Vavilovskii Zhurnal Genetiki i Selektsii最新文献

{"title":"Interrelations between the main seed quality characteristics of narrowleaf lupine from the VIR collection.","authors":"T V Shelenga, A V Salikova, V S Popov, G P Egorova, L L Malyshev, M A Vishnyakova","doi":"10.18699/vjgb-25-05","DOIUrl":"https://doi.org/10.18699/vjgb-25-05","url":null,"abstract":"<p><p>The widespread use of narrowleaf lupine (NLL, Lupinus angustifolius L.) as a feed and food crop requires source material for breeding cultivars with high-quality seeds. The priority criterion for attributing NLL cultivars to the feed or food category is the content of alkaloids. At the same time, equally important seed quality indicators are the protein and oil content, as well as moisture content, which determines the possibility of long-term storage of seeds. For the first time in Russian lupine science, an attempt was made to study the relationships between all the listed characteristics of narrowleaf lupine seeds under the conditions of Northwest Russia (Pushkin town). Sixty-two accessions from the VIR collection were studied in 2019, 2020 and 2022. The range of variability of the studied characteristics was 27.8-37.6 % for protein, 3.9-7.3 % for oil, 1.6-2017.4 mg/100 g of dry matter (D.M.) for alkaloids, and 6.4-7.3 % for moisture. A significant negative correlation between the oil and protein content (-0.33) was observed only in 2019. No significant correlations between the protein and alkaloid content were found in the studied sample. Significant negative relationships were identified between the content of oil and alkaloids only in 2019 and 2020 (-0.38 and -0.27, respectively). In 2022, no correlations were identified. Obviously, the identification of regularities in these correlations requires many years of research taking into account weather conditions. The influence of weather on the concentration of alkaloids in seeds has been proven. The average amount of alkaloids for the sample in 2019 was 504.2 ± 77.7 mg/100 g D.M., 263.7 ± 38.6 mg/100 g D.M. in 2020, and 319.8 ± 51.4 mg/100 g D.M. in 2022. It confirmed the data previously obtained by the authors that the content of alkaloids in seeds increases significantly along with the precipitation deficiency. The temperature regime during this research did not affect this indicator. An increased air temperature contributed to the accumulation of oil, and an increase in precipitation contributed to the accumulation of protein. The most stable indicator independent of environmental conditions was the seed moisture. Accessions with the optimal combination of the main biochemical parameters that determine seed quality have been identified for breeding narrowleaf lupine cultivars in the region in question for feed and food purposes, as well as for green manure.</p>","PeriodicalId":44339,"journal":{"name":"Vavilovskii Zhurnal Genetiki i Selektsii","volume":"29 1","pages":"35-43"},"PeriodicalIF":0.9,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11937010/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143721897","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diurnal fluctuations in the content of soluble sugars and the expression of the TAI and LIN6 invertase genes and the STP1 sugar transporter gene in the leaves of the tomato (Solanum lycopersicum L.).","authors":"M A Filyushin, A V Shchennikova, E Z Kochieva","doi":"10.18699/vjgb-25-07","DOIUrl":"https://doi.org/10.18699/vjgb-25-07","url":null,"abstract":"<p><p>The content of hexoses (fructose, glucose) essential for the fruit of the tomato (Solanum lycopersicum L.) is regulated by the joint activity of sucrose hydrolysis enzymes (including invertases), invertase inhibitors, and sugar transporters. In addition to fruit taste, soluble sugars are closely related to the stress resistance of the tomato plant. In this work, we determined the diurnal dynamics of the content of soluble sugars (sucrose, fructose and glucose) and the expression of genes for sucrose hydrolysis enzymes (vacuolar invertase TAI, cell wall invertase LIN6) and the hexose transporter (STP1) in the leaves of the tomato variety Korneevsky. It was shown that both the amount of sugars and the level of transcripts of the TAI, LIN6 and STP1 genes depend on the circadian rhythm and correspond to the biological processes occurring in the plant at different periods of the day. The content of sucrose and hexoses changes in a similar way during the day. At the beginning of the light phase, the concentration of sugars is minimal, at the end it has the highest daily values; at the beginning of the dark phase, it shows a residual increase and then decreases towards the end of the phase. In silico analysis of organ-specific expression of TAI, LIN6 and STP1 in S. lycopersicum cv. Micro-Tom showed the presence of mRNA of all three genes in all tissues. The TAI gene was expressed most strongly in ripe fruits, while the level of LIN6 and STP1 transcripts was extremely low. The level of TAI mRNA in the leaves was ~2 times higher than that of LIN6 and ~27 times higher than that of STP1. Analysis using qRT-PCR of the diurnal dynamics of TAI, LIN6 and STP1 expression in the cv. Korneevsky leaves showed that all three genes were expressed at all points analyzed. Fluctuations in their expression levels occur in a similar manner: mRNA levels reach peak values in the middle of the light and dark phases. The results obtained are important for understanding the functions of invertases and sugar transporters in the tomato plant, and can be used in predicting the stress resistance of plants in tomato breeding.</p>","PeriodicalId":44339,"journal":{"name":"Vavilovskii Zhurnal Genetiki i Selektsii","volume":"29 1","pages":"55-60"},"PeriodicalIF":0.9,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11933899/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143721881","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Generation and characterisation of seven induced pluripotent stem cell lines from two patients with Parkinson's disease carrying the pathological variant c.1087G>T of the LGR4 gene.","authors":"V S Podvysotskaya, E V Grigor'eva, A A Malakhova, J M Minina, Y V Vyatkin, E A Khabarova, J A Rzaev, S P Medvedev, L V Kovalenko, S M Zakian","doi":"10.18699/vjgb-25-03","DOIUrl":"https://doi.org/10.18699/vjgb-25-03","url":null,"abstract":"<p><p>Parkinson's disease is a neurodegenerative disorder affecting dopaminergic neurons of the substantia nigra pars compacta. The known pathological genetic variants may explain the cause of only 5 % of cases of the disease. In our study, we found two patients with a clinical diagnosis of Parkinson's disease with the genetic variant c.1087G>T (p.Gly363Cys) of the LGR4 gene. The LGR4 gene encodes the membrane receptor LGR4 (leucine rich repeat containing G protein-coupled receptor 4) associated with the G protein. We hypothesize that the LGR4 gene may be either a direct cause or a risk factor for this disease, since it is one of the main participants of the WNT/β-catenin signalling pathway. This signalling pathway is necessary for the proliferation of neurons during their differentiation, which may lead to Parkinson's disease. To study the relationship between this genetic variant and Parkinson's disease, an ideal tool is a cellular model based on induced pluripotent stem cells (iPSCs) and their differentiated derivatives, dopaminergic neurons. We reprogrammed the peripheral blood mononuclear cells of the two patients with the c.1087G>T variant of the LGR4 gene with non-integrating episomal vectors expressing OCT4, SOX2, KLF4, LIN28, L-MYC and mp53DD proteins. The obtained seven lines of induced pluripotent stem cells were characterised in detail. The iPSCs lines obtained meet all the requirements of pluripotent cells, namely, they stably proliferate, form colonies with a morphology characteristic of human pluripotent cells, have a normal diploid karyotype, express endogenous alkaline phosphatase and pluripotency markers (OCT4, NANOG, SSEA-4 and SOX2) and are capable to differentiate into derivatives of the three germ layers. The iPSC lines obtained in this work can be used as a tool to generate a relevant model to study the effect of the pathological variant c.1087G>T of the LGR4 gene on dopaminergic neuron differentiation.</p>","PeriodicalId":44339,"journal":{"name":"Vavilovskii Zhurnal Genetiki i Selektsii","volume":"29 1","pages":"15-25"},"PeriodicalIF":0.9,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11933898/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143721894","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Orthoweb: a software package for evolutionary analysis of gene networks.","authors":"R A Ivanov, A M Mukhin, F V Kazantsev, Z S Mustafin, D A Afonnikov, Y G Matushkin, S A Lashin","doi":"10.18699/vjgb-24-95","DOIUrl":"https://doi.org/10.18699/vjgb-24-95","url":null,"abstract":"<p><p>This article introduces Orthoweb (https://orthoweb.sysbio.cytogen.ru/), a software package developed for the calculation of evolutionary indices, including phylostratigraphic indices and divergence indices (Ka/Ks) for individual genes as well as for gene networks. The phylostratigraphic age index (PAI) allows the evolutionary stage of a gene's emergence (and thus indirectly the approximate time of its origin, known as \"evolutionary age\") to be assessed based on the analysis of orthologous genes across closely and distantly related taxa. Additionally, Orthoweb supports the calculation of the transcriptome age index (TAI) and the transcriptome divergence index (TDI). These indices are important for understanding the dynamics of gene expression and its impact on the development and adaptation of organisms. Orthoweb also includes optional analytical features, such as the ability to explore Gene Ontology (GO) terms associated with genes, facilitating functional enrichment analyses that link evolutionary origins of genes to biological processes. Furthermore, it offers tools for SNP enrichment analysis, enabling the users to assess the evolutionary significance of genetic variants within specific genomic regions. A key feature of Orthoweb is its ability to integrate these indices with gene network analysis. The software offers advanced visualization tools, such as gene network mapping and graphical representations of phylostratigraphic index distributions of network elements, ensuring intuitive interpretation of complex evolutionary relationships. To further streamline research workflows, Orthoweb includes a database of pre-calculated indices for numerous taxa, accessible via an application programming interface (API). This feature allows the users to retrieve pre-computed phylostratigraphic and divergence data efficiently, significantly reducing computational time and effort.</p>","PeriodicalId":44339,"journal":{"name":"Vavilovskii Zhurnal Genetiki i Selektsii","volume":"28 8","pages":"874-881"},"PeriodicalIF":0.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11811495/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143411013","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reconstruction and computer analysis of the structural and functional organization of the gene network regulating cholesterol biosynthesis in humans and the evolutionary characteristics of the genes involved in the network.","authors":"A D Mikhailova, S A Lashin, V A Ivanisenko, P S Demenkov, E V Ignatieva","doi":"10.18699/vjgb-24-94","DOIUrl":"https://doi.org/10.18699/vjgb-24-94","url":null,"abstract":"<p><p>Cholesterol is an essential structural component of cell membranes and a precursor of vitamin D, as well as steroid hormones. Humans and other animal species can absorb cholesterol from food. Cholesterol is also synthesized de novo in the cells of many tissues. We have previously reconstructed the gene network regulating intracellular cholesterol levels, which included regulatory circuits involving transcription factors from the SREBP (Sterol Regulatory Element-Binding Proteins) subfamily. The activity of SREBP transcription factors is regulated inversely depending on the intracellular cholesterol level. This mechanism is implemented with the participation of proteins SCAP, INSIG1, INSIG2, MBTPS1/S1P and MBTPS2/S2P. This group of proteins, together with the SREBP factors, is designated as \"cholesterol sensor\". An elevated cholesterol level is a risk factor for the development of cardiovascular diseases and may also be observed in obesity, diabetes and other pathological conditions. Systematization of information about the molecular mechanisms controlling the activity of SREBP factors and cholesterol biosynthesis in the form of a gene network and building new knowledge about the gene network as a single object is extremely important for understanding the molecular mechanisms underlying the predisposition to diseases. With a computer tool, ANDSystem, we have built a gene network regulating cholesterol biosynthesis. The gene network included data on: (1) the complete set of enzymes involved in cholesterol biosynthesis; (2) proteins that function as part of the \"cholesterol sensor\"; (3) proteins that regulate the activity of the \"cholesterol sensor\"; (4) genes encoding proteins of these groups; (5) genes whose transcription is regulated by SREBP factors (SREBP target genes). The gene network was analyzed and feedback loops that control the activity of SREBP factors were identified. These feedback loops involved the PPARG, NR0B2/SHP1, LPIN1, and AR genes and the proteins they encode. Analysis of the phylostratigraphic age of the genes showed that the ancestral forms of most human genes encoding the enzymes of cholesterol biosynthesis and the proteins of the \"cholesterol sensor\" may have arisen at early evolutionary stages (Cellular organisms (the root of the phylostratigraphic tree) and the stages of Eukaryota and Metazoa divergence). However, the mechanism of gene transcription regulation in response to changes in cholesterol levels may only have formed at later evolutionary stages, since the phylostratigraphic age of the genes encoding the transcription factors SREBP1 and SREBP2 corresponds to the stage of Vertebrata divergence.</p>","PeriodicalId":44339,"journal":{"name":"Vavilovskii Zhurnal Genetiki i Selektsii","volume":"28 8","pages":"864-873"},"PeriodicalIF":0.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11811500/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143411024","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Computational identification of promising genetic markers associated with molecular mechanisms of reduced rice resistance to Rhizoctonia solani under excess nitrogen fertilization using gene network reconstruction and analysis methods.","authors":"E A Antropova, A R Volyanskaya, A V Adamovskaya, P S Demenkov, I V Yatsyk, T V Ivanisenko, Y L Orlov, Ch Haoyu, M Chen, V A Ivanisenko","doi":"10.18699/vjgb-24-103","DOIUrl":"https://doi.org/10.18699/vjgb-24-103","url":null,"abstract":"<p><p>Although nitrogen fertilizers increase rice yield, their excess can impair plant resistance to diseases, particularly sheath blight caused by Rhizoctonia solani. This pathogen can destroy up to 50 % of the crop, but the mechanisms underlying reduced resistance under excess nitrogen remain poorly understood. This study aims to identify potential marker genes to enhance rice resistance to R. solani under excess nitrogen conditions. A comprehensive bioinformatics approach was applied, including differential gene expression analysis, gene network reconstruction, biological process overrepresentation analysis, phylostratigraphic analysis, and non-coding RNA co-expression analysis. The Smart crop cognitive system, ANDSystem, the ncPlantDB database, and other bioinformatics resources were used. Analysis of the molecular genetic interaction network revealed three potential mechanisms explaining reduced resistance of rice to R. solani under excess nitrogen: the OsGSK2-mediated pathway, the OsMYB44-OsWRKY6-OsPR1 pathway, and the SOG1-Rad51-PR1/PR2 pathway. Potential markers for breeding were identified: 7 genes controlling rice responses to various stresses and 11 genes modulating the immune system. Special attention was given to key participants in regulatory pathways under excess nitrogen conditions. Non-coding RNA analysis revealed 30 miRNAs targeting genes of the reconstructed gene network. For two miRNAs (Osa-miR396 and Osa-miR7695), about 7,400 unique long non-coding RNAs (lncRNAs) with various co-expression indices were found. The top 50 lncRNAs with the highest co-expression index for each miRNA were highlighted, opening new perspectives for studying regulatory mechanisms of rice resistance to pathogens. The results provide a theoretical basis for experimental work on creating new rice varieties with increased pathogen resistance under excessive nitrogen nutrition. This study opens prospects for developing innovative strategies in rice breeding aimed at optimizing the balance between yield and disease resistance in modern agrotechnical conditions.</p>","PeriodicalId":44339,"journal":{"name":"Vavilovskii Zhurnal Genetiki i Selektsii","volume":"28 8","pages":"960-973"},"PeriodicalIF":0.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11811503/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143410466","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ontologies in modelling and analysing of big genetic data.","authors":"N L Podkolodnyy, O A Podkolodnaya, V A Ivanisenko, M A Marchenko","doi":"10.18699/vjgb-24-101","DOIUrl":"https://doi.org/10.18699/vjgb-24-101","url":null,"abstract":"<p><p>To systematize and effectively use the huge volume of experimental data accumulated in the field of bioinformatics and biomedicine, new approaches based on ontologies are needed, including automated methods for semantic integration of heterogeneous experimental data, methods for creating large knowledge bases and self-interpreting methods for analyzing large heterogeneous data based on deep learning. The article briefly presents the features of the subject area (bioinformatics, systems biology, biomedicine), formal definitions of the concept of ontology and knowledge graphs, as well as examples of using ontologies for semantic integration of heterogeneous data and creating large knowledge bases, as well as interpreting the results of deep learning on big data. As an example of a successful project, the Gene Ontology knowledge base is described, which not only includes terminological knowledge and gene ontology annotations (GOA), but also causal influence models (GO-CAM). This makes it useful not only for genomic biology, but also for systems biology, as well as for interpreting large-scale experimental data. An approach to building large ontologies using design patterns is discussed, using the ontology of biological attributes (OBA) as an example. Here, most of the classification is automatically computed based on previously created reference ontologies using automated inference, except for a small number of high-level concepts. One of the main problems of deep learning is the lack of interpretability, since neural networks often function as \"black boxes\" unable to explain their decisions. This paper describes approaches to creating methods for interpreting deep learning models and presents two examples of self-explanatory ontology-based deep learning models: (1) Deep GONet, which integrates Gene Ontology into a hierarchical neural network architecture, where each neuron represents a biological function. Experiments on cancer diagnostic datasets show that Deep GONet is easily interpretable and has high performance in distinguishing cancerous and non-cancerous samples. (2) ONN4MST, which uses biome ontologies to trace microbial sources of samples whose niches were previously poorly studied or unknown, detecting microbial contaminants. ONN4MST can distinguish samples from ontologically similar biomes, thus offering a quantitative way to characterize the evolution of the human gut microbial community. Both examples demonstrate high performance and interpretability, making them valuable tools for analyzing and interpreting big data in biology.</p>","PeriodicalId":44339,"journal":{"name":"Vavilovskii Zhurnal Genetiki i Selektsii","volume":"28 8","pages":"940-949"},"PeriodicalIF":0.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11813802/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143410937","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparison of brain activity metrics in Chinese and Russian students while perceiving information referencing self or others.","authors":"Q Si, J Tian, V A Savostyanov, D A Lebedkin, A V Bocharov, A N Savostyanov","doi":"10.18699/vjgb-24-105","DOIUrl":"https://doi.org/10.18699/vjgb-24-105","url":null,"abstract":"<p><p>Neurocomputing technology is a field of interdisciplinary research and development widely applied in modern digital medicine. One of the problems of neuroimaging technology is the creation of methods for studying human brain activity in socially oriented conditions by using modern information approaches. The aim of this study is to develop a methodology for collecting and processing psychophysiological data, which makes it possible to estimate the functional states of the human brain associated with the attribution of external information to oneself or other people. Self-reference is a person's subjective assessment of information coming from the external environment as related to himself/herself. Assigning information to other people or inanimate objects is evaluating information as a message about someone else or about things. In modern neurophysiology, two approaches to the study of self-referential processing have been developed: (1) recording brain activity at rest, then questioning the participant for self-reported thoughts; (2) recording brain activity induced by self-assigned stimuli. In the presented paper, a technology was tested that combines registration and analysis of EEG with viewing facial video recordings. The novelty of our approach is the use of video recordings obtained in the first stage of the survey to induce resting states associated with recognition of information about different subjects in later stages of the survey. We have developed a software and hardware module, i. e. a set of related programs and procedures for their application consisting of blocks that allow for a full cycle of registration and processing of psychological and neurophysiological data. Using this module, brain electrical activity (EEG) indicators reflecting individual characteristics of recognition of information related to oneself and other people were compared between groups of 30 Chinese (14 men and 16 women, average age 23.2 ± 0.4 years) and 32 Russian (15 men, 17 women, average age 22.1 ± 0.4 years) participants. We tested the hypothesis that differences in brain activity in functional rest intervals between Chinese and Russian participants depend on their psychological differences in collectivism scores. It was revealed that brain functional activity depends on the subject relevance of the facial video that the participants viewed between resting-state intervals. Interethnic differences were observed in the activity of the anterior and parietal hubs of the default-mode network and depended on the subject attribution of information. In Chinese, but not Russian, participants significant positive correlations were revealed between the level of collectivism and spectral density in the anterior hub of the default-mode network in all experimental conditions for a wide range of frequencies. The developed software and hardware module is included in an integrated digital platform for conducting research in the field of systems biology and digita","PeriodicalId":44339,"journal":{"name":"Vavilovskii Zhurnal Genetiki i Selektsii","volume":"28 8","pages":"982-992"},"PeriodicalIF":0.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11811493/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143411209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MetArea: a software package for analysis of the mutually exclusive occurrence in pairs of motifs of transcription factor binding sites based on ChIP-seq data.","authors":"V G Levitsky, A V Tsukanov, T I Merkulova","doi":"10.18699/vjgb-24-90","DOIUrl":"https://doi.org/10.18699/vjgb-24-90","url":null,"abstract":"<p><p>ChIP-seq technology, which is based on chromatin immunoprecipitation (ChIP), allows mapping a set of genomic loci (peaks) containing binding sites (BS) for the investigated (target) transcription factor (TF). A TF may recognize several structurally different BS motifs. The multiprotein complex mapped in a ChIP-seq experiment includes target and other \"partner\" TFs linked by protein-protein interactions. Not all these TFs bind to DNA directly. Therefore, both target and partner TFs recognize enriched BS motifs in peaks. A de novo search approach is used to search for enriched TF BS motifs in ChIP-seq data. For a pair of enriched BS motifs of TFs, the co-occurrence or mutually exclusive occurrence can be detected from a set of peaks: the co-occurrence reflects a more frequent occurrence of two motifs in the same peaks, while the mutually exclusive means their more frequent detection in different peaks. We propose the MetArea software package to identify pairs of TF BS motifs with the mutually exclusive occurrence in ChIP-seq data. MetArea was designed to predict the structural diversity of BS motifs of the same TFs, and the functional relation of BS motifs of different TFs. The functional relation of the motifs of the two distinct TFs presumes that they are interchangeable as part of a multiprotein complex that uses the BS of these TFs to bind directly to DNA in different peaks. MetArea calculates the estimates of recognition performance pAUPRC (partial area under the Precision-Recall curve) for each of the two input single motifs, identifies the \"joint\" motif, and computes the performance for it too. The goal of the analysis is to find pairs of single motifs A and B for which the accuracy of the joint A&B motif is higher than those of both single motifs.</p>","PeriodicalId":44339,"journal":{"name":"Vavilovskii Zhurnal Genetiki i Selektsii","volume":"28 8","pages":"822-833"},"PeriodicalIF":0.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11813801/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143410932","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Search for and functional annotation of multi-domain PLA2 family proteins in flatworms.","authors":"M E Bocharnikova, I I Turnaev, D A Afonnikov","doi":"10.18699/vjgb-24-93","DOIUrl":"https://doi.org/10.18699/vjgb-24-93","url":null,"abstract":"<p><p>The phospholipase A2 (PLA2) is a superfamily of hydrolases that catalyze the hydrolysis of phospholipids and play a key role in many molecular processes in the cells and the organism as a whole. This family consists of 16 groups divided into six main types. PLA2 were first isolated from venom toxins and porcine pancreatic juice. The study of these enzymes is currently of great interest, since it has been shown that a number of PLA2 are involved in the processes of carcinogenesis. PLA2 enzymes were characterized in detail in model organisms and humans. However, their presence and functional role in non-model organisms is poorly understood. Such poorly studied taxa include flatworms, a number of species of which are human parasites. Several PLA2 genes have previously been characterized in parasitic flatworms and their possible role in parasite-host interaction has been shown. However, no systematic identification of the PLA2 genes in this taxon has been carried out. The paper provides a search for and a comparative analysis of PLA2 sequences encoded in the genomes of flatworms. 44 species represented by two free-living and 42 parasitic organisms were studied. The analysis was based on identification of orthologous groups of protein-coding genes, taking into account the domain structure of proteins. In flatworms, 12 of the 13 known types of animal A2 phospholipases were found, represented by 11 orthologous groups. Some phospholipases of several types fell into one orthologous group, some types split into several orthogroups in accordance with their domain structure. It has been shown that phospholipases A2 of the calcium-independent type, platelet-activating phospholipases from group G8 and lysosomal phospholipases from group G15 are represented in all large taxa of flatworms and the vast majority of the species studied by us. In free-living flatworms PLA2 genes have multiple copies. In parasitic flatworms, on the contrary, loss of genes occur specifically in individual taxa specifically for groups or subfamilies of PLAs. An orthologous group of secreted phospholipases has been identified, which is represented only in Digenea and this family has undergone duplications in the genomes of opisthorchids. Interestingly, a number of experimental studies have previously shown the effect of Clonorchis sinensis proteins of this orthogroup on the cancer transformation of host cells. Our results made it possible for the first time to systematically identify PLA2 sequences in flatworms, and demonstrated that their evolution is subject to gene loss processes characteristic of parasite genomes in general. In addition, our analysis allowed us to identify taxon-specific processes of duplication and loss of PLA2 genes in parasitic organisms, which may be associated with the processes of their interaction with the host organism.</p>","PeriodicalId":44339,"journal":{"name":"Vavilovskii Zhurnal Genetiki i Selektsii","volume":"28 8","pages":"854-863"},"PeriodicalIF":0.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11811501/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143411093","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}