scholarly journals Comparative Genetic Analysis of Yersinia pestis Strains Isolated on the Ukok Plateau and other Territories of the Altai Mountains

2021 ◽  
pp. 59-69
Author(s):  
G. A. Eroshenko ◽  
A. N. Balykova ◽  
Ya. M. Krasnov ◽  
E. A. Naryshkina ◽  
E. N. Rozhdestvensky ◽  
...  
Keyword(s):  
Yersinia Pestis ◽  
De Novo ◽  
Molecular Genetic ◽  
Genetic Identification ◽  
Likelihood Method ◽  
High Mountain ◽  
Altai Mountains ◽  
Natural Foci ◽  
Ukok Plateau ◽  
Average Size

The aim of the study was molecular-genetic identification and analysis of the phylogenetic relationship of Yersinia pestis strains isolated on the Ukok Plateau in 2020, in order to establish the current boundaries of the natural mega focus of plague in the Altai Mountains in Russia and Mongolia.Materials and methods. 37 strains of Y. pestis of the main subspecies isolated in the Tuva mountain and Gorno-Altai high-mountain plague foci and adjacent territories of Mongolia in 1971–2020 were studied. The whole genome sequencing of the strains was performed using the Ion S5 XL System (Thermo Fischer Scientific). Ion Torrent Suite software package 5.12 and Newbler gsAssembler 2.6 were used to process the data and assemble de novo the sequences of raw reads. The average size of the collected genome was 4.55 million base pairs. Core SNPs were detected by aligning the contigs of Y. pestis strains on the CO92 genome using the Snippy 4.6 program, then 28 SNP homoplasies were removed. The resulting set of SNPs contained only the core region of the genome (955 SNPs). The dendrogram was constructed using the Maximum Likelihood method applying the PhyML 3.1 program.Results and discussion. The current population structure of Y. pestis of the main subspecies, antique biovar, phylogenetic line 4.ANT, endemic to the foci of the Altai Mountains in Russia and Mongolia has been determined. The presence of 4.ANT-21 clone, which became widespread in the territory of these natural foci of plague at the begining of the XXI century, was revealed. It is shown that three strains isolated on the Ukok Plateau in 2020 belong to clone 4.ANT-21. According to phylogenetic analysis, evidence of 4.ANT circulation on the Ukok Plateau before 2018 was obtained. The lesson that has been learned is that it is necessary to study the territories of Mongolia, Kazakhstan and China bordering the Ukok Plateau in order to establish the current boundaries of the 4.ANT mega focus. 

scholarly journals Characteristics and Philogenetic Analysis of Yersinia pseudotuberculosis Strains from the Sarydzhaz High-Mountain Focus in the Tien-Shan

2021 ◽  
pp. 87-93
Author(s):  
A. K. Dzhaparova ◽  
G. A. Eroshenko ◽  
K. A. Nikiforov ◽  
L. M. Kukleva ◽  
Zh. V. Al’khova ◽  
...  
Keyword(s):  
Yersinia Pseudotuberculosis ◽  
De Novo ◽  
Molecular Genetic ◽  
Tien Shan ◽  
Genetic Identification ◽  
Likelihood Method ◽  
Laboratory Diagnostics ◽  
High Mountain ◽  
Snp Analysis ◽  
Whole Genome

The aim of the study was to characterize and carry out molecular-genetic identification of Yersinia pseudotuberculosis strains isolated in the Sarydzhaz high-mountain focus of the Tien-Shan.Materials and methods. The Y. pestis and Y. pseudotuberculosis cultures were differentiated according to their sensitivity to diagnostic bacteriophages, motility, urea fermentation, and pesticin production. Whole genome sequencing was performed using the Ion S5 XL System (Thermo Fischer Scientific). Ion Torrent Suite software package, 5.12 and Newbler gsAssembler 2.6 were used for data processing and de novo assembly of raw read sequences. The dendrogram was constructed using the Maximum Likelihood method applying the PhyML 3.1 software.Results and discussion. Strains of Y. pseudotuberculosis were isolated from museum mixed with Y. pestis cultures obtained from marmots in the Sarydzhaz high-mountain focus. According to whole genome SNP analysis, they belong to the phylogenetic group O:3 serovar, which is widespread throughout the world. Y. pseudotuberculosis is often present in mixed with Y. pestis cultures, isolated from rodents, which should be taken into account when carrying out laboratory diagnostics of plague in natural foci. 

scholarly journals New Epizootic Territory in Gorno-Altai High-Mountain Natural Plague Focus on the Ukok Plateau

2021 ◽  
pp. 103-109
Author(s):  
V. M. Korzun ◽  
A. V. Denisov ◽  
G. Kh. Bazarova ◽  
P. P. Sanarov ◽  
V. V. Shefer ◽  
...  
Keyword(s):  
Yersinia Pestis ◽  
High Mountain ◽  
Target Species ◽  
Serological Tests ◽  
Natural Hosts ◽  
Ukok Plateau ◽  
Predatory Birds ◽  
First Time ◽  
Positive Results ◽  
Bone Remains

The aim of the work – analysis of peculiarities of the plague epizooty found in the southern steppe part of the Ukok Plateau in 2020.Materials and methods. Epizootiological survey was conducted over the area of 1573 km2  in July and August, 2020. 141 mammals, 157 ectoparasites (including 152 fleas), 17 bone remains samples, and 50 regurgitates of predatory birds have been tested for plague.Results and discussion. The background species of mammals – natural hosts of Yersinia pestis in the southern steppe part of the Ukok plateau are gray marmot, long-tailed souslik, and Daurian pika. Abundance of the gray marmot was high and amounted to 1.7±0.18 inhabited burrows per 1 ha (n=30) with 90 % occupancy. Three strains of Yersinia pestis ssp. pestis have been isolated: from Oropsylla alaskensis fleas collected from long-tailed souslik, gray marmot carcass, and regurgitates of predatory birds. Yersinia pestis DNA have been detected in 14 objects. Eight positive results of serological tests have been obtained. The epizooty area that was confirmed by Yersinia pestis isolation totaled 252 km2 . As a result of the survey the circulation of Yersinia pestis ssp. pestis have been for the first time established on the Ukok Plateau. The target species – the gray marmot, as well as the long-tailed souslik, are actively involved into the epizooty. 

scholarly journals Epidemiological Situation on Plague in 2020. Forecast of Episootic Activity of Natural Plague Foci in the Russian Federation and Other CIS Countries for 2021

2021 ◽  
pp. 52-62
Author(s):  
N. V. Popov ◽  
G. A. Eroshenko ◽  
I. G. Karnaukhov ◽  
A. A. Kuznetsov ◽  
A. N. Matrosov ◽  
...  
Keyword(s):  
Russian Federation ◽  
Molecular Genetic ◽  
High Mountain ◽  
Kyrgyz Republic ◽  
Central Asian ◽  
Natural Foci ◽  
The Russian Federation ◽  
Cis Countries ◽  
Epidemiological Characteristics ◽  
Epidemiological Situation

The aim of the work was to substantiate the forecast of the epidemiological and epizootiological situation in natural foci of plague in the Russian Federation, countries of the near and far abroad for the year of 2021. Characteristics of the distribution of Yersinia pestis strains of the main subspecies (subspecies pestis) of medieval and antique biovars, Caucasian (ssp. caucasica) and central Asian (ssp. central asiatica) subspecies by 45 natural foci of the CIS countries are presented in the paper. The persistence of a multidirectional trend in the dynamics of epizootic activity of natural foci of the CIS countries with the circulation of Y. pestis pestis strains of the medieval biovar of the 2.MED1 phylogenetic branch and the antique biovar of the 0.ANT5, 4.ANT phylogenetic branches in the current decade has been outlined. For the Russian Federation, the development of epizootics is predicted in the Gorno-Altai highland and Tuva mountain natural foci caused by the circulation of Y. pestis pestis strains of the antique biovar 4.ANT and Y. pestis of the Altai biovar of the Central Asian subspecies 0.PE4a in 2021. For the Republic of Kazakhstan, there is a high probability of preserving epizootic activity in the North Aral, Aral-Karakum, Balkhash, Mojynkum, Taukum desert and Ili intermountain natural foci with the circulation of Y. pestis pestis strains of the medieval biovar of the phylogenetic branch 2.MED1. For the Kyrgyz Republic, the forecast for the development of plague epizootics caused by Y. pestis pestis strains of the antique biovar 0.ANT5 phylogenetic branch in the Sarydzhaz and Upper Naryn high-mountain natural foci has been substantiated. A high epidemic risk of epizootic manifestations caused by highly virulent strains of Y. pestis pestis of antique biovars 0.ANT5, 4.ANT and medieval biovar 2.MED1 for the entire territory of the CIS countries is noted. The relevance of implementing forecasts of the epidemiological situation into practice, taking into account the molecular-genetic and epidemiological characteristics of Y. pestis strains circulating in areas of expected epizootic manifestations of plague, is highlighted.

GENETIC CERTIFICATION OF FODDER CROPS BREEDING ACHIEVEMENTS

1970 ◽  
pp. 40-46
Author(s):  
V. M. Kosolapov ◽  
N. N. Kozlov ◽  
I. А. Klimenko ◽  
V. N. Zolotarev
Keyword(s):  
Dna Analysis ◽  
Molecular Genetic ◽  
Practical Importance ◽  
Genetic Identification ◽  
Necessary Condition ◽  
Forage Crops ◽  
Fodder Crops ◽  
Long Time ◽  
Analytical Review ◽  
Prospects Of Application

The methods of genetic identification of forage crops varieties and forms have significant scientific and practical importance in breeding and seed multiplication, in protection of author’s rights. At the current moment molecular markers on the base of DNA-polymorphism have been applied widely for these aims. This analytical review examines the possibilities and the prospects of application the different DNA-analysis methods for assessment of forage crops genetic diversity and for development the molecular-genetic passports of breeding achievements. The objective estimation of varieties structure and presence impurities is a necessary condition for improving the methodical approaches in approbation of crops and for decision the problems of timely variety-seed renovation and its systematic replacement. The system of DNA markers that registered in genetic passport will enable to keep the initial genetic structure of variety and to maintain it in production process during long time without fluctuations of agronomic important characteristics and properties. This factor is especially valuable for development the primary seed multiplication.

scholarly journals Prenatal Sonographic Features of CHARGE Syndrome

Diagnostics ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 415
Author(s):  
Kuntharee Traisrisilp ◽  
Wisit Chankhunaphas ◽  
Rekwan Sittiwangkul ◽  
Chureerat Phokaew ◽  
Vorasuk Shotelersuk ◽  
...  
Keyword(s):  
De Novo ◽  
Heart Defects ◽  
Molecular Genetic ◽  
Choanal Atresia ◽  
Charge Syndrome ◽  
Acoustic Stimulation ◽  
Genetic Mutation ◽  
Suspected Case ◽  
Autosomal Dominant Disorder ◽  
Canal Stenosis

CHARGE syndrome is a rare autosomal dominant disorder, associated with coloboma (C), heart defects (H), choanal atresia (A), retardation of growth and/or central nervous system (R), genitourinary anomalies (G) and ear abnormalities (E). Prenatal diagnosis of the syndrome is very rare but may be suspected when a combination of such abnormalities is identified. We describe a prenatally suspected case of CHARGE syndrome due to unique findings of cardiac defects (DORV) in combination with minor clues, including a structurally malformed ear with persistent non-response to an acoustic stimulation (which has never been prenatally described elsewhere), renal malrotation and growth restriction. Postnatal diagnosis was made based on confirmation of the prenatal findings and additional specific findings of bilateral coloboma, choanal atresia and ear canal stenosis. Finally, molecular genetic testing by whole exome sequencing of the neonate and her parents revealed a novel de novo heterozygous frameshift c.3506_3509dup variant in the CHD7 gene, confirming the clinical diagnosis of CHARGE syndrome. In conclusion, we describe unique prenatal features of CHARGE syndrome. Educationally, this is one of the rare examples of CHARGE syndrome, comprising all of the six specific anomalies as originally described; it is also supported by the identification of a specific genetic mutation. The identified genetic variant has never been previously reported, thereby expanding the mutational spectrum of CHD7. Finally, this case can inspire prenatal sonographers to increase awareness of subtle or minor abnormalities as genetic sonomarkers.

Molecular genetic identification of isolates of the hepatitis A virus (HAV) from monkeys at Adler Primate Center

2018 ◽  
Vol 47 (2) ◽  
pp. 87-92 ◽  
Author(s):  
Dmitriy I. Dogadov ◽  
Lydia I. Korzaya ◽  
Anastasia A. Karlsen ◽  
Karen K. Kyuregyan
Keyword(s):  
Hepatitis A ◽  
Hepatitis A Virus ◽  
Molecular Genetic ◽  
Genetic Identification ◽  
Molecular Genetic Identification

scholarly journals De novo adult acute myeloid leukemia with two new mutations in juxtatransmembrane domain of the FLT3 gene: a case report

2021 ◽  
Vol 15 (1) ◽  
Author(s):  
Ismael F. Alarbeed ◽  
Abdulsamad Wafa ◽  
Faten Moassass ◽  
Bassel Al-Halabi ◽  
Walid Al-Achkar ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
De Novo ◽  
Chromosomal Abnormalities ◽  
Molecular Genetic ◽  
Type A ◽  
Chemotherapeutic Treatment ◽  
Acute Myeloid ◽  
New Mutations

Abstract Background Approximately 30% of adult acute myeloid leukemia (AML) acquire within fms-like tyrosine kinase 3 gene (FLT3) internal tandem duplications (FLT3/ITDs) in their juxtamembrane domain (JMD). FLT3/ITDs range in size from three to hundreds of nucleotides, and confer an adverse prognosis. Studies on a possible relationship between of FLT3/ITDs length and clinical outcomes in those AML patients were inconclusive, yet. Case presentation Here we report a 54-year-old Arab male diagnosed with AML who had two FLT3-ITD mutations in addition to NPM1 mutation. Cytogenetic approaches (banding cytogenetics) and fluorescence in situ hybridization (FISH) using specific probes to detect translocations t(8;21), t(15;17), t(16;16), t(12;21), and deletion del(13q)) were applied to exclude chromosomal abnormalities. Molecular genetic approaches (polymerase chain reaction (PCR) and the Sanger sequencing) identified a yet unreported combination of two new mutations in FLT3-ITDs. The first mutation induced a frameshift in JMD, and the second led to a homozygous substitution of c.1836T>A (p.F612L) also in JMD. Additionally a NPM1 type A mutation was detected. The first chemotherapeutic treatment was successful, but 1 month after the initial diagnosis, the patient experienced a relapse and unfortunately died. Conclusions To the best of our knowledge, a combination of two FLT3-ITD mutations in JMD together with an NPM1 type A mutation were not previously reported in adult AML. Further studies are necessary to prove or rule out whether the size of these FLT3-ITDs mutations and potential other double mutations in FLT3-ITD are correlated with the observed adverse outcome.

IV.—The Absence of Glacial Phenomena in large Parts of Western Asia and Eastern Europe, Etc

1892 ◽  
Vol 9 (2) ◽  
pp. 54-64
Author(s):  
Henry H. Howorth
Keyword(s):  
Eastern Europe ◽  
New World ◽  
High Elevation ◽  
High Mountain ◽  
Glacial Period ◽  
Altai Mountains ◽  
Western Asia ◽  
Interesting Area ◽  
Geological Magazine

In some papers which you have done me the favour to print in the GEOLOGICAL MAGAZINE, I have endeavoured to apply a new touchstone to test the age of high mountain chains and of land of high elevation, namely, the presence or absence of distinct and prominent traces of former glaciation, and I have argued that where such traces are not forthcoming in a very unmistakable manner, we are justified in concluding that these highlands have been elevated since the so-called Glacial Period. I have endeavoured to apply the touchstone in question to the Ural and Altai Mountains, to the Thian Shan and Himalaya ranges in Asia, and to the great Cordillera which binds together the two continents forming the New World. I wish to make my survey more complete by an examination of an interesting area comprising Eastern Europe and South Western Asia.

scholarly journals Selecting of Polymorphic Loci of Genome for Identification of Populations of Pinus sylvestris L. on East-Europe Plain

2019 ◽  
Vol 5 (5) ◽  
pp. 25-30
Author(s):  
Ya. Prishnivskaya ◽  
E. Nassonova ◽  
Yu. Vasileva ◽  
S. Boronnikova
Keyword(s):  
Pinus Sylvestris ◽  
Molecular Genetic ◽  
Genetic Identification ◽  
East European Plain ◽  
Data Bases ◽  
East Europe ◽  
Polymorphic Loci ◽  
East European ◽  
Molecular Genetic Identification

10 pairs of primers from 8 related Pinus sylvestris L. populations collected on East-European plain to 10 genes and 4 primer’s pairs to 4 loci of uncoding clDNA regions. 2 loci of uncoding clDNA regions (psbA-trnH, trnL-trnF) were selected from tested 14 primer’s pairs. These two loci are most polymorphic and has homologous consistencies in data bases. Therefore, these loci is recommended for molecular–genetic identification of related Pinus sylvestris L. populations on East–European plain.

scholarly journals Genetic identification of bovine leukaemia virus

2018 ◽  
Vol 6 (2) ◽  
pp. 314-324 ◽  
Author(s):  
Irina Donnik ◽  
Irina Donnik ◽  
Ramil Vafin ◽  
Ramil Vafin ◽  
Aram Galstyan ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Research Methods ◽  
Bovine Leukemia Virus ◽  
Leukemia Virus ◽  
Molecular Genetic ◽  
Genetic Research ◽  
Genetic Identification ◽  
Gene Fragment ◽  
Phylogenetic Classification ◽  
Pcr Rflp

Molecular genetic research methods make it possible to evaluate the genetic diversity of bovine leukemia virus (BLV) and are the most informative approaches to its genetic identification. Molecular genetic research methods work well for the phylogenetic analysis of sequenced nucleotide DNA sequences of the provirus, as well as for the polymerase chain reaction-restriction fragment length polymorphism analysis (PCR-RFLP) according to the phylogenetic classification of the pathogen. The purpose of the research was to study the scientific and methodological approaches to the genetic identification of bovine leukemia virus, integrated into the molecular monitoring of infection of cattle with BLV genotypes. The authors used PCR-RFLP-genotyping and comparative phylogenetic analysis of aligned nucleotide sequences of the env gene fragment of the BLV provirus isolates to detect the genotypic affiliation of the cattle from twenty-one livestock farms of the Republic of Tatarstan. As a result, isolates of four out of ten BLV genotypes were found in the Tatarstani cattle, namely genotypes 1, 4, 7, and 8. The research involved a comparative analysis of 505 nucleotide sequences of a fragment of the BLV env gene, including those deposited in GenBank NCBI. The analysis confirms the inconsistency of several earlier PCR-RFLP typing strategies with the current approach in assessing the genotypic diversity by phylogenetic analysis. The improved strategy of PCR-RFLP genotyping of BLV corresponds with its modern phylogenetic classification. The strategy makes it possible to identify all the known genotypes of the viral pathogen. Its validity has been proved by in silico modelling of restrictogrammes and a phylogenetic analysis of the env gene fragment of 57 reference isolates of ten BLV genotypes that generate 57 genotype-associated combinations of diagnostically significant PCR-RFLP profiles.

Sign in / Sign up

Export Citation Format

Share Document