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1.
Klin Lab Diagn ; 63(7): 410-413, 2018.
Article in Russian | MEDLINE | ID: mdl-30720955

ABSTRACT

The aim of this work was to assess the relationship of rs2230806 SNP of ABCA1 with lipid profile in patients with severe dyslipidemia. The study included 363 patients (42.8% of males), the average age was 48.7 years, 35.5% of patients received hypolipidemic drugs (mainly statins). Quantitative determination of total cholesterol (ТС) and triglycerides (TG) in fasting serum was carried out by a unified enzymatic method, and high density lipoproteins (HDL) - by a direct homogeneous method. Genotype according to the rs2230806 position in the ABCA1 gene was determined by polymerase chain reaction (PCR) «in real time¼ using adjacent samples and melting reaction products after PCR. The frequencies of alleles and genotypes of variant rs2230806 of ABCA1 gene in patients with dyslipidemia did not differ from those in the control group of healthy individuals (athletes). The levels of plasma lipids - TC, TG and HDL cholesterol, on average, in patients with dyslipidemia were 7.8±3,4, 3,4±6,5 and 1.29±0.4 mmol/l, respectively. Compared to different genotypes, the plasma lipid concentrations did not differ significantly, but the analysis of different inheritance models of the allelic variant studied showed a significant association with the level of TG in the additive model, in which each minor allele (a) further enhanced the effect on the level of plasma TG at 1.02 mmol/l (p=0.044). The results of this study demonstrate the effect of a common variant rs2230806 of the ABCA1 gene on the plasma TG level in patients with severe dyslipidemia.


Subject(s)
ATP Binding Cassette Transporter 1/genetics , Dyslipidemias/genetics , Lipids/blood , Alleles , Cholesterol, HDL/blood , Female , Gene Frequency , Genotype , Humans , Male , Middle Aged , Triglycerides/blood
2.
Biomed Khim ; 63(5): 413-417, 2017 Oct.
Article in Russian | MEDLINE | ID: mdl-29080873

ABSTRACT

We aimed to develop a pipeline for the bioinformatic analysis and interpretation of NGS data and detection of a wide range of single-nucleotide somatic mutations within tumor DNA. Initially, the NGS reads were submitted to a quality control check by the Cutadapt program. Low-quality 3¢-nucleotides were removed. After that the reads were mapped to the reference genome hg19 (GRCh37.p13) by BWA. The SAMtools program was used for exclusion of duplicates. MuTect was used for SNV calling. The functional effect of SNVs was evaluated using the algorithm, including annotation and evaluation of SNV pathogenicity by SnpEff and analysis of such databases as COSMIC, dbNSFP, Clinvar, and OMIM. The effect of SNV on the protein function was estimated by SIFT and PolyPhen2. Mutation frequencies were obtained from 1000 Genomes and ExAC projects, as well as from our own databases with frequency data. In order to evaluate the pipeline we used 18 breast cancer tumor biopsies. The MYbaits Onconome KL v1.5 Panel ("MYcroarray") was used for targeted enrichment. NGS was performed on the Illumina HiSeq 2500 platform. As a result, we identified alterations in BRCA1, BRCA2, ATM, CDH1, CHEK2, TP53 genes that affected the sequence of encoded proteins. Our pipeline can be used for effective search and annotation of tumor SNVs. In this study, for the first time, we have tested this pipeline for NGS data analysis of samples from patients of the Russian population. However, further confirmation of efficiency and accuracy of the pipeline is required on NGS data from larger datasets as well as data from several types of solid tumors.


Subject(s)
Computational Biology , DNA Mutational Analysis , High-Throughput Nucleotide Sequencing , Neoplasms/genetics , Data Analysis , Humans , Mutation , Russia
3.
Stomatologiia (Mosk) ; 95(5): 12-18, 2016.
Article in Russian | MEDLINE | ID: mdl-27876716

ABSTRACT

The study revealed positive correlation between bleeding on probing and teeth loss risk with periodontal hypercolonization by Porphyromonas gingivalis, Prevotella intermedia and Treponema denticola. Pathological tooth mobility was associated with hypercolonization by P. intermedia and Tannerella forsythensis. Expression of IL8, TNF-α, MMP8 and MMP9 genes was also assessed in patient groups divided according to the depth of periodontal pockets and-the severity of chronic periodontitis revealing IL8 as positive diagnostic marker.


Subject(s)
Periodontitis/diagnosis , Periodontitis/genetics , Transcriptome , Adult , Chronic Disease , Female , Genetic Markers , Hemorrhage/etiology , Hemorrhage/genetics , Humans , Interleukin-8/genetics , Male , Matrix Metalloproteinase 8/genetics , Matrix Metalloproteinase 9/genetics , Middle Aged , Periodontal Pocket/etiology , Periodontal Pocket/genetics , Periodontitis/complications , Periodontitis/microbiology , Porphyromonas gingivalis/isolation & purification , Prevotella intermedia/isolation & purification , Risk Factors , Tooth Loss/etiology , Tooth Loss/genetics , Tooth Mobility/etiology , Tooth Mobility/genetics , Treponema denticola/isolation & purification , Tumor Necrosis Factor-alpha/genetics , Young Adult
4.
Stomatologiia (Mosk) ; 95(3): 10-16, 2016.
Article in Russian | MEDLINE | ID: mdl-27367192

ABSTRACT

By using qPCR system, women as well as men were found to have an equal periodontal pathogen colonization. However, the women are subjected to have a higher risk of chronic periodontitis onsets. Women with the chronic periodontitis usually expose an evident hypercolonization with a single pathogen. P. gingivalis is the most prevalent causative agent of the chronic periodontitis in women but not in men. In health as well as in the chronic periodontitis a complex of periodontal pathogens forms such as P. gingivalis, P. intermedia, T. forsythensis and T. denticola. T. forsythensis demonstrates the highest correlation with the chronic periodontitis onset in men. Our data allow us to prove T. forsythensis playing the key role in the forming of periodontal pathogen complex.


Subject(s)
Bacteria/classification , Chronic Periodontitis/microbiology , Microbiota , Periodontal Pocket/microbiology , Adult , Bacteria/isolation & purification , Female , Humans , Male , Middle Aged , Sex Factors , Young Adult
5.
Mol Gen Mikrobiol Virusol ; 34(1): 26-30, 2016.
Article in Russian | MEDLINE | ID: mdl-27183718

ABSTRACT

The total of 54 patients with chronic periodontitis of different severity was tested using real-time PCR (Dentoflor kit). The group included 38 patients with chronic gastritis. For the first time, a higher prevalence of Treponema denticola in periodontium of males in comparison with females was demonstrated. The patients with chronic gastritis had more human genome DNA at their periodontium than healthy individuals. Non-parametric statistical analysis demonstrated high association of periodontium colonization with. T. forsythensis and T. denticola (but not Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, and Prevotella intermedia) with the severity of the chronic periodontitis.


Subject(s)
Bacteria/genetics , Chronic Periodontitis/microbiology , Duodenal Diseases/microbiology , Gastrointestinal Microbiome/genetics , Real-Time Polymerase Chain Reaction/methods , Stomach Diseases/microbiology , Adult , Aged , Aged, 80 and over , Female , Humans , Male , Middle Aged
6.
Bull Exp Biol Med ; 160(4): 495-7, 2016 Feb.
Article in English | MEDLINE | ID: mdl-26899837

ABSTRACT

Real-time quantitative PCR (Dentofl or kit) was used to detect DNA of periodontal pathogens in specimens from 92 patients with chronic periodontitis and from a control sample of 12 normal subjects. A bimodal distribution of patients by periodontium colonization with A. actinomycetemcomitans, P. gingivalis, P. intermedia, T. forsythensis, and T. denticola was demonstrated. A new approach to interpretation of the results of quantitative evaluation of periodontal pathogens, including the notion of pathological colonization level, led to classification of all cases with chronic generalized periodontitis into 3 groups: associated with A. actinomycetemcomitans, with T. forsythensis/T. denticola complex, and cases of uncertain genesis.


Subject(s)
Aggregatibacter actinomycetemcomitans/isolation & purification , Chronic Periodontitis/microbiology , Periodontium/microbiology , Porphyromonas gingivalis/isolation & purification , Tannerella forsythia/isolation & purification , Treponema denticola/isolation & purification , Adolescent , Adult , Aged , Aged, 80 and over , Humans , Middle Aged , Periodontium/pathology , Real-Time Polymerase Chain Reaction , Young Adult
7.
Stomatologiia (Mosk) ; 92(4): 28-30, 2013.
Article in Russian | MEDLINE | ID: mdl-23994852

ABSTRACT

The study included 179 patients aged 18-45 years (56 with aggressive periodontal disease and 123 with no clinical signs of periodontitis). Gene polymorphism was analyzed by means of real-time PCR and kissing probes in order to reveal marker panel for aggressive periodontal disease predisposition. Significant difference was found for gene MMP9 in rs17576 position for A allele (55.2% in aggressive periodontal disease patients and 69.5% in control group) and in rs3918242 position for C allele (67.7 and 81.7%, respectively).


Subject(s)
Aggressive Periodontitis/epidemiology , Aggressive Periodontitis/genetics , Genetic Predisposition to Disease , Adolescent , Adult , Alleles , Female , Genetic Markers , Humans , Male , Matrix Metalloproteinase 9/genetics , Middle Aged , Polymorphism, Genetic , Real-Time Polymerase Chain Reaction , Risk , Young Adult
9.
Genetika ; 49(1): 113-24, 2013 Jan.
Article in Russian | MEDLINE | ID: mdl-23662429

ABSTRACT

Allele and genotype frequencies of the -174G/C polymorphism (rs1800795) in the regulatory region of the IL6 gene, which encode anti-inflammatory cytokine interleukin 6, were determined in seven populations representing five ethnic groups from the European part of Russia (440 individuals), as well as in small cohorts that represent populations from 24 countries of Africa and Eurasia (365 individuals). The maps of the geographic distribution of the -174G/C allele frequencies were constructed based on personal (22 populations) and the literature data (66 populations), and the data from dbSNP database obtained by the HapMap project (10 populations). The frequency of the -174G allele varied from 45 to 100% and was characterized by nonrandom geographic distribution. These data could reflect the adaptive load of the alleles examined, which was different in different regions of the world. It is suggested that the level of pathogen prevalence is one of the environmental factors that determine different adaptive values of the IL6*--174G/C alleles. This suggestion is supported by a positive correlation between the -174G allele frequency and level of pathogen prevalence calculated based on historical data (R = 0.768; p < 0.0001).


Subject(s)
Gene Frequency/genetics , Interleukin-6/genetics , Polymorphism, Single Nucleotide/genetics , Regulatory Sequences, Nucleic Acid/genetics , Environment , HapMap Project , Humans , Russia , White People/genetics
10.
Bioorg Khim ; 37(3): 393-8, 2011.
Article in Russian | MEDLINE | ID: mdl-21899055

ABSTRACT

The representation patterns of 15 cytokines RNA in blood plasma and blood cells of patients with breast cancer and apparently healthy women were investigated. Relative levels of RNA IL-8 and IL-18 in plasma of breast cancer patients are significantly increased compared with control group. At the same time no obvious differences were found in relative concentrations of these transcripts in blood cells of patients and control groups. Relative concentration of IL-8 RNA was higher in blood plasma of locally advanced compared with early breast cancer patients.


Subject(s)
Breast Neoplasms/diagnosis , Interleukin-18/biosynthesis , Interleukin-8/biosynthesis , RNA/blood , Adult , Aged , Breast Neoplasms/blood , Breast Neoplasms/pathology , Female , Humans , Middle Aged , Neoplasm Staging , Transcription, Genetic
11.
Stomatologiia (Mosk) ; 90(3): 31-3, 2011.
Article in Russian | MEDLINE | ID: mdl-21716234

ABSTRACT

The introduction of a broad medical practice PCR "real time" is just beginning and dentistry is no exception. Modern molecular genetic methods provide numerous opportunities for diagnosis, assessment and prediction in patients with inflammatory periodontal diseases. Early and accurate diagnosis can allow in the future reduce the incidence of periodontitis and the progression of its course.


Subject(s)
Aggregatibacter actinomycetemcomitans/isolation & purification , Metagenome , Periodontal Pocket/diagnosis , Periodontal Pocket/microbiology , Polymerase Chain Reaction/methods , Deoxyribonucleotides/genetics , Humans , Time Factors
12.
Stomatologiia (Mosk) ; 90(3): 40-2, 2011.
Article in Russian | MEDLINE | ID: mdl-21716237

ABSTRACT

Mouth human populated set of microorganisms that are in dynamic equilibrium and forming microbiocaenosis. In a situation where this balance is disturbed, there is a "activation" of pathogens, including those that lead to the development of inflammatory periodontal diseases. Quantifying the relation parodontopatogenov in this material may be an important diagnostic tool, but data on the profile of individual microbiota subbiotopov mouth so far very little. In this study, we quantified the six pathogenic representatives of the periodontal pocket microbiota in health and periodontitis. Found that when disease development relationship pathogenic representatives of periodontal pocket microbiota varies considerably.


Subject(s)
Aggressive Periodontitis/diagnosis , Aggressive Periodontitis/microbiology , Bacteria/isolation & purification , Mouth/microbiology , Adult , Bacteria/classification , Female , Humans , Middle Aged , Polymerase Chain Reaction
13.
Acta Naturae ; 3(1): 116-22, 2011 Jan.
Article in English | MEDLINE | ID: mdl-22649680

ABSTRACT

Gingivitis and periodontitis are chronic inflammatory diseases of the periodontal tissue in humans caused by both environmental and genetic factors. The human cytokine genes that regulate the immune response may play an important role in the development of these chronic inflammatory diseases. The aim of this study is to analyze the allele status of eight human cytokine genes and to associate it with the inflammation of periodontal tissue in humans. A total of 296 unrelated males of Russian origin were studied. A significant association of theIL1BandIL6 minor alleles and gingivitis was found. In addition, we found a significant association of the OHI-S index with theIL18gene alleles. The influence of genetic factors on gingivitis may contribute to the understanding of the mechanisms of interaction between genetic and environmental factors in periodontal conditions, and to the identification of risk groups for effective prevention and treatment.

14.
Acta Naturae ; 3(2): 99-102, 2011 Apr.
Article in English | MEDLINE | ID: mdl-22649688

ABSTRACT

Periodontitis is a common disease that is considered to be a manifestation of the distortion of the ratio between the normal and conditionally pathogenic microflora of periodontal pockets. In this study, the ratio between the six most important periodontal pathogens and the total microflora of the periodontal pocket in healthy individuals and patients with varying severity of periodontitis was ascertained by quantitative real-time PCR. It was ascertained that the relative content ofPorphyromonas gingivalis,Prevotella intermedia, andTannerella forsythensis(Bacteroides forsythus) persistently develops in the total microflora of the periodontal pocket upon progressing periodontitis; this value is higher than that in the control group by more than two orders of magnitude upon a severe degree of chronic generalized periodontitis.

15.
Acta Naturae ; 2(3): 72-7, 2010 Jul.
Article in English | MEDLINE | ID: mdl-22649653

ABSTRACT

Ankylosing spondylitis (AS) belongs to a group of autoimmune diseases affecting the axial skeleton. Beside thehla-b*27allele, several other human genes that control the variety processes of immune homeostasis are considered to be associated with AS manifestation in different human populations. Among strong associated non-MHC geneserap1 encodingthe endoplasmic reticulum aminopeptidase 1 isoform was recently identified by single nucleotide polymorphisms (SNPs) meta analysis. In our study we inspected the genetic association of five non-synonymous coding SNPs fromerap1 withAS in Caucasians. We implemented the SSP-PCR system for precise genotyping of 87hla-b*27positive AS patients and 77hla-b*27healthy donors from the Russian population. Considerable differences in allele's frequencies within patients vs control cohort were shown for 3 of 5 SNPs under investigation. Using the EM-algorhitm we reconstructed 3-marker haplotypes that distinguish with high probability two cohorts due to differences in the haplotypes frequencies. In such a way both the sensitive, CCT, haplotype and the protective, TTC, one were predicted. To verify the calculation we determined genuine frequencies of 5-marker haplotypes in AS cohort by haplotyping of individual cDNA samples using improved SSP-PCR primer set. We demonstrated that the frequencies ofin silicareconstucted haplotypes and the frequencies of experimentally detected haplotypes are in a good agreement. Frequency of the risk haplotype CCT (rs17482078/10050860/2287987) detected within AS cohort reaches 88%, as well as the frequency calculated by EM-algorhitm.

17.
Mol Gen Mikrobiol Virusol ; (2): 22-4, 2009.
Article in Russian | MEDLINE | ID: mdl-19517806

ABSTRACT

The level of representation of extracellular RNA 14 cytokines in blood plasma in a group of apparently healthy subjects was analyzed. The level of representation of the transcripts of these cytokines in extracellular medium is characterized by specific profile different from the profile of expression of the genes in blood cells.


Subject(s)
Cytokines/genetics , Gene Expression Profiling , RNA, Messenger/blood , Female , Humans , Male
18.
Mikrobiologiia ; 77(3): 396-403, 2008.
Article in Russian | MEDLINE | ID: mdl-18683658

ABSTRACT

Microbial communities from the surface of ancient seeds of higher plants and embedding frozen material dated to the late Pleistocene (formed about 30 thousand years ago) were studied by various methods: scanning electron microscopy, epifluorescence microscopy, and inoculation of nutrient media, followed by identification of isolated cultures. Both prokaryotic and eukaryotic microorganisms were found on the surface of ancient seeds. The total quantity of bacterial cells determined by direct counting and dilution plating (CFU) for the samples of ancient seeds exceeded the value in the embedding frozen material by one to two orders of magnitude. This pattern was not maintained for mycelial fungi; their quantity in the embedding material was also rather high. A significant difference was revealed between the microbial communities of ancient seeds and embedding frozen material. These findings suggest that ancient plant seeds are a particular ecological niche for microorganisms existing in permafrost and require individual detailed study.


Subject(s)
Bacteria/isolation & purification , Fossils , Fungi/isolation & purification , Seeds/microbiology , Bacteria/classification , Bacteria/growth & development , Colony Count, Microbial , Culture Media , Fungi/classification , Fungi/growth & development , Ice Cover , Microscopy, Electron, Scanning , Microscopy, Fluorescence , Siberia
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