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.

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.

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.

[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.

Effect of different drugs on the level of DNA-hydrolyzing polyclonal IgG antibodies in sera of patients with Hashimoto's thyroiditis and nontoxic nodal goiter.

BACKGROUND: DNA-hydrolyzing IgG antibodies have been detected recently in the sera of patients with several autoimmune diseases. MATERIAL AND METHODS: The relative activity of DNA-hydrolyzing IgG from the sera of patients with Hashimoto's thyroiditis and with non-toxic nodal goiter as a function of the patient's condition were measured. The effect of different drugs on the level of DNA-hydrolyzing IgG, functional activity of thyroid gland, and improvement of clinical condition of two groups of patients were analyzed. RESULTS: We demonstrate here for the first time that IgG from peripheral blood of patients with Hashimoto's thyroiditis (65%) and non-toxic nodal goiter (38%) possesses DNAse activity. The relative level-specific activity of IgGs in hydrolysis of DNA increases with the enhancement of the relative amount of antibodies against thyroglobulin and all patients with hypothyroidism (namely a reduced concentration of thyroxine and triiodothyronine and enhanced level of thyrotropic hormone) are characterized by a high level of catalytic antibodies. CONCLUSIONS: The very widely used therapy of patients with thyroxine led only to a temporary change of the hormone concentration in the blood but did not affect the level of DNA-hydrolyzing antibodies. However, treatment with an immunosuppressive drug plaquenil (7-chloro-4(beta-diethylamine-alpha-methylbutylamie)quinoline), significantly decreased the DNA-hydrolyzing activity of Abs, which correlated with enhancement of thyroid hormone concentrations, elevation of functional activity of the thyroid gland, and improvement of the clinical state of the patients.

Methorchiasis in the residents of Novosibirsk area, Russia.

Infection with Methorchis bilis was recognized for the first time in the residents of Novosibirsk area (Russia). During a serological survey (37 patients in toto), it was possible to demonstrate that 48.5% of the serum samples tested possessed antibodies to Opisthorchis felineus antigens, 37.8% to both Opisthorchis felineus and Methorchis bilis antigens, and 13.5% to Methorchis bilis antigens only.

Catalytic heterogenity of polyclonal RNA-hydrolyzing IgM from sera of patients with lupus erythematosus.

Various catalytically active IgG antibodies or abzymes have been detected recently in the sera of patients with several autoimmune pathologies including systemic lupus erythematosus (SLE), where their presence is most probably associated with autoimmunization. Here we show for the first time that IgM from peripheral blood of patients with SLE possesses both DNase and RNase activities: these activities were also present in Fab fragments of the IgM. Both specific enzymic activities of IgM from sera of any single patient are usually 5-10 times higher than those of IgG antibodies. The same preparations of IgM hydrolyze RNA about two order of magnitude faster than DNA. The properties of the RNases of IgM and IgG distinguished them from other known pancreatic and human sera RNases. In addition, the specific activities of the RNase activity of polyclonal IgM with the polymer substrates [RNA > poly(U) > or = poly(A) >> poly(C)], the observed range of optimal pHs, of apparent Km values for substrates and of substrate specificities varied very much for different patients. The findings speak in favor of the generation of a relatively small or an extremely large pool of polyclonal catalytic IgM by the immune system of individual patients.

[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.

Polyclonal antibodies from blood and cerebrospinal fluid of patients with multiple sclerosis effectively hydrolyze DNA and RNA.

It is known that in the blood of patients with some autoimmune diseases catalytically active antibodies hydrolyzing proteins, DNA, and RNA may be detected. In the present work homogeneous preparations of IgG antibodies (Ab) possessing high affinity for nucleic acids (NA) were obtained for the first time from blood and cerebrospinal fluid of patients with multiple sclerosis (MS). The fraction of IgG Ab as well as its Fab fragments and isolated light chains of both kappa- and lambda-types were shown to catalyze effectively the hydrolysis of DNA and RNA. It is shown by different methods that the capability for nucleic acid hydrolysis is an intrinsic property of the polyclonal Ab. NA-hydrolyzing Ab were detected in the blood of 69 of 72 and in the cerebrospinal fluid of 5 of 5 examined MS patients, while they were not detected in the blood of any of 50 healthy donors examined. Comparison of relative rates of RNA hydrolysis and of the substrate specificity in hydrolysis of various model RNAs--cCMP, poly(U), poly(A), and poly(C)--revealed pronounced differences of MS antibodies from ribonucleases of human blood, ribonuclease A, and all earlier described abzymes. The abzymes are usually characterized by relatively low specific activities in comparison with that of normal enzymes catalyzing analogous reactions. Ab from the blood of MS patients are the first example of autoabzymes whose specific activity in RNA hydrolysis is comparable or even higher than that of pancreatic ribonuclease A--one of the most active RNA-hydrolyzing enzymes.

RNA-hydrolyzing antibodies from peripheral blood of patients with lupus erythematosus.

Experiments and hydrolysis of substrates with known spatial structures (such as yeast tRNAPhe, as well as normal and mutant tRNALys from human mitochondria produced by transcription of the appropriate DNA species, that is, RNA genes) were performed to study the ribonuclease activity of antibodies isolated from blood sera of patients with systemic lupus erythematosus (SLE). The antibody preparations contained two types of ribonuclease activities: the first corresponded to the specificity of ribonuclease A and was found during hydrolysis at low salt concentrations, whereas the second was stimulated by Mg2+ and displayed unique specificity toward double-stranded regions of the substrate. The possible use of the antibody preparations as tools for structural studies of conformational differences between RNA molecules was examined. In experiments with unmodified and mutant tRNALys species differing in one base found in the T-loop, we found that hydrolysis with SLE antibodies can detect small local structural changes in RNA under physiological conditions.

DNA- and RNA-hydrolyzing antibodies from the blood of patients with various forms of viral hepatitis.

Antibodies (Abs) hydrolyzing proteins, DNA, and RNA are detected in the blood of patients with various autoimmune diseases. In the present work, homogeneous preparations of IgG Abs from the blood of the healthy donors as well as patients with A, B, C, and delta types of viral hepatitis, influenza, pneumonia, tuberculosis, tonsillitis, duodenal ulcer, and some types of cancer were purified. For the first time, the fraction of IgG and its Fab fragments of patients with viral hepatitis were shown to have high DNA- and RNA-hydrolyzing activity. In case of Abs from the healthy donors and patients with other diseases, high activity of Abs was not detected. The data obtained by various methods indicate that the activity of hepatitis Abs is an intrinsic property of the immunoglobulins. The relative rates of hydrolysis of cCMP, poly(U), poly(A), poly(C), and tRNA(Phe) by hepatitis Abs were compared with those of RNase A and other RNases from human blood. Significant differences in activities of Abs and nucleases in hydrolysis of model substrates were demonstrated. Thus, catalytically active Abs can appear in the blood of patients not only with autoimmune disorders, but with viral diseases as well.

[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.

[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.