O antigen restricts lysogenization of non-O157 Escherichia coli strains by Stx-converting bacteriophage phi24B.

Acquisition of new prophages that are able to increase the bacterial fitness by the lysogenic conversion is believed to be an important strategy of bacterial adaptation to the changing environment. However, in contrast to the factors determining the range of bacteriophage lytic activity, little is known about the factors that define the lysogenization host range. Bacteriophage phi24B is the paradigmal model of Stx-converting phages, encoding the toxins of the Shiga-toxigenic E. coli (STEC). This virus has been shown to lysogenize a wide range of E. coli strains that is much broader than the range of the strains supporting its lytic growth. Therefore, phages produced by the STEC population colonizing the small or large intestine are potentially able to lysogenize symbiotic E. coli in the hindgut, and these secondary lysogens may contribute to the overall patient toxic load and to lead to the emergence of new pathogenic STEC strains. We demonstrate, however, that O antigen effectively limit the lysogenization of the wild E. coli strains by phi24B phage. The lysogens are formed from the spontaneous rough mutants and therefore have increased sensitivity to other bacteriophages and to the bactericidal activity of the serum if compared to their respective parental strains.

The ecogenomics of dsDNA bacteriophages in feces of stabled and feral horses.

The viromes of the mammalian lower gut were shown to be heavily dominated by bacteriophages; however, only for humans were the composition and intervariability of the bacteriophage communities studied in depth. Here we present an ecogenomics survey of dsDNA bacteriophage diversity in the feces of horses (Equus caballus), comparing two groups of stabled horses, and a further group of feral horses that were isolated on an island. Our results indicate that the dsDNA viromes of the horse feces feature higher richness than in human viromes, with more even distribution of genotypes. No over-represented phage genotypes, such as CrAssphage-related viruses found in humans, were identified. Additionally, many bacteriophage genus-level clusters were found to be present in all three geographically isolated populations. The diversity of the horse intestinal bacteriophages is severely undersampled, and so consequently only a minor fraction of the phage contigs could be linked with the bacteriophage genomes. Our study indicates that bacteriophage ecological parameters in the intestinal ecosystems in horses and humans differ significantly, leading them to shape their corresponding viromes in different ways. Therefore, the diversity and structure of the intestinal virome in different animal species needs to be experimentally studied.

[The role of lipids in the classification of astrocytoma and glioblastoma using MS tumor profiling]. / Rol' lipidov pri klassifikatsii astrotsitomy i glioblastomy pri pomoshchi mass-spektrometricheskogo profilirovaniia opukholei.

Express MS identification of biological tissues has become a much more accessible research method due to the application of direct specimen ionization at atmospheric pressure. In contrast to traditional methods of analysis employing GC-MS methods for determining the molecular composition of the analyzed objects it eliminates the influence of mutual ion suppression. Despite significant progress in the field of direct MS of biological tissues, the question of mass spectrometric profile attribution to a certain type of tissue still remains open. The use of modern machine learning methods and protocols (e.g., "random forests") enables us to trace possible relationships between the components of the sample MS profile and the result of brain tumor tissue classification (astrocytoma or glioblastoma). It has been shown that the most pronounced differences in the mass spectrometric profiles of these tumors are due to their lipid composition. Detection of statistically significant differences in lipid profiles of astrocytoma and glioblastoma may be used to perform an express test during surgery and inform the neurosurgeon what type of malignant tissue he is working with. The ability to accurately determine the boundaries of the neoplastic growth significantly improves the quality of both surgical intervention and postoperative rehabilitation, as well as the duration and quality of life of patients.

[The role of lipid metabolism disorders, atypical isoforms of protein kinase C, and mutational status of cytosolic and mitochondrial forms of isocitrate dehydrogenase in carcinogenesis of glial tumors]. / Rol' narushenii lipidnogo obmena, atipicheskikh izoform proteinkinazy S i mutatsionnogo statusa tsitozol'noi i mitokhondrial'noi form izotsitratdegidrogenazy v kantserogeneze glial'nykh opukholei.

The relationship between molecular genetic and metabolic disorders is one of the challenges of modern oncology. In this review, we consider lipid metabolism and its changes as one of the factors of oncogenesis of glial tumors. Also, we demonstrate that the genome and the metabolome are interconnected by a large number of links, and the metabolic pathways, during their reorganization, are able to drastically affect the genetic structure of the cell and, in particular, cause its tumor transformation. Our own observations and analysis of the literature data allow us to conclude that mass spectrometry is a highly accurate current method for assessing metabolic disorders at the cellular level. The use of mass spectrometry during surgery allows the neurosurgeon to obtain real-time data on the level of specific molecular markers in the resected tissue, thereby bringing intraoperative navigation techniques to the molecular level. The generation of molecular fingerprints for each tumor significantly complements the available neuroimaging, molecular genetic, and immunohistochemical data.

Adsorption of Bacteriophages on Bacterial Cells.

The biological functions of bacteriophage virions come down to the solution of three basic problems: to provide protection of viral nucleic acid from the factors of extracellular environment, to recognize a host suitable for phage replication, and to provide the delivery of nucleic acid through bacterial cell envelopes. This review considers the main regularities of phage-cell interaction at the initial stages of infection of tailed bacteriophages, from the reversible binding with receptors on the surface to the beginning of phage DNA entry. Data on the structure and functions of the phage adsorption apparatus, the main quantitative characteristics of the adsorption process, and the mechanisms of adaptation of phages and their hosts to each other effective at the stage of adsorption are presented.

[Modeling the Propagation of Microbial Cells and Phage Particles from the Sites of Permafrost Thawing.]

A method is proposed for integral assessment of the propagation of microbial cells and viral parti- cles during seasonal thawing of relic ice wedge layers. The results of on-site and laboratory investigation car- ried out in the upper part of permafrost exposure at Mamontova Gora (Yakutiya, Russia) are presented. To increase reliability of the results, suspensions of two microbial species and two coliphage species were intro- duced as biomarkers directly on the surface of thaing ice and in the meltwater flow. Each of the four different model biological objects was shown to possess unique parameters of movement in the meltwater flow and is able to move 132 m in 25-35 min with the water flow.

[Genetic and molecular principles for the selection of Pseudomonas and Staphylococcus therapeutic bacteriophages].

The content of empirically selected bacteriophage mixtures, produced by Microgen for the prevention and treatment of staphylococcal and pseudomonade infections, was investigated by negative stain electron microscopy. The main population of phages was shown to belong to the groups suitable for therapeutic purposes based on bioinformatics analysis of known genomes of Pseudomonas and Staphylococcus phages. However, the phage morphology studies did not always reveal the exact correspondence of the phage to the exact group. Therefore, we suggest group genotyping of the therapeutic bacteriophages on thebasis of genetic conservative locus.

A Novel High-Resolving Method for Genomic PCR-Fingerprinting of Enterobacteria.

We developed a novel PCR-fingerprinting system for differentiation of enterobacterial strains using a single oligonucleotide primer IS1tr that matches the inverted terminal repeats of the IS1 insertion element. Compared to widely used BOX-PCR and ribotyping methods, our system features higher resolution allowing differentiation of closely related isolates that appear identical in BOX-PCR and ribotyping but differ in their phage sensitivity. The IS1-profiling system is less sensitive to the quality of the material and equipment used. At the same time, BOX-PCR is more universal and suitable for bacterial strain grouping and reconstruction of the low-distance phylogeny. Thus, our system represents an important supplement to the existing set of tools for bacterial strain differentiation; it is particularly valuable for a detailed investigation of highly divergent and rapidly evolving natural bacterial populations and for studies on coliphage ecology. However, some isolates could not be reliably differentiated by IS1-PCR, because of the low number of bands in their patterns. For improvement of IS1-fingerprinting characteristics, we offer to modify the system by introducing the second primer TR8834 hybridizing to the sequence of a transposase gene that is widely spread in enterobacterial genomes.

[Molecular-genetic characteristics of a medieval population from the northern Russian territory]. / Molekuliarno-geneticheskaia kharakteristika srednevekovykh populiatsii s territorii russkogo severa.

Forty-seven individual mitochondrial DNA (mtDNA) samples isolated from bones samples found in the Nefedyevo, Minino, and Shuygino gravesites have been analyzed to perform molecular genetic study of the medieval (12th to 13th centuries AD) human population from the vicinity of Lake Beloe (Vologda oblast, northern Russia). The mitotypic structure of the population has been determined on the basis of sequencing the mtDNA hypervariable-region segment I (HVSI; positions 15,989-16,410). Three mitotypes characterizing the population studied have been found in the 47 representatives of the medieval population: mitotype 1 corresponding to the Cambridge reference sequence, mitotype 2 (transition G-A at position 16,129), and mitotype 3 (transitions G-A and C-T at loci 16,129 and 16,223, respectively). Mitotypes 1, 2, and 3 have been found in 91.6, 4.2, and 4.2% of the individual samples studied. This high frequency of the Cambridge mitotype is considerably higher than its mean frequencies in European populations. The frequencies of other mitotypes found correspond to their mean European values. The absence of a Mongoloid component has been demonstrated for the female lineage of the population. Comparison of the molecular genetic characteristics of contemporary European ethnic groups and the population studied has demonstrated that it may be assigned to the European population group. The high homogeneity of the mitochondrial pool suggests a strong founder effect, which agrees with the view of archeologists and anthropologists that the first migrant settlers were very few.

The "Linh Duong" Pseudonovibos spiralis (Mammalia, Artiodactyla) is a new buffalo.

The controversial phylogenetic position of the recently described South-East Asian endemic bovid, Pseudonovibos spiralis, was evaluated on the basis of phylogenetic analyses of originally obtained nearly complete 12S mitochondrial rDNA sequences for this species and Bubalus bubalis and 26 sequences of Bovidae from the Genbank using Cervus elaphus (Cervidae) as outgroup. In most of the phylogenetic analyses performed using PAUP 4.0 (maximum parsimony, maximum likelihood and neighbour-joining), Bovidae consisted of two major clades: Bovinae including the tribes Bovini, Tragelaphini and Boselaphini, and Antilopinae + Caprinae, incorporating all other bovids. In most trees P. spiralis fell within the buffalos (subtribe Bovina) between Bubalus and Syncerus. Therefore, our phylogenetic analyses of bovid mitochondrial 12S rRNA gene sequences suggest the close relationship of this enigmatic species with the buffalos and its placement within the subtribe Bovina.

[Mitochondrial DNA sequencing of human hair shafts stored for long time]. / Opredelenie nukleotidnykh posledovatel'nostei mitokhondrial'noi DNK v sterzhniakh volos pri dlitel'nykh srokakh ikh khraneniia.

Mitochondrial DNA (mtDNA) sequencing is commonly used for forensic genetic identification of relation and personality identification based on analysis of tooth and skeletal rudiments. We demonstrated the possibility of DNA extraction and subsequent enzymatic amplification of fragments of a hypervariable segment I of mtDNA control region from hair shafts after long storage (up to 75 years). Shed hairs are the most common biological material evidence in forensic investigations. Low content of DNA and its possible degradation in hair shafts without bulbs may cause artifacts in polymerase chain reaction. However comparative analysis of amplified nucleotide sequences of amplified fragments from hair stored for 75 years was identical to the sequence from hairs cut immediately before experiment. This indicates high quality of the resultant matrices, stability of results, and hence, the possibility of using DNA extracted from hair shafts without bulbs stored for a long time for expert genetic analysis. Theoretical and methodological prospects of using mtDNA polymorphism analysis for forensic expert evaluations are discussed.