bluuebunny/crossref_metadata_2025 huggingface dataset:
Human CRSP interacts with RNA polymerase II CTD and adopts a specific CTD-bound conformation
Authors: Näär Anders M. , Taatjes Dylan J. , Zhai Weiguo , Nogales Eva , Tjian Robert
Published: July 2002

Activation of gene transcription in mammalian cells requires several classes of coactivators that participate in different steps of the activation cascade. Using conventional and affinity chromatography, we have isolated a human coactivator complex that interacts directly with the C-terminal domain (CTD) of RNA polymerase II (Pol II). The CTD-binding complex is structurally and functionally indistinguishable from our previously isolated CRSP coactivator complex. The closely related, but transcriptionally inactive, ARC-L complex failed to interact with the CTD, indicating a significant biochemical difference between CRSP and ARC-L that may, in part, explain their functional divergence. Electron microscopy and three-dimensional single-particle reconstruction reveals a conformation for CTD–CRSP that is structurally distinct from unliganded CRSP or CRSP bound to SREBP-1a, but highly similar to CRSP bound to the VP16 activator. Together, our findings suggest that the human CRSP coactivator functions, at least in part, by mediating activator-dependent recruitment of RNA Pol II via the CTD.
Evolution and Variation of the Yeast (Saccharomyces) Genome
Authors: Mortimer Robert K.
Published: July 2002

In this review we describe the role of the yeastSaccharomycesin the development of human societies including the use of this organism in the making of wine, bread, beer, and distilled beverages. We also discuss the tremendous diversity of yeast found in natural (i.e., noninoculated) wine fermentations and the scientific uses of yeast over the past 60 years. In conclusion, we present ideas on the model of “genome renewal” and the use of this model to explain the mode by which yeast has evolved and how diversity can be generated.
Fourfold Faster Rate of Genome Rearrangement in Nematodes Than in Drosophila
Authors: Coghlan Avril , Wolfe Kenneth H.
Published: July 2002

We compared the genome of the nematode Caenorhabditis elegans to 13% of that of Caenorhabditis briggsae, identifying 252 conserved segments along their chromosomes. We detected 517 chromosomal rearrangements, with the ratio of translocations to inversions to transpositions being ∼1:1:2. We estimate that the species diverged 50–120 million years ago, and that since then there have been 4030 rearrangements between their whole genomes. Our estimate of the rearrangement rate, 0.4–1.0 chromosomal breakages/Mb per Myr, is at least four times that of Drosophila, which was previously reported to be the fastest rate among eukaryotes. The breakpoints of translocations are strongly associated with dispersed repeats and gene family members in the C. elegansgenome.

[The following institution kindly provided reagents, samples or unpublished information as indicated in the paper: Genome Sequencing Center, Washington University School of Medicine, St. Louis.]
A Subtracted cDNA Library from the Zebrafish (Danio rerio) Embryonic Inner Ear: Table 1.
Authors: Coimbra Roney S. , Weil Dominique , Brottier Phillipe , Blanchard Stéphane , Levi Michael , Hardelin Jean-Pierre , Weissenbach Jean , Petit Christine
Published: July 2002

A database was built that consists of 4694 sequence contigs of ∼18,000 reads of cDNAs isolated from the microdissected otocysts of zebrafish embryos at 20–30 hour postfertilization, following subtraction with a pool of liver cDNAs from adult fish. These sequences were compared with those of public databanks. Significant similarity were recorded and organized in a relational database athttp://www.genoscope.cns.fr/zie. A first group of 2067 sequences correspond to 1428 known zebrafish genes or ESTs present in theDanio rerio section of UniGene. A second group of 302 sequences encode putative proteins that showed significant similarity (50%–100%) with 302 nonzebrafish proteins in the nr databank, a public databank containing an exhaustive nonredundant collection of protein sequences from different species (ftp://ftp.ncbi.nlm.nih.gov/blast/db/nr). The remaining 2325 (49.5%) sequence contigs or singletons showed no significant similarity with sequences available in public databanks. Several genes known to be expressed in the developing inner ear were represented in the present database, in particular genes involved in hair cell differentiation or innervation The occurrence of these genes validates the outcome of this study as the first collection of ESTs preferentially expressed in the zebrafish inner ear during the period of hair cell differentiation and neuroblast delamination from the otic vesicle epithelium. Novel zebrafish genes also involved in these processes are thus likely to be represented among the sequences obtained herein, for which no homology was found in the D. rerio section of UniGene.

[The sequence data from this study have been submitted to EMBL under accession nos. AL714032–AL731531].
Tissue-Specific Expression of a Type I Adenylyl Cyclase Rescues the rutabaga Mutant Memory Defect: In Search of the Engram
Authors: Zars Troy , Wolf Reinhard , Davis Ron , Heisenberg Martin
Published: July 2002

Most attempts to localize physical correlates of memory in the central nervous system (CNS) rely on ablation techniques. This approach has the limitation of defining just one of an unknown number of structures necessary for memory formation. We have used theDrosophila rutabaga type I Ca2+/CaM-dependent adenylyl cyclase (AC) gene to determine in which CNS region AC expression is sufficient for memory formation. Using pan-neural and restricted CNS expression with the GAL4 binary transcription activation system, we have rescued the memory defect of the rutabaga mutant in a fast robust spatial learning paradigm. The ventral ganglion, antennal lobes, and median bundle are likely the CNS structures sufficient for rutabaga AC- dependent spatial learning.
Ca2+-Activated Anion Channels and Membrane Depolarizations Induced by Blue Light and Cold in Arabidopsis Seedlings
Authors: Lewis B. D. , Karlin-Neumann G. , Davis R. W. , Spalding E. P.
Published: July 2002

The activation of an anion channel in the plasma membrane of Arabidopsis thaliana hypocotyls by blue light (BL) is believed to be a signal-transducing event leading to growth inhibition. Here we report that the open probability of this particular anion channel depends on cytoplasmic Ca2+ ([Ca2+]cyt) within the concentration range of 1 to 10 [mu]M, raising the possibility that BL activates the anion channel by increasing [Ca2+]cyt. Arabidopsis seedlings cytoplasmically expressing aequorin were generated to test this possibility. Aequorin luminescence did not increase during or after BL, providing evidence that Ca2+ does not play a second-messenger role in the activation of anion channels. However, cold shock simultaneously triggered a large increase in [Ca2+]cyt and a 110-mV transient depolarization of the plasma membrane. A blocker of the anion channel, 5-nitro-2-(3-phenylpropylamino)-benzoic acid, blocked 61% of the cold-induced depolarization without affecting the increase in [Ca2+]cyt. These data led us to propose that cold shock opens Ca2+ channels at the plasma membrane, allowing an inward, depolarizing Ca2+ current. The resulting large increase in [Ca2+]cyt activates the anion channel, which further depolarizes the membrane. Although an increase in [Ca2+]cyt may activate anion channels in response to cold, it appears that BL does so via a Ca2+-independent pathway.
Oxidative Stress Causes Ferredoxin-NADP+ Reductase Solubilization from the Thylakoid Membranes in Methyl Viologen-Treated Plants
Authors: Palatnik J. F. , Valle E. M. , Carrillo N.
Published: July 2002

The flavoenzyme ferredoxin-NADP+ reductase (FNR) is a member of the cellular defense barrier against oxidative damage in Escherichia coli. We evaluated the responses of chloroplast FNR to methyl viologen, a superoxide radical propagator, in wheat (Triticum aestivum L.) plants and chloroplasts. Treatments with the herbicide showed little effect on the levels of FNR protein or transcripts, indicating that expression of this reductase is not up-regulated by oxidants in plants. Viologens and peroxides caused solubilization of active FNR from the thylakoids into the stroma, converting the enzyme from a membrane-bound NADPH producer to a soluble NADPH consumer. This response appeared specific for FNR, since other thylakoid proteins were unaffected by the treatments. The reductase-binding protein was released together with FNR, suggesting that it might be the target of oxidative modification. Stromal accumulation of a functional NADPH reductase in response to oxidative stress is formally analogous to the induction of FNR synthesis observed in E. coli under similar conditions. FNR solubilization may be playing a crucial role in maintaining the NADPH/NADP+ homeostasis of the stressed plastid. The unchecked accumulation of NADPH might otherwise increase the risks of oxidative damage through a rise in the Mehler reaction rates and/or the production of hydroxyl radicals.
Arabidopsis thalianaResponses to Mechanical Stimulation Do Not Require ETR1 or EIN21
Authors: Johnson Keith A. , Sistrunk Melissa L. , Polisensky Diana H. , Braam Janet
Published: July 2002

Plants exposed to repetitive touch or wind are generally shorter and stockier than sheltered plants. These mechanostimulus-induced developmental changes are termed thigmomorphogenesis and may confer resistance to subsequent stresses. An early response of Arabidopsis thaliana to touch or wind is the up-regulation ofTCH (touch) gene expression. The signal transduction pathway that leads to mechanostimulus responses is not well defined. A role for ethylene has been proposed based on the observation that mechanostimulation of plants leads to ethylene evolution and exogenous ethylene leads to thigmomorphogenetic-like changes. To determine whether ethylene has a role in plant responses to mechanostimulation, we assessed the ability of two ethylene-insensitive mutants, etr1–3 and ein2–1, to undergo thigmomorphogenesis and TCH gene up-regulation of expression. The ethylene-insensitive mutants responded to wind similarly to the wild type, with a delay in flowering, decrease in inflorescence elongation rate, shorter mature primary inflorescences, more rosette paraclades, and appropriate TCH gene expression changes. Also, wild-type and mutant Arabidopsis responded to vibrational stimulation, with an increase in hypocotyl elongation and up-regulation of TCH gene expression. We conclude that the ETR1 and EIN2 protein functions are not required for the developmental and molecular responses to mechanical stimulation.
Participation of Mitochondrial Metabolism in Photorespiration1
Authors: Raghavendra Agepati S. , Reumann Sigrun , Heldt Hans W.
Published: July 2002

In this study the interplay of mitochondria and peroxisomes in photorespiration was simulated in a reconstituted system of isolated mitochondria and peroxisomes from spinach (Spinacia oleracea L.) leaves. The mitochondria oxidizing glycine produced serine, which was reduced in the peroxisomes to glycerate. The required reducing equivalents were provided by the mitochondria via the malate-oxaloacetate (OAA) shuttle, in which OAA was reduced in the mitochondrial matrix by NADH generated during glycine oxidation. The rate of peroxisomal glycerate formation, as compared with peroxisomal protein, resembled the corresponding rate required during leaf photosynthesis under ambient conditions. When the reconstituted system produced glycerate at this rate, the malate-to-OAA ratio was in equilibrium with a ratio of NADH/NAD of 8.8 × 10−3. This low ratio is in the same range as the ratio of NADH/NAD in the cytosol of mesophyll cells of intact illuminated spinach leaves, as we had estimated earlier. This result demonstrates that in the photorespiratory cycle a transfer of redox equivalents from the mitochondria to peroxisomes, as postulated from separate experiments with isolated mitochondria and peroxisomes, can indeed operate under conditions of the very low reductive state of the NADH/NAD system prevailing in the cytosol of mesophyll cells in a leaf during photosynthesis.
Nuclear-Gene Mutations Suppress a Defect in the Expression of the Chloroplast-Encoded Large Subunit of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase1
Authors: Hong Seokjoo , Spreitzer Robert J.
Published: July 2002

The green alga Chlamydomonas reinhardtii mutant 76–5EN lacks photosynthesis because of a nuclear-gene mutation that specifically inhibits expression of the chloroplast gene encoding the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco; EC 4.1.1.39). Photosynthesis-competent revertants were selected from mutant 76–5EN to explore the possibility of increasing Rubisco expression. Genetic analysis of 10 revertants revealed that most arose from suppressor mutations in nuclear genes distinct from the original 76–5EN mutant gene. The revertant strains have regained various levels of Rubisco holoenzyme, but none of the suppressor mutations increased Rubisco expression above the wild-type level in either the presence or absence of the 76–5EN mutation. One suppressor mutation, S107–4B, caused a temperature-conditional, photosynthesis-deficient phenotype in the absence of the original 76–5EN mutation. The S107–4B strain was unable to grow photosynthetically at 35°C, but it expressed a substantial level of Rubisco holoenzyme. Whereas the 76–5EN gene encodes a nuclear factor that appears to be required for the transcription of the Rubisco large-subunit gene, the S107–4B nuclear gene may be required for the expression of other chloroplast genes.
Estimating Photosynthesis and Concurrent Export Rates in C3 and C4 Species at Ambient and Elevated CO21,2
Authors: Grodzinski Bernard , Jiao Jirong , Leonardos Evangelos D.
Published: July 2002

The ability of 21 C3 and C4 monocot and dicot species to rapidly export newly fixed C in the light at both ambient and enriched CO2 levels was compared. Photosynthesis and concurrent export rates were estimated during isotopic equilibrium of the transport sugars using a steady-state 14CO2-labeling procedure. At ambient CO2 photosynthesis and export rates for C3 species were 5 to 15 and 1 to 10 μmol C m−2 s−1, respectively, and 20 to 30 and 15 to 22 μmol C m−2 s−1, respectively, for C4 species. A linear regression plot of export on photosynthesis rate of all species had a correlation coefficient of 0.87. When concurrent export was expressed as a percentage of photosynthesis, several C3 dicots that produced transport sugars other than Suc had high efflux rates relative to photosynthesis, comparable to those of C4 species. At high CO2photosynthetic and export rates were only slightly altered in C4 species, and photosynthesis increased but export rates did not in all C3 species. The C3 species that had high efflux rates relative to photosynthesis at ambient CO2 exported at rates comparable to those of C4species on both an absolute basis and as a percentage of photosynthesis. At ambient CO2 there were strong linear relationships between photosynthesis, sugar synthesis, and concurrent export. However, at high CO2 the relationships between photosynthesis and export rate and between sugar synthesis and export rate were not as strong because sugars and starch were accumulated.
The Diageotropica Gene Differentially Affects Auxin and Cytokinin Responses throughout Development in Tomato1
Authors: Coenen Catharina , Lomax Terri L.
Published: July 2002

The interactions between the plant hormones auxin and cytokinin throughout plant development are complex, and genetic investigations of the interdependency of auxin and cytokinin signaling have been limited. We have characterized the cytokinin sensitivity of the auxin-resistantdiageotropica (dgt) mutant of tomato (Lycopersicon esculentum Mill.) in a range of auxin- and cytokinin-regulated responses. Intact, etiolated dgtseedlings showed cross-resistance to cytokinin with respect to root elongation, but cytokinin effects on hypocotyl growth and ethylene synthesis in these seedlings were not impaired by thedgt mutation. Seven-week-old, green wild-type anddgt plants were also equally sensitive to cytokinin with respect to shoot growth and hypocotyl and internode elongation. The effects of cytokinin and the dgt mutation on these processes appeared additive. In tissue culture organ regeneration fromdgt hypocotyl explants showed reduced sensitivity to auxin but normal sensitivity to cytokinin, and the effects of cytokinin and the mutation were again additive. However, although callus induction from dgt hypocotyl explants required auxin and cytokinin, dgt calli did not show the typical concentration-dependent stimulation of growth by either auxin or cytokinin observed in wild-type calli. Cross-resistance of thedgt mutant to cytokinin thus was found to be limited to a small subset of auxin- and cytokinin-regulated growth processes affected by the dgt mutation, indicating that auxin and cytokinin regulate plant growth through both shared and separate signaling pathways.
Rate-Limiting Steps in Selenium Assimilation and Volatilization by Indian Mustard1
Authors: de Souza Mark P. , Pilon-Smits Elizabeth A.H. , Lytle C. Mel , Hwang Seongbin , Tai Jenny , Honma Todd S.U. , Yeh Lucretia , Terry Norman
Published: July 2002

Se can be accumulated by plants and volatilized to dimethylselenide, providing an attractive technology for Se phytoremediation. To determine the rate-limiting steps in Se volatilization from selenate and selenite, time- and concentration-dependent kinetics of Se accumulation and volatilization were studied in Indian mustard (Brassica juncea). Time-dependent kinetic studies showed that selenate was taken up 2-fold faster than selenite. Selenate was rapidly translocated to the shoot, away from the root, the site of volatilization, whereas only approximately 10% of the selenite was translocated. For both selenate- and selenite-supplied plants, Se accumulation and volatilization increased linearly with external Se concentration up to 20 μm; volatilization rates were also linearly correlated with root Se concentrations. Se-volatilization rates were 2- to 3-fold higher from plants supplied with selenite compared with selenate. Se speciation by x-ray absorption spectroscopy revealed that selenite-supplied plants accumulated organic Se, most likely selenomethionine, whereas selenate-supplied plants accumulated selenate. Our data suggest that Se volatilization from selenate is limited by the rate of selenate reduction, as well as by the availability of Se in roots, as influenced by uptake and translocation. Se volatilization from selenite may be limited by selenite uptake and by the conversion of selenomethionine to dimethylselenide.
Spermine Is a Salicylate-Independent Endogenous Inducer for Both Tobacco Acidic Pathogenesis-Related Proteins and Resistance against Tobacco Mosaic Virus Infection
Authors: Yamakawa Hiromoto , Kamada Hiroshi , Satoh Masaya , Ohashi Yuko
Published: July 2002

Intercellular spaces are often the first sites invaded by pathogens. In the spaces of tobacco mosaic virus (TMV)-infected and necrotic lesion-forming tobacco (Nicotiana tabacum L.) leaves, we found that an inducer for acidic pathogenesis-related (PR) proteins was accumulated. The induction activity was recovered in gel-filtrated fractions of low molecular mass with a basic nature, into which authentic spermine (Spm) was eluted. We quantified polyamines in the intercellular spaces of the necrotic lesion-forming leaves and found 20-fold higher levels of free Spm than in healthy leaves. Among several polyamines tested, exogenously supplied Spm induced acidic PR-1 gene expression. Immunoblot analysis showed that Spm treatment increased not only acidic PR-1 but also acidic PR-2, PR-3, and PR-5 protein accumulation. Treatment of healthy tobacco leaves with salicylic acid (SA) caused no significant increase in the level of endogenous Spm, and Spm did not increase the level of endogenous SA, suggesting that induction of acidic PR proteins by Spm is independent of SA. The size of TMV-induced local lesions was reduced by Spm treatment. These results indicate that Spm accumulates outside of cells after lesion formation and induces both acidic PR proteins and resistance against TMV via a SA-independent signaling pathway.
Direct Measurement of Calcium Transport across Chloroplast Inner-Envelope Vesicles
Authors: Roh Michael H. , Shingles Richard , Cleveland Michael J. , McCarty Richard E.
Published: July 2002

The initial rate of Ca2+movement across the inner-envelope membrane of pea (Pisum sativum L.) chloroplasts was directly measured by stopped-flow spectrofluorometry using membrane vesicles loaded with the Ca2+-sensitive fluorophore fura-2. Calibration of fura-2 fluorescence was achieved by combining a ratiometric method with Ca2+-selective minielectrodes to determine pCa values. The initial rate of Ca2+ influx in predominantly right-side-out inner-envelope membrane vesicles was greater than that in largely inside-out vesicles. Ca2+ movement was stimulated by an inwardly directed electrochemical proton gradient across the membrane vesicles, an effect that was diminished by the addition of valinomycin in the presence of K+. In addition, Ca2+ was shown to move across the membrane vesicles in the presence of a K+ diffusion potential gradient. The potential-stimulated rate of Ca2+ transport was slightly inhibited by diltiazem and greatly inhibited by ruthenium red. Other pharmacological agents such as LaCl3, verapamil, and nifedipine had little or no effect. These results indicate that Ca2+ transport across the chloroplast inner envelope can occur by a potential-stimulated uniport mechanism.
Characterization and Immunolocalization of a Cytosolic Calcium-Binding Protein from Brassica napus and Arabidopsis Pollen1
Authors: Rozwadowski Kevin , Zhao Ruohong , Jackman Lisa , Huebert Terry , Burkhart William E. , Hemmingsen Sean M. , Greenwood John , Rothstein Steven J.
Published: July 2002

Two low-molecular-weight proteins have been purified from Brassica napus pollen and a gene corresponding to one of them has been isolated. The gene encodes an 8.6-kD protein with two EF-hand calcium-binding motifs and is a member of a small gene family inB. napus. The protein is part of a family of pollen allergens recently identified in several evolutionarily distant dicot and monocot plants. Homologs have been detected in Arabidopsis, from which one gene has been cloned in this study, and in snapdragon (Antirrhinum majus), but not in tobacco (Nicotiana tabacum). Expression of the gene in B. napus was limited to male tissues and occurred during the pollen-maturation phase of anther development. Both the B. napus and Arabidopsis proteins interact with calcium, and the potential for a calcium-dependent conformational change was demonstrated. Given this affinity for calcium, the cloned genes were termed BPC1 and APC1(B. napus andArabidopsis pollen calcium-binding protein 1, respectively). Immunolocalization studies demonstrated that BPC1 is found in the cytosol of mature pollen. However, upon pollen hydration and germination, there is some apparent leakage of the protein to the pollen wall. BPC1 is also concentrated on or near the surface of the elongating pollen tube. The essential nature of calcium in pollen physiology, combined with the properties of BPC1 and its high evolutionary conservation suggests that this protein plays an important role in pollination by functioning as a calcium-sensitive signal molecule.
The Mechanism of Synthesis of a Mixed-Linkage (1→3),(1→4)β-d-Glucan in Maize. Evidence for Multiple Sites of Glucosyl Transfer in the Synthase Complex1
Authors: Buckeridge Marcos S. , Vergara Claudia E. , Carpita Nicholas C.
Published: July 2002

We examined the mechanism of synthesis in vitro of (1→3),(1→4)β-d-glucan (β-glucan), a growth-specific cell wall polysaccharide found in grasses and cereals. β-Glucan is composed primarily of cellotriosyl and cellotetraosyl units linked by single (1→3)β-linkages. The ratio of cellotriosyl and cellotetraosyl units in the native polymer is strictly controlled at between 2 and 3 in all grasses, whereas the ratios of these units in β-glucan formed in vitro vary from 1.5 with 5 μm UDP-glucose (Glc) to over 11 with 30 mmsubstrate. These results support a model in which three sites of glycosyl transfer occur within the synthase complex to produce the cellobiosyl-(1→3)-d-glucosyl units. We propose that failure to fill one of the sites results in the iterative addition of one or more cellobiosyl units to produce the longer cellodextrin units in the polymer. Variations in the UDP-Glc concentration in excised maize (Zea mays) coleoptiles did not result in wide variations in the ratios of cellotriosyl and cellotetraosyl units in β-glucan synthesized in vivo, indicating that other factors control delivery of UDP-Glc to the synthase. In maize sucrose synthase is enriched in Golgi membranes and plasma membranes and may be involved in the control of substrate delivery to β-glucan synthase and cellulose synthase.
Identification of BFN1, a Bifunctional Nuclease Induced during Leaf and Stem Senescence in Arabidopsis
Authors: Pérez-Amador Miguel A. , Abler Michael L. , De Rocher E. Jay , Thompson Debrah M. , van Hoof Ambro , LeBrasseur Nicole D. , Lers Amnon , Green Pamela J.
Published: July 2002

Nuclease I enzymes are responsible for the degradation of RNA and single-stranded DNA during several plant growth and developmental processes, including senescence. However, in the case of senescence the corresponding genes have not been reported. We describe the identification and characterization of BFN1 of Arabidopsis, and demonstrate that it is a senescence-associated nuclease I gene. BFN1 nuclease shows high similarity to the sequence of a barley nuclease induced during germination and a zinnia (Zinnia elegans) nuclease induced during xylogenesis. In transgenic plants overexpressing the BFN1 cDNA, a nuclease activity of about 38 kD was detected on both RNase and DNase activity gels. Levels of BFN1 mRNA were extremely low or undetectable in roots, leaves, and stems. In contrast, relatively highBFN1 mRNA levels were detected in flowers and during leaf and stem senescence. BFN1 nuclease activity was also induced during leaf and stem senescence. The strong response of theBFN1 gene to senescence indicated that it would be an excellent tool with which to study the mechanisms of senescence induction, as well as the role of the BFN1 enzyme in senescence using reverse genetic approaches in Arabidopsis.
Molecular Cloning and Characterization of ATP-Phosphoribosyl Transferase from Arabidopsis, a Key Enzyme in the Histidine Biosynthetic Pathway
Authors: Ohta Daisaku , Fujimori Ko , Mizutani Masaharu , Nakayama Yumiko , Kunpaisal-Hashimoto Rosarin , Münzer Silvia , Kozaki Akiko
Published: July 2002

We have characterized two isoforms of ATP-phosphoribosyl transferase (ATP-PRT) from Arabidopsis (AtATP-PRT1 [accession no.AB025251] and AtATP-PRT2), catalyzing the first step of the pathway of hisidine (His) biosynthesis. The primary structures deduced from AtATP-PRT1 and AtATP-PRT2cDNAs share an overall amino acid identity of 74.6% and contain N-terminal chloroplast transit peptide sequences. DNA-blot analyses indicated that the ATP-PRTs in Arabidopsis are encoded by two separate genes with a closely similar gene structural organization. Both gene transcripts were detected throughout development, and protein-blot analysis revealed predominant accumulation of the AtATP-PRT proteins in Arabidopsis leaves. The His auxotrophy of a his1 mutant of Saccharomyces cerevisiae was suppressed by the transformation with AtATP-PRT1 andAtATP-PRT2 cDNAs, indicating that both isoforms are functionally active ATP-PRT enzymes. The K  mvalues for ATP and phosphoribosyl pyrophosphate of the recombinant AtATP-PRT proteins were comparable to those of the native ATP-PRTs from higher plants and bacteria. It was demonstrated that the recombinant AtATP-PRTs were inhibited by l-His (50% inhibition of initial activity = 40–320 μm), suggesting that His biosynthesis was regulated in plants through feedback inhibition byl-His.
Identification of a New Glucosinolate-Rich Cell Type in Arabidopsis Flower Stalk
Authors: Koroleva Olga A. , Davies Andrew , Deeken Rosalia , Thorpe Michael R. , Tomos A. Deri , Hedrich Rainer
Published: July 2002

Distribution of K, Ca, Cl, S, and P in freeze-dried sections of Arabidopsis flower stalk was analyzed by energy dispersive x-ray imaging. Concentrations of these elements in different cell types were quantified by microanalysis of single-cell samples and phloem exudates. Results showed a differential pattern of distribution for all five elements. K concentration was found to be highest in the parenchymatous tissue around vascular bundles. Ca and Cl were present mainly in the central part of the flower stalk. P was largely located in the bundles and in the parenchyma surrounding them. S signal was extraordinary high in groups of cells (S-cells) situated between the phloem of every vascular bundle and the endodermis. Enzymatic hydrolysis by thioglucosidase of cell sap collected from S-cells using a glass microcapillary resulted in the release of glucose, indicating that these cells contain glucosinolates at high (> 100 mm) concentration, which is consistent with the concentration of S (> 200 mm) estimated by x-ray analysis of cell sap samples. Since their position outside of the phloem is ideally suited for protecting the long-distance transport system from feeding insects, the possible roles of these cells as components of a plant defense system are discussed.
Hydrogen Peroxide Yields during the Incompatible Interaction of Tobacco Suspension Cells Inoculated with Phytophthora nicotianae
Authors: Able Amanda J. , Guest David I. , Sutherland Mark W.
Published: July 2002

Rates of H2O2 production by tobacco suspension cells inoculated with zoospores from compatible or incompatible races of the pathogen Phytophthora nicotianae were followed by direct measurement of oxygen evolution from culture supernatants following catalase addition. Rates of HO2  ./O2  −production were compared by following the formation of the formazan of sodium, 3′-[1-[phenylamino-carbonyl]-3,4-tetrazolium]-bis(4-methoxy-6-nitro) benzene-sulfonic acid hydrate. In the incompatible interaction only, both reactive oxygen species (ROS) were produced by the cultured host cells in a minor burst between 0 and 2 h and then in a major burst between 8 and 12 h after inoculation. Absolute levels of H2O2 could not be accurately measured due to its metabolism by host cells, but results are consistent with the majority of H2O2 being formed via dismutation of HO2  ./O2  −. The effects of inhibitors of endogenous Cu/Zn superoxide dismutase (diethyldithiocarbamate) and catalase (3-amino-1,2,4-triazole and salicylic acid) were also examined. Yields of ROS in the presence of the inhibitors diphenylene iodonium, allopurinol, and salicylhydroxamic acid suggest that ROS were generated in incompatible host responses by more than one mechanism.
A Cytosolic ADP-Glucose Pyrophosphorylase Is a Feature of Graminaceous Endosperms, But Not of Other Starch-Storing Organs
Authors: Beckles Diane M. , Smith Alison M. , ap Rees Tom
Published: July 2002

The occurrence of an extra-plastidial isoform of ADP-glucose (Glc) pyrophosphorylase (AGPase) among starch-storing organs was investigated in two ways. First, the possibility that an extra-plastidial isoform arose during the domestication of cereals was studied by comparing the intracellular distribution of enzyme activity and protein in developing endosperm of noncultivated Hordeum species with that previously reported for cultivated barley (Hordeum vulgare). As in cultivated barley, the AGPase of H. vulgare subsp. spontaneum and Hordeum murinum endosperm is accounted for by a major extra-plastidial and a minor plastidial isoform. Second, the ratio of ADP-Glc to UDP-Glc was used as an indication of the intracellular location of the AGPase activity in a wide range of starch-synthesizing organs. The ratio is expected to be high in organs in which UDP-Glc and ADP-Glc are synthesized primarily in the cytosol, because the reactions catalyzed by AGPase and UDP-Glc pyrophosphorylase will be coupled and close to equilibrium. This study revealed that ADP-Glc contents and the ratio of ADP-Glc to UDP-Glc were higher in developing graminaceous endosperms than in any other starch-storing organs. Taken as a whole the results indicate that an extra-plastidial AGPase is important in ADP-Glc synthesis in graminaceous endosperms, but not in other starch-storing organs.
Phytochelatins Are Involved in Differential Arsenate Tolerance inHolcus lanatus
Authors: Hartley-Whitaker Jeanette , Ainsworth Gillian , Vooijs Riet , Bookum Wilma Ten , Schat Henk , Meharg Andrew A.
Published: July 2002

Arsenate tolerance is conferred by suppression of the high-affinity phosphate/arsenate uptake system, which greatly reduces arsenate influx in a number of higher plant species. Despite this suppressed uptake, arsenate-tolerant plants can still accumulate high levels of As over their lifetime, suggesting that constitutive detoxification mechanisms may be required. Phytochelatins are thiol-rich peptides, whose production is induced by a range of metals and metalloids including arsenate. This study provides evidence for the role of phytochelatins in the detoxification of arsenate in arsenate-tolerant Holcus lanatus. Elevated levels of phytochelatin were measured in plants with a range of tolerance to arsenate at equivalent levels of arsenate stress, measured as inhibition of root growth. The results suggest that arsenate tolerance in H. lanatus requires both adaptive suppression of the high-affinity phosphate uptake system and constitutive phytochelatin production.
Alteration of Auxin Polar Transport in the Arabidopsisifl1 Mutants
Authors: Zhong Ruiqin , Ye Zheng-Hua
Published: July 2002

The INTERFASCICULAR FIBERLESS/REVOLUTA(IFL1/REV) gene is essential for the normal differentiation of interfascicular fibers and secondary xylem in the inflorescence stems of Arabidopsis. It has been proposed thatIFL1/REV influences auxin polar flow or the transduction of auxin signal, which is required for fiber and vascular differentiation. Assay of auxin polar transport showed that the ifl1 mutations dramatically reduced auxin polar flow along the inflorescence stems and in the hypocotyls. The null mutant allele ifl1-2was accompanied by a significant decrease in the expression level of two putative auxin efflux carriers. The ifl1 mutants remained sensitive to auxin and an auxin transport inhibitor. Theifl1-2 mutant exhibited visible phenotypes associated with defects in auxin polar transport such as pin-like inflorescence, reduced numbers of cauline branches, reduced numbers of secondary rosette inflorescence, and dark green leaves with delayed senescence. The visible phenotypes displayed by the ifl1 mutants could be mimicked by treatment of wild-type plants with an auxin polar transport inhibitor. In addition, the auxin polar transport inhibitor altered the normal differentiation of interfascicular fibers in the inflorescence stems of wild-type Arabidopsis. Taken together, these results suggest a correlation between the reduced auxin polar transport and the alteration of cell differentiation and morphology in theifl1 mutants.
The Three-Dimensional Structure of Cystathionine β-Lyase from Arabidopsis and Its Substrate Specificity
Authors: Breitinger Ulrike , Clausen Tim , Ehlert Stephan , Huber Robert , Laber Bernd , Schmidt Frank , Pohl Ehmke , Messerschmidt Albrecht
Published: July 2002

The pyridoxal 5′-phosphate-dependent enzyme cystathionine β-lyase (CBL) catalyzes the penultimate step in the de novo biosynthesis of Met in microbes and plants. Absence of CBL in higher organisms makes it an important target for the development of antibiotics and herbicides. The three-dimensional structure of cystathionine β-lyase from Arabidopsis was determined by Patterson search techniques, using the structure of tobacco (Nicotiana tabacum) cystathionine γ-synthase as starting point. At a resolution of 2.3 Å, the model was refined to a final crystallographic R-factor of 24.9%. The overall structure is very similar to other pyridoxal 5′-phosphate-dependent enzymes of the γ-family. Exchange of a few critical residues within the active site causes the different substrate preferences betweenEscherichia coli and Arabidopsis CBL. Loss of interactions at the α-carboxyl site is the reason for the poorer substrate binding of Arabidopsis CBL. In addition, the binding pocket of Arabidopsis CBL is larger than that of E. coli CBL, explaining the similar binding of l-cystathionine andl-djenkolate in Arabidopsis CBL in contrast to E. coli CBL, where the substrate binding site is optimized for the natural substrate cystathionine.
Estimation of statistical uncertainties in quantitative phase analysis using the Rietveld method and the whole-powder-pattern decomposition method
Authors: Toraya H.
Published: July 2002

Formulae for estimating statistical uncertainties in quantitative phase analysis using the Rietveld method and the whole-powder-pattern decomposition method have been derived. The relative magnitude of statistical uncertainty for a derived weight fraction of a component in a mixture is given by σ(Wm)/Wm= (1/Wm− 1)1/2F(D\textstyle\sum_{i = 1}^NYoi)−1/2, whereWmis the weight fraction of themth component,Fis the goodness-of-fit index,D(≤1) is a factor depending on the degree of peak overlap, and ∑Yoiis the total sum of profile intensities in the 2θ range used for whole-powder-pattern fitting. If the step width Δ2θ in step scanning is halved, ∑Yoiis almost doubled; on the other hand, ∑Yoiis proportional to the fixed counting timeT. Therefore, σ(Wm)/Wm∝ (Δ2θ/T)1/2. Extension of the 2θ range for whole-powder-pattern fitting towards the high-angle region is not effective for improving the precision of the derived weight fractions if the profile intensities in that region are weak. The formulae provide guidelines for optimizing experimental parameters in order to obtain a required precision.
Completion of crystal structures from powder data: the use of the coordination polyhedra
Authors: Altomare Angela , Giacovazzo Carmelo , Guagliardi Antonietta , Moliterni Anna Grazia Giuseppina , Rizzi Rosanna
Published: July 2002

Direct methods applied to powder diffraction data often provide well located heavy atoms and unreliable light-atom positions. The completion of the crystal structure is then not always straightforward and may require a considerable amount of user intervention. The heavy-atom connectivity provided by the trial solution may be used to guess the nature of the coordination polyhedra. A Monte Carlo procedure is described which, in the absence of a well defined structural model, is able to locate the light atoms correctly under the restraints of the experimental heavy-atom connectivity model. The correctness of the final model is assessed by criteria based on the agreement between the whole experimental diffraction pattern and the calculated one. The procedure requires little CPU computing time and has been implemented as a routine ofEXPO[Altomareet al.(1999).J. Appl. Cryst.32, 339–340]. The method has proved to be sufficiently robust against the distortion of the coordination polyhedra and has been successfully applied to some test structures.
Estimating nanoparticle size from diffraction measurements
Authors: Hall B. D. , Zanchet D. , Ugarte D.
Published: July 2002

Nanometre-sized particles are of considerable current interest because of their special size-dependent physical properties. Debye–Scherrer diffraction patterns are often used to characterize samples, as well as to probe the structure of nanoparticles. Unfortunately, the well known `Scherrer formula' is unreliable at estimating particle size, because the assumption of an underlying crystal structure (translational symmetry) is often invalid. A simple approach is presented here which takes the Fourier transform of a Debye–Scherrer diffraction pattern. The method works well on noisy data and when only a narrow range of scattering angles is available.
Quantitative X-ray standing-wave phase analysis by means of photoelectrons
Authors: Mukhamedzhanov E. Kh. , Bocchi C.
Published: July 2002

Quantitative information on a subsurface layer structure is obtained through the determination of the photoelectron escape depth by using the photoelectrons emitted by an X-ray standing wavefield in the range of dynamical X-ray diffraction from high-quality crystals. A simple method to determine the mean escape depthLof low-energy-loss photoelectrons is proposed, based on the analysis of the phase of the X-ray standing wavefield in a specially designed epitaxic structure grown by molecular-beam epitaxy. The valueL= 24 nm is obtained for GaSb crystals with CuKα1radiation as a probe. As an example of the complimentary application of the technique, an Sb-based single-quantum-well structure was analysed by using both high-resolution X-ray diffraction and the X-ray standing-wave method.
Bayesian estimation of hyperparameters for indirect Fourier transformation in small-angle scattering
Authors: Hansen Steen
Published: July 2002

Bayesian analysis is applied to the problem of estimation of hyperparameters, which are necessary for indirect Fourier transformation of small-angle scattering data. The hyperparameters most frequently needed are the overall noise level of the experiment and the maximum dimension of the scatterer. Bayesian methods allow the posterior probability distribution for the hyperparameters to be determined, making it possible to calculate the distance distribution function of interest as the weighted mean of all possible solutions to the indirect transformation problem. Consequently no choice of hyperparameters has to be made. The applicability of the method is demonstrated using simulated as well as real experimental data.
SANS polarization analysis with nuclear spin-polarized 3He
Authors: Gentile T.R. , Jones G.L. , Thompson A.K. , Barker J. , Glinka C.J. , Hammouda B. , Lynn J.W.
Published: July 2002

A neutron spin filter based on transmission through nuclear-spin-polarized 3He gas has been applied to polarization analysis of small angle neutron scattering (SANS). Such spin filters, which are based on the large spin dependence of the absorption of neutrons by 3He, make SANS polarization analysis possible because of their large angular acceptance. In the present experiment, a 3He-based analyzer was employed to separate nuclear scattering into its coherent and spin-incoherent components. Polarized 3He analyzers were prepared by two different optical pumping methods and installed on the NG3 SANS instrument at the NIST Center for Neutron Research (NCNR). Measurements were taken on cellophane tape and silica gel, for which the scattering is almost completely incoherent and coherent, respectively, and on a combined sample. For the combined sample, separation of the coherent part from the incoherent part was successfully demonstrated using polarization analysis.
New approach to stress analysis based on grazing-incidence X-ray diffraction
Authors: Skrzypek S. J. , Baczmański A. , Ratuszek W. , Kusior E.
Published: July 2002

A new development in the determination of residual stresses in thin surface layers and coatings is presented. The procedure, based on the grazing-incidence X-ray diffraction geometry (referred to here as the `g-sin2 ψ' geometry), enables non-destructive measurement at a chosen depth below the sample surface. The penetration depth of the X-ray radiation is well defined and does not change during the experiment. The method is particularly useful for the analysis of non-uniform stresses in near-surface layers. The g-sin2 ψ geometry was applied for measurements of the residual stresses in TiN coatings. Anisotropic diffraction elastic constants of textured material were used to determine the stress value from the measured lattice strains. A new method of data treatment enables reference-free measurements of residual stresses.
Peak labelling in electron density maps from powder data: the use of crystal chemical information
Authors: Altomare Angela , Giacovazzo Carmelo , Ianigro Massimo , Moliterni Anna Grazia Giuseppina , Rizzi Rosanna
Published: July 2002

Direct methods applied to powder diffraction data often provide electron density maps of which the quality is usually affected by systematic and/or random phase errors, by amplitude truncation effects in the series representation of the electron density,etc. The frequent incorrect labelling of the peaks can strongly affect the efficiency of the procedures used for crystal structure refinement. For example, the success of alternative techniques, such asPOLPO[Altomareet al. (2000).J. Appl. Cryst.33, 1305–1310], requires that all the heavy atoms be positioned and exactly labelled.
Two-dimensional intensity profiles of effective satellites
Authors: Morelhão S. L. , Avanci L. H. , Quivy A. A. , Abramof E.
Published: July 2002

The observation of a new X-ray scattering process with synchrotron radiation is reported. The phenomenon is analogous to three-beam diffraction in a single crystal; however, the features in the azimuthal scans are provided by superlattice-satellite reflections instead of bulk reflections. These features were named effective satellites and they are observed over the ordinary satellite reflections as a function of the azimuthal angle. Their occurrences have been monitored in completely different superlattices by mapping the incidence and azimuthal angles of the incident X-ray beam. Effects of structural parameters of the superlattices on the effective satellites as well as the information that can be extracted by measuring their positions are discussed.
The electronic structure of the 3d transition metals
Authors: Weiss R. J. , Mazzone G.
Published: July 2002

The measurements and calculations of the charge, spin and momentum density of the metallic elements Ti to Ni are examined. Both the Compton profiles (momentum density) and X-ray scattering factors (charge density) are shown to provide a direct determination of the cohesive energy. It generally appears that the 3d spin density is contracted relative to the free atom while the 3d charge density builds up at the Wigner–Seitz cell boundary relative to the free atom particularly near the bottom of the band. No theoretical calculation is available which evaluates charge, spin and momentum density as well as cohesive energy. In addition, a significant disparity between theory and experiment exists for the momentum and charge density anisotropies in the b.c.c. metals. Suggested areas for further work are given.
Facilities for solution scattering and fibre diffraction at the Daresbury SRS
Authors: Nave C. , Helliwell J. R. , Moore P. R. , Thompson A. W. , Worgan J. S. , Greenall R. J. , Miller A. , Burley S. K. , Bradshaw J. , Pigram W. J. , Fuller W. , Siddons D. P. , Deutsch M. , Tragear R. T.
Published: July 2002

The small-angle scattering facility at Daresbury has been constructed for diffraction studies of a wide range of naturally occurring and synthetic materials. The high brightness of the SRS is combined with focusing optics, resulting in exposure times that can be two or three orders of magnitude less than those required on a conventional source. Spacings of 2000 Å in the vertical direction and 300 Å in the horizontal direction can be observed, while the resolution between diffraction orders is 5000 and 600 Å. In addition, preliminary results have been obtained on a double-crystal diffractometer that has a resolution, in one dimension, of better than 26 000 Å. For high-angle fibre diffraction studies, a camera with pinhole collimation has been constructed. Examples from solution scattering and fibre diffraction are used to illustrate the performance of these facilities.
Comments on The accuracy of experimental radial distribution functions for metallic glasses by B.J. Thijsse (1984)
Authors: Hajdu F. , Herms G.
Published: July 2002

The interpretation of a relationship between measured intensities and the radial distribution function given in the paper `The accuracy of experimental radial distribution functions for metallic glasses' [Thijsse (1984). J. Appl. Cryst.
17, 61–76] is disputed.