bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization, lateral variability and lateral extent of discontinuity surfaces on a Carbonate Platform (Barremian to Lower Aptian, Oman)
Authors: SATTLER UTE , IMMENHAUSER ADRIAN , HILLGÄRTNER HEIKO , ESTEBAN MATEU 
Published: March 2005

AbstractHiati of various duration in carbonates are commonly expressed as discontinuity surfaces. The understanding of processes that form and affect these surfaces leads to an improved sequence‐stratigraphic interpretation, a reliable outcrop correlation, and better models for reservoir compartmentalization. Various intraformational discontinuities were analysed and interpreted in a well‐exposed study window, 2·5 km in lateral length and 60 m in height comprising the Barremian‐Aptian Qishn Formation (Haushi‐Huqf area, central Oman). This study focuses on the lateral extent and morphology of the surfaces, the petrography of the underlying rocks, and the facies changes and geochemical trends across these discontinuities. Furthermore, the lateral variability of discontinuity surfaces was documented. Three genetic types of discontinuities are differentiated: (i) erosion surfaces; (ii) omission surfaces (hard‐ and firmgrounds); and (iii) composite surfaces with evidence for both subaerial exposure and submarine boring. Field observations, combined with petrographic and geochemical data, suggest that 17 surfaces are laterally extensive for at least 20 km and record relative sea‐level fluctuations of regional scale. In contrast, a large number of laterally limited surfaces (<1 km) are related to locally active processes such as waves and current erosion. The lateral variability along extensive surfaces is the result of the depositional environment below the discontinuity, the sea‐floor topography, waves and currents and differential erosion. The most pronounced lateral variability is present along six laterally extensive composite surfaces that record terrestrial exposure and subsequent flooding of a tidal flat environment. This variability is caused by spatial variability in the tidal flat environment, meteoric alteration and differential erosion. This study emphasizes the spatial and temporal complexity of processes that form and modify discontinuity surfaces. This variability must be kept in mind when interpretations and correlations are based on one‐dimensional sections or cores.
3D and 4D controls on carbonate depositional systems: sedimentological and sequence stratigraphic analysis of an attached carbonate platform and atoll (Miocene, Níjar Basin, SE Spain)
Authors: WARRLICH GEORG , BOSENCE DAN , WALTHAM DAVE 
Published: March 2005

AbstractThis study investigates the controls on three‐dimensional stratigraphic geometries and facies of shallow‐water carbonate depositional sequences. A 15 km2area of well‐exposed Mid to Late Miocene carbonates on the margin of the Níjar Basin of SE Spain was mapped in detail. An attached carbonate platform and atoll developed from a steeply sloping basin margin over a basal topographic unconformity and an offshore dacite dome (Late Miocene). The older strata comprise prograding bioclastic (mollusc and coralline algae) dominated sediments and later MessinianPoritesreefs form prograding and downstepping geometries (falling stage systems tract). Seven depositional sequences, their systems tracts and facies have been mapped and dated (using Sr isotopes) to define their morphology, stratigraphic geometries, and palaeo‐environments. A relative sea‐level curve and isochore maps were constructed for the three Messinian depositional sequences that precede the late Messinian evaporative drawdown of the Mediterranean. The main 3D controls on these depositional sequences are interpreted as being: (i) local, tectonically driven relative sea‐level changes; (ii) the morphology of the underlying sequence boundary; (iii) the type of carbonate producers [bioclastic coralline algal and mollusc‐dominated sequences accumulated in lows and on slopes of < 14° whereas thePoritesreef‐dominated sequence accumulated on steep slopes (up to 25°) and shallow‐water highs]. Further controls were: (iv) the inherited palaeo‐valleys and point‐sourced clastics; (v) the amount of clastic sediments; and (vi) erosion during the following sequence boundary development. The stratigraphy is compared with that of adjacent Miocene basins in the western Mediterranean to differentiate local (tectonics, clastic supply, erosion history, carbonate‐producing communities) versus regional (climatic, tectonic, palaeogeographic, sea‐level) controls.
Stacked fluvial and tide‐dominated estuarine deposits in high‐frequency (fourth‐order) sequences of the Eocene Central Basin, Spitsbergen
Authors: PLINK‐BJÖRKLUND PIRET 
Published: March 2005

AbstractEighteen coastal‐plain depositional sequences that can be correlated to shallow‐ to deep‐water clinoforms in the Eocene Central Basin of Spitsbergen were studied in 1 × 15 km scale mountainside exposures. The overall mud‐prone (>300 m thick) coastal‐plain succession is divided by prominent fluvial erosion surfaces into vertically stacked depositional sequences, 7–44 m thick. The erosion surfaces are overlain by fluvial conglomerates and coarse‐grained sandstones. The fluvial deposits show tidal influence at their seaward ends. The fluvial deposits pass upwards into macrotidal tide‐dominated estuarine deposits, with coarse‐grained river‐dominated facies followed further seawards by high‐ and low‐sinuosity tidal channels, upper‐flow‐regime tidal flats, and tidal sand bar facies associations. Laterally, marginal sandy to muddy tidal flat and marsh deposits occur. The fluvial/estuarine sequences are interpreted as having accumulated as a series of incised valley fills because: (i) the basal fluvial erosion surfaces, with at least 16 m of local erosional relief, are regional incisions; (ii) the basal fluvial deposits exhibit a significant basinward facies shift; (iii) the regional erosion surfaces can be correlated with rooted horizons in the interfluve areas; and (iv) the estuarine deposits onlap the valley walls in a landward direction. The coastal‐plain deposits represent the topset to clinoforms that formed during progradational infilling of the Eocene Central Basin. Despite large‐scale progradation, the sequences are volumetrically dominated by lowstand fluvial deposits and especially by transgressive estuarine deposits. The transgressive deposits are overlain by highstand units in only about 30% of the sequences. The depositional system remained an estuary even during highstand conditions, as evidenced by the continued bedload convergence in the inner‐estuarine tidal channels.
The characterization of novel mycorrhiza‐specific phosphate transporters from Lycopersicon esculentum and Solanum tuberosum uncovers functional redundancy in symbiotic phosphate transport in solanaceous species
Authors: Nagy Réka , Karandashov Vladimir , Chague Véronique , Kalinkevich Katsiaryna , Tamasloukht M'Barek , Xu Guohua , Jakobsen Iver , Levy Avraham A. , Amrhein Nikolaus , Bucher Marcel 
Published: March 2005

SummarySolanaceous species are among the >200 000 plant species worldwide forming a mycorrhiza, that is, a root living in symbiosis with soil‐borne arbuscular‐mycorrhizal (AM) fungi. An important parameter of this symbiosis, which is vital for ecosystem productivity, agriculture, and horticulture, is the transfer of phosphate (Pi) from the AM fungus to the plant, facilitated by plasma membrane‐spanning Pi transporter proteins. The first mycorrhiza‐specific plant Pi transporter to be identified, was StPT3 from potato [Nature414 (2004) 462]. Here, we describe novel Pi transporters from the solanaceous species tomato, LePT4, and its orthologue StPT4 from potato, both being members of the Pht1 family of plant Pi transporters. Phylogenetic tree analysis demonstrates clustering of both LePT4 and StPT4 with the mycorrhiza‐specific Pi transporter from Medicago truncatula [Plant Cell, 14 (2002) 2413] and rice [Proc. Natl Acad. Sci. USA, 99 (2002) 13324], respectively, but not with StPT3, indicating that two non‐orthologous mycorrhiza‐responsive genes encoding Pi transporters are co‐expressed in the Solanaceae. The cloned promoter regions from both genes, LePT4 and StPT4, exhibit a high degree of sequence identity and were shown to direct expression exclusively in colonized cells when fused to the GUS reporter gene, in accordance with the abundance of LePT4 and StPT4 transcripts in mycorrhized roots. Furthermore, extensive sequencing of StPT4‐like clones and subsequent expression analysis in potato and tomato revealed the presence of a close paralogue of StPT4 and LePT4, named StPT5 and LePT5, respectively, representing a third Pi transport system in solanaceous species which is upregulated upon AM fungal colonization of roots. Knock out of LePT4 in the tomato cv. MicroTom indicated considerable redundancy between LePT4 and other Pi transporters in tomato.
Comparative genomics enabled the isolation of the R3a late blight resistance gene in potato
Authors: Huang Sanwen , Van Der Vossen Edwin A.G. , Kuang Hanhui , Vleeshouwers Vivianne G.A.A. , Zhang Ningwen , Borm Theo J.A. , Van Eck Herman J. , Baker Barbara , Jacobsen Evert , Visser Richard G.F. 
Published: March 2005

SummaryComparative genomics provides a tool to utilize the exponentially increasing sequence information from model plants to clone agronomically important genes from less studied crop species. Plant disease resistance (R) loci frequently lack synteny between related species of cereals and crucifers but appear to be positionally well conserved in the Solanaceae. In this report, we adopted a local RGA approach using genomic information from the model Solanaceous plant tomato to isolate R3a, a potato gene that confers race‐specific resistance to the late blight pathogen Phytophthora infestans. R3a is a member of the R3 complex locus on chromosome 11. Comparative analyses of the R3 complex locus with the corresponding I2 complex locus in tomato suggest that this is an ancient locus involved in plant innate immunity against oomycete and fungal pathogens. However, the R3 complex locus has evolved after divergence from tomato and the locus has experienced a significant expansion in potato without disruption of the flanking colinearity. This expansion has resulted in an increase in the number of R genes and in functional diversification, which has probably been driven by the co‐evolutionary history between P. infestans and its host potato. Constitutive expression was observed for the R3a gene, as well as some of its paralogues whose functions remain unknown.
The phytotoxin coronatine and methyl jasmonate impact multiple phytohormone pathways in tomato
Authors: Uppalapati Srinivasa Rao , Ayoubi Patricia , Weng Hua , Palmer David A. , Mitchell Robin E. , Jones William , Bender Carol L. 
Published: March 2005

SummaryCoronatine (COR) is a phytotoxin produced by several pathovars of Pseudomonas syringae and consists of coronafacic acid (CFA), an analog of methyl jasmonic acid (MeJA), and coronamic acid (CMA), which resembles 1‐aminocyclopropane‐1‐carboxylic acid (ACC), a precursor to ethylene. An understanding of how COR functions, is perceived by different plant tissues, and the extent to which it mimics MeJA remain unclear. In this study, COR and related compounds were examined with respect to structure and function. The results indicate that conjugation of CFA to an amino acid is required for optimal activity in tomato, including chlorosis, changes in chloroplast structure, cell wall thickening, accumulation of proteinase inhibitors, induction of anthocyanins, and root growth inhibition. cDNA microarrays were utilized to understand the molecular processes that are regulated by MeJA, COR, CFA and CMA in tomato leaves. A comparison of COR‐ and MeJA‐regulated transcriptomes revealed that COR regulated 35% of the MeJA‐induced genes. There was significant overlap in the number of COR and CFA‐regulated genes with CFA impacting the expression of 39.4% of the COR‐regulated genes. Taken together, the results of biological assays, ultrastructural studies, and gene expression profiling demonstrate that: (1) the intact COR molecule impacts signaling in tomato via the jasmonic acid, ethylene, and auxin pathways; (2) CMA does not function as a structural analog of ACC; (3) COR has a broader range of functions than either CFA or CMA; and (4) COR and MeJA share similar, but not identical activities and impact multiple phytohormone pathways in tomato.
Roles of isoamylase and ADP‐glucose pyrophosphorylase in starch granule synthesis in rice endosperm
Authors: Kawagoe Yasushi , Kubo Akiko , Satoh Hikaru , Takaiwa Fumio , Nakamura Yasunori 
Published: March 2005

SummaryAmyloplast‐targeted green fluorescent protein (GFP) was used to monitor amyloplast division and starch granule synthesis in the developing endosperm of transgenic rice. Two classical starch mutants, sugary and shrunken, contain reduced activities of isoamylase1 (ISA1) and cytosolic ADP‐glucose pyrophosphorylase, respectively. Dividing amyloplasts in the wild‐type and shrunken endosperms contained starch granules, whereas those in sugary endosperm did not contain detectable granules, suggesting that ISA1 plays a role in granule synthesis at the initiation step. The transition from phytoglycogen to sugary‐amylopectin was gradual in the boundary region between the inner and outer endosperms of sugary. These results suggest that the synthesis of sugary‐amylopectin and phytoglycogen involved a stochastic process and that ISA1 activity plays a critical role in the stochastic process in starch synthesis in rice endosperm. The reduction of cytosolic ADP‐glucose pyrophosphorylase activity in shrunken endosperm did not inhibit granule initiation but severely restrained the subsequent enlargement of granules. The shrunken endosperm often developed pleomorphic amyloplasts containing a large number of underdeveloped granules or a large cluster of small grains of amyloplasts, each containing a simple‐type starch granule. Although constriction‐type divisions of amyloplasts were much more frequent, budding‐type divisions were also found in the shrunken endosperm. We show that monitoring GFP in developing amyloplasts was an effective means of evaluating the roles of enzymes involved in starch granule synthesis in the rice endosperm.
Plant‐specific mitotic targeting of RanGAP requires a functional WPP domain
Authors: Jeong Sun Yong , Rose Annkatrin , Joseph Jomon , Dasso Mary , Meier Iris 
Published: March 2005

SummaryThe small GTPase Ran is involved in nucleocytoplasmic transport, spindle formation, nuclear envelope (NE) formation, and cell‐cycle control. In vertebrates, these functions are controlled by a three‐dimensional gradient of Ran‐GTP to Ran‐GDP, established by the spatial separation of Ran GTPase‐activating protein (RanGAP) and the Ran guanine nucleotide exchange factor RCC1. While this spatial separation is established by the NE during interphase, it is orchestrated during mitosis by association of RCC1 with the chromosomes and RanGAP with the spindle and kinetochores. SUMOylation of vertebrate RanGAP1 is required for NE, spindle, and centromere association. Arabidopsis RanGAP1 (AtRanGAP1) lacks the SUMOylated C‐terminal domain of vertebrate RanGAP, but contains a plant‐specific N‐terminal domain (WPP domain), which is necessary and sufficient for its targeting to the NE in interphase. Here we show that the human and plant RanGAP‐targeting domains are kingdom specific. AtRanGAP1 has a mitotic trafficking pattern uniquely different from that of vertebrate RanGAP, which includes targeting to the outward‐growing rim of the cell plate. The WPP domain is necessary and sufficient for this targeting. Point mutations in conserved residues of the WPP domain also abolish targeting to the nuclear rim and the cell plate, suggesting that the same mechanism is involved in both targeting events. These results indicate that plant and animal RanGAPs undergo different migration patterns during cell division, which require their kingdom‐specific targeting domains.
Complex regulation of Arabidopsis AGR1/PIN2‐mediated root gravitropic response and basipetal auxin transport by cantharidin‐sensitive protein phosphatases
Authors: Shin Heungsop , Shin Hwa‐Soo , Guo Zibiao , Blancaflor Elison B. , Masson Patrick H. , Chen Rujin 
Published: March 2005

SummaryPolar auxin transport, mediated by two distinct plasma membrane‐localized auxin influx and efflux carrier proteins/complexes, plays an important role in many plant growth and developmental processes including tropic responses to gravity and light, development of lateral roots and patterning in embryogenesis. We have previously shown that the Arabidopsis AGRAVITROPIC 1/PIN2 gene encodes an auxin efflux component regulating root gravitropism and basipetal auxin transport. However, the regulatory mechanism underlying the function of AGR1/PIN2 is largely unknown. Recently, protein phosphorylation and dephosphorylation mediated by protein kinases and phosphatases, respectively, have been implicated in regulating polar auxin transport and root gravitropism. Here, we examined the effects of chemical inhibitors of protein phosphatases on root gravitropism and basipetal auxin transport, as well as the expression pattern of AGR1/PIN2 gene and the localization of AGR1/PIN2 protein. We also examined the effects of inhibitors of vesicle trafficking and protein kinases. Our data suggest that protein phosphatases, sensitive to cantharidin and okadaic acid, are likely involved in regulating AGR1/PIN2‐mediated root basipetal auxin transport and gravitropism, as well as auxin response in the root central elongation zone (CEZ). BFA‐sensitive vesicle trafficking may be required for the cycling of AGR1/PIN2 between plasma membrane and the BFA compartment, but not for the AGR1/PIN2‐mediated root basipetal auxin transport and auxin response in CEZ cells.
Dimerization of the bacterial effector protein AvrBs3 in the plant cell cytoplasm prior to nuclear import
Authors: Gürlebeck Doreen , Szurek Boris , Bonas Ulla 
Published: March 2005

SummaryThe effector protein AvrBs3 from the bacterial phytopathogen Xanthomonas campestris pv. vesicatoria is translocated into the plant cell where it specifically induces hypertrophy symptoms or the hypersensitive reaction. Activity of AvrBs3 depends on nuclear localization signals (NLSs) and an acidic activation domain, suggesting a role in regulation of plant transcription. Here, we show that AvrBs3 dimerizes in the plant cell prior to its nuclear import. AvrBs3 deletion derivatives were tested in the yeast two‐hybrid system revealing that the repeat region, which confers specific recognition in resistant plants and is crucial for virulence function, is also essential for the self‐interaction. GST pull‐down assays showed that the AvrBs3–AvrBs3 interaction occurs independent of plant proteins. Coexpression of two different inactive mutant AvrBs3 derivatives in Bs3‐resistant pepper plants resulted in ‘trans‐complementation’, i.e., the induction of a hypersensitive reaction. This clearly indicates that AvrBs3‐dimerization occurs in planta. Interestingly, ‘trans‐complementation’ was not observed in susceptible plants suggesting that wild‐type homodimers are needed for the AvrBs3 virulence function in plants. Furthermore, a green fluorescent protein (GFP) fusion of AvrBs3 deleted in the NLSs (AvrBs3ΔNLS‐GFP), normally localized in the cytoplasm, was imported into the nucleus upon coexpression with wild‐type AvrBs3 in Nicotiana benthamiana. Thus, AvrBs3 dimerization takes place in the cytoplasm of the plant cell prior to nuclear import. Given the fact that dimerization is a common feature of transcriptional regulators, our data are consistent with the idea that AvrBs3 manipulates expression of plant genes involved in the establishment of compatible and incompatible interactions.
Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over‐expressing an MYB transcription factor
Authors: Tohge Takayuki , Nishiyama Yasutaka , Hirai Masami Yokota , Yano Mitsuru , Nakajima Jun‐ichiro , Awazuhara Motoko , Inoue Eri , Takahashi Hideki , Goodenowe Dayan B. , Kitayama Masahiko , Noji Masaaki , Yamazaki Mami , Saito Kazuki 
Published: March 2005

SummaryThe integration of metabolomics and transcriptomics can provide precise information on gene‐to‐metabolite networks for identifying the function of unknown genes unless there has been a post‐transcriptional modification. Here, we report a comprehensive analysis of the metabolome and transcriptome of Arabidopsis thaliana over‐expressing the PAP1 gene encoding an MYB transcription factor, for the identification of novel gene functions involved in flavonoid biosynthesis. For metabolome analysis, we performed flavonoid‐targeted analysis by high‐performance liquid chromatography‐mass spectrometry and non‐targeted analysis by Fourier‐transform ion‐cyclotron mass spectrometry with an ultrahigh‐resolution capacity. This combined analysis revealed the specific accumulation of cyanidin and quercetin derivatives, and identified eight novel anthocyanins from an array of putative 1800 metabolites in PAP1 over‐expressing plants. The transcriptome analysis of 22 810 genes on a DNA microarray revealed the induction of 38 genes by ectopic PAP1 over‐expression. In addition to well‐known genes involved in anthocyanin production, several genes with unidentified functions or annotated with putative functions, encoding putative glycosyltransferase, acyltransferase, glutathione S‐transferase, sugar transporters and transcription factors, were induced by PAP1. Two putative glycosyltransferase genes (At5g17050 and At4g14090) induced by PAP1 expression were confirmed to encode flavonoid 3‐O‐glucosyltransferase and anthocyanin 5‐O‐glucosyltransferase, respectively, from the enzymatic activity of their recombinant proteins in vitro and results of the analysis of anthocyanins in the respective T‐DNA‐inserted mutants. The functional genomics approach through the integration of metabolomics and transcriptomics presented here provides an innovative means of identifying novel gene functions involved in plant metabolism.
The H2O2‐regulated Ep5C gene encodes a peroxidase required for bacterial speck susceptibility in tomato
Authors: Coego Alberto , Ramirez Vicente , Ellul Phillipe , Mayda Esther , Vera Pablo 
Published: March 2005

SummaryBacterial speck caused by the pathogen Pseudomonas syringae pv. tomato (P. s. tomato) is a devastating disease of tomato plants. Here we show that inhibition of Ep5C gene expression, which encodes a secreted cationic peroxidase, is sufficient to confer resistance against P. s. tomato. The inhibition of Ep5C protein accumulation in antisense tomato plants established resistance that was not accompanied by the pre‐activation of known defense pathways. Therefore, Ep5C inhibition represents a novel form of disease resistance based on a loss‐of‐gene function in the plant required for successful infection by a compatible bacterial pathogen. Ep5C expression is rapidly induced by H2O2, a reactive oxygen intermediate normally generated during the course of a plant–pathogen interaction. This was corroborated by monitoring the expression of an Ep5C‐GUS gene in transgenic Arabidopsis plants. Collectively, these results identify a signaling pathway that uses early signals generated during the oxidative burst, such as H2O2, for the selective activation of host factors required for mounting a compatible interaction. Thus, Ep5C provides a new resource for developing bacterial speck disease‐resistant varieties.