1 gene interferes with the normal development of chloroplasts and etioplasts, but does not seem to affect amyloplast structure. Microscopic analysis also shows a pleiotropic effect of theCLA1 gene mutation in mesophyll tissue formation.
Characterization of Arabidopsis Acid Phosphatase Promoter and Regulation of Acid Phosphatase Expression
Authors: Haran Shoshan , Logendra Sithes , Seskar Mirjana , Bratanova Margarita , Raskin Ilya
Published: July 2002

The expression and secretion of acid phosphatase (APase) was investigated in Indian mustard (Brassica juncea L. Czern.) plants using sensitive in vitro and activity gel assays. Phosphorus (P) starvation induced two APases in Indian mustard roots, only one of which was secreted. Northern-blot analysis indicated transcriptional regulation of APase expression. Polymerase chain reaction and Southern-blot analyses revealed two APase homologs in Indian mustard, whereas in Arabidopsis, only one APase homolog was detected. The Arabidopsis APase promoter region was cloned and fused to the β-glucuronidase (GUS) and green fluorescent protein (GFP) reporter genes. GUS expression was first evident in leaves of the P-starved Arabidopsis plants. In P-starved roots, the expression of GUS initiated in lateral root meristems followed by generalized expression throughout the root. GUS expression diminished with the addition of P to the medium. Expression of GFP in P-starved roots also initiated in the lateral root meristems and the recombinant GFP with the APase signal peptide was secreted by the roots into the medium. The APase promoter was specifically activated by low P levels. The removal of other essential elements or the addition of salicylic or jasmonic acids, known inducers of gene expression, did not activate the APase promoter. This novel APase promoter may be used as a plant-inducible gene expression system for the production of recombinant proteins and as a tool to study P metabolism in plants.
An Investigation of the Storage and Biosynthesis of Phenylpropenes in Sweet Basil
Authors: Gang David R. , Wang Jihong , Dudareva Natalia , Nam Kyoung Hee , Simon James E. , Lewinsohn Efraim , Pichersky Eran
Published: July 2002

Plants that contain high concentrations of the defense compounds of the phenylpropene class (eugenol, chavicol, and their derivatives) have been recognized since antiquity as important spices for human consumption (e.g. cloves) and have high economic value. Our understanding of the biosynthetic pathway that produces these compounds in the plant, however, has remained incomplete. Several lines of basil (Ocimum basilicum) produce volatile oils that contain essentially only one or two specific phenylpropene compounds. Like other members of the Lamiaceae, basil leaves possess on their surface two types of glandular trichomes, termed peltate and capitate glands. We demonstrate here that the volatile oil constituents eugenol and methylchavicol accumulate, respectively, in the peltate glands of basil lines SW (which produces essentially only eugenol) and EMX-1 (which produces essentially only methylchavicol). Assays for putative enzymes in the biosynthetic pathway leading to these phenylpropenes localized many of the corresponding enzyme activities almost exclusively to the peltate glands in leaves actively producing volatile oil. An analysis of an expressed sequence tag database from leaf peltate glands revealed that known genes for the phenylpropanoid pathway are expressed at very high levels in these structures, accounting for 13% of the total expressed sequence tags. An additional 14% of cDNAs encoded enzymes for the biosynthesis of S-adenosyl-methionine, an important substrate in the synthesis of many phenylpropenes. Thus, the peltate glands of basil appear to be highly specialized structures for the synthesis and storage of phenylpropenes, and serve as an excellent model system to study phenylpropene biosynthesis.
Cavitation Fatigue. Embolism and Refilling Cycles Can Weaken the Cavitation Resistance of Xylem
Authors: Hacke Uwe G. , Stiller Volker , Sperry John S. , Pittermann Jarmila , McCulloh Katherine A.
Published: July 2002

Although cavitation and refilling cycles could be common in plants, it is unknown whether these cycles weaken the cavitation resistance of xylem. Stem or petiole segments were tested for cavitation resistance before and after a controlled cavitation-refilling cycle. Cavitation was induced by centrifugation, air drying of shoots, or soil drought. Except for droughted plants, material was not significantly water stressed prior to collection. Cavitation resistance was determined from “vulnerability curves” showing the percentage loss of conductivity versus xylem pressure. Two responses were observed. “Resilient” xylem (Acer negundo and Alnus incanastems) showed no change in cavitation resistance after a cavitation-refilling cycle. In contrast, “weakened” xylem (Populus angustifolia, P. tremuloides, Helianthus annuusstems, and Aesculus hippocastanum petioles) showed considerable reduction in cavitation resistance. Weakening was observed whether cavitation was induced by centrifugation, air dehydration, or soil drought. Observations from H. annuus showed that weakening was proportional to the embolism induced by stress. Air injection experiments indicated that the weakened response was a result of an increase in the leakiness of the vascular system to air seeding. The increased air permeability in weakened xylem could result from rupture or loosening of the cellulosic mesh of interconduit pit membranes during the water stress and cavitation treatment.
Function and Dynamics of Auxin and Carbohydrates during Earlywood/Latewood Transition in Scots Pine
Authors: Uggla Claes , Magel Elisabeth , Moritz Thomas , Sundberg Björn
Published: July 2002

In temperate regions the annual pattern of wood development is characterized by the formation of radially narrow and thick walled latewood cells. This takes place at the later part of the growing season when cambial cell division declines. To gain new insight into the regulation of this process, micro-analytical techniques were used to visualize the distribution of indole-3-acetic acid (IAA), soluble carbohydrates, and activities of sucrose (Suc)-metabolizing enzymes across the cambial region tissues in Scots pine (Pinus sylvestris). The total amount of IAA in the cambial region did not change with latewood initiation. But its radial distribution pattern was altered, resulting in an increased concentration in the cambial meristem and its recent derivatives. Thus, initiation of latewood formation and cessation of cambial cell division is not a consequence of decreased IAA concentrations in dividing and expanding cells. Rather, IAA most likely has a role in defining the altered developmental pattern associated with latewood formation. Carbohydrates and enzyme activities showed distinctive radial distribution patterns. Suc peaked in the phloem and decreased sharply to low levels across the cambial zone, whereas fructose and glucose reached their highest levels in the maturing tracheids. Suc synthase was the dominating Suc cleaving enzyme with a peak in the secondary wall-forming tracheids and in the phloem. Soluble acid invertase peaked in dividing and expanding cells. Suc-phosphate synthase had its highest activities in the phloem. Activities of cell wall bound invertase were low. The absence of major seasonal variations indicates that carbohydrate availability is not a trigger for latewood initiation. However, steep concentration gradients of the sugars suggest a role for sugar signaling in vascular development.
AtCSLD3, A Cellulose Synthase-Like Gene Important for Root Hair Growth in Arabidopsis
Authors: Wang Xuan , Cnops Gerda , Vanderhaeghen Rudy , De Block Sabine , Van Montagu Marc , Van Lijsebettens Mieke
Published: July 2002

A member of the cellulose synthase-like (subfamily D) gene family of Arabidopsis, AtCSLD3, has been identified by T-DNA tagging. The analysis of the corresponding mutant,csld3-1, showed that the AtCSLD3 gene plays a role in root hair growth in plants. Root hairs grow in phases: First a bulge is formed and then the root hair elongates by polarized growth, the so-called “tip growth.” In the mutant, root hairs were initiated at the correct position and grew into a bulge, but their elongation was severely reduced. The tips of the csld3-1root hairs easily leaked cytoplasm, indicating that the tensile strength of the cell wall had changed at the site of the tip. Based on the mutant phenotype and the functional conservation between CSLD3 and the genuine cellulose synthase proteins, we hypothesized that the CSLD3 protein is essential for the synthesis of polymers for the fast-growing primary cell wall at the root hair tip. The distinct mutant phenotype and the ubiquitous expression pattern indicate that the CSLD3 gene product is only limiting at the zone of the root hair tip, suggesting particular physical properties of the cell wall at this specific site of the root hair cell.
First results from a macromolecular crystallography system with a polycapillary collimating optic and a microfocus X-ray generator
Authors: Gubarev Mikhail , Ciszak Ewa , Ponomarev Igor , Gibson Walter , Joy Marshall
Published: July 2002

The design and performance of a high-flux X-ray crystallography system, optimized for diffraction measurements from small macromolecular crystals, is described. This system combines a microfocus X-ray generator [40 µm full width at half-maximum (FWHM) spot size at a power level of 40 W] and a short focal length (F= 2.6 mm) polycapillary collimating optic, and produces a small-diameter quasi-parallel X-ray beam. Measurements of the X-ray flux, divergence and spectral purity of the resulting X-ray beam are presented. The X-ray flux through an aperture of 250 µm diameter produced by the microfocus system is 16 times higher than that from a 3.15 kW rotating-anode generator equipped with a pyrolytic graphite monochromator. Diffraction data from lysozyme test crystals collected with the microfocus X-ray system are of high quality and can be reduced with standard crystallographic software, yielding an overall merging factorRsym≤ 6%. Significant additional improvements in flux are possible, and plans for achieving these goals are discussed.
High-energy X-ray diffuse scattering using Weissenberg flat-cone geometry
Authors: Butler B. D. , Haeffner D. R. , Lee P. L. , Welberry T. R.
Published: July 2002

A technique for the measurement of diffuse X-ray scattering on individual reciprocal-space planes using high-energy X-ray photons is described. The method is demonstrated using a disordered crystal of the compound TlSbOGeO4and compared to data collected with a sealed-tube Cu anode source. Measurements were made on a synchrotron undulator beamline at an energy of 45 keV using Weissenberg flat-cone geometry and a storage phosphor (image) plate to detect the scattered X-rays. Advantages of the method include: extension of the accessible diffraction space to both higherandlower wavevectors, the ability to use crystals of irregular shape without the need for complicated absorption corrections, less need to prepare sample surfaces carefully, and the ability to filter fluorescence simply.
Towards general diffractometry. III. Beyond the normal-beam geometry
Authors: Dera Przemysław , Katrusiak Andrzej
Published: July 2002

The concept of a general four-circle diffractometer has been realised by introducing axial misalignments into mathematical formulae describing the diffractometer geometry. The advantage of using the described diffractometer formalism for routine measurements is discussed. Transformations of the setting angles of the reflections between different diffractometers, as well as the propagation of errors arising from the misalignment of axes, are taken into account.
A new version of the method for analysing peak broadening caused by local tilt distribution in double-crystal X-ray diffraction measurements
Authors: Nakashima Kiichi
Published: July 2002

A new method of analysing X-ray peak broadening caused by local tilt distribution in mosaic structures is proposed for double-crystal X-ray diffraction measurements. In the new method, the dependence of whole peak profiles on various reflection indiceshklis analysed, whereas that of only the peak full width at half-maximum (FWHM) is analysed in a conventional broadening analysis. The theoretical formula tells us that not only the FWHM values but also the whole profiles become independent ofhklafter rescaling the horizontal axis Δθ of measured patterns to Δθ/cosθc, where θcis the angle between the (001) and (hkl) planes. A new criterion is proposed to judge whether X-ray peak broadening is caused by the local tilt distribution or not; the advantage provided by the new criterion, using whole peak profiles, is high accuracy in making this judgment. It is experimentally verified that thehklindependence holds in terms of whole peak profiles. The advantage of the method is demonstrated experimentally by applying it to InAsP/InGaAsP strained layer superlattice samples.
X-ray topographic dislocation contrast visible in reflections orthogonal to the Burgers vectors of axial screw dislocations in hexagonal silicon carbide
Authors: Vetter W. M. , Dudley M.
Published: July 2002

Contrast is associated with micropipes in X-ray topographs of SiC crystals obtained with prismatic reflections, representing an apparent violation of theg·b= 0 invisibility criterion. This is explained as a population of basal-plane dislocations with Burgers vectors of the setb= {\textstyle{1 \over 3}}〈11{\bar{2}}0〉 that occur in a high density within a few micrometers of the micropipes, below the resolution of X-ray topography. These basal-plane dislocations could be observed under an electron microscope. The presence of the surfaces of the micropipes influences the dislocation images in the topographs taken with prismatic reflections, often resulting in a band of light contrast along the axes of the micropipes.
Determination of the crystallized fractions of a largely amorphous multiphase material by the Rietveld method
Authors: Orlhac X. , Fillet C. , Deniard P. , Dulac A. M. , Brec R.
Published: July 2002

The Rietveld method has proved to be a very effective means to characterize and quantify the crystalline phases and the amorphous phase in glass ceramic materials using X-ray powder diffraction data. The technique was applied to a borosilicate glass of the type used for high-level nuclear-waste containment, in order to measure the proportions of the crystallized phases after heat treatment and, thus, to qualify the thermal stability of the glass. Six crystalline phases were analysed in this way in an almost entirely (>95 wt%) amorphous material after adding a known proportion of an internal standard (TiO2). The quantitative analyses were corrected to allow for microabsorption effects resulting from grain-size and absorption-contrast effects. In addition to the quantitative data, unit-cell parameters and site-occupancy refinements revealed solid-solution and substitution phenomena in the crystal.
A comparison of various commonly used correlation functions for describing total scattering
Authors: Keen David A.
Published: July 2002

Total scattering, an increasingly important crystallographic research area, is defined theoretically in terms of correlation functions. Different researchers use different definitions for these functions, frequently leading to confusion in the literature. Here, a consistent set of equations for total-scattering correlation functions are developed and explicitly compared with other, often encountered, definitions. It is hoped that this will lead to increased transparency for newcomers to the field of total scattering.
Elastic strain and stress determination by Rietveld refinement: generalized treatment for textured polycrystals for all Laue classes
Authors: Popa N. C. , Balzar D.
Published: July 2002

A novel approach to model diffraction line shifts caused by elastic residual or applied stresses in textured polycrystals is proposed. The model yields the complete strain and stress tensors as a function of crystallite orientation, as well as the average values of the macroscopic strain and stress tensors. It is particularly suitable for implementation in Rietveld refinement programs. The requirements on refinable parameters for all crystal Laue classes are given. The effects of sample symmetry are also included and the conditions for strain invariance to both the sample symmetries (texture and stress/strain) are discussed.
EXPGUI, a graphical user interface forGSAS
Authors: Toby Brian H.
Published: July 2002

A description and justification of theEXPGUIprogram is presented. This program implements a graphical user interface and shell for theGSASsingle-crystal and Rietveld package. Use of the Tcl/Tk scripting language allowsEXPGUIto be platform independent. Also included is a synopsis of how the program is implemented.
Integrating biocrystallography into traditional biology and chemistry curricula
Authors: Jaskólski Mariusz
Published: July 2002

New academic courses for teaching protein crystallography to biology and chemistry students have been developed. The general aim of the lecture courses is to introduce crystallographic terminology and modern diffraction methodology, to discuss the principles of macromolecular structure, to develop confidence in assessing macromolecular models, and to develop skills in extracting biostructural information from crystallographic literature as well as from bioinformatics resources available on the Internet. Emphasis on structural biology (chemists) or on crystallographic concepts and methodology (biologists) differs depending on the background of the students. In practical classes, the students work with real models of crystals and lattices, and use construction kits to build models of protein secondary structure. Diffraction images of oriented protein crystals are used for determination of unit-cell parameters. An Internet-based multiple-choice quiz is used for tests, self-assessment and practice.
MASSHA– a graphics system for rigid-body modelling of macromolecular complexes against solution scattering data
Authors: Konarev P. V. , Petoukhov M. V. , Svergun D. I.
Published: July 2002

A program,MASSHA, for three-dimensional rendering and rigid-body refinement is presented. The program allows display and manipulation of high-resolution atomic structures and low-resolution models represented as smooth envelopes or ensembles of beads.MASSHAis coupled with a computational module to align structural models of different nature and resolution automatically. The main feature is the possibility for rigid-body refinement of the quaternary structure of macromolecular complexes. If high- or low-resolution models of individual subunits are available, the complex can be constructed on the computer display and refined to fit the experimental solution scattering data.MASSHAprovides both interactive and automated refinement modes to position subunits in a heterodimeric complex (general case) and in a homodimeric complex with a twofold symmetry axis. Examples of application of the program (running on IBM PC compatible machines under Windows 9x/NT/2000) are given.
Estimation of errors in the measurement of unit-cell parameters. I. Statistical uncertainties of peak positions of powder diffraction lines determined by individual profile fitting
Authors: Toraya H.
Published: July 2002

A formula for estimating the statistical uncertainty of peak positions, determined by individual profile fitting, has been derived. The magnitude of the statistical uncertainty is given by (sum of peak profile intensities)−1/2× (full width at half-maximum) ×F×G×Q× (goodness-of-fit index). The factorFdepends on the shape of the diffraction profile; it becomes smaller by 40% when the profile shape changes from Lorentzian to Gaussian. The factorGrepresents the parameter correlation between the peak position and the parameter for profile asymmetry; it becomes unity when the profile shape is symmetric or the parameter for profile asymmetry is fixed during the least-squares fitting. The factorQdepends on the peak-to-background ratio. The formula was experimentally verified by using diffraction data sets for CeO2and Si powders. The statistical uncertainty is essentially based on the counting statistics and profile width. Therefore, the peak position of a strong and sharp peak in the low-angle region can be determined more precisely than that of a weak and broadened peak in the high-angle region. The formula provides a guideline for optimizing experimental parameters for required precision.
Micro X-ray diffraction on capillary powder samples: a novel and effective technique for overcoming preferred orientation
Authors: Bergese P. , Bontempi E. , Colombo I. , Depero L. E.
Published: July 2002

In past years, both experimental and analytical approaches have been developed for eliminating preferred orientation effects on powder X-ray diffraction patterns. The state of the art does not allow one to face the problem without difficult sample treatments, mechanical randomization, pole-figure study or pattern fitting based on the Rietveld approach. These methods are time consuming or need the knowledge of all the structural parameters, and, moreover, must be managed by specialized operators. Besides, none of the above techniques can be applied to powder samples of drugs loaded into polymeric carriers, the diffraction patterns of which present a structured amorphous halo from which the crystalline drug peaks rise up. In this paper, it is shown that micro X-ray diffraction on capillary powder samples, combined with a two-dimensional detector, is a promising solution to preferred orientation problems, since it provides easy and rapid preparation of randomly oriented powder samples, fast measurements (acquisition times of a few minutes) and correct powder diffraction patterns.
Salts of aromatic carboxylates: the crystal structures of nickel(II) and cobalt(II) 2,6-naphthalenedicarboxylate tetrahydrate
Authors: Kaduk James A. , Hanko Jason A.
Published: July 2002

The crystal structures of isostructural 2,6-naphthalenedicarboxylate tetrahydrate salts of nickel(II) and cobalt(II) have been determined using Monte Carlo simulated annealing techniques and laboratory X-ray powder diffraction data. These compounds crystallize in the triclinic space groupP\bar{1}, withZ= 2;a= 10.0851 (4),b= 10.9429 (5),c= 6.2639 (3) Å, α = 98.989 (2), β = 87.428 (3), γ = 108.015 (2)°,V= 649.32 (5) Å3for [Ni(C12H6O4)(H2O)4], anda= 10.1855 (6),b= 10.8921 (6),c= 6.2908 (5) Å, α = 98.519 (4), β = 87.563 (4), γ = 108.304 (3)°,V= 655.28 (8) Å3for [Co(C12H6O4)(H2O)4]. The water-molecule H atoms were located by quantum chemical geometry optimization usingCASTEP. The structure consists of alternating hydrocarbon and metal/oxygen layers parallel to theacplane. Each naphthalenedicarboxylate anion bridges two metal cations; each carboxyl group is monodentate. The resulting structure contains infinite chains parallel to [111]. The octahedral coordination sphere of the metal cations containstranscarboxylates and four equatorial water molecules. The carboxyl groups are rotated by 15–20° out of the naphthalene plane. The metal/oxygen layers are characterized by an extensive hydrogen-bonding network. The orientations of the carboxyl groups are determined by the formation of short (O...O = 2.53 Å) hydrogen bonds between the carbonyl O atoms and theciswater molecules. Molecular mechanics energy minimizations suggest that coordination and hydrogen-bonding interactions are most important in determining the crystal packing.
Measurement of subtle strain modifications in heterostructures by using X-ray mapping in reciprocal space
Authors: Shilo D. , Lakin E. , Zolotoyabko E.
Published: July 2002

The application of X-ray mapping in reciprocal space to the measurement of subtle strain modifications in heterostructures is analysed, focussing on strain analysis in non-cubic crystals. Special attention is paid to the enhancement of the precision of the mapping technique in comparison with conventional diffraction profile measurements. The capabilities of the mapping-based strain analysis are illustrated by selected examples of epitaxially grown structures (obeying Vegard's rule), as well as implanted structures with unknown mismatches between the lattice parameters of the damaged layer and of the crystal bulk.
Rietveld refinements on laboratory energy dispersive X-ray diffraction (EDXD) data
Authors: Ballirano Paolo , Caminiti Ruggero
Published: July 2002

Rietveld refinements of corundum, a rutile and anatase nanocrystalline synthetic mixture, and gypsum, on laboratory energy dispersive X-ray diffraction (EDXD) data are reported. Cell parameters, positional and displacement parameters are in reasonable agreement with single-crystal reference data, despite the rather poor resolution of EDXD data. In particular, good results were obtained for gypsum (unrestrained refinement) with counting times as short as 1000 s.
Crystal structures of the relaxor oxide Pb2(ScTa)O6in the paraelectric and ferroelectric states
Authors: Woodward P. M. , Baba-Kishi K. Z.
Published: July 2002

The crystal structure of the relaxor ferroelectric Pb2ScTaO6has been refined from high-resolution neutron time-of-flight powder diffraction data recorded at various temperatures from 4 to 400 K. Upon warming, Pb2ScTaO6undergoes a first-order transition at 295 K from the rhombohedral ferroelectric state into the cubic paraelectric state. At 4.2 K, in the ferroelectric state, this compound adoptsR3 space-group symmetry, witha= 8.15231 (7) Å and α = 89.8488 (3)°. At 400 K, in the paraelectric state, this compound adoptsFm\bar{3}mspace-group symmetry, witha= 8.15345 (3) Å. In the ferroelectric state, the Pb2+coordination polyhedra are quite asymmetric, clearly indicating the presence of a stereoactive electron lone pair. The Sc3+and Ta5+ions are also shifted away from the centers of their respective octahedra, each toward an octahedral face. The large displacement parameters associated with both the Pb and the O ions, in the 400 K structure reveal significant local shifts of these ions from their ideal sites in the paraelectric state. Thus, the paraelectric to ferroelectric transition is driven by long-range cooperative ordering of the cation displacements. Synchrotron X-ray powder diffraction measurements are used to estimate the domain size of the Sc3+/Ta5+ordering and the ferroelectric cation displacements as 88 nm and 10 nm, respectively.
The approximation of symmetric X-ray peaks by Pearson type VII distributions
Authors: Hall M. M. , Veeraraghavan V. G. , Rubin H. , Winchell P. G.
Published: July 2002

Some symmetric X-ray diffraction peaks can be approximated in shape by Pearson type VII distributions: y(x) = y_0[1 + (x - \bar x)^{2}/ma^2]^{-m}.This distribution is Cauchy for m = 1, modified Lorentzian for m = 2, and Gaussian for m = ∞. Some properties of the distribution and some illustrative applications are presented.
Energy-dispersive powder profile refinement using synchrotron radiation
Authors: Glazer A. M. , Hidaka M. , Bordas J.
Published: July 2002

Results of powder-profile refinement using a solid-state detector with synchrotron radiation are presented. The data are collected very rapidly and the usual structural parameters are refined together with line-shape, zero error and instrument function. The results are in excellent agreement with previously published parameters. The rapidity and precision of the method means that it will be possible in the near future to find structural parameters of a powdered material in a few s or min and thus allow simultaneous structure refinement with changing sample environment.
Crystal cooling for protein crystallography with synchrotron radiation
Authors: Bartunik H. D. , Schubert P.
Published: July 2002

A new crystal cooling device for protein data collection with a rotation camera at temperatures between 323 and 100 K is described. It includes a flow cell for solvent exchange at low temperatures. The crystal is mounted in a double chamber with thin Mylar walls. The temperature is controlled to better than 0.5 K by N2 or He gas flowing through the inner chamber. Since cooling is isotropic, temperature gradients near the sample are avoided. Dry gas circulating through the outer chamber prevents the windows from icing. The system has been routinely used for synchrotron radiation data collection at the instrument X ll at DORIS. The scope of applications in low-temperature protein crystallography with synchrotron radiation is discussed.
Crystallographic characteristics of the process of σ-phase precipitation in chromium–nickel austenitic steels
Authors: Barcik J.
Published: July 2002

Transmission electron microscopy has been used to determine the crystallographic characteristics of the σ-phase precipitation process in austenitic steels. The σ-phase precipitating inside the austenite grains was found to exhibit a close similarity to the austenite described by Nenno, Tagaya & Nishijama [Trans. Jpn. Inst. Met. (1962), 3, 82–91]. Transition matrices of the austenite planes and direction indices to the a phase have been determined. The σ-phase lamellae were found to lie on the {111} austenite plane which is their habit plane and grow most rapidly in the 〈112〉
γ
direction. The habit of these lamellae are bound by four {110}σ and two {001}σ σ-phase planes.
Quantitative analysis of intensitities in X-ray topographs by enhanced microfluorescence
Authors: Weissmann S. , Greenhut V. A. , Chaudhuri J. , Kalman Z. H.
Published: July 2002

A method is presented for enhancing the fluorescence of the silver precipitates in the microfluorescent analysis of X-ray topographs by scanning electron microscopy or similar electron microprobes. The method is based on the indirect excitation of the silver fluorescence by depositing a thin suitable metal film on the emulsion of a nuclear track plate. Theoretical aspects of the method are presented and experimentally verified. The method was applied to determine the elastic strain distribution in a bent silicon plate containing a hole by measuring the opacities of the exposed and developed topograph obtained from the specimen.