Comparative Whole-Transcriptome Profiling of Liver Tissue from Wistar Rats Fed with Diets Containing Different Amounts of Fat, Fructose, and Cholesterol.

Differential expression of 30,003 genes was studied in the liver of female Wistar rats fed with isocaloric diets with the excess of fat, fructose, or cholesterol, or their combinations for 62 days using the method of whole-transcriptome profiling on a microchip. Relative mRNA expression levels of the Asah2, Crot, Crtc2, Fmo3, GSTA2, LOC1009122026, LOC102551184, NpY, NqO1, Prom1, Retsat, RGD1305464, Tmem104, and Whsc1 genes were also determined by RT-qPCR. All the tested diets affected differently the key metabolic pathways (KEGGs). Significant changes in the expression of steroid metabolism gene were observed in the liver of animals fed with the tested diets (except the high-fat high fructose diet). Both high-fat and high-fructose diets caused a significant decrease in the expression of squalene synthase (FDFT1 gene) responsible for the initial stage of cholesterol synthesis. On the contrary, in animals fed with the high-cholesterol diet (0.5% cholesterol), expression of the FDFT1 gene did not differ from the control group; however, these animals were characterized by changes in the expression of glucose and glycogen synthesis genes, which could lead to the suppression of glycogen synthesis and gluconeogenesis. At the same time, this group demonstrated different liver tissue morphology in comparison with the animals fed with the high-fructose high-fat diet, manifested as the presence of lipid vacuoles of a smaller size in hepatocytes. The high-fructose and high-fructose high-fat diets affected the metabolic pathways associated with intracellular protein catabolism (endocytosis, phagocytosis, proteasomal degradation, protein processing in the endoplasmic reticulum), tight junctions and intercellular contacts, adhesion molecules, and intracellular RNA transport. Rats fed with the high-fructose high-fat or high-cholesterol diets demonstrated consistent changes in the expression of the Crot, Prom1, and RGD1305464 genes, which reflected a coordinated shift in the regulation of lipid and carbohydrate metabolisms.

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.

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.

Associations of single nucleotide polymorphisms with malignant and borderline bone tumors.

Bone neoplasms - are a rare group of diseases, which ethiology and pathogenesis are not fully understood. We have studied 6 single nucleotide polymorphisms rs792/(GHI), rs7956547(IGFI), rs3761243(GNRH2), rs11737764(FGF2), rs6599400(FGFR3), and rs1690916(MDM2) associations with bone tumors. In our work we've detected significant associations with some single nucleotide polymorphisms: IGFl.rs7956547, GNRH2.rs3761243 and FGFR3.rs6599400 in patients with malignant and borderline bone tumors.

Association of FGFR3 and MDM2 gene nucleotide polymorphisms with bone tumors.

Association study of 6 candidate single-nucleotide polymorphisms (rs7921, rs7956547, rs3761243, rs11737764, rs6599400, rs1690916) was carried out in a group of patients with bone tumors of different histological structure (n=68) and control group of normal subjects (n=96). Significant associations of rs6599400 and rs1690916 polymorphisms with disease risk were detected (odds ratio 2.15 [1.06-4.24] and 0.39 [0.19-0.78], respectively). These polymorphisms were located in untranslated genome regions: polymorphism rs6599400 in the 5' region of fibroblast growth factor-3 receptor gene (FGFR3), rs1690916 in the 3' region of mouse MDM2 p53-binding protein homolog (MDM2). These data indicated a possible role of hereditary genetic factors in the formation of predisposition to bone sarcomas and confirmed previous findings according to which these genes should be regarded among the most probable factors involved in tumor development, including tumors of the bone and cartilage tissues.

[Construction of probes for hybridization with hepatitis A virus RNA based on phage M13]. / Konstruirovanie zondov dlia gibridizatsii s RNK virusa gepatita A na osnove faga M13.

Three fragments of a DNA copy complementary to tre hepatitis A virus RNA have been isolated from the pHAV-VPI-22 plasmid and cloned in M 13 mp 8 vector. The 140, 250 and 390 b. p. fragments corresponded to the viral genome fragment coding for VP1 protein. Single-stranded DNAs of the hybrid phages with 250 b. p. and 390 b. p. inserts have been used for radioactive probe synthesis. The specificity of the probes for viral RNA was confirmed in hybridization with hepatitis A virus RNA purified from the virus-infected cell culture. The hybridization was shown to detect up to 10(-12)-10(-13) g of the virus. A principal possibility to use the probes in diagnostic purposes was demonstrated by the virus detection in blood samples obtained from patients with hepatitis A infection.

[Use of non-radioactive biotin-labelled probes for detecting hepatitis A virus]. / Ispol'zovanie neradioaktivnykh biotin-mechennykh zondov dlia detektsii virusa gepatita A.

The biotin-labeled DNA probes were constructed on the basis of the hybrid bacteriophage M13nip 9 single-stranded DNA containing the fragments of the hepatitis A viral cDNA. The probes were biotin treated by chemical modification of the DNA by the peraminating reagent or photochemically. The labeled DNA probes were used in molecular hybridization experiments with the nuclear acids fixed on the nitrocellulose filters. The biotin treated DNA was determined by the avidin-gold colloid conjugate with the subsequent physical silver amplification or by the streptavidin-alkaline phosphatase conjugate. The sensitivity of both probes was identical and permitted the determination of 5 x 10(-11)-5 x 10(-12) g of the control DNA and 10(-9) g of the hepatitis A virus. The developed test systems were used for detection of the viral RNA in blood from patients.

[The use of a biotinated probe for the detection of the genomic RNA of the hepatitis A virus in clinical specimens]. / Ispol'zovanie biotinirovannogo zonda dlia detektsii genomnoi RNK virusa gepatita A v klinicheskikh obraztsakh.

A detection technique for hepatitis A virus (HAV) RNA by means of molecular hybridization using ss-biotinated DNA probe on the basis of M13 bacteriophage is described. The technique sensitivity reached 1-10 pg of control DNA or 100-500 pg of HAV. The experiments for detection of HAV carriers among the patients and contacts from foci of HAV outbreaks were carried out. A comparative analysis of the above technique and enzyme immunoassay and amplification technique was done and good coincidence of the results was demonstrated.

[The use of a molecular probe containing a specific cDNA consisting of bacteriophage M13 for detecting the hepatitis A virus in clinical specimens]. / Ispol'zovanie molekuliarnogo zonda, soderzhashchego spetsificheskuiu kDNK v sostave bakteriofaga M13, dlia detektsii virusa gepatita A v klinicheskikh obraztsakh.

A probe was constructed containing a fragment of DNA replica of hepatitis A virus (HAV) RNA within bacteriophage M13 single-stranded DNA which allowed 10(-12) g of viral RNA to be tested. Hybridization of 32P-labeled probe with total RNA from 559 samples of blood, saliva, and urine from patients with viral hepatitis A revealed the presence of HAV RNA in 14% of the samples. In the 1st week of the jaundice period HAV RNA was detected in 40% (15 positive samples out of the 39 tested), in the 2nd week 26% (14 out of 54). HAV RNA was demonstrated in 20 out of 236 blood samples from subjects in a focus of HA outbreak. Six out of 9 subjects subsequently developing the disease were detected 7-10 days before the onset of the clinical symptoms. The proposed method may be useful for detection of HAV carriers in the latent period for their isolation in order to prevent further development of epidemic.

[Development of a two-site immunoassay using polyclonal antibodies for determination of lactoferrin in human blood]. / Razrabotka dvukhsaitnogo immunoanaliza s ispol'zovaniem poliklonal'nykh antitel dlia opredeleniia laktoferrina v syvorotke krovi cheloveka.

The two-site enzyme-linked immunosorbent assay (ELISA) for lactoferrin using polyclonal antibodies to spatially distant epitopes has been developed. The assay sensitivity defined as minimal detectable lactoferrin concentration for p = 0.05 is 0.5 ng/ml. Accuracy of the assay (variance coefficient) is 7% within the clinical range of antigen concentrations. Human albumin, hemoglobin, and transferrin in concentrations up to 5 mg/ml practically do not interfere with the measurement. Sera of healthy donors and viral hepatitis patients were investigated using the two-site ELISA. The lactoferrin content in 44 donors' sera was 130 +/- 40 ng/ml (medium +/- standard deviation). A study of the serum specimens of 95 patients with hepatitis A, B, and C showed significant increase in serum lactoferrin concentration: 850 +/- 420, 780 +/- 580, and 680 +/- 500 ng/ml respectively. The assay showed good characteristics and may be recommended for lactoferrin measurement in patients' sera.

[Some real problems of human opisthorchiasis]. / O nekotorykh aktual'nykh voprosakh problemy opistorkhidozov cheloveka.

Forty six sera from residents of the Novosibirsk Region in whom the diagnosis of chronic opisthorchiasis had been helminthoovoscopically verified were examined. In the thin layer immunoassay, of them 14 (30.4%) sera were responsive to excretory O. felineus antigens, 3 (7.9%) were to M. bilis antigens, and 29 (63.2%) were to the above antigens simultaneously. The results of these studies determine it possible to regard M. bilis methorchiasis as a zooanthroponous disease and a human being as a final host of this helminth.

[Comparative analysis of methods of diagnosis of chlamydia infection]. / Sravnitel'nyi analiz metodov diagnostiki khlamidioza.

In case of a correct sampling, the diagnostic value of optic and electron microscopy for detecting Chlamydia infection is not inferior to that of direct microimmunofluorescence (DMIF) and higher than that of enzyme immunoassay (EIA). Optic microscopy showed that basal vaginal epithelium and buccal mucosa can be infected with Chlamydia. Provazek bodies were detected in the buccal mucosa of the overwhelming majority of patients with genital chlamydiasis. These results were confirmed by DMIF and EIA. Since none of the diagnostic methods is 100% reliable, we recommend using two methods: inexpensive optic microscopy and polymerase chain reaction or DMIF.

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.