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Vol 21, No 4 (2023)

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From the Editorial Board

Ecological genetics. What is it? 20 years later

Inge-Vechtomov S.G., Barabanova L.V.

Abstract

This article deals with the 20th anniversary of the publication of the first issue of the Journal “Ecological Genetics”. The authors list the main prerequisites that determined the creation of the Journal with the aim of combining scientific research conducted in different areas of ecological genetics. The modern vision of ecological genetics within the framework of general biology is emphasized.

Ecological genetics. 2023;21(4):293-297
pages 293-297 views

Human ecological genetics

Environmental genetics and predictive medicine: 20 years later. New trends and old basis

Glotov A.S.

Abstract

This review, based on previously formulated hypotheses and our own research, examines the main modern trends in molecular medicine related to assessing the effect of environmental factors on the human genome. Information is provided about all programs for analyzing the human genome, their connection with biobanks, polymorphism and errors of the genome, and the importance of genomic clinical databases. Ten trends in molecular medicine over the past 20 years are separately highlighted. The formation of genetic dialectics between monogenic and multifactorial diseases is reflected. The path of development of molecular methods, the expansion of the role of the genetic laboratory in decision-making, and the emergence of genetic consultants are noted. The review presents new challenges in predictive medicine related to carrier screening and the development of preimplantation genetic testing. The situation with genetic testing related to an individual's susceptibility to environmental factors and diseases is summarized. Some attention is paid to evidence-based pharmacogenetic studies. Some new areas are considered — psychogenetics, sports genetics, genetics of sensitivity to coronavirus infection and others. In conclusion, the forecast of multifactorial diseases is reviewed, which is based on gene technologies and mathematical modeling and the creation of a new paradigm of a genetic passport — an omics map of reproductive health.

Ecological genetics. 2023;21(4):299-315
pages 299-315 views

Differential effect of estrogen and progesterone on in vitro growth of uterine leiomyoma cells with chromosome 7 deletions

Koltsova A.S., Efimova O.A., Baranov V.S., Yarmolinskaya M.I., Polenov N.I., Pendina A.A.

Abstract

BACKGROUND: The studies on how sex steroid hormones affect growth of uterine leiomyoma cells with chromosomal abnormalities is highly relevant for development of personalized tumor therapy.

AIM: To study in vitro the isolated and combined effects of estrogen and progesterone on uterine leiomyoma cells with chromosomal aberrations — deletions in 7q.

MATERIALS AND METHODS: The study was performed on 15 uterine leiomyomas, excised from 15 women of 26–44 years of age who were not treated with hormones. Uterine leiomyoma cells were cultured in hormone-free medium, in the medium supplemented with estrogen, progesterone or both hormones. The chromosome preparations were made and stained with QFH/AcD to perform conventional karyotyping and fluorescence in situ hybridization (FISH) to accurately describe chromosomal rearrangements. The frequency of uterine leiomyoma cells with chromosomal aberrations was assessed by interphase FISH.

RESULTS: Deletions in 7q were identified in 6 out of 15 karyotyped uterine leiomyomas; four of them had one clone with deletion in 7q whereas two others comprised two clones with 7q deletions of different length. The frequency of cells carrying deletions in 7q greatly varied in uterine leiomyoma samples cultured in hormone-free medium: from 3.5% to 93.6%. Exposure of cell cultures to estrogen and progesterone resulted in a fold change frequency increase in some of the uterine leiomyomas and decrease in the others. The most significant changes in the frequency of cells with deletions in 7q were registered in response to the isolated estrogen and, to a lesser extent, to progesterone exposure; less significant changes were observed after combined hormonal effect.

CONCLUSIONS: In uterine leiomyomas with deletions in 7q, the frequency of abnormal cells may either increase or decrease in response to estrogen and progesterone in vitro supplementation. The isolated effect of estrogen or progesterone on the frequency of uterine leiomyoma cells with deletion in 7q is more pronounced compared to the combined one.

Ecological genetics. 2023;21(4):317-328
pages 317-328 views

Genetic toxicology

M.E. Lobashev’s physiological theory of the mutation process and the formation of contemporary views on mutational changes in genetic material

Zhuk A.S., Stepchenkova E.I., Inge-Vechtomov S.G.

Abstract

Changes in mutation rates can significantly impact population size and its genetic structure, leading to the emergence of new traits and species. At the same time, the destabilization of genetic material is the main cause of hereditary and oncological diseases and aging. M.E. Lobashev was the first to point out the connection between mutations and repair. He introduced the concept of a premutation state or primary lesion of genetic material and suggested that mutagenesis is a physiological process in which mutations occurs during the repair of damaged genetic material due to non-identical restoration of its structure. The theories of M.E. Lobashev laid the groundwork for understanding the causes and mechanisms of inherited changes in genetic material, which have been experimentally confirmed in studies of replication, repair, and recombination. It is now known that mutations arise through a multistep process over time, due to ambiguity of one of template processes — DNA synthesis. Recent research made it possible to establish the physical nature of primary lesions and mutations, to develop various methods for their identification, and estimate the impact of primary lesions and mutations in the phenotype formation.

Ecological genetics. 2023;21(4):329-342
pages 329-342 views

Genetic basis of ecosystems evolution

Genetic diversity and autozygosity estimates in wild european boars and domesticated pigs

Bakoev S.Y., Romanets T.S., Korobeinikova A.V., Mishina A.I., Kolosova M.A., Romanets E.A., Kolosov A.Y., Getmantseva L.V.

Abstract

BACKGROUND: Pigs are one of the most widely distributed domestic animals. The study of their genetic diversity and selection loci is of great interest both in the field of genetics and animal breeding, and in the aspect of conservation and development of breeding resources and food security.

AIM: The aim of the presented work is to evaluate the autozygosity and the distribution of autozygosity segments (HBD) in wild boars and pigs of the main commercial breeds: Large White, Landrace and Duroc, and to search for selection loci related to adaptation to habitat conditions and selection pressure.

MATERIALS AND METHODS: The aim of the presented work is to evaluate the autozygosity and distribution of autozygosity segments (HBD) in wild boars and domestic pigs of the main commercial breeds: Large White, Landrace and Duroc, and to search for selection loci related to adaptation to habitat conditions and selection pressure.

RESULTS: Based on the results of the genome scan, the average autozygosity values in boars and pigs were in the range of 0.23–0.29, but in boars about 0.08 of the genome share is covered by HBD segments, presumably originating from ancestors who lived about 206 years ago; in pigs — originating from ancestors who lived about 64 years ago.

CONCLUSIONS: Only 3 segments met the criteria for top-HBD (frequency of at least 60% and at least 10 SNPs) in boars. In Large White, Landrace and Duroc pigs, 18, 9 and 35 segments were identified, respectively. In general, the analysis of HBD segments showed that they reflect the main breeding strategies aimed at developing commercial pigs.

Ecological genetics. 2023;21(4):343-355
pages 343-355 views

Analysis of arctic char (Salvelinus alpinus) haplotypes in the largest lakes of the North-West Region of Russia for genetic monitoring

Kiseleva M.N., Mitryushkina D.K., Filatova T.A., Golotin V.A., Zhukova A.A., Rozhkovan K.V., Mamaeva A.E., Apalikova O.V.

Abstract

BACKGROUND: Arctic char is a residential form of the Arctic char Salvelinus alpinus and a commercial target in Ladoga Lake. Caused by fishing the gradual decline in the number of ones in the largest lakes of the North-Western Region of Russia is compensated by measures for its artificial reproduction.

AIM: The aim of this work was to carry out gaplotyping of the arctic char (Salvelinus alpinus) population in the largest lakes of the northwestern region of Russia.

MATERIALS AND METHODS: The gaplotyping by PCR amplification in combination with restriction fragment length polymorphism (PCR-RFLP) of several amplified mtDNA regions, sequencing of the D-loop of mtDNA.

RESULTS: Screening studies of the genetic diversity of arctic char were carried out in three geographical population of the North-Western region of Russia and also the lake form of Arctic char from Sobachye Lake (Putorana Plateau, Western Siberia). The variability of a significant part (more than 35%) of the mitochondrial genome was analyzed including the regions of 16S rRNA/ND1/ND2 (2000 bp), COXI (567 bp), ND5/ND6 (2490 bp) and D-loop (1097 bp). Analysis of the nucleotide sequences of the control region mtDNA revealed 6 different haplotypes that were included in a single Eurasian group of char.

CONCLUSIONS: The panel of PCR-RFLP markers can serve as a tool for monitoring the genetic structure of the arctic char populations of Ladoga Lake under conditions of ones artificial maintenance.

Ecological genetics. 2023;21(4):357-368
pages 357-368 views

Metabolic profiling of leaves of four Ranunculus species

Smirnov P.D., Puzanskiy R.K., Vanisov S.A., Dubrovskiy M.D., Shavarda A.L., Shishova M.F., Yemelyanov V.V.

Abstract

BACKGROUND: Plant ability to survive oxygen deficiency is associated with the presence of various adaptations, majority of which are mediated by significant changes of metabolism. These alterations allow resistant wetland plants to grow even in an oxygen-depleted environment.

AIM: To compare metabolic profiles of the leaves of the wetland species Ranunculus lingua, R. repens and R. sceleratus, and the mesophyte species R. acris growing in their natural habitat in order to identify the most characteristic metabolic traits of hypoxia-resistant plants.

MATERIALS AND METHODS: Metabolite profiling was performed by GC-MS. Statistical analysis of metabolomics data was processed using R 4.3.1 Beagle Scouts.

RESULTS: The resulting profile included 360 compounds. 74 of these were identified and 114 compounds were determined to a class. Sugars (114) were the most widely represented in the obtained profiles. 10 amino and 23 carboxylic acids, lipids and phenolic compounds have been identified. Significant differences were revealed between the profiles of leaf metabolomes of all tested species, which were clustered according to phylogenetic relation. The hydrophytic R. sceleratus, growing under submergence, showed the most unique metabolome, in which the level of sugars was reduced and intermediates of anaerobic metabolism, nitrogen metabolism, and alternative pathways of NAD(P)H reoxidation were accumulated. The profile of mesophytic R. acris was markedly different by decreased levels of amino acids, fatty acids and sterols. The metabolite profiles of waterlogged hydrophytes R. lingua and R. repens occupied an intermediate position.

CONCLUSIONS: The identified differences of metabolomes of Ranunculus species are due to genetic determinants, ecological niche and direct impact of a stressor.

Ecological genetics. 2023;21(4):369-382
pages 369-382 views

Methodology in ecological genetics

Review of heterozygosity visualization approaches in the context of conservation research

Tomarovsky A.A., Totikov A.A., Yakupova A.R., Graphodatsky A.S., Kliver S.F.

Abstract

The assessment of heterozygosity level is one of the key metrics in conservation biology, as it contributes to the accurate design of conservation programs for endangered species. With the development of whole-genome sequencing technologies, it is now possible to more accurately estimate heterozygosity not only at the organismal level, but also at the population and species level. Contemporary conservation studies involve the processing of large volumes of whole-genome data, leading to problems of interpretation and necessitates the study of modern visualization methods for clear and correct presentation of results. In this review, we comprehensively examine the main types of visualization of heterozygosity assessments obtained using various approaches. We delve into the theory underlying each visualization method and discuss their characteristics using examples from studies of non-model species with different conservation statuses. The review provides insight into current tools for heterozygosity assessment and subsequent visualization, as well as current trends in this field.

Ecological genetics. 2023;21(4):383-400
pages 383-400 views

Opinions, discussions

The peculiarities of cell elongation growth of cereal coleoptiles under normal and flooding conditions

Kirpichnikova A.A., Kudoyarova G.R., Yemelyanov V.V., Shishova M.F.

Abstract

The review examines modern knowledge on the mechanisms of the early stages of plant cell elongation growth. Coleoptiles are used as a model object representing juvenile organs of cereal seedlings. Elongation growth is considered to be a protective morphophysiological stage of seedling development during hypogeal germination. The molecular mechanisms of elongation growth include: changes in the properties of the cell wall, activation of proton pumps, as well as aquaporins of plasma membrane and tonoplast. Particular attention is paid to the hormonal system of regulation, including auxin and ethylene. Coleoptiles of rice, a semi-aquatic plant tolerant to oxygen deficiency, demonstrate that the mechanisms of elongation growth are changing intensively under submergence, but they completely ensure cell growth. There is also a redistribution of importance and abundance between phytohormones. The data presented in the review indicate the necessity to continue investigations on the mechanisms of elongation growth under normal and stress conditions.

Ecological genetics. 2023;21(4):401-417
pages 401-417 views


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