Recent Rice stripe virus Epidemics in Zhejiang Province, China, and Experiments on Sowing Date, Disease-Yield Loss Relationships, and Seedling Susceptibility

Rice stripe virus, transmitted by the small brown planthopper Laodelphax striatellus, has recently reemerged as a major disease in Zhejiang province, eastern China. Intensive surveys during 2003 to 2006 demonstrated how the disease has spread rapidly from the northern to central and eastern regions with increasing incidence each year. In bioassays, the highest proportions of viruliferous vectors were from regions where the disease was most severe. The greatest disease incidence was in the earliest sown plants, and substantial control could be achieved by delaying planting from late May to mid-June. In experiments where different proportions of infected plants were established (by inoculation or varying the sowing date), average yield losses were 0.8% for every 1% increase in disease incidence. In inoculation experiments, young seedlings, particularly those at the three- to five-leaf stage, were the most susceptible, whereas ≤1% of plants inoculated at or after the elongation stage developed symptoms. Recent epidemics appear to have resulted from large populations of viruliferous vectors colonizing rice seedlings at the most susceptible stage. This is probably because of changes in cropping practice, recent warmer winters in Zhejiang province, and the development of resistance or tolerance to the insecticides widely used (triazophos, synthetic pyrethroids, and Imidacloprid).

Molecular cloning and characterization of the Dicer-like 2 gene from Brassica rapa

Dicer-like proteins (DCLs) are involved in small RNA-mediated development and viral defense in plants. In model plants, at least four DCLs have been found and a number of studies have helped to understand their function. However, the function of the Dicer or DCLs in other plants is still unclear. Here, we report the full-length cDNA sequence of Brassica rapa ssp. chinensis DCL2 (BrDCL2) gene, which contains a 4,179 bp open reading frame (ORF) encoding a protein of 1,392 amino acids. At the 3' end of BrDCL2, clones with three different lengths of 3' untranslated region were found. An alternative splice variant of BrDCL2, BrDCL2sv, in which one intron was retained between exon9 and exon10, was also cloned. Because of a change in the coding sequence resulting in a premature terminal codon, BrDCL2sv was expected to translate a short peptide containing the whole DEXHc domain.

Range-wide phylogeographic analysis of the spotted frog complex (Rana luteiventris and Rana pretiosa) in northwestern North America

The dynamic geological and climatic history of northwestern North America has made it a focal region for phylogeography. We conducted a range-wide phylogeographic analysis of the spotted frog complex (Rana luteiventris and Rana pretiosa) across its range in northwestern North America to understand its evolutionary history and the distribution of clades to inform conservation of R. pretiosa and Great Basin R. luteiventris, candidates for listing under the US Endangered Species Act. Mitochondrial DNA sequence data from a segment of the cytochrome b gene were obtained from 308 R. luteiventris and R. pretiosa from 96 sites. Phylogenetic analysis revealed one main R. pretiosa clade and three main R. luteiventris clades, two of which overlapped in southeastern Oregon. The three R. luteiventris clades were separated from each other by high levels of sequence divergence (average of 4.75-4.97%). Two divergent clades were also uncovered within the Great Basin. Low genetic variation in R. pretiosa and the southeastern Oregon clade of R. luteiventris suggests concern about their vulnerability to extinction.

A potyvirus P1 protein interacts with the Rieske Fe/S protein of its host

ABSTRACT Yeast two-hybrid (Y2H) screens were used to test for interactions between the P1 protein of Soybean mosaic virus Pinellia isolate (SMV-P) and a cDNA expression library of its host, the aroid Pinellia ternata. Of the 13 independent interacting clones identified, ten were identical and had an open reading frame predicted to encode a 23.7-kDa protein closely related to the cytochrome b6/f complex Rieske Fe/S genes of plants. The interaction between SMV-P-P1 and the mature Rieske Fe/S protein (without transit peptide) of the host was confirmed by in vitro co-immunoprecipitation of the two proteins. Y2H assays using different parts of the two proteins showed that only the N-terminal part (amino acids 1-82) of SMV-P P1 was responsible for the interaction with the Rieske Fe/S protein and that amino acids 1-33 interacted only with the transit peptide, while amino acids 34-82 could interact with the entire Rieske Fe/S protein. SMV-P P1 also interacted moderately with the Rieske Fe/S protein of its other hosts, soybean and Zantedeschia aethiopica, but weakly with that of the non-host Arabidopsis thaliana. The P1-Rieske Fe/S protein interactions are likely to be involved in symptom development, and the very variable N-terminus of P1 may play an important role in host adaptation.

Analysis of SFM dynamics in solitary and optically-injected VCSELs

The aim of this paper is to use the spin-flip model (SFM) to investigate how the fundamental parameters of birefringence, spin relaxation and pumping affect the dynamics of solitary and optically-injected vertical-cavity surface-emitting lasers (VCSELs). The SFM predicts that a solitary VCSEL can exhibit diverse polarisation behaviour, including elliptical and linear stability, which can be used in polarisation switching. For given values of pumping, spin relaxation and birefringence, we analyse the electric field components, the carrier densities corresponding to spin-up and spin-down, and the relaxation oscillation frequency for a solitary VCSEL and the stability map for an optically-injected VCSEL.

Molecular characterization of the largest and smallest genome segments, S1 and S12, of Rice gall dwarf virus

The nucleotide sequences of segments S1 and S12 of a Chinese isolate of Rice gall dwarf virus (RGDV) were determined. This provides the first complete sequences of these segments. The complete sequence of S1, the largest genome segment of RGDV, was 4,505 nucleotides in length and was predicted to encode a large protein of 1,458 amino acids with a calculated molecular mass of nearly 166.2 kDa. The protein was related to that encoded by S1 of Rice dwarf virus (RDV; 50% identity and 67% similarity) and (to a lesser extent) to some large proteins of other reoviruses. It appears to be an RNA-dependent RNA polymerase (RdRp) and is probably present in particles as a minor core protein. S12, the smallest genome segment of RGDV, was 853 nucleotides in length, encoding a single major protein of 206 amino acids with a calculated molecular mass of nearly 23.6 kDa. This protein, though a little larger than those of RDV S11 and Wound tumor virus (WTV) S12 in size, showed some similarity to them, especially in the conserved N-terminal region and may have RNA-binding properties. Despite having a common host plant, RDV and RGDV were not more closely related to one another than either of them was to WTV. Phylogenetic analysis of the RdRp showed that members of the genus Phytoreovirus were more closely related to those of the genus Rotavirus than to any other genus within the family Reoviridae.

Nandrolone Potentiates Arrhythmogenic Effects of Cardiac Ischemia in the Rat

Anabolic steroid abuse has been associated with thrombosis and arteriosclerosis, both of which predispose to myocardial ischemia and infarction. However, there are reports of sudden cardiac death in the absence of thrombus and atheroma following anabolic steroid use. Although treatment with the commonly abused steroid, nandrolone, has been shown to decrease recovery of systolic function following ischemia in isolated rat hearts, it is unknown whether anabolic steroids can increase the incidence of fatal arrhythmia associated with cardiac ischemia. Anesthetized male Sprague-Dawley rats were administered vehicle or nandrolone (10-160 microg/kg/min iv) 10 min prior to 15-min occlusion of the left anterior descending coronary artery followed by 10-min reperfusion. Nandrolone, in this dose range, did not significantly change heart rate, blood pressure, or cardiac rhythm in the absence of ischemia. However, the fraction of rats surviving ischemia was significantly (p < 0.05) decreased by nandrolone at both 40 and 160 microg/kg/min, while survival time during ischemia was decreased significantly (p < 0.001) by nandrolone 160 microg/kg/min. An increase (p < 0.05) in the duration of ventricular fibrillation was noted at the highest compared to the lowest dose of nandrolone, corresponding to a significant increase in the fraction of rats experiencing ventricular fibrillation (p < 0.01). Nandrolone had no effect on the frequency or duration of ventricular fibrillation or survival time during reperfusion. Although the mechanisms underlying these effects are currently unclear, they indicate that exposure to anabolic steroids in combination with transient reductions in coronary blood flow may explain some reports of sudden cardiac death in anabolic steroid users.

Effects of parallel and orthogonal polarization on nonlinear optical characteristics of a 1550 nm VCSOA

Experimental observation of Optical Bistability (OB) and nonlinear gain is reported in a 1550-nm Vertical Cavity Semiconductor Optical Amplifier (VCSOA) under parallel and orthogonal polarized optical injection into the two orthogonal polarizations of the fundamental mode. Different nonlinear switching mechanisms, including anticlockwise and clockwise nonlinear gain and bistability, have been found when the polarization of the externally injected signal matches that of the injected mode, whilst a linear response is measured when the polarization is orthogonal to that of the mode under injection. This diversity of behavior with input polarization offers promise for the potential use of VCSOAs for all-optical signal processing and all-optical switching/routing applications.

Genomic analysis of rice stripe virus Zhejiang isolate shows the presence of an OTU-like domain in the RNA1 protein and a novel sequence motif conserved within the intergenic regions of ambisense segments of tenuiviruses

The complete genome sequence of the four RNAs of rice stripe virus Zhejiang isolate was determined. In addition to polymerase modules, the pc1 protein encoded on RNA1 harbours an ovarian tumour (OTU) - like cysteine protease signature near its N-terminus, suggesting that the protein might yield the viral polymerase and one or more additional proteins by autoproteolytic cleavage and/or have deubiquitination activity. A novel inverted repeat sequence motif was found to be universal within the intergenic regions of ambisense genome segments of tenuiviruses, supporting the possibility that it may be functionally important, perhaps in regulating transcription termination.

Molecular characterization of the genome segments S4, S6 and S7 of rice gall dwarf virus

Rice gall dwarf virus (RGDV) is a member of the genus Phytoreovirus within the family Reovirdae. Its genome has 12 segments of double-stranded RNA (dsRNA), of which the nucleotide sequences of segments S4, S6, and S7 were determined, providing the first complete genome sequence of RGDV. Each of the segments S4, S6, and S7 contained conserved terminal sequences conforming to the RGDV consensus, 5'-GGXA ... UGAU-3' (X = U or C). Each segment had a single predicted open reading frame encoding proteins with calculated molecular weights of 79.8, 58.6, and 53.3 kDa. These proteins appeared to be homologous to those encoded by the corresponding segments of rice dwarf virus and wound tumor virus, the other known members of the same genus, having about 20-30% amino acid identity to them. It is therefore likely that RGDV S4 and S6 encode non-structural proteins and S7 an inner core protein. Probable homologies between the segments of all known phytoreoviruses are summarized. Beyond these similarities, the RGDV proteins displayed no significant similarity to any other reported viral proteins.

Comparison of ITS sequences from UK and North American sugar-beet powdery mildews and the designation of Erysiphe betae

Powdery mildew of sugar beet, a disease of major economic significance, was first described at the beginning of the 20th century, and since then there has been some confusion over the correct taxonomic identity of the causal agent. In Europe, the fungus was initially classified as the novel species Microsphaera betae, later re-named Erysiphe betae, whilst in America it was identified as E. polygoni, despite sugar-beet isolates from both regions having a host range restricted to Beta species. It is possible that more than one fungus causes the disease, as published descriptions of conidiogenesis have differed. In this study, isolates of the fungus collected from sugar beet in the UK and USA were investigated for polymorphisms in the rDNA ITS region to determine if the same species caused the disease in both countries, whether there was any justification for the retention of the name E. polygoni in the USA, and to search for evidence of a second species infecting sugar beet. From a total of 18 isolates examined, 23 ITS sequences were obtained. Fifteen of these, which included the UK and USA isolates, were identical and the remainder had single-base substitutions, indicating that the fungi were conspecific. Dendrogram analysis of Erysiphales ITS regions revealed that the UK and North American isolates were more closely related to E. heraclei than to E. polygoni. It is proposed that the species name Erysiphe betae be used for the powdery mildew fungus that infects sugar beet. No evidence was found in this study for a second sugar-beet powdery mildew species.

Analysis of the dimensional dependence of semiconductor optical amplifier recovery speeds

We investigate the dependence of the speed of recovery of optically excited semiconductor optical amplifiers (SOAs) on the active region dimensions. We use a picosecond pump-probe arrangement to experimentally measure and compare the gain and phase dynamics of four SOAs with varying active region dimensions. A sophisticated time domain SOA model incorporating amplified spontaneous emission (ASE) agrees well with the measurements and shows that, in the absence of a continuous wave (CW) beam, the ASE plays a similar role to such a holding beam. The experimental results are shown to be consistent with a recovery rate which is inversely proportional to the optical area. A significant speed increase is predicted for an appropriate choice of active region dimensions.

Family Flexiviridae: a case study in virion and genome plasticity

The plant virus family Flexiviridae includes the definitive genera Potexvirus, Mandarivirus, Allexivirus, Carlavirus, Foveavirus, Capillovirus, Vitivirus, Trichovirus, the putative genus Citrivirus, and some unassigned species. Its establishment was based on similarities in virion morphology, common features in genome type and organization, and strong phylogenetic relationships between replicational and structural proteins. In this review, we provide a brief account of the main biological and molecular properties of the members of the family, with special emphasis on the relationships within and among the genera. In phylogenetic analyses the potexvirus-like replicases were more closely related to tymoviruses than to carlaviruses. We postulate a common evolutionary ancestor for the family Tymoviridae and the two distinct evolutionary clusters of the Flexiviridae, i.e., a plant virus with a polyadenylated genome, filamentous virions, and a triple gene block of movement proteins. Subsequent recombination and gene loss would then have generated a very diverse group of plant and fungal viruses.

The Sbm1 locus conferring resistance to Soil-borne cereal mosaic virus maps to a gene-rich region on 5DL in wheat

A mosaic disease caused by Soil-borne cereal mosaic virus (SBCMV) is becoming increasingly important, particularly in winter wheat in Europe. As there are currently no effective cultural practices or practical environmentally friendly chemicals for disease control, host plant resistance is an important objective in breeding programs. However, development of resistant cultivars is slow owing to difficulties in germplasm screening for resistance. Therefore, there is a need to identify molecular markers linked to SBCMV-resistance gene(s), so that quick and accurate laboratory-based marker-assisted selection rather than prolonged field-based screens for resistance can be used in developing resistant cultivars. We previously demonstrated that resistance to SBCMV in Triticum aestivum ‘Cadenza’ is controlled by a single locus. In this work, we used AFLP and microsatellite technology to map this resistance locus, with the proposed name Sbm1, to the distal end of chromosome 5DL. Interestingly, several expressed disease-resistance gene analogues also map to this gene-rich region on 5DL. Closely linked (~17 cM interval) markers, BARC110 and WMC765, RRES01 and BARC144, that flank Sbm1 will be very useful in breeding for selection of germplasm carrying Sbm1.

Characterisation of an isolate of Narcissus degeneration virus from Chinese narcissus (Narcissus tazetta var. chinensis)

A potyvirus from Chinese narcissus was transmitted mechanically to three species of Narcissus and to Lycoris radiata but not to 22 other test species. In western blot, the coat protein reacted strongly with Narcissus degeneration virus (UK isolate) antiserum. Antiserum raised to the Chinese virus did not react with eighteen other potyviruses. The complete nucleotide sequence (9816 nt) had the typical genome organisation for a member of the genus Potyvirus. Sequence comparisons and phylogenetic analysis showed that the Chinese virus was different from all previously sequenced potyviruses but distantly related to onion yellow dwarf and shallot yellow stripe viruses.

Narcissus symptomless virus: a new carlavirus of daffodils

A filamentous virus, with particles 600-650 nm long, was purified from Narcissus pseudonarcissus (daffodil) in Hangzhou and an antiserum prepared. After mechanical inoculation, the virus could be detected serologically in Narcissus species but not in some commonly used virus indicators. Infection was symptomless. The complete sequence of the genomic RNA (8281 nt) showed six predicted ORFs typical of carlaviruses. Pairwise comparisons of gene sequences and phylogenetic analysis demonstrated that the new virus should be classified as a carlavirus but that it was not closely related to members of any current species. We propose the name Narcissus symptomless virus (NSV).

Dietary fish oil dose-response effects on ileal phospholipid fatty acids and contractility

We have reported that dietary fish oil (FO) leads to the incorporation of long-chain n-3 PUFA into the gut tissue of small animal models, affecting contractility, particularly of rat ileum. This study examined the FO dose response for the incorporation of n-3 PUFA into ileal tissue and how this correlated with in vitro contractility. Groups of ten to twelve 13-wk-old Wistar-Kyoto rats were fed 0, 1, 2.5, and 5% FO-supplemented diets balanced with sunflower seed oil for 4 wk, after which ileal total phospholipid FA were determined and in vitro contractility assessed. For the total phospholipid fraction, increasing the dietary FO levels led to a significant increase first evident at 1% FO, with a stepwise, nonsaturating six-fold increase in n-3 PUFA as EPA (20:5n-3), DPA (docosapentaenoic acid, 22:5n-3), and DHA, but mainly as DHA (22:6n-3), replacing the n-6 PUFA linoleic acid (18:2n-6) and arachidonic acid (20:4n-6) over the dosage range. There was no difference in KCl-induced depolarization-driven contractility. However, a significant increase in receptor-dependent maximal contractility occurred at 1% FO for carbachol and at 2.5% FO for prostaglandin E2, with a concomitant increase in sensitivity for prostaglandin E2 at 2.5 and 5% FO. These results demonstrate that significant increases in ileal membrane n-3 PUFA occurred at relatively low doses of dietary FO, with differential receptor-dependent increases in contractility observed for muscarinic and prostanoid agonists.

DPVweb: a comprehensive database of plant and fungal virus genes and genomes

DPVweb () provides a central source of information about viruses, viroids and satellites of plants, fungi and protozoa. Comprehensive taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences are provided. The database also holds detailed, curated, information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene (currently, n ≈ 9000). For comparative purposes, it also contains a single representative sequence of all other fully sequenced virus species with an RNA or single-stranded DNA genome. The start and end positions of each feature (gene, non-translated region and the like) have been recorded and checked for accuracy. As far as possible, nomenclature for genes and proteins are standardized within genera and families. Sequences of features (either as DNA or amino acid sequences) can be directly downloaded from the website in FASTA format. The sequence information can also be accessed via client software for PC computers (freely downloadable from the website) that enable users to make an easy selection of sequences and features of a chosen virus for further analyses.