Single Nucleotide Polymorphisms in hsp65 and MACPPE12 Genes of Mycobacterium avium subsp. hominissuis

Russian Journal of Genetics - Mycobacterium avium subsp. hominissuis (MAH) are typical inhabitants of the environment, which are known as opportunistic pathogens of animals and humans. The aim of...     

Integrated computer system for regulating eukaryotic gene expression

The review describes several modules of the GeneExpress integrated computer system concerning the regulation of gene expression in eukaryotes. Approaches to the presentation of experimental data in databases are considered. The employment of GeneExpress in computer analysis and modeling of the organization and function of genetic systems is illustrated with examples. GeneExpress is available at http://wwwmgs.bionet.nsc.ru/mgs/gnw/.     

Computer System “Gene Discovery” to Search for Patterns in Eukaryotic Regulatory Nucleotide Sequences

A method is proposed to automatically search for patterns in the mutual location of context signals in regulatory DNA sequences. The procedure is based on the methods of Data Mining and Knowledge Discovery software, implemented in a computer system Gene Discovery. This system was used to study erythroid-specific promoters and promoters of the endocrine-system genes from TRRD. We detected some trends in occurrence and localization of specific oligonucleotide groups.     

At Baltic crossroads: a molecular snapshot of Mycobacterium tuberculosis population diversity in Kaliningrad, Russia

The Kaliningrad region is the westernmost part of the Russian Federation; it includes an enclave on the Baltic Sea inside the European Union separated from mainland Russia by Lithuania and Poland. The incidence of tuberculosis in Kaliningrad has shown a steady and dramatic increase from 83/100 000 in 2000 to 134/100 000 in 2006; the rate of multidrug-resistant tuberculosis (MDR-tuberculosis) in the Kaliningrad region was reported to be 30.5% among newly diagnosed tuberculosis patients. This study presents a first molecular snapshot of the population diversity of Mycobacterium tuberculosis in this region. A total of 90 drug-resistant and susceptible M. tuberculosis strains from Kaliningrad were subjected to spoligotyping, 12-locus MIRU typing and mutation analysis of the drug resistance genes rpoB and katG . A comparison with international databases showed that the M. tuberculosis population in this region shares a joint pool of strains with the European part of Russia, and also exhibits a certain affinity with those of its northern European neighbours, such as Poland and Germany. Comparison of the genotyping and drug resistance data emphasized that the high prevalence of the MDR Beijing genotype strains is a major cause of the adverse epidemiological situation of MDR-tuberculosis in the Kaliningrad region.     

N-terminal region of Saccharomyces cerevisiae eRF3 is essential for the functioning of the eRF1/eRF3 complex beyond translation termination

Background  

Termination of translation in eukaryotes requires two release factors, eRF1, which recognizes all three nonsense codons and facilitates release of the nascent polypeptide chain, and eRF3 stimulating translation termination in a GTP-depended manner. eRF3 from different organisms possess a highly conservative C region (eRF3C), which is responsible for the function in translation termination, and almost always contain the N-terminal extension, which is inessential and vary both in structure and length. In the yeast Saccharomyces cerevisiae the N-terminal region of eRF3 is responsible for conversion of this protein into the aggregated and functionally inactive prion form.     

Analysis of the nucleotide context of Arabidopsis thaliana mitochondrial mRNA editing sites

We have studied the effects of 1 mM solutions of L-amino acids on the X-ray- and heat-induced generation of hydrogen peroxide and hydroxyl radicals in phosphate buffer (5 mM, pH 7.4). Hydrogen peroxide was estimated by enhanced chemiluminescence in the luminol/p-iodophenol/peroxidase system; hydroxyl radicals were detected with a fluorescent probe coumarin-3-carboxylic acid. We demonstrate that amino acids can be grouped into three categories by their effect on X-ray-induced H₂O₂ production: those that reduce, increase, and have no influence on H₂O₂ yield. Similar amino acid effects were observed upon heating; however, the composition of respective amino acid groups was different. All amino acids lowered the X-ray-induced hydroxyl radical production, and the most effective were Cys > His > Phe = Met = Trp > > Tyr (in descending order). Hydroxyl radical generation induced by heating was inhibited by Met, His, and Phe; enhanced by Ser; and not affected by Tyr and Pro. Thus, amino acids have different effects on the production of reactive oxygen species by X-rays and heating, and some amino acids appear to be effective natural antioxidants.     

Computer System mRNA-FAST (mRNA Function,Activity, STructure)

Computer system mRNA-FAST (mRNA Function, Activity, STructure; http://wwwmgs.bionet.nsc.ru/mgs/dbases/trsig/) is described. The system has been developed to analyze nucleotide sequences of mRNA and to measure their essential properties. The system compiles the data base on translation signals including nucleotide sequences of the regulatory regions with structural and experimental information on their specific activities. It also contains programs to search for local homology between mRNA and translation signals, to search for potential signals basing on analysis of the oligonucleotide dictionaries, and to model secondary RNA structure. Possible applications of the system mRNA-FAST are discussed.     

Mycobacterium tuberculosis Population in Northwestern Russia: An Update from Russian-EU/Latvian Border Region

This study aimed to characterize the population structure of Mycobacterium tuberculosis in Pskov oblast in northwestern Russia, to view it in the geographical context, to compare drug resistance properties across major genetic families. Ninety M. tuberculosis strains from tuberculosis (TB) patients, permanent residents in Pskov oblast were subjected to LAM-specific IS6110-PCR and spoligotyping, followed by comparison with SITVITWEB and MIRU-VNTRplus databases. The Beijing genotype (n = 40) was found the most prevalent followed by LAM (n = 18), T (n = 13), Haarlem (n = 10), Ural (n = 5), and Manu2 (n = 1); the family status remained unknown for 3 isolates. The high rate of Beijing genotype and prevalence of LAM family are similar to those in the other Russian settings. A feature specific for M. tuberculosis population in Pskov is a relatively higher rate of Haarlem and T types. Beijing strains were further typed with 12-MIRU (followed by comparison with proprietary global database) and 3 hypervariable loci QUB-3232, VNTR-3820, VNTR-4120. The 12-MIRU typing differentiated 40 Beijing strains into 14 types (HGI = 0.82) while two largest types were M2 (223325153533) prevalent throughout former USSR and M11 (223325173533) prevalent in Russia and East Asia. The use of 3 hypervariable loci increased a discrimination of the Beijing strains (18 profiles, HGI = 0.89). Both major families Beijing and LAM had similar rate of MDR strains (62.5 and 55.6%, respectively) that was significantly higher than in other strains (21.9%; P = 0.001 and 0.03, respectively). The rpoB531 mutations were more frequently found in Beijing strains while LAM drug resistant strains mainly harbored rpoB516 and inhA −15 mutations. Taken together with a high rate of multidrug resistance among Beijing strains from new TB cases (79.3% versus 44.4% in LAM), these findings suggest the critical impact of the Beijing genotype on the current situation with MDR-TB in the Pskov region in northwestern Russia.     

Analysis and Recognition of Erythroid-Specific Gene Promoters Basing on Degenerate Oligonucleotide Motifs

We developed a method to search for degenerate oligonucleotide motifs specific for certain regions in eukaryotic gene promoters. A procedure of promoter recognition based on these motifs is presented. The methods are integrated within the program package ARGO available for Internet users (http://wwwmgs.bionet.nsc.ru/mgs/programs/argo). This method was applied to study erythroid-specific gene promoters. High efficiency of their recognition is demonstrated.