Noncontiguous finished genome sequence of Megasphaera sp. ASD88, isolated from faeces of a child with autism spectrum disorder.

We report here a draft genome sequence of Megasphaera sp. ASD88, a strain from the intestinal microbiota of a child with autism spectrum disorder, representing a previously undescribed species of the genus Megasphaera. The assembled sequence consists of 88 scaffolds, and the total size is 2.59 Mb.

Transcription profile analysis of the endometrium revealed molecular markers of the personalized 'window of implantation' during in vitro fertilization.

To determine the most informative markers for assessing the functional state of endometrium during the 'window of implantation' and creating a model for assessment of the readiness of endometrium for embryo implantation. Forty-seven women with tubal infertility and a successful IVF pregnancy participated in the study. Pipelle endometrial sample was performed during the supposed 'window of implantation' in natural cycle with subsequent histological study, and transcriptional profile of genes GPX3, PAEP, DPP4, TAGLN, HABP2, IMPA2, AQP3, HLA-DOB, MSX1, POSTN determined by real-time quantitative polymerase chain reaction (qRT-PCR). Differences in the level of mRNA expression of all the studied genes in the receptive endometrium were found in comparison to the prereceptive one, which allowed us to classify two functional states of the endometrium. The results of histological examination responded to the stage of maturation of the endometrium in 78.7% of cases. Receptive endometrial status can be determined based on the integral evaluation of mRNA expression level of 4 PAEP, DPP4, MSX1, and HLA-DOB genes. The model for determining a personalized `window implantation' is offered for practical application in ART.

[Metabolomic profiling in culture media of day-5 human embryos]. / Profilirovanie metabolitov v pitatel'nykh sredakh piatidnevnykh émbrionov cheloveka.

The aim of this study was to determine the changes of metabolomic profiles in embryonic culture media (ECM) for the evaluation of quality and implantation potential of human embryos. ECM (n=163) were collected on day 5 before transfer or cryopreservation. Some embryos were used in preimplantation genetic screening for detection of aneuploidy karyotypes. Samples were subdivided into groups according to embryo morphological classification (by Gardner), genetic analysis and implantation data. ECM were extracted with methanol, precipitates were separated by centrifugation and metabolite production of individual embryo was analysed by LC-MS (the positive ion mode). After peak detection and retention time alignment, data were analysed using the PCA algorithm. MS fingerprinting analysis of embryo culture medium showed significant differences between morphologically divided groups. Intragroup comparisons did not reveal differences between subclasses. Genetic screening of embryos revealed 33 aneuploid karyotypes. It was shown that chromosome number did not affect the metabolite profiles comparing with the normal group. The culture media of embryos that were positive or negative for successful implantation showed specific signatures that allowed to distinguish embryos with different outcomes.The characterization of ECMs by LC-MS may facilitate more accurate selection of the best embryo for the implantation, improving single-embryo transfer and thus eliminating the risk and undesirable effects of multiple pregnancies.

Method of Selection of Bacteria Antibiotic Resistance Genes Based on Clustering of Similar Nucleotide Sequences.

A new method for selection of bacterium antibiotic resistance genes is proposed and tested for solving the problems related to selection of primers for PCR assay. The method implies clustering of similar nucleotide sequences and selection of group primers for all genes of each cluster. Clustering of resistance genes for six groups of antibiotics (aminoglycosides, ß-lactams, fluoroquinolones, glycopeptides, macrolides and lincosamides, and fusidic acid) was performed. The method was tested for 81 strains of bacteria of different genera isolated from patients (K. pneumoniae, Staphylococcus spp., S. agalactiae, E. faecalis, E. coli, and G. vaginalis). The results obtained by us are comparable to those in the selection of individual genes; this allows reducing the number of primers necessary for maximum coverage of the known antibiotic resistance genes during PCR analysis.

[Comparative results of preimplantation genetic screening by array comparative genomic hybridization and new-generation sequencing].

Aneuploidies as quantitative chromosome abnormalities are a main cause of failed development of morphologically normal embryos, implantation failures, and early reproductive losses. Preimplantation genetic screening (PGS) allows a preselection of embryos with a normal karyotype, thus increasing the implantation rate and reducing the frequency of early pregnancy loss after IVF. Modern PGS technologies are based on a genome-wide analysis of the embryo. The first pilot study in Russia was performed to assess the possibility of using semiconductor new-generation sequencing (NGS) as a PGS method. NGS data were collected for 38 biopsied embryos and compared with the data from array comparative genomic hybridization (array-CGH). The concordance between the NGS and array-CGH data was 94.8%. Two samples showed the karyotype 47,XXY by array-CGH and a normal karyotype by NGS. The discrepancies may be explained by loss of efficiency of array-CGH amplicon labeling.

Description of a new HLA-A*02 allele, A*02:658, in a Russian individual.

Sequence of the novel allele, HLA-A*02:658, differs from HLA-A*02:01:01:01 by one-nucleotide exchange in exon 2.

[Twin reversed arterial perfusion syndrome in the monochorionic diamniotic placenta with the development of an acardiac fetus]. / Sindrom obratnoi arterial'noi perfuzii v monokhorial'noi diamnioticheskoi platsente s razvitiem ploda-akardiusa.

The article describes an acardiac fetus in a patient with monochorionic diamniotic twin pregnancy with reversed arterial perfusion syndrome at 30 weeks' gestation. It gives postmortem fetal computed tomographic and pathoanatomic data. Microarray of acardiac fetal tissues revealed that there was deletion of chromosome 19 - arr [hg19] 19p13.3q11 (260,911-23,005,001) x1; size, 23 Mbp; the signal level in about 30% of fetal tissue cells containing deletion.

Comparison of the results of preimplantation genetic screening obtained by a-CGH and NGS methods from the same embryos.

Chromosomal aneuploidies are known for being the main cause of abnormal development of embryos with normal morphology, their implantation failure and early reproductive losses in IVF treatments. Preimplantation genetic screening (PGS) allows selecting embryos with normal chromosomal content and increases IVF treatment efficiency due to higher implantation rates and less frequent early pregnancy losses. New technologies used for PGS allow making genome-wide analysis of the presence of all chromosomes in embryos. This article presents our study of evaluation of two techniques used for PGS: previously developed and used in our laboratory a-CGH assay based on Agilent technology and newly tested semi-conductive NGS technique (Torrent technology).

[SAFETY AND IMMUNOGENICITY OF A NATIONAL COMBINED VACCINE AGAINST PERTUSSIS, DIPHTHERIA, TETANUS, HEPATITIS B AND Hib-INFECTION, CONTAINING ACELLULAR PERTUSSIS COMPONENT, DURING IMMUNIZATION OF ADULTS].

AIM: Study safety, reactogenicity and immunologic effectiveness of a national combined vaccine against diphtheria, pertussis (acellular component), tetanus, hepatitis B and Hib-infection during immunization of volunteers aged 18-60 years. MATERIALS AND METHODS: The study was carried out in accordance with ethical standards and requirements, regulated by Helsinki declaration and Good clinical practice (ICHGCP). In a simple non-randomized clinical trial 20 adult volunteers took part, the mean age of those was 46.9 years. RESULTS: Registered: post-vaccination reactions (both local and systemic) were mild and of moderate degree of severity, stopped independently after 2-3 days without administration of drug treatment. Postvaccinal complications were not noted. Parameters of general and biochemical analysis of blood, urine, IgE content in dynamics of immunization were within normal limits. A single administration of aAPDT--HepB+Hib to individuals aged 18-60 years resulted in development of antibodies against all the components of the preparation. Seroconversion factor fluctuated from 6.9 to 53.5: CONCLUSION: The results obtained allow to recommend the vaccine for evaluation of its safety, reactogenicity, immunologic and prophylaxis effectiveness in randomized clinical observation trials in children.

[Conditionally pathogenic microorganisms in patients with bisphosphonate jaw osteonecrosis].

The objective of the study was to define treatment strategy in cases of facial bones bisphosphonate induced osteonecrosis based on the study of the role of conditionally pathogenic oral microorganisms. Three typical clinical cases of bisphosphonate osteonecrosis of the facial bones were analyzed and 15 conditionally pathogenic oral microorganisms were identified in these patients using real-time PCR in saliva, wound and bone samples. A comparative analysis was carried out with purulent-inflammatory diseases of maxillofacial area. The study results proved an important role of conditionally pathogenic microorganisms of the oral cavity in the development of osteonecrosis of the facial bones. Wide range of bacterial species was identified in osteonecrosis of the facial bones patients. While bone tissue is most exposed to microbial communities, surgical treatment results in effective rehabilitation for a long period.

Role of Collagen Gene Polymorphisms in the Structure of Early Gestation Loss.

Studies of collagen gene polymorphisms associated with predisposition to early recurrent miscarriages revealed significant differences in the distribution of COL1A1 C-1997A C>A (rs1107946) genotypes and alleles in the group of pregnant patients with early miscarriages in comparison with controls (normal pregnancy). Identification of COL1A1 C-1997A C>A (rs1107946) collagen gene polymorphisms at the stage of pregnancy planning will make it possible to form early miscarriage risk groups for more thorough preparation to gestation and optimization of follow up of this patient population.

[Genetic determinants of resistance of hospital-associated strains of Klebsiella pneumoniae to ß-lactam antibiotics isolated in neonates].

According to the results of analysis of whole genome sequencing, the presence of genes having resistance to ß-lactam antibiotics in hospital-associated strains of Klebsiella pneumoniae was studied. The strains were isolated from neonatal intensive care units. The data obtained were compared with the results of antimicrobial susceptibility testing of isolated microorganisms. Among other strains resistant to cephalosporins, the dominance of genes of CTX-M-type extended-spectrum ß-lactamases was shown. It was revealed that one of eight strains phenotypically resistant and moderately resistant to carbapenems have the blaOXA-48 carbapenemase gene.

Comparison of the expression of immunomodulatory factors in cultures of mesenchymal stromal cells from human extraembryonic tissues.

mRNA of genes (tgfß, il6, il10, il1ß, and vegf165) involved in cell proliferation, inflammatory, anti-inflammatory, and angiogenic processes were detected and quantified in cultures of mesenchymal stromal cells of different passages derived from human extraembryonic tissues (amniotic sac, umbilical cord, chorionic villi and trophoblast of the placenta). The concentrations of IL-10, IL-6, IL-1ß, and TGFß were measured.

Expression of immunomodulator gene mRNA in co-culture of mesenchymal stromal cells from the placenta and human mononuclear blood cells.

The expression of mRNA of cytokines and immunoregulatory molecules characterizing the interaction of mesenchymal stromal cells from chorionic villi of postpartum placenta and allogenic mononuclear blood cells was studied during 3-day co-culturing of these cells. The expression of foxp3, il2ra, and il10 mRNA in floating mononuclear cells increased from day 1 to 3 in co-culture, which can refl ect the process of induction of regulatory T cells in the lymphocyte population under the action of mesenchymal stromal cells.

Actn3 genotype is associated with testosterone levels of athletes.

UNLABELLED: α-Actinin-3 (ACTN3) has been proposed to regulate skeletal muscle differentiation and hypertrophy through its interaction with the signalling protein calcineurin. Since the inhibition of calcineurin potentiates the production of testosterone, we hypothesized that α-actinin-3 deficiency (predicted from the ACTN3 XX genotype) may influence serum levels of testosterone of athletes. OBJECTIVE: To investigate the association of ACTN3 gene R577X polymorphism with resting testosterone levels in athletes. METHODS: A total of 209 elite Russian athletes from different sports (119 males, 90 females) were genotyped for ACTN3 gene R577X polymorphism by real-time PCR. Resting testosterone was examined in serum of athletes using enzyme immunoassay. RESULTS: The mean testosterone levels were significantly higher in both males and females with the ACTN3 R allele than in XX homozygotes (males: RR: 24.9 (5.7), RX: 21.8 (5.5), XX: 18.6 (4.9) ng · mL(-1), P = 0.0071; females: RR: 1.43 (0.6), RX: 1.21 (0.71), XX: 0.79 (0.66) ng · mL(-1), P = 0.0167). CONCLUSIONS: We found that the ACTN3 R allele was associated with high levels of testosterone in athletes, and this may explain, in part, the association between the ACTN3 RR genotype, skeletal muscle hypertrophy and power athlete status.

SOD2 gene polymorphism and muscle damage markers in elite athletes.

Exercise-induced oxidative stress is a state that primarily occurs in athletes involved in high-intensity sports when pro-oxidants overwhelm the antioxidant defense system to oxidize proteins, lipids, and nucleic acids. During exercise, oxidative stress is linked to muscle metabolism and muscle damage, because exercise increases free radical production. The T allele of the Ala16Val (rs4880 C/T) polymorphism in the mitochondrial superoxide dismutase 2 (SOD2) gene has been reported to reduce SOD2 efficiency against oxidative stress. In the present study we tested the hypothesis that the SOD2 TT genotype would be underrepresented in elite athletes involved in high-intensity sports and associated with increased values of muscle and liver damage biomarkers. The study involved 2664 Caucasian (2262 Russian and 402 Polish) athletes. SOD2 genotype and allele frequencies were compared to 917 controls. Muscle and liver damage markers [creatine kinase (CK), creatinine, alanine transaminase (ALT), aspartate transaminase (AST), alkaline phosphatase (ALP)] were examined in serum from 1444 Russian athletes. The frequency of the SOD2 TT genotype (18.6%) was significantly lower in power/strength athletes (n = 524) compared to controls (25.0%, p = 0.0076) or athletes involved in low-intensity sports (n = 180; 33.9%, p < 0.0001). Furthermore, the SOD2 T allele was significantly associated with increased activity of CK (females: p = 0.0144) and creatinine level (females: p = 0.0276; males: p = 0.0135) in athletes. Our data show that the SOD2 TT genotype might be unfavorable for high-intensity athletic events.

[A method of quantitative assessment of cytokine gene mRNA expression levels using real-time PCR in homogenous low cell number populations].

We propose a method of quantitative functional activity assessment in cells isolated via sorting on a flow cytometer. We show that cell populations vary in the mRNA expression of cytokine genes immediately after isolation and sorting, while the maintenance of homogenous populations in culture without stimulation results in an increase in these gene mRNA expression. Using the original system, it is now possible to detect mRNA cytokine genes with high sensitivity, starting from 90 cells per specimen. This approach permits genetic and immunogenetic analysis of gene expression with the goal of determining their functions in the in vitro studies.

[Detection of Staphylococcus aureus toxins using immuno-PCR].

A highly sensitive test system, based on the method of immuno-PCR, was developed for the detection of two staphylococcal toxins: enterotoxin A (SEA) and toxic shock syndrome toxin (TSST). A key element of the developed systems was obtaining supramolecular complexes of bisbiotinylated oligodeoxynucleotides and streptavidin, which were used as DNA tags. Specificity studies showed no cross-reactivity when determining SEA and TSST. The sensitivity of detection of these toxins in the culture supernatants S. aureus was not less than 10 pg/mL.

[Immunogenetic aspects of early rheumatoid arthritis].

The study is aimed to investigate the distribution of alleles of HLA-DRB1 gene in patients with early rheumatoid arthritis and healthy individuals in Russian population, and evaluate their significance as molecular genetic markers of rheumatoid arthritis predisposition and protection. The association between alleles of HLA-DRB1 genes, antibodies to cyclic citrullinated peptides and IgM rheumatoid factor was also studied. Low and high resolution HLA-DRB1 genotyping were compared. In the cohort of patients with early rheumatoid arthritis, the alleles of HLA-DRB1 gene were found to be markers of rheumatoid arthritis protection/risk, especially in the homozygous state. They determined production of antibodies to cyclic citrullinated peptides but were not associated with rheumatoid factor IgM levels. These findings support different autoimmune mechanisms of rheumatoid arthritis pathogenesis.

[Immunogenetic predictors of a rapid virologic response to antiviral therapy in patients with chronic hepatitis C].

AIM: To determine the correlation between interleukin 28B (IL28B) gene polymorphism in patients with chronic hepatitis C (CHC), the presence or absence a rapid virologic response to antiviral therapy, and a number of immunological characteristics as a basis for a personalized approach to treating the patients. SUBJECTS AND METHODS: Seventeen CHC patients infected with hepatitis C virus genotype 1b were examined and underwent genetic testing for IL28B gene polymorphism for rs12979860 (CC, CT or TT genotypes) and rs8099917 (TT, TG or GG genotypes) using the modified method of adjacent samples, which revealed single nucleotide substitutions in the genes. Their immunological parameters were identified by a flow cytometry technique by taking into account whether a rapid virologic response had been achieved. RESULTS: The key phenomena of a rapid virologic response in the representatives of different IL28B genotypes are the nonspecific proliferative activity of blood natural killer cells before treatment, as well as the count of regulatory T cells before and 4 weeks after therapy start. CONCLUSION: To predict the efficiency of antiviral therapy for CHC, it is desirable to supplement genetic studies with immunological data.