Vol 34, No 2 (2019)

The activation of mobile genetic elements is a prerequisite for controlling the expression of genes in successive cell divisions, with their change specifically depending on the tissue and developmental stage. These activation patterns are characteristic of totipotent and pluripotent embryo cells, as well as for stem cells in the postnatal period. We have suggested that in the evolution of multicellular eukaryotes, optimal ratios are selected in the arrangement of transposons relative to exons and introns of host genes. These ratios, specific to each species, can be the basis for controlling the sequential differentiation of stem cells necessary for the development of the whole organism. Despite the fact that cell differentiation in ontogenesis is controlled by a very conservative set of genes, mobile genetic elements are involved in the fine-tuning of regulatory networks that control the expression of these genes, which is reflected in the phenotypic characteristics of each species. Transposons are important sources of genome structures that are actively used to regulate the multicellular embryonic development. These structures include binding sites with transcription factors, enhancers and silencers, promoters, insulators, alternative splicing sites, non-coding RNA. Moreover, transposons are involved in the emergence and evolution of new protein-coding genes through exonization, domestication, and the formation of retrogenes. The activation of transposons is needed to regulate the differentiation and reproduction of cells in the body; however, in terminally differentiated cells, upon reaching predetermined sizes of organs, molecular systems are activated that block a further cascade of transposon activation. We suggest that the imperfection of systems aimed at specific suppression of transposon activity in mature cells may be the cause of aging and age-related diseases due to the pathological activation of mobile genetic elements. Identifying the tissue-specific mechanisms of inherited transposon activation in stem cells, as well as their pathological activation in terminally differentiated cells, may be the basis for finding ways to fight aging.

In spite of effective anti-retroviral therapy, HIV-1 infection may still lead to neurological impairment in patients. The underlying mechanism of neurodegeneration remains mysterious. HIV-1 does not infect neurons, but does infect microglia cells in the brain. It is controversial whether HIV-1 productively infects astrocytes, an abundant glial cell type in the brain. Thirty years of investigation have led to conflicting reports concerning the entry, infection, and production of progeny virions from astrocytes. New models from studies in primary human fetal astrocytes suggest phagocytosis of HIV-1 with little productive infection. The retroviral life cycle requires integration of the viral genome to the host genome. The host protein LEDGF/p75 is required for efficient HIV-1 integration. In the absence of LEDGF/p75, HIV-1 integration and infection efficiency is reduced ten fold. Differentiated astrocytes do not appear to express LEDGF/p75, which suggests these cells are disabled for efficient integration. Phagocytosis of HIV-1 virions and the lack of LEDGF/p75 expression in astrocytes suggest that this cell type is not efficiently infected in vivo.

This review summarizes the results of a comprehensive multi-year molecular-epidemiological research on HCV (2001–2016) in Altai krai and Novosibirsk oblast. The first eight cases of infection with the CRF01_1b2k recombinant form of HCV were revealed during this research. The recombination point in the NS2 gene was confirmed for all CRF01_1b2k Siberian isolates, which agrees with the data on the previously identified recombinants of the same form in other regions of Russia and the rest of the world. An analysis of the nucleotide sequences of the Core, E1, NS2, and NS5b gene fragments in the genomes of eight recombinant isolates of the 2k/1b type identified in Siberia showed a close phylogenetic relationship between them, as well as with 27 recombinants described in St. Petersburg, Azerbaijan, Armenia, Estonia, The Netherlands, Ireland, France, and the United States. The levels of homology for the Core, Е1, NS2, and NS5b genes were 97, 94, 92, and 96%, respectively. Phylogenetic analysis of the genomes of recombinants indicated the common origin of isolates of the 2k/1b type and their broad circulation in the territory of Russia. Analysis of the 5'‑region of the genome of recombinant isolates of subtype 2k showed that, apart from Russia, the closest isolates of the 2k subtype were previously identified in Moldova and Uzbekistan in 1996–2013. The incidence of recombinant isolates in the Siberian region is estimated at 1%. The molecular clock method has shown that the most probable time of the appearance of the CRF01_1b2k recombinant form is between 1957 and 1970.

Plague is a zoonotic infection whose pathogenic agent has caused hundreds of million human deaths. A broad range of hosts and vectors, along with the geographical dispersion of natural plague foci characterized by different ecological conditions, contribute to the formation of the polytypic Y. pestis species, the result of selection of the genetic variants specific for certain natural foci. Through the efforts of a world consortium of scientists, a global coordinated phylogram of the SNP types of the plague pathogen has been developed. However, debates on the intraspecies Y. pestis taxonomy still continue on the vast Russian expanses. The work of a taxonomist has many specific, individual features, formed on the basis of individual experience. It is important in this kind of work to follow an old rule which requires that borders should be placed where they have been put by nature, and should not be put where nature has not put them. With that in mind, we suggest here the rational variant of the plague pathogen nomenclature constructed in accordance with the rules set out in the International Code of Bacterial Nomenclature and Evolutionary Taxonomy.

Accurate library quantification is very important during post-pooling captured target sequencing. There are a number of methods available to quantify libraries prior to sequencing, but no gold standard for the quantification of libraries exists. In this study, we compared common library quantification methods (Labchip, Qubit 3.0, qPCR with three primer sets) with ultra-low coverage sequencing (MiSeq with and without insert size correction). Cost, time and quantification accuracy were considered. We found that Qubit and MiSeq were better than qPCR and LabChip at predicting the final concentration. Also we revealed that MiSeq with insert size correction was the most accurate method for library quantification prior to target sequencing. This method allows for correction shifts in the ratio due to enrichment. Ultra-low coverage sequencing by Illumina MiSeq is the most accurate method for library quantification prior to pooling and post-pooling target enrichment.

The gastric cancer is one of the most common carcinomas and the second cancer-related death in the world. The risk factors for this cancer include genetic factors and environmental factors such as Helicobacter pylori infection. The protein HcpD (HP0160) of H. pylori is a member of the cysteine-rich protein family that interacts with host immune systems. One of the modern approaches to stimulate the humoral and cellular immune systems against diseases is utilization of DNA vaccines. Using qPCR method, this study aimed to evaluate the expression level of cytokines genes including IL17, IL4, and interferon gamma (IFNγ) in BALB/c mice vaccinated with pCDNA3.1(–)-hcpD DNA vaccine against H. pylori. In this study, pCDNA3.1(–)-hcpD recombinant vector was prepared and transformed into E. coli to obtain a large number of plasmids. After plasmid purification and confirmation of the transformation by digestion and PCR, the chitosan nanoparticles were synthesized using ionic gelation method. The injectable solutions containing pCDNA3.1(–)-hcpD, pCDNA3.1(–)-hcpD + nanoparticles or pCDNA3.1 (empty vector as control group) were injected into BALB/c mice, separately. Then, the blood and tissues samples from each animal were collected and the expression levels of cytokine genes were examined by a qRT-PCR method. The IL-4 expression level was significantly decreased in pcDNA3.1(–)-hcpD + nanoparticle and pcDNA3.1(–)-hcpD groups (p < 0.001). Conversely, the expression level of IFNγ gene in both groups was increased significantly (p < 0.001). The expression level of IL17 gene showed no significant difference between DNA vaccine containing nanoparticle compare with pcDNA3.1(–)-hcpD (p > 0.05). During 15, 30 and 45 post-injection days, the expression level of hcpD decreased in hip tissue of mice vaccinated with pcDNA3.1(–)-hcpD and pcDNA3.1(–)-hcpD + nanoparticle although no significant difference found between the vaccinated groups (p > 0.05). pcDNA3.1(–)-hcpD vaccine can stimulate the immune system in vaccinated mice either as the sole agent or combined with chitosan nanoparticles. Therefore this method can be an effective way for immunization against H. pylori infection.