bluuebunny/crossref_metadata_2025_split huggingface dataset:
First Report of Bacterial Leaf Spot on Snow Lotus Caused by Pseudomonas syringae in China
Authors: Zhao S. F. , Luo Y. N. , Zhao H. Y. , Du J. , Fang X. Y. 
Published: January 2009

Snow lotus (Saussurea involucrata (Kar. & Kir.) Sch. Bip.) is an economically important medicinal herb increasingly grown in China in recent years. During the summer and autumn of 2005, 2006, and 2007, a necrosis of unknown etiology was observed on leaves in commercial production areas in Xinjiang Province of China. Disease incidence was approximately 40 to 50% of the plants during the 2005 and 2007 growing seasons. Initial symptoms consisted of pronounced water-soaked, dark brown-to-black spots that were 1 to 2 mm in diameter on young, expanding leaves. Later, some leaf spots on older leaves enlarged and coalesced, causing leaf desiccation. Leaf samples were collected in 2005, 2006, and 2007 from the affected hosts. Bacterial streaming was evident from these samples, and 28 strains were isolated on nutrient agar or King's medium B (KMB). All strains were gram negative and fluoresced bluegreen under UV light after 48 h of growth at 28°C on KMB. On the basis of LOPAT tests, the strains were identified as Pseudomonas syringae (1). The identity of two strains was confirmed by sequencing the 16S rDNA gene, which revealed 98% similarity to P. syringae strains in NCBI (Accession Nos. FJ001817 and FJ001818 for XJSNL 111 and 107, respectively). Infiltration of tobacco leaves with bacterial suspensions resulted in typical hypersensitivity reactions within 24 h. Pathogenicity of the strains was confirmed by spray inoculating five snow lotus leaves of a six-leaf stage plant with 108 CFU ml–1 bacterial suspensions in sterile water and five plants sprayed with sterile distilled water served as controls. Inoculated and sterile water-sprayed controls were maintained in the growth chamber with 90% relative humidity for 15 days at 15 ± 2°C. Symptoms similar to the original symptoms were observed on inoculated plants after 2 weeks. No symptoms developed on controls. Bacteria reisolated from inoculated plants were identified as strains of P. syringae. Isolates were deposited at the Key Laboratory for Oasis Crop Disease Prevention and Cure, Shihezi University. Rust caused by Puccinia carthami and leaf spot disease caused by Alternaria carthami of snow lotus have been reported (2,3). To our knowledge, this is the first report of P. syringae as the cause of bacterial leaf spot on snow lotus in China. References: (1) A. Braun-Kiewnick and D. C. Sands. Pseudomonas. Page 84 in: Laboratory Guide for the Identification of Plant Pathogenic Bacteria. 3rd ed. N. W. Schaad et al., eds. The American Phytopathological Society, St. Paul, MN, 2001. (2) S. Zhao et al. Plant Dis. 91:772, 2007. (3) S. Zhao et al. Plant Dis. 92:318, 2008.
Compromised Virus-Induced Gene Silencing in RDR6-Deficient Plants
Authors: Vaistij Fabián E. , Jones Louise 
Published: January 2009

Abstract
RNA silencing in plants serves as a potent antiviral defense mechanism through the action of small interfering RNAs (siRNAs), which direct RNA degradation. siRNAs can be derived directly from the viral genome or via the action of host-encoded RNA-dependent RNA polymerases (RDRs). Plant genomes encode multiple RDRs, and it has been demonstrated that plants defective for RDR6 hyperaccumulate several classes of virus. In this study, we compared the effectiveness of virus-induced gene silencing (VIGS) and RNA-directed DNA methylation (RdDM) in wild-type and RDR6-deficient Nicotiana benthamiana plants. For the potexvirus Potato virus X (PVX) and the potyvirus Plum pox virus (PPV), the efficiency of both VIGS and RdDM were compromised in RDR6-defective plants despite accumulating high levels of viral siRNAs similar to infection of wild-type plants. The reduced efficiency of VIGS and RdDM was unrelated to the size class of siRNA produced and, at least for PVX, was not dependent on the presence of the virus-encoded silencing suppressor protein, 25K. We suggest that primary siRNAs produced from PVX and PPV in the absence of RDR6 may not be good effectors of silencing and that RDR6 is required to produce secondary siRNAs that drive a more effective antiviral response.
Cell Culture-Induced Gradual and Frequent Epigenetic Reprogramming of Invertedly Repeated Tobacco Transgene Epialleles
Authors: Krizova Katerina , Fojtova Miloslava , Depicker Ann , Kovarik Ales 
Published: January 2009

AbstractUsing a two-component transgene system involving two epiallelic variants of the invertedly repeated transgenes in locus 1 (Lo1) and a homologous single-copy transgene locus 2 (Lo2), we have studied the stability of the methylation patterns and trans-silencing interactions in cell culture and regenerated tobacco (Nicotiana tabacum) plants. The posttranscriptionally silenced (PTGS) epiallele of the Lo1 trans-silences and trans-methylates the target Lo2 in a hybrid (Lo1/Lo2 line), while its transcriptionally silenced variant (Lo1E) does not. This pattern was stable over several generations in plants. However, in early Lo1E/Lo2 callus, decreased transgene expression and partial loss of Lo1E promoter methylation compared with leaf tissue in the parental plant were observed. Analysis of small RNA species and coding region methylation suggested that the transgenes were silenced by a PTGS mechanism. The Lo1/Lo2 line remained silenced, but the nonmethylated Lo1 promoter acquired partial methylation in later callus stages. These data indicate that a cell culture process has brought both epialleles to a similar epigenetic ground. Bisulfite sequencing of the 35S promoter within the Lo1 silencer revealed molecules with no, intermediate, and high levels of methylation, demonstrating, to our knowledge for the first time, cell-to-cell methylation diversity of callus. Regenerated plants showed high interindividual but low intraindividual epigenetic variability, indicating that the callus-induced epiallelic variants were transmitted to plants and became fixed. We propose that epigenetic changes associated with dedifferentiation might influence regulatory pathways mediated by trans-PTGS processes.
The Proteome of Seed Development in the Model Legume Lotus japonicus
Authors: Dam Svend , Laursen Brian S. , Ørnfelt Jane H. , Jochimsen Bjarne , Stærfeldt Hans Henrik , Friis Carsten , Nielsen Kasper , Goffard Nicolas , Besenbacher Søren , Krusell Lene , Sato Shusei , Tabata Satoshi , Thøgersen Ida B. , Enghild Jan J. , Stougaard Jens 
Published: January 2009

Abstract
We have characterized the development of seeds in the model legume Lotus japonicus. Like soybean (Glycine max) and pea (Pisum sativum), Lotus develops straight seed pods and each pod contains approximately 20 seeds that reach maturity within 40 days. Histological sections show the characteristic three developmental phases of legume seeds and the presence of embryo, endosperm, and seed coat in desiccated seeds. Furthermore, protein, oil, starch, phytic acid, and ash contents were determined, and this indicates that the composition of mature Lotus seed is more similar to soybean than to pea. In a first attempt to determine the seed proteome, both a two-dimensional polyacrylamide gel electrophoresis approach and a gel-based liquid chromatography-mass spectrometry approach were used. Globulins were analyzed by two-dimensional polyacrylamide gel electrophoresis, and five legumins, LLP1 to LLP5, and two convicilins, LCP1 and LCP2, were identified by matrix-assisted laser desorption ionization quadrupole/time-of-flight mass spectrometry. For two distinct developmental phases, seed filling and desiccation, a gel-based liquid chromatography-mass spectrometry approach was used, and 665 and 181 unique proteins corresponding to gene accession numbers were identified for the two phases, respectively. All of the proteome data, including the experimental data and mass spectrometry spectra peaks, were collected in a database that is available to the scientific community via a Web interface (http://www.cbs.dtu.dk/cgi-bin/lotus/db.cgi). This database establishes the basis for relating physiology, biochemistry, and regulation of seed development in Lotus. Together with a new Web interface (http://bioinfoserver.rsbs.anu.edu.au/utils/PathExpress4legumes/) collecting all protein identifications for Lotus, Medicago, and soybean seed proteomes, this database is a valuable resource for comparative seed proteomics and pathway analysis within and beyond the legume family.
System Potentials, a Novel Electrical Long-Distance Apoplastic Signal in Plants, Induced by Wounding
Authors: Zimmermann Matthias R. , Maischak Heiko , Mithöfer Axel , Boland Wilhelm , Felle Hubert H. 
Published: January 2009

Abstract
Systemic signaling was investigated in both a dicot (Vicia faba) and a monocot (Hordeum vulgare) plant. Stimuli were applied to one leaf (S-leaf), and apoplastic responses were monitored on a distant leaf (target; T-leaf) with microelectrodes positioned in substomatal cavities of open stomata. Leaves that had been injured by cutting and to which a variety of cations were subsequently added caused voltage transients at the T-leaf, which are neither action potentials nor variation potentials: with respect to the cell interior, the initial polarity of these voltage transients is hyperpolarizing; they do not obey the all-or-none rule but depend on both the concentration and the type of substance added and propagate at 5 to 10 cm min−1. This response is thought to be due to the stimulation of the plasma membrane H+-ATPase, a notion supported by the action of fusicoccin, which also causes such voltage transients to appear on the T-leaf, whereas orthovanadate prevents their propagation. Moreover, apoplastic ion flux analysis reveals that, in contrast to action or variation potentials, all of the investigated ion movements (Ca2+, K+, H+, and Cl−) occur after the voltage change begins. We suggest that these wound-induced “system potentials” represent a new type of electrical long-distance signaling in higher plants.
Cytological features of chromophobe renal cell carcinoma, classic type. A report of nine cases
Authors: Tejerina E. , González‐Peramato P. , Jiménez‐Heffernan J. A. , Vicandi B. , Serrano A. , López‐Ferrer P. , Viguer J. M. 
Published: January 2009

Objective:  To review our experience with nine cases of chromophobe renal cell carcinoma (ChRCC), classic type. The cytological descriptions of this entity are still rare, and information concerning the diagnostic value of cytology is needed.Methods:  Nine cases of ChRCC evaluated using fine needle aspiration (n = 6) or intraoperative scrape cytology (n = 3) were selected. Expression of vimentin was evaluated in four cases using immunocytochemistry, which was performed on alcohol‐fixed material. In all cases a complete pathological study was available.Results:  The neoplastic cells were arranged mainly as single cells and small, discohesive, monolayered groups. A polymorphous cellular population was identified, with coexisting large, small and intermediate‐sized cells. The large neoplastic cells showed clear, flocculent cytoplasm with small, eccentric nuclei and frequent binucleation. Dense, homogeneous cytoplasm was most commonly seen in smaller cells. Clear cytoplasmic spaces resembling perinuclear halos were frequently observed, best appreciated in cells with more dense cytoplasm. Binucleation and a marginal nuclear location were commonly seen. Necrosis, basement membrane or other stromal material were absent. Vimentin was not expressed in the four cases analysed. Precise cytological recognition was possible in the last five cases.Conclusions:  There is increasing evidence that a cytological diagnosis of ChRCC is possible. In our experience the histopathological features of ChRCC were well reflected in cytological samples, allowing specific recognition. In our cases the main differential diagnosis considered was clear cell carcinoma. Cytology can be especially helpful in the evaluation of intraoperative samples.
Effect ofMucuna prurienson oxidative stress mediated damage in aged rat sperm
Authors: Suresh Sekar , Prithiviraj Elumalai , Prakash Seppan 
Published: January 2009

SummaryMucuna pruriensLinn., a leguminous plant, has been recognized as an aphrodisiac and spermatogenic agent. Protective efficacy ofM. prurienson reactive oxygen species (ROS)‐induced pathophysiological alterations in structural and functional integrity of epididymal sperm in aged Wister albino rat was analysed. Animals were grouped as groups I, II, III and IV, i.e. young (control), aged, aged treated with ethanolic extract (200 mg/kg b.w.) ofM. pruriensand young rats treated withM. pruriens, respectively. At the end of the experimental period, i.e. after 60 days animals were sacrificed, epididymal sperm were collected and subjected to count, viability, motility, morphology and morphometric analysis. Enzymatic and non‐enzymatic antioxidants, ROS, lipid peroxidation (LPO), DNA damage, chromosomal integrity and mitochondrial membrane potential were estimated. Results obtained from the aged animals showed significant reduction in sperm count, viability and motility, increased morphological damage and an increase in the number of sperm with cytoplasmic remnant, and these alterations were significantly reversed inM. prurienstreated group. Significant increase in LPO, HO˙ and H2O2production and significant decline in the levels of the enzymatic and non‐enzymatic antioxidants were observed in the aged animals. Supplementation ofM. prurienssignificantly reduced ROS and LPO production and significant increase in both enzymatic and non‐enzymatic antioxidant levels. There were significant DNA damage, loss of chromosomal integrity and increase in mitochondrial membrane permeability in aged rat sperm. This was significantly reduced in group III. Present observation indicates the antioxidant enhancing property, free radical quenching ability and spermatogenic efficacy of theM. pruriens. Collectively, sperm damage in ageing was significantly reduced by quenching ROS, improving antioxidant defence system and mitochondrial function.
Gauging the effects of sampling failure in biogeographical analysis
Authors: Turner Alan H. , Smith Nathan D. , Callery John A. 
Published: January 2009

AbstractAim  Various methods are employed to recover patterns of area relationships in extinct and extant clades. The fidelity of these patterns can be adversely affected by sampling error in the form of missing data. Here we use simulation studies to evaluate the sensitivity of an analytical biogeographical method, namely tree reconciliation analysis (TRA), to this form of sampling failure.Location  Simulation study.Methods  To approximate varying degrees of taxonomic sampling failure within phylogenies varying in size and in redundancy of biogeographical signal, we applied sequential pruning protocols to artificial taxon–area cladograms displaying congruent patterns of area relationships. Initial trials assumed equal probability of sampling failure among all areas. Additional trials assigned weighted probabilities to each of the areas in order to explore the effects of uneven geographical sampling. Pruned taxon–area cladograms were then analysed with TRA to determine if the optimal area cladograms recovered match the original biogeographical signal, or if they represent false, ambiguous or uninformative signals.Results  The results indicate a period of consistently accurate recovery of the true biogeographical signal, followed by a nonlinear decrease in signal recovery as more taxa are pruned. At high levels of sampling failure, false biogeographical signals are more likely to be recovered than the true signal. However, randomization testing for statistical significance greatly decreases the chance of accepting false signals. The primary inflection of the signal recovery curve, and its steepness and slope depend upon taxon–area cladogram size and area redundancy, as well as on the evenness of sampling. Uneven sampling across geographical areas is found to have serious deleterious effects on TRA, with the accuracy of recovery of biogeographical signal varying by an order of magnitude or more across different sampling regimes.Main conclusions  These simulations reiterate the importance of taxon sampling in biogeographical analysis, and attest to the importance of considering geographical, as well as overall, sampling failure when interpreting the robustness of biogeographical signals. In addition to randomization testing for significance, we suggest the use of randomized sequential taxon deletions and the construction of signal decay curves as a means to assess the robustness of biogeographical signals for empirical data sets.
Can herbarium records be used to map alien species invasion and native species expansion over the past 100 years?
Authors: Crawford Priscilla H. C. , Hoagland Bruce W. 
Published: January 2009

AbstractAim  To determine if the temporal and spatial pattern of alien plant invasion and native plant expansion can be observed using 100 years of herbarium data from Oklahoma, USA, and to eliminate herbarium collection biases in such analyses.Location  Oklahoma, USA.Methods  Using herbarium records from the Oklahoma Vascular Plants Database from 1903 to 2004, we reconstructed the spatial and temporal collection history of two alien invasive taxa (Lonicera japonica and Tamarix spp.) and three native expansive species (Ambrosia psilostachya, Amphiachyris dracunculoides and Juniperus virginiana). To compare the overall collecting trend, groups of native non‐expansive taxa were selected as counterparts. We recorded the year of the first collection in each township in Oklahoma for all taxa. The cumulative number of occupied townships was log‐transformed, plotted against time and modelled with linear regression. The slope of the linear regression represented collection trend over time for the non‐expansive counterpart group. However, for the invasive and expansive species, the regression slope represented the collection effort plus the invasion or expansion rate. We calculated the proportion of invasive and expansive species to non‐expansive species by dividing the cumulative number of townships for each invasive or expansive species by the cumulative number of townships occupied by the counterpart group (proportion curve).Results  Maps of the collection records of invasive and expansive taxa illustrated no discernible spatial invasion or expansion pattern. The slopes of the linear regression for alien invasive taxa were significantly steeper than those of their associated native non‐expansive counterparts, indicating an increase in abundance. Juniperus virginiana, L. japonica and Tamarix spp. exhibited one or more periods during which they were collected at a disproportionately higher rate than their native non‐expansive counterparts.Main conclusions  Patterns of species invasion and expansion in Oklahoma were detected using techniques developed for regions with longer collecting plant histories. The proportion curve analysis eliminated some biases inherent in herbarium data by reducing the effect of collecting effort. Both the regression model and proportion curve analyses illustrate the temporal invasion patterns of alien invasive species. The native species did not show a clear expansion pattern. The information found in recently established herbaria may not be sensitive enough to detect the increase in abundance of native species.
Mapping of pachytene bivalents of female codling moth Cydia pomonella (Linnaeus) (Lep., Tortricidae)
Authors: Makee H. , Tafesh N. , Harrown H. 
Published: January 2009

AbstractSpread pachytene nuclei of codling moth Cydia pomonella (Linnaeus) (Lep., Tortricidae) females of a Syrian strain (SY) were used to investigate chromomere patterns of chromosome bivalents and determine their length. The karyotype of female codling moths consists of 28 chromosome bivalents, of which seven are clearly distinguishable using chromosome length and the number and size of the chromomeres in the pachytene stage. One autosome bivalent has two nucleolar organizing regions (NORs) that are located at the opposite ends of the chromosome and appear as distinct structural landmarks. In female codling moths, the WZ sex chromosome bivalent was easily identified in pachytene oocytes according to the heterochromatic thread of the W chromosome. This study contributed to the knowledge and identification of pachytene chromosomes of female codling moths.
Effects of lipopolysaccharide on platelet‐derived growth factor isoform and receptor expression in cultured rat common bile duct fibroblasts and cholangiocytes
Authors: Kim Tae‐Hyeon , Moon Jong Ho , Savard Christopher E , Kuver Rahul , Lee Sum P 
Published: January 2009

AbstractBackground and Aim:  Little is known about the role of platelet‐derived growth factor (PDGF) in biliary fibrosis in the setting of bacterial colonization of the biliary tree. We therefore sought to investigate whether exposure to bacterial lipopolysaccharide (LPS) alters PDGF isoform and receptor expression in cultured rat common bile duct fibroblasts (CBDF) and normal rat cholangiocytes (NRC).Methods:  Collagen content in cells and media was assessed by colorimetric assay and gel electrophoresis. mRNA levels of PDGF‐A and ‐B, and PDGF‐Receptors (PDGF‐R) α and β were measured by relative quantitative real‐time PCR. Protein levels of PDGF‐AA, AB and BB were measured by ELISA, and PDGF‐Rα and PDGF‐Rβ by Western blot.Results:  In CBDF, LPS increased total soluble collagen synthesis and secretion. PDGF‐Rα and β mRNA and protein were also increased by LPS treatment in CBDF. Lipopolysaccharide treatment elicited an increase in PDGF‐A and ‐B mRNA levels in CBDF. In NRC, levels of PDGF‐A mRNA increased in a dose‐dependent fashion following LPS treatment, whereas PDGF‐B mRNA showed no response. PDGF‐AA secretion was higher by CBDF than by NRC. PDGF‐BB levels were also higher in CBDF than in NRC. While PDGF‐BB levels did not respond to LPS treatment in CBDF, there was a dose‐dependent response of this isoform to LPS in NRC. Intracellular and secreted PDGF‐AB increased with LPS treatment in NRC.Conclusions:  These results support a model in which chronic bacterial colonization of the biliary tree induces fibrosis through PDGF‐dependent mechanisms.
Immunophenotyping of interstitial infiltrate does not distinguish between BK virus nephropathy and acute cellular rejection
Authors: ROGERS NATASHA M , RUSS GRAEME R , COOPER JOHN , COATES P TOBY 
Published: January 2009

SUMMARYIntroduction:  BK virus nephropathy (BKVN) is a significant cause of late renal allograft loss. It is characterized histologically by an interstitial nephritis that can be difficult to distinguish from acute cellular rejection (ACR). We investigated whether immunophenotyping of the infiltrate would aid this distinction.Methods:  Ten cases of biopsy‐proven BKVN, following renal transplantation, were identified from a single transplant centre. The infection was confirmed by renal biopsy and staining for SV‐40 T‐antigen. Biopsies from 20 consecutive patients with ACR were identified and used as controls. There was no evidence of BK infection serologically or histologically in these patients. Immunohistochemical staining with anti‐CD20, perforin and granzyme B was performed on remaining tissue samples.Results:  Clustered B cells were demonstrated in both BKVN and ACR. Hence, the CD20‐stained component within the interstitial infiltrate was not useful in distinguishing these biopsies. Perforin‐stained slides demonstrated fewer cytotoxic T cells in the biopsies with BK virus (average 2.4 ± 1.4 cells per 100 lymphocytes per field) compared with those samples with acute rejection (8.6 ± 5.7 cells per 100 lymphocytes, P < 0.0001). No significant difference in granzyme B staining was detected between ACR and BKVN.Conclusion:  Clustered B cells and granzyme B staining did not differentiate between ACR and BKVN. However, ACR cellular infiltrate was rich in perforin positive cells suggesting that perforin staining may be a useful marker to discriminate between these conditions.