Molecular characterization of a novel mycovirus from Rhizoctonia fumigata AG-Ba isolate C-314 Baishi.

The complete genome sequence of a novel dsRNA virus isolated from Rhizoctonia fumigata AG-Ba isolate C-314 Baishi (designated as Rhizoctonia fumigata virus 1, RfV1) was determined. The RfV1 genome was 9,907 bp in length and contained two open reading frames (ORFs). ORF1 potentially coded for a 198.10-kDa protein (P1). P1 shared low but significant amino acid sequence similarity to the putative protein encoded by Lentinula edodes mycovirus (LeV) ORF1. P1 contained a NUDIX domain, which was also present in the putative proteins encoded by the ORF1s of LeV and Phlebiopsis gigantea large virus 1 (PgLV-1). ORF2 potentially coded for a 146.72-kDa protein (P2) that contained the conserved motifs of the RNA-dependent RNA polymerase (RdRp). ORF1 and ORF2 were overlapping, and it was predicted that ORF2 could be translated as a fusion with ORF1 via a ribosomal -1 frameshifting mechanism. Phylogenetic analysis indicated that RfV1 clustered with PgLV-1, LeV and Rosellinia necatrix megabirnavirus 1 (RnMBV1) in a separate clade independent of other virus genera. We propose that RfV1, along with PgLV-1 and LeV, should be grouped into a new viral genus related to the family Megabirnaviridae. This is the first report of the full-length genome sequence of a novel mycovirus isolated from R. fumigata.

[Influence of spectrometer scanning requirements in homemade grating diffuse NIR instrument on NIR veracity].

The influence of instrument parameters, such as scan internal, length of instrument run, frequency of scan background etc, on NIR veracity was studied with a homemade grating diffuse NIR instrument using Yunnan flue-cured tobacco. Results showed that scan interval, such as 8 nm or 16 nm, had no evident influence on NIR quantitative analysis. To improve scan speed, the scan interval the authors decided to use was 16 nm. NIR model was set up which could revise the influence of the length of instrument run. This instrument can clue on baseline shift to decide the frequency of background scanning, which can deduce NIR analysis error and improve NIR veracity.

[New technology for sample preprocessing in NIR analysis].

Sample's moisture content and granularity would have an important influence on NIR veracity. Preprocesssing methods have been used for NIR analysis to achieve better NIR veracity. With Yunnan flue-cured tobacco as study materials, the authors innovatively applied microwave fast drying technology and home pulverizer to tobacco preprocessing, which could finish the preprocessing in 5 min, faster than the traditional methods such as oven drying and sifting. Results showed that: microwave fast drying technology could improve NIR analysis veracity when samples' moisture content had a wide range; influence of samples' granularity on NIR veracity could be eliminated after 25 s home pulverizer shatter. This study can offer a new method for NIR analysis workers to simplify NIR preprocessing.

[Influence of LPLS algorithm parameters on NIR veracity].

The theory of local partial least square (LPLS) algorithm was described based on locally weighted regression algorithm (LWR). The influence of data processing parameters, such as principal component numbers and local set-up sample number in LPLS mode, on the NIR veracity was studied with homemade grating diffuse NIR instrument using Yunnan flue-cured tobacco. Results showed that for nicotine model, the principal component number decided by cross validation was not the best choice, and better results could be achieved by reducing the principal component number; using 30-50 samples to set up NIR model, the veracity of total sugar, total nitrogen, and nicotine could be improved by 7%, 14% and 10%, respectively. So, LPLS algorithm can effectively improve NIR model's veracity, and is a good method to set up robust NIR models.

[Influence of sample loading and test conditions on NIR veracity and study of analysis error source].

The influence of sample test conditions on the NIR veracity was studied with homemade grating diffuse NIR instrument using Yunnan flue-cured tobacco. Deducing analysis error was achieved by model self-emendation when a global NIR model was set up. Without regarding the influence of loading samples and test conditions, the test repetition error, re-loading error and samples tightness error, which were brought by instrument S/N, accounted for 50%, 30% and 20% of the total error, respectively. Depressing sample could reduce errors brought by sample tightness. Changes in test conditions could bring more analysis error, which was larger than the total of repetition error. These results theoretically explain the influence of sample test conditions on the NIR analysis veracity, which can provide basic theory data for farther improvement of homemade instrument and offer a new idea for resolving this problem.

[Influence of sample annum and distribution of chemical values on NIR veracity].

The influence of sample annum and the distribution of sample component on NIR veracity was studied with homemade grating diffuse NIR instrument using Yunnan flue-cured tobacco. Results showed that sample annum had an obvious influence on the total sugar and nicotine models, but had an unconspicuous influence on the total-nitrogen model. Models set up by samples, whose component content distribution was normal school, was better than those set up by even distribution. The conclusion in this study has a significant referenced value for the method and principle to select representative samples to modeling from a large amount of specimens.

Genome Sequencing of Ralstonia solanacearum CQPS-1, a Phylotype I Strain Collected from a Highland Area with Continuous Cropping of Tobacco.

Ralstonia solanacearum, an agent of bacterial wilt, is a highly variable species with a broad host range and wide geographic distribution. As a species complex, it has extensive genetic diversity and its living environment is polymorphic like the lowland and the highland area, so more genomes are needed for studying population evolution and environment adaptation. In this paper, we reported the genome sequencing of R. solanacearum strain CQPS-1 isolated from wilted tobacco in Pengshui, Chongqing, China, a highland area with severely acidified soil and continuous cropping of tobacco more than 20 years. The comparative genomic analysis among different R. solanacearum strains was also performed. The completed genome size of CQPS-1 was 5.89 Mb and contained the chromosome (3.83 Mb) and the megaplasmid (2.06 Mb). A total of 5229 coding sequences were predicted (the chromosome and megaplasmid encoded 3573 and 1656 genes, respectively). A comparative analysis with eight strains from four phylotypes showed that there was some variation among the species, e.g., a large set of specific genes in CQPS-1. Type III secretion system gene cluster (hrp gene cluster) was conserved in CQPS-1 compared with the reference strain GMI1000. In addition, most genes coding core type III effectors were also conserved with GMI1000, but significant gene variation was found in the gene ripAA: the identity compared with strain GMI1000 was 75% and the hrpII box promoter in the upstream had significantly mutated. This study provided a potential resource for further understanding of the relationship between variation of pathogenicity factors and adaptation to the host environment.

Exposure to Umbelliferone Reduces Ralstonia solanacearum Biofilm Formation, Transcription of Type III Secretion System Regulators and Effectors and Virulence on Tobacco.

Ralstonia solanacearum is one of the most devastating phytopathogens and causes bacterial wilt, which leads to severe economic loss due to its worldwide distribution and broad host range. Certain plant-derived compounds (PDCs) can impair bacterial virulence by suppressing pathogenic factors of R. solanacearum. However, the inhibitory mechanisms of PDCs in bacterial virulence remain largely unknown. In this study, we screened a library of coumarins and derivatives, natural PDCs with fused benzene and α-pyrone rings, for their effects on expression of the type III secretion system (T3SS) of R. solanacearum. Here, we show that umbelliferone (UM), a 7-hydroxycoumarin, suppressed T3SS regulator gene expression through HrpG-HrpB and PrhG-HrpB pathways. UM decreased gene expression of six type III effectors (RipX, RipD, RipP1, RipR, RipTAL, and RipW) of 10 representative effector genes but did not alter T2SS expression. In addition, biofilm formation of R. solanacearum was significantly reduced by UM, though swimming activity was not affected. We then observed that UM suppressed the wilting disease process by reducing colonization and proliferation in tobacco roots and stems. In summary, the findings reveal that UM may serve as a plant-derived inhibitor to manipulate R. solanacearum T3SS and biofilm formation, providing proof of concept that these key virulence factors are potential targets for the integrated control of bacterial wilt.

Conflicting evidence combination based on uncertainty measure and distance of evidence.

Dempster-Shafer evidence theory is widely used in many fields of information fusion. However, the counter-intuitive results may be obtained when combining with highly conflicting evidence. To deal with such a problem, we put forward a new method based on the distance of evidence and the uncertainty measure. First, based on the distance of evidence, the evidence is divided into two parts, the credible evidence and the incredible evidence. Then, a novel belief entropy is applied to measure the information volume of the evidence. Finally, the weight of each evidence is obtained and used to modify the evidence before using the Dempster's combination rule. Numerical examples show that the proposed method can effectively handle conflicting evidence with better convergence.