bluuebunny/crossref_metadata_2025 huggingface dataset:
OpenAlea: a visual programming and component-based software platform for plant modelling
Authors: Pradal Christophe , Dufour-Kowalski Samuel , Boudon Frédéric , Fournier Christian , Godin Christophe
Published: November 2008

The development of functional–structural plant models requires an increasing amount of computer modelling. All these models are developed by different teams in various contexts and with different goals. Efficient and flexible computational frameworks are required to augment the interaction between these models, their reusability, and the possibility to compare them on identical datasets. In this paper, we present an open-source platform, OpenAlea, that provides a user-friendly environment for modellers, and advanced deployment methods. OpenAlea allows researchers to build models using a visual programming interface and provides a set of tools and models dedicated to plant modelling. Models and algorithms are embedded in OpenAlea ‘components’ with well defined input and output interfaces that can be easily interconnected to form more complex models and define more macroscopic components. The system architecture is based on the use of a general purpose, high-level, object-oriented script language, Python, widely used in other scientific areas. We present a brief rationale that underlies the architectural design of this system and we illustrate the use of the platform to assemble several heterogeneous model components and to rapidly prototype a complex modelling scenario.
Why Leaves Turn Red in Autumn. The Role of Anthocyanins in Senescing Leaves of Red-Osier Dogwood
Authors: Feild Taylor S. , Lee David W. , Holbrook N. Michele
Published: November 2008

Why the leaves of many woody species accumulate anthocyanins prior to being shed has long puzzled biologists because it is unclear what effects anthocyanins may have on leaf function. Here, we provide evidence for red-osier dogwood (Cornus stolonifera) that anthocyanins form a pigment layer in the palisade mesophyll layer that decreases light capture by chloroplasts. Measurements of leaf absorbance demonstrated that red-senescing leaves absorbed more light of blue-green to orange wavelengths (495–644 nm) compared with yellow-senescing leaves. Using chlorophyll afluorescence measurements, we observed that maximum photosystem II (PSII) photon yield of red-senescing leaves recovered from a high-light stress treatment, whereas yellow-senescing leaves failed to recover after 6 h of dark adaptation, which suggests photo-oxidative damage. Because no differences were observed in light response curves of effective PSII photon yield for red- and yellow-senescing leaves, differences between red- and yellow-senescing cannot be explained by differences in the capacities for photochemical and non-photochemical light energy dissipation. A role of anthocyanins as screening pigments was explored further by measuring the responses PSII photon yield to blue light, which is preferentially absorbed by anthocyanins, versus red light, which is poorly absorbed. We found that dark-adapted PSII photon yield of red-senescing leaves recovered rapidly following illumination with blue light. However, red light induced a similar, prolonged decrease in PSII photon yield in both red- and yellow-senescing leaves. We suggest that optical masking of chlorophyll by anthocyanins reduces risk of photo-oxidative damage to leaf cells as they senesce, which otherwise may lower the efficiency of nutrient retrieval from senescing autumn leaves.
Low Ascorbic Acid in the vtc-1 Mutant of Arabidopsis Is Associated with Decreased Growth and Intracellular Redistribution of the Antioxidant System
Authors: Veljovic-Jovanovic Sonja D. , Pignocchi Cristina , Noctor Graham , Foyer Christine H.
Published: November 2008

Ascorbic acid has numerous and diverse roles in plant metabolism. We have used the vtc-1 mutant of Arabidopsis, which is deficient in ascorbate biosynthesis, to investigate the role of ascorbate concentration in growth, regulation of photosynthesis, and control of the partitioning of antioxidative enyzmes. The mutant possessed 70% less ascorbate in the leaves compared with the wild type. This lesion was associated with a slight increase in total glutathione but no change in the redox state of either ascorbate or glutathione. In vtc-1, total ascorbate in the apoplast was decreased to 23% of the wild-type value. The mutant displayed much slower shoot growth than the wild type when grown in air or at high CO2 (3 mL L−1), where oxidative stress is diminished. Leaves were smaller, and shoot fresh weight and dry weight were lower in the mutant. No significant differences in the light saturation curves for CO2 assimilation were found in air or at high CO2, suggesting that the effect on growth was not due to decreased photosynthetic capacity in the mutant. Analysis of chlorophyll a fluorescence quenching revealed only a slight effect on non-photochemical energy dissipation. Hydrogen peroxide contents were similar in the leaves of thevtc-1 mutant and the wild type. Total leaf peroxidase activity was increased in the mutant and compartment-specific differences in ascorbate peroxidase (APX) activity were observed. In agreement with the measurements of enzyme activity, the expression of cytosolic APX was increased, whereas that for chloroplast APX isoforms was either unchanged or slightly decreased. These data implicate ascorbate concentration in the regulation of the compartmentalization of the antioxidant system in Arabidopsis.
Control of Specific Gene Expression by Gibberellin and Brassinosteroid
Authors: Bouquin Thomas , Meier Carsten , Foster Randy , Nielsen Mads Eggert , Mundy John
Published: November 2008

We identified a recessive, brassinolide-insensitive mutant caused by a deletion allele (bri1-201) of the brassinosteroid (BR) receptor BRI1. The bri1-201 mutant displayed altered expression levels of genes differentially regulated by gibberellin (GA). RNA-blot analysis revealed that BR and GA antagonistically regulate the accumulation of mRNAs of the GA-responsive GASA1 gene, as well as the GA-repressibleGA5 gene. Expression studies with cycloheximide indicated that the antagonistic effects of GA and BR onGA5 require de novo protein synthesis. Reporter transgene analyses and RNA-blot analysis showed that BR and GA modulateGA5 expression, at least in part, at the transcriptional level, and that the signals are independent and subtractive.
Brachypodium distachyon. A New Model System for Functional Genomics in Grasses
Authors: Draper John , Mur Luis A.J. , Jenkins Glyn , Ghosh-Biswas Gadab C. , Bablak Pauline , Hasterok Robert , Routledge Andrew P.M.
Published: November 2008

A new model for grass functional genomics is described based on Brachypodium distachyon, which in the evolution of the Pooideae diverged just prior to the clade of “core pooid” genera that contain the majority of important temperate cereals and forage grasses. Diploid ecotypes of B.distachyon (2n = 10) have five easily distinguishable chromosomes that display high levels of chiasma formation at meiosis. The B. distachyonnuclear genome was indistinguishable in size from that of Arabidopsis, making it the simplest genome described in grasses to date.B. distachyon is a self-fertile, inbreeding annual with a life cycle of less than 4 months. These features, coupled with its small size (approximately 20 cm at maturity), lack of seed-head shatter, and undemanding growth requirements should make it amenable to high-throughput genetics and mutant screens. Immature embryos exhibited a high capacity for plant regeneration via somatic embryogenesis. Regenerated plants display very low levels of albinism and have normal fertility. A simple transformation system has been developed based on microprojectile bombardment of embryogenic callus and hygromycin selection. SelectedB. distachyon ecotypes were resistant to all tested cereal-adapted Blumeria graminis species and cereal brown rusts (Puccinia reconditia). In contrast, different ecotypes displayed resistance or disease symptoms following challenge with the rice blast pathogen (Magnaporthe grisea) and wheat/barley yellow stripe rusts (Puccinia striformis). Despite its small stature, B.distachyon has large seeds that should prove useful for studies on grain filling. Such biological characteristics represent important traits for study in temperate cereals.
Native and Artificial Reticuloplasmins Co-Accumulate in Distinct Domains of the Endoplasmic Reticulum and in Post-Endoplasmic Reticulum Compartments
Authors: Torres Esperanza , Gonzalez-Melendi Pablo , Stöger Eva , Shaw Peter , Twyman Richard M. , Nicholson Liz , Vaquero Carmen , Fischer Rainer , Christou Paul , Perrin Yolande
Published: November 2008

We compared the subcellular distribution of native and artificial reticuloplasmins in endosperm, callus, and leaf tissues of transgenic rice (Oryza sativa) to determine the distribution of these proteins among endoplasmic reticulum (ER) and post-ER compartments. The native reticuloplasmin was calreticulin. The artificial reticuloplasmin was a recombinant single-chain antibody (scFv), expressed with an N-terminal signal peptide and the C-terminal KDEL sequence for retrieval to the ER (scFvT84.66-KDEL). We found that both molecules were distributed in the same manner. In endosperm, each accumulated in ER-derived prolamine protein bodies, but also in glutelin protein storage vacuoles, even though glutelins are known to pass through the Golgi apparatus en route to these organelles. This finding may suggest that similar mechanisms are involved in the sorting of reticuloplasmins and rice seed storage proteins. However, the presence of reticuloplasmins in protein storage vacuoles could also be due to simple dispersal into these compartments during protein storage vacuole biogenesis, before glutelin deposition. In callus and leaf mesophyll cells, both reticuloplasmins accumulated in ribosome-coated vesicles probably derived directly from the rough ER.
Inhibition of Plastocyanin to P700 +Electron Transfer inChlamydomonas reinhardtiiby Hyperosmotic Stress
Authors: Cruz Jeffrey A. , Salbilla Brian A. , Kanazawa Atsuko , Kramer David M.
Published: November 2008

Oxygen electrode and fluorescence studies demonstrate that linear electron transport in the freshwater alga Chlamydomonas reinhardtii can be completely abolished by abrupt hyperosmotic shock. We show that the most likely primary site of inhibition of electron transfer by hyperosmotic shock is a blockage of electron transfer between plastocyanin (PC) or cytochromec6 and P700. The effects on this reaction were reversible upon dilution of the osmolytes and the stability of plastocyanin or photosystem (PS) I was unaffected. Electron micrographs of osmotically shocked cells showed a significant decrease in the thylakoid lumen volume. Comparison of estimated lumenal width with the x-ray structures of plastocyanin and PS I suggest that lumenal space contracts during HOS so as to hinder the movement of docking to PS I of plastocyanin or cytochromec  6.
Different Myrosinase and Idioblast Distribution in Arabidopsis and Brassica napus
Authors: Andréasson Erik , Jørgensen Lise Bolt , Höglund Anna-Stina , Rask Lars , Meijer Johan
Published: November 2008

Myrosinase (EC 3.2.3.1) is a glucosinolate-degrading enzyme mainly found in special idioblasts, myrosin cells, in Brassicaceae. This two-component system of secondary products and degradative enzymes is important in plant-insect interactions. Immunocytochemical analysis of Arabidopsis localized myrosinase exclusively to myrosin cells in the phloem parenchyma, whereas no myrosin cells were detected in the ground tissue. In Brassica napus, myrosinase could be detected in myrosin cells both in the phloem parenchyma and in the ground tissue. The myrosin cells were similar in Arabidopsis and B. napus and were found to be different from the companion cells and the glucosinolate-containing S-cells present in Arabidopsis. Confocal laser scanning immunomicroscopy analysis of myrosin cells inB. napus embryos showed that the myrosin grains constitute a continuous reticular system in the cell. These findings indicate that in the two species studied, initial cells creating the ground tissue have different potential for making idioblasts and suggest that the myrosinase-glucosinolate system has at least partly different functions. Several myrosinases in B. napusextracts are recovered in complex together with myrosinase-binding protein (MBP), and the localization of MBP was therefore studied in situ. The expression of MBP was highest in germinating seedlings ofB. napus and was found in every cell except the myrosin cells of the ground tissue. Rapid disappearance of the MBP from the non-myrosin cells and emergence of MBP in the myrosin cells resulted in an apparent colocalization of MBP and myrosinase in 7-d-old seedlings.
Expression of β-Expansins Is Correlated with Internodal Elongation in Deepwater Rice
Authors: Lee Yi , Kende Hans
Published: November 2008

Fourteen putative rice (Oryza sativa) β-expansin genes, Os-EXPB1 through Os-EXPB14, were identified in the expressed sequence tag and genomic databases. The DNA and deduced amino acid sequences are highly conserved in all 14 β-expansins. They have a series of conserved C (cysteine) residues in the N-terminal half of the protein, an HFD (histidine-phenylalanine-aspartate) motif in the central region, and a series of W (tryptophan) residues near the carboxyl terminus. Five β-expansin genes are expressed in deepwater rice internodes, with especially high transcript levels in the growing region. Expression of four β-expansin genes in the internode was induced by treatment with gibberellin and by wounding. The wound response resulted from excising stem sections or from piercing pinholes into the stem of intact plants. The level of wound-induced β-expansin transcripts declined rapidly 5 h after cutting of stem sections. We conclude that the expression of β-expansin genes is correlated with rapid elongation of deepwater rice internodes, it is induced by gibberellin and wounding, and wound-induced β-expansin mRNA appears to turn over rapidly.
The Glyoxylate Cycle in an Arbuscular Mycorrhizal Fungus. Carbon Flux and Gene Expression
Authors: Lammers Peter J. , Jun Jeongwon , Abubaker Jehad , Arreola Raul , Gopalan Anjali , Bago Berta , Hernandez-Sebastia Cinta , Allen James W. , Douds David D. , Pfeffer Philip E. , Shachar-Hill Yair
Published: November 2008

The arbuscular mycorrhizal (AM) symbiosis is responsible for huge fluxes of photosynthetically fixed carbon from plants to the soil. Lipid, which is the dominant form of stored carbon in the fungal partner and which fuels spore germination, is made by the fungus within the root and is exported to the extraradical mycelium. We tested the hypothesis that the glyoxylate cycle is central to the flow of carbon in the AM symbiosis. The results of 13C labeling of germinating spores and extraradical mycelium with13C2-acetate and13C2-glycerol and analysis by nuclear magnetic resonance spectroscopy indicate that there are very substantial fluxes through the glyoxylate cycle in the fungal partner. Full-length sequences obtained by polymerase chain reaction from a cDNA library from germinating spores of the AM fungus Glomus intraradices showed strong homology to gene sequences for isocitrate lyase and malate synthase from plants and other fungal species. Quantitative real-time polymerase chain reaction measurements show that these genes are expressed at significant levels during the symbiosis. Glyoxysome-like bodies were observed by electron microscopy in fungal structures where the glyoxylate cycle is expected to be active, which is consistent with the presence in both enzyme sequences of motifs associated with glyoxysomal targeting. We also identified among several hundred expressed sequence tags several enzymes of primary metabolism whose expression during spore germination is consistent with previous labeling studies and with fluxes into and out of the glyoxylate cycle.
Overexpression of Malate Dehydrogenase in Transgenic Alfalfa Enhances Organic Acid Synthesis and Confers Tolerance to Aluminum
Authors: Tesfaye Mesfin , Temple Stephen J. , Allan Deborah L. , Vance Carroll P. , Samac Deborah A.
Published: November 2008

Al toxicity is a severe impediment to production of many crops in acid soil. Toxicity can be reduced through lime application to raise soil pH, however this amendment does not remedy subsoil acidity, and liming may not always be practical or cost-effective. Addition of organic acids to plant nutrient solutions alleviates phytotoxic Al effects, presumably by chelating Al and rendering it less toxic. In an effort to increase organic acid secretion and thereby enhance Al tolerance in alfalfa (Medicago sativa), we produced transgenic plants using nodule-enhanced forms of malate dehydrogenase and phosphoenolpyruvate carboxylase cDNAs under the control of the constitutive cauliflower mosaic virus 35S promoter. We report that a 1.6-fold increase in malate dehydrogenase enzyme specific activity in root tips of selected transgenic alfalfa led to a 4.2-fold increase in root concentration as well as a 7.1-fold increase in root exudation of citrate, oxalate, malate, succinate, and acetate compared with untransformed control alfalfa plants. Overexpression of phosphoenolpyruvate carboxylase enzyme specific activity in transgenic alfalfa did not result in increased root exudation of organic acids. The degree of Al tolerance by transformed plants in hydroponic solutions and in naturally acid soil corresponded with their patterns of organic acid exudation and supports the concept that enhancing organic acid synthesis in plants may be an effective strategy to cope with soil acidity and Al toxicity.
A Chloroplast Protein Homologous to the Eubacterial Topological Specificity Factor MinE Plays a Role in Chloroplast Division
Authors: Itoh Ryuuichi , Fujiwara Makoto , Nagata Noriko , Yoshida Shigeo
Published: November 2008

We report the identification of a nucleus-encodedminE gene, designated AtMinE1, of Arabidopsis. The encoded AtMinE1 protein possesses both N- and C-terminal extensions, relative to the eubacterial and algal chloroplast-encoded MinE proteins. The N-terminal extension functioned as a chloroplast-targeting transit peptide, as revealed by a transient expression assay using an N terminus:green fluorescent protein fusion. Histochemical β-glucuronidase staining of transgenic Arabidopsis lines harboring an AtMinE1promoter::uidA reporter fusion unveiled specific activation of the promoter in green tissues, especially at the shoot apex, which suggests a requirement for cell division-associatedAtMinE1 expression for proplastid division in green tissues. In addition, we generated transgenic plants overexpressing a full-length AtMinE1 cDNA and examined the subcellular structures of those plants. Giant heteromorphic chloroplasts were observed in transgenic plants, with a reduced number per cell, whereas mitochondrial morphology remained similar to that of wild-type plants. Taken together, these observations suggest that MinE is the third conserved component involved in chloroplast division.
Differential Regulation of Transcripts Encoding Cytosolic NADP-Malic Enzyme in C3 and C4 FlaveriaSpecies
Authors: Lai Lien B. , Tausta S. Lorraine , Nelson Timothy M.
Published: November 2008

A cytosolic NADP-malic enzyme (CYTME) has been described previously in several plants, all C3 species. CYTME is distinct from the chloroplastic NADP-malic enzyme (CHLME) that is highly active in C4 species. We show that at least oneCytMe gene is present in all Flaveriaspp., including C3, C4, and C3-C4 intermediate types. Based on theCytMe expression patterns in Flaveria pringlei (C3) and Flaveria trinervia(C4), we suggest CYTME has several distinct roles, including the supplying of NADPH for cytosolic metabolism, the supporting of wound response or repair, and the balancing of cellular pH in illuminated leaves. These three roles are likely correlated withCytMe mRNAs of apparent sizes 2.0, 2.2, and 2.4 kb, respectively, which differ in the length of the 5′ untranslated regions. Various regulatory mechanisms involving RNA processing and translational efficiency are discussed.
The Arabidopsis Gene Tardy Asynchronous Meiosis Is Required for the Normal Pace and Synchrony of Cell Division during Male Meiosis
Authors: Magnard Jean-Louis , Yang Ming , Chen Yun-Chia Sophia , Leary Michele , McCormick Sheila
Published: November 2008

Male meiosis in higher organisms features synchronous cell divisions in a large number of cells. It is not clear how this synchrony is achieved, nor is it known whether the synchrony is linked to the regulation of cell cycle progression. Here, we describe an Arabidopsis mutant, named tardy asynchronous meiosis(tam), that exhibits a phenotype of delayed and asynchronous cell divisions during male meiosis. In Arabidopsis, two nuclear divisions occur before simultaneous cytokinesis yields a tetrad of haploid cells. In tam, cell divisions are delayed, resulting in the formation of abnormal intermediates, most frequently dyad meiotic products, or in rare cases, dyad pollen (two gametophytes within one exine wall). Temperature-shift experiments showed that the percentage of the abnormal intermediates increased at 27°C. Analysis of tam and thetam/quartet1 double mutant showed that most of these abnormal intermediates could continue through the normal rounds of cell divisions and form functional pollen, though at a slower than normal pace. The asynchrony of cell division started at the G2/M transition, with cells entering metaphase at different time points, during both meiosis I and II. In addition, chromosome condensation defects and mis-segregation were sometimes observed intam. These observations suggest that the TAM protein positively regulates cell cycle progression, perhaps by promoting the G2/M transition. We speculate that there is a signal, perhaps TAM, that couples the normal pace of cell cycle progression with the synchrony of cell division during male meiosis.
Characterization of a Tomato Xyloglucan Endotransglycosylase Gene That Is Down-Regulated by Auxin in Etiolated Hypocotyls
Authors: Catalá Carmen , Rose Jocelyn K.C. , York William S. , Albersheim Peter , Darvill Alan G. , Bennett Alan B.
Published: November 2008

The reorganization of the cellulose-xyloglucan matrix is proposed to serve as an important mechanism in the control of strength and extensibility of the plant primary cell wall. One of the key enzymes associated with xyloglucan metabolism is xyloglucan endotransglycosylase (XET), which catalyzes the endocleavage and religation of xyloglucan molecules. As with other plant species, XETs are encoded by a gene family in tomato (Lycopersicon esculentum cv T5). In a previous study, we demonstrated that the tomato XET gene LeEXT was abundantly expressed in the rapidly expanding region of the etiolated hypocotyl and was induced to higher levels by auxin. Here, we report the identification of a new tomato XET gene, LeXET2, that shows a different spatial expression and diametrically opposite pattern of auxin regulation fromLeEXT. LeXET2 was expressed more abundantly in the mature nonelongating regions of the hypocotyl, and its mRNA abundance decreased dramatically following auxin treatment of etiolated hypocotyl segments. Analysis of the effect of several plant hormones on LeXET2 expression revealed that the inhibition of LeXET2 mRNA accumulation also occurred with cytokinin treatment. LeXET2 mRNA levels increased significantly in hypocotyl segments treated with gibberellin, but this increase could be prevented by adding auxin or cytokinin to the incubation media. Recombinant LeXET2 protein obtained by heterologous expression in Pichia pastoris exhibited greater XET activity against xyloglucan from tomato than that from three other species. The opposite patterns of expression and differential auxin regulation of LeXET2 and LeEXT suggest that they encode XETs with distinct roles during plant growth and development.
Inactivation of the Phloem-Specific Dof Zinc Finger GeneDAG1Affects Response to Light and Integrity of the Testa of Arabidopsis Seeds
Authors: Papi Maura , Sabatini Sabrina , Altamura Maria Maddalena , Hennig Lars , Schäfer Eberhard , Costantino Paolo , Vittorioso Paola
Published: November 2008

We show here that seeds from the knockout mutant of the Arabidopsis DAG1 gene encoding a Dof zinc finger transcription factor have an altered response to red and far-red light. Mutant dag1 seeds are induced to germinate by much lower red light fluence rates, and germination reaches more quickly a point where it is independent of phytochrome signaling. Moreover, although microscopic analysis reveals no obvious structural alterations in the seed coat (testa) of dag1 seeds, staining assays with different dyes point to an abnormal fragility of the testa. By extensive in situ mRNA hybridization analysis we show here that the gene, which is not expressed in the embryo, is specifically expressed in the phloem of all organs of the mother plant.
Quantitative Analysis of Indole-3-Acetic Acid Metabolites in Arabidopsis
Authors: Kowalczyk Mariusz , Sandberg Göran
Published: November 2008

A general gas chromatography/mass spectrometry (MS)-based screen was performed to identify catabolites and conjugates of indole-3-acetic acid (IAA) during vegetative growth of Arabidopsis. This experiment revealed the existence of two new conjugates:N-(indole-3-acetyl)-alfa-alanine (IA-Ala) andN-(indole-3-acetyl)-alfa-leucine (IA-Leu). A method for quantitative analysis of IAA metabolites in plant extracts by liquid chromatography-electrospray tandem MS has been developed. The accuracy and precision of the new method are better than 10% for standards close to the detection limit, and are between 6% and 16% for the entire protocol applied to plant extracts. The low detection limits, 0.02 to 0.1 pmol for the different metabolites, made it possible to use as little as 50 to 100 mg of tissue for quantitative analysis. The analysis was performed on different tissues of an Arabidopsis plant at two stages of development, using heavy labeled internal standards of the catabolite 2-oxoindole-3-acetic acid as well as IAA conjugated to amino acids: aspartate, glutamate, Ala, and Leu. Expanding leaves and roots that generally contain high amounts of the free hormone also contained the highest levels of IA-aspartate, IA-glutamate, and 2-oxoindole-3-acetic acid, supporting their role as irreversible catabolic products. The levels of IA-Leu and IA-Ala did not follow the general distribution of IAA. Interestingly, the level of IA-Leu was highest in roots and IA-Ala in the aerial tissues.
A Condensing Enzyme from the Seeds of Lesquerella fendleri That Specifically Elongates Hydroxy Fatty Acids
Authors: Moon Hangsik , Smith Mark A. , Kunst Ljerka
Published: November 2008

Lesquerella fendleri seed oil contains up to 60% hydroxy fatty acids, nearly all of which is the 20-carbon hydroxy fatty acid lesquerolic acid (d-14-hydroxyeicos-cis-11-enoic acid). Previous work suggested that lesquerolic acid inL. fendleri was formed by the elongation of the 18-carbon hydroxy fatty acid, ricinoleic acid. To identify a gene encoding the enzyme involved in hydroxy fatty acid elongation, anL. fendleri genomic DNA library was screened using the coding region of the Arabidopsis Fatty Acid Elongation1gene as a probe. A gene, LfKCS3, with a high sequence similarity to known very long-chain fatty acid condensing enzymes, was isolated. LfKCS3 has a 2,062-bp open reading frame interrupted by two introns, which encodes a polypeptide of 496 amino acids. LfKCS3 transcripts accumulated only in the embryos of L. fendleri and first appeared in the early stages of development. Fusion of theLfKCS3 promoter to the uidA reporter gene and expression in transgenic Arabidopsis resulted in a high level of β-glucuronidase activity exclusively in developing embryos. Seeds of Arabidopsis plants transformed with LfKCS3 showed no change in their very long-chain fatty acid content. However, when these Arabidopsis plants were crossed with the transgenic plants expressing the castor oleate 12-hydroxylase, significant amounts of 20-carbon hydroxy fatty acids accumulated in the seed, indicating that the LfKCS3 condensing enzyme specifically catalyzes elongation of 18-carbon hydroxy fatty acids.
Components of the Arabidopsis C-Repeat/Dehydration-Responsive Element Binding Factor Cold-Response Pathway Are Conserved inBrassica napus and Other Plant Species
Authors: Jaglo Kirsten R. , Kleff Susanne , Amundsen Keenan L. , Zhang Xin , Haake Volker , Zhang James Z. , Deits Thomas , Thomashow Michael F.
Published: November 2008

Many plants increase in freezing tolerance in response to low, nonfreezing temperatures, a phenomenon known as cold acclimation. Cold acclimation in Arabidopsis involves rapid cold-induced expression of the C-repeat/dehydration-responsive element binding factor (CBF) transcriptional activators followed by expression of CBF-targeted genes that increase freezing tolerance. Here, we present evidence for a CBF cold-response pathway in Brassica napus. We show thatB. napus encodes CBF-like genes and that transcripts for these genes accumulate rapidly in response to low temperature followed closely by expression of the cold-regulatedBn115 gene, an ortholog of the Arabidopsis CBF-targetedCOR15a gene. Moreover, we show that constitutive overexpression of the Arabidopsis CBF genes in transgenic B. napus plants induces expression of orthologs of Arabidopsis CBF-targeted genes and increases the freezing tolerance of both nonacclimated and cold-acclimated plants. Transcripts encoding CBF-like proteins were also found to accumulate rapidly in response to low temperature in wheat (Triticum aestivumL. cv Norstar) and rye (Secale cereale L. cv Puma), which cold acclimate, as well as in tomato (Lycopersicon esculentum var. Bonny Best, Castle Mart, Micro-Tom, and D Huang), a freezing-sensitive plant that does not cold acclimate. An alignment of the CBF proteins from Arabidopsis, B. napus, wheat, rye, and tomato revealed the presence of conserved amino acid sequences, PKK/RPAGRxKFxETRHP and DSAWR, that bracket the AP2/EREBP DNA binding domains of the proteins and distinguish them from other members of the AP2/EREBP protein family. We conclude that components of the CBF cold-response pathway are highly conserved in flowering plants and not limited to those that cold acclimate.
Different Sugar Kinases Are Involved in the Sugar Sensing ofGaldieria sulphuraria
Authors: Oesterhelt Christine , Gross Wolfgang
Published: November 2008

The unicellular acidophilic red alga Galdieria sulphuraria is a facultative heterotroph with a complex uptake system for sugars and polyols, consisting of at least 14 transporters. Upon transfer to heterotrophic conditions, these transporters were induced simultaneously. Once induced, transporters for common hexoses and pentoses are apparently not down-regulated under heterotrophic conditions. Uptake of deoxysugars (FUC/Rha), however, was repressed by substrates metabolized via gluco-, galacto-, glycero-, or hexokinase, whereas substrates phosphorylated by xylulokinase had no effect. This indicates that several sugar kinases play a key role in sugar sensing. In contrast, polyol transporters were repressed only by glucose or its analogs but not by other sugars. This repression does not involve the activity of kinases. Most likely this type of glucose sensing is independent of metabolism and takes place prior to or during uptake. In its natural environment, these two different sensing mechanisms would enable the alga to utilize a mixture of different substrates in a most economic way by repressing dispensible transporters.
Voltage-Dependent Cation Channels Permeable to NH4
+, K+, and Ca2+ in the Symbiosome Membrane of the Model Legume Lotus japonicus
Authors: Roberts Daniel M. , Tyerman Stephen D.
Published: November 2008

The symbiosome of nitrogen fixing root nodules mediates metabolite exchange between endosymbiotic rhizobia bacteria and the legume host. In the present study, the ion currents of the symbiosome membrane of the model legume Lotus japonicus were analyzed by patch-clamp recording. Both excised and symbiosome-attached patches exhibited a large inward (toward the cytosolic side of the membrane) current that is activated in a time-dependent manner by negative (on the cytosolic side) potentials. Based on reversal potential determinations and recordings with the impermeant cationN-methyl-glucamine, this current shows a high permeability for monovalent cations with no apparent permeability for anions. The current also showed a finite Ca2+ permeability. However, the currents were predominantly carried by univalent cations with a slightly greater selectivity for NH4  +over K+. Increased Ca2+ concentration inhibited the current with a K  0.5 for inhibition of 0.317 mm. The current showed strong rectification that is mediated by divalent cations (either Mg2+ or Ca2+). The influence of divalent cations is symmetrical in nature, because rectification can be exerted in either direction depending upon which side of the membrane has the highest concentration of divalent cations. However, based on observations with symbiosome-attached patches, the direction of the current in vivo is proposed to be toward the cytosol with cytosolic Mg2+acting as the putative gating regulator. The findings suggest thatL. japonicus possesses a voltage-dependent cation efflux channel that is capable of exporting fixed NH4  +, and may also play an additional role in Ca2+ transport.
FQR1, a Novel Primary Auxin-Response Gene, Encodes a Flavin Mononucleotide-Binding Quinone Reductase
Authors: Laskowski Marta J. , Dreher Kate A. , Gehring Mary A. , Abel Steffen , Gensler Arminda L. , Sussex Ian M.
Published: November 2008

FQR1 is a novel primary auxin-response gene that codes for a flavin mononucleotide-binding flavodoxin-like quinone reductase. Accumulation of FQR1 mRNA begins within 10 min of indole-3-acetic acid application and reaches a maximum of approximately 10-fold induction 30 min after treatment. This increase in FQR1 mRNA abundance is not diminished by the protein synthesis inhibitor cycloheximide, demonstrating thatFQR1 is a primary auxin-response gene. Sequence analysis reveals that FQR1 belongs to a family of flavin mononucleotide-binding quinone reductases. Partially purified His-tagged FQR1 isolated fromEscherichia coli catalyzes the transfer of electrons from NADH and NADPH to several substrates and exhibits in vitro quinone reductase activity. Overexpression of FQR1 in plants leads to increased levels of FQR1 protein and quinone reductase activity, indicating that FQR1 functions as a quinone reductase in vivo. In mammalian systems, glutathione S-transferases and quinone reductases are classified as phase II detoxification enzymes. We hypothesize that the auxin-inducible glutathioneS-transferases and quinone reductases found in plants also act as detoxification enzymes, possibly to protect against auxin-induced oxidative stress.
Biochemical and Molecular Characterization of a Mutation That Confers a Decreased Raffinosaccharide and Phytic Acid Phenotype on Soybean Seeds
Authors: Hitz William D. , Carlson Thomas J. , Kerr Phil S. , Sebastian Scott A.
Published: November 2008

A single, recessive mutation in soybean (Glycine max L. Merr.), which confers a seed phenotype of increased inorganic phosphate, decreased phytic acid, and a decrease in total raffinosaccharides, has been previously disclosed (S.A. Sebastian, P.S. Kerr, R.W. Pearlstein, W.D. Hitz [2000] Soy in Animal Nutrition, pp 56–74). The genetic lesion causing the multiple changes in seed phenotype is a single base change in the third base of the codon for what is amino acid residue 396 of the mature peptide encoding a seed-expressed myo-inositol 1-phospate synthase gene. The base change causes residue 396 to change from lysine to asparagine. That amino acid change decreases the specific activity of the seed-expressed myo-inositol 1-phosphate synthase by about 90%. Radio tracer experiments indicate that the supply ofmyo-inositol to the reaction, which converts UDP-galactose and myo-inositol to galactinol is a controlling factor in the conversion of total carbohydrate into the raffinosaccharides in both wild-type and mutant lines. That same decrease in myo-inositol 1-phosphate synthetic capacity leads to a decreased capacity for the synthesis ofmyo-inositol hexaphosphate (phytic acid) and a concomitant increase in inorganic phosphate.
Characterization of Calcium Oxalates Generated as Biominerals in Cacti
Authors: Monje Paula V. , Baran Enrique J.
Published: November 2008

The chemical composition and morphology of solid material isolated from various Cactaceae species have been analyzed. All of the tested specimens deposited high-purity calcium oxalate crystals in their succulent modified stems. These deposits occurred most frequently as round-shaped druses that sometimes coexist with abundant crystal sand in the tissue. The biominerals were identified either as CaC2O4.2H2O (weddellite) or as CaC2O4.H2O (whewellite). Seven different species from the Opuntioideae subfamily showed the presence of whewellite, and an equal number of species from the Cereoideae subfamily showed the deposition of weddellite. The chemical nature of these deposits was assessed by infrared spectroscopy. The crystal morphology of the crystals was visualized by both conventional light and scanning electron microscopy. Weddellite druses were made up of tetragonal crystallites, whereas those from whewellite were most often recognized by their acute points and general star-like shape. These studies clearly demonstrated that members from the main traditional subfamilies of the Cactaceae family could synthesize different chemical forms of calcium oxalate, suggesting a definite but different genetic control. The direct relationship established between a given Cactaceae species and a definite calcium oxalate biomineral seems to be a useful tool for plant identification and chemotaxonomy.
Leaf Senescence Induced by Mild Water Deficit Follows the Same Sequence of Macroscopic, Biochemical, and Molecular Events as Monocarpic Senescence in Pea
Authors: Pic Emmanuelle , de la Serve Bernard Teyssendier , Tardieu François , Turc Olivier
Published: November 2008

We have compared the time course of leaf senescence in pea (Pisum sativum L. cv Messire) plants subjected to a mild water deficit to that of monocarpic senescence in leaves of three different ages in well-watered plants and to that of plants in which leaf senescence was delayed by flower excision. The mild water deficit (with photosynthesis rate maintained at appreciable levels) sped up senescence by 15 d (200°Cd), whereas flower excision delayed it by 17 d (270°Cd) compared with leaves of the same age in well-watered plants. The range of life spans in leaves of different ages in control plants was 25 d (340°Cd). In all cases, the first detected event was an increase in the mRNA encoding a cysteine-proteinase homologous to Arabidopsis SAG2. This happened while the photosynthesis rate and the chlorophyll and protein contents were still high. The 2-fold variability in life span of the studied leaves was closely linked to the duration from leaf unfolding to the beginning of accumulation of this mRNA. In contrast, the duration of the subsequent phases was essentially conserved in all studied cases, except in plants with excised flowers, where the degradation processes were slower. These results suggest that senescence in water-deficient plants was triggered by an early signal occurring while leaf photosynthesis was still active, followed by a program similar to that of monocarpic senescence. They also suggest that reproductive development plays a crucial role in the triggering of senescence.
Insights into the Functional Architecture of the Catalytic Center of a Maize β-Glucosidase Zm-p60.1
Authors: Zouhar Jan , Vévodová Jitka , Marek Jaromı́r , Damborský Jir̆ı́ , Su Xiao-Dong , Brzobohatý Br̆etislav
Published: November 2008

The maize (Zea mays) β-glucosidase Zm-p60.1 has been implicated in regulation of plant development by the targeted release of free cytokinins from cytokinin-O-glucosides, their inactive storage forms. The crystal structure of the wild-type enzyme was solved at 2.05-Å resolution, allowing molecular docking analysis to be conducted. This indicated that the enzyme specificity toward substrates with aryl aglycones is determined by aglycone aromatic system stacking with W373, and interactions with edges of F193, F200, and F461 located opposite W373 in a slot-like aglycone-binding site. These aglycone-active site interactions recently were hypothesized to determine substrate specificity in inactive enzyme substrate complexes of ZM-Glu1, an allozyme of Zm-p60.1. Here, we test this hypothesis by kinetic analysis of F193I/Y/W mutants. The decreasedK  m of all mutants confirmed the involvement of F193 in determining enzyme affinity toward substrates with an aromatic aglycone. It was unexpected that a 30-fold decrease ink  cat was found in F193I mutant compared with the wild type. Kinetic analysis and computer modeling demonstrated that the F193-aglycone-W373 interaction not only contributes to aglycone recognition as hypothesized previously but also codetermines catalytic rate by fixing the glucosidic bond in an orientation favorable for attack by the catalytic pair, E186 and E401. The catalytic pair, assigned initially by their location in the structure, was confirmed by kinetic analysis of E186D/Q and E401D/Q mutants. It was unexpected that the E401D as well as C205S and C211S mutations dramatically impaired the assembly of a catalysis-competent homodimer, suggesting novel links between the active site structure and dimer formation.
Constitutive Overexpression of Cystathionine γ-Synthase in Arabidopsis Leads to Accumulation of Soluble Methionine andS-Methylmethionine
Authors: Kim Jungsup , Lee Minsang , Chalam Radhika , Martin Melinda Neal , Leustek Thomas , Boerjan Wout
Published: November 2008

The committing step in Met andS-adenosyl-l-Met (SAM) synthesis is catalyzed by cystathionine γ-synthase (CGS). Transgenic Arabidopsis plants overexpressing CGS under control of the cauliflower mosaic virus 35S promoter show increased soluble Met and its metaboliteS-methyl-Met, but only at specific stages of development. The highest level of Met and S-methyl-Met was observed in seedling tissues and in flowers, siliques, and roots of mature plants where they accumulate 8- to 20-fold above wild type, whereas the level in mature leaves and other tissues is no greater than wild type. CGS-overexpressing seedlings are resistant to ethionine, a toxic Met analog. With these properties the transgenic lines resemblemto1, an Arabidopsis, CGS-mutant inactivated in the autogenous control mechanism for Met-dependent down-regulation of CGS expression. However, wild-type CGS was overexpressed in the transgenic plants, indicating that autogenous control can be overcome by increasing the level of CGS mRNA through transcriptional control. Several of the transgenic lines show silencing of CGS resulting in deformed plants with a reduced capacity for reproductive growth. Exogenous feeding of Met to the most severely affected plants partially restores their growth. Similar morphological deformities are observed in plants cosuppressed for SAM synthetase, even though such plants accumulate 250-fold more soluble Met than wild type and they overexpress CGS. The results suggest that the abnormalities associated with CGS and SAM synthetase silencing are due in part to a reduced ability to produce SAM and that SAM may be a regulator of CGS expression.
Scatterless hybrid metal–single-crystal slit for small-angle X-ray scattering and high-resolution X-ray diffraction
Authors: Li Youli , Beck Roy , Huang Tuo , Choi Myung Chul , Divinagracia Morito
Published: November 2008

A simple hybrid design has been developed to produce practically scatterless aperture slits for small-angle X-ray scattering and high-resolution X-ray diffraction. The hybrid slit consists of a rectangular single-crystal substrate (e.g.Si or Ge) bonded to a high-density metal base with a large taper angle (> 10°). The beam-defining single-crystal tip is oriented far from any Bragg peak position with respect to the incident beam and hence produces none of the slit scattering commonly associated with conventional metal slits. It has been demonstrated that the incorporation of the scatterless slits leads to a much simplified design in small-angle X-ray scattering instruments employing only one or two apertures, with dramatically increased intensity (a threefold increase observed in the test setup) and improved low-angle resolution.
A tutorial for learning and teaching macromolecular crystallography
Authors: Faust Annette , Panjikar Santosh , Mueller Uwe , Parthasarathy Venkataraman , Schmidt Andrea , Lamzin Victor S. , Weiss Manfred S.
Published: November 2008

Five experiments have been designed to be used for teaching macromolecular crystallography. The three proteins used in this tutorial are all commercially available; they can be easily and reproducibly crystallized and mounted for diffraction data collection. For each of the five experiments the raw images and the processed data of a sample diffraction data set as well as the refined coordinates and phases are provided for teaching the steps of data processing and structure determination.
Neutron transmission of single-crystal magnesium fluoride
Authors: Barker J. G. , Mildner D. F. R. , Rodriguez J. A. , Thiyagarajan P.
Published: November 2008

The neutron attenuation through single-crystal magnesium fluoride has been measured as a function of wavelength at both room temperature and 77 K. These data confirm a total cross section that is lower than that of MgO for wavelengths greater than 0.2 nm. MgF2cooled to 77 K is a slightly better filter of epithermal neutrons than MgO for obtaining a thermal neutron beam.
From space to superspace and back: Superspace Group Finder
Authors: Orlov Ivan , Palatinus Lukas , Chapuis Gervais
Published: November 2008

The symmetry of a commensurately modulated crystal structure can be described in two different ways: in terms of a conventional three-dimensional space group or using the superspace concept in (3 +d) dimensions. The three-dimensional space group is obtained as a real-space section of the (3 +d) superspace group. A complete network was constructed linking (3 + 1) superspace groups and the corresponding three-dimensional space groups derived from rational sections. A database has been established and is available at http://superspace.epfl.ch/finder/. It is particularly useful for finding common superspace groups for various series of modular (`composition-flexible') structures and phase transitions. The use of the database is illustrated with examples from various fields of crystal chemistry.
From Policy to Practice: The Implementation and Negotiation of Technologies in Everyday Child Welfare
Authors: Peckover Sue , Hall Christopher , White Sue
Published: November 2008

A central element of the Every Child Matters reforms in England are measures which aim at improving information sharing. Amongst these are the children’s database and the Common Assessment Framework, both representing technological solutions to long‐standing concerns about information sharing in child welfare. This article reports some findings from an Economic and Social Research Council (ESRC)‐funded study which examined their introduction and use in everyday professional practice. Substantial differences in policy implementation, access to and use of the technologies, draw attention to the importance of the localised and situated contexts into which these technologies are being introduced, raising serious questions about their future development as national standard systems.