Snapper: high-sensitive detection of methylation motifs based on Oxford Nanopore reads

MOTIVATION

The Oxford Nanopore technology has a great potential for the analysis of methylated motifs in genomes, including whole-genome methylome profiling. However, we found that there are no methylation motifs detection algorithms, which would be sensitive enough and return deterministic results. Thus, the MEME suit does not extract all Helicobacter pylori methylation sites de novo even using the iterative approach implemented in the most up-to-date methylation analysis tool Nanodisco.

RESULTS

We present Snapper, a new highly sensitive approach, to extract methylation motif sequences based on a greedy motif selection algorithm. Snapper does not require manual control during the enrichment process and has enrichment sensitivity higher than MEME coupled with Tombo or Nanodisco instruments that was demonstrated on H.pylori strain J99 studied earlier by the PacBio technology and on four external datasets representing different bacterial species. We used Snapper to characterize the total methylome of a new H.pylori strain A45. At least four methylation sites that have not been described for H.pylori earlier were revealed. We experimentally confirmed the presence of a new CCAG-specific methyltransferase and inferred a gene encoding a new CCAAK-specific methyltransferase.

AVAILABILITY AND IMPLEMENTATION

Snapper is implemented using Python and is freely available as a pip package named "snapper-ont." Also, Snapper and the demo dataset are available in Zenodo (10.5281/zenodo.10117651).

Inhibition of Chlamydial Infection by CRISPR/Cas9-SAM Mediated Enhancement of Human Peptidoglycan Recognition Proteins Gene Expression in HeLa Cells

The global problem of emerging resistance of microorganisms to antibiotics makes the search for new natural substances with antibacterial properties relevant. Such substances include peptidoglycan recognition proteins (PGLYRP), which are the components of the innate immunity of many organisms, including humans. These proteins have a unique mechanism of action that allows them to evade the resistance of bacteria to them, as well as to be active against both Gram-positive and Gram-negative bacteria. However, the use of antimicrobial recombinant proteins is not always advisable due to the complexity of local delivery of the proteins and their stability; in this regard it seems appropriate to activate the components of the innate immunity. The aim of this study was to increase the expression level of native peptidoglycan recognition protein genes in HeLa cells using genome-editing technology with synergistic activation mediators (CRISPR/Cas9-SAM) and evaluate antichlamydial effect of PGLYRP. We demonstrated activation of the chlamydial two-component gene system (ctcB-ctcC), which played a key role in the mechanism of action of the peptidoglycan recognition proteins. We generated the HeLa cell line transduced with lentiviruses encoding CRISPR/Cas9-SAM activation system with increased PGLYRP gene expression. It was shown that activation of the own peptidoglycan recognition proteins gene expression in the cell line caused inhibition of the chlamydial infection development. The proposed approach makes it possible to use the capabilities of innate immunity to combat infectious diseases caused by Gram-positive and Gram-negative bacteria.

Transcription-facilitating histone chaperons interact with genomic and synthetic G4 structures

Affinity for G-quadruplex (G4) structures may be a common feature of transcription-facilitating histone chaperons (HCs). This assumption is based on previous unmatched studies of HCs FACT, nucleolin (NCL), BRD3, and ATRX. We verified this assumption and considered its implications for the therapeutic applications of synthetic (exogenous) G4s and the biological significance of genomic G4s. First, we questioned whether exogenous G4s that recognize cell-surface NCL and could trap other HCs in the nucleus are usable as anticancer agents. We performed in vitro binding assays and selected leading multi-targeted G4s. They exhibited minor effects on cell viability. The presumed NCL-regulated intracellular transport of G4s was inefficient or insufficient for tumor-specific G4 delivery. Next, to clarify whether G4s in the human genome could recruit HCs, we compared available HC ChIP-seq data with G4-seq/G4-ChIP-seq data. Several G4s, including the well-known c-Myc quadruplex structure, were found to be colocalized with HC occupancy sites in cancer cell lines. As evidenced by our molecular modeling data, c-Myc G4 might interfere with the HC function of BRD3 but is unlikely to prevent the BRD3-driven assembly of the chromatin remodeling complex. The c-Myc case illustrates the intricate role of genomic G4s in chromatin remodeling, nucleosome remodeling, and transcription.

Two novel transcriptional reporter systems for monitoring Helicobacter pylori stress responses

Helicobacter pylori, a human pathogen linked to many stomach diseases, is well adapted to colonize aggressive gastric environments, and its virulence factors contribute this adaptation. Here, we report the construction of two novel H. pylori vectors, pSv2 and pSv4, carrying a reporter gene fused to the promoters of virulence factor genes for monitoring the response of single H. pylori cells to various stresses. H. pylori cryptic plasmids were modified by the introduction of the Escherichia coli origin of replication, chloramphenicol resistance cassette, and promoterless gfp gene to produce E. coli/H. pylori shuttle vectors. The promoter regions of vacA and ureA genes encoding well-characterized H. pylori virulence factors were fused to the promoterless gfp gene. Recording the GFP fluorescence signal from the genetically modified H. pylori cells immobilized in specifically designed microfluidic devices revealed the response of transcriptional reporter systems to osmotic stress, acidic stress, elevated Ni²⁺ concentration or iron chelation. Our observations validate the utility of the pSv2 and pSv4 vectors to monitor the regulation of virulence factor genes in diverse strains and clinical isolates of H. pylori.

Medicinal leech antimicrobial peptides lacking toxicity represent a promising alternative strategy to combat antibiotic-resistant pathogens

The rise of antibiotic resistance has necessitated the development of alternative strategies for the treatment of infectious diseases. Antimicrobial peptides (AMPs), components of the innate immune response in various organisms, are promising next-generation drugs against bacterial infections. The ability of the medicinal leech Hirudo medicinalis to store blood for months with little change has attracted interest regarding the identification of novel AMPs in this organism. In this study, we employed computational algorithms to the medicinal leech genome assembly to identify amino acid sequences encoding potential AMPs. Then, we synthesized twelve candidate AMPs identified by the algorithms, determined their secondary structures, measured minimal inhibitory concentrations against three bacterial species (Escherichia coli, Bacillus subtilis, and Chlamydia thrachomatis), and assayed cytotoxic and haemolytic activities. Eight of twelve candidate AMPs possessed antimicrobial activity, and only two of them, 3967 (FRIMRILRVLKL) and 536-1 (RWRLVCFLCRRKKV), exhibited inhibition of growth of all tested bacterial species at a minimal inhibitory concentration of 10 μmol. Thus, we evidence the utility of the developed computational algorithms for the identification of AMPs with low toxicity and haemolytic activity in the medicinal leech genome assembly.

[Recombinant small heat shock protein from Acholeplasma laidlawii increases the Escherichia coli viability in thermal stress by selective protein rescue]

In both prokaryotes and eukaryotes, the survival at temperatures considerably exceeding the optimum is supported by intense synthesis of the so-called heat shock proteins (HSPs), which act to overcome the adverse effects of heat stress. Among mycoplasmas (class Mollicutes), which have significantly reduced genomes, only some members of the Acholeplasmataceae family possess small HSPs of the α-crystallin type. Overproduction of a recombinant HSP IbpA (Hsp20) from the free-living mycoplasma Acholeplasma laidlawii was shown to increase the resistance of Escherichia coli to short-term heat shock. It has been long assumed that IbpA prevents protein aggregation and precipitation thereby increasing viability of E. coli cells. Several potential target proteins interacting with IbpA under heat stress were identified, including biosynthetic enzymes, enzymes of energy metabolism, and components of the protein synthesis machinery. Statistical analysis of physicochemical properties indicated that IbpA interaction partners significantly differ in molecular weight, charge, and isoelectric point from other members of the E. coli proteome. Upon shortterm exposure to increased temperature, IbpA was found to preferentially interact with high-molecular weight proteins having a pI of about 5.1, significantly lower than the typical values of E. coli proteins.

Role of isopeptidolysis in the process of thrombolysis

INTRODUCTION

Known thrombolytic agents either break peptide bonds in the fibrin molecule or act as plasminogen activators, which also results in peptide bond cleavage. In thrombi, fibrin molecules are known to be cross-linked by isopeptide bonds, the formation of which is mediated by factor XIIIa. In this work, we studied the dissolution of thrombi via isopeptide bond cleavage using a recombinant destabilase. Destabilase is an enzyme secreted from the medicinal leech salivary gland. This enzyme exhibits muramidase (lysozyme) activity, in addition to endo-ε-(γ-Glu)-Lys-isopeptidase activity, which is responsible for isopeptide bond cleavage.

METHODS

Venous (jugular vein) and arterial (carotid artery) thrombosis was induced in rats. Rats were intravenously injected with both recombinant destabilase produced in Escherichia coli and a commercial streptokinase preparation. After 24 h, the weight and degree of cross-linking in the thrombi were analysed. Amidolytic activity in rat blood serum was measured in order to evaluate destabilase levels in the blood.

RESULTS

Destabilase was definitively shown to cause a 47.6% and 74.6% decrease in the weight of venous and arterial thrombi, respectively. The enzyme proved to be more efficient at dissolving thrombi compared to streptokinase. The combined administration of destabilase and streptokinase has a greater effect than the injection of individual enzymes. Destabilase reduces fibrin stabilization in thrombi.

CONCLUSION

Cumulatively, we find that the medicinal leech destabilase is a more efficient thrombolytic agent for dissolving thrombi, which could help increase the overall effectiveness of conventional thrombolytic drugs.

[Conformational polymorphysm of G-rich fragments of DNA ALU-repeats. I. Potential noncanonical structures]

In this paper, we report results of systematic studies of conformational polymorphism of G-rich DNA fragments from Alu repeats. Alu retrotransposones are primate-specific short interspersed elements. Using the Alu sequence from the prooncogen bcl2 intron and the consensus AluSx sequence as representative examples, we determined characteristic Alu sites that are capable of adopting G-quadruplex (GQ) conformations (i.e., potential quadruplex sites - PQSAlu), and demonstrated by bioinformatics methods that those sites are Alu-specific in the human genome. Genomic frequencies of PQSAlu were assessed (~1/10000 b.p.). The sites were found to be characteristic of young (active) Alu families (Alu-Y). A recombinant DNA sequence bearing the Alu element from the human bcl2 gene (304 b.p.) and its PQS-mutant (Alu-PQS) were constructed. The formation of noncanonical structures in Alubcl2 dsDNA and the absence of such structures in the case of Alu-PQS were shown using DMS-footprinting and AFM microscopy. Expression vectors bearing wild-type and mutant Alu insertions in the promoter regions were obtained, and the effects of these insertions on the expression of the reporter gene in НЕК293 and HeLa cell lines were compared. Our findings on the spatial organization of Alu repeats may provide insight into the mechanisms of genomic rearrangements which underlie many oncological and neurodegenerative diseases.

Destabilase-lysozyme-2 - original recombinant thrombolytic preparation of medicinal leech inhibits horse platelets aggregation

The purpose. Identifying the capacity of the medicinal leech novel original recombinant thrombolytic preparation Destabilase-Lysozyme-2 to inhibit the blood platelet aggregation.

METHODS

Gene of destabilase-lysozyme. ds2 (mlDL-Ds2 ), was cloned in E.coli cells. Recombinant protein was isolated in denaturing conditions using metal-chelate chromatography followed by denaturation of the polypeptide by rapid dilution in exact accordance with the procedure described by Kurdyumov A.S. et al. ( 2016, Russian Journal of Bioorganic Chemistry, v.42, s. 42-52). Blood was collected from the jugular vein of 18 horses. The functional status of platelets in the presence of different destabilase-lysozyme concentrations were evaluated for their aggregation in Platelet Rich Plasma ( PRP) and in Washed Platelet suspension (WP) using aggregometers Chrono-Log-700 and Сhrono-Log-560, USA560, США. As used aggregation inducers of ADP, collagen type III and human thrombin.

RESULTS

First demonstrated the ability of newly synthesized (Kurdyumov A.S. et al. 2016, Russian Journal of Bioorganic Chemistry, v42, s. 42-52) thrombolytic recombinant enzyme destabilase-lyzosyme to inhibit more than 40% of ADP-stimulated PRP aggregation and ADP- stimulated aggregation of horse blood washed platelets.

CONCLUSION

The ability of destabilase-lyzosyme -2 to inhibit platelets aggregation extends biological properties of recombinant thrombolytic enzyme, pre-clinical trials which resulted in the end of 2015.

[The modern approaches to organization of delivery system in Nizhniy Novgorod]

The article presents data concerning reproductive demographic processes in Nizhniy Novgorod. The numbers of women of fertility age and indicator of maternity mortality were selected as objects for analysis. The structure of causes of maternal mortality is presented and on its basis the corresponding classification was developed. To prevent maternal losses the development of specialized centers was proposed and implementation of high-tech blood-preserving techniques as well. The routing and accompaniment of women being in critical ("closer to death") conditions are considered.

Purification and characterisation of recombinant Bacteroides fragilis toxin-2

Fragilysin (BFT) is metalloprotease that is secreted by enterotoxigenic Bacteroides fragilis. Studying the mechanism of BFT interaction with intestinal epithelial cells requires a pure protein sample. In this study, we cloned DNA-fragments coding for the catalytic domain of fragilysin-2 and profragilysin-2 into an E. coli expression vector. Purification methods for the recombinant fragilysin-2 catalytic domain and profragilysin-2 were developed. In addition, we obtained mature active fragilysin-2 from recombinant proprotein by limited tryptic digestion. We tested the biological activity of the recombinant protein samples and revealed that E-cadherin was cleaved when HT-29 cells were treated with mature fragilysin-2 but not with profragilysin-2. Azocoll, azocasein and gelatin were not proteolytically cleaved by mature fragilysin-2. Proteins released in culture medium after HT-29 cells treatment with mature active BFT-2 were identified.

[Laser microdissection for biology and medicine]

For routine extraction of DNA, RNA, proteins and metabolites, small tissue pieces are placed into lysing solution. These tissue pieces in general contain different cell types. For this reason, lysate contains components of different cell types, which complicates the interpretation of molecular analysis results. The laser microdissection allows overcoming this trouble. The laser microdissection is a method to procure tissue samples contained defined cell subpopulations, individual cells and even subsellular components under direct microscopic visualization. Collected samples can be undergone to different downstream molecular assays: DNA analysis, RNA transcript profiling, cDNA library generation and gene expression analysis, proteomic analysis and metabolite profiling. The laser microdissection has wide applications in oncology (research and routine), cellular and molecular biology, biochemistry and forensics. This paper reviews the principles of different laser microdissection instruments, examples of laser microdissection application and problems of sample preparation for laser microdissection.

[The characteristics of functioning of hospice in the conditions of megapolis]

The article deals with the analysis of volume and structure of specific care exemplified by the field service of hospice of Nijny Novgorod and compared with specialized hospital department. The priority nosology and patients age categories are established as included into the care services of hospice field team.

Destabilase-lysozyme of medicinal leech. Multifunctionality of recombinant protein

Preparation and purification of a recombinant protein are described along with characteristics of its specific (for ε-(γ-Glu)-Lys and D-dimer substrates) and nonspecific (for L-γ-Glu-pNA) isopeptidase activities; the absence of peptidase function for α-(α-Glu)-Lys substrate is noted. It is shown that the protein exhibits muramidase (cell walls of Micrococcus lysodeikticus) and specific glycosidase activities. The latter was determined towards the fluorogenic substrate 4-methylumbelliferyl-tetra-N-acetyl-β-chitotetraoxide. Antimicrobial activity of recombinant destabilase-lysozyme protein (recDest-Lys) and its 11-membered amphipathic peptide was revealed towards cells of the strict anaerobic Archaean Methanosarcina barkeri, whose cell walls contain no murein. Possible mechanisms of the effect of recDest-Lys on these cells are discussed.

[Oligomeric forms, functions and cellular localization of alpha-crystallin type protein from Acholeplasma laidlawii]

Alpha-Crystallin type heat shock protein (alpha-HSP) IbpA from Acholeplasma laidlawii was expressed in Escherichia coil and isolated from cell extract on Ni-sepharose column. Recombinant IbpA, like other alpha-HSPs, spontaneously formed oligomeres in vitro. High resolution electron microscopy revealed regular structures with 15 nm in diameter. Evaluation of molecular mass of IbpA oligomers was performed by gel filtration. Most of oligomers consist of 24 subunits. Recombinant IbpA prevents heat denaturation of soluble proteins in cell extract of E. coli and displays a mild positive effect on thermotolerance of E. coli cells during severe heat shock. We investigated a localization of IbpA in A. laidlawii cell by immunocytochemistry. We suppose that IbpA may protect various intracellular structures from damage during heat shock.

The Genes of Antimicrobial Peptides for the Therapy of Intracellular Infections

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[Localization of the division protein FtsZ in mycoplasma cells Mycoplasma hominis]

Localization of the protein FtsZ in Mycoplasma hominis cells was determined. Ultra thin sections were treated by rabbit polyclonal antibodies against FtsZ M. hominis: a conjugate of protein A with colloidal gold particles was used instead of secondary antibodies. Considerable polymorphism of cells was seen on electron microscopy pictures of M. hominis cells, which is typical for mycoplasmas. Among a wide variety of cell shapes we distinguished dumbbell-shaped dividing cells, and the cells connected with each other with the aid of thin membrane tubules (former constrictions). Dominants distribution of the label in the constriction area of dividing M. hominis cells and in the area of the thin membrane tubules was observed. We revealed the cross septum in the mycoplasma cells for the first time, as well as the gold labeling of this structure. Furthermore, in some rounded and oval cells colloidal gold particles labeled the whole plasma membrane in ring-shaped manner. Probably, the label in these cases marks a submembrane contractile ring (Z-ring). The facts mentioned above confirm that FtsZ of M. hominis plays an active role in the mycoplasma cytokinesis. In a series of cases spiral-like distribution of gold particles was observed. Probably, FtsZ protofilaments in M. hominis cells can form spiral structures similar to Z-spirals of Bacillus subtilis and Escherichia coli. Its presence in mycoplasma cells may be considered as an important argument in favour of model of Z-ring assembling through reorganization of Z-spirals. FtsZ also may participate in maintenance of mycoplasma cell shape (membrane localization).

Recombinant plasmid constructs expressing gene for antimicrobial peptide melittin for the therapy of Mycoplasma and chlamydia infections

In view of growing number of pathogenic microbial strain resistant to routine antibiotics, antimicrobial peptides become promising agents for the therapy of infectious diseases. We studied in vivo effects of melittin, an antimicrobial peptide expressed in a recombinant plasmid vector, on infection with urogenital pathogens Chlamydia trachomatis, Mycoplasma hominis, and Mycoplasma gallisepticum. We obtained recombinant plasmid constructs, where melittin gene is under the control of tetracycline-dependent human cytomegalovirus promoter. Inhibition of experimental C. trachomatis, M. hominis, and M. gallisepticum infection after administration of recombinant plasmid vectors expressing melittin gene to BALB/c mice was demonstrated.

[The heat shock protein of alpha-crystallin type from mycoplasma (Acholeplasma laidlawii)]

A considerable increase in several heat shock proteins (HSPs) amount in Acholeplasma laidlawii cells has been revealed after temperature rising of liquid culture; and the quantity of small HSP, named p17, was increased in a hundred of times. The p17 protein was isolated and identified as HSP of alpha-crystallin type (alpha-HSP). It became possible as a result of sequencing of 15 amino acids from N-terminal of the p17 polypeptide chain, followed by revealing of a corresponding open reading frame (ORF) in a completely sequenced genome of A. laidlawii PG 8A. Computer-based search for homologous ORFs in all 17 genomes of Mycoplasmataceae family (the mycoplasmas themselves) that had been completely sequenced to date, gives negative result. But among the representatives of Mollicutes (mycoplasma) class, the genes coding alpha-HSPs were found in two Phytoplasma species (Phytoplasmataceae family) and the acholeplasma examined (Acholeplasmataceae family). It supposed that presence or absence of alpha-HSPs in microorganisms might be connected with the fact that representatives of Acholeplasmataceae and Phytoplasmataceae families inhabit principally in plant tissues in contrast to majority of Mycoplasmataceae family, that inhabit animal and human tissues, i. e. use ecological niches with relatively constant temperature.

[Inclusion membrane proteins of Chlamydiaceae]

Inclusion membrane proteins belong to the family of unique chlamydial proteins. Members of this family attract attention of scientists because of the following characteristics: Inc-proteins are localized in the inclusion membrane, these proteins have been found in all chlamydial species, expression of the most part of its genes begins during first hours from the infection of cell culture. Biological functions of Inc-proteins remain unknown, but these proteins are suggested to play a key role in process of the development the chlamydial infection.

Proteomic analysis methods for characterization of proteins from the salivary gland secretions of the medicinal leech during different seasons

Salivary gland secretion (SGS) of the medicinal leech Hirudo medicinalis in summer and winter was studied by proteomic analysis methods, and season-associated difference was found in the distribution of fractionated proteins with the same pattern of their positions. Differences were detected for proteins with molecular weights from 15 to 250 kD fractionated by two-dimensional SDS-PAGE and for 2-10- and 10-60-kD proteins analyzed by SELDI-MS. Thirty-two and 20 proteins were detected by MALDI-TOF-MS in the high-molecular-weight fraction of the summer and winter SGS, respectively, isolated from the corresponding two-dimensional electrophoregrams, and this was less than 20% of the total SGS protein. The N-terminal amino acid sequences were determined for 12 proteins. The peptide maps and N-terminal amino acid sequences of the proteins studied were identified, and no known proteins were revealed. These findings suggest a high content of newly revealed proteins in SGS of medicinal leech, and this correlates with multiple positive clinical effects of hirudotherapy realized through SGS, but the mechanisms of these effects remain unclear.

Expression of Chlamydia trachomatis inclusion membrane protein genes IncB and IncC in Escherichia coli

In this study, we have cloned the Chlamydia trachomatis genes incB and incC into the expression plasmid vectors from pET series for the subsequent isolation of recombinant proteins. As a result, we have obtained the first full-length recombinant C. trachomatis proteins IncB and IncC, which can be used for following antibody production and for study of their protein-protein interaction.

Identification of serovar-specific single-nucleotide polymorphisms of C. Trachomatis omp1 gene

Complete sequences of omp1 gene encoding chlamydial main outer membrane protein were analyzed in 76 clinical strains of C. trachomatis. Thirty-four serovar-specific single-nucleotide polymorphisms were identified, 20 of them meet two criteria: unique position of the nucleotide and unique nucleotide substitution. Evaluation of serovar-specific single-nucleotide polymorphisms of omp1 gene can appreciably simplify and accelerate genetic diagnosis of C. trachomatis serovars.

Effect of induced expression of an antimicrobial peptide melittin on Chlamydia trachomatis and Mycoplasma hominis infections in vivo

A plasmid construct was designed in which the gene of antimicrobial peptide melittin is controlled by the tetracycline-responsive promoter of human cytomegalovirus, aided by a constitutively expressed trans-activator protein gene. Its vaginal administration and induction of melittin gene transcription with doxycycline markedly suppressed subsequent genital tract infection of mice by Mycoplasma hominis and Chlamydia trachomatis. At least half of the melittin-protected animals proved free of either pathogen within 3-4 weeks. Recombinant plasmids expressing genes of antimicrobial peptides hold much promise as agents for prevention and control of urogenital latent infections.

Location of C. trachomatis Inc Proteins during Expression of Their Genes in HeLa Cell Culture

Plasma constructions including genes encoding C. trachomatis inclusion membrane protein as composite proteins with reporter green fluorescent protein were obtained. After transfection of HeLa cell culture with the resultant plasmid constructions the location of inclusion membrane proteins in transfected cell was for the first time detected by confocal microscopy.

Experimental Mycoplasma hominis infection of the genital tract in BALB/c mice

We studied the ability of laboratory and clinical strains of Mycoplasma hominis to colonize the genital tract mucosa in BALB/c mice. Colonization with mycoplasma occurred only in mice receiving estrogen. Mycoplasma hominis strains obtained after 3-fold passage through the vaginal mucosa in mice and administered intravaginally in a dose of 0.5 x 10(8) CFU/ml caused infection in 100% animals. Inflammation in the lower genital tract was reduced by the 8th week after infection.

Mutations in a 23S rRNA gene of Chlamydia trachomatis associated with resistance to macrolides

For six clinical isolates of Chlamydia trachomatis, in vitro susceptibility to erythromycin, azithromycin, and josamycin has been determined. Four isolates were resistant to all the antibiotics and had the mutations A2058C and T2611C (Escherichia coli numbering) in the 23S rRNA gene. All the isolates had mixed populations of bacteria that did and did not carry 23S rRNA gene mutations.

[Structural-functional motifs of sterol 14-alpha demethylases (CYP51)]

CYP51 family of cytochromes P450 (sterol 14-alpha-demethylases) comprises the representatives from different kingdoms of living world, thus positioning itself as the most ancient member of the superfamily. In the course of the present research the collection of 36 full-length CYP51 amino acid sequences was submitted to cluster analysis. Each node of the clustering dendrogram corresponds to the groups of proteins, located on the branches descending from the node. By making the multiple alignment of each group of protein sequences we obtained the node-specific consensus sequences. The informational content of the consensus was defined as the presence of the compact conserved sites, the motifs. The assessment of informational content was computed using Sherman's non-parametric statistical criterion. The high informational content was observed for the 100% conserved consensus sequences of the following CYP51,s groups: fungi, animal+plant, plant+protista and bacteria. These selected consensus sequences were next aligned all together to get the final consensus for the whole family. To enrich the informational content of the CYP51 consensus the level of its conservation was dropped to 75%. Regions of statistically significant conservation were unraveled in the CYP51 consensus sequence. These regions (motifs) were then correlated with the information on secondary structure elements and substrate recognition sites reported for CYP51 from Mycobacterium tuberculosis. Seven motifs appeared to be obligatory for every CYP51 protein. The motifs thus obtained were searched for among all the known cytochrome P450 proteins. Some motifs were found to be absolutely specific for 14-alpha-demethylases, whereas others were common to different species of cytochromes P450.

[Analysis of point mutations in the ygeD, gyrA and parC genes in fluoroquinolones resistant clinical isolates of Chlamydia trachomatis]

Resistance of 14 clinical isolates of C. trachomatis to fluoroquinolones, i.e. of ciprofloxacin, pefloxaxin and ofloxacin, was assayed. Three isolates with a high resistance degree to all 3 drugs (MIC equal or above 64 microg/ml) were detected. MIC was found to be equal to or below 4 microg/ml for 3 isolates. The remaining isolates had an intermediate resistance level. The nucleotide sequence was established for the Quinolone-Resistance Determining Region (QRDR) genes coding the DNA-gyrase subunit A (gyrA) and DNA-topoisomerase IV subunit C (parC) as well as for the 3'-region of ygeD coding, presumably, the efflux protein. In none of the isolates, the gyrA and gyrC QRDR differed from the corresponding regions in the published C. trachomatis genome sequence. Several silent mutations and mutations resulting in amino acid substitutions were observed in the ygeD 3' region of 2 isolates resistant to high FQ concentrations and in 1 isolate with the intermediate resistance level.

[Sparing conservative surgery in children with chronic purulent otitis media]

A novel method of treatment of otitis media purulenta chronica in children implies administration of donor (from the parents or donor with the same blood group) plasm possessing a complete set of humoral and cellular immunity components. As a monotherapy, plasm treatment proved highly effective both before surgery and after it.

[Expression of the Mycobacterium tuberculosis cytochrome CYP51 gene in Escherichia coli]

Mycobacterium tuberculosis sterol 14 alpha-demethylase CYP51 is currently considered a promising target for a new generation of antitubercular drugs. Similarly to eucaryotic sterol 14 alpha-demethylases, candidate selective inhibitors of M. tuberculosis CYP51 belong to azoles, the N-substituted derivatives of imidazole and triazole. We have constructed a highly effective system for heterologous expression of MT CYP51 in E. coli. The recombinant protein was purified by metalloaffinity chromatography for primary in vitro screening of novel antitubercular azole compounds for their high affinity to the molecular target. Yield of the purified recombinant MT CYP51 was about 1.5 micromoles of the purified native protein per 1 l of E. coli cell culture. The recombinant protein interacted with ketoconazole with a Kd of 7.7 microM. MT CYP51 produced by our system for heterologous expression in E. coli may be used for initial testing of novel antimycobacterial azole drugs.

[Cloning and expression of the Mycoplasma hominis ftsZ for a cell division protein]

A Mycoplasma hominis chromosomal fragment containing the full-length ftsZ gene was cloned and sequenced. Natural expression of this gene was demonstrated by reverse transcription-polymerase chain reaction (RT-PCR) with total RNA. The M. hominis FtsZ protein was shown to differ substantially from its counterparts of two other Mycoplasma species, M. genitalium and M. pneumoniae. The possibility of M. hominis ftsZ expression in Escherichia coli was demonstrated with several bacterial strains. The M. hominis FtsZ protein was isolated from E. coli cells transformed with recombinant plasmids carrying the M. hominis ftsZ gene. Complementation between the E. coli and M. hominis FtsZ proteins was observed in transformants.

[Characteristics of autonomic dystonia in children with vasomotor rhinitis]

Data obtained at analysis of tables of screening diagnosis, cardiointervalograms, tilt tests used in examination of 57 children with neurovegetative vasomotor rhinitis point to disorders in the autonomic nervous system (by initial vegetative tone), vegetative reactivity. Parasympathetic prevalence in the initial vegetative tone and cardiointervalograms stems from sympathetic hypoactivity in the majority of the patients. The above vegetative shifts dictate the necessity of vegetotropic medication inclusion into combined therapy of vasomotor rhinitis.

[Genetic heterogeneity of cytochrome CYP51 in clinical strains of Mycobacterium tuberculosis]

Information on the complete genome sequences of a number of organisms available recently offers essentially new opportunities for the development of new, highly effective antimicrobial compounds. In particular, the search for new effective antituberculosis drugs remains an important problem, due to the recent increase of number of patients suffering with tuberculosis. In this respect considerable attention is paid to the cyp51-like gene Rv0764c encoding sterol-14 alpha-demethylase belonging to the cytochrome P450 superfamily, which has been discovered by computer analysis of the Mycobacterium tuberculosis genome sequence. We have screened 64 clinical isolates of M. tuberculosis for functionally relevant mutations in the coding sequence of the gene encoding Cyp 51-demethylase by single-strand conformation polymorphism analysis (SSCP) and sequencing of PCR-amplified gene fragments. Structural analysis of the gene in the isolates revealed no mutations leading to amino acid substitutions in the corresponding protein. 10 isolates had a silent nucleotide substitution 114 GCT-->GCC. Computer analysis of cyp51 sequence of the CDC1551 strain also revealed a similar nucleotide substitution, which has not been mentioned previously. The data obtained demonstrate that the sequence of the gene is highly conserved, supporting the advisability of M. tuberculosis Cyp51 protein to be considered as a molecular target for new antitubercular drugs. The SNP found in the gene coding sequence may be employed in the studies of M. tuberculosis population genetics.

Evaluation of antibiotic sensitivity of Chlamydia trachomatis using RT-PCR

The sensitivity of 11 clinical strains of Chlamydia trachomatis to azithromycin, ofloxacin, doxycycline, and erythromycin was evaluated. The minimum inhibiting concentrations of all antibiotics for 90% strains, determined by PCR with reverse transcription of omp3B gene RNA (GenBank U68443) corresponded to, and those with reverse transcription of 16S rRNA gene RNA (GenBank X54451) far surpassed the minimum bactericidal concentrations for 90% strains determined by direct immunofluorescence with monoclonal antibodies to the major outer membrane protein.

Induced expression of melittin, an antimicrobial peptide, inhibits infection by Chlamydia trachomatis and Mycoplasma hominis in a HeLa cell line

As the number of pathogenic microbial strains resistant to different antibiotics increases, amphipathic peptides with antimicrobial activity are promising agents for the therapy of infectious diseases. This work deals with the effect of an amphipathic antimicrobial peptide, melittin, expressed within recombinant plasmid vectors, on infection with urogenital pathogens Chlamydia trachomatis and Mycoplasma hominis in HeLa cell culture. Recombinant plasmid constructs with the melittin gene under the control of the tetracycline-responsive promoter of human cytomegalovirus were obtained. We showed inhibition of C. trachomatis and M. hominis infection after the introduction of recombinant plasmid vectors expressing the melittin gene into the infected cell culture.

[Infectious complications in electric cardiac stimulation]

There were 4424 patients operated for alterations of the cardiac rhythm. Primary electrocardiostimulation was performed in 3183 of them, reoperations in 1241 patients (39%). Infectious complications took place in 146 patients (3.3%). Based on their experiences the authors developed the strategy of treatment of patients with purulent complications and sepsis depending on their character and time of their appearance.

[Gene therapy of chronic infections of the urogenital system using cytotoxic peptides]

Gene therapy of chronic infectious diseases of urogenital tract represents a new perspective field in the modern biological and medical sciences. In the review discuss one of the new directions in gene therapy of urogenital infections caused by Mycoplasma: inhibition of mycoplasmal infection after administration of recombinant plasmid vectors, expressed the genes of cytotoxic peptides.

[The specific features of the functional status of the pituitary- adrenal and sympatho-adrenal system in children with angiofibromas of the skull base]

Analyzing the results of examination of 14 boys aged 6 to 13 years who had angiofibromas of the skull base has led to the conclusion that the disease runs in the presence of the markedly activated sympathoadrenal and pituitary-adrenal systems and lipid oxidation products. While choosing a therapy, it is necessary to take into account hormonally metabolic and antioxidative imbalance and to prescribe metabolic and membrane-stabilizing drugs.

Inhibition of influenza A virus reproduction by a ribozyme targeted against PB1 mRNA

A ribozyme gene directed at a specific cleavage of mRNA coding for PB1 protein, a component of RNA-dependent RNA-polymerase of influenza A virus, was constructed. The avian adenovirus CELO virus-associated RNA (VA RNA CELO) promoter and human cytomegalovirus (CMV) promoter were used for the permanent expression of the ribozyme in cell lines. The cells were infected with influenza A virus strains A/Singapore/1/57 and A/WSN/33, and the suppression of the virus reproduction and virus-specific protein synthesis was measured. The maximal level of the inhibition of virus reproduction as compared to the reproduction in non-transformed cells was 93.5%. Defective recombinant adenoviruses were constructed carrying the genes of functional and non-functional ribozymes under the control of human cytomegalovirus (CMV) promoter. The reproduction of A/WSN/33 virus in CV-1 cells preinfected with recombinant adenoviruses was shown to be suppressed.

[Combined treatment of chronic hypertrophic pharyngitis in children]

The trial of fluctuating current in combined treatment of 94 children (age 3-14 years) with chronic hypertrophic pharyngitis proved superior to the conventional treatment in the control patients: the response rate 85.7-92.5% versus 52.9%, respectively. Combined treatment including fluctuating current is thought effective in children with chronic hypertrophic pharyngitis.

[The status of autonomic nervous system in children with chronic sinusitis]

Such parameters of autonomic nervous system as initial vegetative tonicity, vegetative reactivity, vegetative support of activity were for the first time assessed in children with chronic sinusitis. The vegetative dysfunction was found in purulent and purulent-polypous sinusitis. The above vegetative unbalance dictates the necessity of addition of various vegetotropic modalities to combined treatment of chronic sinusitis.

[Natural humoral and cellular factors of nonspecific defense in the treatment of chronic sinusitis in children]

Sparing treatment of chronic purulent sinusitis in children is an urgent problem of rhinology. Usage of preparations of donor (parental, of the same group) autoleukomass and blood plasm which possess all the components of humoral and cellular immunity proved highly effective against chronic purulent sinusitis in children. The drawback of this method is the necessity of regular lavage of the sinuses after insertion of the leukomass and heparinized plasm. The use of donor serum (parental, of the same group) also produced a good effect in purulent sinusitis. The serum advantage over the leukomass or plasm is that it can be left in the sinuses until the next procedure.

[Hormonal-metabolic and immune status in recurrent laryngeal papillomatosis in children]

Clinical, biochemical and immunological findings in 12 children with recurrent laryngeal papillomatosis evidence for defects in hormonal--metabolic and immune profiles in terms of depressed sympathoadrenal, adrenocortical functions and secondary immunodeficiency. To correct the above disorders it is advisable to practice immunocorrective therapy and drugs (prospidin) stimulating adrenal function.

[The characteristics of the membrane-destabilizing mechanisms in chronic suppurative and suppurative-polypous sinusitis in children]

It is found that chronic purulent and pyopolypous sinusitis in children causes activation of lipid peroxidation and endogenic phospholipases in red cell membranes. There are shifts in structural and functional pattern of cytomembranes in inflammation focus (exudate from the sinuses). Membrane destabilization was maximal in pyopolypous sinus inflammation.

[Peripheral nervous system in children with chronic inflammatory otorhinolaryngologic diseases]

A comparative evaluation of central and vegetative nervous as well as cardiovascular systems in 20 normal children and 45 patients with ENT problems found out vegetative lability in 8 children. Three of them were from the control healthy group, 4 had tonsillitis, 1 purulent sinusitis. These children were referred to the vegetative dystonia risk group. In 28 patients (9.3 and 16 cases of purulent-polypous, purulent and decompensated tonsillitis, respectively) parasympathicotonic and sympathicotonic shifts revealed in the baseline vegetative tone and vegetative reactivity require adequate therapeutic correction.