Aim. To improve the method of the quality assessment of single nucleotide polymorphisms, which are used for SNP-typing, based on the analysis of their distribution in the primary data of whole genome ...sequencing (reads).Materials and methods. Data of the whole genome sequencing of 56 Vibrio cholerae strains obtained using different types of sequencers were used. The software was developed using Java programming language. Cluster analysis and construction of the dendrogram were performed with the author's software using the UPGMA method.Results and discussion. The «instability» of detection the number of SNP in the genome of cholera causative agent was shown. The method of selection of the SNP list for phylogenetic analysis based on the analysis of the primary data of whole genome sequencing (reads), has been developed. The method of using «control genomes» for cluster analysis of whole genome sequencing data has been proposed.Conclusion. The list of 3198 «stable SNP» for phylogenetic analysis has been composed. Genetic affinity between the non-toxigenic strains that contain the tcpA gene (ctxAB–tcpA+) and preCTX-strains of V. cholerae was shown.
Systematic studies of micro-channel plate PMTs Lehmann, A.; Britting, A.; Cowie, E. ...
Nuclear instruments & methods in physics research. Section A, Accelerators, spectrometers, detectors and associated equipment,
05/2011, Letnik:
639, Številka:
1
Journal Article
Recenzirano
DIRC Cherenkov detectors will be the main devices for
π
/
K
separation at the PANDA experiment at FAIR. Due to their advantageous properties in terms of time resolution and especially inside magnetic ...fields micro-channel plate photo multipliers (MCP-PMTs) are very attractive sensor candidates. In this paper we present the investigation of several types of multi-anode MCP-PMTs. The darkcount rate, the behavior inside a magnetic field of up to 2
T, the time resolution, the gain homogeneity and crosstalk of multi-pixel MCP-PMTs were found to be well suitable for the PANDA requirements. Even the rate capability of the latest models from Burle-Photonis and Hamamatsu is satisfactory. Although a big step forward was accomplished with these recently available MCP-PMTs, the lifetime is still not sufficient for the photon densities expected for the PANDA DIRCs.
Objective
: To compare the genomic diversity of SARS-CoV-2 strains that were spread in the Rostov region and the Republic of Crimea in the period from March to June 2021.
Materials and Methods
: A ...total of 194 samples were sequenced and 186 genovariants were recognized among them using the Pangolin program. Multiple alignment was performed and dendrograms were constructed for the samples belonging to the alpha and delta genovariants.
Results
: Changes of the predominant genovariants were revealed for territories of the Rostov Region and the Republic of Crimea from March to June. An increasing percent of the alpha variant was observed in both regions during the spring followed by the rapid emergence of the delta variant, which became predominant in June.
Conclusion
: It was shown that alpha variant samples from the Rostov region share a pool of common mutations, while in contrast, alpha variant samples from the Republic of Crimea are closer to those sampled from Moscow and Moscow region. At the end of May, the delta gene variant begins to be revealed, which is rapidly replacing other lines in all the territories considered in this study.
Comparative study of antibiotics resistance and VNTR-typing of Vibrio cholerae non O1/ non O139 strains, isolated on the territory of Rostov region in 2014.
Antibioticogramms of strains were ...determined by serial dilution method in dense nutrient medium according to MG 4.2.2495-09 (2009). Pheno-, sero- and VNTR-typing was carried out by conventional-methods.
The studied strains belonged to V. cholerae species, did not agglutinate with O1 and O139 sera, were atoxigenic hemolysis-positive, did not contain genes of cholera toxin and toxin-coregulating pili of adhesion, contained genes of hemagglutinin/protease, protease PrtV, collagenase, cytotonic factor Cef, outer membrane protein-OmpW, tol- and -vps-clusters, regulatory genes toxR and hapR. Antibioticogramms of the strains have shown the presence of cultures, resistant to ampicillin, ceftazidime-furazolidone, trimethoprim/sulfamethoxazole with intermediate resistance to streptomycin, kanamycin, gentamycin, amikacin, netilmicin, Approximately 20% of isolates had multiple drug resistance. Data of VNTR- and genotyping confirmed a possibility of water transmission route of the infection.
Execution of monitoring of cultures from environmental samples is necessary for timely detection of genetic characteristics, antibiotics resistance.
N-ACETYL-β-D-GLUCOSAMINIDASE OF VIBRIO CHOLERAE Duvanova, O V; Mishankin, B N; Vodopianov, A S ...
Žurnal mikrobiologii, èpidemiologii i immunobiologii,
2016 Mar-Apr, Letnik:
93, Številka:
2
Journal Article
Recenzirano
Odprti dostop
Study N-acetyl-β-D-glucosaminidase (chitobiase) (EC 3.2.1.30) in strains of Vibrio cholerae of O1/non-O1 serogroups of various origin, that is a component of chitinolytic complex taking into account ...object of isolation and epidemiologic significance of strains.
Cultures of V. cholerae O1/non-O1 serogroup strains were obtained from the museum of live culture of Rostov RIPC. Enzymatic activity analysis was carried out in Hitachi F-2500 fluorescent spectrophotometer using FL Solutions licensed software. NCBI databases were used during enzyme characteristics.
N-acetyl-β-D-glucosaminidase in Vcholerae O1/non-O1 serogroup strains was detected, purified by column chromatography, studied and characterized by a number of physical-chemical and biological properties. Comparative computer analysis of amino acid sequence of N-acetyl-β-D-glucosaminidases of V. cholerae (VC2217 gene), Serratia marcescens etc. has allowed. to attribute the enzyme from V. cholerae to glycosyl-hydrolases (chitobiases) of family 20 and classify it according to enzyme nomenclature as EC 3.2.1.30.
N-acetyl-β-D-glucosaminidase in V. cholerae of O1/non-O1 serogroups of various origin and epidemiologic significance, participating in chitin utilization was studied and characterized for the first time, and its possible role in biology of cholera causative agent was shown.
Application of the authors' GIS <<Cholera 1989-2014>> for systematization of atoxigenic strains ofserogroup 01 choleravibrios (ctxAB-tcpA-, ctxAB-tcpA+), isolated from aquatic objects of the ...environment by pheno- and genotype.
A sample of 304 Vibrio cholerae 01 strains was studied. Isolation of 39 genes related to pathogenicity was carried out Discrimination ability of a set of genes was determined by Simpson formula. Cluster analysis was carried out by UPGMA method.
Analysis of multi-year data on aquatic V cholerae Ο1 strains in country's subject was carried out using GIS. Apossibility of systematization ofphenotypes of the isolated strains by defined parameters was shown. An experimental program for detectior of presence/lack ofvarious genes and their combinations for genotyping was developed. Conclusion GIS was established to allow to carry out analysis of phenotypes by defined parameters, as well as implement approximate systematization of genotypes of atoxigenic strains of cholera vibrios Ο1 by optimally sufficient detection of 14 genes.
Aim. Search for potential INDEL-markers in genomes of Burkholderia pseudomallei strains, as well as evaluation of the possibility of their use for intra-species genotyping. Materials and methods. ...Full-genome sequences of 25 В. pseudomallei strains with known geographic regions of isolation from GenBank database were studied. INDEL-marker search was carried out using authors’ program Gene Expert. Cluster analysis was carried out using genetic distance by R. Sokal and C. Michener and neighbor joining method. Results. 11 INDEL-markers were detected that allowed to split the studied strains into 13 genotypes. Spectrum of INDEL-patterns characteristic for Australian strains was determined. A possibility of existence of certain phylogeographic patterns of Thailand isolates is shown. Conclusion. A possibility of INDEL-markers to differentiate isolates of B. pseudomallei into 2 geographic populations (Australian and South-eastern Asia origin) that allows to determine the source of melioidosis outbreak and transmission routes of the pathogen is detected.
Development of DIRC counters for the PANDA experiment at FAIR Seitz, B.; Bettoni, D.; Branford, D. ...
Nuclear instruments & methods in physics research. Section A, Accelerators, spectrometers, detectors and associated equipment,
02/2011, Letnik:
628, Številka:
1
Journal Article
Recenzirano
Odprti dostop
The PANDA experiment at the planned FAIR facility at GSI, Darmstadt, aims at measuring hadronic final states with unprecedented precision and luminosity. Superior particle identification of charged ...and neutral particles is mandatory to fulfil PANDA's physics aims. DIRC (Detection of Internally Reflected Cherenkov light) counters are foreseen for charged particle identification. A barrel DIRC will cover the central region while a disc DIRC will provide particle identification in the forward region.
Three DIRC concepts differing in the radiator geometry and method for dispersion correction are studied. The barrel DIRC uses a novel imaging system and aims at exploiting a 3D reconstruction to mitigate dispersion effects. Two concepts are investigated for the forward disc DIRC. One concept employs passive dispersion correction and focussing light guides for image reconstruction. Alternatively, time-of-propagation measurements and a wave-length dependent photon detection system are investigated. The three detector designs share common developments such as investigating radiator properties and photon detection systems, and use the same test beam facilities.
Objective of the study was to develop the methodology for identification of administratively independent areas under potential risk of “external” epidemiological threat realization, by the example of ...cholera.Materials and methods. Analysis was conducted using free software package with open source code (QGIS 2.8 and GRASS GIS 7.0) on the basis of the data received from Rosgranitsa and the Federal State Statistics Service. The construction of risk cartogram was performed on the base of Euclidean distance and estimation of nuclear density.Results and conclusions. In accordance with the obtained results, the GIS containing information about the checkpoints on the Russian border, settlements, roads and railway lines was worked out. The method of identification of risk areas due to importation of infectious diseases based on the cholera model has been developed, and the total area of such territories was less than 1 % of the total area of the country. It was found that in some cases the risk area is located at a certain distance from the checkpoint, but the existence of checkpoint does not lead to the formation of risk areas. The developed GIS is available on the geo-information portal of FGHI Rostov-on-Don Research Anti-Plague Institute of Rospotrebnadzor.
A focussing disc DIRC for PANDA Cowie, E.N.; Britting, A.; Clarkson, A. ...
Nuclear instruments & methods in physics research. Section A, Accelerators, spectrometers, detectors and associated equipment,
05/2011, Letnik:
639, Številka:
1
Journal Article
Recenzirano
The PANDA experiment at the FAIR upgrade to GSI, Darmstadt, aims to study modern hadronic physics with unprecedented precision. Excellent particle identification of both charged and neutral particles ...is necessary to achieve the physics aims of PANDA. Two DIRC detectors are foreseen for charged particle identification, one in a barrel configuration for the central region, and the second in a disc configuration for the forward endcap. The design of the forward disc DIRC centres around the novel application of passive chromatic dispersion correction elements, allied with focussing optics, to achieve excellent resolution of Chernekov angle. A system of comprehensive prototype development will show the feasibility of the system. Key to the success of the prototype is fully understanding the production, transport and detection of the Cherenkov photons within the detector. Photon yield and its dependence on the polar angle of the detector have been measured. Observed photon yield is also the basis for subsequent studies into the benefit of chromatic dispersion correction elements, focussing and overall detector performance.
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