bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ricinosomes Predict Programmed Cell Death Leading to Anther Dehiscence in Tomato
Authors: Senatore Adriano , Trobacher Christopher P. , Greenwood John S. 
Published: December 2008

Abstract
Successful development and dehiscence of the anther and release of pollen are dependent upon the programmed cell death (PCD) of the tapetum and other sporophytic tissues. Ultrastructural examination of the developing and dehiscing anther of tomato (Solanum lycopersicum) revealed that cells of the interlocular septum, the connective tissue, the middle layer/endothecium, and the epidermal cells surrounding the stomium all exhibit features consistent with progression through PCD. Ricinosomes, a subset of precursor protease vesicles that are unique to some incidents of plant PCD, were also present in all of these cell types. These novel organelles are known to harbor KDEL-tailed cysteine proteinases that act in the final stages of corpse processing following cell death. Indeed, a tomato KDEL-tailed cysteine proteinase, SlCysEP, was identified and its gene was cloned, sequenced, and characterized. SlCysEP transcript and protein were restricted to the anthers of the senescing tomato flower. Present in the interlocular septum and in the epidermal cells surrounding the stomium relatively early in development, SlCysEP accumulates later in the sporophytic tissues surrounding the locules as dehiscence ensues. At the ultrastuctural level, immunogold labeling localized SlCysEP to the ricinosomes within the cells of these tissues, but not in the tapetum. It is suggested that the accumulation of SlCysEP and the appearance of ricinosomes act as very early predictors of cell death in the tomato anther.
Multidrug and Toxic Compound Extrusion-Type Transporters Implicated in Vacuolar Sequestration of Nicotine in Tobacco Roots
Authors: Shoji Tsubasa , Inai Koji , Yazaki Yoshiaki , Sato Yasutaka , Takase Hisabumi , Shitan Nobukazu , Yazaki Kazufumi , Goto Yumi , Toyooka Kiminori , Matsuoka Ken , Hashimoto Takashi 
Published: December 2008

AbstractNicotine is a major alkaloid accumulating in the vacuole of tobacco (Nicotiana tabacum), but the transporters involved in the vacuolar sequestration are not known. We here report that tobacco genes (NtMATE1 and NtMATE2) encoding transporters of the multidrug and toxic compound extrusion (MATE) family are coordinately regulated with structural genes for nicotine biosynthesis in the root, with respect to spatial expression patterns, regulation by NIC regulatory loci, and induction by methyl jasmonate. Subcellular fractionation, immunogold electron microscopy, and expression of a green fluorescent protein fusion protein all suggested that these transporters are localized to the vacuolar membrane. Reduced expression of the transporters rendered tobacco plants more sensitive to the application of nicotine. In contrast, overexpression of NtMATE1 in cultured tobacco cells induced strong acidification of the cytoplasm after jasmonate elicitation or after the addition of nicotine under nonelicited conditions. Expression of NtMATE1 in yeast (Saccharomyces cerevisiae) cells compromised the accumulation of exogenously supplied nicotine into the yeast cells. The results imply that these MATE-type proteins transport tobacco alkaloids from the cytosol into the vacuole in exchange for protons in alkaloid-synthesizing root cells.
Characterization of Raphanus sativus Pentatricopeptide Repeat Proteins Encoded by the Fertility Restorer Locus for Ogura Cytoplasmic Male Sterility
Authors: Uyttewaal M. , Arnal N. , Quadrado M. , Martin-Canadell A. , Vrielynck N. , Hiard S. , Gherbi H. , Bendahmane A. , Budar F. , Mireau H. 
Published: December 2008

Abstract
Cytoplasmic male sterility is a maternally inherited trait in higher plants that prevents the production of functional pollen. Ogura cytoplasmic male sterility in radish (Raphanus sativus) is regulated by the orf138 mitochondrial locus. Male fertility can be restored when orf138 accumulation is suppressed by the nuclear Rfo locus, which consists of three genes putatively encoding highly similar pentatricopeptide repeat proteins (PPR-A, -B, and -C). We produced transgenic rapeseed (Brassica napus) plants separately expressing PPR-A and PPR-B and demonstrated that both encoded proteins accumulated preferentially in the anthers of young flower buds. Immunodetection of ORF138 showed that, unlike PPR-B, PPR-A had no effect on the synthesis of the sterility protein. Moreover, immunolocalization experiments indicated that complete elimination of ORF138 from the tapetum of anthers correlated with the restoration of fertility. Thus, the primary role of PPR-B in restoring fertility is to inhibit ORF138 synthesis in the tapetum of young anthers. In situ hybridization experiments confirmed, at the cellular level, that PPR-B has no effect on the accumulation of orf138 mRNA. Lastly, immunoprecipitation experiments demonstrated that PPR-B, but not PPR-A, is associated with the orf138 RNA in vivo, linking restoration activity with the ability to directly or indirectly interact with the orf138 RNA. Together, our data support a role for PPR-B in the translational regulation of orf138 mRNA.
Dynamic Evolution ofOryzaGenomes Is Revealed by Comparative Genomic Analysis of a Genus-Wide Vertical Data Set
Authors: Ammiraju Jetty S.S. , Lu Fei , Sanyal Abhijit , Yu Yeisoo , Song Xiang , Jiang Ning , Pontaroli Ana Clara , Rambo Teri , Currie Jennifer , Collura Kristi , Talag Jayson , Fan Chuanzhu , Goicoechea Jose Luis , Zuccolo Andrea , Chen Jinfeng , Bennetzen Jeffrey L. , Chen Mingsheng , Jackson Scott , Wing Rod A. 
Published: December 2008

AbstractOryza (23 species; 10 genome types) contains the world's most important food crop — rice. Although the rice genome serves as an essential tool for biological research, little is known about the evolution of the other Oryza genome types. They contain a historical record of genomic changes that led to diversification of this genus around the world as well as an untapped reservoir of agriculturally important traits. To investigate the evolution of the collective Oryza genome, we sequenced and compared nine orthologous genomic regions encompassing the Adh1-Adh2 genes (from six diploid genome types) with the rice reference sequence. Our analysis revealed the architectural complexities and dynamic evolution of this region that have occurred over the past ∼15 million years. Of the 46 intact genes and four pseudogenes in the japonica genome, 38 (76%) fell into eight multigene families. Analysis of the evolutionary history of each family revealed independent and lineage-specific gain and loss of gene family members as frequent causes of synteny disruption. Transposable elements were shown to mediate massive replacement of intergenic space (&gt;95%), gene disruption, and gene/gene fragment movement. Three cases of long-range structural variation (inversions/deletions) spanning several hundred kilobases were identified that contributed significantly to genome diversification.
Scale‐dependent effects of land use on plant species richness of mountain grassland in the European Alps
Authors: Spiegelberger Thomas , Matthies Diethart , Müller‐Schärer Heinz , Schaffner Urs 
Published: December 2008

Traditionally managed mountain grasslands in the Alps are species‐rich ecosystems that developed during centuries of livestock grazing. However, changes in land use including fertilisation of well accessible pastures and gradual abandonment of remote sites are increasingly threatening this diversity. In five regions of the Swiss and French Alps we assessed the relationship between land use, soil resource availability, cover of the unpalatable speciesVeratrum album,species richness and vegetation composition of mountain grasslands across four spatial scales ranging from 1 to 1000 m2.Mean species richness and the increase in the number of species with increasing area were lower in intensively grazed, fertilised pastures than in traditional pastures or in abandoned pastures. Species composition of abandoned pastures differed from that of the other management types. Plant species richness was influenced by different factors at different spatial scales. At the 1 m2scale, plant species richness was negatively related to soil nitrate and influenced by the cover ofV. album,depending on land use: species richness and cover ofV. albumwere negatively correlated in abandoned pastures, but positively correlated in fertilised grasslands. At the 1000 m2scale, a negative effect of fertilization on richness was evident. These results indicate that at small scales species richness in mountain grasslands is determined by competition for light, which should be more important if nutrient availability is high, and by positive and negative interactions with unpalatable plants. In contrast, species richness at the large scale appears to be mainly influenced by land use. This result emphasizes the importance of studying such inter‐relationships at multiple scales. Our study further suggests that the maintenance of the traditional land use scheme is crucial for the conservation of plant species richness of mountain pastures as both intensification and abandonment changed species composition and reduced plant species diversity.
Emus as non‐standard seed dispersers and their potential for long‐distance dispersal
Authors: Calviño‐Cancela María , R. Dunn Robert , Van Etten Eddie J. B. , B. Lamont Byron 
Published: December 2008

Long‐distance seed dispersal may have important consequences for species range, migration rates, metapopulation dynamics, and gene flow. Plants have evolved various adaptations for seed dispersal by standard agents, with typical dispersal distances associated with them. Seeds may also be dispersed by non‐standard agents for which they do not show any apparent adaptation and may reach long distances. By sampling the droppings of emus Dromaius novaehollandiae at three localities in Western Australia, we investigated their potential to act as long‐distance dispersers of seeds with adaptations for dispersal modes other than endozoochory, such as unassisted, ant, wind and exozoochory, for which they act as non‐standard agents. Seventy‐seven plant species with five types of dispersal syndromes were found in the 112 droppings analysed, with at least 68 having viable seeds. Although endozoochory was the most frequent syndrome, the presence of other syndromes was important in terms of number of species (61%) and seeds (50%). Estimates of species richness indicated that an increase in sampling effort would increase the number of species observed, especially among non‐endozoochores. As a consequence of their long gut retention times and high mobility, emus can provide long‐distance dispersal opportunities that may be especially relevant for species with dispersal modes of typically short distances (unassisted, ant).Our results suggest that the role of emus as non‐standard agents for long‐distance dispersal should be taken into account for understanding current geographic ranges, gene flow and metapopulation dynamics of some plant species, as well as for predicting their future responses to climate change and fragmentation.
Patient acceptance and clinical impact of Bravo monitoring in patients with previous failed catheter‐based studies
Authors: SWEIS R. , FOX M. , ANGGIANSAH R. , ANGGIANSAH A. , BASAVARAJU K. , CANAVAN R. , WONG T. 
Published: December 2008

SummaryBackground  Standard pH monitoring is performed over 24 h with a naso‐oesophageal catheter (C‐pH). Limitations include naso‐pharyngeal discomfort, nausea and social embarrassment resulting in reduced reflux‐provoking activities. Recently a catheter‐free pH‐monitoring technique has become available. The tolerability and diagnostic yield of this system in patients who failed standard monitoring remain unknown.Aim  To examine the tolerability and diagnostic outcome of catheter‐free pH‐monitoring technique in patients who failed standard monitoring.Methods  Patients referred for C‐pH and catheter‐free pH monitoring completed a tolerability questionnaire. Acid exposure in the distal oesophagus and symptom index (SI) were reviewed.Results  Over 4 years, 883/1751 (50%) of patients with typical reflux symptoms referred for C‐pH were diagnosed with gastro‐oesophageal reflux disease (GERD) based on a pathological percentage time acid exposure (%time pH <4);134 (8%) patients failed C‐pH and, of these, 129 successfully completed 2‐day catheter‐free pH monitoring. Ninety‐eight (76%) of these patients had a pathological percentage pH <4 on either day compared with 49/102 (49%) of contemporaneous C‐pH patients (P < 0.01). There was no difference in SI for heartburn (35% vs. 42%; P = 0.49). The questionnaire demonstrated a preference for catheter‐free pH monitoring (96%) with less restriction in activities of daily living, naso‐pharyngeal discomfort, dysphagia and chest pain.Conclusions Tolerance and satisfaction with catheter‐free pH monitoring are high in patients who had previously failed C‐pH; catheter‐free pH monitoring assists the definitive diagnosis of GERD in this group.
Proton pump inhibitors increase significantly the risk ofClostridium difficileinfection in a low‐endemicity, non‐outbreak hospital setting
Authors: DALTON B. R. , LYE‐MACCANNELL T. , HENDERSON E. A. , MACCANNELL D. R. , LOUIE T. J. 
Published: December 2008

SummaryBackground Proton pump inhibitors (PPI) have been linked to higher risk ofClostridium difficileinfection (CDI). The relevance of this association in hospitals with low disease activity, where an outbreak strain is nondominant, has been assessed in relatively few studies.Aim To assess the association of PPI and CDI in a setting of low disease activity.Methods A retrospective cohort study was conducted at two hospitals. Patients admitted for ≥7 days receiving antibiotics were included. Demographics, exposure to PPI, antibiotics and other drugs in relation to diagnosis of CDI were assessed by univariate and multivariate analyses.Results Of 14 719 patients, 149 (1%) first episode CDI were documented; PPI co‐exposure increased CDI [1.44 cases/100 patients vs. 0.74 cases/100 non‐exposed (OR: 1.96, 95% CI: 1.42–2.72)]. By logistic regression, PPI days (adjusted OR: 1.01 per day, 95% CI: 1.00–1.02), histamine‐2 blockers, antidepressants, antibiotic days, exposure to medications, age, admission service and length of admission were significant predictors.Conclusions A statistically significant increase in CDI was observed in antibiotic recipients who received PPI, but the absolute risk increase is modest. In settings of with low rates of CDI, the benefit of PPI therapy outweighs the risk of developing CDI. These data support programmes to decrease inappropriate use of PPI in hospitalized patients.
Primary particle size distribution of eroded material affected by degree of aggregate slaking and seal development
Authors: Warrington D. N. , Mamedov A. I. , Bhardwaj A. K. , Levy G. J. 
Published: December 2008

SummaryPrimary particle size distribution (PSD) of eroded sediment can be used to estimate potential nutrient losses from soil and pollution hazards to the environment. We studied eroded sediment PSDs from three saturated soils, packed in trays (20 × 40 × 4 cm), that had undergone either minimal aggregate slaking (MAS) or severe aggregate slaking (SAS) prior to a 60 mm simulated rainstorm (kinetic energy, 15.9 kJ m−3; droplet diameter, 2.97 mm) and collected runoff at regular intervals. The degree of aggregate slaking was controlled by the rate at which soils were wetted to saturation. The PSDs of eroded materials and of parent soils were determined using a laser particle size analyser. For each soil, PSD frequency curves of eroded sediments and parent soils were generally of a similar shape but most eroded sediments had larger clay contents than their parent soils. In the SAS treatment, cumulative clay enrichment in the eroded materials was inversely related to the parent soil clay content, these being 28.5, 26.6 and 22.8% richer in clay than their parent soils for the loam, sandy clay and clay, respectively. Generally, total clay loss was greater from soils with SAS than from those with MAS because of erosion rates; however, clay enrichment of sediments, compared with parent soil clay contents, was mostly greater in samples with MAS. Greater clay enrichment took place during the early seal development stage in the loam, but could not readily be associated with specific stages of seal development for the clay. In the sandy clay, the relation between seal development and clay enrichment in the eroded material depended on the initial degree of aggregate slaking. The observed large preferential loss of clay by erosion in cultivated soils re‐emphasizes the need to employ erosion control measures.
SWORM: an agent‐based model to simulate the effect of earthworms on soil structure
Authors: Blanchart E. , Marilleau N. , Chotte J.‐L. , Drogoul A. , Perrier E. , Cambier Ch. 
Published: December 2008

SummarySoil structure can be defined as the spatial organization of solid mineral and organic particles, and pore space. It is of great importance for soil functioning as it drives ecosystem functions (carbon sequestration, emission of greenhouse gases, nutrient cycling, primary productivity, etc.). Soil structure results from biotic and abiotic factors. Among biotic factors, numerous studies have shown the importance of organic matter, microorganisms, roots and invertebrates. Earthworms are known to play a key role in soil structure formation and maintenance through a continuous production of biogenic structures (casts and burrows). As far as we know, no models describe or quantify the effect of soil invertebrates on soil aggregation and porosity. It is a challenge to describe the physical soil environment for purposes of modelling because a soil is a multi‐scale heterogeneous, three‐dimensional and dynamic environment. An approach based on fractal theory (often used in soil sciences) was chosen to model such a real complex environment; it was integrated into a multi‐agent system (MAS), which allows us to simulate agents (e.g. earthworms) situated in a virtual world (e.g. soil). It is a bottom‐up approach that allows us to describe a system at a micro level (e.g. earthworms and their local soil environment) in order to observe, during simulations, macroscopic changes (e.g. soil structure evolution, organic matter dynamics, and microbial functions). In this paper we describe the SWORM (for ‘Simulated Worms’) model and the simulator, and present the results of the simulation applied to a case study. The effect of compacting and decompacting earthworm species on the structure of humid savanna soil at Lamto in Côte d’Ivoire has been widely studied. Quantitative and graphical outputs (e.g. thin sections of the virtual soil) indicate that the simulator was able to reproduce the effects of both compacting and decompacting species. Different ways to improve the model are discussed.
Airborne radiometric survey data and a DTM as covariates for regional scale mapping of soil organic carbon across Northern Ireland
Authors: Rawlins B. G. , Marchant B. P. , Smyth D. , Scheib C. , Lark R. M. , Jordan C. 
Published: December 2008

SummarySoil scientists require cost‐effective methods to make accurate regional predictions of soil organic carbon (SOC) content. We assess the suitability of airborne radiometric data and digital elevation data as covariates to improve the precision of predictions of SOC from an intensive survey in Northern Ireland. Radiometric data (K band) and, to a lesser extent, altitude are shown to increase the precision of SOC predictions when they are included in linear mixed models of SOC variation. However the statistical distribution of SOC in Northern Ireland is bimodal and therefore unsuitable for geostatistical analysis unless the two peaks can be accounted for by the fixed effects in the linear mixed models. The upper peak in the distribution is due to areas of peat soils. This problem may be partly countered if soil maps are used to classify areas of Northern Ireland according to their expected SOC content and then different models are fitted to each of these classes. Here we divide the soil in Northern Ireland into three classes, namely mineral, organo‐mineral and peat. This leads to a further increase in the precision of SOC predictions and the median square error is 2.2 %2. However a substantial number of our observations appear to be mis‐classified and therefore the mean squared error in the predictions is larger (30.6 %2) since it is dominated by large errors due to mis‐classification. Further improvement in SOC prediction may therefore be possible if better delineation between areas of large SOC (peat) and small SOC (non‐peat) could be achieved.
Co‐operative action of interleukin‐10 and interferon‐γ to regulate dendritic cell functions
Authors: Yanagawa Yoshiki , Iwabuchi Kazuya , Onoé Kazunori 
Published: December 2008

SummaryInterleukin‐10 (IL‐10) and interferon‐γ (IFN‐γ) double producer is found in a subpopulation of T regulatory type 1 (Tr1) and T helper type 1 (Th1) cells. Consequently, it is of interest how IL‐10 and IFN‐γ influence the immune system. However, few studies have addressed the co‐operative action of these ‘immunosuppressive’ and ‘immunostimulatory’ cytokines. Here, we examine the effect of IL‐10 combined with IFN‐γ on dendritic cell (DC) functions. Murine bone marrow‐derived conventional DCs were stimulated with IL‐10 and/or IFN‐γ for 24 hr. Tumour necrosis factor‐α and IL‐12 p40 production by DCs treated with both IL‐10 and IFN‐γ was significantly lower than that by DCs treated with IL‐10 or IFN‐γ alone. Major histocompatibility complex class II expression on DCs treated with both cytokines was attenuated compared with that on DCs treated with either cytokine alone. In contrast, levels of inducible nitric oxide synthase and indoleamine 2,3‐dioxygenase, which appear to suppress T‐cell responses and promote tolerance, in DCs treated with both cytokines were higher than those in DCs treated with IL‐10 or IFN‐γ alone. Simultaneous treatment with IL‐10 and IFN‐γ significantly suppressed the ability of DCs to activate CD4+ T cells compared with treatment with either cytokine. Therefore, IL‐10 and IFN‐γ co‐operatively suppress the immunostimulatory functions of DCs.
Yersinia pestis and host macrophages: immunodeficiency of mouse macrophages induced by YscW
Authors: Bi Yujing , Du Zongmin , Han Yanping , Guo Zhaobiao , Tan Yafang , Zhu Ziwen , Yang Ruifu 
Published: December 2008

SummaryThe virulence of the pathogenic Yersinia species depends on a plasmid‐encoded type III secretion system (T3SS) that transfers six Yersinia outer protein (Yop) effector proteins into the cytoplasm of eukaryotic cells, leading to disruption of host defence mechanisms. It is shown in this study that Yersinia pestis YscW, a protein of the T3SS injectisome, contributes to the induction of a deficiency in phagocytosis in host macrophages and a reduction in their antigen‐presenting capacity. A Y. pestis strain lacking yscW had no effect on uptake by host macrophages. In mice infected with wild‐type Y. pestis, the yscW mutant or a complement strain, immunodeficiency was observed in host macrophages compared with those from uninfected mice. However, the phagocytosis and antigen presenting capacities of macrophages infected by yscW mutant strain both in vivo and in vitro were significantly higher than those by wild type strain. Consistent with this finding, when YscW was expressed in the RAW264·7 macrophage cell line, phagocytosis and antigen‐presenting capacities were significantly lower than those of the control groups. These results indicate that Y. pestis YscW may directly induce immunodeficiency in murine macrophages by crippling their phagocytosis and antigen‐presenting capacities. These data provide evidences to Y. pestis pathogenesis that some proteins in T3SS injectisome, such as YscW protein, might play independent roles in disrupting host defense apart from their known functions.