bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expression of Arabidopsis MIRNA Genes
Authors: Xie Zhixin , Allen Edwards , Fahlgren Noah , Calamar Adam , Givan Scott A. , Carrington James C. 
Published: July 2005

Abstract
MicroRNAs (miRNAs) are approximately 21-nucleotide noncoding RNAs that regulate target transcripts in plants and animals. In addition to miRNAs, plants contain several classes of endogenous small interfering RNAs (siRNAs) involved in target gene regulation and epigenetic silencing. Small RNA libraries were constructed from wild-type Arabidopsis (Arabidopsis thaliana) and mutant plants (rdr2 and dcl3) that were genetically enriched for miRNAs, and a computational procedure was developed to identify candidate miRNAs. Thirty-eight distinct miRNAs corresponding to 22 families were represented in the libraries. Using a 5′ rapid amplification of cDNA ends procedure, the transcription start sites for 63 miRNA primary transcripts from 52 MIRNA loci (99 loci tested) were mapped, revealing features consistent with an RNA polymerase II mechanism of transcription. Ten loci (19%) yielded transcripts from multiple start sites. A canonical TATA box motif was identified upstream of the major start site at 45 (86%) of the mapped MIRNA loci. The 5′-mapping data were combined with miRNA cloning and 3′-PCR data to definitively validate expression of at least 73 MIRNA genes. These data provide a molecular basis to explore regulatory mechanisms of miRNA expression in plants.
Analysis of the Rice Mutant dwarf and gladius leaf 1. Aberrant Katanin-Mediated Microtubule Organization Causes Up-Regulation of Gibberellin Biosynthetic Genes Independently of Gibberellin Signaling
Authors: Komorisono Masahiko , Ueguchi-Tanaka Miyako , Aichi Ikuko , Hasegawa Yasuko , Ashikari Motoyuki , Kitano Hidemi , Matsuoka Makoto , Sazuka Takashi 
Published: July 2005

Abstract
Molecular genetic studies of plant dwarf mutants have indicated that gibberellin (GA) and brassinosteroid (BR) are two major factors that determine plant height; dwarf mutants that are caused by other defects are relatively rare, especially in monocot species. Here, we report a rice (Oryza sativa) dwarf mutant, dwarf and gladius leaf 1 (dgl1), which exhibits only minimal response to GA and BR. In addition to the dwarf phenotype, dgl1 produces leaves with abnormally rounded tip regions. Positional cloning of DGL1 revealed that it encodes a 60-kD microtubule-severing katanin-like protein. The protein was found to be important in cell elongation and division, based on the observed cell phenotypes. GA biosynthetic genes are up-regulated in dgl1, but the expression of BR biosynthetic genes is not enhanced. The enhanced expression of GA biosynthetic genes in dgl1 is not caused by inappropriate GA signaling because the expression of these genes was repressed by GA3 treatment, and degradation of the rice DELLA protein SLR1 was triggered by GA3 in this mutant. Instead, aberrant microtubule organization caused by the loss of the microtubule-severing function of DGL1 may result in enhanced expression of GA biosynthetic genes in that enhanced expression was also observed in a BR-deficient mutant with aberrant microtubule organization. These results suggest that the function of DGL1 is important for cell and organ elongation in rice, and aberrant DGL1-mediated microtubule organization causes up-regulation of gibberellin biosynthetic genes independently of gibberellin signaling.
An RNA-Dependent RNA Polymerase Prevents Meristem Invasion by Potato Virus X and Is Required for the Activity But Not the Production of a Systemic Silencing Signal
Authors: Schwach Frank , Vaistij Fabian E. , Jones Louise , Baulcombe David C. 
Published: July 2005

Abstract
One of the functions of RNA silencing in plants is antiviral defense. A hallmark of RNA silencing is spreading of the silenced state through the plant. Little is known about the nature of the systemic silencing signal and the proteins required for its production, transport, and reception in plant tissues. Here, we show that the RNA-dependent RNA polymerase RDR6 in Nicotiana benthamiana is involved in defense against potato virus X at the level of systemic spreading and in exclusion of the virus from the apical growing point. It has no effect on primary replication and cell-to-cell movement of the virus and does not contribute significantly to the formation of virus-derived small interfering (si) RNA in a fully established potato virus X infection. In grafting experiments, the RDR6 homolog was required for the ability of a cell to respond to, but not to produce or translocate, the systemic silencing signal. Taking these findings together, we suggest a model of virus defense in which RDR6 uses incoming silencing signal to generate double-stranded RNA precursors of secondary siRNA. According to this idea, the secondary siRNAs mediate RNA silencing as an immediate response that slows down the systemic spreading of the virus into the growing point and newly emerging leaves.
Fractionation of the Three Stable Oxygen Isotopes by Oxygen-Producing and Oxygen-Consuming Reactions in Photosynthetic Organisms
Authors: Helman Yael , Barkan Eugeni , Eisenstadt Doron , Luz Boaz , Kaplan Aaron 
Published: July 2005

Abstract
The triple isotope composition (δ 17O and δ 18O) of dissolved O2 in the ocean and in ice cores was recently used to assess the primary productivity over broad spatial and temporal scales. However, assessment of the productivity with the aid of this method must rely on accurate measurements of the 17O/16O versus 18O/16O relationship in each of the main oxygen-producing and -consuming reactions. Data obtained here showed that cleavage of water in photosystem II did not fractionate oxygen isotopes; the δ 18O and δ 17O of the O2 evolved were essentially identical to those of the substrate water. The fractionation slopes for the oxygenase reaction of Rubisco and respiration were identical (0.518 ± 0.001) and that of glycolate oxidation was 0.503 ± 0.002. There was a considerable difference in the slopes of O2 photoreduction (the Mehler reaction) in the cyanobacterium Synechocystis sp. strain PCC 6803 (0.497 ± 0.004) and that of pea (Pisum sativum) thylakoids (0.526 ± 0.001). These values provided clear and independent evidence that the mechanism of O2 photoreduction differs between higher plants and cyanobacteria. We used our method to assess the magnitude of O2 photoreduction in cyanobacterial cells maintained under conditions where photorespiration was negligible. It was found that electron flow to O2 can be as high as 40% that leaving photosystem II, whereas respiratory activity in the light is only 6%. The implications of our findings to the evaluation of specific O2-producing or -consuming reactions, in vivo, are discussed.
Sites and Regulation of Polyamine Catabolism in the Tobacco Plant. Correlations with Cell Division/Expansion, Cell Cycle Progression, and Vascular Development
Authors: Paschalidis Konstantinos A. , Roubelakis-Angelakis Kalliopi A. 
Published: July 2005

Abstract
We previously gave a picture of the homeostatic characteristics of polyamine (PA) biosynthesis and conjugation in tobacco (Nicotiana tabacum) plant organs during development. In this work, we present the sites and regulation of PA catabolism related to cell division/expansion, cell cycle progression, and vascular development in the tobacco plant. Diamine oxidase (DAO), PA oxidase (PAO), peroxidases (POXs), and putrescine N-methyltransferase expressions follow temporally and spatially discrete patterns in shoot apical cells, leaves (apical, peripheral, and central regions), acropetal and basipetal petiole regions, internodes, and young and old roots in developing plants. DAO and PAO produce hydrogen peroxide, a plant signal molecule and substrate for POXs. Gene expression and immunohistochemistry analyses reveal that amine oxidases in developing tobacco tissues precede and overlap with nascent nuclear DNA and also with POXs and lignification. In mature and old tissues, flow cytometry indicates that amine oxidase and POX activities, as well as pao gene and PAO protein levels, coincide with G2 nuclear phase and endoreduplication. In young versus the older roots, amine oxidases and POX expression decrease with parallel inhibition of G2 advance and endoreduplication, whereas putrescine N-methyltransferase dramatically increases. In both hypergeous and hypogeous tissues, DAO and PAO expression occurs in cells destined to undergo lignification, suggesting a different in situ localization. DNA synthesis early in development and the advance in cell cycle/endocycle are temporally and spatially related to PA catabolism and vascular development.
Characteristics of Electrical Signals in Poplar and Responses in Photosynthesis
Authors: Lautner Silke , Grams Thorsten Erhard Edgar , Matyssek Rainer , Fromm Jörg 
Published: July 2005

Abstract
To gain an understanding of the role of electrical signaling in trees, poplar (Populus trichocarpa, Populus tremula × P. tremuloides) shoots were stimulated by chilling as well as flaming. Two kinds of signal propagation were detected by microelectrode measurements (aphid technique) in the phloem of leaf veins: (1) basipetal, short-distance signaling that led to rapid membrane hyperpolarization caused by K+-efflux within the leaf lamina; and (2) acropetal, long-distance signaling that triggered depolarization of the membrane potential in the leaf phloem. In the latter, the depolarizing signals travel across the stem from the manipulated leaves to adjacent leaves where the net CO2 uptake rate is temporarily depressed toward compensation. With regard to photosystem II, both heat-induced long-distance and short-distance signaling were investigated using two-dimensional “imaging” analysis of chlorophyll fluorescence. Both types of signaling significantly reduced the quantum yield of electron transport through photosystem II. Imaging analysis revealed that the signal that causes yield reduction spreads through the leaf lamina. Coldblocking of the stem proved that the electrical signal transmission via the phloem becomes disrupted, causing the leaf gas exchange to remain unaffected. Calcium-deficient trees showed a marked contrast inasmuch as the amplitude of the electrical signal was distinctly reduced, concomitant with the absence of a significant response in leaf gas exchange upon flame wounding. In summary, the above results led us to conclude that calcium as well as potassium is involved in the propagation of phloem-transmitted electrical signals that evoke specific responses in the photosynthesis of leaves.
Molecular Identification and Characterization of the Arabidopsis Δ3,5,Δ2,4-Dienoyl-Coenzyme A Isomerase, a Peroxisomal Enzyme Participating in the β-Oxidation Cycle of Unsaturated Fatty Acids
Authors: Goepfert Simon , Vidoudez Charles , Rezzonico Enea , Hiltunen J. Kalervo , Poirier Yves 
Published: July 2005

Abstract
Degradation of unsaturated fatty acids through the peroxisomal β-oxidation pathway requires the participation of auxiliary enzymes in addition to the enzymes of the core β-oxidation cycle. The auxiliary enzyme Δ3,5,Δ2,4-dienoyl-coenzyme A (CoA) isomerase has been well studied in yeast (Saccharomyces cerevisiae) and mammals, but no plant homolog had been identified and characterized at the biochemical or molecular level. A candidate gene (At5g43280) was identified in Arabidopsis (Arabidopsis thaliana) encoding a protein showing homology to the rat (Rattus norvegicus) Δ3,5,Δ2,4-dienoyl-CoA isomerase, and possessing an enoyl-CoA hydratase/isomerase fingerprint as well as aspartic and glutamic residues shown to be important for catalytic activity of the mammalian enzyme. The protein, named AtDCI1, contains a peroxisome targeting sequence at the C terminus, and fusion of a fluorescent protein to AtDCI1 directed the chimeric protein to the peroxisome in onion (Allium cepa) cells. AtDCI1 expressed in Escherichia coli was shown to have Δ3,5,Δ2,4-dienoyl-CoA isomerase activity in vitro. Furthermore, using the synthesis of polyhydroxyalkanoate in yeast peroxisomes as an analytical tool to study the β-oxidation cycle, expression of AtDCI1 was shown to complement the yeast mutant deficient in the Δ3,5,Δ2,4-dienoyl-CoA isomerase, thus showing that AtDCI1 is also appropriately targeted to the peroxisome in yeast and has Δ3,5,Δ2,4-dienoyl-CoA isomerase activity in vivo. The AtDCI1 gene is expressed constitutively in several tissues, but expression is particularly induced during seed germination. Proteins showing high homology with AtDCI1 are found in gymnosperms as well as angiosperms belonging to the Monocotyledon or Dicotyledon classes.
Arabidopsis ARP7 Is an Essential Actin-Related Protein Required for Normal Embryogenesis, Plant Architecture, and Floral Organ Abscission
Authors: Kandasamy Muthugapatti K. , McKinney Elizabeth C. , Deal Roger B. , Meagher Richard B. 
Published: July 2005

AbstractThe actin-related proteins (ARPs) that are localized to the nucleus are present as components of various chromatin-modifying complexes involved in chromatin dynamics and transcriptional regulation. Arabidopsis (Arabidopsis thaliana) ARP7 is a constitutively expressed nuclear protein belonging to a novel plant-specific ARP class. In this study, we demonstrate a vital role for ARP7 protein in embryogenesis and plant development. Knocking out the expression of ARP7 in an arp7-1 T-DNA mutant produced morphologically aberrant, homozygous embryos that were arrested at or before the torpedo stage of development. Hence, the arp7-1 null mutation is homozygous lethal. Knocking down the expression levels of ARP7 protein with RNA interference produced viable Arabidopsis lines affected in multiple developmental pathways and induced dosage-dependent, heritable defects in plant architecture. The transgenic plants containing greatly reduced levels of ARP7 in the nucleus were severely dwarfed with small rosette leaves that are defective in cell expansion and trichome morphology. Moreover, the ARP7-deficient RNA interference plants exhibited retarded root growth, altered flower development, delayed perianth abscission, and reduced fertility. These pleiotropic phenotypic changes suggest a critical role for the Arabidopsis ARP7 protein in the regulation of various phases of plant development through chromatin-mediated, global regulation of gene expression.
The Tobacco Mosaic Virus 126-Kilodalton Protein, a Constituent of the Virus Replication Complex, Alone or within the Complex Aligns with and Traffics along Microfilaments
Authors: Liu Jian-Zhong , Blancaflor Elison B. , Nelson Richard S. 
Published: July 2005

Abstract
Virus-induced cytoplasmic inclusion bodies (referred to as virus replication complexes [VRCs]) consisting of virus and host components are observed in plant cells infected with tobacco mosaic virus, but the components that modulate their form and function are not fully understood. Here, we show that the tobacco mosaic virus 126-kD protein fused with green fluorescent protein formed cytoplasmic bodies (126-bodies) in the absence of other viral components. Using mutant 126-kD:green fluorescent fusion proteins and viral constructs expressing the corresponding mutant 126-kD proteins, it was determined that the size of the 126-bodies and the corresponding VRCs changed in synchrony for each 126-kD protein mutation tested. Through colabeling experiments, we observed the coalignment and intracellular trafficking of 126-bodies and, regardless of size, VRCs, along microfilaments (MFs). Disruption of MFs with MF-depolymerizing agents or through virus-induced gene silencing compromised the intracellular trafficking of the 126-bodies and VRCs and virus cell-to-cell movement, but did not decrease virus accumulation to levels that would affect virus movement or prevent VRC formation. Our results indicate that (1) the 126-kD protein modulates VRC size and traffics along MFs in cells; (2) VRCs traffic along MFs in cells, possibly through an interaction with the 126-kD protein, and the negative effect of MF antagonists on 126-body and VRC intracellular movement and virus cell-to-cell movement correlates with the disruption of this association; and (3) virus movement was not correlated with VRC size.
Effect of Temperature on Geminivirus-Induced RNA Silencing in Plants
Authors: Chellappan Padmanabhan , Vanitharani Ramachandran , Ogbe Francis , Fauquet Claude M. 
Published: July 2005

Abstract
Short-interfering RNAs (siRNAs), the molecular markers of posttranscriptional gene silencing (PTGS), are powerful tools that interfere with gene expression and counter virus infection both in plants and animals. Here, we report the effect of temperature on geminivirus-induced gene silencing by quantifying virus-derived siRNAs and by evaluating their distribution along the virus genome for isolates of five species of cassava geminiviruses in cassava (Manihot esculenta, Crantz) and Nicotiana benthamiana. Cassava geminivirus-induced RNA silencing increased by raising the temperature from 25°C to 30°C, with the appearance of less symptomatic newly developed leaves, irrespective of the nature of the virus. Consequently, nonrecovery-type geminiviruses behaved like recovery-type viruses under high temperature. Next, we evaluated the distribution of virus-derived siRNAs on the respective virus genome at three temperatures (25°C, 25°C–30°C, and 30°C). For recovery-type viruses, siRNAs accumulated at moderately higher levels during virus-induced PTGS at higher temperatures, and there was no change in the distribution of the siRNA population along the virus genome. For nonrecovery-type viruses, siRNAs accumulated at strikingly higher levels than those observed for infections with recovery-type viruses at high temperature. As determined for an RNA virus, temperature influences gene silencing for single-stranded DNA geminiviruses. It is possible that other mechanisms besides gene silencing also control geminivirus accumulation at high temperatures. The findings presented here should be taken into consideration when implementing PTGS-based strategies to control plant virus accumulation.
Arabidopsis SENESCENCE-ASSOCIATED GENE101 Stabilizes and Signals within an ENHANCED DISEASE SUSCEPTIBILITY1 Complex in Plant Innate Immunity
Authors: Feys Bart J. , Wiermer Marcel , Bhat Riyaz A. , Moisan Lisa J. , Medina-Escobar Nieves , Neu Christina , Cabral Adriana , Parker Jane E. 
Published: July 2005

Abstract
Plant innate immunity against invasive biotrophic pathogens depends on the intracellular defense regulator ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1). We show here that Arabidopsis thaliana EDS1 interacts in vivo with another protein, SENESCENCE-ASSOCIATED GENE101 (SAG101), discovered through a proteomic approach to identify new EDS1 pathway components. Together with PHYTOALEXIN-DEFICIENT4 (PAD4), a known EDS1 interactor, SAG101 contributes intrinsic and indispensable signaling activity to EDS1-dependent resistance. The combined activities of SAG101 and PAD4 are necessary for programmed cell death triggered by the Toll-Interleukin-1 Receptor type of nucleotide binding/leucine-rich repeat immune receptor in response to avirulent pathogen isolates and in restricting the growth of normally virulent pathogens. We further demonstrate by a combination of cell fractionation, coimmunoprecipitation, and fluorescence resonance energy transfer experiments the existence of an EDS1–SAG101 complex inside the nucleus that is molecularly and spatially distinct from EDS1–PAD4 associations in the nucleus and cytoplasm. By contrast, EDS1 homomeric interactions were detected in the cytoplasm but not inside the nucleus. These data, combined with evidence for coregulation between individual EDS1 complexes, suggest that dynamic interactions of EDS1 and its signaling partners in multiple cell compartments are important for plant defense signal relay.
The low-temperature and high-pressure crystal structures of cyclobutanol (C4H7OH)
Authors: McGregor Pamela A. , Allan David R. , Parsons Simon , Pulham Colin R. 
Published: July 2005

The low-temperature and high-pressure crystal structures of cyclobutanol (C4H7OH) have been determined using single-crystal X-ray diffraction techniques. At temperatures below 220 K, cyclobutanol crystallizes in the Aba2 space group (Z′ = 2) and its crystal structure is composed of pseudo-threefold hydrogen-bonded molecular catemers [assigned as C_2^2(4) in graph-set notation], which lie parallel to the crystallographic a axis. At a pressure of 1.3 GPa, the crystal symmetry changes to Pna21 (Z′ = 1) and the molecular catemers [expressed as C(2) in graph-set notation] adopt a pseudo-twofold arrangement. This structural behaviour is in agreement with our previous observations for phenol and its halogenated derivatives 2-chlorophenol and 4-fluorophenol, where pressure was found to favour a molecular packing more closely associated with small alkyl groups rather than that of relatively bulky alkyl groups. In addition, an examination of the molecular coordination environment in the low-temperature and high-pressure structures of cyclobutanol reveals that the change in structure on application of pressure appears to be driven by the molecules assuming a packing arrangement which more closely resembles that adopted in hard-sphere structures.
European Union scientific production on alcohol and drug misuse (1976–2000)
Authors: Sánchez‐Carbonell Xavier , Guardiola Elena , Bellés Ana , Beranuy Marta 
Published: July 2005

ABSTRACTBackground  Alcohol and drug misuse is a social and health phenomenon of great relevance in the European Union (EU). One indicator of scientific production in a given area is the analysis of publications included in bibliographic databases. Scientific production on alcohol and drug misuse was analysed in EU member countries, and comparisons were made between countries.Methods  Analysis of articles on alcohol and drug misuse published during the period 1976–2000 by institutions based in a country of the EU, indexed by PsycINFO.Results  A total of 4825 citations was retrieved. Great Britain published 38.6%, while Sweden, Germany and Spain accounted for a further 30%. The articles dealt with drug and alcohol usage (12.8%), substance abuse (53.5%) and drug and alcohol rehabilitation (34.5%). The articles were published in 13 different languages, more than three‐quarters being in English. Spanish was the second language, and was followed by French, German, Dutch and Italian. The articles were published in 521 different journals, and 62 of these published more than 10 articles. The journals publishing most were Addiction, Alcohol and Alcoholism and Drug and Alcohol Dependence. Sixty‐eight per cent of the articles were signed by more than one author, and the index of collaboration, between 1996 and 2000, was 3.24.Discussion and conclusions  PsycINFO is useful for making comparisons between countries, because it includes the name and country of the institution. The number of publications in the EU on alcohol and drug misuse increased over the quarter‐century analysed. The most used language was English, as it also is for PsycINFO as a whole, and a tendency towards its increased use was observed. Classification of the articles by subject by the Classification Code is too general, and makes it difficult to distinguish between the areas it proposes. Production tends to be concentrated in journals dealing specifically with drug dependence and psychiatry. The index of collaboration is similar to that found in other scientific areas.