Abstract. The rediscovery of Mendel’s laws in 1900 marked the beginning of the “age of Mendelism” in biology. A significant moment was the shift of researchers’ interests from the physiological mechanisms of the development of inherited traits in ontogenesis to the fixation of specific genes, their structure and localization in chromosomes. The resulting extremely rapid evolution of knowledge in the field of heredity and variability led to the emergence of “molecular biology” in the middle of the 20th century to study the biochemistry of matrix processes. And only after that, science returned to studying the physiological mechanisms of developmental genetics. The article examines the role of Mendel and the laws of heredity revealed by him in the history of biology of the 20th century.
Key words: Gregor Mendel; Carl Correns; Hugo de Vries; Erich von Tschermak-Seysenegg; history of genetics
For citation: Ermolaev A.I. Mendelism as a stage in the development of biology. Pisma v Vavilovskii Zhurnal Genetiki i Selektsii = Lett Vavilov J Genet Breed. 2025;11(4):145-153. doi 10.18699/letvjgb-2025-11-21 (in Russian)
Funding. This work was supported by the S.I. Vavilov Institute for the History of Science and Technology RAS.
Acknowledgements. I am grateful to Professor N.P. Goncharov and the respected reviewers for careful attention to the article and valuable advice.

Abstract. Assessment of ornamental plants seed propagation prospects is one of the important tasks of Botanical Gardens in the search for new crops for landscaping interiors. Representatives of the Malvaceae Juss. family have long established themselves as resistant ornamental and flowering plants. They have been used for the “green” decoration of apartments, offices and conservations for many years. The genus Pavonia Cav. is still little known in the indoor plant market, due to its lack of representation in flower shops. As a part of the study diasporas program formed by introduced species in the greenhouse of the Botanical Garden of Samara University, was conducted a study on the quality of seeds of 3 species of genus Pavonia: P. missionum, P. spinifex, P. hastata. The morphometric parameters of the seeds, the weight of 1000 seeds, their completeness and germination were measured during the study. The internal structure of seeds study, carried out by digital microfocus radiography in the scientific research laboratory of Innovative methods for studying and preserving biological Diversity at Samara University on a mobile X-ray diagnostic unit, revealed the following types of defects: unfulfilled and puny seeds in all 3 species; cracks and gnawing in P. spinifex seeds. No signs of pests infestation were found. The number of fully completed seeds in all three species exceeded 65 % in all the years of research. The first signs of seed germination in laboratory conditions were noted on day 2 in P. spinifex and P. missionum, and on day 5 in P. hastata. The germination rate of seeds exceeded 80 % for P. missionum seeds stored for 3 years, and for P. spinifex seeds stored from 1 to 5 years. The seeds of P. hastata, apparently, had an internal infection with fungi, which led to their rotting, even despite the preliminary pre-sowing treatment. Thus, the seed material of the Botanical Garden greenhouse’s own reproduction, which has been stored for less than 3 years, can be used for further reproduction of these species of genus Pavonia.
Key words: 1,000 seeds weight; microfocus radiography; seed quality; seed size; shelf life; seed viability; seed germination; method of noninvasive assessment of the internal structure of seeds
For citation: Roguleva N.O., Ghukasyan S.A. Evaluation of the seed quality of some genus Pavonia species from the Botanical Garden of Samara University greenhouse collection. Pisma v Vavilovskii Zhurnal Genetiki i Selektsii = Lett Vavilov J Genet Breed. 2025;11(4):154-163. doi 10.18699/letvjgb-2025-11-22 (in Russian)

Abstract. The regulation of eukaryotic gene transcription is controlled by transcription factors (TFs) recognizing specific DNA sequences, TF binding sites (TFBSs) in the regulatory regions of genes. The TFBS search is essential to clarify the mechanisms of gene transcription regulation. The high-throughput sequencing technology ChIP-seq allows to map TFBSs genome-wide that radically expands the abilities for DNA-protein interaction study. The ChIP-seq data analysis includes the following processing steps: read mapping; peak calling implying detection of genomic loci where a TF bound DNA; de novo motif search identifying the enriched nucleotide context patterns for TF-DNA complexes in these loci; and the analysis of obtained TFBS motifs. The last two steps are the most important, thereby we propose the pipeline MultiDeCA (Multi-model De novo discovery of motifs and their Combinatorial Analysis) including the following tools. BSMotif tool clusters TFs by TFBS motif similarity based on TF classifications by DNA-binding domain structure. AntiNoise tool prepares the negative DNA sequences for de novo motif discovery. MultiDeNA tool uniformly applies the motif models PWM, BaMM, InMoDe, and SiteGA. MCOT/MetArea tools detect the motif co-occurrence/mutual exclusive occurrence in motif pairs. BSMotif/AntiNoise/MultiDeNA tools allow simplifying the detection of involved TFs/to increase the TFBS motif search accuracy/reflect the variety of detected TFBS motifs. MCOT/MetArea tools provide additional motif analysis to reveal the potential partner TFs/indirect binding of the target TF. The pipeline was successfully applied for the analysis of the target TF JunD ChIP-seq data.
Key words: transcription factors binding sites; TFBSs; ChIP-seq; motifs; de novo search; bioinformatics pipeline
For citation: Tsukanov A.V., Levitsky V.G. MultiDeCA: pipeline for discovery and analysis of transcription factor binding site motifs based on ChIP-seq data. Pisma v Vavilovskii Zhurnal Genetiki i Selektsii = Lett Vavilov J Genet Breed. 2025;11(4):164-173. doi 10.18699/ letvjgb-2025-11-23 (in Russian)
Funding. This work was supported by State Budgeted Project FWNR-2022-0020.

Abstract. The renin-angiotensin-aldosterone system (RAAS) plays a key role in the hormonal regulation of blood pressure. In this study, we investigated the evolutionary characteristics of the human RAAS association gene network, which we had previously reconstructed using the ANDSystem software package and which contained 145 genes. For each of these genes, we calculated two evolutionary characteristics using our own web service, OrthoWeb: the phylogenetic age index (PAI), an estimate of the gene’s evolutionary age, and the divergence index (DI), an estimate of the gene’s evolutionary mode. The PAI corresponds to the age of the phylogenetic tree node in which the evolutionary branch leading to the gene in question arose. The DI is equal to the arithmetic mean of the ratio of the number of nonsynonymous dN substitutions to the number of synonymous dS substitutions (dN/dS) in the protein-coding region of the gene under study. Based on PAI estimates with a significance level of p < 0.05 in comparison with all human protein-coding genes, a significantly large number of 59 of 145 RAAS genes (41 %) were shown to have evolutionary ages corresponding to the formation of the taxon of multicellular organisms (Metazoa) before the emergence of the circulatory system. Based on DI estimates with a significance level of p < 0.05 in the taxon Hominidae, it was shown that 89 RAAS genes evolved under stabilizing selection, 54 genes under neutral drift, and two genes, EDN1 and PLA2G2A, under driving selection (adaptive evolution). Key words: renin-angiotensin-aldosterone system (RAAS); evolutionary genetics; bioinformatics; phylostratigraphic analysis; endothelin; phospholipase; natural selection; neutral drift; index of evolutionary age of a gene; divergence index
For citation: Suslov V.V., Kuzminykh H.I., Levanova N.M., Ivanov R.A., Kondratyuk E.Yu., Chadaeva I.V., Ponomarenko M.P. Evolutionary characteristics of the associative gene network of the renin-angiotensin-aldosterone system (RAAS). Pisma v Vavilovskii Zhurnal Genetiki i Selektsii = Lett Vavilov J Genet Breed. 2025;11(4):174-180. doi 10.18699/letvjgb-2025-11-24 (in Russian)
Funding. The work was supported by the budget project FWNR-2022-0020.
Acknowledgements. The authors are grafeful to the Bioinformatics Shared Use Centre for the used computational resources.

Abstract. Currently, there is an increase in the spread of functional abnormalities in the development of cognitive functions in schoolchildren 7–12 years old studying in elementary grades, including disorders of attention, motor control and speech recognition. For the timely correction of such violations, it is necessary to develop a comprehensive technology for the early diagnosis of cognitive dysfunctions, adapted to estimation of primary school students. Genetic methods, including analysis of gene networks of behavior regulation, make it possible to establish a hereditary predisposition to the occurrence of cognitive abnormalities. Behavioral tests, such as the Go/noGo task, the stop-signal paradigm, the Stroop task and the grammatical error recognition task, are reliable and wellvalidated tools for assessing the degree of impairment of various cognitive functions at the level of their external manifestations. The combination of behavioral tests with the recording of brain’s bioelectric signals (EEG) allows assessing the neurophysiological causes of cognitive impairment. The comparison of psychophysiological testing results with data obtained from the reconstruction of gene networks of behavior regulation opens up prospects for the effective prediction of the possible clinical consequences of childhood cognitive deviations. The Children Neurocognitive Testing software pipeline we are developing allows accumulating and analyzing behavioral, genetic and neurophysiological markers that reflect the hereditary features and functional state of attention systems, activation and inhibitory executive control, as well as recognition of written speech in schoolchildren. The use of a pipeline enables rapid and non-invasive assessment of the degree of children cognitive development.
Key words: brain cognitive functions; children; genes networks of behavioral regulation; Go/noGo; stop-signal paradigm; Stroop task; software pipeline
For citation: Pershin A.D., Zorina K.A., Savostyanov V.A., Saprygin A.E., Savostyanov A.N. “Children Neurocognitive Testing” software pipeline for searching and analyzing genetic, behavioral and neurophysiological markers of cognitive impairment in schoolchildren. Pisma v Vavilovskii Zhurnal Genetiki i Selektsii = Lett Vavilov J Genet Breed. 2025;11(4):181-187. doi 10.18699/letvjgb-2025-11-25
Funding. The pipeline development was supported by State Budgeted Project FWNR-2022-0020 for the Institute of Cytology and Genetics, Siberian Branch of the RAS. The collection of EEG data in a group of children aged from 6 to 12 years for pipeline testing was supported by State Budgeted Project 122042700001-9 at the Scientific Research Institute of Neurosciences and Medicine.