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Study of RNA-protein interactions and identification of RNA targets are among the key aspects of under-standing RNA biology. Currently, various methods are available to investigate these interactions with, RNA immunoprecipitation (RIP) being the most common. The search for RNA targets has largely been conducted using antibodies to an endogenous protein or to GFP-tag directly. Having to be dependent on the expression level of the target protein and having to spend time selecting highly specific antibodies make immunoprecipitation complicated. Expression of the GFP-fused protein can lead to cytotoxicity and, consequently, to improper recognition or degradation of the chimeric protein. Over the past few years, multifunctional tags have been developed. SNAP-tag and HaloTag allow the target protein to be studied from different perspectives. Labeling of the fusion protein with custom-made fluorescent dyes makes it possible to study protein expression and to localize it in the cell or the whole organism. A high-affinity substrate has been created to allow covalent binding by chimeric proteins, minimizing protein loss during protein isolation. In this paper, a HaloTag-based method, which we called Halo-RPD (HaloTag RNA PullDown), is presented. The proposed protocol uses plants with stable fusion protein expression and Magne® HaloTag® magnetic beads to capture RNA-protein complexes directly from the cytoplasmic lysate of transgenic Arabidopsis thaliana plants. The key stages described in the paper are as follows: (1) preparation of the magnetic beads; (2) tissue homogenization and collection of control samples; (3) precipitation and wash of RNA-protein complexes; (4) evaluation of protein binding efficiency; (5) RNA isolation; (6) analysis of the RNA obtained. Recommendations for better NGS assay designs are provided.

The animal models used in biomedical research cover virtually every human disease. RatDEGdb, a knowledge base of the differentially expressed genes (DEGs) of the rat as a model object in biomedical research is a collection of published data on gene expression in rat strains simulating arterial hypertension, age-related diseases, psychopathological conditions and other human afflictions. The current release contains information on 25,101 DEGs representing 14,320 unique rat genes that change transcription levels in 21 tissues of 10 genetic rat strains used as models of 11 human diseases based on 45 original scientific papers. RatDEGdb is novel in that, unlike any other biomedical database, it offers the manually curated annotations of DEGs in model rats with the use of independent clinical data on equal changes in the expression of homologous genes revealed in people with pathologies. The rat DEGs put in RatDEGdb were annotated with equal changes in the expression of their human homologs in affected people. In its current release, RatDEGdb contains 94,873 such annotations for 321 human genes in 836 diseases based on 959 original scientific papers found in the current PubMed. RatDEGdb may be interesting first of all to human geneticists, molecular biologists, clinical physicians, genetic advisors as well as experts in biopharmaceutics, bioinformatics and personalized genomics. RatDEGdb is publicly available at https://www.sysbio.ru/RatDEGdb.

Periodic processes of gene network functioning are described with good precision by periodic trajectories (limit cycles) of multidimensional systems of kinetic-type differential equations. In the literature, such systems are often called dynamical, they are composed according to schemes of positive and negative feedback between components of these networks. The variables in these equations describe concentrations of these components as functions of time. In the preparation of numerical experiments with such mathematical models, it is useful to start with studies of qualitative behavior of ensembles of trajectories of the corresponding dynamical systems, in particular, to estimate the highest likelihood domain of the initial data, to solve inverse problems of parameter identification, to list the equilibrium points and their characteristics, to localize cycles in the phase portraits, to construct stratification of the phase portraits to subdomains with different qualities of trajectory behavior, etc. Such an à priori geometric analysis of the dynamical systems is quite analogous to the basic section “Investigation of functions and plot of their graphs” of Calculus, where the methods of qualitative studies of shapes of curves determined by equations are exposed. In the present paper, we construct ensembles of trajectories in phase portraits of some dynamical systems. These ensembles are 2-dimensional surfaces invariant with respect to shifts along the trajectories. This is analogous to classical construction in analytic mechanics, i. e. the level surfaces of motion integrals (energy, kinetic moment, etc.). Such surfaces compose foliations in phase portraits of dynamical systems of Hamiltonian mechanics. In contrast with this classical mechanical case, the foliations considered in this paper have singularities: all their leaves have a non-empty intersection, they contain limit cycles on their boundaries. Description of the phase portraits of these systems at the level of their stratifications, and that of ensembles of trajectories allows one to construct more realistic gene network models on the basis of methods of statistical physics and the theory of stochastic differential equations.

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An infrared thermometer was first used to assess drought and heat tolerance in plant breeding more than 40 years ago. Soon afterward, this method became widely used throughout the world. However, Russia has not yet applied the described method for evaluating stress tolerance. This paper presents an overview of using infrared thermometry in plant breeding. Taking wheat as an example, it shows major advantages and disadvantages of canopy temperature depression (CTD) values measured by the infrared thermometer. The paper also demonstrates that genotypes with higher CTD values, and therefore with a lower canopy temperature, use more available soil moisture under drought stress to cool the canopy by transpiration. It refers to CTD as an integrative trait that reflects an overall plant water status. Its coefficient of variation lies in the interval of 10 to 43 %. A large number of publications illustrate a close relation between CTD values and yield and indicate a high heritability of the former. Meanwhile, the same works show that yield has a higher heritability. Moreover, some researchers doubt that CTD should be used in applied wheat breeding as there are many factors that influence it. CTD has a high correlation with other traits that reflect plant water status or their adaptation to drought or heat stress. Quantitative trait loci (QTLs) associated with CTD are localized in all chromosomes, except for 3D. These QTLs often explain a small part of phenotypic variance (10–20 %, more likely less than 10 %), which complicates the pyramiding of canopy temperature genes through marker-assisted selection. The paper concludes that the evaluation of CTD appears to be a reliable, relatively simple, labor-saving, objective, and non-invasive method that sets it apart from other methods as well as shows the best results under terminal drought and heat stress conditions.

Metapolycentromeres consist of multiple sequential domains of centromeric chromatin associated with a centromere-specific variant of histone H3 (CENP-A), functioning collectively as a single centromere. To date, they have been revealed in nine flowering plant, five insect and six vertebrate species. In this paper, we focus on their structure and possible mechanisms of emergence and evolution. The metapolycentromeres may vary in the number of centromeric domains and in their genetic content and epigenetic modifications. However, these variations do not seem to affect their function. The emergence of metapolycentromeres has been attributed to multiple Robertsonian translocations and segmental duplications. Conditions of genomic instability, such as interspecific hybridization and malignant neoplasms, are suggested as triggers for the de novo emergence of metapolycentromeres. Addressing the “centromere paradox” – the rapid evolution of centromeric DNA and proteins despite their conserved cellular function – we explore the centromere drive hypothesis as a plausible explanation for the dynamic evolution of centromeres in general, and in particular the emergence of metapolycentromeres and holocentromeres. Apparently, metapolycentromeres are more common across different species than it was believed until recently. Indeed, a systematic review of the available cytogenetic publications allowed us to identify 27 candidate species with metapolycentromeres. Тhe list of the already established and newly revealed candidate species thus spans 27 species of flowering plants and eight species of gymnosperm plants, five species of insects, and seven species of vertebrates. This indicates an erratic phylogenetic distribution of the species with metapolycentromeres and may suggest an independent emergence of the metapolycentromeres in the course of evolution. However, the current catalog of species with identified and likely metapolycentromeres remains too short to draw reliable conclusions about their evolution, particularly in the absence of knowledge about related species without metapolycentromeres for comparative analysis. More studies are necessary to shed light on the mechanisms of metapolycentromere formation and evolution.

The transition of detached fragments of mitochondrial DNA into the nucleus and their integration into chromosomal DNA is a special kind of genetic variability that highlights the relation between the two genomes and their interaction in a eukaryotic cell. The human genome contains several hundreds of insertions of mtDNA fragments (NUMTS). This paper presents an overview of the current state of research in this area. To date, evidence has been obtained that the occurrence of new mtDNA insertions in the nuclear genome is a seldom but not exceptionally rare event. The integration of new mtDNA fragments into the nuclear genome occurs during double-strand DNA break repair through the non-homologous end joining mechanism. Along with evolutionarily stable “genetic fossils” that were integrated into the nuclear genome millions of years ago and are shared by many species, there are NUMTS that could be species-specific, polymorphic in a species, or “private”. Partial copies of mitochondrial DNA in the human nuclear genome can interfere with mtDNA during experimental studies of the mitochondrial genome, such as genotyping, heteroplasmy assessment, mtDNA methylation analysis, and mtDNA copy number estimation. In some cases, the insertion of multiple copies of the complete mitochondrial genome sequence may mimic paternal inheritance of mtDNA. The functional significance of NUMTS is poorly understood. For instance, they may be a source of variability for expression and splicing modulation. The role of NUMTS as a cause of hereditary diseases is negligible, since only a few cases of diseases caused by NUMTS have been described so far. In addition, NUMTS can serve as markers for evolutionary genetic studies. Of particular interest is the meaning of NUMTS in eukaryotic genome evolution. The constant flow of functionally inactive DNA sequences from mitochondria into the nucleus and its significance could be studied in view of the modern concepts of evolutionary theory suggesting non-adaptive complexity and the key role of stochastic processes in the formation of genomic structure.

One of promising areas of wheat breeding is the creation of varieties with a high concentration of anthocyanins in the grain for the production of functional food products. Nonetheless, the question of how these compounds affect seed viability after long-term storage has remained unexplored. A comparative study on seed viability was conducted using a set of near-isogenic lines on the background of spring wheat variety Saratovskaya 29. These sister lines carry different combinations of recombinant DNA regions (on chromosomes 2A and 7D) containing dominant and recessive alleles at loci Pp3 and Pp-D1 (Pp: Purple pericarp), which determine the anthocyanin color of coleoptiles and of the pericarp. Seeds were germinated on two layers of water-moistened filter paper in a climatic chamber at a constant temperature of 20 °C on a 12-hour daylight cycle. During long-term natural storage of the seeds for up to 9 years in a dry ventilated room in Kraft bags at 20 ± 2 °C, the tested wheat samples experienced a loss of seed germination capacity of ~50 %; anthocyanins were found to not participate in the preservation of germination capacity. Nonetheless, anthocyanins contributed to the preservation of seed viability under unfavorable short-term conditions of a temperature rise to 48 °C at 100 % humidity. The accelerated aging test did not predict poor germination capacity after long-term seed storage. The results showed a neutral role of anthocyanins in the maintenance of seed germination capacity for 6–9 years under natural storage conditions at 20 ± 2 °C. A small statistically significant increase in grain germination capacity during natural aging was associated with the presence of a recombinant region containing the Pp-D1 gene on wheat chromosome 7D.

This survey paper contains a brief analysis of publications included in current issue of scientific journal «Cytology and Genetics» dedicated to its 50th anniversary. These papers reflect scientific achievements of their authors in the field of genetics and cell biology and underine the potential of these two biological disciplines, forming «double helix» of the journal.

Analysis of hyperspectral images is of great interest in plant studies. Nowadays, this analysis is used more and more widely, so the development of hyperspectral image processing methods is an urgent task. This paper presents a hyperspectral image processing pipeline that includes: preprocessing, basic statistical analysis, visualization of a multichannel hyperspectral image, and solving classification and clustering problems using machine learning methods. The current version of the package implements the following methods: construction of a confidence interval of an arbitrary level for the difference of sample averages; verification of the similarity of intensity distributions of spectral lines for two sets of hyperspectral images on the basis of the Mann–Whitney U-criterion and Pearson’s criterion of agreement; visualization in two-dimensional space using dimensionality reduction methods PCA, ISOMAP and UMAP; classification using linear or ridge regression, random forest and catboost; clustering of samples using the EM-algorithm. The software pipeline is implemented in Python using the Pandas, NumPy, OpenCV, SciPy, Sklearn, Umap, CatBoost and Plotly libraries. The source code is available at: https://github.com/igor2704/Hyperspectral_images. The pipeline was applied to identify melanin pigment in the shell of barley grains based on hyperspectral data. Visualization based on PCA, UMAP and ISOMAP methods, as well as the use of clustering algorithms, showed that a linear separation of grain samples with and without pigmentation could be performed with high accuracy based on hyperspectral data. The analysis revealed statistically significant differences in the distribution of median intensities for samples of images of grains with and without pigmentation. Thus, it was demonstrated that hyperspectral images can be used to determine the presence or absence of melanin in barley grains with great accuracy. The flexible and convenient tool created in this work will significantly increase the efficiency of hyperspectral image analysis.

On January 1, 2024, Academician of the Russian Academy of Sciences Igor Anatolyevich Tikhonovich, an outstanding specialist in the field of genetics of plant-microbial interactions, a prominent higher education teacher and organizer of science, turned 75 years old. He has published more than 250 papers in peer-reviewed journals, prepared 10 monographs and textbooks, and received 12 patents. Academician Tikhonovich led the All-Russian Institute of Agricultural Microbiology for more than forty years, which under his leadership developed into a leading internationally recognized scientific school in the field of symbiogenetics. One of the most important conceptual generalizations formulated by I.A. Tikhonovich was the principle of complementarity of genomes. Under the leadership and with the direct participation of Igor Anatolyevich, the formation and development of new Master’s degree programs in agrobiotechnology and molecular biology of plants was started at St. Petersburg State University and the Sirius University of Science and Technology. During the leadership of Igor Anatolyevich, the Vavilov Society of Genetics and Breeders was replenished with new departments and held a number of important scientific events, including the VII Congress of VOGiS and the “Russian Genetic Resources” Forums.Friends and associates, the community of geneticists and breeders of the Russian Federation warmly congratulate Igor Anatolyevich on his anniversary and wish him major scientific discoveries, new pedagogical achievements and the attainment of all his goals.

Collections of common potato maintained in the field genebanks suffer significant losses due to the impact of extreme environmental factors, diseases and pests. The solution of the problem of safe long-term preservation of common potato accessions is to create doublet in vitro and cryo-collections. Cryogenic collections are stored at ultra-low temperatures in cryobanks. Several methods of potato cryoconservation are known, of which the droplet vitrification method developed by B. Panis with colleagues in 2005 is the most widely used in genebanks. This paper provides a detailed description of the modified method of droplet vitrification, which is used for cryopreservation of apexes (shoot tips) of potato in vitro plants at the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR). The method modified at VIR includes the main steps of the original droplet-vitrification method developed by B. Panis and colleagues: 1) preparation of plant material, 2) isolation of shoot tips, 3) treatment of explants with cryoprotector solutions, 4) freezing/immersion in liquid nitrogen, 5) thawing, 6) post-cryogenic recovery and evaluation of viability and regeneration capacity. The modifications of stages 1, 2 and 6 proposed at VIR lead to a significant reduction in the duration of cryopreservation experiments in comparison with the original method of B. Panis. This paper presents the results of cryopreservation of modern potato cultivars and South American landraces which were obtained using the method of droplet vitrification as modified at VIR. The majority (76.7 %) of the studied accessions of cultivated potato were characterized by high rates of postcryogenic recovery (40–95 %) and 23.3 % of the samples had the values of postcryogenic regeneration from 20 to 39 %, which corresponds to the minimal permissible values for long-term storage in a cryobank. Currently the modified droplet-vitrification method is used for further expanding of the VIR potato cryocollection.

With the advent of the new genome editing tool of target-specifically customizable endonucleases, a huge variety of novel opportunities have become feasible. The crop improvement is one of the main applications of genome editing in plant science and plant biotechnology. The amount of publications referring to genome editing and CRISPR/Cas system based molecular tools application in crops is permanently growing. The aim of this study is the systematization and cataloging of these data. Earlier we published the first catalog of targeted crop genome modifications as of February 10, 2017. The current review is an update of the catalog; it covers research papers on crop genome modifications from February 10, 2017 to August 17, 2018, found by searching 47 crop names in the Scopus database. Over one year and a half, 377 articles mentioning CRISPR/Cas and crop names have been published, of which 131 articles describe an experimental application of this tool for editing 193 genes in 19 crops, including rice with the largest number of genes modified (109 genes). Editing 50 of 193 genes was aimed at crop improvement. The catalog presented here includes these 50 genes, specifying the cultivars, each gene and gene product function, modification type and delivery method used. The current full list of genes modified with CRISPR/Cas with the aim of crop improvement is 81 in 16 crops (for 5 years from August 2013 to August 2018). In this paper, we also summarize data on different modifications types in different crops and provide a brief review of some novel methods and approaches that have appeared in crop genome editing research over the reviewed period. Taken together, these data provide a clear view on current progress in crop genome modifications and traits improvement using CRISPR/Cas based genome editing technology.

Wheat is one of three main food crops around the world, which has the largest distribution area due to its adaptation to the different environments. This review considers polymorphisms and allelic variation of the vernalization response genes Vrn controlling the major adaptation traits in wheats (the genus Triticum L.): growth habit (spring vs. winter) and length of vegetative period (earliness). The review summarizes available information on the allelic diversity of the Vrn genes and discusses molecular-level relationships between Vrn polymorphisms and their effect on growth habit (spring vs. winter) and earliness (length vegetative period in spring plants) in di-, tetra- and hexaploid wheat species. A unique attempt has been made to relate information on mutations (polymorphisms) in dominant Vrn alleles to the values of the commercially most important trait “length of plant vegetative period (earliness)”. The effects of mutations (polymorphisms) in the recessive vrn genes on vernalization requirement in winter wheats are considered, and this trait was formalized. The evolution of the winter/spring growth habit in the genus Triticum species is discussed. A scheme of phylogenetic interactions between Vrn alleles was constructed on the basis of these polymorphisms; the paper considers the possibilities to enhance the diversity of polymorphisms for the dominant Vrn genes and their alleles using wheat related species and rarely used alleles and discusses the prospects of breeding for improved earliness for concrete agroecological zones.

Meta-analysis of transcriptomic data from different experiments has become increasingly prevalent due to a significantly increasing number of genome-wide experiments investigating gene expression changes under various conditions. Such data integration provides greater accuracy in identifying candidate genes and allows testing new hypotheses, which could not be validated in individual studies. To increase the relevance of experiment integration, it is necessary to optimize the selection of experiments. In this paper, we propose a set of quantitative indicators for a comprehensive comparative description of transcriptomic data. These indicators can be easily visualized and interpreted. They include the number of differentially expressed genes (DEGs), the proportion of experiment-specific (unique) DEGs in each data set, the pairwise similarity of experiments in DEG composition and the homogeneity of DEG profiles. For automatic calculation and visualization of these indicators, we have developed the program InterTransViewer. We have used InterTransViewer to comparatively describe 23 auxin- and 16 ethylene- or 1-aminocyclopropane-1-carboxylic acid (ACC)-induced transcriptomes in Arabidopsis thaliana L. We have demonstrated that analysis of the characteristics of individual DEG profiles and their pairwise comparisons based on DEG composition allow the user to rank experiments in the context of each other, assess the tendency towards their integration or segregation, and generate hypotheses about the influence of non-target factors on the transcriptional response. As a result, InterTransViewer identifies potentially homogeneous groups of experiments. Subsequent estimation of the profile homogeneity within these groups using resampling and setting a significance threshold helps to decide whether these data are appropriate for meta-analysis. Overall, InterTransViewer makes it possible to efficiently select experiments for meta-analysis depending on its task and methods.

The participants of Hepatitis C virus (HCV) replication are both viral and host proteins. Therapeutic approaches based on activity inhibition of viral non-structural proteins NS3, NS5A, and NS5B are undergoing clinical trials. However, rapid mutation processes in the viral genome and acquisition of drug resistance to the existing drugs remain the main obstacles to fighting HCV. Identifying the host factors, exploring their role in HCV RNA replication, and studying viral effects on their expression is essential for understanding the mechanisms of viral replication and developing novel, effective curative approaches. It is known that the host factors PREB (prolactin regulatory element binding) and PLA2G4C (cytosolic phospholipase A2 gamma) are important for the functioning of the viral replicase complex and the formation of the platforms of HCV genome replication. The expression of PREB and PLA2G4C was significantly elevated in the presence of the HCV genome. However, the mechanisms of its regulation by HCV remain unknown. In this paper, using a text-mining technology provided by ANDSystem, we reconstructed and analyzed gene networks describing regulatory effects on the expression of PREB and PLA2G4C by HCV proteins. On the basis of the gene network analysis performed, we put forward hypotheses about the modulation of the host factors functions resulting from protein-protein interaction with HCV proteins. Among the viral proteins, NS3 showed the greatest number of regulatory linkages. We assumed that NS3 could inhibit the function of host transcription factor (TF) NOTCH1 by protein-protein interaction, leading to upregulation of PREB and PLA2G4C. Analysis of the gene networks and data on differential gene expression in HCV-infected cells allowed us to hypothesize further how HCV could regulate the expression of TFs, the binding sites of which are localized within PREB and PLA2G4C gene regions. The results obtained can be used for planning studies of the molecular-genetic mechanisms of viral-host interaction and searching for potential targets for anti-HCV therapy.

Identification of the mechanisms underlying the genetic control of spatial structure formation is among the relevant tasks of developmental biology. Both experimental and theoretical approaches and methods are used for this purpose, including gene network methodology, as well as mathematical and computer modeling. Reconstruction and analysis of the gene networks that provide the formation of traits allow us to integrate the existing experimental data and to identify the key links and intra-network connections that ensure the function of networks. Mathematical and computer modeling is used to obtain the dynamic characteristics of the studied systems and to predict their state and behavior. An example of the spatial morphological structure is the Drosophila bristle pattern with a strictly defined arrangement of its components – mechanoreceptors (external sensory organs) – on the head and body. The mechanoreceptor develops from a single sensory organ parental cell (SOPC), which is isolated from the ectoderm cells of the imaginal disk. It is distinguished from its surroundings by the highest content of proneural proteins (ASC), the products of the achaete-scute proneural gene complex (AS-C). The SOPC status is determined by the gene network we previously reconstructed and the AS-C is the key component of this network. AS-C activity is controlled by its subnetwork – the central regulatory circuit (CRC) comprising seven genes: AS-C, hairy, senseless (sens), charlatan (chn), scratch (scrt), phyllopod (phyl), and extramacrochaete (emc), as well as their respective proteins. In addition, the CRC includes the accessory proteins Daughterless (DA), Groucho (GRO), Ubiquitin (UB), and Seven-in-absentia (SINA). The paper describes the results of computer modeling of different CRC operation modes. As is shown, a cell is determined as an SOPC when the ASC content increases approximately 2.5-fold relative to the level in the surrounding cells. The hierarchy of the effects of mutations in the CRC genes on the dynamics of ASC protein accumulation is clarified. AS-C as the main CRC component is the most significant. The mutations that decrease the ASC content by more than 40 % lead to the prohibition of SOPC segregation.

At the beginning of the paper, the level of necessary phenomenology of complex models is discussed. When working with complex systems, which of course include living organisms and ecological systems, it is necessary to use a phenomenological description. An illustration of the phenomenological approach is given, which captures the most significant general principles or patterns of interactions; the specific values of the parameters cannot be calculated from the first principles, but are determined empirically. An appropriate interpretation is also chosen empirically and pragmatically. However, in order to simulate a wider range of situations, it becomes necessary to lower the level of phenomenology, switch to a more detailed description of the system, introducing interaction between selected elements of the system. The requirements for a system model combining ecological, metabolic and genetic levels of cell culture description are formulated. A mathematical model of quorum sensing dynamics during the growth of batch culture of luminescent bacteria at different concentrations of the nutrient substrate has been developed. The model contains four blocks describing ecological, energy, quorum and luminescent aspects of bacterial culture growth. The model demonstrated good agreement with the experimental data obtained. When analyzing the model, three oddities in the behavior of the culture were noted, which presumably can change the idea of some processes taking place during the development of a culture of luminescent bacteria. The results obtained suggest the presence of some additional control system for the luminescent reaction via the synthesis pathways of FMN · Н2 or aliphatic aldehyde. In this case, the generalized description of the contribution of energy metabolism to luminescence only through ATP is too strong a simplification. As a result of comparing the model dynamics with the experiment, a discrepancy arose between the concentration of the substrate (peptone) measured in the experiment and its effective influence on the bacterial population growth. This discrepancy seems to indicate peptone is not the leading substrate, and growth is limited by nutrients contained in the yeast extract, the concentration of which did not change in these experiments. The discrepancies noted between the expectations and the results of experimental data processing, together with the assumptions about the causes of these discrepancies, set the direction for further experimental and theoretical studies of quorum sensing mechanisms in a culture of luminescent bacteria.

Development and improvement of mathematical methods used in modeling biological systems represents a topical issue of mathematical biology. In this paper, we considered a general form of a system of first-order delayed differential equations, traditionally used for describing the function of biological systems of different hierarchical levels. The main feature of this class of models is that some inherent processes (for example, elongation of DNA, RNA, and protein synthesis) are described in a subtle form and can be explicitly specified only through delayed arguments. In this paper, we propose an algorithm for rewriting systems with constant delayed arguments in an equivalent form that represents a system of partial differential equations with transfer equations. The algorithm is universal, since it does not impose any special conditions on the form of the right-hand parts of systems with delayed arguments. The proposed method is a multivariant algorithm. That is, based on one system of differential equations with delayed arguments, the algorithm allows writing out a number of special systems of partial differential equations, which are equivalent to the original system with delayed argument in the entire solution set. The results obtained indicate that delayed arguments and transfer equations are equivalent mathematical tools for describing all types of dynamic processes of energy and/or matter transfer in biological, chemical, and physical systems, indicating a deep-level similarity between properties of dynamic systems, regardless of their origin. At the same time, those processes that are subtle when retarded argument is used can be explicitly described in the form of transfer equations using systems of partial differential equations. This property is extremely important for the modeling of molecular genetic systems in which processes of DNA, RNA, and protein synthesis proceed at variable rates and need to be considered in certain problems, what can easily be done in models constructed using the mathematical tool of partial derivatives.

Studies of genomic background of neurological disorders are very actual in view of their high population prevalence, severe course, serious impact on patients' disability and progressive mental and physical de-adaptation. In the paper, problems of genetic heterogeneity of hereditary neurological disorders and character of the respective genetic burden in the regions of Russian Federation are discussed in detail, a 'dynamic' type of mutations (increase in number of microsatellite repeats copies) attributable to many neurodegenerative diseases is analyzed, and achievements of Russian researchers in the identification of genes for hereditary neurological disorders and in the realization of pilot protocols of gene therapy are presented. Problems related to studies of genetic predisposition to common multifactorial diseases of the nervous system are discussed.

Introduction and objective: The purpose of this paper is a systematic review of articles and research in the context of the relationship between genetic determinants of migraine and thyroid dysfunction. Materials and methods: A non-systematic review of the scientific literature was carried out according to the following keywords: PubMed was searched and 76 articles published up to 2023 were analyzed. Description of the state of knowledge: Epidemiological studies confirm the co-occurrence of migraine and thyroid dysfunction, especially hypothyroidism, which are considered to be diseases with a strong genetic background. Thyroid function parameters such as TSH and fT4 are susceptible to genetic influences. However, there is a lack of consistent interpretation of the observational results, which highlights the need for further research. Analysis of gene overlaps and links between headache and thyroid function, based on GWAS data, could shed light on the complex genetic interactions underlying this association. Summary: The genetic associations revealed in the study enhance our comprehension of the intricate relationship between migraine and thyroid dysfunction. These findings not only offer the prospect of developing biomarkers for identifying migraine patients who might benefit from thyroid hormone therapy but also underscore the promising potential of future genetic studies in providing biological insights to advance clinical decision-making in understanding and addressing these interconnected phenomena.

Professor Vladimir Pavlovich Efroimson is one of the most prominent Russian geneticists, a former student of N.K. Kolt'tsov, who was among the geneticists that had to struggle against the presecution of genetics in the Soviet Union. Efroimson has discovered the formula of mutation rate in human (1932). He was a laeding specialist in genetics and breeding of silkworm and defended his condidate (1941) and doctoral (1947) dissertations on the subiect. He wrote the first Russian monograph on genetics The Introduction to Medical Genetics (1964)--the book that triddered the revival of human genetics in the Soviet Union. Efroimson was a veteran of the World War II, he fought in the army in 1941 through 1945 and was awarded military decorations. He was presecuted two times in 1932 ans 1949. Efroimson spent 10 years in Gulag and for 25 years was banned from scientific work. He was the autor of three monographs and over 100 scientific papers and the editor of many books on different issues of genetics. Efroimson entered the annals of Russian science as an outstsnding researcher, but also as an inblinking fighter for the truth, an uncompromising opponent of antiscientific directions in biology, an ardent advocate of genetics and the moral standart of a true scientist.

The results of up-to-date researches made on the interaction of vitaminology and genetics are assumed. Publications, which were issued after the completion of superlative scientific career of academician R. V. Chagovets, the scientist who stood at the source of up-to-date genetico-biochemical trend in vitaminology were used in the paper. Information of the last years concerning three urgent problems of biochemistry and genetics is presented: studies of the structure, functions and genetic determination of vitamin-binding and transporting proteins; investigation of genetic determination of vitamin synthesis enzymes; study of vitamins and their derivatives role in genome function regulation. It is stressed in the review that genetico-biochemical investigations in vitaminology, despite their urgency and scientific importance, had not been developed in the right way. This makes the meeting of practical needs of microbiological industry, medicine and animal breeding more difficult.

Arid habitats have recently attracted increasing attention in terms of biodiversity research and the disco very of new bacterial species. These habitats are among the target ecosystems suitable for isolating new strains of actinobacteria that are likely to produce new metabolites. This paper presents the results on the isolation of actinobacteria from soils of the dry steppe zone of the Selenga Highlands, the characterization of their taxonomic diversity, as well as ecological and trophic properties. The bacterial counts on ISP 4 medium ranged from 6.6 × 105 to 7.1 × 106 CFU/g. The highest bacterial counts were observed in the subsurface and middle horizons of the studied soils. 28 strains of Gram-positive bacteria represented by thin-branched mycelium, coccoid and bacilliform forms were isolated. According to the results of 16S rRNA gene analysis, the isolated strains were representatives of Streptomyces, Arthrobacter, Glycomyces, Kocuria, Microbacterium, Micromonospora, Nocardioides, Pseudarthrobacter, and Rhodococcus (Actinomycetota). One isolate that showed low 16S rRNA gene sequence similarity with previously isolated and validly described species was a new species of the genus Glycomyces. It was shown that all tested strains are mesophilic, prefer neutral or slightly alkaline conditions, have growth limits in the temperature range of 5–45 °C and pH 6–9. The optimal NaCl concentration for growth of most strains was 0–1 %. The strains under study were capable of utilizing a wide range of mono- and disaccharides and polyatomic alcohols as a carbon source. The isolated strains were capable of using both organic (proteins and amino acids) and inorganic (ammonium salts and nitrates) compounds as nitrogen sources. The examinations of extracellular enzymes showed that all isolates were capable of producing catalase and amylase; 78.6 % of the total number of isolates produced protease and lipase; 53.6 %, cellulase; and 28.6 %, urease. The data obtained expand current knowledge about the diversity of microbial communities in soils of the Selenga Highlands and also confirm the potential of searching for new actinobacteria species in these soils.

To date, many derivatives and analogs of nucleic acids (NAs) have been developed. Some of them have found uses in scientific research and biomedical applications. Their effective use is based on the data about their properties. Some of the most important physicochemical properties of oligonucleotides are thermodynamic parameters of the formation of their duplexes with DNA and RNA. These parameters can be calculated only for a few NA derivatives: locked NAs, bridged oligonucleotides, and peptide NAs. Existing predictive approaches are based on an analysis of experimental data and the consequent construction of predictive models. The ongoing pilot studies aimed at devising methods for predicting the properties of NAs by computational modeling techniques are based only on knowledge about the structure of oligonucleotides. In this work, we studied the applicability of the weighted histogram analysis method (WHAM) in combination with umbrella sampling to the calculation of thermodynamic parameters of DNA duplex formation (changes in enthalpy ∆H°, entropy ∆S°, and Gibbs free energy ∆G37° ). A procedure was designed involving WHAM for calculating the hybridization properties of oligodeoxyribonucleotides. Optimal parameters for modeling and calculation of thermodynamic parameters were determined. The feasibility of calculation of ∆H°, ∆S°, and ∆G37° was demonstrated using a representative sample of 21 oligonucleotides 4–16 nucleotides long with a GC content of 14–100 %. Error of the calculation of the thermodynamic parameters was 11.4, 12.9, and 11.8 % for ∆H°, ∆S°, and ∆G37° , respectively, and the melting temperature was predicted with an average error of 5.5 °C. Such high accuracy of computations is comparable with the accuracy of the experimental approach and of other methods for calculating the energy of NA duplex formation. In this paper, the use of WHAM for computation of the energy of DNA duplex formation was systematically investigated for the first time. Our results show that a reliable calculation of the hybridization parameters of new NA derivatives is possible, including derivatives not yet synthesized. This work opens up new horizons for a rational design of constructs based on NAs for solving problems in biomedicine and biotechnology.

Cancer is a complex and heterogeneous disease characterized by the accumulation of genetic alterations that drive uncontrolled cell growth and proliferation. Evolutionary dynamics plays a crucial role in the emergence and development of tumors, shaping the heterogeneity and adaptability of cancer cells. From the perspective of evolutionary theory, tumors are complex ecosystems that evolve through a process of microevolution influenced by genetic mutations, epigenetic changes, tumor microenvironment factors, and therapy­induced changes. This dynamic nature of tumors poses significant challenges for effective cancer treatment, and understanding it is essential for developing effective and personalized therapies. By uncovering the mechanisms that determine tumor heterogeneity, researchers can identify key genetic and epigenetic changes that contribute to tumor progression and resistance to treatment. This knowledge enables the development of innovative strategies for targeting specific tumor clones, minimizing the risk of recurrence and improving patient outcomes. To investigate the evolutionary dynamics of cancer, researchers employ a wide range of experimental and computational approaches. Traditional experimental methods involve genomic profiling techniques such as next­generation sequencing and fluorescence in situ hybridization. These techniques enable the identification of somatic mutations, copy number alterations, and structural rearrangements within cancer genomes. Furthermore, single­cell sequencing methods have emerged as powerful tools for dissecting intratumoral heterogeneity and tracing clonal evolution. In parallel, computational models and algorithms have been developed to simulate and analyze cancer evolution. These models integrate data from multiple sources to predict tumor growth patterns, identify driver mutations, and infer evolutionary trajectories. In this paper, we set out to describe the current approaches to address this evolutionary complexity and theories of its occurrence.

The paper analyzes the genetic profile of the domestic cat population of the Aoshima Island. The population has been established in the middle of the last century, after a small group of animals was imported for rodent control. Based on three photographs, the genotypes of the cats in three overlapping groups (75, 56, and 70 individuals) were determined. The mutant allele frequencies of the sex-linked O (Orange) locus and the three autosomal loci a, W, and l (Agouti, White, and Long hair) responsible for coat color and length were estimated. The population lacks the mutant alleles d (Dilution locus), W and wg (White), tab (Tabby), TiA (Ticked) present in other populations of Japan. This is an almost monomorphic population with prevailing red and tortoiseshell individuals. Most cats have interrupted stripes (genotype Ti+Ti+TaM-). The island’s population differs from the other populations of the Japanese islands in the frequencies of two mutant alleles, O and a. The frequency of the O allele (q(O) = 0.580) is one of the highest in the region, while the frequency of the a allele (q(a) = 0.276) is two times lower than in the other populations. In both cases, the differences in frequencies between the neighbouring populations are significant (p < 0.0001). An independent study of the same population revealed a similar genetic structure. However, it detected the presence of the d allele, the frequency of the a allele was higher (0.534 versus 0.276, p < 0.020). The genetic profile, frequencies of mutant alleles in the population, and history of its origin indicate a significant influence of the founder effect on the genetic structure of the island’s domestic cat population.

The paper is devoted to A.S. Serebrovskiĭ's studies on induced mutagenesis. His first publication on X-ray induction of mutations in Drosophila appeared in 1928; this became a classical work and entered the golden fund of modern radiation genetics. Investigations of the scientists in the A.S. Serebrovskiĭ's laboratory as will as his own works on the analysis of radiation mutations at the achaete-scute complex have led to the development of the teaching about gene subdivision and made it possible to draw up a linear array of a gene from elementary subgenes, which have laid down the foundations of the modern molecular-genetic theory of gene.

Abstract: The paper is devoted to the development of Soviet genetics in the higher school in the second half of the 1960s. Currently history of Russian genetics is becoming a popular research subject among Russian and foreign historians. Tragic events, which befell Soviet genetics in mid 20th century have been thoroughly examined both in scientific and popular accounts. Thus development of genetics during the later period of Soviet history makes a more suitable subject for a rigorous historical investigation. In the late 1960s Soviet science and technology policy in regard to biological research was aimed at the restoration of losses suffered due to the rise of Lysenkoism. This period has not yet been duly investigated and there are almost no publications authored by professional historians dedicated to genetics research in the Soviet Union in the 1960-80s. To a certain extent this gap has been covered in the author’s earlier publications. The research is based on the wide range of archive documents from the archives of Moscow, Saint- Petersburg and Novosibirsk. Also, significant place is given to oral sources. The paper underlines that Leningrad and Novosibirsk Universities made a great contribution to the revival of human resources in the Soviet genetics. At the same time many other biological departments and institutes were going through the reorganization of the Soviet biology with lots of difficulties. The examples of the All-Union Institute of Plant Industry of the VASKhNIL and the Novosibirsk agricultural institute vividly illustrated that Lysenkoists still held an important positions in the field of science and education. Besides, the lack of material supplies of the chairs and laboratories had a destructive influence.

Experimental genetic studies of Drosophila were initiated by T.H. Morgan in 1910, when he discovered the sex-linked white-eyed mutation, white. This discovery commenced the transformation of Mendel’s “hereditary factors” to more specific but no less enigmatic W.L. Johanssen’s “genes”. Owing to Drosophila’s biologic features, it became a universal eukaryotic model for genetic, embryological, morphological, physiological, molecular, and cellular studies. Actually, the history of discoveries done on Drosophila species reflects the course of genetics development. That was Drosophila studies to lay foundation for genetic notions of the nature of genes, genetic linkage, mitotic and meiotic chromosome segregation, mechanisms governing mutagenesis and recombination, genetic instability, mobile genetic elements, regularities and genetics of individual development, and microevolutionary processes in populations. The paper considers steps and milestones of genetics development by examples of the American and Russian genetic schools. The American genetics was characterized by “reductionism”, whereas the Russian genetics was inclined to “cosmism”, where emphasis was placed on the understanding of macroevolutionary processes. Drosophila has become a test ground to try new genetic methods, and its studies contribute much to biomedical science. The paper outlines several top priority fields in modern Drosophila studies.

Abstract: The paper is devoted to the development of Soviet genetics in the higher school in the second half of the 1960s. Currently history of Russian genetics is becoming a popular research subject among Russian and foreign historians. Tragic events, which befell Soviet genetics in mid 20th century have been thoroughly examined both in scientific and popular accounts. Thus development of genetics during the later period of Soviet history makes a more suitable subject for a rigorous historical investigation. In the late 1960s Soviet science and technology policy in regard to biological research was aimed at the restoration of losses suffered due to the rise of Lysenkoism. This period has not yet been duly investigated and there are almost no publications authored by professional historians dedicated to genetics research in the Soviet Union in the 1960-80s. To a certain extent this gap has been covered in the author’s earlier publications. The research is based on the wide range of archive documents from the archives of Moscow, Saint- Petersburg and Novosibirsk. Also, significant place is given to oral sources. The paper underlines that Leningrad and Novosibirsk Universities made a great contribution to the revival of human resources in the Soviet genetics. At the same time many other biological departments and institutes were going through the reorganization of the Soviet biology with lots of difficulties. The examples of the All-Union Institute of Plant Industry of the VASKhNIL and the Novosibirsk agricultural institute vividly illustrated that Lysenkoists still held an important positions in the field of science and education. Besides, the lack of material supplies of the chairs and laboratories had a destructive influence.

The paper presents an analysis of the data obtained for pea accessions from the VIR collection studied at the Adler Experiment Station in the setting of the Krasnodar Territory in 2017–2019. It was for the first time that these accessions were studied for a set of phenotypic traits. The object of the study was a sample of 494 pea accessions originated from 43 countries and 18 regions and territories of the Russian Federation. The work was carried out in compliance with the methodological guidelines developed at VIR. Statistica 13.3 software was employed for statistical data processing. An assessment of four qualitative, 10 quantitative and four phenological traits in the accessions made it possible to differentiate them by the type of use, that is, as dry, forage and garden peas. The varieties differing in the type of use significantly differed by the values of such traits as stem length, number of pods per plant, number of nodes to the first flower, number of flowers in the inflorescence, the maximum number of seeds per pod, pod length, and a narrower pod of forage pea compared to that of dry and garden peas. The average values of these traits were recorded for the peas with different types of use. The maximum difference was noted between garden and forage pea varieties. Dry pea varieties occupied an intermediate position. The complex of phenotypic traits identified determines the differences between three types of pea use, which is important when selecting the initial material for breeding appropriate varieties.

The snowballing growth of scientific data obtained using modern techniques of genome editing (GE) calls for their critical evaluation and comparison against previously applied methods such as induced mutagenesis, which was a leading method of genome modification for many decades of the past century, and its application has resulted in a huge diversity of cultivars. However, this method was relatively long and included a number of stages from inducing multiple mutations using different mutagenic factors to crossing and selecting the most valuable cultivars for several generations. A new technology of genetic engineering and transgenesis enabled us to radically reduce the time required to obtain a new genetically-modified cultivar to one generation and make the modification process more effective and targeted. The main drawback of this approach was that an introduced transgene might uncontrollably affect the other genes of a recipient plant, which led to the limitations imposed on transgenesis application in many countries. These limitations have been effectively surmounted thanks to the development of GE techniques allowing for a precise modification within a single gene that in many characteristics make it similar to a natural allele (especially when it comes to ribonucleoprotein complexes), which has paved the way for wide application of GE in routine breeding. The paper reviews the main stages of GE development in its application in plants. It provides short descriptions of different GE techniques, including those using protein editors such as zinc-finger and transcription activator-like effector nucleases (TALEN), and the CRISPR/Cas9 technology. It lists a number of achievements in using GE to produce new cultivars of higher yield that are resistant to unfavorable factors and have good nutritional properties. The review also considers the de novo domestication approach, which allows for faster obtaining of new cultivars from natural varieties. In the conclusion, the future ways of GE development are discussed.

Dystonia-6 (DYT-THAP1, DYT6) is an autosomal dominant movement disorder characterized by early involvement of craniofacial muscles with secondary generalization. DYT6 is caused by heterozygous variants in the THAP domain-containing protein 1 (THAP1) gene. Currently, more than 90 different pathogenic missense and truncating THAP1 variants have been reported – mainly in people from Europe but also from China and Brazil. However, no cases of genetically confirmed DYT6 have been described in Central Asian countries. Here the first case of genetically confirmed DYT6-dystonia from Central Asia is described. The proband had adolescent-onset focal dystonia with secondary generalization, trihexyphenidyl induced persistent chorea and robust and sustained response to globus pallidus internus deep brain stimulation. Her definitive diagnosis has been made 39 years after the onset of the disease keeping her for almost 4 decades disabled. This paper highlights the urgent need for movement disorders specialists in Central Asia as well as access to free genetic testing and deep brain stimulation surgery.

Wheatgrass (Th. intermedium) has been traditionally used in wheat breeding for obtaining wheat-wheatgrass hybrids and varieties with introgressions of new genes for economically valuable traits. However, in the 1980s in the United States wheatgrass was selected from among perennial plant species as having promise for domestication and the development of dual-purpose varieties for grain (as an alternative to perennial wheat) and hay. The result of this work was the creation of the wheatgrass varieties Kernza (The Land Institute, Kansas) and MN-Clearwater (University of Minnesota, Minnesota). In Omsk State Agrarian University, the variety Sova was developed by mass selection of the most winter-hardy biotypes with their subsequent combination from the population of wheatgrass obtained from The Land Institute. The average grain yield of the variety Sova is 9.2 dt/ha, green mass is 210.0 dt/ ha, and hay is 71.0 dt/ha. Wheatgrass is a crop with a large production potential, beneficial environmental properties, and valuable grain for functional food. Many publications show the advantages of growing the Kernza variety compared to annual crops in reducing groundwater nitrate contamination, increasing soil carbon sequestration, and reducing energy and economic costs. However, breeding programs for domestication of perennial crops are very limited in Russia. This paper presents an overview of main tasks faced by breeders, aimed at enhancing the yield and cultivating wheatgrass efficiency as a perennial grain and fodder crop. To address them, both traditional and modern biotechnological and molecular cytogenetic approaches are used. The most important task is to transfer target genes of Th. intermedium to modern wheat varieties and decrease the level of chromatin carrying undesirable genes of the wild relative. The first consensus map of wheatgrass containing 10,029 markers was obtained, which is important for searching for genes and their introgressions to the wheat genome. The results of research on the nutritional and technological properties of wheatgrass grain for the development of food products as well as the differences in the quality of wheatgrass grain and wheat grain are presented.

April 2, 2022 marks the anniversary of Lyudmila Andreevna Bespalova, an Academician of the Russian Academy of Sciences, one of the prominent wheat and triticale breeders, the author of many varieties introduced into agricultural practice both in our country and abroad, which are cultivated in areas encompassing millions of hectares, thus making a significant contribution to solving the global food security problem. Lyudmila A. Bespalova is a recognized classic in the field of wheat breeding and seed production, she has published over 300 scientific papers, and received about 120 copyright certificates and patents. Acad. Bespalova is a bright representative of domestic breeders, who maintains the traditions of one of the largest scientific schools and takes an active part in the life of the community of geneticists and breeders in this country by training young specialists and increasing the prestige of and demand for the profession of a breeder.

Investigation of the frequencies of functionally signif icant gene variants in the context of medical biology and gene geography is a relevant issue for studying the genetic structure of human populations. The transition from a traditional to an urbanized lifestyle leads to a higher incidence of civilizational diseases associated with metabolic disorders, including type 2 diabetes mellitus. The goal of the present paper is to analyze the frequencies of functionally signif icant gene alleles in the metabolic prof iles of indigenous Siberian peoples to identify the gene pool resilience, evaluate the susceptibility of various ethnic groups to metabolic disorders under changing environmental conditions, and predict the epidemiological situation that may occur in the near future. The study was performed in the monoethnic samples of eastern and western Buryats, Teleuts, Dolgans, and two territorial groups of Yakuts. A real-time PCR was used to determine the frequencies of single nucleotide polymorphisms (SNPs) G103894T, rs12255372, and C53341T, rs7903146 in the TCF7L2 gene. The results obtained were compared to the frequencies identif ied for Russians from Eastern Siberia and the values available in the literature. The frequencies of the polymorphic variants studied in the samples from the indigenous Siberian peoples place them in between Caucasian and East Asian populations, following the geographic gradient of polymorphism distribution. A signif icantly lower occurrence of type 2 diabetes risk alleles TCF7L2 (103894T) and TCF7L2 (53341T) in the samples of indigenous Siberian peoples compared to Russians was observed, which agrees with their lower susceptibility to metabolic disorders compared to the newcomer Caucasian population. Taking into account urbanization, a reduced growth in type 2 diabetes incidence may be predicted in indigenous Siberian peoples, i. e. Buryats, Yakuts, Dolgans, and Teleuts, compared to the newcomer Caucasian population. A further study of population structure with respect to different metabolic prof ile genes is required to better understand the molecular genetic foundations of the adaptive potential of indigenous Siberian peoples.

Correlations between the morphological features of f lower buds and the developmental stages of the male gametophyte are of great practical interest as a reliable marker that accelerates and simplif ies the selection of appropriate plant material for isolated microspore culture. Microspore culture enables one to quickly obtain many pure lines of different vegetable crops, but it has not yet been widely applied in the melon (Cucumis melo L.). To successfully apply this technique in a new culture, one has to optimize many of its elements: f irst, f ind the biological markers for selecting the f lower buds containing the microspores of certain development stages. The paper presents the results of research estimating the correlations between the length and diameter of the f lower buds, the length of the visual part of the corolla, the length of the anthers and the development stages of the male gametophyte in the F1 hybrid of the Kim Hong Ngoc melon. The strongest correlation (CC = 0.885) was found for the f lower bed diameter and a strong correlation (CC = 0.880), for the bud length. The corolla’s visual part was a less reliable morphological feature, and the anther’s length should not be used as a parameter to predict the developmental stages of the melon’s male gametophyte. It was also found that one anther could contain the microspores and pollen grains of different developmental stages. In the f lower buds less than 4 mm in length and 1.51 ± 0.02 mm in diameter prevailed tetrads, and in the buds 4.0–4.9 mm in length and 2.30 ± 0.02 mm in diameter, early microspores. The microspores of a middle stage of development prevailed in the f lower buds 5.0–5.9 mm in length and 2.32 ± 0.00 mm in diameter; mid and late vacuolated microspores, in the buds 6.0–8.9 mm in length and 2.96 ± 0.37 mm in diameter; and two-celled pollen, in the buds more than 9 mm in length and more than 3.97 ± 0.34 mm in diameter.

It is generally accepted that during the domestication of food plants, selection was focused on their productivity, the ease of their technological processing into food, and resistance to pathogens and environmental stressors. Besides, the palatability of plant foods and their health benefits could also be subjected to selection by humans in the past. Nonetheless, it is unclear whether in antiquity, aside from positive selection for beneficial properties of plants, humans simultaneously selected against such detrimental properties as allergenicity. This topic is becoming increasingly relevant as the allergization of the population grows, being a major challenge for modern medicine. That is why intensive research by breeders is already underway for creating hypoallergenic forms of food plants. Accordingly, in this paper, albumin, globulin, and β­amylase of common wheat Triticum aestivum L. (1753) are analyzed, which have been identified earlier as targets for attacks by human class E immunoglobulins. At the genomic level, we wanted to find signs of past negative selection against the allergenicity of these three proteins (albumin, globulin, and β­amylase) during the domestication of ancestral forms of modern food plants. We focused the search on the TATA­binding protein (TBP)­binding site because it is located within a narrow region (between positions –70 and –20 relative to the corresponding transcription start sites), is the most conserved, necessary for primary transcription initiation, and is the best­studied regulatory genomic signal in eukaryotes. Our previous studies presented our publicly available Web service Plant_SNP_TATA_Z­tester, which makes it possible to estimate the equilibrium dissociation constant (KD) of TBP complexes with plant proximal promoters (as output data) using 90 bp of their DNA sequences (as input data). In this work, by means of this bioinformatics tool, 363 gene promoter DNA sequences representing 43 plant species were analyzed. It was found that compared with non­food plants, food plants are characterized by significantly weaker affinity of TBP for proximal promoters of their genes homologous to the genes of commonwheat globulin, albumin, and β­amylase (food allergens) (p< 0.01, Fisher’s Z­test). This evidence suggests that in the past humans carried out selective breeding to reduce the expression of food plant genes encoding these allergenic proteins.

This paper describes an attempt to analyze, with the aid of bioinformatics resources (programs and databases), the probable cause of the cross-interaction of antibodies against HPV16 L1 with antigenic protein HPV6 L1, which has been revealed in the investigation of the candidate vaccine obtained on the base of a plant expression system (tomato plants). In our opinion, the most likely reason for the cross-interaction of antibodies with antigens of different pathogenic HPV types is the similarity of their antigenic determinants. In this work, the amino acid sequences of HPV16 L1 and HPV6 L1 used for the development of a binary vaccine against cervical cancer and anogenital papillomatosis have been analyzed. For the analysis of antigenic determinants, the programs BepiPred-2.0: Sequential B-Cell Epitope Predictor, DiscoTope 2.0 Server and SYFPEITHI have been used. As a result of the analysis of probable B-cell linear determinants (epitopes), it has been found that in both types of HPV the proteins have approximately the same location and size of linear antigenic determinants; the difference is observed only in the form of small shifts in the size of several amino acid residues. However, there are some differences in the amino acid composition of epitopes; therefore, the possibility for cross-interaction of the antibodies with the antigens due to the similarity of linear antigenic determinants for B-cells is very small. The analysis of potential threedimensional epitopes for B-cells has shown that due to little difference between them the HPV16 L1 and HPV6 L1 proteins have no prerequisites for cross-interaction of the antibodies with the antigens belonging to the two different pathogenic HPV types. The analysis of probable linear epitopes for T-cells has revealed a common antigenic determinant in the two protein sequences. According to the rank made with the SYFPEITHI program, the amino acid sequence AQL(I)FNKPYWL is the second most likely antigenic determinant for T-cells. Meanwhile, the amino acid sequences of this determinant in HPV16 L1 and HPV6 L1 are virtually identical. There is a difference in only one position, but it is not critical due to the similarity of the physicochemical properties of amino acids, for which there is a replacement in the amino acid sequence of antigenic determinants. Consequently, some moderate cross-interaction of the antibodies to HPV16 L1 with the antigens of HPV6 L1 may be expected.

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This paper presents the results on the breeding work carried out by the Subtropical Scientific Centre of the Russian Academy of Sciences. Currently, the Centre’s breeders are doing a lot of work aimed at breeding new fine yielding cultivars of subtropical and flower crops that will be resistant to growing conditions; they include kaki persimmon, feijoa, mandarin, freesia, crown anemone, pelargonium and chrysanthemum. The sources of high-level priority traits in flower crops that are valuable for further breeding in order to improve decorative (colour, flower shape, inflorescence), economic and biological traits (flowering period, a large number of flowers in the inflorescence, storage period of cut flowers, disease resistance, high reproduction coefficient) were recorded. The aim of the research is to improve the subtropical and flower crops assortment. The objects of the research were 989 hybrid forms: 136 citrus crops, 56 persimmon, 36 feijoa, 38 tea plant, 11 pear, 24 hazel, 108 freesia, 398 crown anemone, 120 pelargonium and 62 chrysanthemum hybrids. New cultivars with a complex of valuable traits have been created as a result of the scientific work. Over the past five years, FRC SSC of RAS has created 50 new cultivars: 26 pelargonium, 15 anemone, 5 freesia, 2 chrysanthemum, 1 persimmon and 1 apple and submitted them to the State Cultivar Commission. The “State Register of Selection Achievements Authorized for Use for Production Purposes” has included 63 cultivars developed by FRC SSC RAS, including 26 pelargonium, 13 anemone, 9 chrysanthemum, 7 freesia, 4 hazel, 3 feijoa and 1 tea plant cultivars. 46 patents for breeding achievements have been obtained.

In this review, the authors considered the promising species of vegetable crops for introduction and breeding in the Russian Federation. An attempt was made to assess the possibilities of their breeding improvement from the standpoint of the presence of traits that limit large-scale production. Species that could potentially serve as sources of a high content of functional food ingredients (FFI) have been identified and characterized. For the successful introgression of these species in the Russian Federation, we proposed the methodological approaches including the assessment of the potential cold resistance of thermophilic crops in the mature male gametophyte in vitro (e. g., asparagus bean). The increase in the biodiversity of vegetable plants and improving of their nutritional value should be recognized as one of the main tasks, along with the growth of crop productivity. It is proposed to use the ratio of the total number of the registered cultivars of a particular crop to the number of years since the first cultivar of that crop has been included in the State Register of Breeding Achievements Admitted for Use as a measure of demand. It is advisable to formalize the trait“high content of FFI” in crops, taking as a basis, for example, a 2–4-fold excess of the content of any FFI or their complex in a cultivar over the crop’s standard (reference) value. Such varieties should be included in the State Register of Breeding Achievements Approved for Use as a separate list. The purpose of their separation in the State Register is to ensure the potential interest of investors and business structures in the sale of functional food on the market. The paper discusses in detail the most promising species of introduced vegetable crops from five families (Brassicaceae, Amaranthaceae, Solanaceae, Leguminosae, Cucurbitaceae). The following species are proposed as potential sources of high FPI content: Brassica oleracea ssp. oleracea, B. oleraceae var. alboglabra, B. rapa ssp. chinensis, B. rapa ssp. narinosa, B. rapa ssp. nipposinica, B. rapa ssp. rapa, B. uncea, Cochlearia officinalis, Lepidium sativum, Amaranthus caudatus, A. cruentus, A. hypochondriacus, A. dubius, A. tricolor, lividus, species in the genus Physalis L., Momordica charantia, Benincasa hispida, Cucumis metuliferus, Vigna unguiculata.

Many processes in living organisms are subject to periodic oscillations at different hierarchical levels of their organization: from molecular-genetic to population and ecological. Oscillatory processes are responsible for cell cycles in both prokaryotes and eukaryotes, for circadian rhythms, for synchronous coupling of respiration with cardiac contractions, etc. Fluctuations in the numbers of organisms in natural populations can be caused by the populations’ own properties, their age structure, and ecological relationships with other species. Along with experimental approaches, mathematical and computer modeling is widely used to study oscillating biological systems. This paper presents classical mathematical models that describe oscillatory behavior in biological systems. Methods for the search for oscillatory molecular-genetic systems are presented by the example of their special case – oscillatory enzymatic systems. Factors influencing the cyclic dynamics in living systems, typical not only of the molecular-genetic level, but of higher levels of organization as well, are considered. Application of different ways to describe gene networks for modeling oscillatory molecular-genetic systems is considered, where the most important factor for the emergence of cyclic behavior is the presence of feedback. Techniques for finding potentially oscillatory enzymatic systems are presented. Using the method described in the article, we present and analyze, in a step-by-step manner, first the structural models (graphs) of gene networks and then the reconstruction of the mathematical models and computational experiments with them. Structural models are ideally suited for the tasks of an automatic search for potential oscillating contours (linked subgraphs), whose structure can correspond to the mathematical model of the molecular-genetic system that demonstrates oscillatory behavior in dynamics. At the same time, it is the numerical study of mathematical models for the selected contours that makes it possible to confirm the presence of stable limit cycles in them. As an example of application of the technology, a network of 300 metabolic reactions of the bacterium Escherichia coli was analyzed using mathematical and computer modeling tools. In particular, oscillatory behavior was shown for a loop whose reactions are part of the tryptophan biosynthesis pathway.

De novo transcriptome assembly is an important stage of RNA-seq data computational analysis. It allows the researchers to obtain the sequences of transcripts presented in the biological sample of interest. The availability of accurate and complete transcriptome sequence of the organism of interest is, in turn, an indispensable condition for further analysis of RNA-seq data. Through years of transcriptomic research, the bioinformatics community has developed a number of assembler programs for transcriptome reconstruction from short reads of RNA-seq libraries. Different assemblers makes it possible to conduct a de novo transcriptome reconstruction and a genome-guided reconstruction. The majority of the assemblers working with RNA-seq data are based on the De Bruijn graph method of sequence reconstruction. However, specif ics of their procedures can vary drastically, as do their results. A number of authors recommend a hybrid approach to transcriptome reconstruction based on combining the results of several assemblers in order to achieve a better transcriptome assembly. The advantage of this approach has been demonstrated in a number of studies, with RNA-seq experiments conducted on the Illumina platform. In this paper, we propose a hybrid approach for creating a transcriptome assembly of the barley Hordeum vulgare isogenic line Bowman and two nearly isogenic lines contrasting in spike pigmentation, based on the results of sequencing on the IonTorrent platform. This approach implements several de novo assemblers: Trinity, Trans-ABySS and rnaSPAdes. Several assembly metrics were examined: the percentage of reference transcripts observed in the assemblies, the percentage of RNA-seq reads involved, and BUSCO scores. It was shown that, based on the summation of these metrics, transcriptome meta-assembly surpasses individual transcriptome assemblies it consists of.