Ecological genetics

medical and biology peer-review journal publishes from 2003

English version Russian Journal of Genetics: Applied Research was published from 2011 to 2018

Since 2019 the journal publishes papers in Russian and English in parallel.


professor Sergei G. Inge-Vechtomov 


Journal mission

The journal Ecological genetics accepts for consideration original manuscripts that clarify all aspects of interactions between genetic and ecological processes on any types of organisms and on all levels of living system organization, from molecular to ecosystem one.


The editorial board accepts manuscripts that reflect the results of field and experimental studies, and fundamental research of broad conceptual and/or comparative context.

We welcome the publication of materials that:

  • make a significant contribution to the development of general biological theory and methodology of ecological and genetic research;
  • contribute to a better understanding of genetic mechanisms of the regulation of intra– and inter–species interactions of organisms, as well as ‘organism–environment’ interactions;
  • contribute to a better understanding of modern issues in general biology.

Publications of the journal would be of interest to a wide range of specialists in the fields of ecology, genetics, biochemistry, general biology, evolutionary theory, as well as for physicians and teachers and students of various biological and medical profiles.

The official languages of the journal are English and Russian. The English version of the article appears on the website three months after the publication of the Russian version.


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Vol 20, No 4 (2022)

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Genetic basis of ecosystems evolution

Identification of cryptic forms of the hybridogenic complex of European water frogs (Pelophylax esculentus complex) in the conditions of transformed biotopes of the south of the Central Russian Upland based on DNA markers
Barkhatov A.S., Snegin E.A.

AIM: The aim of the study was to carry out species identification of the hybridogenic complex of European water frogs (Pelophylax esculentus complex) in the conditions of transformed biotopes of the south of the Central Russian Upland based on molecular genetic markers

MATERIALS AND METHODS: The study included 36 local populations (770 individuals) living in conditions of transformed biotopes of the south of the Central Russian Upland. Identification of cryptic forms was carried out by a Multiplex PCR. Two molecular genetic markers were used for amplification: intron 1 of the SAI-1 DNA serum albumin gene to determine hybrids and cryptic forms, and a fragment of the first subunit of the cytochrome oxidase COI mtDNA gene to determine maternal lines.

RESULTS: According to the data obtained, “pure” R-type population systems predominate (58.33%) in the study region. Mixed RE-type population systems were identified in 14 localities, REL-type in the region is extremely rare and is noted only in one locality. No pure L-type, E-type, or mixed LE-type population systems have been identified. The study revealed a statistically significant (p < 0.001) predominance of haplotypes of the “Western” form (Pelophylax ridibundus).

CONCLUSIONS: The data obtained indicate active adaptive changes in the population structure of European water frogs in the study area. Degradation of water bodies caused by abiotic and anthropogenic factors forces amphibians to migrate to neighboring reservoirs in which hybridization of representatives of this complex occurs. Introgressive and hybrid forms of the marsh frog, as well as hybrid edible individuals with greater ecological plasticity and tolerance to anthropogenic pressure, displace populations of Pelophylax lessonae. Based on the above, we consider it necessary to include the pond frog (P. lessonae) in the Red Book of the Belgorod region.

Ecological genetics. 2022;20(4):247-260
pages 247-260 views
Genetic structure and differentiation of Scots pine (Pinus sylvestris L.) populations in the Middle and Upper Volga Regions
Sheikina O.V.

BACKGROUND: Due to broad geographical and ecological distribution of Scots pine we witness the shaping of a significant species heterogeneity. There is a demand in researching the features of the genetic structure and differentiation of Scots pine populations in different parts of the range.

MATERIALS AND METHODS: 12 populations were scrutinized with the use of ISSR markers. The genetic structure was assessed by estimating basic indicators of genetic diversity (the number of alleles per locus, the number of effective alleles, and the expected heterozygosity) and by the analysis of molecular variance (AMOVA). Genetic differentiation was assessed by Nei’s GST statistic, Mantel test, Principal Coordinates Analysis (PCoA), and creating a tree diagram.

RESULTS: Populations that grow on the right bank of the Volga in the northern and central parts of the Volga Uplands are characterized by a higher genetic diversity (Na = 1.84–1.89; Ne = 1.34–1.39; He = 0.217–0.241) and a lower subdivision (GST = 0.092). Populations that grow on the left bank proved lower rates of genetic variability (Na = 1.68–1.81; Ne = 1.27–1.35; He = 0.174–0.218) while the divergence was higher (GST = 0.179). Much of the genetic variability is within the populations (more than 80%).

CONCLUSIONS: The study determined differences in the genetic structure and the degree of differentiation of Scots pine populations, that grow on different banks of the Volga in the Middle and Upper Volga Regions.

Ecological genetics. 2022;20(4):261-270
pages 261-270 views
Diversity of PsSym29 and PsNRLK1 genes in the VIR germplasm collection of pea (Pisum sativum L.)
Zhukov V.A., Zhernakov A.I., Belozerova M.Y., Dodueva I.E., Lebedeva M.A., Lutova L.A., Tikhonovich I.A.

BACKGROUND: N.I. Vavilov Institute of Plant Genetic Resources (VIR) (Saint Petersburg, Russia) maintains a large collection of pea (Pisum sativum L.). Earlier, several growth and yield parameters were recorded for plants of 99 accessions grown under inoculation with nodule bacteria and arbuscular mycorrhizal fungi.

MATERIALS AND METHODS: Polymorphism of genes encoding symbiotic receptor kinase PsSym29 [participating in the autoregulation of nodulation (AON) system] and closely related receptor kinase PsNRLK1 (with yet unknown function in symbiosis) was assessed in 99 pea genotypes from the VIR collection. Nucleotide diversity, Tajima’s D, and Fay and Wu’s H statistics were calculated using DNAsp 5.0 software. The significance of associations of allelic state of the sequenced genes with the growth and yield parameters was tested by two-way ANOVA followed by FDR correction and by regression analysis.

RESULTS: Nucleotide diversity and the ratio of synonymous to non-synonymous substitutions was greater in PsNRLK1 as compared to PsSym29. The analysis of Fay and Wu’s H in sliding window revealed signatures of positive selection in one site of PsSym29 and in three sites of PsNRLK1 gene sequences located in 1st exons encoding LRR (leucine rich repeat) domains. No significant associations of allelic state of neither PsSym29 nor PsNRLK1 genes was found with plant growth and yield parameters.

CONCLUSIONS: The sequences of both PsSym29 and PsNRLK1 genes undergo positive selection, but the conditions in which specific allelic states of the genes become adaptive are to be elucidated in future.

Ecological genetics. 2022;20(4):271-278
pages 271-278 views
Metabolite profiling of leaves of three Epilobium species
Puzanskiy R.K., Smirnov P.D., Vanisov S.A., Dubrovskiy M.D., Shavarda A.L., Shishova M.F., Yemelyanov V.V.

BACKGROUND: The ability of plants to adapt to oxygen deficiency is associated with the presence of various adaptations, many of which are mediated by significant changes of metabolism. These changes allow resistant wetland plants to grow even in oxygen-deficient environment.

AIM: The aim of the study was to carry out metabolic profiling of the leaves of the wetland species Epilobium palustre and Epilobium hirsutum, and the mesophyte species Epilobium angustifolium in order to identify the most characteristic metabolome traits of hypoxia-resistant plants.

MATERIALS AND METHODS: Metabolite profiling was performed by GC-MS. Statistical analysis of metabolomics data was processed using R 4.2.1 Funny-Looking Kid.

RESULTS: The resulting profile included about 360 compounds. 70 of these were identified and 50 compounds were determined to a class. Sugars (64) were the most widely represented in the obtained profiles. 16 amino and 20 carboxylic acids, lipids and secondary compounds have been identified. Significant differences were revealed between the profiles of leaf metabolomes of mesophyte E. angustifolium and hydrophytes E. hirsutum and E. palustre. The mesophyte was characterized by high levels of sugars. The metabolomes of wetland Epilobium species practically did not differ from each other and were characterized by the accumulation of amino acids, including GABA shunt intermediates, dicarboxylic acids of the Krebs cycle, and metabolites of glycolysis and lactic acid fermentation, which reflects the stimulation of anaerobic respiration, nitrogen metabolism, and alternative pathways of NAD(P)H reoxidation in wetland plants.

CONCLUSIONS: Traits of metabolic profiles detected in hydrophyte Epilobium species can be used to assess the degree of plant resistance to oxygen deficiency.

Ecological genetics. 2022;20(4):279-293
pages 279-293 views

Genetic toxicology

Genotoxic effects of antiepileptic drugs. Literature review
Eremina N.V., Zhanataev A.K., Durnev A.D.

Based on the selected criteria data from studies of the genotoxic activity of antiepileptic drugs in eukaryotic test systems in vitro and in vivo, performed by DNA comet assay, chromosomal aberrations and micronuclei assays, published in the period 1995–2022, were selected and summarized.

Among the 20 drugs reviewed, for one drug (N03AA05 Benzobarbital), there are no data on studies of genotoxic activity; for 7 drugs information is presented only as a summary on the FDA and EMA websites without primary data and information on experimental designs. Among the remaining 12 drugs, only three drugs (phenobarbital, valproic acid and levetiracetam) have information on in vivo studies, both by DNA damage assay and by cytogenetic methods. Based on known publications, it is impossible to draw reasonable conclusions about the genotoxic potential of individual drugs. The available data are fragmentary, incomplete and contradictory. It remains to state the facts of detection of genotoxic effects in individual drugs in separate studies. In general, there is no doubt about the potential genotoxic hazard of this group the drugs in.

Additional studies are needed to clarify the data on the genotoxicity of antiepileptic drugs including beyond the standard protocols. In the course of their implementation, one should take into account the possible tissue-specific manifestation of antiepileptics genotoxicity, as indicated by the facts of genotoxic effects detection in tissue cells that are not targets in classical genotoxic studies. The expediency of objectifying approaches when choosing a drug for safe therapy, taking into account information about its genotoxicity, is emphasized, and the prospects for possible studies on antigenotoxic prophylaxis in patients with epilepsy are pointed out.

Ecological genetics. 2022;20(4):295-313
pages 295-313 views
Relationship between methylation of promoters of apoptosis genes in blood lymphocytes with the frequency of chromosomal aberrations and the dose of radiation
Isubakova D.S., Tsymbal O.S., Litviakov N.V., Milto I.V., Takhauov R.M.

BACKGROUND: Impaired apoptosis can have serious consequences: the accumulation of mutant cells, the development of teratogenic effects and malignant neoplasms. In this regard, the study of the mechanisms of changes in the activity of apoptosis due to methylation under the influence of long-term irradiation is urgent.

AIM: The study of the degree of methylation of gene promoters involved in the induction of apoptosis in the personnel of the Siberian Chemical Plant, exposed to long-term technogenic irradiation of ionizing radiation in the course of their professional activities.

MATERIALS AND METHODS: The study was performed on peripheral blood samples of employees of the Siberian Chemical Plant, with a total dose of external exposure from 100 to 300 mSv. Chromosomal aberrations were detected by standard karyotyping of cultured blood lymphocytes. The degree of gene promoters methylation was determined using MethylScreen technology.

RESULTS: The degree of gene methylation BIRC2, CASP3, CASP9, CIDEB, CRADD, DAPK1, DFFA, FADD, GADD45A, LTBR, TNFRSF21, TNFRSF25 ranges from 0.31 to 41.75%. A strong negative correlation was found between the degree of methylation of GADD45A (r = –0.7364, р = 0.009) with an increased frequency of aberrant cells, moderate negative correlation GADD45A (r = –0.6347, р = 0.035) with an increased frequency of dicentric chromosomes, moderate negative correlation CASP9 (r = –0.6606, р = 0.026), and strong negative correlation CIDEB (r = –0.7982, р = 0.003) with an increased frequency of chromatid fragments. A moderate negative correlation of the methylation degree of CASP9 (r = –0.6636, р = 0.026), and CIDEB (r = –0.6636, р = 0.026) with the total dose of external exposure was shown.

CONCLUSIONS: The decrease in the level of apoptosis at doses of 100–300 mSv can be explained by the achievement of the demethylation threshold for the promoters of the proapoptotic genes GADD45A, CASP9, CIDEB. This once again testifies in favor of the threshold model of the dependence of the radiation effect on the radiation dose.

Ecological genetics. 2022;20(4):315-323
pages 315-323 views
Chronic dust bronchitis: composition of the sputum bacterial microbiome and its association with chromosome damage in blood lymphocytes
Druzhinin V.G., Baranova E.D., Demenkov P.S., Matskova L.V., Paradnikova S.A., Volobaev V.P., Larionov A.V.

BACKGROUND: Recent studies show that the bacterial microbiome of the respiratory tract can influence the development of a number of diseases of the human respiratory system. Changes in the composition of the microbiome in patients are associated with dysbiosis, and in addition, many bacteria have a genotoxic potential and can directly or indirectly damage the genome in the cells of the host organism.

AIM: The aim of the study was to analyze the composition of the sputum microbiome and its relationship with chromosome damage in the blood leukocytes of patients with chronic dust bronchitis (CDB).

MATERIALS AND METHODS: The taxonomic composition of the sputum microbiome of 22 patients with CKD and 22 sputum donors from the control group was studied using next-generation sequencing (NGS) technology of 16S rRNA of bacterial genes. At the same time, the basic frequencies of chromosomal aberrations and micronuclei were determined in blood leukocytes.

RESULTS: The sputum microbiome of chronic dust bronchitis patients had a significant reduction in alpha and beta diversity parameters compared to healthy study participants. In addition, an increase in the relative abundance of the genus Streptococcus (29.97 ± 3.03 vs. 18.78 ± 2.47; p = 0.003) was found in the sputum of CP patients compared with the control. Thus, the results of metagenome sequencing indicate a common dysbiotic process with a predominance of one dominant genus of bacteria in this pulmonary pathology. The results of cytogenetic analysis of blood leukocytes showed a significant increase in the proportion of aberrant metaphases in CKD patients compared with healthy donors (3.41% vs. 1.84%; p < 0.01) and the absence of significant differences in frequency leukocytes with micronuclei between the compared groups (1.28% vs. 1.11%). Correlation analysis revealed the presence of significant direct relationships between the frequency of aberrant metaphases and the percentage of representatives of the genera Bacteroides in the sputum of patients with chronic dust bronchitis (r = 0.471; p = 0.031); Lachnoanaerobaculum (r = 0.446; p = 0.043) and Alloprevotella (r = 0.444; p = 0.044). Further studies should be devoted to the search for possible mechanisms of influence of these bacteria on clastogenic effects in the cells of the host organism.

Ecological genetics. 2022;20(4):325-337
pages 325-337 views

Methodology in ecological genetics

The synthesis of Broccoli RNA fluorescent aptamer in Saccharomyces cerevisiae yeast cells
Shanaa O.A., Rumyantsev A.M., Sambuk E.V., Padkina M.V.

BACKGROUND: RNA aptamers are short, single-stranded oligonucleotides, with remarkable binding ability to target molecules characterized by high specificity and affinity. Such targets are vastly diverse and range from specific ions to entire cells. RNA aptamers are widely used in biology and medicine for basic research, as well as for practical purposes as in therapy and diagnostics. At present, chemical or in vitro methods of synthesis are mainly used to obtain RNA aptamers. However, such methods are expensive and time-consuming with low productivity. Therefore, in vivo methods are becoming more attractive to researchers working on optimizing high-scale production of RNA aptamers.

AIM: The aim of this work is to develop a reporter system for optimizing the synthesis of small RNA molecules in Saccharomyces cerevisiae yeast cells.

MATERIALS AND METHODS: We used the Broccoli fluorescent RNA aptamer to develop a reporter system allowing us to optimize the conditions for in vivo short RNA synthesis in yeast cells. This aptamer is about 112 bp in size and binds to the fluorogenic dye DFHBI-1T. Only upon binding, the aptamer-dye complex exhibits fluorescence properties. After excitation using light with a wavelength of 482 nm, the aptamer-dye complex emission is observed with a peak at 505 nm.

RESULTS: We have designed a reporter system providing the synthesis of the fluorescent Broccoli RNA aptamer in S. cerevisiae yeast cells. Transcription of RNA molecules containing the aptamer is carried out by the regulated promoter of the GAL1 gene. The synthesized transcripts contain the HH and HDV ribozymes to ensure precise cleavage of the RNA aptamer sequences.

CONCLUSIONS: This reporter system is based on the Broccoli RNA aptamer, and it can be used to optimize the in vivo synthesis of RNA aptamers in S. cerevisiae yeast cells. This work serves an urgent task in connection with the active use of such aptamers in scientific research, biotechnology and medicine.

Ecological genetics. 2022;20(4):339-348
pages 339-348 views
Application of the IR spectrometry method in the screening study of various oat species
Khoreva V.I., Popov V.S., Kon'kova N.G.

BACKGROUND: The infrared reflection spectroscopy application method for rapid assessment of biochemical parameters in various types of oats is shown. On the basis of the biochemical data obtained in the laboratory of VIR, calibration models of protein, oil and starch content were constructed.

AIM: The aim of the study is to develop an express method of near-infrared spectroscopy (NIRS) spectroscopy to determine the main biochemical parameters in oat seeds and to build calibration models for the MATRIX-I IR analyser to quantify the mass fraction of protein, oil and starch in oat seeds based on data obtained by traditional methods.

MATERIALS AND METHODS: Biochemical quality indicators (protein, oil, starch) were studied on seeds of filmy oats (Avena sativa L.) grown in 2015–2016 in the North-Western Region of the Russian Federation. Calibration models for the determination of protein, oil and starch in oat seeds (98 samples, harvest 2014–2015) were developed for the MATRIX-I IR analyzer by Bruker Optics (Germany). Values obtained by traditional chemical methods of analysis were used to construct calibration models. Oat seed oil was determined by the Soxlet method, protein by the Kjeldahl method, starch by the Evers polarimetric method. All indicators were recalculated for dry weight.

RESULTS AND CONCLUSION: The reliability of the developed models was checked by the results of protein, oil and starch determination in the seeds of the test batch according to the indicator of the calibration correctness. The data obtained using the calibration curve on the MATRIX-I device had no significant differences with the results of chemical studies. Therefore, calibration can be used for screening analysis for protein, oil and starch content in oat samples. This method allows you to save valuable material, increase labour productivity due to the speed of obtaining data, does not require reagents and is safe.

Ecological genetics. 2022;20(4):349-357
pages 349-357 views
Comparasion of the effectiveness of anchor proteins ScAGα1p, KpCW51p, KpCW61p for surface display in yeast Komagataella phaffii
Tsygankov M.A., Rumyantsev A.M., Makeeva A.S., Padkina M.V.

BACKGROUND: Yeast display is an effective technology for exposure target proteins to the cell surface by fusing them with cell wall proteins. This technique, among other things, makes it possible to obtain vaccine preparations based on yeast by exposing antigen proteins on their cell surface. Finding and selecting proteins that allow effective exposure of target proteins on the surface of yeast cells is an urgent task.

AIM: The aim of this work was to evaluate the efficiency of cell wall proteins ScAGα1p, KpCW51p, KpCW61p for displaying the reporter protein on the Komagataella phaffii cell surface, including the study of several variants of the ScAGα1 gene coding sequence.

MATERIALS AND METHODS: The studied gene sequences were cloned under the control of the AOX1 gene promoter in the same reading frame as the eGFP reporter protein gene and integrated into the genome of the K. Phaffii yeast strain X-33.

RESULTS: Cytoimmunochemical analysis and confocal microscopy of strains displaying the eGFP protein on their surface under conditions of induction of the AOX1 gene promoter made it possible to identify the most effective anchor protein. The best efficiency was demonstrated for the sequence of the ScAGα1 gene without the native 3' non-coding region.

CONCLUSIONS: The plasmids obtained in the work will make it possible to obtain a yeast strain K. phaffii that effectively exposure proteins, including antigens, on its surface, which can be used as a vaccine preparation.

Ecological genetics. 2022;20(4):359-371
pages 359-371 views

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