Ivanov MK, Bragin AG, Prasolova MA
… +2 more, Vedernikov VE, Dymshits GM
Mol Gen Mikrobiol Virusol
· 2009 · PMID 19705776
An uncompetitive exogenous internal amplification control method (EIAC) was developed on the basis of short synthetic DNA segment, whose amplification can be detected in real time by UFA spectroscopy principle. The EIAC...An uncompetitive exogenous internal amplification control method (EIAC) was developed on the basis of short synthetic DNA segment, whose amplification can be detected in real time by UFA spectroscopy principle. The EIAC was shown to be useful as internal control in diagnostic test systems based on DNA or RNA detection by multiplex real-time PCR. It can be applied to assess the quality of extracted DNA or RNA, and also to detect and study the factors causing PCR inhibition and earlier plateau effect.
Comparative analysis of distribution of pseudogenes (YPO1582, YPO1728, YPO1967, and YPO4008) of strains of basic and supplementary species of the plague infection agent and pseudotuberculosis infection agent was performe...Comparative analysis of distribution of pseudogenes (YPO1582, YPO1728, YPO1967, and YPO4008) of strains of basic and supplementary species of the plague infection agent and pseudotuberculosis infection agent was performed. The genome of basic subspecies of plague infection agent species strain contains 3 different variants: intact genes, genes with IS-element inserts, or individual fragments. The pseudogene profile can be used as genetic marker of the Y. Pestis strains of basic subspecies from natural foci of plague. Strains of supplementary subspecies of Y. Pestis and Y. pseudotuberculosis contain these genes as the wild-type gene alleles. In addition to other factors, this fact can be regarded as evidence of ancient origin of plague infection agent supplementary subspecies and their similarity to pseudotuberculosis infection agent.
This review discusses the available data on molecular mechanism of penetration of baculoviruses into cell and structural features of proteins involved in this process. These data are discussed in terms of basic postulate...This review discusses the available data on molecular mechanism of penetration of baculoviruses into cell and structural features of proteins involved in this process. These data are discussed in terms of basic postulates of contemporary model of fusion of biological membranes and other large DNA-containing viruses.
Methods and macros used for processing of samples of NP bacteria retrieved from GenBank are described. The goal of the processing is to transform lists of NP bacteria retrieved from GenBank into Excel table with classifi...Methods and macros used for processing of samples of NP bacteria retrieved from GenBank are described. The goal of the processing is to transform lists of NP bacteria retrieved from GenBank into Excel table with classification of data concerning bacterial genes, species, and genomes of bacteria, as well as accompanying information about NP bacteria. The list is processed using several macros and the result of processing is stored in table. Each line of the table contains information about one record of initial list of NP bacteria. Information about genes, species, and genomes of NP bacteria is contained in columns of table. The capacity of the macros is demonstrated using the list of NP bacteria of the genus Ureaplasma. The developed macros can be applied to lists of NP bacteria and viruses available from GenBank. This information can be used in studies of interspecies and intraspecies genetic polymorphism and genetic targets for various problems of molecular biology (genotyping of viruses and bacteria).
Shedova EN, Lunina NA, Berezina OV
… +3 more, Zverlov VV, Schwarz V, Velikodvorskaia GA
Mol Gen Mikrobiol Virusol
· 2009 · PMID 19517808
The glycosyl hydrolase genes cel5A and xyl3A previously isolated by ourselves within a fragment of DNA from the methagenomic library of cow rumen microflora DNA were sub-cloned and expressed in E. coli. The recombinant p...The glycosyl hydrolase genes cel5A and xyl3A previously isolated by ourselves within a fragment of DNA from the methagenomic library of cow rumen microflora DNA were sub-cloned and expressed in E. coli. The recombinant proteins Cel5A and Xyl3A were purified and characterized. Cellulase Cel5A belongs to the Family 5 glycosyl hydrolases and is a one-module 38.2 kDa enzyme that hydrolyses the 1,4-glycoside bonds of soluble cellulose substrates and amorphous cellulose, showing its maximal activity (31200 u/mg) on lichenan, a soluble substrate with mixed (beta-1,3-1,4) bonds. The end product of the amorphous cellulose hydrolysis is cellobiose. Cel5A is inactive toward the crystal forms of cellulose. Cel5A is an endoglucanase capable of exohydrolysis. The molecular mass of beta-xylosidase Xyl3A belonging to the Family 3 glycosyl hydrolases is 83.7 kDa. The enzyme is active only on xylooligosaccharides, with the maximal activity shown on xylobiose, the end product of the reaction being xylose. No activity on xylane was hitherto observed. Recombinant Cel5A and Xyl3A are stable over a wide range of pH and temperatures, their maximal activity being observed at pH 6.5 and at 55 degrees C.
Logunov DIu, Shchebliakov DV, Zubkova OV
… +5 more, Shmarov MM, Rakovskaia IV, Gintsburg LA, Gudkov AV, Naroditskiĭ BS
Mol Gen Mikrobiol Virusol
· 2009 · PMID 19517807
Various strains of mycoplasmas cause activation of transcriptional factor NF-kB as a result of interaction with different combinations of Toll-like receptors (TLR). It is well known that the MALP-2 protein of M. fermenta...Various strains of mycoplasmas cause activation of transcriptional factor NF-kB as a result of interaction with different combinations of Toll-like receptors (TLR). It is well known that the MALP-2 protein of M. fermentans activates the NF-kB through interaction with the TLR2/6, lipid-associated membrane lipopeptides (LAMPs) of M. penetrans through the TLR1/2, LAMPs of M. pneumoniae through combinations of Toll-like receptors (TLR2/6 and TLR1/2), and superantigene of M. arthritidis through the TLR2 and TLR4-dependent pathways. In this study, we defined specific Toll-like receptors for LAMPs of M. arginini. For carrying out the research we used cell lines 293-null, 293-hTLR2, 293-hTLR1/2, 293-hTLR2/CD14, 293-hTLR2/6, 293-hTLR4/ CD14-MD2 expressing certain combinations of TLR and their coreceptors. It was shown that LAMPs of M. arginini cause activation of NF-kB interacting with TLR2/1, TLR2/6 and TLR2/ CD14, but not with TLR2 alone or TLR4.
The level of representation of extracellular RNA 14 cytokines in blood plasma in a group of apparently healthy subjects was analyzed. The level of representation of the transcripts of these cytokines in extracellular med...The level of representation of extracellular RNA 14 cytokines in blood plasma in a group of apparently healthy subjects was analyzed. The level of representation of the transcripts of these cytokines in extracellular medium is characterized by specific profile different from the profile of expression of the genes in blood cells.
Zinov'eva MV, Vaĭshlia NA, Vinogradova TV
… +2 more, Kopantsev EP, Sverdlov ED
Mol Gen Mikrobiol Virusol
· 2009 · PMID 19517805
Polyfunctional protein PML contributes significantly in vital activity of cell. 11 isoforms of PML differ from one another by C-terminal domain. In spite of intensive research into the protein, the role of the isoforms i...Polyfunctional protein PML contributes significantly in vital activity of cell. 11 isoforms of PML differ from one another by C-terminal domain. In spite of intensive research into the protein, the role of the isoforms in cellular processes remains obscure. In addition, the literature contains various names of the isoforms. The goal of this work was to review the structure of the PML gene, variants of alternative splicing of mPNA, and domain organization of corresponding protein forms. The PML isoforms were classified and functional specificity of each PML isoform was characterized: contribution to gene transcription, contribution to cell apoptosis, cell growth, immune response, formation of nuclear bodies.
Mingaleeva RN, Chernov IP, Kopantsev EP
… +3 more, Stukacheva EA, Skaptsova NV, Sverdlov ED
Mol Gen Mikrobiol Virusol
· 2009 · PMID 19517804
An important problem in the development of gene therapy approaches in oncology is the necessity of using promoters providing specific and high level of gene expression in tumor cells. To solve this problem, we used induc...An important problem in the development of gene therapy approaches in oncology is the necessity of using promoters providing specific and high level of gene expression in tumor cells. To solve this problem, we used inducible system of gene expression regulation (Tat-TAR-system), which is utilized by human immunodeficiency virus (HIV). tat and tk-HSV genes, as well as a fragment of LTR HIV-1, were cloned in the retrovirus vector, tk-HSV gene was under control of the LTR HIV-1 fragment. Potential capacity of these constructions for transactivating tk-HSV gene transcription was studied. Basal expression level of this gene was defined in transient transfection of HEK293 cells. It was shown that specific transactivation of the tk-HSV gene was controlled by the LTR HIV-1 fragment in lung carcinoma cells Calu-1, permanently transfected by the tat gene construction. The effect of transactivation of tk-HSV transcription in Tat-TAR-system was demonstrated in Calu-1 cells in conditions of control of cancer-specific tat gene over BIRC5 promoter.
Inactivation of the rpoS gene encoding for sigma S subunit of RNA polymerase of the rhizospheric strain Pseudomonas chlororaphis 449 results in a sharp decrease (5-8 fold) of phenazine antibiotics synthesis, decline of a...Inactivation of the rpoS gene encoding for sigma S subunit of RNA polymerase of the rhizospheric strain Pseudomonas chlororaphis 449 results in a sharp decrease (5-8 fold) of phenazine antibiotics synthesis, decline of acid and alkaline phosphatases (pH 2.5 and 8.8, respectively) activities and antagonistic activity of this strain against phytopathogenic fungus Rhizoctonia solani. A mutation in the rpoS gene causes a small decrease of lipase and proteolytic activities in supernatants of Pseudomonas chlororaphis 449 cultures, as well as does not substantially affect the synthesis of three types of N-acyl-homoserinelactones that are signal molecules of Quorum Sensing regulation, and the capacity of bacteria to motility on the surface of the medium (swarming).
Butovskaia PR, Pavlova GV, Martirosian IA
… +2 more, Sukhikh GT, Ryskov AP
Mol Gen Mikrobiol Virusol
· 2009 · PMID 19283907
99 DNA samples of organs and tissues of 18 mice were examined using the method of PCR amplification with random primers. Among 27 oligonucleotide primers tested, 4 producing stable, well-reproducible profiles of amplific...99 DNA samples of organs and tissues of 18 mice were examined using the method of PCR amplification with random primers. Among 27 oligonucleotide primers tested, 4 producing stable, well-reproducible profiles of amplification products were chosen for further analysis. Using 2 of these primers we detected differences in RAPD-profiles in some tissues in several individuals. These differences were associated with the modification of mobility, or with the fragment gain/loss in the RAPD profile, and could be caused either by genomic rearrangements, or mutations involving the regions of the DNA-primer pairing. Different epigenetic factors may also contribute to this process.
The influenza virus A/gull/Moscow/3100/2006 (H6N2) was isolated from gull feces within the precincts of Moscow in autumn 2006. The nucleotide sequence of the complete genome (GenBank, EU152234-EU152241) and genotype (K,...The influenza virus A/gull/Moscow/3100/2006 (H6N2) was isolated from gull feces within the precincts of Moscow in autumn 2006. The nucleotide sequence of the complete genome (GenBank, EU152234-EU152241) and genotype (K, G, D, 6B, F, 2D, F, 1E) for this virus were determined. Phylogenetic analysis suggests that the H6N2 virus derived by numerous reassortment between viruses that have been circulating among different birds in Europe since 1999 and in South-East Asia (NA gene) for last years. Migratory birds probably introduced some of these viruses from South-East Asia earlier. The strain A/gull/Moscow/3100/2006 is nonpathogenic for chicken embryos and mice and induces specific antibody production in mice. Similar to all avian influenza viruses A/gull/Moscow/3100/ 2006 it binds to Neu5Ac(2-3Gal receptors, but reveals higher affinity for fucosylated sialosugars (SLex) in contrast to the duck viruses, as was shown in receptor specificity assay and clarified due to modeling the accommodation of SLex into receptor binding site of duck and gull influenza virus hemagglutinin.
Tutykhina IL, Bezborodova OA, Verkhovskaia LV
… +6 more, Shmarov MM, Logunov DIu, Nemtsova ER, Narodnotskiĭ BS, Iakubovskaia RI, Gintsburg AL
Mol Gen Mikrobiol Virusol
· 2009 · PMID 19280990
The Ad5-Lf pseudoadenovirus nanostructure (RPAN) was produced using homologous recombination in E. coli cells. This construction provided efficient expression of the Lf gene in permissive cell culture with high productio...The Ad5-Lf pseudoadenovirus nanostructure (RPAN) was produced using homologous recombination in E. coli cells. This construction provided efficient expression of the Lf gene in permissive cell culture with high production rate of recombinant protein similar to native human Lf in some physical, chemical, and biological properties. Single intravenous injection of the construction into mice and rats was effective for prolonged production and circulation of recombinant human Lf in blood of experimental animals without toxic effects. The produced construction is promising for providing prolonged production of recombinant human Lf in the human body.
Development of new technology allows different antigens of a necessary degree of cleanliness to be obtained. This development is a major problem of modern medical biotechnology. A promising approach to this problem inclu...Development of new technology allows different antigens of a necessary degree of cleanliness to be obtained. This development is a major problem of modern medical biotechnology. A promising approach to this problem includes use of the affinity domains (tags) incorporated in structure of a recombinant antigen and capable to bind to corresponding sorbents. The method of preparation of ready-for-use injections containing complexes formed by soluble antigens on insoluble cellulose immunosorbent (not chemical conjugates) in one stage is based on the fusion protein technology. This approach includes preparation of two-component recombinant proteins containing an antigen of interest and the cellulose-binding domain (CBD), which spontaneously binds to cellulose containing sorbents with high binding constant. Research into the immunogenic properties of the CBD in the complex with cellulose and in the preparation of recombinant CBD in a rat model was performed. The titers of specific antibodies in rat serum induced by recombinant CBD and CBD in the complex with cellulose was evaluated. The CBD in the complex with cellulose was more immunogenic in comparison with CBD alone. The spectrum and levels of cytokines in collected rat serum induced by developed preparations was also measured using the microsphere-based Luminex Flowmetrix system (BioPlex). It was found that the amorphous cellulose was not an immunotolerant sorbent, because it induced the expression of the proinfammatory cytokines in vivo.
The purpose of this work was to find the character of the dependence between the GC-content of the gene and the level of preterminal codons usage inside it. 84 codon usage tables were used as the material (each of them c...The purpose of this work was to find the character of the dependence between the GC-content of the gene and the level of preterminal codons usage inside it. 84 codon usage tables were used as the material (each of them contains average frequencies of codon usage for all encoding districts belonging to one bacterial specie). We also used nucleotide sequences encoding for active centers of bacterial adenylate cyclases. Inverse correlation between the GC-content (G+C) and the total level of preterminal codons usage (PCU) was observed (R = - 0.97). For nucleotide sequences encoding for active centers from adenylate cyclases class I the coefficient of correlation between G+C and PCU is -0.75. For sequences encoding for active centers from adenylate cyclases class III the coefficient of correlation between G+C and PCU is -0.91. Preterminal codons are mostly GC-deficient relative to their synonymous nonpreterminal codons and in absolute terms. The cause of the inverse correlation between G+C and the level of preterminal codons usage is an increase in their frequencies of usage due to mutational AT-pressure and the decrease of their frequencies of usage due to mutational GC-pressure. The evidence of the frequent fixation of nonsense mutations in GC-deficient bacteria was found. The practical conclusion is the following: the higher is the GC-content of gene or genome, the lower is the probability of nonsense mutation inside it.
Shedova EN, Berezina OV, Lunina NA
… +3 more, Zverlov VV, Schwartz WH, Velikodvorskaia GA
Mol Gen Mikrobiol Virusol
· 2009 · PMID 19280987
The problem of search for and characterization of enzymes synthesized by non-cultivated microorganisms is presently being settled by creating metagenomic libraries. A 6000-clone library with the average size of its inser...The problem of search for and characterization of enzymes synthesized by non-cultivated microorganisms is presently being settled by creating metagenomic libraries. A 6000-clone library with the average size of its inserts amounting to 15 bp has been constructed on the basis of total DNA isolated from cow rumen microorganisms. As the result of the screening of the library on plates with different substrates, a clone was selected that efficiently hydrolyzed lichenan and carboxymethylcellulose. The clone contained the recombinant plasmid pBlue-13 bearing a 12071 bp.-long metagenomic fragment carrying ten open reading frames, two of them being identified as glycosyl hydrolase genes. No homology of the metagenomic DNA with any known microorganism genomes was revealed. The amino acid sequence, deduced on the basis of frame 4 and denoted by Xyl3A, bears resemblance with beta-xylosidases of glycosyl hydrolase Family 3. Frame 6 encodes polypeptide Cel5A homologous to cellulases of glycosyl hydrolase Family 5. The amino acid sequences deduced on the basis of seven out of ten open reading frames were homologous to proteins of microorganisms belonging to the Bacteroides sp. family, the bacteria inhabiting mammalian intestines.
More than 99% of bacteria exist in natural ecosystems as specifically organized biofilms adhering to solid surfaces. Biofilms have a typical architecture and are enclosed in exopolymeric matrix. Bacteria living in biofil...More than 99% of bacteria exist in natural ecosystems as specifically organized biofilms adhering to solid surfaces. Biofilms have a typical architecture and are enclosed in exopolymeric matrix. Bacteria living in biofilms are extremely resistant to antibacterial factors. In this work we studied the role of some global regulators of gene expression on biofilm formation by Escherichia coli K12. The Histone-like proteins H-NS and StpA were shown to play an essential role in the regulation of biofilm formation. Mutant strains deficient in HNS or StpA had lower levels of biofilm formation than the wild-type isogenic strain. A double mutant deficient in the two proteins was virtually incapable of forming the biofilms. The mutations in the rpoN gene encoding for the sigma N subunit of RNA-polymerase and in lon gene encoding for Lon-proteinase induced a 40-60% increase in the biofilm formation.
The aim of this work was to evaluate the prevalence mutations in the rpoB, katG, inhA, ahpC gene of rifampicin and isoniazid resistant M. tuberculosis (Tb) isolates from Kyrgyz Republic using OA Biochip MDR. In the rifam...The aim of this work was to evaluate the prevalence mutations in the rpoB, katG, inhA, ahpC gene of rifampicin and isoniazid resistant M. tuberculosis (Tb) isolates from Kyrgyz Republic using OA Biochip MDR. In the rifampicin-resistant strains, the mutations were identified in the codons 531, 526, 516, 511, 513, 512, 533, and 522. The most prevalent point mutations were Ser531RLeu at the codon 531 (59.7%). Resistance to INH was associated with mutations found in the katG gene (94.5%), inhA gene (3.5%), and ahpC gene (1.0%). The most prevalent mutations were SerRThr at the codon 315 (93.0%). The rifampicin and isoniasid resistance of the M. Tb strains isolated in Kyrgyzstan is associated mostly with Ser531RLeu mutation of the rpoB gene, Ser315RThr mutation of the katG gene, and InhT15 mutation.
Malysheva DN, Vergun AA, Martirosian IA
… +2 more, Tokarskaia ON, Ryskov AP
Mol Gen Mikrobiol Virusol
· 2008 · PMID 19172877
Using a pair of primers selected for the loci deltau 215, deltau 281, and deltau 323 of Darevskia unisexualis monolocus PCR analysis of orthologous loci was carried out in populations of the related parthenogenetic speci...Using a pair of primers selected for the loci deltau 215, deltau 281, and deltau 323 of Darevskia unisexualis monolocus PCR analysis of orthologous loci was carried out in populations of the related parthenogenetic species D. armeniaca and in populations of bisexual parental species D. valentini and D. mixta. It was shown that the studied loci were polymorphic and represented in populations of D. armeniaca by several allelic variants. We cloned and sequenced PCR amplification products of the allelic variants of deltau 215, deltau 281, and deltau 323 loci. It was found that allelic differences of microsatellite loci were caused by variation in a number of tandem repeats in the microsatellite clusters and point mutations in the flanking regions. Interspecies comparison of the orthologous locus deltau 215 between parthenogenetic species D. armeniaca and parental species showed that two allelic variants of deltau 215 in D. armeniaca were inherited from the parental bisexual species D. mixta and D. valentini. The third allelic variant was not found in parental species and appeared because of mutation processes in genome of parthenospecies. For the first time, the information about the molecular nature of allelic polymorphism of these microsatellite loci of parthenogenetic species D. armeniaca was received in this study.
Tutykhina IL, Shmarov MM, Logunov DIu
… +4 more, Grabko VI, Sevast'ianova GA, Naroditskiĭ BS, Gintsburg AL
Mol Gen Mikrobiol Virusol
· 2008 · PMID 19172876
Aviadenovirus CELO is a promising vector for gene delivery to eukaryotic cells, including mammalian cells. In the present state of affairs, it gives a chance to apply recombinant adenoviruses CELO against animal pathogen...Aviadenovirus CELO is a promising vector for gene delivery to eukaryotic cells, including mammalian cells. In the present state of affairs, it gives a chance to apply recombinant adenoviruses CELO against animal pathogens. High expression level of transgene consisting of virus vector is necessary to reach protective humoral and T-cell immune answer. One of the approaches to enhance the expression level of transgene consisting of viral vectors is inclusion of addition 5'- and 3'- untranslated regulatory elements (PARS, IRES, WPRE) to the expression cassette. In this work, 5'-untranslated regulatory elements of major late transcription unit of CELO genome (a bipartite leader and gene hexon leader) were used for construction of the expression cassette consisting of the recombinant adenovirus CELO to provide high expression level of reporter gene of secreted alkaline phosphatase in nonpermissive cell system. It was shown in our experiments that the obtained recombinant adenovirus CELO was characterized by enhanced (2.4-3.5 times) expression level of reporter gene in transduced mammalian cells in vitro and in vivo.