Targeted Sequencing for Studying Economically Useful Traits and Phylogenetic Diversity of Ancient Sheep

Russian Journal of Genetics - Sheep were one of the first animals to be domesticated. The history of sheep domestication and their widespread distribution dates to about ten thousand years ago,...     

KatG Ser3 15Thr mutation as the main reason of isoniazid resistance in Mycobacterium tuberculosis isolated in the Novosibirsk and Kemerovo Regions

KatG Ser3 15Thr mutation is one of the main reasons of resistance to isoniazid in Mycobacterium tuberculosis isolates. The frequency rate of the above mutation among isoniazid-resistant isolates made 94% in Novosibirsk Region and 93% in Kemerovo Region. The use of PCR-restriction fragment length polymorphism (PCR-RFLP) can be regarded as an adequate method for rapid screening of isoniazid resistance in Mycobacterium tuberculosis isolated in the West-Siberian Region.     

Function of hypothalamic-pituitary-adrenocortical system in hypertensive rats of ISIAH strain

Functional activity of hypothalamic-pituitary-adrenocortical axis has been studied under control and restraint stress conditions in rats with inherited stress-sensitive arterial hypertension (ISIAH strain) and in normotensive WAG (Wistar Albino Glaxo) strain. The levels of hypothalamic CRH-mRNA (in control and 2 hrs stress), pituitary and plasma ACTH and plasma corticosterone (in control and after 5, 15 or 30 min of restraint stress), were evaluated. Hypothalamic CRH-mRNA level was found to be approximately the same in the control rats of both strains. In control conditions, the pituitary and plasma ACTH content in ISIAH rats was significantly lower whereas the corticosterone level in the plasma differed from each other in both strain. The restraint stress resulted in a statistically significant increase of the CRH-mRNA in ISIAH rats and not in the WAG rats. Moreover, in spite of the lower ACTH level in stressed ISIAH rats, the corticosterone blood plasma concentration in hypetensive rats was significantly higher. The data obtained confirm the idea that the stress-dependent hypertension might be related to an enhanced sensitivity of the main endocrine links involved in the stress response organization.     

Expression of CYP1A in liver of A/Sn and CC57BR mice differing in sensitivity to hepatocarcinogenesis induced by o-aminoazotoluene

The induction of P450 cytochromes Cyp1a1 and Cyp1a2 in the liver of male mice differing in sensitivity to the carcinogenic effect of o-aminoazotoluene (OAT) has been studied. The level of Cyp1a1 and Cyp1a2 mRNA was assayed by quantitative competitive polymerase chain reaction (PCR). In both OAT-treated strains, the level of Cyp1a1 mRNA increased more than 1000-fold, while the amount of Cyp1a2 mRNA increased only two- or threefold. Interstrain differences in the Cyp1a mRNA level were revealed. The level of Cyp1a1 mRNA in liver of OAT-induced A/Sn mice was three times higher than in CC57BR mice. The amount of Cyp1a2 mRNA in control and OAT-treated mice was 7 and 13 times higher, respectively, than in CC57BR mice. The enzyme activities of cytochromes P450 1a were assayed. An increase in Cyp1a1 mRNA level in OAT-treated mice correlated with an enhancement of the benzo[a]pyrene hydrolase and 7-ethoxyresofurin o-deethylase activities; the correlation between the level of Cyp1a2 mRNA and 7-ethoxyresofurin o-demethylase activity was much less pronounced. Interstrain variation in Cyp1a1 and Cyp1a2 activities was also shown at the enzyme activity level. We suppose that quantitative differences in the Cyp1a2 mRNA level play a key role in OAT-induced hepatocarcinogenesis.     

Effect of point substitutions in the <Emphasis Type="Italic">MnSOD,GPX1</Emphasis>, and <Emphasis Type="Italic">GSTP1</Emphasis> genes on the risk of familial and sporadic breast cancers in residents of Altai Krai

The frequencies of the polymorphic gene variants MnSOD Ala₉Val, GPX1 Pro₁₉₈Leu, and GSTP1 Ile₁₀₅Val were estimated in female residents of Altai krai with breast cancer. The frequency distributions of the genotypes for all genes studied in both patients and control subjects fit the Hardy-Weinberg equilibrium. The estimated frequencies of the genotypes for the studied genes in the control group did not differ from those earlier reported for Caucasoid women living in Europe. The T (rs1050450) allele of the GPX1 gene was demonstrated to protect against sporadic breast cancer (OR = 0.74 (95% CI = 0.58−0.94), p = 0.012). Carriers of the genotype combination MnSOD CC + GPX1 CC were found to have a 1.6 times higher risk of sporadic breast cancer compared to the control group (OR = 1.59 (1.05−2.41), p = 0.0258). The polymorphic loci GSTP1 (rs1695) and MnSOD (rs4880) were not found to be significantly associated with the risk of familial or sporadic breast cancer.     

Polymorphic variants of folate metabolizing genes (C677T and A1298C MTHFR, C1420T SHMT1 and G1958A MTHFD) are not associated with the risk of breast cancer in West Siberian Region of Russia

Breast cancer is the most incident cancer among women. We investigated the role of polymorphisms of folate metabolizing genes MTHFR (C677T and A1298C), SHMT1 (C1420T) and MTHFD (G1258A) in genetic susceptibility to this type of cancer. We determined allele and genotype frequencies in case (850 women with sporadic form of breast cancer) and control (810 women) groups. None of these polymorphisms was significantly associated with breast cancer risk. To increase statistical power of our study, we conducted a meta-analysis which included published genotype data and the results of our work. Meta-analysis also revealed no significant association of studied SNPs with breast cancer.     

Analysis of integration sites of T-DNA insertions in transgenic tobacco plants

DNA fragments containing T-DNA/plant DNA junctions isolated from 17 transgenic tobacco plants were amplified using inverse PCR. Analysis of the nucleotide sequences of 34 cloned DNA fragments revealed 100% homology with vector sequences outside T-DNA in 10 cases. Nine nucleotide sequences had homology with the repeats in the tobacco genome. The percentage of homology varied from 70 to 90%, with the identified repeats belonging to different types. In most clones no homology was revealed with the GENEBANK sequences. Alignment of the sequences truncated during the integration of the left and the right borders of the T-DNA insertions demonstrated significant clusterization (10 bp region) of truncation sites for the left border. Five sequences had identical truncation sites (+23 T) that showed the perferable use of this nucleotide. The AT content varied from 51 to 72% which was close to the total percentage of AT pairs in the tobacco genome.     

Spontaneous spectinomycin resistance mutations of the chloroplast <Emphasis Type="Italic">rrn16</Emphasis> gene in <Emphasis Type="Italic">Daucus carota</Emphasis> callus lines

Bioballistic transformation of carrot (Daucus carota L.) callus cultures with a plasmid containing the aadA (aminoglycoside 3′-adenyltransferase) gene and subsequent selection of transformants on a selective medium containing spectinomycin (100–500 mg/l) yielded ten callus lines resistant to this antibiotic. PCR analysis did not detect exogenous DNA in the genomes of spectinomycin-resistant calluses. Resistance proved to be due to spontaneous mutations that occurred in two different regions of the chloroplast rrn16 gene, which codes for the 16S rRNA. Six lines displayed the G > T or G > C transverions in position 1012 of the rrn16 gene, and three lines had the A > G transition in position 1138 of the gene. Chloroplast mutations arising during passages of callus cultures in the presence of spectinomycin were described in D. carota for the first time. The cause of spectinomycin resistance was not identified in one line. The mutations observed in the D. carota plastid genome occurred in the region that is involved in the formation of a double-stranded region at the 3′ end of the 16S rRNA and coincided in positions with the nucleotide substitutions found in spectinomycin-resistant plants of tobacco Nicotiana tabacum L. and bladderpod Lesquerella fendleri L.     

Clinical application of VNTR-typing of Mycobacteria tuberculosis strains: monitoring of treatment quality and of laboratory service

An early diagnosis of super-infection and mixed infection of Mycobacteria tuberculosis is highly important for the correction of an assigned treatment and for a positive prognostication. An analysis of loci with varying tandem repeats (VNTR) is a simple in use and reproducible method of M. tuberculosis genotyping. Thirty-seven serial isolates of M. tuberculosis from 12 patients with pulmonary tuberculosis including changing resistance to TB drugs registered in follow-up and treatment underwent VNTR-typing for 6 loci: ETR-A, C, E, V1, V3 and V4. Both super-infection and mixed infection were shown in 33.3% of cases to cause changes in the profile of resistance to TB drugs. In 3 patients, changes in the drug resistance profile were accompanied by a substitution of a colonizing strain for an epidemic clonal variant of the Beijing family with the 445446 genotype. Whereas in one patient, there was a substitution of the Beijing strain for the genotype 222422 strain, which is typical of M. tuberculosis with the S42 spoligotype. One intermediate serial isolate from the above patient had a mixed culture of 2 polyresistant strains of M. tuberculosis (445476 + 222422). In one case, the substitution of the infecting strain for a strain with changed genotypes and profiles of resistance to antibiotics occurred twice within an interval of 5-6 months. The 343543 genotype strain changed for the 452562 genotype strain and then--for the 445466 genotype strain; the final genotype variant belonged to the Beijing family. Serial isolates from 8 patients retained their original genotype (Beijing). In such cases, the changing spectrum of resistance to TB drugs can be associated with the secondary drug resistance acquired by strains in the process of treatment or with errors of laboratory equipment. Finally, the VNTR analysis is a rapid, easy-in-use and effective tool for the systemic typing of M. tuberculosis isolates in clinical practice.