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Vol 18, No 2 (2020)

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Opinions, discussions
Von Willebrand factor and endothelial damage: a possible association with COVID-19
Aksenova A.Y.
Abstract

COVID-19 caused by the SARS-CoV-2 virus is a new type of infection which has caused an enormous social and economic burden across the world. While most people will develop a mild-to-moderate form of the disease or even stay asymptomatic, a certain proportion will get critically ill. COVID-19 mortality risk is higher in elderly patients and in patients with cardiovascular diseases and diabetes. Molecular mechanisms which underlie these risks are not yet understood for COVID-19. Here I discuss a possible association of COVID-19 complications with von Willebrand factor (VWF) level and endothelial damage. VFW is an important prognostic marker of endothelial dysfunction and its level fluctuates depending on age. VWF level is also variable depending on sex and race. Importantly, chloroquine, a drug that showed potential efficacy for COVID-19 treatment, can influence VWF secretion and consequently its level and activity. I propose that VWF level and activity might be predictors of the COVID-19 morbidity and mortality; moreover the VWF might be involved in the pathogenesis of the disease. I suggest that a comprehensive study of VWF level in SARS-CoV-2 positive groups of people with mild and severe course of the disease should be undertaken.

Ecological genetics. 2020;18(2):135-138
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Genetic basis of ecosystems evolution
Genetic differentiation of two phenotypes of Plantago media L. In South Timan
Zakhozhiy I.G., Shadrin D.M., Pylina Y.I., Chadin I.F., Golovko T.K.
Abstract

Background. The investigation of the genetic nature of plant phenotypic variability is of great importance for understanding biological diversity, distribution and adaptation of plants to environmental conditions.

The aim of our work was to study the genetic differentiation of two phenotypes of Plantago media in South Timan.

Materials and methods. The genetic differentiation of light and shadow phenotypes of Plantago media plants was evaluated using intersimple sequence repeats (ISSR) markers.

Results. The population-genetic analysis of 210 loci revealed two clusters, which boundaries coincided with the boundaries between plants of light and shadow phenotypes. The results of the discriminatory analysis of the main components and AMOVA (FST = 0.07, p = 0.001) confirmed that there are statistically significant genetic differences between these phenotypes even though they possess a high genetic similarity.

Conclusion. Light and shadow Plantago media phenotypes adapted to different ecological conditions are genetically differentiated. The population genetic analysis using ISSR markers is a sensitive tool for identifying the genetic diversity of phenotypic plant variations formed under the influence of environmental factors.

Ecological genetics. 2020;18(2):139-148
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Expression of the ToxA and PtrPF2 genes of the phytopathogenic fungus Pyrenophora tritici-repentis at the beginning of the infection process
Mironenko N.V., Orina A.S., Kovalenko N.M.
Abstract

Background. Pyrenophora tritici-repentis causing a tan spot of wheat produces host-specific toxins.

Materials and methods. Two P. tritici-repentis isolates with different ability to cause necrosis on the leaves of wheat cultivar Glenlea (nec+ and nec) and with different expression level of ToxA and PtrPf2 (factor transcription gene) in vitro were used for analysis. ToxA gene expression in P. tritici-repentis isolates in planta was characterized using quantitative PCR.

Results. The expression of the ToxA gene in P. tritici-repentis ToxA+ isolates significantly increased when infected the wheat leaves compared to ToxA expression results obtained in vitro. The levels of ToxA expression in both isolates differed significantly after 24, 48 and 96 h after inoculation, however, the dynamics of the trait change over time were similar. However, the highest ToxA expression in the virulent (nec+) isolate in contrast with the avirulent (nec) isolate was observed at a point of 48 h. Whereas the expression of regulating transcription factor PtrPf2 in planta differed imperceptibly from expression in vitro throughout the observation period.

Conclusion. Obviously, the role of the fungal transcription factor in regulating the effector gene expression weakens in planta, and other mechanisms regulating the expression of pathogen genes at the biotrophic stage of the disease develop.

Ecological genetics. 2020;18(2):149-155
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Phylogenetic characteristic of nodul bacteria endemic for Southern Ural species of the genus Oxytropis (fabaceae)
Baymiev A.K., Vladimirova A.A., Akimova E.S., Gumenko R.S., Muldashev A.A., Chemeris A.V., Baymiev A.K.
Abstract

Background. An analysis of the spatial distribution of some taxonomically and ecologically related legumes in the Ural showed a nontrivial spatial distribution of related species of the genus Oxytropis DC of the Orobia Bunge section within the Uchalinsky uplands. Despite the similarities in ecology, these species practically do not grow together. Explicit spatial segregation of closely related plants over a relatively small area allows this phenomenon to be used as a convenient model for studying the effect of segregation of closely related legume species on the genetic composition of their nodule bacteria.

Materials and methods. The genetic diversity of nodule bacteria entering into symbiosis with O. kungurensis, O. baschkiriensis, O. approximata and O. gmelinii plants was studied. In addition, the polymorphism of their symbiotic genes has also been analyzed.

Results. Phylogenetic characteristics of nodule bacteria endemic for the Southern Ural belonging to 4 species of leguminous plants of the genus Oxytropis of the section Orobia: O. kungurensis, O. baschkiriensis, O. approximata, O. gmelinii which are characterized by spatial separation of the growth sites, also called plant segregation, are given. It was shown that all of them belong to the genus Mesorhizobium despite certain phylogenetic differences of bacteria. Analysis of the symbiotic genes of the analyzed strains revealed a lack of congruence of their phylogeny with the core part of the genome. It was found that the microsymbionts of O. baschkiriensis plants differ in the phylogeny of nod-genes from nodule bacteria of other plants of the Oxytropis genus and are close to microsymbionts of plants of the Lupinaster genus growing in the Southern Urals.

Conclusion. Acquisition of the property to enter into symbiosis with nodule bacteria of plants of the genus Lupinaster may turn out to be an adaptive mechanism that arose as a result of segregation of O. baschkiriensis from other species of Oxytropis.

Ecological genetics. 2020;18(2):157-167
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Culturable endophytic bacteria from stems and leaves of garden pea (Pisum sativum L.)
Vasileva E.N., Akhtemova G.A., Afonin A.M., Borisov A.Y., Tikhonovich I.A., Zhukov V.A.
Abstract

Background. Endophytic microorganisms inhabit internal tissues of most plants. However, little is known about endophytic community of the garden pea (Pisum sativum L.), an agriculturally important crop.

Materials and methods. Culturable endophytic bacteria were isolated from sterilized stems and leaves of three pea genotypes: K-8274 (cv. Vendevil), K-3358 (unnamed cultivar), and cv. Triumph. The taxonomic position of isolates was determined by 16S rRNA gene sequencing. The plant growth-promoting capabilityof identified bacteria was tested on the roots of watercress (Lepidium sativum L.).

Results. In total, out of 118 morphotypes of culturable endophytic bacteria identified, for 80 the taxonomic position was determined. Proteobacteria and Firmicutes were dominant phyla, and Actinobacteria were present in minority. Eight bacterial isolates demonstrated the plant growth-promoting capability, and one of them – KV17 (Rahnella sp.) maintained this capability after several passages and prolonged storage.

Conclusion. The plant growth-promoting bacteria isolated from pea stems and leaves can become a component of microbiological preparations.

Ecological genetics. 2020;18(2):169-184
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The state of gene pool of the basic forest-forming species of the white sea watershed (on the example of a Picea × fennica (Regel) kom. And Pinus sylvestris L.)
Ilinov A.A., Raevsky B.V., Chirva O.V.
Abstract

Background. The genetic diversity of forest tree species populations is a key factor contributing to their resistance against negative effects of human activity, and the global climate change. The aim of the present study was to evaluate the state of gene pools of the main forest-forming species in the White Sea watershed.

Materials and methods. Five populations of Norway spruce and seven populations of Scotch pine have been selected within the Arctic zone of the European part of Russia (the western part of the White Sea watershed), along with two boundary ones located near the northern borders of the abovementioned species areas. The analysis of the spruce samples had been performed using five nuclear SSR loci, while for the pine samples it was four. DNA fragments were separated on a sequencer CEQ 8000. The main criteria of the genetic diversity (A99%, Ho, He) and F-statistics were calculated.

Results. The marginal spruce populations were characterized by the largest magnitude of the genetic diversity (Ho = 0.46; He = 0.47) and isolation (FST = 0.33) compared to other populations of the same species. The differences were statistically significant. All pine populations studied demonstrated a higher level of genetic diversity (Ho = 0.50, He = 0.63) compared to spruce populations. The differences between the boundary and in-area populations were not statistically reliable (FST = 0.04).

Conclusion. Our investigation revealed a sufficiently high level of spruce and pine northern populations’ genetic diversity making them able to withstand expected negative effects of anthropogenic activity and global climate change.

Ecological genetics. 2020;18(2):185-202
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Genetic toxicology
Technical aspects of the electrophoresis stage in the comet assay
Zhanataev A.K., Anisina E.A., Pligina K.L., Lisitsyn A.A., Durnev A.D.
Abstract

Inter- and intralaboratory variability of results is still a serious issue in the comet assay. There are several technical conditions of procedure, which may critically affect the results and electrophoresis terms were identified as main. A comparative assessment of the expected and actual electric field strength in five electrophoretic tanks and the contribution of the revealed differences to the variability in DNA damage carried out. Only for one tank, the measured electric field strength coincided with the expected 1 V/cm, while for four it ranged from 0.6 to 2.0 V/cm. The values of DNA damage assessed in the same samples of mouse kidney cells differed between tanks up to 4.7-fold for induced and up to 10-fold for spontaneous DNA damage. High local variations in the electric field strength and solution temperature across the platform as well as in %DNA in the tail of identical cell samples within electrophoresis runs also revealed. These variations were reduced by recirculation of electrophoresis solution. The results show that discrepancy between the estimated and the actual electric field strength can be reason of inter-laboratory variation of the comet assay results. Recirculation of the solution during electrophoresis will be useful to control of intra-laboratory and intra-assay variations.

Ecological genetics. 2020;18(2):203-214
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Human ecological genetics
Genetic and biochemical investigation of the gamma-glutamylcyclotransferase role in predisposition to type 2 diabetes mellitus
Azarova I.E., Klyosova E.Y., Churilin M.I., Samgina T.A., Konoplya A.I., Polonikov A.V.
Abstract

Background. Imbalance in the system of redox homeostasis is an important link in the pathogenesis of type 2 diabetes (T2D). Gamma-glutamyl cyclotransferase is an antioxidant defense enzyme directly involved in the metabolism of glutathione, an endogenous antioxidant.

The aim of the study was to examine the association of single nucleotide polymorphisms (SNP) rs38420 (G > A), rs4270 (T > C), rs6462210 (C > T) and rs28679 (G > A) in GGCT gene with the risk of developing T2D.

Materials and Methods. The study included 1022 T2D patients and 1064 healthy volunteers. Genotyping of GGCT gene loci was performed using iPLEX technology on a MassARRAY Analyzer 4 genome time-of-flight mass spectrometer (Agena Bioscience).

Results. As a result, we identified for the first time the association of SNP rs4270 in the GGCT gene with the risk of T2D in the Russian population. We have also established genetic and environmental interactions associated with predisposition to the disease: protective effect of gamma-glutamyl cyclotransferase gene was observed only in non-smokers under condition of daily consumption of fresh vegetables and fruits, whereas in persons with insufficient consumption of plant foods, as well as in all smoking patients protective effect of GGCT was not observed. In patients with T2D, the level of hydrogen peroxide and glutathione monomer was sharply increased compared to the controls. SNP rs4270 was also found to be associated with elevated levels of reduced glutathione in the plasma of type 2 diabetics.

Conclusion. Thus, for the first time it was established that polymorphic locus rs4270 in the GGCT gene is associated with a predisposition to T2D, but its relationship with the disease is modulated by smoking and fresh plant foods consumption.

Ecological genetics. 2020;18(2):215-228
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Human diseases associated with NTE gene
Melentev P.A., Agranovich O.E., Sarantseva S.V.
Abstract

Evolutionary conserved NTE gene is important for survival and functioning of nervous system cells, its dysfunction leads to various pathologies. Here we describe characteristics of different disorders induced by NTE protein activity inhibition (OPIDN) or by NTE gene mutations: hereditary spastic paraplegia (SPG39), Boucher – Neuhaüser, Gordon Holmes, Laurence – Moon, Oliver – McFarlane syndromes, Leber congenital amaurosis, pure cerebellar ataxia. Current review summarises accumulated data about clinical features of NTE associated diseases, presenting them in a historical way of biomedical studies, and observes molecular and genetic causes of these disorders.

Ecological genetics. 2020;18(2):229-242
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Polymorphism of GC gene, encoding vitamin D binding protein, in aboriginal populations of Siberia
Malyarchuk B.A.
Abstract

The analysis of the nucleotide sequences of exons and adjacent non-coding regions of the GC gene in 108 representatives of various ethnic groups of aboriginal population of Siberia was carried out. Polymorphism was found in four nucleotide positions: non-synonymous substitutions at the rs4588 and rs7041 loci, a synonymous substitution at the rs4752 locus, and a replacement in the non-coding region at the rs3733359 locus. Seven haplotypes of the GC gene were identified. Of these, 4 haplotypes encode the Gc1F isoform, 2 haplotypes encode the Gc1S isoform, and 1 haplotype encodes the Gc2 isoform. Between-regional differences were found in the distribution of variants of the GC gene: in the northeast and in the central part of Siberia, the highest prevalence of the Gc1F and Gc1F/Gc1F variants is observed, and in the south and west of Siberia, the Gc2, Gc1S/Gc2 and Gc2/Gc2 variants are most common. In the case of the GC gene, gene-environment interactions are apparently aimed at creating a balance between the activity of vitamin D-binding protein and the level of 25-hydroxyvitamin D in the blood serum.

Ecological genetics. 2020;18(2):243-250
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Methodology in ecological genetics
Selective system based on fragments of the M1 virus for the yeast Saccharomyces cerevisiae transformation
Muzaev D.M., Rumyantsev A.M., Al Shanaa O.R., Sambuk E.V.
Abstract

Background. A selective system based on the M1 virus of the yeast Saccharomyces cerevisiae was proposed.

Methods. To create a recipient strain, a DNA fragment encoding the killer toxin of the M1 virus under the control of the regulated promoter of the GAL1 gene was inserted into the genome of S. cerevisiae strains Y-1236 and Y-2177.

Results. Integration of such expression cassette leads to the conditional lethality – resulting strains die on a medium with galactose when killer toxin synthesis occurs. A linear DNA fragment containing the gene of interest flanked by sequences homologous to the promoter of the GAL1 gene and the termination region of the CYC1 gene is used to transform the obtained strains. During transformation due to homologous recombination, the sequence encoding the killer toxin is cleaved and the transformants grow on a medium with galactose.

Conclusion. The proposed selective system combines the main advantages of other systems: the use of simple media, without the need to add expensive antibiotics, and a simplified technique for constructing expression cassettes and selecting transformants.

Ecological genetics. 2020;18(2):251-263
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