ABSTRACT
Contamination of the sample with DNA is a problem when isolating RNA by phenol-chloroform extraction, and DNase treatment introduces an additional error in the analysis of gene expression. Bearing in mind the ability of LiCl to precipitate RNA selectively, we studied the possibility and advantage of using LiCl as a precipitation agent in the protocol for RNA precipitation [3] from frozen segments of large vessels. Combined use of LiCl with isopropanol as precipitating agents (optimal ratio 2.5 M and 40%, respectively) significantly eliminates negative effects of using this salt (inhibition of reverse transcription and low RNA yield).
Subject(s)
Lithium Chloride , RNA , DNA , Lithium , Lithium Chloride/pharmacology , Phenol , RNA/geneticsABSTRACT
We studied the effects of single nucleotide polymorphisms in the promoter regions of matrix metalloproteinase genes rs1799750 (-1607dupG) MMP1, rs243865 (C-1306T) MMP2, rs3025058 (-1171dupA) MMP3, and rs11568818 (A-181G) MMP7 on the risk of varicose vein of the lower extremities in ethnical Russians, residents of the Russian Federation. We genotyped 536 patients with this pathology and 273 healthy participants without history of chronic venous disease. Association was examined using logistic regression analysis. None of the studied polymorphisms showed statistically significant association with the risk of varicose veins of the lower extremities. Our results provide evidence that these polymorphisms are not involved in the pathogenesis of varicose veins and cannot serve as markers of predisposition to this pathology.
Subject(s)
Lower Extremity/pathology , Matrix Metalloproteinase 1/genetics , Matrix Metalloproteinase 2/genetics , Matrix Metalloproteinase 3/genetics , Matrix Metalloproteinase 7/genetics , Varicose Veins/epidemiology , Varicose Veins/genetics , Adult , Female , Gene Frequency/genetics , Genetic Predisposition to Disease/genetics , Genotype , Humans , Logistic Models , Male , Middle Aged , Polymorphism, Single NucleotideABSTRACT
We analyzed associations between single nucleotide polymorphisms (SNP) rs13155212 and rs7704267 in the AGGF1 gene (angiogenic factor with G patch and FHA domains 1) and the risk of risk of varicose veins of the legs in ethnic Russians. Frequencies of alleles, genotypes, and haplotypes were estimated in the sample of patients with this disease (474 patients) and in the control group of participants (478 volunteers) without a history of chronic venous disease. None of the studied polymorphisms was associated with the risk of this pathology. The whole AGGF1 gene sequence lies in a single block of high linkage disequilibrium, and both studied polymorphic variants are representative of all other SNP within this region. From these results, a conclusion was made that AGGF1 gene polymorphism does not affect the risk of varicose veins of the legs in ethnic Russians, or its contribution is low and can be revealed only after analysis of larger cohorts.
Subject(s)
Angiogenic Proteins/genetics , Leg/blood supply , Varicose Veins/genetics , Adult , Age of Onset , Case-Control Studies , Female , Gene Frequency , Genetic Association Studies , Genetic Predisposition to Disease , Haplotypes , Humans , Linkage Disequilibrium , Male , Middle Aged , Polymorphism, Single Nucleotide , Risk , RussiaABSTRACT
We performed transcriptome analysis of some human induced pluripotent stem cells, embryonic stem cells, and human somatic cells using DNA microarrays. PluriTest bioinformatic system was used for evaluation of cell pluripotency. Changes in the genome structure and status of X-chromosome gene expression was analyzed using microarray technology.
Subject(s)
Embryonic Stem Cells/physiology , Genes, X-Linked , Induced Pluripotent Stem Cells/physiology , Transcriptome , Cells, Cultured , DNA/genetics , Embryonic Stem Cells/cytology , Gene Expression , Gene Expression Profiling , Humans , Induced Pluripotent Stem Cells/cytology , Oligonucleotide Array Sequence AnalysisABSTRACT
Transcription factors of the FoxA family (forkhead box A) regulate cell metabolism and differentiation and maintain specificity of liver cell proteome and phenotype of mature hepatocytes. The relationship between hepatocarcinogenicity of azo compounds o-aminoazotoluene (OAT) and 3'-methyl-4-dimethylaminobenzene (3'MeDAB) for GR mice and one of the early events, modulation of the DNA-binding activity of FoxA transcription factor, was studied. Single injection of 3'MeDAB to 12-day-old mice caused liver tumors in 100% males and females similarly as OAT, a well-known mouse hepatocarcinogene. The DNA-binding activity of FoxA in the liver decreased 2.5-3 times by OAT, this resulting in a 40% reduction of glucocorticoid induction of tyrosine aminotransferase (liver-specific gene). In contrast to these, 3'MeDAB did not modify FoxA protein activities or the degree of glucocorticoid induction of tyrosine aminotransferase.
Subject(s)
Azo Compounds/toxicity , Benzene Derivatives/toxicity , Hepatocyte Nuclear Factors/metabolism , Liver Neoplasms/chemically induced , o-Aminoazotoluene/toxicity , Animals , Azo Compounds/pharmacology , Benzene Derivatives/pharmacology , Female , Glucocorticoids , Liver/drug effects , Liver/metabolism , Liver Neoplasms/metabolism , Male , Mice , Protein Binding , Proto-Oncogene Proteins c-ets/metabolism , Transcriptional Activation/drug effects , o-Aminoazotoluene/pharmacologyABSTRACT
Selective increase of DNA-binding activity of constitutive androstane receptor was detected in rat and mouse liver in response to aminoazo dyes exhibiting hepatocarcinogenic activity for these species (ortho-aminoazotoluene for mice and 3'-methyl-4-dimethylaminobenzene for rats). Competition of azo dyes with 3H-5alpha-androst-16-ene-3alpha-ol (a well-known ligand of constitutive androstane receptor) for binding to liver cell cytosol proteins was studied. Ortho-aminoazotoluene and 3'-methyl-4-dimethylaminobenzene were better competitors for cytosol proteins from mouse and rat liver, respectively.
