Vavilovskii Zhurnal Genetiki i Selektsii最新文献

We recently proposed a novel class of nucleic acid derivatives - phosphoramidate benzoazole oligonucleotides (PABAOs). In these compounds, one of the non-bridging oxygen atoms is replaced by a phosphoramidate N-benzoazole group, such as benzimidazole, dimethylbenzimidazole, benzoxazole, or benzothiazole. Studies of the properties of these derivatives have shown that their use in PCR enhances the specificity and selectivity of the analysis. The study investigates the effect of phosphoramide N-benzimidazole modification of DNA primers on their elongation by Taq DNA polymerase using molecular dynamics simulations. We examined perfectly matched primer-template complexes with modifications at positions one through six from the 3'-end of the primer. Prior experimental work demonstrated that the degree of elongation suppression depends on the modification position: the closer to the 3'-end, the stronger the inhibition, with maximal suppression observed for the first position, especially in mismatched complexes. Furthermore, incomplete elongation products were experimentally observed for primers modified at the fourth position. Our molecular dynamics simulations and subsequent analysis revealed the molecular mechanisms underlying the interaction of modified primers with the enzyme. These include steric hindrance that impedes polymerase progression along the modified strand and local distortions in the DNA structure, which explain the experimentally observed trends. We established that both different stereoisomers of the phosphoramidate groups and conformers of the phosphoramidate N-benzimidazole moiety differentially affect the structure of the enzyme-substrate complex and the efficiency of Taq DNA polymerase interaction with the modified DNA complex. Modification of the first and second internucleoside phosphate from the 3'-end of the primer causes the most significant perturbation to the structure of the protein-nucleic acid complex. When the modification is located at the fourth phosphate group, the N-benzimidazole moiety occupies a specific pocket of the enzyme. These findings provide a foundation for the rational design of specific DNA primers bearing modified N-benzimidazole moieties with tailored properties for use in PCR diagnostics.

Major depressive disorder (MDD) is one of the most widespread mental illnesses, which necessitates the search for factors of increased predisposition to this disorder. Single nucleotide polymorphisms in genes of the brain's neurotransmitter systems are often considered as molecular genetic markers of MDD. Indicators of individual single nucleotide variability in neurotransmitter genes are used to assess the risk of MDD before its symptomatology at the behavioral level. However, the predictive capabilities of analyzing genomic variations to assess the risk of depression are not yet sufficiently reliable and are complemented by behavioral and neurophysiological information about patients. Neurophysiological markers of MDD provide the most reliable estimates of the severity of pathological symptoms, but they reflect a person's state at the time of examination, and not a predisposition to the occurrence of this pathological state and do not allow assessing the risk of its appearance in the future. Major depressive disorder is often accompanied by abnormalities in a person's ability to control motor responses, including the ability to voluntary suppress inappropriate behavior. The "stop-signal paradigm" (SSP) is an experimental method for assessing the functional balance between the inhibitory and activation systems of the brain during targeted movements. Combined with EEG recording, this experimental method allows for the consideration of not only participants' behavioral characteristics, such as speed or accuracy of responses, but also the brain's neurophysiological features associated with behavior control. The objective of this study was to evaluate the relationship between EEG responses in the stop-signal paradigm and individual single nucleotide variability in candidate genes for MDD detection. Dimensionality in the original genetic and neurophysiological experimental data was reduced by principal component analysis (PCA) to subsequently detect an association between EEG response components recorded during the control of random motor responses and single nucleotide variations in genes, the variability of which is asso-ciated with MDD risk. Variability in these genes has been shown to be associated with the amplitude of brain responses under the conditions of test subjects using the PCA method. The results obtained can be used to develop systems for the early diagnosis of depression, identify individual patterns of impairment in the brain, select methods for correcting the disease and control the effectiveness of therapy.

The nature of the last universal common ancestor (LUCA) of all living organisms remains a controversial issue in biology. There is evidence of both thermophilic and mesophilic LUCA origin. The increasing complexity of the cellular apparatus during the evolution from early life forms to modern organisms could have manifested itself in long-term evolutionary changes in the nucleotide composition of genetic sequences. This work is devoted to the identification of such trends in tRNA sequences. The results of an evolutionary analysis of single-nucleotide substitutions in tRNAs of 123 species from three domains - Bacteria, Archaea and Eukaryota - are presented. A universal vector of directed evolutionary change in tRNA sequences has been discovered, in which substitutions of guanine (G) to adenine (A) and cytosine (C) to uracil (U) occur more frequently than the reverse. The most striking asymmetry in the number of substitutions is observed in the following transitions: a) purine-to-purine, where G→A outnumbers A→G, b) pyrimidine-to-pyrimidine, where C→U outnumbers U→C, and c) purine-to-pyrimidine and vice versa, where G→U outnumbers U→G. As a result, tRNAs could lose "strong" three-hydrogen-bond complementary pairs formed by guanine and cytosine and fix "weak" two-hydrogen-bond complementary pairs formed by adenine and uracil. 16 out of 20 tRNA families are susceptible to the detected change in sequence composition, which corresponds to the significance level p = 0.006 according to the one-sided binomial test. The identified pattern indicates a high GC content in the common ancestor of modern tRNAs, supporting the hypothesis that the last universal common ancestor (LUCA) lived in a hotter environment than do most contemporary organisms.

The study of molecular genetic mechanisms of plant responses to specific growth conditions and stress factors is a central focus of scientific research aimed at developing new valuable crop varieties, particularly rice and wheat. These factors include abiotic stresses (high or low temperatures, drought, salinity, soil metal contamination), biotic stresses (pathogens, pests), as well as plant responses to regulatory factors (fertilizers, hormones, elicitors, and other compounds). Modern research in plant genetics is based on the understanding that the formation of any phenotypic characteristics (molecular genetic, biochemical, physiological, morphological, etc.) is controlled by gene networks - groups of coordinately functioning genes interacting through their products (RNA, proteins, and metabolites). Previously, we developed the ANDSystem intelligent technology designed to extract knowledge from scientific publication texts for the reconstruction of gene networks in biology and biomedicine. In this work, using an adapted version of ANDSystem for plants, we created the SmartCrop knowledge base designed to address challenges related to studying molecular genetic mechanisms of genotype-phenotype-environment interactions for agriculturally valuable rice and wheat crops. SmartCrop is designed to assist researchers in solving tasks such as interpreting omics technology results (establishing connections between gene sets and biological processes, phenotypic traits, etc.); reconstructing gene networks describing relationships between molecular genetic objects and concepts in breeding, phenomics, seed production, phytopathology, diagnostics, protective agents, etc.; identifying regulatory and signaling pathways of plant responses to specific growth conditions and biotic and abiotic stresses; predicting candidate genes for genotyping; searching for markers for marker-assisted selection; and identifying potential targets for substances (including external factors) affecting plants to ensure timely and uniform germination, better vegetative growth, efficient nutrient uptake, and improved stress resistance.

The development of high-throughput sequencing has expanded the possibilities for studying the regulation of gene expression, including the reconstruction of gene regulatory networks and transcription factor regulatory networks (TFRNs). Identifying the molecular aspects for regulation of biological processes via these networks remains a challenge. Solving this problem for plants will significantly advance the understanding of the mechanisms shaping agronomically important traits. Previously, we developed the PlantReg program to reconstruct the transcriptional regulation of biological processes in the model species Arabidopsis thaliana L. The links established by this program between TFRNs and the genes regulating biological processes specify the type of regulation (activation/suppression). However, the program does not determine whether activation/suppression of the target gene is due to the cooperative or competitive interaction of transcription factors (TFs). We assumed that using information on the mutual arrangement of TF binding sites (BSs) in the target gene promoter as well as data on the activity type of TF effector domains would help to identify the cooperative/competitive action of TFs. We improved the program and created PlantReg 1.1, which enables precise localization of TF BSs in extended TF binding regions identified from genome-wide DAP-seq profiles (https://plamorph.sysbio.ru/fannotf/). To demonstrate the capabilities of the program, we used it to investigate the regulation of target genes in previously reconstructed TFRNs for auxin response and early reaction to salt stress in A. thaliana. The study focused on genes encoding proteins involved in chlorophyll and lignin biosynthesis, ribosome biogenesis, and abscisic acid (ABA) signaling. We revealed that the frequency of competitive regulation under the influence of auxin or salt stress could be quite high (approximately 30 %). We demonstrated that competition between bZIP family TFs for common BS is a significant mechanism of transcriptional repression in response to auxin, and that auxin and salt stress can engage common competitive regulatory mechanisms to modulate the expression of some genes in the ABA signaling pathway.

The rapid advancement of omics technologies (genomics, transcriptomics, proteomics, metabolomics) and other high-throughput methods for experimental studies of molecular genetic systems and processes has led to the generation of an unprecedentedly vast amount of heterogeneous and complex biological data. Effective use of this information resource requires systematic approaches to its analysis. One such approach involves the creation of domain-specific knowledge/data repositories that integrate information from multiple sources. This not only enables the storage and structuring of heterogeneous data distributed across various resources but also facilitates the acquisition of new insights into biological systems and processes. A systematic approach is also critical to solving the fundamental problem of biology - clarifying the regularities of morphogenesis. Morphogenesis is regulated through evolutionarily conserved signaling pathways (Hedgehog, Wnt, Notch, etc.). The Hedgehog (HH) pathway plays a key role in this process, as it begins functioning earlier than others in ontogenesis and determines the progression of every stage of an organism's life cycle: from structuring embryonic primordia, histo- and organogenesis, to maintaining tissue homeostasis and regeneration in adults. Our work presents HH_Signal_pathway_db, a knowledge base that integrates curated data on the molecular components and functional roles of the human Hedgehog (HH) signaling pathway. The first release of the database (available upon request at bukharina@bionet.nsc.ru) contains information on 56 genes, their protein products, the regulatory interaction network, and established associations with pathological conditions in humans. HH_Signal_pathway_db provides researchers with a tool for gaining new knowledge about the role of the Hedgehog pathway in health and disease, and its potential applications in developmental biology and translational medicine.

Organismal aging is accompanied by the accumulation of senescent cells - damaged, non-functional cells that exhibit cell cycle arrest, resistance to apoptosis, metabolic dysfunction, and production of a wide range of pro-inflammatory substances. The age-related accumulation of these cells is associated with impaired tissue function, contributes to chronic inflammation (inflammaging), and promotes the development of various age-associated diseases. Conversely, the elimination of senescent cells restores tissue functions and positively affects overall metabolism. Under normal conditions, senescent cells are removed by the innate immune system; however, the efficiency of this process declines with age. The involvement of adaptive immunity and the role of T cells in the clearance of senescent cells remain poorly understood. The aim of this study was to identify alterations in local T cell immunity associated with the accumulation of senescent cells in human skin. The analysis was performed on publicly available single-cell RNA-sequencing data from skin biopsies, and the senescent status was assessed using the SenePy algorithm with Gaussian mixture models. It was found that the emergence of senescent cells occurs heterogeneously across cell types within the tissue. The accumulation of these cells is associated with alterations in the CD4+ to CD8+ T cell ratio, as well as with an increased abundance of regulatory T cells. Functional analysis revealed that these quantitative age-related shifts were accompanied by more pronounced activation of regulatory T cells together with features of anergy and exhaustion in CD8+ T cells, whereas functional changes in CD4+ T cells were heterogeneous. These findings underscore the importance of adaptive immunity in maintaining tissue homeostasis and suggest potential age-related dysfunction of tissue-resident T cells. Understanding the mechanisms underlying the interaction between adaptive immunity and senescent cells is crucial for the development of senolytic vaccines and other immunological approaches aimed at enhancing endogenous elimination of senescent cells.

Mathematical models represent a powerful theoretical tool for studying complex biological systems. They provide an opportunity to track non-obvious interactions and conduct in silico experiments to address practical problems. Iron plays a key role in oxygen transport in the mammals. However, a high concentration of this microelement can damage cellular structures through the production of reactive oxygen species and can also lead to ferroptosis (programmed cell death associated with iron-dependent lipid peroxidation). The immune system contributes greatly to the regulation of iron metabolism - hypoferritinemia (decreased ferritin concentration in the blood) during infection -which is a result of the innate immune response. In the study of iron metabolism, many aspects of regulation remain insufficiently studied and require a deeper understanding of the structural-functional organization and dynamics of all components of this complex process in both normal and pathological conditions. Consequently, mathematical modeling becomes an important tool to identify key regulatory interactions and predict the behavior of the iron metabolism regulatory system in the human body under various conditions. This article presents a review of iron metabolism models applicable to humans presented in chronological order of their development to illustrate the evolution and priorities in modeling iron metabolism. We focused on the formulation of numerical problems in the analyzed models, their structure and reproducibility, thereby highlighting their advantages and drawbacks. Advanced models can numerically simulate various experimental scenarios: blood transfusion, signaling pathway disruption, mutation in the ferroportin gene, and chronic inflammation. However, existing mathematical models of iron metabolism are difficult to scale and do not account for the functioning of other organs and systems, which severely limits their applicability. Therefore, to enhance the utility of computational models in solving practical problems related to iron metabolism in the human body, it is necessary to develop a scalable and verifiable mathematical model of iron metabolism that considers interactions with other functional human systems (e. g., the immune system) and state-of-the-art standards for representing mathematical models of biological systems.

The causal agent of net blotch Pyrenophora teres Drechs. f. teres (Ptt) is a dangerous pathogen of barley. The development of genetic protection against this disease is a necessary link in resource-saving and environmentally friendly barley cultivation technologies. Effective QTL markers controlling both qualitative and quantitative resistance are required for breeding for resistance to Ptt. As a result of GWAS, we identified barley accessions of different origins, the SNP haplotypes of which were associated with resistance loci simultaneously on different barley chromosomes (VIR catalogue numbers: k-5900, k-8829, k-8877, k-14936, k-30341 and k-18552). The aim of the study was to validate SNP markers (MM) of Ptt resistance loci on chromosomes 3H, 4H and 6H in F2 from crossing six resistant accessions with the susceptible variety Tatum. The observed segregation for resistance in all crossing combinations confirmed the presence of several genetic determinants of resistance in the studied accessions. To study the polymorphism of the parents from the crosses and the correspondence between the phenotypes to the presence/absence of the markers in the segregating populations, primers with a specific 3'-end, CAPS markers, and KASP markers were developed. A significant association (p < 0.05) between the presence of the CAPS marker JHI-Hv50k-2016-391380 HindIII on chromosome 6H and the phenotype of resistance to Ptt in F2 plants was revealed in crosses between the susceptible cultivar Tatum and accessions k-5900, k-8829, k-8877 and k-18552. On chromosome 4H, a significant association with the resistance phenotype in the F2 population from the cross with accession k-8877 was revealed for marker JHI-Hv50k-2016-237924, and in that from the cross with accession k-5900, for marker SCRI_RS_181886. The presence of QTL on chromosome 6H, which controls qualitative resistance in four barley accessions, masks the expression of other genes, which explains the discrepancy between the resistance phenotype and the presence of molecular markers in the segregating populations. Resistance donors and molecular markers with proven efficacy can be used in marker-assisted selection (MAS) to develop barley cultivars resistant to net blotch.

Hepatocellular Carcinoma (HCC) is the most common primary liver cancer characterized by rapid progression, high mortality rate and therapy resistance. One of the key areas in studying the molecular mechanisms of HCC development is the analysis of disturbances in apoptosis processes in hepatocytes. Throughout life apoptosis ensures the elimination of old and defective cells while the attenuation of this process serves as one of the leading factors in carcinogenesis. In this study we reconstructed and analyzed the gene network regulating hepatocyte apoptosis in humans based on single-cell transcriptome sequencing (scRNA-seq) data and the ANDSystem knowledge base which employs artificial intelligence and computational systems biology methods. Comparative analysis of gene expression revealed weakened transcription of genes involved in the regulation of inflammatory processes and apoptosis in tumor hepatocytes compared to hepatocytes of normal liver tissue. The reconstructed network included 116 differentially expressed genes annotated in Gene Ontology as genes involved in the apoptotic process (apoptotic process GO:0006915), along with their 116 corresponding protein products. It also included 16 additional proteins that, while lacking GO apoptosis annotation, were differentially expressed in HCC and interacting with genes and proteins participating in the apoptosis process. Computational analysis of the gene network identified several key protein products encoded by the genes NFKB1, MMP9, BCL2, A4, CDKN1A, CDK1, ERBB2, G3P, MCL1, FOXO1. These proteins exhibited both a high degree of connectivity with other network objects and differential expression in HCC. Of particular interest are proteins CDKN1A, ERBB2, IL8, and EGR1, which are not annotated in Gene Ontology as apoptosis participants but have a statistically significant number of interactions with genes involved in apoptosis. This indicates their role in regulating programmed cell death. The obtained results can guide the design of new experiments studying the role of apoptosis in carcinogenesis and aid in the search for novel therapeutic targets and approaches for HCC therapy using apoptosis modulation in malignant hepatocytes. Furthermore, the proposed approach to reconstructing and analyzing the apoptosis regulation gene network in hepatocellular carcinoma can be applied to analyze other tumor forms providing a systemic understanding of disturbances in key regulatory processes in oncogenesis and potential therapy targets.