bluuebunny/crossref_metadata_2025 huggingface dataset:
Different natural killer (NK) receptor expression and immunoglobulin E (IgE) regulation by NK1 and NK2 cells
Authors: Aktas E , Akdis M , Bilgic S , Disch R , Falk C S , Blaser K , Akdis C , Deniz G
Published: March 2005

Many studies concerning the role of T cells and cytokines in allergy have been performed, but little is known about the role of natural killer (NK) cells. Accordingly, the expression of co-stimulatory, inhibitory and apoptosis receptors, cytokine profiles and their effect on immunoglobulin isotypes were investigated in polyallergic atopic dermatitis (AD) patients with hyper immunoglobulin E (IgE) and healthy individuals. AD patients showed significantly decreased peripheral blood NK cells compared to healthy individuals. Freshly isolated NK cells of polyallergic patients spontaneously released higher amounts of interleukin (IL)-4, IL-5, IL-13 and interferon (IFN)-γ compared to healthy individuals. NK cells were differentiated to NK1 cells by IL-12 and neutralizing anti-IL-4 monoclonal antibodies (mAb), and to NK2 cells by IL-4 and neutralizing anti-IL-12 mAb. Following IL-12 stimulation, NK cells produced increased levels of IFN-γ and decreased IL-4. In contrast, stimulation of NK cells with IL-4 inhibited IFN-γ, but increased IL-13, production. The effect of NK cell subsets on IgE regulation was examined in co-cultures of in vitro differentiated  NK  cells  with  peripheral  blood  mononuclear  cells  (PBMC) or B cells. NK1 cells significantly inhibited IL-4- and soluble CD40-ligand-stimulated IgE production; however, NK2 cells did not have any effect. The inhibitory effect of NK1 cells on IgE production was blocked by neutralization of IFN-γ. Except for CD40, NK cell subsets showed different expression of killer-inhibitory receptors and co-stimulatory molecules between the polyallergic and healthy subjects. These results indicate that human NK cells show differences in numbers, surface receptor and cytokine phenotypes and functional properties in AD.
Simultaneous degradation estimation and restoration of confocal images and performance evaluation by colocalization analysis
Authors: ROOMS F. , PHILIPS W. , LIDKE D. S.
Published: March 2005

A novel method for joint restoration and estimation of the degradation of confocal microscope images is presented. The observed images are degraded due to two sources: blurring due to the band‐limited nature of the optical system [modelled by the point spread function (PSF)], and Poisson noise contaminates the observations due to the discrete nature of the photon detection process. The proposed method iterates noise reduction, blur estimation and deblurring, and applies these steps in two phases, i.e. a training phase and a restoration phase. In the first phase, these three steps are iterated until the blur estimation converges. Noise reduction and blur estimation are performed using steerable pyramids, and the deblurring is performed by the Richardson–Lucy algorithm. The second phase is the actual restoration. From then on, the blur estimation is used as a criterion to measure the image quality. The iterations are stopped when this measure converges, a result that is guaranteed. The integrated method is completely automatic, and no prior information on the image is required. The method has been given the name SPERRIL (Steerable Pyramid‐based Estimation and Regularized Richardson–Lucy restoration). Compared with existing techniques by both objective measures and visual observation, in the SPERRIL‐restored images noise is better suppressed.
A fast method to study the secretory activity of neuroendocrine cells at the ultrastructural level
Authors: VAN HERP F. , COENEN T. , GEURTS H. P. M. , JANSSEN G. J. A. , MARTENS G. J. M.
Published: March 2005

Cryo field emission scanning electron microscopy (cryo‐FE‐SEM) is a versatile technique that allows the investigation of the three‐dimensional organization of cells at the ultrastructural level over a wide range of magnifications. Unfortunately, cryopreparation of the specimens for this technique remains cumbersome, in particular because ice crystal formation must be prevented during freezing. Here we report that a light prefixation with glutaraldehyde and incubation in glycerol as cryoprotectant or a high‐pressure freezing approach are both excellent procedures for cryopreparation of animal cells to be used in combination with cryo‐FE‐SEM. Using the proopiomelanocortin‐producing intermediate pituitary melanotrope cells of Xenopus laevis as a physiologically inducible neuroendocrine system, we compared the ultrastructural characteristics of inactive and hyperactive neuroendocrine cells. The overall quality of the ultrastructural images was comparable for the two cryopreparation procedures, although some fine structures were better conserved using high‐pressure freezing. Melanotrope cells in a secretory inactive state contained numerous storage granules and a poorly developed endoplasmic reticulum (ER), while large amounts of rough ER were present in hyperactive cells. Thus, the cryo‐FE‐SEM approach described here allows a fast ultrastructural study on the secretory activity of neuroendocrine cells.
A procedure to determine the correct thickness of an object with confocal microscopy in case of refractive index mismatch
Authors: KUYPERS L. C. , DECRAEMER W. F. , DIRCKX J. J. J. , TIMMERMANS J.‐P.
Published: March 2005

A difference in refractive index (n) between immersion medium and specimen results in increasing loss of intensity and resolution with increasing focal depth and in an incorrect axial scaling in images of a confocal microscope. Axial thickness measurements of an object on such images are therefore not exact. The present paper describes a simple procedure to determine the correct axial thickness of an object with confocal fluorescence microscopy. We study this procedure for a specimen that has a higher refractive index than the immersion medium and with a thickness up to 100 µm. The measuring method was experimentally tested by comparing the thickness of polymer layers measured on axial images of a confocal microscope in case of a water–polymer mismatch to reference values obtained from an independent technique, i.e. scanning electron microscopy. The case when the specimen has a lower refractive index than the immersion medium is also shown by way of illustration. Measured thickness data of a water layer and an oil layer with the same actual thickness were obtained using an oil‐immersion objective lens with confocal microscopy. Good agreement between theory and experiment was found in both cases, consolidating our method.
Comparative imaging of a bacterial surface‐located GFP fusion protein by epifluorescence and scanning near‐field optical microscopy
Authors: GUNNING A. P. , BONGAERTS R. J. M. , KIRBY A. R. , HINTON J. C. D. , MORRIS V. J.
Published: March 2005

IcsA is an autotransporter protein that plays a role in the virulence of Shigella bacteria. We have examined the cellular localization of a fusion of an IcsA fragment to the green fluorescent protein (GFP) expressed in Escherichia coli using a dual epifluorescence and scanning near‐field optical microscope. By combining the data obtained from far‐field with near‐field microscopy of the same sample, discrimination between surface‐bound fusion proteins and fusion proteins located in the cellular cytoplasm becomes possible. Furthermore, and for the first time, the inherent advantages in resolution of the near‐field images provides highly specific details of the location of a GFP fusion protein on a bacterial cell surface.
Reconstruct: a free editor for serial section microscopy
Authors: FIALA J. C.
Published: March 2005

Many microscopy studies require reconstruction from serial sections, a method of analysis that is sometimes difficult and time‐consuming. When each section is cut, mounted and imaged separately, section images must be montaged and realigned to accurately analyse and visualize the three‐dimensional (3D) structure. Reconstruct is a free editor designed to facilitate montaging, alignment, analysis and visualization of serial sections. The methods used by Reconstruct for organizing, transforming and displaying data enable the analysis of series with large numbers of sections and images over a large range of magnifications by making efficient use of computer memory. Alignments can correct for some types of non‐linear deformations, including cracks and folds, as often encountered in serial electron microscopy. A large number of different structures can be easily traced and placed together in a single 3D scene that can be animated or saved. As a flexible editor, Reconstruct can reduce the time and resources expended for serial section studies and allows a larger tissue volume to be analysed more quickly.
Microfabric analysis by manual and automated stereological procedures: a methodological approach to Antarctic tillite
Authors: STROEVEN ARJEN P. , STROEVEN PIET , VAN DER MEER JAAP J. M.
Published: March 2005

Fabric analysis is commonly used to infer former movement directions of diamictons; however, analysis techniques are typically time consuming and partly subjective. Stereological analysis provides an alternative for objective determination of the preferred orientation of particles. The ability of manual and automated stereological procedures to determine the preferred orientation of particles (120–4000 µm) in tillite is assessed, using core samples from Mount Feather, McMurdo Dry Valleys, Antarctica. Orthogonal sets of vertical thin sections were subjected to directed secant analysis involving the determination of the number of intersections between particle outlines and a rotating series of parallel lines. The manual analysis reveals a weakly developed three‐dimensional tilt angle (plunge) of 68°. This reflects the depth‐averaged subglacial deformational structure of the deposit. Because the preferred orientation signal is weak, in the automated set‐up this signal is obscured by the effect of digitization, hampering the reliable assessment of the orientation direction. The study shows microfabric variability within the studied cored section that is interpreted as a shear fabric. Reliable macrostructural information that might constrain ice flow directions requires a larger number of randomly or systematically drawn core samples from which averaged microstructural fabrics can be derived.
Mass movement‐induced fold‐and‐thrust belt structures in unconsolidated sediments in Lake Lucerne (Switzerland)
Authors: SCHNELLMANN MICHAEL , ANSELMETTI FLAVIO S. , GIARDINI DOMENICO , McKENZIE JUDITH A.
Published: March 2005

High‐resolution seismic imaging and piston coring in Lake Lucerne, Switzerland, have revealed surprising deformation structures in flat‐lying, unconsolidated sediment at the foot of subaqueous slopes. These deformation structures appear beneath wedges of massflow deposits and resemble fold‐and‐thrust belts with basal décollement surfaces. The deformation is interpreted as the result of gravity spreading induced by loading of the slope‐adjacent lake floor during massflow deposition. This study investigated four earthquake‐triggered lateral mass‐movement deposits in Lake Lucerne affecting four sections of the lake floor with areas ranging from 0·25 to 6·5 km2 in area. Up to 6 m thick sediment packages draping the subaqueous slopes slid along the acoustic basement. The resulting failure scars typically lie in water depths of >30 m on slopes characterized by downward steepening and inclinations of >10°. From the base‐of‐slope to several hundred metres out onto the flat plains, the wedges of massflow deposits overlie deeply (10–20 m) deformed basin‐plain sediment characterized by soft sediment fold‐and‐thrust belts with arcuate strikes and pronounced frontal thrusts. The intensity of deformation decreases towards the more external parts of the massflow wedges. Beyond the frontal thrust, the overridden lake floor remains mostly undisturbed. Geometrical relationships between massflow deposits and the deformed basin‐plain sediment indicate that deformation occurred mainly during massflow deposition. Gravity spreading induced by the successive collapse of the growing slope‐adjacent massflow wedge is proposed as the driving mechanism for the deformation. The geometry of fjord‐type lakes with sharp lower slope breaks favours the deposition of thick, basin‐marginal massflow wedges, that effectively load and deform the underlying sediment. In the centre of the basins, the two largest massflow deposits described are directly overlain by thick contained (mega‐)turbidites, interpreted as combined products of the suspension clouds set up by subaqueous mass movements and related tsunami and seiche waves.
Estimating palaeobathymetry of wave‐graded continental shelves from sediment texture
Authors: DUNBAR G. B. , BARRETT P. J.
Published: March 2005

The concept of the wave‐graded continental shelf, with sea floor sediment coarsening from offshore mud to shoreface sand, has been well known from the time of Johnson (1919). Although most of the modern shelf shows textures unrelated to water depth on account of relict features or sediment starvation, the geological record is more likely to preserve sites where sediment is being fed to a subsiding inner‐shelf. These consistently show the landward‐coarsening pattern of the wave‐graded shelf, recording past water depth history in accumulated sea floor sediment. The landward‐coarsening pattern is driven primarily by wave‐induced bed shear stress, which increases shoreward exponentially, although it also varies from place to place with wave climate, and can be influenced by sediment concentration and currents. In this study, the relationship between bed shear stress, sediment texture and water depth has been investigated by comparing per cent mud and wave climate data from shore‐normal transects of three modern wave‐graded coastal settings: Wellington Harbour (low energy) and the Manawatu coast (moderate energy) in New Zealand, and Monterey Bay in California (moderate–high energy). Samples from all three locations show a progressive change from poorly sorted mud offshore to well‐sorted fine sand nearshore, with the sand–mud transition ranging from 3 m (low energy) to 50 m (moderate–high energy), reflecting differences in average bed shear. Repeat measurements of per cent mud on seasonal, annual and decadal time scales along a Manawatu coastal transect showed no measurable change, demonstrating equilibrium between sediment supply, wave energy, water depth and sediment texture. A simple model based on the relationship between wave climate, shear stress and per cent mud, and using data and conditions from the modern Manawatu coast, is applied to two mid‐Pliocene cyclothems exposed 50 km inland, giving results comparable with estimates from foraminifera and the deep‐sea isotope record. Per cent mud offers more detail for palaeobathymetric trends in shallow water shelf strata than other proxy depth recorders, although it is limited to depths above wave base and requires an independent estimate of wave climate if depths are to be quantified.
Normal faulting as a control on the stratigraphic development of shallow marine syn‐rift sequences: the Nukhul and Lower Rudeis Formations, Hammam Faraun fault block, Suez Rift, Egypt
Authors: JACKSON C. A. L. , GAWTHORPE R. L. , CARR I. D. , SHARP I. R.
Published: March 2005

Tectono‐stratigraphic analysis of the East Tanka fault zone (ETFZ), Suez Rift, indicates that the evolution of normal fault segments was an important control on syn‐rift depositional patterns and sequence stratigraphy. Sedimentological and stratigraphic analysis of the Nukhul Formation indicates that it was deposited in a narrow (ca 1–2 km), elongate (ca 5 km), fault‐bounded, tidally influenced embayment during the low subsidence rift‐initiation phase. The Nukhul Formation is composed of transgressive (TST) and highstand (HST) systems tract couplets interpreted as reflecting fault‐driven subsidence and the continuous creation of accommodation in the hangingwall to the ETFZ. The overlying Lower Rudeis Formation was deposited during the high subsidence rift‐climax phase, and is composed of forced regressive systems tract (FRST) shallow marine sandbodies, and TST to HST offshore mudstones. Activity on the ETFZ led to marked spatial variability in stratal stacking patterns, systems tracts and key stratal surfaces, as footwall uplift, coupled with regressive marine erosion during deposition of FRST sandbodies, led to the removal of intervening TST–HST mudstone‐dominated units, and the amalgamation of FRST sandbodies and the stratal surfaces bounding these units in the footwall. This study indicates that the evolution of normal fault segments over relatively short (i.e. <1 km) length‐scales has the potential to enhance or suppress a eustatic sea‐level signal, leading to marked spatial variations in stratal stacking patterns, systems tracts and key stratal surfaces. Crucially, these variations in sequence stratigraphic evolution may occur within time‐equivalent stratal units, thus caution must be exercised when attempting to correlate syn‐rift depositional units based solely on stratal stacking patterns. Furthermore, local, tectonically controlled variations in relative sea level can give rise to syn‐rift stacking patterns which are counterintuitive in the context of the structural setting and perceived regional subsidence rates.
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

Hiati 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

This 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

Eighteen 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.
Phylogeny of the neotropical rove beetle genus Nordus (Coleoptera: Staphylinidae) with a special reference to the evolution of coloration and secondary sexual characters
Authors: Chatzimanolis Stylianos
Published: March 2005

Abstract.  A phylogenetic analysis for Nordus is provided; the monophyly of the genus is established and the phylogenetic relationships of its thirty‐eight species are resolved. Analysis of eighty‐seven morphological characters, including two coloration characters, produced four equally most‐parsimonious trees (tree length = 365, consistency index = 0.38, retention index = 0.66). The coloration of the head and thorax is examined in the context of the reconstructed phylogeny and the evolution of heterochromy is discussed. Golden‐orange coloration of the head and thorax evolved in the ancestor of Nordus. Black coloration of the head evolved at least five times, and black coloration of the thorax at least six times within the genus. The evolution of secondary sexual structures in Nordus is also examined in the context of the phylogeny. In males, a medial emarginate abdominal sternum VIII is the ancestral condition. The presence of a single large median lobe on sternum VIII or the presence of two elongate median lobes with a medial emargination on sternum VIII each represent independent evolution of modifications to the male sternum VIII in different lineages. In females, an unmodified abdominal sternum VIII is the ancestral condition. Evolution of an emargination, small lobe or pointed lobe on the margin of sternum VIII in females occurred in different lineages.
The ant subfamily Pseudomyrmecinae (Hymenoptera: Formicidae): phylogeny and evolution of big‐eyed arboreal ants
Authors: Ward Philip S. , Downie Douglas A.
Published: March 2005

Abstract. The ant subfamily Pseudomyrmecinae comprises three genera of hyperoptic, arboreal ants, widely distributed in tropical and subtropical regions:Pseudomyrmex(∼200 species, New World),Myrcidris(two species, South America) andTetraponera(∼100 species, Palaeotropics). The phylogenetic relationships among these ants were investigated using DNA sequence data (∼5.2 kb from 18S rDNA, 28S rDNA, wingless, abdominal‐A, and long‐wavelength rhodopsin genes) and 144 morphological characters, both separately and in combination. Data were gathered from a representative set of forty‐nine pseudomyrmecine species, plus eighteen species from various outgroups. There was substantial agreement among the results obtained from different datasets, and from different methods of phylogenetic inference (parsimony, Bayesian inference). The monophyly of the following groups is strongly supported (100% bootstrap support and 1.00 posterior probability in the molecular dataset): Pseudomyrmecinae,Pseudomyrmex, andPseudomyrmex + Myrcidris. The status of the genusTetraponerais less clear: the DNA sequence data indicate that the genus is paraphyletic, but morphological features and a unique insertion in the 28S gene support the monophyly of this taxon. Seven of ninePseudomyrmexspecies groups, established previously on the basis of morphology alone, are strongly upheld, but monophyly is rejected for theP. pallensgroup and theP. viduusgroup. In the latter case, molecular evidence indicates the existence of two independent clades, associated with the ant‐plantsTriplarisandTachigali, respectively, whose convergent morphological features had caused them to be placed erroneously in the same species group. The present results confirm an earlier assertion that obligate associations with domatia‐bearing plants have arisen at least twelve times in the subfamily. Molecular and morphological data support the hypothesis of a sister‐group relationship between Pseudomyrmecinae and Myrmeciinae (84% parsimony bootstrap, combined dataset), which implies a Cretaceous origin of the stem‐group pseudomyrmecines in the southern hemisphere. Pseudomyrmecines appear to have arisen in the Palaeotropics and later dispersed from Africa to South America, where they experienced a pronounced burst of diversification.
A systematic revision of the New World species of Trypeta Meigen (Diptera: Tephritidae)
Authors: Han Ho‐Yeon , Norrbom Allen L.
Published: March 2005

Abstract.  The tephritid genus Trypeta is revised for the New World and a key, descriptions, illustrations, and phylogeny provided for the eighteen species recognized: Trypeta bifasciata, sp.n., californiensis, sp.n., chiapasensis, sp.n., concolor (Wulp), costaricana, sp.n., denticulata, sp.n., flaveola Coquillett, flavifasciata, sp.n., footei, sp.n., fractura (Coquillett), inclinata, sp.n., maculata, sp.n., maculosa (Coquillett), melanoura, sp.n., reducta, sp.n., rufata (Wulp), striata (Wulp), and wulpi, sp.n. Lectotypes are designated for Spilographa fractura Coquillett and Spilographa maculosa Coquillett. Trypeta (Acidia) tortile Coquillett, Acidia sigma Phillips, and Trypeta angustigena Foote are synonymized with Trypeta flaveola Coquillett. Based upon many specimens, we redefine Trypeta flaveola as a widely distributed and morphologically highly variable species. New host plant records are provided for five species, and host data and other information on the biology and immature stages of all of the New World Trypeta species are summarized and discussed. Our phylogenetic analysis suggests that the majority of New World Trypeta species form a monophyletic group that diversified in the southwestern U.S.A. and Mesoamerica.
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

Solanaceous 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

Comparative 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

Coronatine (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

Amyloplast‐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

The 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

Polar 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

The 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

The 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

Bacterial 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.
Diacylglycerol pyrophosphate is a second messenger of abscisic acid signaling in Arabidopsis thaliana suspension cells
Authors: Zalejski Christine , Zhang Zongshen , Quettier Anne‐Laure , Maldiney Régis , Bonnet Magda , Brault Mathias , Demandre Chantal , Miginiac Emile , Rona Jean‐Pierre , Sotta Bruno , Jeannette Emmanuelle
Published: March 2005

In plants, the importance of phospholipid signaling in responses to environmental stresses is becoming well documented. The involvement of phospholipids in abscisic acid (ABA) responses is also established. In a previous study, we demonstrated that the stimulation of phospholipase D (PLD) activity and plasma membrane anion currents by ABA were both required for RAB18 expression in Arabidopsis thaliana suspension cells. In this study, we show that the total lipids extracted from ABA‐treated cells mimic ABA in activating plasmalemma anion currents and induction of RAB18 expression. Moreover, ABA evokes within 5 min a transient 1.7‐fold increase in phosphatidic acid (PA) followed by a sevenfold increase in diacylglycerol pyrophosphate (DGPP) at 20 min. PA activated plasmalemma anion currents but was incapable of triggering RAB18 expression. By contrast, DGPP mimicked ABA on anion currents and was also able to stimulate RAB18 expression. Here we show the role of DGPP as phospholipid second messenger in ABA signaling.