Modern approaches to the detection and analysis of low-copy-number RNAs are often based on the use of RNA-dependent DNA polymerases, for example, in reverse-transcription PCR. The accuracy and efficiency of cDNA synthesis in the reverse-transcription reaction catalyzed by reverse transcriptase (RNA-dependent DNA polymerase) significantly affect the correctness of the results of PCR diagnostic assays and/or RNA sequencing. In this regard, many studies are focused on the optimization of the reverse-transcription reaction, including the search for more perfect primers necessary to obtain a full-length DNA copy of RNA under study. The best-known completely uncharged analogs of oligonucleotides – morpholine oligonucleotides and peptide nucleic acids – cannot be substrates for enzymes that process nucleic acids. The aim of this work was to conduct a pilot study of uncharged phosphoryl guanidine oligodeoxyribonucleotides (PGOs) as primers for mouse leukemia virus reverse transcriptase (MMLV H-). Specific features of elongation of partially and completely uncharged PGO primers were investigated. It was demonstrated that PGOs can be elongated efficiently, e.g., in the presence of a fragment of human ribosomal RNA having complex spatial structure. It was shown that the proportion (%) of abortive elongation products of a PGO primer depends on buffer ionic strength, nucleotide sequence of the primer, and the presence and location of phosphoryl guanidine groups in the primer. The results indicate the suitability of PGOs, including completely electroneutral ones, as primers for reverse-transcription PCR, thereby opening up new prospects for the creation of experimental models for the analysis of highly structured RNA. 

The stromal elements of a malignant tumor can promote cancer progression and metastasis. The structure of the tumor stroma includes connective tissue elements, blood vessels, nerves, and extracellular matrix (ECM). Some of the cellular elements of the tumor stroma are cancer-associated fibroblasts (CAFs). The origin and function of CAFs have been actively studied over the past thirty years. CAFs produce collagen, the main scaffold protein of the extracellular matrix. Collagen in the tumor stroma stimulates fibrosis, enhances the rigidity of tumor tissue, and disrupts the transmission of proliferation and differentiation signaling pathways. CAFs control tumor angiogenesis, cell motility, tumor immunogenic properties, and the development of resistance to chemo- and immunotherapy. As a result of metabolic adaptation of rapidly growing tumor tissue to the nutrients and oxygen deprivation, the main type of energy production in cells changes from oxidative phosphorylation to anaerobic glycolysis. These changes lead to sequential molecular alterations, including the induction of specified transcriptional factors that result in the CAFs activation. The molecular phenotype of activated CAFs is similar to fibroblasts activated during inflammation. In activated CAFs, alpha-smooth muscle actin (α-SMA) is synthetized de novo and various proteases and fibronectin are produced. Since CAFs are found in all types of carcinomas, these cells are potential targets for the development of new approaches for anticancer therapy. Some CAFs originate from resident fibroblasts of the organs invaded by the tumor, while others originate from epithelial tumor cells, which are undergoing an epithelial-mesenchymal transition (EMT). To date, many molecular and metabolic inducers of the EMT have been discovered including the transforming growth factor-beta (TGF-β), hypoxia, and inflammation. This review classifies modern concepts of molecular markers of CAFs, their functional features, and discusses the stages of epithelial-mesenchymal transition, and the potential of CAFs as a target for antitumor therapy.

The generic complex Miscanthus Anderss. (Poaceae) is a unique example among herbaceous plants characterized by high values of growth of aboveground vegetative mass and practical use as a valuable source of alternative energy. Miscanthus is one of the most efficient solar energy accumulators, and since phytomeliorative use implies the cultivation of these resource plants in inconvenient and semi-shady areas, the question about the effect of insufficient lighting on the productivity of Miscanthus arises. As a result of a long-lasing introduction effort, the Central Siberian Botanical Garden SB RAS created a population of Miscanthus sacchariflorus (Maxim.) Benth., which has good prospects for growing under the conditions of the forest-steppe area in Western Siberia. The goals of our study were: (1) to determine the peculiarities of shoot formation, (2) to assess the cellulose and lignin accumulation in M. sacchariflorus populations under different lighting conditions and (3) to perform a DNA passportization of the Miscanthus population by ISSR marking. Evaluation of shoot formation and the amount of accumulated cellulose and lignin in plants was carried out under different degrees of illumination: one variant was grown in a sunny area, and the other, in partial shade. As a result of analysis of variance, it was found that the number of shoots does not depend on environmental conditions, but on the age of the plant, while environmental conditions have a significant effect on plant height. Although the samples of both M. sacchariflorus variants were characterized by different rates of creation of a continuous projective cover, plants in semi-shaded areas formed up to 89.34 % of shoots compared to their peers in illuminated areas, which did not affect significantly the size of the aboveground mass and the cellulose content in it. As a result of ISSR-analysis of genomic DNA in the M. sacchariflorus population, unique molecular polymorphic fragments were identified, which can be used for identification and DNA passportization at the inter-population level. Thus, the complex use of M. sacchariflorus as a valuable meliorative and bioenergetic culture is due to the high adaptive potential of this species. It was found that the illumination factor has virtually no effect on the amount of the cellulose content in the shoot, and a reduced content of the technologically undesirable lignin was observed in plants growing in the partial shade conditions.

The table beet, a widespread edible root crop known for its medicinal and antioxidant properties, early maturation, good shelf life, and high contents of bioactive compounds, vitamins and minerals, is used for the production of a natural red food dye. The relevance of this study is dictated by the lack of knowledge about the dynamic changes in the content of betanin during the growing season when developing table beet cultivars with a focus on pigment extraction. The article presents the results of a study of 29 red-colored table beet accessions from the collection of the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR). Dynamic changes in the content of the pigment during the growing season were observed on two beet accessions, cvs. ‘Russkaya odnosemyannaya’ and ‘Bordo odnosemyannaya’. Four pH versions of the buffer solution were tested, and the test results are presented. A buffer solution with pH 6.5 is recommended for research purposes. The amplitude of variability in the content of betanin in the peel (39.9–239.2 mg/100 g) and flesh (14.4–127.5 mg/100 g) of beets was determined. It was confirmed that the content of betanin in the peel exceeded that in the flesh in all samples. A positive relationship between these indicators was revealed (r = 0.74, p ≤ 0.05). It was found that betanin accumulation did not occur in beet roots during the growing season. The pigment showed considerable fluctuations associated with abiotic environmental factors. Correlation analysis showed a significant positive relationship between air temperature and betanin content in the root flesh (r = 0.32–0.31, p ≤ 0.05). A negative impact of environmental temperature on betanin content in the peel manifested itself on the third day (r = –0.34…–0.35, p ≤ 0.05). The negative response to precipitation was less expressed in cv. ‘Bordo odnosemyannaya’ due to the genotype’s more active metabolism and plasticity. Structural morphological features of the photosynthetic apparatus were described for the tested accessions, and their interrelations with the studied character were specified. Recommendations are given concerning the choice of a planting pattern and the timing of table beet harvesting for pigment extraction.

The key factor of genome instability during aging is transposon dysregulation. This may be due to senile changes in the expression of lamins, which epigenetically modulate transposons. Lamins directly physically interact with transposons. Epigenetic regulators such as SIRT7, BAF, and microRNA can also serve as intermediaries for their interactions. There is also an inverse regulation, since transposons are sources of miRNAs that affect lamins. We suggest that lamins can be attributed to epigenetic factors, since they are part of the NURD, interact with histone deacetylases and regulate gene expression without changing the nucleotide sequences. The role of lamins in the etiopathogenesis of premature aging syndromes may be associated with interactions with transposons. In various human cells, LINE1 is present in the heterochromatin domains of the genome associated with lamins, while SIRT7 facilitates the interaction of this retroelement with lamins. Both retroelements and the nuclear lamina play an important role in the antiviral response of organisms. This may be due to the role of lamins in protection from both viruses and transposons, since viruses and transposons are evolutionarily related. Transposable elements and lamins are secondary messengers of environmental stressors that can serve as triggers for aging and carcinogenesis. Transposons play a role in the development of cancer, while the microRNAs derived from them, participating in the etiopathogenesis of tumors, are important in human aging. Lamins have similar properties, since lamins are dysregulated in cancer, and microRNAs affecting them are involved in carcinogenesis. Changes in the expression of specific microRNAs were also revealed in laminopathies. Identification of the epigenetic mechanisms of interaction of lamins with transposons during aging can become the basis for the development of methods of life extension and targeted therapy of age-associated cancer.

Transcriptional activity of genes involved in maintaining genetic homeostasis (genes for repair, cell cycle and apoptosis: TP53, MDM2, ATM, BAX, BCL-2, CDKN1A, OGG1, XPC, PADI4, MAPK8, NF-KB1, STAT3, GATA3) was studied in chronically exposed persons with an increased intensity of early and late stages of apoptosis and necrosis of peripheral blood lymphocytes. The object of this study was peripheral blood mononuclear cells obtained from 132 chronically exposed residents of the Techa riverside villages. The mean accumulated dose to red bone marrow was 426.4±48.2 mGy (1.3–2930.0 mGy), to thymus and peripheral immune organs, 58.9±7.9 mGy (0.1–489.0 mGy). The study was performed more than 60 years after the onset of exposure, the average age of exposed persons was 68±0.6 years (55–86 years). The study of apoptotic and necrotic death of peripheral blood lymphocytes was based on the presence of phosphatidylserine on the cell membrane surface, as well as on its permeability for DNA-intercalating dye. Evaluation of the relative content of mRNA genes for repair, cell cycle, and apoptosis was carried out using real-time PCR. An increased relative content of PADI4 gene mRNA was registered in the group of chronically exposed persons with the increased intensity of early apoptosis (p = 0.006). Modulation of the relative content of mRNA of the TP53 (p = 0.013) and BCL-2 (p = 0.021) genes was detected in the group of chronically exposed individuals with the increased intensity of the late stage of apoptosis. A statistically significant increase in the transcriptional activity of the TP53 gene was observed in the group of chronically exposed persons with the increased intensity of peripheral blood lymphocyte necrosis in the long-term period (p = 0.015). In the course of the study it was noted that exposed people with increased intensity of apoptosis, first of all, demonstrate changes in the transcriptional activity of apoptotic genes. These data are consistent with current views on the activation of programmed cell death.

The risk of cervical cancer is caused by persistent human papillomavirus (HPV) infection. Cervical cancer is the most frequent cancer among women. Our purpose was to investigate the association between TP53 215C>G (Pro72Arg), MDM2 -410T>G, and NQO1 609C>T gene polymorphisms with a high HPV load and the influence of gene-gene interactions on prolonged HPV infection. Eighty-nine women with a high HPV viral load and 114 healthy women were involved in a case–control study. Genotyping for TP53 215C>G (Pro72Arg) and MDM2 -410T>G SNPs was carried out by allele-specific PCR and genotyping for NQO1 609C>T was performed by a TaqMan assay. Quantitative analysis of HPV DNA was performed by AmpliSens® HPV HCR screen-titer-FRT test system. Gene-gene interactions were analyzed using the multifactor dimensionality reduction (MDR) method. The study of separate SNPs of MDM2 -410T>G and NQO1 609C>T genes did not reveal any statistically significant difference in genotype and allele frequencies among women within the two groups. The frequency of the 215G (72Arg) allele and 215GG (72Arg/Arg) genotype of the TP53 gene was significantly higher in the case group than in the control group (OR = 1.74, 95 % CI = 1.10–2.73; p = 0.02 and OR = 1.97, 95 % CI = 1.13–3.46; p = 0.04, respectively). MDR analysis showed the significance of intergenic interactions of the three studied loci TP53 (rs1042522) – MDM2 (rs2279744) – NQO1 (rs1800566) for the formation of a high HPV load (OR = 3.05, 95 % CI = 1.73–5.46; p = 0.0001).

Cardiovascular diseases (CVDs), the leading cause of death worldwide, generally refer to a range of pathological conditions with the involvement of the heart and the blood vessels. A sizable fraction of the susceptibility loci is known, but the underlying mechanisms have been established only for a small proportion. Therefore, there is an increasing need to explore the functional relevance of trait-associated variants and, moreover, to search for novel risk genetic variation. We have reported the bioinformatic approach allowing effective identification of functional non-coding variants by integrated analysis of genome-wide data. Here, the analysis of 1361 previously identified regulatory SNPs (rSNPs) was performed to provide new insights into cardiovascular risk. We found 773,471 coding co-segregating markers for input rSNPs using the 1000 Genomes Project. The intersection of GWAS-derived SNPs with a relevance to cardiovascular traits with these markers was analyzed within a window of 10 Kbp. The effects on the transcription factor (TF) binding sites were explored by DeFine models. Functional pathway enrichment and protein– protein interaction (PPI) network analyses were performed on the targets and the extended genes by STRING and DAVID. Eighteen rSNPs were functionally linked to cardiovascular risk. A significant impact on binding sites of thirteen TFs including those involved in blood cells formation, hematopoiesis, macrophage function, inflammation, and vasoconstriction was found in K562 cells. 21 rSNP gene targets and 5 partners predicted by PPI were enriched for spliceosome and endocytosis KEGG pathways, endosome sorting complex and mRNA splicing REACTOME pathways. Related Gene Ontology terms included mRNA splicing and processing, endosome transport and protein catabolic processes. Together, the findings provide further insight into the biological basis of CVDs and highlight the importance of the precise regulation of splicing and alternative splicing.

In this article, the system of the green microalgal genus Micractinium, based on morphological, physiological, ecological and molecular data, is considered. The main diagnostic species characteristics and the taxonomic placement of some taxa are also discussed. Phylogenetic analysis showed that the genus Micractinium is characterized by high cryptic diversity. The algorithms used for species delimitation had different results on the number of potentially species-level clusters allocated. The ABGD method was less “sensitive”. The tree-based approaches GMYC and PTP showed a more feasible taxonomy of the genus Micractinium, being an effective additional tool for distinguishing species. The clustering obtained by the latter two methods is in good congruence with morphological (cell size and shape, ability to form colonies, production of bristles, chloroplast type), physiological (vitamin requirements, reaction to high and low temperatures), molecular (presence of introns, level of genetic differences, presence of CBCs or special features of the secondary structure in ITS1 and ITS2) and ecological characteristics (habitat). The polyphyly of the holotype of the genus M. pusillum as well as M. belenophorum is shown. The intron was effective as an additional tool for distinguishing species, and the results of the intron analysis should be taken into account together with other characteristics. The CBC approach, based on the search for compensatory base changes in conservative ITS2 regions, was successful only for distinguishing cryptic species from “true” members of M. pusillum. Therefore, to distinguish species, it is more effective to take into account all the CBC in ITS1 and ITS2 and analyze characteristic structural differences (molecular signatures) in the secondary structure of internal transcribed spacers. The genetic distances analysis of 18S–ITS1–5.8S–ITS2 nucleotide sequences showed that intraspecific differences in the genus ranged from 0 to 0.5 % and interspecific differences, from 0.6 to 4.7 %. Due to the polyphasic approach, it was possible to characterize 29 clusters and phylogenetic lines at the species level within the genus Micractinium and to make assumptions about the species.

Here we report new data describing the biodiversity of phytobenthic communities based on DNA-metabarcoding using the 18S rDNA marker and the Illumina MiSeq system. The study was initiated due to the blooming of filamentous algae (mainly of the genus Spirogyra) and cyanobacteria in the coastal zone of Lake Baikal under climate change and anthropogenic impact. The composition and taxonomic diversity of algae and other organisms associated with them on different sites of Lake Baikal (near Bolshoi Ushkaniy Island, in Listvennichny Bay) and in the Kaya (within the city of Irkutsk, located in the same drainage basin as Lake Baikal) were determined using DNAmetabarcoding. About 15 thousand reads of the 18S rRNA marker were obtained by applying NGS (next-generation sequencing). The species of algae dominating in the number of reads, as well as the difficult-to-identify taxa (Stramenopiles, Alveolata, Euglenozoa, Chromista, Rhizaria, Amoebozoa, etc.), which play an important role in the functioning and formation of the structure of algal communities, were revealed. The Shannon index of the communities studied ranges from 1.56 to 2.72. The advantages and weaknesses of using DNA-metabarcoding based on the 18S rRNA gene fragment for studying the structure of algal communities are shown. The advantage of this method is the possibility to more fully determine the diversity of eukaryotes taxa, which are difficult to identify by morphology, without involving a large number of specialists, while the disadvantage of the method is the distortion that may occur during the PCR. Here, ways of solving this problem are proposed. The results of the study show that the analysis of the minor component of the eukaryotic community in samples (organisms with low biomass) consisting of a mixture of multicellular and unicellular organisms requires a read-depths of at least 100,000 sequences per sample. In general, the DNA-metabarcoding method is recommended for studying the structure of algal communities and eukaryotes associated with them.

One of the greatest achievements of genetics in the 20th century is D.K. Belyaev’s discovery of destabilizing selection during the domestication of animals and that this selection affects only gene expression regulation (not gene structure) and influences systems of neuroendocrine control of ontogenesis in a stressful environment. Among the experimental data generalized by Belyaev’s discovery, there are also findings about accelerated extinction of testes’ hormonal function and disrupted seasonality of reproduction of domesticated foxes in comparison with their wild congeners. To date, Belyaev’s discovery has already been repeatedly confirmed, for example, by independent observations during deer domestication, during the use of rats as laboratory animals, after the reintroduction of endangered species such as Przewalski’s horse, and during the creation of a Siberian reserve population of the Siberian grouse when it had reached an endangered status in natural habitats. A genome-wide comparison among humans, several domestic animals, and some of their wild congeners has given rise to the concept of self-domestication syndrome, which includes autism spectrum disorders. In our previous study, we created a bioinformatic model of human self-domestication syndrome using differentially expressed genes (DEGs; of domestic animals versus their wild congeners) orthologous to the human genes (mainly, nervous-system genes) whose changes in expression affect reproductive potential, i.e., growth of the number of humans in the absence of restrictions caused by limiting factors. Here, we applied this model to 68 human genes whose changes in expression alter the reproductive health of women and men and to 3080 DEGs of domestic versus wild animals. As a result, in domestic animals, we identified 16 and 4 DEGs, the expression changes of which are codirected with changes in the expression of the human orthologous genes decreasing and increasing human reproductive potential, respectively. The wild animals had 9 and 11 such DEGs, respectively. This difference between domestic and wild animals was significant according to Pearson’s χ2 test (p < 0.05) and Fisher’s exact test (p < 0.05). We discuss the results from the standpoint of restoration of endangered animal species whose natural habitats are subject to an anthropogenic impact.

The Siberian wood frog Rana amurensis Boulenger, 1886 is the most hypoxia-tolerant amphibian. It can survive for several months in an almost complete absence of oxygen. Little is known about the mechanisms of this remarkable resilience, in part because studies of amphibian genomes are impeded by their large size. To make the Siberian wood frog more amenable for genetic analysis, we performed transcriptome sequencing and de novo assembly for the R. amurensis brain under hypoxia and normoxia, as well as for the normoxic heart. In order to build a de novo transcriptome assembly of R. amurensis, we utilized 125-bp paired-end reads obtained from the brain under normoxia and hypoxia conditions, and from the heart under normoxia. In the transcriptome assembled from about 100,000,000 reads, 81.5 % of transcripts were annotated as complete, 5.3 % as fragmented, and 13.2 % as missing. We detected 59,078 known transcripts that clustered into 22,251 genes; 11,482 of them were assigned to specific GO categories. Among them, we found 6696 genes involved in protein binding, 3531 genes involved in catalytic activity, and 576 genes associated with transporter activity. A search for genes encoding receptors of the most important neurotransmitters, which may participate in the response to hypoxia, resulted in a set of expressed receptors of dopamine, serotonin, GABA, glutamate, acetylcholine, and norepinephrine. Unexpectedly, no transcripts for histamine receptors were found. The data obtained in this study create a valuable resource for studying the mechanisms of hypoxia tolerance in the Siberian wood frog, as well as for amphibian studies in general.