Diferenciace kmenu viru sarky svestky a vyuziti ELISA pri slechteni merunek na rezistenci k tomuto viru

Available from STL Prague, CZ / NTK - National Technical LibrarySIGLECZCzech Republi

Extraesophageal Reflux: What Is the Best Parameter for pH-Monitoring Data Analysis from the Perspective of Patient Response to Proton Pump Inhibitors?

Objectives. To analyze the pH-monitoring records of patients with suspected extraesophageal reflux (EER) using three different parameters (number of refluxes (NOR), acid exposure time (AET), and reflux area index (RAI)), with a view to determining which type of analysis is best at selecting the patients who will respond to a proton pump inhibitor (PPI). Methods. Demographic data were obtained and the level of the complaint was assessed using the Visual Analogue Scale. A dual probe pH-monitoring study was conducted. NOR greater than six, AET more than 0.1%, and RAI higher than 6.3 mpH were taken to be the thresholds for EER. Subsequently the response to a 12-week PPI trial was analyzed. Results. A total of 81 patients were analyzed. The percentages of patients with substantial EER based on NOR, AET, and RAI were 36%, 28% and 26%, respectively. Statistically significant, often positive PPI trials were confirmed in the group identified as having substantial EER using all three types of analysis. When using AET and RAI, the significance was more pronounced (P=0.012 and P=0.013, resp.) in comparison with NOR (P=0.033). Conclusions. Patients with EER diagnosed using AET or RAI will respond to PPI significantly often

Characterisation of a novel virus infecting orchids of the genus Pleione

<p>Plants of the genus Pleione, originating from hobby growers in the Netherlands and in the Czech Republic, were conspicuous for viral infection, showing symptoms of leaf mosaic or flower breaking. Using Sanger and high throughput sequencing, the full genome sequence of a novel potyvirus was obtained from sequencing data. The genome sequence was annotated and compared to the genome of other potyviruses. The virus was experimentally transmitted by aphids into Pleione and Chenopodium quinoa plants. The name Pleione flower breaking virus (PlFBV) was suggested for the new virus. The presence of the virus was confirmed using RT-PCR, with newly designed primers targeting this new species. The incidence of the virus was contrasted between both countries and might have been influenced by the growth conditions and the exposure of the plants to aphids.</p

Molecular characterization of divergent grapevine Pinot gris virus isolates and their detection in Slovak and Czech grapevines

Analysis of complete genome sequences of three Slovak isolates of grapevine Pinot gris virus (GPGV) showed their low heterogeneity (reaching 1.7 %) and a close relationship to the Italian NC_015782 isolate (4.2-4.5 % divergence). Comparison of Slovak and Italian isolates revealed an unusual accumulation of 21 indel mutations in ORF1, resulting in a localized high divergence in the encoded amino acid sequences. An elevated divergence in the 5&#39; extremity of the GPGV genomes is suggestive of a recombination between Slovak isolates and grapevine berry inner necrosis virus. RT-PCR allowed the frequent detection of closely related GPGV isolates in grapevines from Slovakia and the Czech Republic

Detection of single nucleotide polymorphisms in virus genomes assembled from high-throughput sequencing data: large-scale performance testing of sequence analysis strategies

Recent developments in high-throughput sequencing (HTS) technologies and bioinformatics have drastically changed research in virology, especially for virus discovery. Indeed, proper monitoring of the viral population requires information on the different isolates circulating in the studied area. For this purpose, HTS has greatly facilitated the sequencing of new genomes of detected viruses and their comparison. However, bioinformatics analyses allowing reconstruction of genome sequences and detection of single nucleotide polymorphisms (SNPs) can potentially create bias and has not been widely addressed so far. Therefore, more knowledge is required on the limitations of predicting SNPs based on HTS-generated sequence samples. To address this issue, we compared the ability of 14 plant virology laboratories, each employing a different bioinformatics pipeline, to detect 21 variants of pepino mosaic virus (PepMV) in three samples through large-scale performance testing (PT) using three artificially designed datasets. To evaluate the impact of bioinformatics analyses, they were divided into three key steps: reads pre-processing, virus-isolate identification, and variant calling. Each step was evaluated independently through an original, PT design including discussion and validation between participants at each step. Overall, this work underlines key parameters influencing SNPs detection and proposes recommendations for reliable variant calling for plant viruses. The identification of the closest reference, mapping parameters and manual validation of the detection were recognized as the most impactful analysis steps for the success of the SNPs detections. Strategies to improve the prediction of SNPs are also discussed

COST Action FA1407: Empowering NGS technologies for the study and diagnostic of plant viruses

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