bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic Introgression in Populations of Two Related Species Adalia frigida (Schneider, 1792) and Adalia bipunctata (Linnaeus, 1758) (Coleoptera: Coccinellidae) in the Zone of Sympatry
Authors: Romanov D. A. , Shaikevich E. V. , Zakharov I. A.
Published: April 2024

The haplotype diversity of mtDNA of the circumpolar species of ladybirds Adalia frigida collected in Yakutsk and Salekhard was studied. Based on the analysis of the nucleotide sequences of the cox1 gene, 18 mitochondrial haplotypes were identified, of which 14 were new. Of the 18 haplotypes of A. frigida, two (H32 and H9) are the most common. In the Salekhard region, the range of A. frigida overlaps with that of another closely related species, A. bipunctata. The value of divergence in the cox1 gene between A. frigida and A. bipunctata reaches 4.1–4.3% and corresponds to the level of differences characteristic of closely related species. These species are able to interbreed, the share of hybrid individuals (A. frigida and A. bipunctata) in Salekhard is 56.5%. Hybridization between A. frigida and A. bipunctata led to mutual mitochondrial introgression, which resulted in the acquisition of the H1 haplotype by the A. frigida beetles and the H9 haplotype by the A. bipunctata beetles.
Mathematical Model Development for Schizophrenia Risk Prediction Based on Assessment of Polymorphic Alleles Carriage in 13 Genetic Loci Affecting Pterin Metabolism
Authors: Zhilyaeva T. V. , Bavrina A. P. , Kasyanov E. D. , Blagonravova A. S. , Mazo G. E.
Published: April 2024

Real-time PCR was used to analyze the carriage of alleles in 13 genetic loci that affect pterin metabolism in 116 patients with schizophrenia and 62 healthy volunteers. To analyze the accuracy of predicting the risk of schizophrenia, we used the binary logistic regression method with the assessment of the contribution of all studied loci. Results: A mathematical model was developed that makes it possible to predict the risk of schizophrenia manifestation in a carrier of the combination of genotypes MTHFD1 1958CC/MTRR 66GG with a probability of 90.6%, MTHFD1 1958CC/MTRR66AG with a probability of 81.9%. The use of this model is expedient in routine psychiatric practice among individuals at high risk of schizophrenia manifestation after replication in other samples and obtaining a larger volume of observations.
A Genome-Wide Search of New Meat Productivity Candidate Genes in North Caucasian Meat and Wool Sheep Breed
Authors: Krivoruchko A. Yu. , Zuev R. V. , Surov A. I. , Skokova A. V. , Kanibolotskaya A. A. , Likhovid A. A. , Yatsyk O. A.
Published: April 2024

The search for new genes that affect the growth and development of muscle tissue and associated with meat productivity traits in sheep is an actual task. The implementation of this is inextricably linked with the prospects for the development of marker-assisted and genomic selection. Research presents data of new approach in the detection of candidate genes for sheep meat productivity. Animal genotyping was performed using Ovine Infinium HD BeadChip 600K DNA, association search was performed using PLINK v1.07 software. As a result of the work, identified SNPs that were significantly associated with phenotypic traits directly related to the level of meat productivity in the North-Caucasian meat and wool sheep: height at the withers, live weight at birth, thickness of adipose tissue, width of the muscle “eye”. To search for candidate genes, 19 polymorphisms with the highest association reliability were selected. Determining the location of the analyzed SNPs made it possible to identify 16 new candidate genes associated with lifetime meat productivity traits in North-Caucasian meat and wool sheep: CILK1, ENO4, CTPS2, GABRB2, SLC44A1, C12ORF45, SLC41A2, CASD1, SINE2, SLC35F1, RP, SH3KBP1, LRRIQ1, SWAP70, THBS1 and FSIP. Animal genotyping for these genes should be used in marker-associated breeding to improve sheep meat productivity and study their effect on the phenotype.
The Y-Chromosome Lineage Variation in Ancient and Modern Populations of the Sakha (Yakuts)
Authors: Fedorova S. A. , Zvénigorosky V. , Alekseev A. N.
Published: April 2024

This review presents the results of paleogenetic studies on the ancient population of Yakutia in the Middle Ages. The diversity of haplogroups and STR haplotypes of the Y chromosome of 74 men from Yakut burials from the 15th–19th centuries was considered and compared with the data on modern ethnogeographical groups of the Yakuts. A comparison of genetic reconstructions with historical data and the legends of the Sakha people was performed.
Analysis of the Allelofund of Semi-Fine-Wool Sheep of the Pechora Population Using STR Markers
Authors: Kaneva L. A. , Matyukov V. S. , Zharikov Ya. A.
Published: April 2024

The polymorphism of microsatellites was studied in semi-fine-wool sheep in the Romney-Marsh type of the Pechora population, bred with the participation of the now extinct northern short-tailed aboriginal sheep. Evaluation of the differentiation of groups of sheep of different genesis by the frequencies of STR loci genes, identification of private alleles and cluster analysis did not allow to obtain information about the allelofund of the aboriginal sheep. Absorption crossing into an improved breed with the selection of a crossbred population according to the target standards of semi-fine-wool breeds, apparently, led to the loss of the gene pool characteristic of the northern aboriginal sheep by the Pechora sheep.
About the Genetic Divergence of Populations Coupled by Migrations: Modern Modeling Based on Experimental Results of Yu.P. Altukhov and Coauthors
Authors: Zhdanova O. L. , Frisman E. Ya.
Published: April 2024

The existence possibility of stable differences in a selection-homogeneous range looks somewhat paradoxical from the population genetics point of view, but it is disruptive selection that can give such a divergence. Examples of population systems with stable divergence of the genetic structures of subpopulations living in a homogeneous area occur in nature and experimental systems. Comparison of these observations and modeling results allow us to explain the persistence of the stability of natural genetic divergence by the mechanism of interaction between disruptive selection (in the form of reduced fitness of hybrid forms) and a weak migration process. The results of experiments performed by Yu.P. Altukhov et al. with box populations of Drosophila melanogaster, in which the primary divergence of the genetic structures of the subpopulation at the α-GDH locus appeared, are in good agreement with this statement. One can assume the disruptive selection, in this case, the reduced fitness of heterozygotes in α-HDG, played the significant role in maintaining this divergence. An alternative hypothesis is genetic drift that fixed the differences. To identify and substantiate the possibility of the presence of this factor in a given system, and to assess the significant role that disruptive selection plays in maintaining the stability of primary genetic divergence, we analyzed mathematical models of the allele frequencies’ dynamics in a large panmictic population and in a system of 30 local migration coupled populations. Comparison of the simulation results with those of the experiment allows us to conclude with a high probability, in the considered experimental population system, there was a disruptive selection at the α‑GDH locus that facilitated the primary genetic divergence.
Flavin-Containing Monooxygenases (FMO) Genes in Garlic Allium sativum L.: Genome-Wide Identification, Characterization, and Expression Analysis in Response to Fusarium proliferatum
Authors: Anisimova O. K. , Shchennikova A. V. , Kochieva E. Z. , Filyushin M. A.
Published: April 2024

In this study, 39 flavin-containing monooxygenase genes were identified in the garlic (Allium sativum L.) genome. The distribution of AsFMOs into three phylogenetic clades associated with N-oxygenation (22 proteins), auxin biosynthesis (13 proteins), and S-oxygenation (4 proteins) has been shown. FAD and NADPH binding, FMO-identifying, and FATGY motifs were found in the AsFMO sequences. AsFMOs transcripts were present in all garlic organs with a maximum in roots, leaves, peduncle, and aerial bulbs. In response to infection with the pathogenic fungus Fusarium proliferatum, differential expression of clade I genes (AsFMO4, AsFMO11, AsFMO12, and AsFMO35) was detected in the roots of cv. Sarmat and Strelets, contrasting in Fusarium rot resistance. At the same time, the expression response of the clade III AsFMO18 gene involved in the alliin biosynthesis was similar for both cultivars, regardless of their resistance/susceptibility to Fusarium. This suggests the clades I and III genes redundancy in plant responses to infection. The AsFMO35 coding and regulatory sequences were analyzed in the Sarmat and Strelets cultivars. It was shown that the AsFMO35 promoter differs in the presence of the ABA-associated cis-regulatory element ABRE in cv. Strelets susceptible to Fusarium rot.
Genetic Variation in Titin in Patients with Hypertrophic and Non-Compact Cardiomyopathy
Authors: Chakova N. N. , Shulinski R. S. , Komissarova S. M. , Dolmatovich T. V. , Niyazova S. S. , Mazur O. Ch. , Ivanova A. S. , Liaudanski A. D.
Published: April 2024

Using NGS, the coding sequence of the TTN gene was sequenced in patients with left ventricular non-compaction cardiomyopathy (LVNC, 44 individuals) and hypertrophic cardiomyopathy (HCM, 74 individuals), as well as in the control (194 individuals), and 9 nucleotide variants leading to truncated titin (TTNtv) and 372 missense variants were identified. A comparative analysis of the genetic variability of titin between the groups of patients with LVNC and HCM and the control sample was carried out in terms of the type of mutations and their localization in the exons of genes, as well as in the sarcomeric and functional domains of the protein. The role of TTNtv in the development of LVNC was confirmed, and the significance of additional variants in the same gene or in other genes associated with various cardiomyopathies for the phenotypic implementation of TTNtv was demonstrated. 75% of patients with TTNtv had a dilated LVNC phenotype. Missense substitutions in the TTN gene were found both among the patients with LVNC and HCM, and in people in the control sample, which indirectly confirms that most missense variants in this gene are benign. The paper identifies and lists highly mutable and conserved exons of the TTN gene and also presents a list of missense mutations with possible clinical significance in relation to the structural pathology of the myocardium, including new variants. It was shown that the majority of pathogenic and potentially significant mutations were located in the A-zone of the sarcomere. In all the groups, about 30–50% of new variants were identified. Probably, many of them are neutral and are of exclusively population interest.
Population-Genetic Characteristics Ingush in the North Ossetia-Alania
Authors: Elchinova G. I. , Balinova N. V. , Kadyshev V. V. , Tebieva I. S. , Revazov Yu. A. , Zinchenko R. A.
Published: April 2024

In accordance with the Protocol of the genetic and epidemiological survey of the population, the study of the population-genetic characteristics of the Ingush of North Ossetia-Alania was carried out. The extended nature of reproduction was found (3.62). The Crow index is calculated in two ways – the classical one and according to the method proposed by N.H. Spitsina, which takes into account not only pre-productive, but also prenatal losses. The age parameters of reproduction are within the limits of those for other surveyed populations. A graphical comparative analysis of the components of the Crow’s index obtained by different methods is carried out. Low endogamy was revealed (0.13), positive but low ethnic marital assortativness (1.96). The scheme of the surname landscape shows two clusters corresponding to the Ingush and Ossetian populations.
Chromosomal Location of the b-Amy-A1 Gene and Distribution of Its Alleles in Winter Common Wheat Culture
Authors: Netsvetaev V. P. , Kozelets Ya. O. , Ascheulova A. P. , Petrenko A. V. , Akinshina O. V.
Published: April 2024

The analysis of the chromosomal location of the b-Amy-A1 gene, which controls the synthesis of wheat beta-amylase isoenzymes, was carried out by assessing the linkage with the B1 (Awnless) marker gene located in the long arm of chromosome 5A. Results based on F2 and F→∞ Delta × Selection 2092 study. The b-Amy-A1 locus showed 6.55 ± 2.10% linkage to the B1 gene. In parallel, alleles of the Rht8 locus, which causes dwarfing of plants, were identified and its linkage to the C gene (Compact spike) was established in 22.59 ± 6.28% (F2) and 24.22 ± 1.18% (F→∞) of recombination in chromosome 2D. The Delta variety carries the Rht8a allele, and the Selection 2092 accession carries the Rht8c allele. A collection of winter common wheat varieties created and released in the Russia was studied. The selected cultivars carried identical b-Amy-B1a and b-Amy-D1a alleles of the 4B and 4D chromosome loci. At the same time, the most common b-Amy-A1a and b-Amy-A1b alleles of chromosome 5A differed. It was found that in the direction from south to north of European part, the frequency of the b-Amy-A1a allele increases from 24.2% (Northern Caucasus) to 72.50% (Moscow–Ulyanovsk regions). Accordingly, the frequency of the alternative allele b-Amy-A1b decreased from 75.8% (Northern Caucasus) to 25.0% (Moscow–Ulyanovsk regions). In the Rostov region, the ratio of the occurrence of alleles b-Amy-A1a to b-Amy-A1b was 42.5 to 57.5%. At the same time, already in the Central Chernozem region+, a significant dominance of the b-Amy-A1a allele over b-Amy-A1b was manifested. Using the collection of varieties as a population of F→∞ demonstrated the linkage of b-Amy-A1 with B1 value in 5.56 ± 1.90% recombination.
Pilot Study to Detect the Repertoires of T-Cell Receptor Gamma Chains in Patients with Juvenile Schizophrenia
Authors: Plotnikova M. Yu. , Patrikeev A. D. , Levchenko A. Yu. , Fedorenko O. Yu. , Andreeva T. V. , Rogaev E. I.
Published: April 2024

Disfunction of immune system and neuroinflammation may play a role in pathogenesis of schizophrenia. The role of adaptive immune system has to be elucidated. We present a pilot study to test the methodology of profiling of immune repertoires of the TCR gamma chain by deep sequencing using several patients with juvenile schizophrenia and unaffected control subjects. The clonotype profiles were revealed and their diversity and presumable differences in structure of CDR3 TRG region of functional clones in juvenile schizophrenia and controls were estimated. This approach is perspective for further comprehensive study of changes in adaptive immune system in representative cohorts of patients with different forms of schizophrenia.
Variability of Supernumerary Chromosome Morphotypes and the Emergence of Micro-B-Chromosomes in the Karyotype of Apodemus peninsulae (Rodentia) in the Russian Far East
Authors: Roslik G. V. , Kartavtseva I. V.
Published: April 2024

Variability in the number and morphotypes of macro, as well as mini and micro B-chromosomes of Apodemus peninsulae in the valley Zeya River from Amur region is described. Micro B chromosomes were found in the karyotypes of the Korean field mice from the Far East of Russia for the first time. Two opposite trends in the geographic variability of B chromosome morphotypes have been identified. The first one is due to the presence/absence of mini and/or micro, in addition to macro B-chromosomes, in animals from the right and left river banks in the northeastern part of the Upper Zeya Plain, as well as in the northern part of the Amur-Zeya Plain. The second is a clinal variability is characterized by a gradual increase in three combined geographic populations of A. peninsulae of numerical parameters of B-chromosomes: index x̄В Max micro, x̄В Max macro, the number of morphotypes, the number of clones in mosaics, and the proportion of mosaics in the direction from north to south of the Zeya River valley. The revealed diversity of A. peninsulae B-chromosome morphotypes for 13 regions allows us to re-evaluate the geographical variability of additional chromosomes of this species in the Russian Far East Adaptive value of B-chromosome morphotypes for the species has been also assumed.
Phylogeography of Oak Species in the Caucasus Based on the Results of Chloroplast DNA Analysis
Authors: Semerikova S. A. , Aliev Kh. U. , Semerikov N. V. , Semerikov V. L.
Published: April 2024

In order to study the biogeography and history of the temperate biota of the Caucasian region, one of the centers of biological diversity of Eurasia, the phylogeographic structure of the chloroplast DNA of roburoid oaks (Quercus L. sect. Quercus, Fagaceae) was studied. We analyzed 926 trees of five species (Quercus robur, Q. petraea, Q. pubescens, Q. hartwissiana, Q. macranthera) from 70 populations located in different parts of the Caucasus. Sequencing of five fragments with a total length of more than 10 000 bp revealed eight haplotypes, which were typed using chloroplast microsatellite loci (cpSSR), sequencing, and restriction analysis. The Quercus phylogenetic tree, which includes 34 chloroplast haplotypes of Western Eurasian and East Asian roburoid species, confirmed the monophyly of roburoid oaks, which form several lines that do not have supported topological relationships with each other. The haplotypes identified in the Caucasus belong to two divergent Western Eurasian lineages. These haplotypes are endemic for the Eastern Black Sea and Caucasian region and do not have related haplotypes beyond its borders, which indicates the long-term presence of oaks in the Caucasus and the historical links of the oaks of the Caucasian region with the Eastern Crimea and Eastern Turkey in the absence of chloroplast DNA exchanges with the Eastern European part of the range. The results of the present study indicate that Caucasian populations could not significantly contribute to the colonization of northern territories, and were not influenced by more northern populations, at least through seed transfer. The distribution zones of the Caucasian haplotypes almost do not intersect with each other, occupying certain geographical areas, probably due to the settlement from individual glacial refugia and genetic drift. The geographical structure of chloroplast DNA variability indicates a long-term presence of oak in addition to Western Transcaucasia (Colchis refugium), in the regions of the Northwestern, Central, Eastern Caucasus and the Lesser Caucasus. The coincident composition of the haplotypes of the studied oak species within the geographic regions indicates the long-term coexistence of different species in different parts of the Caucasus.
Search for Candidate Genes for Mutations Disrupting Synaptonemal Complex Formation in the Sequenced Genome of Rye Secale cereale
Authors: Sopova J. V. , Zykin P. A. , Dolmatovich T. V. , Sosnikhina S. P.
Published: April 2024

The formation of a synaptonemal complex between homologous chromosomes during prophase I of meiosis is of great importance for the normal course of the recombination process. Disturbances in the formation of the synaptonemal complex can lead to both asynapsis (in this case, univalents will be present at the metaphase I stage) and heterologous synapsis (both univalents and multivalents will be detected at the metaphase I stage). Previously, we obtained rye mutants in which no formation of synaptonemal complexes (sy1 and sy9) was observed or the synapsis was heterologous (sy10, sy18 and sy19). We performed a bioinformatics analysis of the annotated rye genome and identified potential candidate genes for each of these mutants. The choice of candidate genes was carried out on the basis of microsatellite mapping data and their comparison with annotated sequences of the rye genome. As a result, the following genes were selected: Mei2-like for the sy1 mutant, MAD2 for the sy9 mutant, BUB3.3 and BUB3.1 for sy10 and sy18, respectively, and Meiosis 5 for sy19.
The Colonization History of Iturup Island by the Red-Backed Vole Craseomys rufocanus according to the Analysis of the Cytochrome b (cytb) Fragment
Authors: Abramson N. I. , Tursunova L. S. , Petrova T. V. , Popov I. Yu. , Platonov V. V. , Abramov A. V.
Published: April 2024

The hypotheses on colonization history of red-backed vole of Iturup Island comparative analysis of distribution and number of haplotypes of mitochondrial cytochrome b gene (662 bp) in vole sampled at various sites along the Iturup Island perimeter and Hokkaido, Kunashir and Sakhalin Islands and adjacent regions of the mainlandhas been carried out. All studied samples from the Iturup Island (68) belonged to the only one haplotype most close to the haplotypes of voles from the Sakhalin Island. The only sample from the Kunashir Island, nearest to the Iturup Island possessed the same haplotype, three additional samples from this island have haplotypes related to haplotypes of voles from the Sakhalin Island and fall within the so called “Sakhalin” clade, while the majority of haplotypes of voles from the Kunashir Island appeared to be close to haplotypes of voles from the Hokkaido Island and make up with them one independent clade, genetically very different from clade of Sakhalin and Iturup samples. The obtained data on the genetic variability of voles from the Iturup Island provides convincing evidence in favour of the recent introduction of the red-backed vole C. rufocanus to the Iturup Island, most likely with sea transport from Sakhalin.
B-Chromosome Variability in Plants and Animals under Extreme Environments
Authors: Borisov Yu. M. , Sedel’nikova T. S.
Published: April 2024

A review of data on B-chromosomes in populations of various systematic groups of plants and animals from their extreme habitats – the borders of the range and areas of the range exposed to unfavorable environmental factors is given. The analysis showed a rather similar picture of the distribution of B chromosomes in species from extreme habitats: there is a tendency to increase the number, occurrence and polymorphism of B chromosomes, which is accompanied by changes in the karyotype, genomic and chromosomal anomalies in their carriers. B chromosomes are often found in species with wide ranges. The possible adaptive role of B chromosomes in the vital activity of the organism and the evolution of genomes is discussed.
Methods for ChIP-seq Normalization and Their Application for Analysis of Regulatory Elements in Brain Cells
Authors: Gusev F. E. , Andreeva T. V. , Rogaev E. I.
Published: April 2024

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) has become one of the major tools to elucidate gene expression programs. Similar to other molecular profiling methods, ChIP-seq is sensetive to several technical biases which affect downstream results, especially in cases when material quality is difficult to control, for example, frozen post-mortem human tissue. However methods for bioinformatics analysis improve every year and allow to mitigate these effects after sequencing by adjusting for both technical ChIP-seq biases and more general biological biases like post-mortem interval or cell heterogenity of the sample. Here we review a wide selection of ChIP-seq normalization methods with a focus on application in specific experimental settings, in particular when brain tissue is investigated.
The Content of Carotoids and the Expression Profile of Carotenoid Biogenesis Genes during Long-Term Cold Storage of Potato Tubers
Authors: Kulakova A. M. , Shchennikova A. V. , Kochieva E. Z.
Published: April 2024

Carotenoids are secondary metabolites that are synthesized and stored in all types of plant plastids. These pigments play a significant role in protection against oxidative stress, as well as in the color of flowers and sink organs. Tubers of potato Solanum tuberosum L. synthesize carotenoids, including during post-harvest storage. The state of physiological dormancy and cold stress response are controlled, among other things, by abscisic acid (ABA), which is an apocarotenoid. In this study, we analyzed the expression of carotenoid biogenesis pathway genes (PSY1, PSY2, PSY3, PDS, ZDS, Z-ISO, CRTISO, LCYB1, LCYB2, LCYE, VDE, ZEP, NSY, NCED1, NCED2, and NCED6), as well as genes putatively involved in initiation of chromoplast differentiation (OR1 and OR2), in the dynamics of long-term cold storage (September, February, April) of tubers of potato cultivars Barin, Utro, Krasavchik, Sevemoe siyanie and Nadezhda. It was shown that OR1, and OR2 mRNAs are present in tubers of all cultivars at all stages of storage. The expression profile of all analyzed carotenoid biosynthesis genes during tuber storage was characterized by a significant decrease in transcript levels in February compared to September, with some exceptions. In the period from February to April, the level of gene transcripts changed insignificantly. The biochemical analysis of the carotenoid content in the dynamics of cold storage showed that at the time of harvesting, the highest carotenoid content was in tubers of the cv. Utro; tubers of other cultivars were characterized by a similar amount of carotenoids. During storage from September to April, the total carotenoids changed in a genotype-dependent manner without any trend common to all cultivars.
Transcriptomic Analysis of the Levilactobacillus brevis 47f Strain under Oxidative Stress
Authors: Pouektova E. U. , Averina O. V. , Kovtun A. S. , Danilenko V. N.
Published: April 2024

Levilactobacillus brevis 47f is a heterofermentative aerotolerant lactic acid bacterium isolated from the microbiota of the gastrointestinal tract of a healthy person. Previously, the strain showed anti-inflammatory properties and protects the murine intestine from enteropathy induced by 5-fluorouracil as part of preclinical studies. At the same time, the molecular mechanisms that account for the properties of the strain and its response to the action of reactive oxygen species, remain unexplored. The aim of this work was to study the response of the strain to the action of oxidizing agents – hydrogen peroxide and oxygen – using the method of transcriptional RNAseq analysis. Both oxidants exhibited a strong effect on the strain, increasing or decreasing the expression of several hundred genes – both general and specific for each oxidant. The characteristics of proteins whose expression was increased the most (DE ≥ 5) are provided. The genes activated under the action of both oxidants encode proteins related to stress, antioxidant activity, protein and nucleotide repair, cell wall, carbohydrate transport and metabolism, and catabolic energy storage pathways. Peroxide mainly activated the transcription of defense proteins, namely, stress response and molecular chaperones, antioxidant activity, DNA repair, and proteins involved in the formation of the cell wall. Under aerobic conditions, the genes that encode proteins involved in energy conversion (the use of fatty acids, nucleosides, fructose in addition to glucose as an energy source; proteins of the phosphoketolase pathway) and the import of peptides, amino acids, and sugars, were activated to a large extent. The data obtained in this work will be used by us to conduct an integrated analysis of transcriptomic, proteomic, and metabolomic data derived from this strain. This will make a significant contribution to the creation of a pharmacobiotic based on L. brevis 47f for the treatment of various inflammatory diseases.
Peculiarities of Transcriptional Activity of Long Non-Coding RNAs (COOLAIR, COLDAIR, and COLDWRAP) during the Vernalization of the Plant Arabidopsis thaliana of Northern Natural Populations
Authors: Zaretskaya M. V. , Lebedeva O. N. , Fedorenko O. M.
Published: April 2024

Peculiarities of the lncRNA expression – COOLAIR, COLDAIR, and COLDWRAP, which perform an important function in the vernalization-mediated epigenetic mechanism of the transition to flowering in A. thaliana plants of northern natural populations (Karelia), were revealed. The results obtained are partly differ from the data of other authors performing studies on pure lines and other ecotypes of this species. It is suggested that the genetic and epigenetic mechanisms involved in the process of vernalization and control of flowering times may differ in plant populations from different geographic regions.
Cellular and Epigenetic Aspects of Trained Immunity and Prospects for Creation of Universal Vaccines in the Face of Increasingly Frequent Pandemics
Authors: Alekseenko I. V. , Vasilov R. G. , Kondratyeva L. G. , Kostrov S. V. , Chernov I. P. , Sverdlov E. D.
Published: April 2024

The inevitability of pandemics creates an urgent requirement for emergency action to develop effective technologies to reduce harm to the human population in the period between the onset of an epidemic and the development and production of a vaccine. In this review we discuss the possibility of engineering universal vaccines. Such vaccines would exploit the nonspecific potential of innate immunity, would allow the population to be vaccinated when an unidentified pathogen appears, and would reduce disease severity until pathogen-specific vaccines become available. There are strong evidences that bacterial or viral vaccines such as BCG, measles and polio have heterologous protective effects against unrelated pathogens. This is attributed to the innate immune system’s ability to maintain the memory of past infections and use it to develop immune defenses against new ones. This effect has been called “trained” immunity. The use of trained immunity may also represent an important new approach to improving existing vaccines or to developing new vaccines that combine the induction of classical adaptive immune memory and innate immune memory. Such approaches can be boosted by genetic technology and prove extremely useful against future pandemics.
Elimination of Chromosomes as a Mechanism for the Formation of Diploid Plants in Diploid–Tetraploid Crosses in Maize (Zea mays L.)
Authors: Elkonin L. A. , Mavlyutova L. I. , Kolesova A. Yu. , Panin V. M. , Tsvetova M. I.
Published: April 2024

One of the main components of apomictic plant reproduction is the formation of unreduced embryo sacs (ESs). Heteroploid crosses, in which maternal diploid plants are pollinated by pollen of tetraploid paternal parent, can be used as an effective tool for identifying the ability to form unreduced ESs. In maize, in crosses 2n(♀) × 4n(♂), as a rule, shrunken kernels with a triploid embryo are formed, in which the development of the endosperm is impaired due to the deviation of the balance of the maternal (m) to paternal (p) genomes from the ratio of 2m : 1p. In our experiments, in several diploid maize lines, after their pollination with tetraploid pollen, the formation of large plump kernels was observed, from which diploid maternal-type plants developed, the maternal-type phenotype, as well as the hybrid endosperm phenotype, were confirmed by the expression of genetic markers. It has been suggested that the plump kernels in 2n × 4n crosses arise on the basis of unreduced embryo sacs (ESs) and pseudogamous apomixis, since the fusion of diploid sperms with diploid polar nuclei provides a 2 : 1 ratio of maternal to paternal genomes in the endosperm. In order to clarify the genetic nature of diploid plants phenotypically similar to maternal lines that developed from plump kernels in 2n × 4n crosses, we carried out their genotyping for all 10 chromosomes of the maize genome using polymorphic codominant SSR- and Indel-markers that differentiate the paternal line from maternal lines. As maternal lines, we used HPL AT, which has the ability to haploid parthenogenesis, KM, YuV-11, as well as the F2 B47/HPL AT hybrid plants; and as a paternal line – Chernaya Tetra(4n). It was found that in all the plants studied, when markers of five chromosomes (1, 2, 3, 4, and 9) were used, amplification of only maternal alleles was observed. However, in each of the studied plant, when using markers of other chromosomes, cases of amplification of alleles characteristic of the paternal line were noted. A hypothesis is put forward on the formation of diploid plants in 2n × 4n crosses in maize as a result of fertilization of the unreduced ESs and the subsequent elimination of chromosomes, predominantly of the pollen parent.
Relationship of the Anthocyanian Content with the Expression Level of the Anthocyanian Biosynthesis Pathway Regulatory and Structural Genes in Capsicum L. Species
Authors: Filyushin M. A. , Shchennikova A. V. , Kochieva E. Z.
Published: April 2024

In this study, the content of anthocyanins and the expression pattern of regulatory (CaMYB113, CaMYB1, and CaMYB1-like) and structural (CaCHS, CaCHI, CaF3H, CaDFR, CaANS, CaUFGT1, and CaGSTF12) genes of the anthocyanin biosynthesis pathway in leaves, flower petals, and peel of unripe fruits of pepper Capsicum frutescens L. cultivars (Samotsvet, Rozhdestvenskii buket and Eureka), which differ in the pattern of anthocyanin-mediated pigmentation of aboveground organs. A positive correlation was found between the levels of CaCHS, CaF3H, CaDFR, CaANS, and CaCSTF12 transcripts with the amount of anthocyanins in the leaves of these cultivars. It was shown that out of three regulatory genes only CaMYB113 is expressed. Using ten cultivars of three Capsicum species as an example, the presence of 5'-UTR in CaMYB113 mRNA was confirmed. The second variant of the CaMYB113 allele with the insertion of the LINE-1 retrotransposon in intron I was found in the genome of cv. Rozhdestvensky buket and Samotsvet with purple color of the analyzed organs.
Genetic Structure of Russian Riding Horse Breed
Authors: Nikolaeva E. A. , Voronkova V. N. , Politova M. A. , Ryabova E. V. , Demin V. A. , Stolpovsky Yu. A.
Published: April 2024

166 horses of the russian riding breed were studied using 17 microsatellite loci recommended by ISAG. Microsatellite polymorphism data of thirty European breeds (7874 individuals) was used for comparative analysis of genetic diversity. According to the level of allelic richness, the Russian riding horse has high values – 5. 4 alleles per microsatellite locus. In total, 122 alleles were found in the breed, including private 14 allele at the HTG7 locus. The population genetic structure was revealed for the Russian riding, Arabian, Akhal-Teke, German riding and thoroughbred breeds. Clustering of horse breeds on a circular UPGMA dendrogram revealed six main clusters. the Russian ridinghorse forms a single group with German and thoroughbred horses in PCA. Breeds were divided into three populations in STRUCTURE program: 1) Arabian, 2) Russian Riding, Akhal-Teke, thoroughbred riding, 3) German half-breed. Analysis of differentiation between breeds using the F-st method showed the greatest values (differences) between all breeds with the Akhal-Tekehorses. The smallest value (Fst = 0.22) between the Russian riding and German riding breed. Differences for each pair of breeds were significant (p-value 0.001).
The Law of Homological Series of N.I. Vavilov and Its Possible Fate
Authors: Rozanov* A. Yu.
Published: April 2024

On the world material on one of the most ancient groups of invertebrates – archeocyats, the applicability of the law of homologous series of N.I. Vavilov to construct a system of this group. It is proved that the laws of evolutionary morphology are special cases of the law of homological series. An analysis of the features of the development of our galaxy before the formation of the Earth raises the question that the law of homological series is the final part of a more general law of autocombinatorics.
The Genetic History of the Russian Old Settlers of the Arctic Coast of Yakutia from the Village Russkoye Ust’ye
Authors: Solovyev A. V. , Borisova T. V. , Romanov G. P. , Teryutin F. M. , Pshennikova V. G. , Nikitina S. E. , Alekseev A. N. , Barashkov N. A. , Fedorova S. A.
Published: April 2024

There are various hypotheses on the origin and time of the appearance of Russian settlements in the Arctic Ocean shores of Eastern Siberia. In order to study the history of the formation of the russian old-settlers of Yakutia, we analyzed the lineages of the Y-chromosome in three groups of residents of the village of Russkoye Ust’ye, located in the delta of the Indigirka River (“Pomors”, “Cossacks” and “Zashivertsy”), comparable with the main migration waves of settlement of Russians on the Arctic coast of Eastern Siberia. For the first time, the characteristic features of the genetic structure of the population of Russkoustinans are described by the data of a genome-wide analysis of 740,000 single nucleotide polymorphisms. The results of the study to a greater extent testify in favor of the “Pomor” hypothesis of the origin of the Russkoustinians.
The Influence of Deletion in the Non-Catalytic Domain of GdpP Mediated by Genome Editing with CRISPR/Cas9 on the Phenotype of Staphylococcus aureus
Authors: Sopova Yu. V. , Velizhanina M. E. , Кandina D. А. , Gostev V. V. , Chulkova P. S. , Sulian O. S. , Sidorenko S. V.
Published: April 2024

The high cellular level of cyclic di-adenosine monophosphate (c-di-AMP), which in turn results in resistance to cell-wall targeted antibiotics in Staphylococcus aureus. An increase in intracellular molecules of c-di-AMP is due to mutations in the DHH/DHHA1 domain of the GdpP protein. The influence of mutations in the other domains of GdpP has not been fully studied. The aim of this study was to obtain a targeted non-frameshifting deletion in the GdpP protein’s linker region between the GGDEF and DHH/DHHA1 domains. Restriction-modification deficient strain S. aureus RN4220 was used for genome editing. Two vectors with thermosensitive origins of replication were used. The first pCN-EF2132tet vector contained the Enterococcus faecalis EF2132 recombinase gene; the second pCAS9counter vector contained the Streptococcus pyogenes RNA-directed Cas9 nuclease gene. The S. aureus RN4220 strain was transformed with the pCN-EF2132tet vector to obtain recombining competent cells, and then a donor oligonucleotide was introduced simultaneously with the counterselection vector. A recombinant strain with a target deletion (90 bp) in GdpP (amino acids 308–337) was obtained after two sequential transformations. The mutant strain showed no changes in the phenotype: lag phase, growth rate, doubling time, and colony morphology did not differ from the progenitor strain. Susceptibility to cell-wall targeted antibiotics was the same as in the progenitor strain. Thus, mutations in the linker region between the GGDEF and DHH/DHHA1 domains of the GdpP do not affect susceptibility to antibiotics in S. aureus.
Molecular Marking in Brassica oleracea L. Breeding for Resistance to Fusarium Wilt
Authors: Dubina E. V. , Makukha Yu. A. , Artem’eva A. M. , Fateev D. A. , Garkusha S. V. , Gorun O. L. , Lesnyak S. A.
Published: April 2024

This article presents the results of research on the identification of informative DNA marker systems, providing reliable control of the resistance gene to fusarium wilt Foc1 presence in white cabbage breeding material. At the beginning of the work 14 molecular markers, taken from VegMarks database and literature sources were tested on isogenic white cabbage lines with contrasting resistance to fusarium wilt (resistant line DT-46 and susceptible line Kb1P). InDel-marker M10 and SSR-markers Frg13 and O110-D01 have been ascertained to show polymorphism between white cabbage forms with contrasting resistance to fusarium wilt. Also PCR-analysis of segregating F2-population plants of hybrid combination DT-46 × Kb1P using these markers and phytopathology testing have been conducted. As a result of statistical analysis of segregation it has been found that SSR-marker Ol10-D01 only is cosegregated with the trait of resistance to fusarium wilt as expected segregation of F2-plants by genotype 1 : 2 : 1 according to Mendel’s law, the least recombination frequency between the resistance gene Foc1 and the marker (1.6%) has just been observed by this locus only and highly polymorphic (PIC = 0.51).
Genetic Factors of Reflex Epilepsies
Authors: Dudko N. A. , Kunizheva S. S. , Andreeva T. V. , Adrianova I. Yu. , Rogaev E. I.
Published: April 2024

Reflex epilepsy is a relatively rare form of epilepsy, occurring only in five percent of all cases of this disease. The genetic factors of reflex epilepsy are diverse and, in general, poorly studied. This review examines the main results obtained in recent years in the study of molecular genetic factors of reflex epilepsy, including new data on the mechanisms of genetic regulation in reflex epilepsy caused by triggers such as audio and video stimulation, food consumption, reading, contact with water and hypoxia. The results obtained in studies on animal models and patients using next-generation sequencing technology are presented.
Polymorphism of the MAOA Gene (rs1137070) and Internet Addiction in Adolescents
Authors: Kopylova K. V. , Marchenko I. V. , Shubina M. V. , Gorbacheva N. N. , Novitckii I. A. , Smolnikova M. V.
Published: April 2024

Monoamine oxidase A (MAOA) catalyzes the degradation of norepinephrine, dopamine, and serotonin, i.e. neurotransmitters involved in the pathogenesis of pathological addictions, including internet addiction (IA). Gene MAOA has been actively studied in terms of genetic predisposition to the development of aggressive behavior potentially involved in the formation of IA. The study included 602 adolescents (9–18 years old, mean age = 14.6, SD 1.7) from the Angara-Yenisei macroregion (Russians n = 329, Tuvans n = 158, Khakasses n = 158). The type of IA was assessed according to the Chen scale (Chen Internet Addiction Scale, CIAS), gene polymorphism was detected using real-time PCR. The distribution of the TT genotype of MAOA rs1137070 polymorphism associated with low activity of the monoamine oxidase A enzyme and aggressive behavior affected by IA, was found to be significantly higher in Tuvan adolescents compared with Russians (31.1/21.2% p = = 0.02). Pathological internet addiction (more than 65 points by Chen scale) often observed among Khakass adolescents compared to Russian (26.4/15.5%, p = 0.03). Thus, the allelic variant T of MAOA rs1137070 polymorphism appears to be potential marker for dependent and aggressive behavior to form, Asian representatives being more susceptible to the development of pathological addictions than Caucasian populations.
The Genetic Resource of Thinopyrum elongatum (Host) D.R. Dewey in Breeding Improvement of Wheat
Authors: Korostyleva T. V. , Shiyan A. N. , Odintsova T. I.
Published: April 2024

Thinopyrum elongatum (Host) D.R. Dewey is a valuable resource for the application of genomic engineering and modern genetic technologies aimed at wheat improvement because it carries genome Е, the parent genome of the Thinopyrum genus. Its representatives are successfully used in distant hybridization and production of introgressive lines for transferring genes of economically valuable traits into new wheat varieties. This review presents the available data on the main genetically characterized traits of Th. elongatum that have been or can be used for transfer into the wheat genome. These traits include resistance to fusariosis, septoriosis, rust diseases, and abiotic environmental factors – overwatering, soil salinity and low temperatures, as well as the traits that determine the quality of bakery products. The latest studies of Th. elongatum genome by genome and transcriptome sequencing are also considered.
Study of the Association of Polymorphic Variants rs2295080 and rs1883965 of the MTOR Gene with the Development of Pulmonary Sarcoidosis
Authors: Malysheva I. E. , Topchieva L. V. , Tikhonovich E. L.
Published: April 2024

The aim of the study was to study the association of polymorphic variants rs2295080 and rs1883965 of the MTOR gene with the risk of developing pulmonary sarcoidosis. The study included 253 people (122 patients diagnosed with morphologically verified sarcoidosis with lung involvement (average age – 41.00 ± 12.56 years) and 131 healthy people (control group) (average age – 44.00 ± 14.23). The distribution of alleles and genotypes of polymorphic markers rs2295080 and rs1883965 of the MTOR gene was analyzed in the study groups. There was a statistically significant increase in the level of mRNA expression of the MTOR gene in PBL of patients with pulmonary sarcoidosis compared with the control group (p = 0.007). A decrease in the number of transcripts of this gene was noted in patients receiving therapy compared with patients without therapy (p = = 0.025). There were no statistically significant differences in the distribution of allele and genotype frequencies for polymorphic markers rs2295080 and rs1883965 of the MTOR gene in the group of patients with pulmonary sarcoidosis and in the control group: (χ2 = 0.196, d.f. = 1, p = 0.658 and χ2 = 0.637, d.f. = 2, p = = 0.728) and (χ2 = 0.034, d.f. = 1, p = 0.855 and χ2 = 0.051, d.f. = 2, p = 0.975) respectively. Conclusion: аn increased level of expression of the MTOR gene in peripheral blood leukocytes of patients with pulmonary sarcoidosis may indicate the involvement of this gene in the pathogenesis of this disease. Polymorphic markers rs2295080 and rs1883965 of the MTOR gene are not associated with the risk of developing pulmonary sarcoidosis. Probably, an increase in the expression level of the MTOR gene in patients with pulmonary sarcoidosis is due to the development of inflammation.
Phylogeny of the Genus Eleginus (Gadidae) according to the Analysis of the Variability of Microsatellite Locus and mtDNA CO1 Fragment
Authors: Stroganov A. N. , Ponomareva E. V. , Ponomareva M. V. , Shubina E. A. , Zhukova K. A. , Smirnov A. A. , Rakitskaya T. A. , Rakitina M. V.
Published: April 2024

Genetic methods based on the study of the variability of mitochondrial (CO1) and nuclear (microsatellites) DNA were used to study the processes of morphogenesis in the genus Eleginus. The revealed level of genetic differentiation characterizes the Pacific Saffron cod (Eleginus gracilis) and Navaga (Eleginus nawaga) as independent species that diverged in a relatively recent period at the boundary of the Pliocene and Pleistocene. The White Sea Navaga’s populations were by microsatellites markers differed from the Navaga inhabiting the basins of the Kara and the Barents seas. At the same time, it is assumed that the Kara-Barents Sea region could act as a “glacial refugium”, which ensured the post-glacial settlement of Navaga, including in the “watered” White Sea depression. Phylogenetic analysis based on CO1 haplotypes diversity reveals demand of possible reorganization in order Gadiformes, including Eleginus in an independent subfamily – sister in relation to the subfamilies Gadinae, Lotinae, Merlucciinae. The prospects of improving genetic methodological approaches in the framework of the development of research on Saffron cod are noted.
Effect of Chronic Radiation Exposure on Human microRNA Expression
Authors: Yanishevskaya M. A. , Blinova E. A. , Akleyev A. V.
Published: April 2024

Relative expression of mature microRNA assessed in peripheral blood cells in persons chronically exposed to low-dose radiation in the long-term period. The study included people exposed in the 1950s on the Techa River (Southern Urals, Russia). The cumulative red bone marrow doses (RBM) of the persons in the main study group (33 persons) ranged from 77.7 to 2869.8 mGy (mean value – 698.5 mGy). The comparison group consisted of 30 people with RBM dose not exceeding 70 mGy over their lifetime. Reverse transcription of RNA samples was performed using specific stem-loop primers (“stem-loop”). Changes in the relative content of microRNA were assessed by real-time PCR on the CFX96 detection system (BioRad, USA). Statistical analysis of the results was performed using Mann–Whitney U-criterion. A significant increase in hsa-miR-125b, hsa-miR-181a, and hsa-miR-16-5p content was detected in exposed people after 60 years, and their expression was found to depend on the RBM dose.