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Vol 59, No 2 (2023)

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ОБЗОРНЫЕ И ТЕОРЕТИЧЕСКИЕ СТАТЬИ

Association of Allelic Variants A and B of the Beta-Lactoglobulin Gene with Dairy Productivity of Cattle

Parygina E.V., Kozhevnikova I.S.

Abstract

The effectiveness of cattle selection for quantitative and qualitative traits that are of economic importance in dairy cattle breeding largely depends on the identification of the genes that control these traits, as well as their allelic polymorphism. One such gene is the gene LGB encoding the protein beta-lactoglobulin. The review provides brief information about the structure and biological role of this protein, gene polymorphism. An analysis of the literature data of various studies was carried out, which made it possible to identify and evaluate the effect of the two most common alleles of the gene LGB (A and B) on the efficiency indicators of dairy production.

Genetika. 2023;59(2):127-134
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Symbiogenetics and Symbiogenesis: Molecular and Ecological Bases of Integrative Evolution

Provorov N.A., Tikhonovich I.A.

Abstract

Symbiogenetics is presented as a discipline aimed to study the combined genetic systems resulted from co-evolution of unrelated organisms. Their research complements the methodology of genetic analysis with the approaches of “genetic synthesis” aimed at characterizing the molecular and ecological factors of integration of heterologous genomes. Hologenomes and symbiogenomes that arise via integrative evolution (symbiogenesis) are dissected, like prokaryotic pangenomes, into the core and accessory parts. In hologenome, the core part, which is constant in composition, is represented by the host genome (nuclear-cytoplasmic system of heredity), and the variable accessory part composed by metagenome of the microbial community which is associated with the host and performs functions useful for it. Mechanisms of symbiogenesis go beyond the factors of evolution of free-living organisms and include: (a) interspecies altruism associated with the refusal of symbionts from autonomous existence, and upon a deep reduction, from the ability to maintain the genome; (b) inheritance by host of symbionts as of “acquired” genetic determinants (pangenesis). Under the impacts of these factors, symbionts can be transformed into cellular organelles that have lost their genetic individuality and sometimes lack genomes. Symbiogenesis is presented as a multi-stage process, including the emergence of: (i) genome-containing prokaryotic cell; (ii) multi-genomic eukaryotic cell; (iii) multicellular eukaryotes as holobionts composed of host organisms and associated microbial communities. Genome-free organelles that have retained the basic reproductive and metabolic functions can be used as models for reconstructing the early stages of cell evolution, including the emergence of cellular genome.

Genetika. 2023;59(2):135-146
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МОЛЕКУЛЯРНАЯ ГЕНЕТИКА

Structure and Diversity of Tc1/mariner Transposons in the Genome of the Jellyfish Aurelia aurita

Ulupova Y.N., Puzakova L.V., Puzakov M.V.

Abstract

Transposable elements, DNA transposons and retrotransposons are DNA sequences capable of movement within the genome. It is assumed that they play one of their key roles in adaptive and evolutionary processes. One of the most studied groups of DNA transposons is the infraclass ITm, and in particular the superfamily Tc1/mariner. In this work, we considered the representation, structure, and evolution of Tc1/mariner DNA transposons in the jellyfish Aurelia aurita. It was found that the predominant proportion of Tc1/mariner elements of the jellyfish is represented by the TLE family. A new subfamily of TLE elements called Aurum has been identified. In addition, two groups of elements VS-aura and VS-beplau were found in the Visitor family, which are probably also separate subfamilies. Analysis of the structure and diversity of Tc1/mariner elements showed that at the moment Tc1/mariner transposons in the jellyfish genome are at the stage of degradation and elimination. Almost all elements are deleted or have structural changes, and, accordingly, do not have potentially functional copies.

Genetika. 2023;59(2):147-156
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ГЕНЕТИКА ЖИВОТНЫХ

Polymorphism and Differentiation of the Evoron Vole Three Populations according to the mtDNA Control Region Variability

Sheremetyeva I.N., Kartavtseva I.V., Frisman L.V.

Abstract

As a result of the control region mtl DNA analysis for the Evoron vole, a high haplotype (97%) and nucleotide (1.53%) diversity was found. The data obtained indicate a low level of genetic differentiation populations. At the same time, populations geographically located closer are subdivided more strongly than remote ones. In general, there is agreement between the data on the variability of the mitochondrial DNA control region and chromosome races. However, if the data of chromosomal analysis indicate the preservation of the karyotype more ancient variants in the Evoron-Chukchagir lowland (“evoron” chromosomal race), then the data of molecular genetic analysis testify in favor of the preservation of the most ancient mt haplotype (106-19) in the upper Bureya depression population (“argi” chromosomal race).

Genetika. 2023;59(2):157-169
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Mitochondrial DNA Evolution Trends of Baikal Endemic Sponges. I. Mitochondrial Genome of S. khanaevi

Maikova О.О., Sherbakov D.Y.

Abstract

The nucleotide sequence of the mitochondrial genome of a new species of sponge from the Baikal endemic family Lubomirskiidae – Swartschewskia khanaevi was determined, the length of which was 26 638 bp. An increase in the rate of accumulation of nucleotide substitutions in protein-coding genes from 2 to 3 times relative to other species of sponges of the Lubomirskiidae family was revealed. On the phylogenetic tree, the species S. khanaevi clusters with another representative of the genus Swartschewskia. It was shown that all studied mitochondrial genomes of Lubomirskiidae are characterized by the presence of a large number and diversity of inverted repeats in intergenic regions, which distinguishes them from other members of the Demospongiae class.

Genetika. 2023;59(2):170-175
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Long-Term and Seasonal Dynamics of Inversion Polymorphism of the Malaria Mosquito Anopheles messeae Fall. (Diptera: Culicidae) in the Population of the Central Part of the Species Range (Western Siberia, Tomsk Region)

Sibataev A.K., Wasserlauf I.E., Usov K.E., Alekseeva S.S., Abylkassymova G.M., Stegniy V.N.

Abstract

The assessment of the level of genetic variability from 1974 to 2020 in the population of the malaria mosquito Anopheles messeae Fall. in the village of Kolarovo (Tomsk region) was carried out on the basis of cytogenetic analysis of polytene chromosomes. Analysis of the dynamics of inversion polymorphism of the malaria mosquito Anopheles messeae Fall. in the period from 1974 to 2020, according to the frequencies of inversion variants of chromosomes and gametes in the population village Kolarovo showed the replacement of “northern” variants in the period of the 90s of the last century with “southern” variants and the stabilization of these changes until 2020. The correlation of the frequency distribution of chromosomal inversions from 1972 to 2020 was revealed with an annual temperature including a semi-annual average April–September and semi-annual average October–March temperature. The results obtained made it possible to reveal the nature of dynamic processes associated with the modification of a specific ecological niche during a long period due to climate warming. The spatiotemporal stationarity (dynamic stability) of adaptive inversion polymorphism is evidence of high population-genetic (or rather species-specific) homeostasis and the absence of tendencies to speciation.

Genetika. 2023;59(2):176-183
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Genetic Differentiation of the Fourhorn Sculpin Myoxocephalus quadricornis (Linnaeus, 1758) and Its Position in the Tribe Myoxocephalini Taranetz (Cottidae: Myoxocephalinae)

Moreva I.N., Radchenko O.A., Petrovskaya A.V.

Abstract

A molecular genetic and karyological study of the fourhorn sculpin Myoxocephalus quadricornis (Linnaeus, 1758) was carried out. The karyotype was studied for the first time and the results of Ag-staining of the chromosomes of specimens of the species from the East Siberian Sea are presented. The karyotype of M. quadricornis is stable, contains 32 (10 metacentrics, 2 submetacentrics, 20 subtelocentrics) chromosomes, the number of chromosome arms is 44. Nucleolar organizers were found in the telomeric regions of the short arms of two homologous medium-sized subtelocentrics. Variability in the number of nucleolarforming chromosomes and stained blocks of nucleolar organizers was found. Common features in the chromosome sets of M. quadricornis and Megalocottus platycephalus indicate their greater similarity compared to species of the genus Myoxocephalus. The results of the karyological analysis are consistent with the molecular genetic data about the sister relationships between M. quadricornis and Megalocottus platycephalus. A complex of karyological and molecular-genetic features has been identified that allow one to reliably distinguish M. quadricornis from species of the tribe Myoxocephalini and indicate the need for its removal from the genus Myoxocephalus.

Genetika. 2023;59(2):184-195
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ГЕНЕТИКА ЧЕЛОВЕКА

Polygenic Analysis of Cytokine and Inflammatory Genes Polymorphisms in Chronic Obstructive Pulmonary Disease

Korytina G.F., Aznabaeva Y.G., Kochetova O.V., Nasibullin T.R., Akhmadishina L.Z., Khusnutdinova N.N., Zagidullin N.S., Victorova T.V.

Abstract

Chronic obstructive pulmonary disease (COPD) is a complex lung disease characterized by progressive airflow limitation and abnormal inflammatory response of the lungs to inhaled noxious particles or gases. COPD pathogenesis was linked to oxidative stress and systemic inflammation. We aimed to assess the association of cytokines and inflammatory genes polymorphisms and their combinations with COPD. SNPs of inflammatory genes FASLG (rs763110), IL19 (rs2243193), IL20 (rs2981573), IL24 (rs291107), PPBP (rs352010), IL4 (rs2243250), IL4 (rs2070874), С5 (rs17611), FAS (rs1800682), IL4RA (rs1805010), TGFb1 (rs1800469) was genotyped by the real-time polymerase chain reaction (PCR) among 601 COPD patients and 617 controls. Significant associations with COPD in the study group under additive genetic model were identified for IL19 (rs2243193) (P = 0.00001, OR = 0.73), IL4 (rs2243250) (P = 0.024, OR = 1.27), IL4 (rs2070874) (P = 0.00001, OR = 0.62), and for PPBP (rs352010) under the recessive model (P = 0.00001, OR = 2.34). Using the APSampler algorithm, we obtained gene-gene combinations that remained significantly associated with COPD; A allele of IL19 (rs2243193) and C allele of PPBP (rs352010) were the core element of the majority of protective patterns associated with COPD. The highest risk of COPD was conferred by combination of alleles: G of IL12A (rs2243115) with A of IL13 (rs20541) and C of IL4 (rs2070874) (OR = 2.72). The receiver operating characteristic (ROC) analysis resulted in an area under the curve (AUC) of 0.895 (95%CI 0.874–0.916) for model including SNPs: A allele of IL19 (rs2243193) and AA genotype of IL20 (rs2981573) combination, IL19 (rs2243193), IL12A (rs2243115), PPBP (rs352010), IL4 (rs2070874) together with age and smoking pack years, indicating a high ability of the model to correctly classify individuals with and without COPD.

Genetika. 2023;59(2):196-208
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Characterization of Novel F5 Intronic Variant Associated with Aberrant Splicing and Severe Factor V Deficiency

Pshenichnikova O.S., Yakovleva E.V., Zozulya N.I., Poznyakova Y.M., Demidova E.Y., Surin V.L.

Abstract

Congenital factor V deficiency is a rare autosomal recessive bleeding disorder, caused by defects in F5 gene and associated with bleeding manifestations of variable severity. In this study we report molecular and functional characterization of a novel F5 variant which causes aberrant splicing and significantly reduces protein expression in a patient with severe FV deficiency. We performed F5 mutation screening and functional study in a proband (FV:C 0.4%) with a history of gastrointestinal bleeding, post-traumatic bleeding, hematomas, ecchymoses, and discomfort in ankle joints since infancy. Sequencing revealed a novel homozygous F5 gene variant NC_000001.10:169519985G>C (or NM_000130.5:c.1297 –8C>G). Bioinformatics sequence analysis predicted that this variant would lead to the acceptor site loss of the intron 8/exon 9 junction. However mRN-A analysis identified, that it also activated the aberrant splice site located 7 nucleotides upstream of the normal one and was associated with the production of an anomalous F5 transcript with retention of seven nucleotides of intron 8 resulting in a premature stop codon. We revealed no traces of normal transcript in the patient. Our findings confirm that not only changes in canonical splicing dinucleotides could significantly disrupt the splicing sites and impair pre-mRNA processing.

Genetika. 2023;59(2):209-216
pages 209-216 views

Gene–Gene Interactions and Biological Network Analysis of Diseases with Disturbances of Human Cognitive Functions

Bocharova A.V., Stepanov V.A.

Abstract

Neurological and mental diseases, such as schizophrenia, Alzheimer’s disease, bipolar disorder, Parkinson’s disease, have complex phenotypes with cognitive impairment. These diseases are socially significant pathologies and serious problems for world health and are distinguished by the multilevel nature of the implementation of genetic information. A number of active genes are involved in the formation of the final phenotype. Thereby, it is necessary to apply the analysis of biological networks aimed at identifying the interacting genes and proteins that lead to the pathogenesis of the disease, in order to understand the molecular mechanisms underlying the studied pathology. In this study, various online resources and databases were used to implement this approach: WebGestalt, Gene Ontology, STRING. The protein-protein interaction network was obtained, where two subnets are distinguished, one of which is involved in the risk of developing schizophrenia, and the other in the risk of developing Alzheimer’s disease.

Genetika. 2023;59(2):217-225
pages 217-225 views

Associations of Polymorphic Loci of Matrix Metalloproteinase Genes with the Development of Breast Cancer in Women Central Chernozem Region of Russia

Pavlova N.V., Ponomarenko I.V., Orlova V.S., Batlutskaya I.V., Efremova O.A., Churnosov M.I.

Abstract

The association of polymorphic variants of matrix metalloproteinase (MMP) genes with breast cancer (BC) in women of the Central Chernozem region of Russia, taking into account the presence/absence of a burdened family history, was studied. The study included 358 patients with breast cancer (68 patients had a burdened family history) and 746 women of the control group. Genotyping of 10 polymorphic loci of MMP genes (rs1799750 MMP1; rs243865 MMP2; rs679620 MMP3; rs1940475 MMP8; rs17576, rs17577, rs3918242, rs2250889, rs3787268, rs3918249 MMP9) was performed. To study the associations of polymorphic variants of MMP genes with breast cancer in two subgroups, taking into account the presence/absence of a burdened family history (the control group for these two subgroups was the same), the method of logistic regression analysis was used. It was revealed that a low risk of developing the disease among women with a burdened family history is associated with polymorphisms rs243865 MMP2 (OR = 0.53–0.54, pperm ≤ 0.03) and rs2250889 MMP9 (OR = 0.36–0.37, pperm ≤ 0.04). In women without burdened heredity, an increased risk of developing breast cancer is associated with rs3787268 MMP9 (OR = 2.16, pperm = 0.03) and haplotypes of polymorphic loci of the MMP9 gene (pperm ≤ 0.05): CA rs3918249–rs17576 (OR = 2.15), CCA rs3918242–rs3918249–rs17576 (OR = 1.69), CCAG rs3918242–rs3918249–rs17576–rs3787268 (OR = 1.69), CAGCG rs3918249–rs17576–rs3787268–rs2250889–rs17577 (OR = 3.06). Three haplotypes are associated with a low risk of breast cancer in women without burdened heredity: GG rs17576–rs3787268 (OR = 0.60), GGC rs17576–rs3787268–rs2250889 (OR = 0.63), and CGG rs3918249–rs17576–rs3787268 (OR = 0.62).

Genetika. 2023;59(2):226-237
pages 226-237 views

КРАТКИЕ СООБЩЕНИЯ

The CRP Gene’s Role in the Relations between Childhood Adversity and History of Suicide Attempts in Schizophrenia

Alfimova M.V., Lezheiko T.V., Gabaeva M.V., Plakunova V.V., Mikhailova V.A., Kaleda V.G., Golimbet V.E.

Abstract

Research suggests that, in contrast to circulating C-reactive protein (CRP), genetic variants conferring higher CRP levels have protective effects against schizophrenia and moderate influences of season of birth on the development of the disease. This study aimed to explore whether the CRP gene also moderates the relations between childhood adversity and clinical characteristics of schizophrenia. The relations between childhood adversity, genotypes at rs2794521within the CRP locus, syndromes measured as five factors and two negative subfactors of the Positive and Negative Syndrome Scale, and history of suicide attempts were analyzed in 921 schizophrenia patients using analyses of covariances, Pearson’s chi-squared test, and logistic regression. A significant effect of genotype on suicide attempts in patients exposed to childhood adversity was found. The result suggests a moderating role of genetic determinants of inflammation in translating early life psychological stress effects into risk of suicide attempts in schizophrenia.

Genetika. 2023;59(2):238-243
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ХРОНИКА

pages 244 views

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