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1.
Tissue Antigens ; 83(2): 106-12, 2014 Feb.
Article in English | MEDLINE | ID: mdl-24397488

ABSTRACT

The human leukocyte antigen (HLA) system has a major role in the regulation of the immune response as it is involved in the defense against pathogens. Some studies have reported that HLA class II genes play a strong role in severe cases of pulmonary tuberculosis (PTB) in several populations. Thus the aim of the study was to compare the HLA-class II alleles of patients with drug resistant tuberculosis with those of healthy controls from the same ethnic group in Kazakhstan. The aim of the present study was to evaluate the correlation of HLA-class II alleles by patients with drug resistant tuberculosis and the healthy controls of the same ethnic group in Kazakhstan. The HLA-class II alleles of 76 patients with tuberculosis (TB) and 157 healthy volunteers were investigated using sequence-based typing (SBT)-method. HLA-DQA1*03:02 HLA-DRB1*08:01 and DRB1*08:03 occurred more frequently (P = 0.05) in patients with drug resistant tuberculosis than in controls. We observed a possible association between certain HLA alleles and TB that are specific for the Kazakh population. Further studies are needed to confirm our findings using a larger number of patients with drug resistant tuberculosis.


Subject(s)
Genetic Predisposition to Disease , HLA-DQ alpha-Chains/genetics , HLA-DRB1 Chains/genetics , Haplotypes , Tuberculosis, Multidrug-Resistant/genetics , Tuberculosis, Pulmonary/genetics , Adult , Antitubercular Agents/therapeutic use , Case-Control Studies , Female , Gene Frequency , HLA-DQ alpha-Chains/classification , HLA-DQ alpha-Chains/immunology , HLA-DRB1 Chains/classification , HLA-DRB1 Chains/immunology , Histocompatibility Testing , Humans , Kazakhstan , Male , Middle Aged , Mycobacterium tuberculosis/drug effects , Mycobacterium tuberculosis/immunology , Tuberculosis, Multidrug-Resistant/drug therapy , Tuberculosis, Multidrug-Resistant/immunology , Tuberculosis, Multidrug-Resistant/microbiology , Tuberculosis, Pulmonary/drug therapy , Tuberculosis, Pulmonary/immunology , Tuberculosis, Pulmonary/microbiology
2.
Pediatr Transplant ; 16(2): 151-9, 2012 Mar.
Article in English | MEDLINE | ID: mdl-22300090

ABSTRACT

BKV reactivation is associated with impaired graft function in kidney transplant patients. The objective of our study was to determine the prevalence of BKV infection in consecutive pediatric kidney transplant recipients at our center. Fifty-eight pediatric kidney transplant recipients were studied. The mean age at screening was 9.4 ± 2.8 yr, and samples were obtained at a median of 2.4 ± 1.4 yr after transplantation. BKV-DNA was analyzed in urine and plasma by quantitative PCR. Occurrences of BK-DNAuria and BK-DNAemia did not change in the first two yr after transplantation in children and amounted to 21-23% and 7-8%, respectively (p > 0.05). In the third year, the occurrences of BK-DNAuria and BK-DNAemia increased insignificantly to 27% and 9% in the pediatric patients. We also determined the subtypes and subgroups of BK virus isolated from Russian renal transplant recipients and found that BKV isolates were composed of subtypes Ib-2 and IV/c2. The data we obtained indicate that although only 5% of BKVAN cases occurred between years two and five post-transplantation, it seems necessary to regularly monitor pediatric patients for BKV infection through the third year after transplantation.


Subject(s)
BK Virus/isolation & purification , Kidney Transplantation , Polyomavirus Infections/epidemiology , Postoperative Complications/epidemiology , Tumor Virus Infections/epidemiology , Adult , BK Virus/classification , BK Virus/genetics , Base Sequence , Case-Control Studies , Child , DNA, Viral/analysis , Female , Genotype , Humans , Male , Molecular Sequence Data , Phylogeny , Polyomavirus Infections/diagnosis , Polyomavirus Infections/etiology , Polyomavirus Infections/virology , Postoperative Complications/diagnosis , Postoperative Complications/virology , Real-Time Polymerase Chain Reaction , Retrospective Studies , Russia , Tumor Virus Infections/diagnosis , Tumor Virus Infections/etiology , Tumor Virus Infections/virology , Viral Load
4.
Tissue Antigens ; 78(3): 217-8, 2011 Sep.
Article in English | MEDLINE | ID: mdl-21732918

ABSTRACT

Eight novel alleles, two HLA-A and six HLA-B, are described in Kazakh individuals.


Subject(s)
HLA-A Antigens/genetics , HLA-B Antigens/genetics , Alleles , Humans , Kazakhstan , Sequence Analysis, DNA
5.
Tissue Antigens ; 77(3): 263-4, 2011 Mar.
Article in English | MEDLINE | ID: mdl-21299539

ABSTRACT

Seven novel human leukocyte antigen (HLA)-DRB1 alleles were identified during routine sequence-based typing (SBT) of healthy Kazakh individuals.


Subject(s)
HLA-DR Antigens/genetics , Alleles , Base Sequence , DNA Mutational Analysis/methods , HLA-DRB1 Chains , Health , Humans , Kazakhstan , Polymorphism, Genetic/physiology , Sequence Analysis, DNA/methods
7.
Genetika ; 45(2): 275-9, 2009 Feb.
Article in Russian | MEDLINE | ID: mdl-19334624

ABSTRACT

A high-throughput method based on the minisequencing reaction followed by MALDI-TOF mass spectrometry has been developed for detecting C-->T transitions in 291 methylation sites of M.Hpy99XI Helicobacter pylori J99. The study has shown an absolute (100%) accuracy of the new method.


Subject(s)
DNA Methylation/genetics , DNA, Bacterial/genetics , Helicobacter pylori/genetics , Point Mutation , DNA Mutational Analysis/methods , Sensitivity and Specificity
8.
Klin Med (Mosk) ; 87(2): 35-9, 2009.
Article in Russian | MEDLINE | ID: mdl-19348299

ABSTRACT

Recent studies of cytochrome P-450 gene polymorphism showed that it may influence the outcome of treatment of Helicobacter pylori (Hp) infection. The literature data concerning effects of genetic factors on the results of eradication therapy of peptic ulcer in the Russian population are scarce and the problem needs further investigation. The aim of this work was to examine CYP2C19 polymorphism in a mixed population of the city and region of Moscow and evaluate its effect on the efficiency of eradication therapy of Hp infection. The prospective study of a cohort of 82 patients with Hp-induced gastric and duodenal ulcers examined in conformity with the current health care standards. All the patients received first line eradication therapy during 7 days. Its efficiency was found to be dependent on CYP2C19 polymorphism among other factors.


Subject(s)
Aryl Hydrocarbon Hydroxylases/genetics , DNA, Bacterial/genetics , Duodenal Ulcer/genetics , Helicobacter Infections/genetics , Helicobacter pylori/genetics , Polymorphism, Genetic , Stomach Ulcer/genetics , Adult , Biopsy , Cytochrome P-450 CYP2C19 , Cytochrome P-450 Enzyme System/genetics , Duodenal Ulcer/drug therapy , Duodenal Ulcer/microbiology , Endoscopy, Gastrointestinal , Female , Follow-Up Studies , Helicobacter Infections/drug therapy , Helicobacter Infections/microbiology , Helicobacter pylori/drug effects , Helicobacter pylori/isolation & purification , Humans , Intestinal Mucosa/microbiology , Intestinal Mucosa/pathology , Male , Prospective Studies , Stomach Ulcer/drug therapy , Stomach Ulcer/microbiology
9.
Antibiot Khimioter ; 54(9-10): 10-5, 2009.
Article in Russian | MEDLINE | ID: mdl-20415256

ABSTRACT

The frequence of mutations in the rifampicin resistant (RIF(r)) clones of microorganisms after adaption to ofloxacin and metronidazole was investigated to estimate the biological cost of H. pylori rifampicin (RIF) resistance. Mutations in rpoB gene responsible for RIF resistance of H. pylori were shown to have biological cost and be compensated by additional mutations in the microorganism genome. Comparison of the mutation frequency in the presence of metroniazole demonstrated that the acquired resistance to RIF resulted in changing of the adaptative capacity of the RIF(r) clones of H. pylori to metronidazole. Thus, a significant increase of the mutation frequency (> 700 times) in one of the RIF(r) clones and a broad spectrum of the mutations responsible for resistance to metronidazole vs. the H. pylori initial strain 26695 were observed. The findings could be evident of the fact that the adaptation to RIF changed the properties of the cell on one hand in such a way that its mutation capacity increased and that the target selection on the other hand revealed hypermutable cells, likely usual for the bacterial population.


Subject(s)
Anti-Bacterial Agents/pharmacology , Drug Resistance, Bacterial/drug effects , Helicobacter pylori/drug effects , Adaptation, Biological , Bacterial Proteins/genetics , DNA-Directed RNA Polymerases/genetics , Genes, Bacterial , Helicobacter pylori/genetics , Metronidazole/pharmacology , Mutation , Ofloxacin/pharmacology
11.
Bull Exp Biol Med ; 144(3): 413-5, 2007 Sep.
Article in English | MEDLINE | ID: mdl-18457047

ABSTRACT

Analysis of 16S ribosomal RNA gene was carried out in 2 DNA samples isolated from vaginal epithelial smears from women suffering from bacterial vaginosis. The composition of vaginal epithelial microbiocenosis in bacterial vaginosis was determined and its significant difference from normocenosis was shown. A laboratory protocol for identification of vaginal epithelial microflora was developed on the basis of 16S ribosomal RNA gene analysis.


Subject(s)
Epithelium/microbiology , RNA, Ribosomal, 16S/genetics , Vagina , Bacteria/genetics , Female , Humans , Vagina/anatomy & histology , Vagina/microbiology , Vaginosis, Bacterial/microbiology
12.
Genetika ; 41(10): 1338-44, 2005 Oct.
Article in Russian | MEDLINE | ID: mdl-16316005

ABSTRACT

To detect point mutations A2115C, A2143G/C, and A2143G in the 23S rRNA gene of Helicobacter pylori associated with resistance of the microorganism to clarithromycin, a new powerful way of analysis was used. This method involved the reaction of minisequencing followed by MALDI-TOF mass spectrometry of reaction products. In ten analyzed clarithromycin-resistant clinical isolates of H. pylori obtained in Russia, the resistance was found to be mediated only by mutation A2144G in the 23S rRNA gene.


Subject(s)
Anti-Bacterial Agents , Clarithromycin , Drug Resistance, Bacterial/genetics , Helicobacter pylori/genetics , Point Mutation , RNA, Bacterial/genetics , RNA, Ribosomal, 23S/genetics , Anti-Bacterial Agents/pharmacology , Clarithromycin/pharmacology , Genes, Bacterial/genetics , Genes, rRNA/genetics , Humans
13.
Genetika ; 41(10): 1434-7, 2005 Oct.
Article in Russian | MEDLINE | ID: mdl-16316017

ABSTRACT

Using multilocus sequence typing (MLST), 22 Helicobacter pylori isolates from Russia have been characterized. All of the Russian strains were assigned to a single population, hpEurope.


Subject(s)
Genes, Bacterial/genetics , Helicobacter pylori/genetics , Phylogeny , Genetics, Population , Humans , Russia , Sequence Analysis, DNA
14.
Mol Biol (Mosk) ; 39(6): 945-51, 2005.
Article in Russian | MEDLINE | ID: mdl-16358730

ABSTRACT

Comparison of open-reading frames (ORFs) H. pylori 26695 and J99 strains has been revealed prevalence of nucleotide replacements as transitions (more than 3%) above transversions (less than 1%). Prevalence of nucleotide transitions is caused by high speed of C : G to T : A transitions in a coding strand of DNA (3.5-5.3%) and not coding strand (2.9-3.9%). The correspondence rate of transversion (A --> C, A --> T, C --> A, C --> G, G --> C, G --> T, T --> A and T --> G) did not exceed 0.84%. The highest correspondence frequency between C and T was detected in ACGT-ATGT (28.3%) - the site of methylation by active methyltransferase M.Hpy99XI in H. pylori 26695 and J99. Thus one can speculate that predominant transition taking place in H. pylori is mutation of C into T, which is realized through cytosine methylation-deamination mechanism.


Subject(s)
DNA Methylation , Genome, Bacterial/genetics , Helicobacter pylori/genetics , Open Reading Frames/genetics , Point Mutation , Bacterial Proteins/genetics , Site-Specific DNA-Methyltransferase (Adenine-Specific)/genetics , Species Specificity
15.
Biochemistry (Mosc) ; 70(4): 383-90, 2005 Apr.
Article in English | MEDLINE | ID: mdl-15892605

ABSTRACT

The transcription profiles of four Helicobacter pylori clinical isolates (two cag-negative and two cag-positive) were compared in stationary growth phase using a cDNA-macroarray. The correlation coefficient value between total transcription profiles of clinical isolates H. pylori varied from 0.70 to 0.83. For 44 groups of genes (total number 66) belonging to various functional classes of H. pylori, the correlation coefficient value between these isolates exceeded 0.7, and for 14 groups the value exceeded 0.9. These groups included genes encoding components involved in cell division, adaptations to atypical conditions, electron transport, salvage of nucleosides and nucleotides, glycolysis/gluconeogenesis, folding and stabilization of proteins, translation factors, anaerobic metabolism, and amino acids and amine metabolism. Expression of 52 genes significantly differed between H. pylori clinical isolates. Some of these genes determine microorganism virulence. They include: cytotoxin-associated gene (cagA), genes encoding neutrophil-activating protein (napA), major flagellar protein (flaA), and vacuolizing cytotoxin (vacA), some genes encoding outer membrane proteins (omp), urease alpha and beta subunits (ureA and ureB), and some regulatory proteins, and genes encoding stress-related proteins, such as the chaperone and heat shock protein genes (groEL and dnaK).


Subject(s)
Genes, Bacterial , Helicobacter pylori/genetics , Transcription, Genetic , Adhesins, Bacterial/genetics , Antigens, Bacterial/genetics , Bacterial Proteins/genetics , Helicobacter pylori/isolation & purification , Humans , Oligonucleotide Array Sequence Analysis
16.
Bull Exp Biol Med ; 137(2): 197-9, 2004 Feb.
Article in English, Russian | MEDLINE | ID: mdl-15273774

ABSTRACT

Complete nucleotide cDNA sequence (29715 nucleotides) of SARS-associated coronavirus (strain SoD) isolated for the first time in the territory of the Russian Federation was determined. Phylogenetic analysis revealed maximum similarity between strain SoD genome and Frankfurt 1 strain genome. Three nucleotide substitutions determining two amino acid substitutions were detected.


Subject(s)
Genome, Viral , Severe acute respiratory syndrome-related coronavirus/genetics , Severe acute respiratory syndrome-related coronavirus/isolation & purification , Amino Acid Substitution , DNA, Complementary/genetics , DNA, Viral/genetics , Humans , Phylogeny , Polymerase Chain Reaction , Russia , Severe acute respiratory syndrome-related coronavirus/classification , Severe Acute Respiratory Syndrome/virology
17.
Biochemistry (Mosc) ; 69(5): 536-41, 2004 May.
Article in English | MEDLINE | ID: mdl-15193128

ABSTRACT

The goal of the present work was to compare different techniques of molecular typing using as an example clinical isolates of Helicobacter pylori obtained from patients in different regions of Russia. DNA-macroarray genome scanning using individual genes was employed to set up our basic classification of isolates that did or did not contain pathogenicity islands. In parallel, DNA of the same isolates was used in the conventional random amplified polymorphic DNA (RAPD) PCR analysis, and the isolates were also genotyped (cagA, vacA, iceA, and babA status) and their proteomic maps were obtained by means of unidimensional SDS polyacrylamide gel electrophoresis (1D-SDS-PAGE) coupled with identification using peptide mass fingerprinting by MALDI-TOF mass spectrometry. A statistically significant correlation (coefficient of correlation r = 0.25, p = 0.005) was observed between the results of genome scanning and 1D-SDS-PAGE. No correlation was found between RAPD-PCR typing and genome scanning.


Subject(s)
Bacterial Typing Techniques/methods , Helicobacter pylori/classification , DNA, Bacterial/analysis , Electrophoresis, Polyacrylamide Gel , Genomic Islands/genetics , Helicobacter pylori/isolation & purification , Humans , Molecular Probe Techniques , Polymerase Chain Reaction , Proteomics , Random Amplified Polymorphic DNA Technique , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
18.
Mol Biol (Mosk) ; 37(4): 625-33, 2003.
Article in Russian | MEDLINE | ID: mdl-12942635

ABSTRACT

DNA macroarrays were used to characterize 17 Helicobacter pylori strains isolated in four geographic regions of Russia (Moscow, St. Petersburg, Kazan, and Novosibirsk). Of all genes, 1272 (81%) proved to occur in all strains and to constitute a functional core of the genome, and 293 (18.7%) were strain-specific and greatly varied among the H. pylori strains. Most (71%) of the latter had unknown functions; the remainder included restriction-modification genes (3-9%), transposition genes (2-4%), and genes coding for outer membrane proteins (2-4%). The Russian H. pylori strains did not differ in genome organization or in the number and distribution of strain-specific genes from strains isolated in other countries.


Subject(s)
Genetic Variation , Genome, Bacterial , Helicobacter pylori/genetics , Bacterial Proteins/genetics , Gene Order , Genes, Bacterial , Helicobacter pylori/pathogenicity , Membrane Glycoproteins/genetics , Multigene Family , Oligonucleotide Array Sequence Analysis , Open Reading Frames , Russia , Species Specificity , Virulence/genetics
20.
Genetika ; 39(3): 318-25, 2003 Mar.
Article in Russian | MEDLINE | ID: mdl-12722630

ABSTRACT

A Mycoplasma hominis chromosomal fragment containing the full-length ftsZ gene was cloned and sequenced. Natural expression of this gene was demonstrated by reverse transcription-polymerase chain reaction (RT-PCR) with total RNA. The M. hominis FtsZ protein was shown to differ substantially from its counterparts of two other Mycoplasma species, M. genitalium and M. pneumoniae. The possibility of M. hominis ftsZ expression in Escherichia coli was demonstrated with several bacterial strains. The M. hominis FtsZ protein was isolated from E. coli cells transformed with recombinant plasmids carrying the M. hominis ftsZ gene. Complementation between the E. coli and M. hominis FtsZ proteins was observed in transformants.


Subject(s)
Bacterial Proteins/genetics , Cytoskeletal Proteins , Mycoplasma hominis/genetics , Amino Acid Sequence , Bacterial Proteins/metabolism , Cell Division/genetics , Cloning, Molecular , Escherichia coli/genetics , Gene Expression Regulation, Bacterial , Genetic Complementation Test , Molecular Sequence Data , Mycoplasma/genetics , Mycoplasma hominis/cytology , Mycoplasma hominis/metabolism , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Sequence Homology, Amino Acid
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