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Ignatieva EV, Lashin SA, Mustafin ZS, Kolchanov NA. Evolution of human genes encoding cell surface receptors involved in the regulation of appetite: an analysis based on the phylostratigraphic age and divergence indexes. Vavilovskii Zhurnal Genet Selektsii 2023; 27:829-838. [PMID: 38213702 PMCID: PMC10777300 DOI: 10.18699/vjgb-23-96] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 01/13/2024] Open
Abstract
Genes encoding cell surface receptors make up a significant portion of the human genome (more than a thousand genes) and play an important role in gene networks. Cell surface receptors are transmembrane proteins that interact with molecules (ligands) located outside the cell. This interaction activates signal transduction pathways in the cell. A large number of exogenous ligands of various origins, including drugs, are known for cell surface receptors, which accounts for interest in them from biomedical researchers. Appetite (the desire of the animal organism to consume food) is one of the most primitive instincts that contribute to survival. However, when the supply of nutrients is stable, the mechanism of adaptation to adverse factors acquired in the course of evolution turned out to be excessive, and therefore obesity has become one of the most serious public health problems of the twenty-first century. Pathological human conditions characterized by appetite violations include both hyperphagia, which inevitably leads to obesity, and anorexia nervosa induced by psychosocial stimuli, as well as decreased appetite caused by neurodegeneration, inflammation or cancer. Understanding the evolutionary mechanisms of human diseases, especially those related to lifestyle changes that have occurred over the past 100-200 years, is of fundamental and applied importance. It is also very important to identify relationships between the evolutionary characteristics of genes in gene networks and the resistance of these networks to changes caused by mutations. The aim of the current study is to identify the distinctive features of human genes encoding cell surface receptors involved in appetite regulation using the phylostratigraphic age index (PAI) and divergence index (DI). The values of PAI and DI were analyzed for 64 human genes encoding cell surface receptors, the orthologs of which were involved in the regulation of appetite in model animal species. It turned out that the set of genes under consideration contains an increased number of genes with the same phylostratigraphic age (PAI = 5, the stage of vertebrate divergence), and almost all of these genes (28 out of 31) belong to the superfamily of G-protein coupled receptors. Apparently, the synchronized evolution of such a large group of genes (31 genes out of 64) is associated with the development of the brain as a separate organ in the first vertebrates. When studying the distribution of genes from the same set by DI values, a significant enrichment with genes having a low DIs was revealed: eight genes (GPR26, NPY1R, GHSR, ADIPOR1, DRD1, NPY2R, GPR171, NPBWR1) had extremely low DIs (less than 0.05). Such low DI values indicate that most likely these genes are subjected to stabilizing selection. It was also found that the group of genes with low DIs was enriched with genes that had brain-specific patterns of expression. In particular, GPR26, which had the lowest DI, is in the group of brain-specific genes. Because the endogenous ligand for the GPR26 receptor has not yet been identified, this gene seems to be an extremely interesting object for further theoretical and experimental research. We believe that the features of the genes encoding cell surface receptors we have identified using the evolutionary metrics PAI and DI can be a starting point for further evolutionary analysis of the gene network regulating appetite.
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Affiliation(s)
- E V Ignatieva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - S A Lashin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Z S Mustafin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - N A Kolchanov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Ivanisenko VA, Basov NV, Makarova AA, Venzel AS, Rogachev AD, Demenkov PS, Ivanisenko TV, Kleshchev MA, Gaisler EV, Moroz GB, Plesko VV, Sotnikova YS, Patrushev YV, Lomivorotov VV, Kolchanov NA, Pokrovsky AG. Gene networks for use in metabolomic data analysis of blood plasma from patients with postoperative delirium. Vavilovskii Zhurnal Genet Selektsii 2023; 27:768-775. [PMID: 38223851 PMCID: PMC10784323 DOI: 10.18699/vjgb-23-89] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/12/2023] [Accepted: 08/24/2023] [Indexed: 01/16/2024] Open
Abstract
Postoperative delirium (POD) is considered one of the most severe complications, resulting in impaired cognitive function, extended hospitalization, and higher treatment costs. The challenge of early POD diagnosis becomes particularly significant in cardiac surgery cases, as the incidence of this complication exceeds 50 % in certain patient categories. While it is known that neuroinflammation, neurotransmitter imbalances, disruptions in neuroendocrine regulation, and interneuronal connections contribute significantly to the development of POD, the molecular, genetic mechanisms of POD in cardiac surgery patients, along with potential metabolomic diagnostic markers, remain inadequately understood. In this study, blood plasma was collected from a group of patients over 65 years old after cardiac surgery involving artificial circulation. The collected samples were analyzed for sphingomyelin content and quantity using high-performance liquid chromatography coupled with mass spectrometry (HPLC-MS/MS) methods. The analysis revealed four significantly different sphingomyelin contents in patients with POD compared to those who did not develop POD (control group). Employing gene network reconstruction, we perceived a set of 82 regulatory enzymes affiliated with the genetic coordination of the sphingolipid metabolism pathway. Within this set, 47 are assumed to be regulators of gene expression, governing the transcription of enzymes pivotal to the metabolic cascade. Complementing this, an additional assembly of 35 regulators are considered to be regulators of activity, degradation, and translocation dynamics of enzymes integral to the aforementioned pathway. Analysis of the overrepresentation of diseases with which these regulatory proteins are associated showed that the regulators can be categorized into two groups, associated with cardiovascular pathologies (CVP) and neuropsychiatric diseases (NPD), respectively. The regulators associated with CVP are expectedly related to the effects on myocardial tissue during surgery. It is hypothesized that dysfunction of NPD-associated regulators may specifically account for the development of POD after cardiac surgery. Thus, the identified regulatory genes may provide a basis for planning further experiments, in order to study disorders at the level of expression of these genes, as well as impaired function of proteins encoded by them in patients with POD. The identified significant sphingolipids can be considered as potential markers of POD.
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Affiliation(s)
- V A Ivanisenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - N V Basov
- Novosibirsk State University, Novosibirsk, Russia N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A A Makarova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A S Venzel
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - A D Rogachev
- Novosibirsk State University, Novosibirsk, Russia N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - P S Demenkov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - T V Ivanisenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - M A Kleshchev
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E V Gaisler
- Novosibirsk State University, Novosibirsk, Russia N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - G B Moroz
- E. Meshalkin National Medical Research Center of the Ministry of Health of Russian Federation, Novosibirsk, Russia
| | - V V Plesko
- E. Meshalkin National Medical Research Center of the Ministry of Health of Russian Federation, Novosibirsk, Russia
| | - Y S Sotnikova
- Novosibirsk State University, Novosibirsk, Russia N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Boreskov Institute of Catalysis of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Y V Patrushev
- Novosibirsk State University, Novosibirsk, Russia Boreskov Institute of Catalysis of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - V V Lomivorotov
- E. Meshalkin National Medical Research Center of the Ministry of Health of Russian Federation, Novosibirsk, Russia Penn State Health Milton S. Hershey Medical Center, Hershey, PA, USA
| | - N A Kolchanov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
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Klimenko AI, Lashin SA, Kolchanov NA, Afonnikov DA, Matushkin YG. [Molecular Mechanisms to Optimize Gene Translation Elongation Differ Significantly in Bacteria with and without Nonribosomal Peptides]. Mol Biol (Mosk) 2023; 57:155-165. [PMID: 37000645 DOI: 10.31857/s002689842302012x, edn: eggoic] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 08/31/2022] [Indexed: 04/01/2023]
Abstract
Nonribosomal peptides play an important role in the vital activity of bacteria and have an extremely broad field of biological activity. In particular, they act as antibiotics, toxins, surfactants, siderophores, and also perform a number of other specific functions. Biosynthesis of these molecules does not occur on ribosomes but by special enzymes that form gene clusters in bacterial genomes. We hypothesized that the presence of nonribosomal peptide synthesis pathways is a specific feature of bacterial metabolism, which may affect other vital processes of the cell, including translational ones. This work was the first to show the relationship between the translation regulation mechanism of protein-coding genes in bacteria, which is largely determined by the efficiency of translation elongation, and the presence of gene clusters in the genomes for the biosynthesis of nonribosomal peptides. Bioinformatic analysis of the translation elongation efficiency of protein-coding genes was performed in 11679 bacterial genomes, some of which contained gene clusters of nonribosomal peptide biosynthesis and some of which did not. The analysis showed that bacteria whose genomes contained clusters of nonribosomal peptide biosynthetic genes and those without such gene clusters differ significantly in the molecular mechanisms that ensure translation efficiency. Thus, among microorganisms whose genomes contain gene clusters of nonribosomal peptide synthetases, a significantly smaller part of them is characterized by optimized regulation of the number of local inverted repeats, while most of them have genomes optimized by the averaged energy of inverted repeats studs in mRNA and additionally by codon composition. Our results suggest that the presence of nonribosomal peptide biosynthetic pathways in bacteria may influence the structure of the overall bacterial metabolism, which is also expressed in the specific mechanisms of ribosomal protein biosynthesis.
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Affiliation(s)
- A I Klimenko
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - S A Lashin
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - N A Kolchanov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - D A Afonnikov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - Yu G Matushkin
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
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Savinkova LK, Sharypova EB, Kolchanov NA. On the Role of TATA Boxes and TATA-Binding Protein in Arabidopsis thaliana. Plants (Basel) 2023; 12:1000. [PMID: 36903861 PMCID: PMC10005294 DOI: 10.3390/plants12051000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/13/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
For transcription initiation by RNA polymerase II (Pol II), all eukaryotes require assembly of basal transcription machinery on the core promoter, a region located approximately in the locus spanning a transcription start site (-50; +50 bp). Although Pol II is a complex multi-subunit enzyme conserved among all eukaryotes, it cannot initiate transcription without the participation of many other proteins. Transcription initiation on TATA-containing promoters requires the assembly of the preinitiation complex; this process is triggered by an interaction of TATA-binding protein (TBP, a component of the general transcription factor TFIID (transcription factor II D)) with a TATA box. The interaction of TBP with various TATA boxes in plants, in particular Arabidopsis thaliana, has hardly been investigated, except for a few early studies that addressed the role of a TATA box and substitutions in it in plant transcription systems. This is despite the fact that the interaction of TBP with TATA boxes and their variants can be used to regulate transcription. In this review, we examine the roles of some general transcription factors in the assembly of the basal transcription complex, as well as functions of TATA boxes of the model plant A. thaliana. We review examples showing not only the involvement of TATA boxes in the initiation of transcription machinery assembly but also their indirect participation in plant adaptation to environmental conditions in responses to light and other phenomena. Examples of an influence of the expression levels of A. thaliana TBP1 and TBP2 on morphological traits of the plants are also examined. We summarize available functional data on these two early players that trigger the assembly of transcription machinery. This information will deepen the understanding of the mechanisms underlying transcription by Pol II in plants and will help to utilize the functions of the interaction of TBP with TATA boxes in practice.
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Ritter GS, Nikolin VP, Popova NA, Proskurina AS, Kisaretova PE, Taranov OS, Dubatolova TD, E V Dolgova EV, Potter EA, Kirikovich SS, Efremov YR, Bayborodin SI, Romanenko MV, Meschaninova MI, Venyaminova AG, Kolchanov NA, Bogachev SS. [Characteristic of the active substance of the Saccharomyces cerevisiae preparation having radioprotective properties]. Vavilovskii Zhurnal Genet Selektsii 2021; 24:643-652. [PMID: 33659850 PMCID: PMC7716560 DOI: 10.18699/vj20.658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The paper describes some biological features of the radioprotective effect of double-stranded RNA preparation. It was found that yeast RNA preparation has a prolonged radioprotective effect after irradiation by a lethal dose of 9.4 Gy. 100 % of animals survive on the 70th day of observation when irradiated 1 hour or 4 days after 7 mg RNA preparation injection, 60 % animals survive when irradiated on day 8 or 12. Time parameters of repair of double-stranded breaks induced by gamma rays were estimated. It was found that the injection of the RNA preparation at the time of maximum number of double-stranded breaks, 1 hour after irradiation, reduces the efficacy of radioprotective action compared with the injection 1 hour before irradiation and 4 hours after irradiation. A comparison of the radioprotective effect of the standard radioprotector B-190 and the RNA preparation was made in one experiment. It has been established that the total RNA preparation is more efficacious than B-190. Survival on the 40th day after irradiation was 78 % for the group of mice treated with the RNA preparation and 67 % for those treated with B-190. In the course of analytical studies of the total yeast RNA preparation, it was found that the preparation is a mixture of single-stranded and double-stranded RNA. It was shown that only double-stranded RNA has radioprotective properties. Injection of 160 μg double-stranded RNA protects 100 % of the experimental animals from an absolutely lethal dose of gamma radiation, 9.4 Gy. It was established that the radioprotective effect of double-stranded RNA does not depend on sequence, but depends on its double-stranded form and the presence of "open" ends of the molecule. It is supposed that the radioprotective effect of double-stranded RNA is associated with the participation of RNA molecules in the correct repair of radiation-damaged chromatin in blood stem cells. The hematopoietic pluripotent cells that have survived migrate to the periphery, reach the spleen and actively proliferate. The newly formed cell population restores the hematopoietic and immune systems, which determines the survival of lethally irradiated animals.
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Affiliation(s)
- G S Ritter
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - V P Nikolin
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - N A Popova
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - A S Proskurina
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - P E Kisaretova
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - O S Taranov
- State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk region, Russia
| | - T D Dubatolova
- Institute of Molecular and Cellular Biology of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E V E V Dolgova
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E A Potter
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - S S Kirikovich
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Y R Efremov
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - S I Bayborodin
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | | | - M I Meschaninova
- Institute of Chemical Biology and Fundamental Medicine of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A G Venyaminova
- Institute of Chemical Biology and Fundamental Medicine of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - N A Kolchanov
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - S S Bogachev
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Chadaeva IV, Rasskazov DA, Sharypova EB, Drachkova IA, Oshchepkova EA, Savinkova LK, Ponomarenko PM, Ponomarenko MP, Kolchanov NA, Kozlov VA. Сandidate SNP-markers of rheumatoid arthritis that can significantly alter the affinity of the TATA-binding protein for human gene promoters. Vavilovskii Zhurnal Genet Selektsii 2020. [DOI: 10.18699/vj19.586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Rheumatoid polyarthritis (RA) is an autoimmune disease with autoantibodies, including antibodies to citrullant antigens and proinflammatory cytokines, such as TNF-α and IL-6, which are involved in the induction of chronic synovitis, bone erosion, followed by deformity. Immunopathogenesis is based on the mechanisms of the breakdown of immune tolerance to its own antigens, which is characterized by an increase in the activity of T-effector cells, causing RA symptomatology. At the same time, against the background of such increased activity of effector lymphocytes, a decrease in the activity of a number of regulatory cells, including regulatory T-cells (Treg) and myeloid suppressor cells, is recorded. There is reason to say that it is the change in the activity of suppressor cells that is the leading element in RA pathogenesis. That is why only periods of weakening (remission) of RA are spoken of. According to the more powerful female immune system compared to the male one, the risk of developing RA in women is thrice as high, this risk decreases during breastfeeding and grows during pregnancy as well as after menopause in proportion to the level of sex hormones. It is believed that 50 % of the risk of developing RA depends on the conditions and lifestyle, while the remaining 50 % is dependent on genetic predisposition. That is why, RA fits the main idea of postgenomic predictive-preventive personalized medicine that is to give a chance to those who would like to reduce his/her risk of diseases by bringing his/her conditions and lifestyle in line with the data on his/her genome sequenced. This is very important, since doctors consider RA as one of the most frequent causes of disability. Using the Web service SNP_TATA_Z-tester (http://beehive.bionet.nsc.ru/cgi-bin/mgs/tatascan_fox/start.pl), 227 variants of single nucleotide polymorphism (SNP) of the human gene promoters were studied. As a result, 43 candidate SNP markers for RA that can alter the affinity of the TATA-binding protein (TBP) for the promoters of these genes were predicted.
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Affiliation(s)
- I. V. Chadaeva
- Institute of Cytology and Genetics, SB RAS; Novosibirsk State University
| | | | | | | | | | | | | | - M. P. Ponomarenko
- Institute of Cytology and Genetics, SB RAS; Novosibirsk State University
| | - N. A. Kolchanov
- Institute of Cytology and Genetics, SB RAS; Novosibirsk State University
| | - V. A. Kozlov
- Research Institute of Fundamental and Clinical Immunology
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Oshevski SI, Ragino YI, Kashtanova EV, Polonskaya YV, Stakhneva EM, Nikolin VP, Popova NA, Kolchanov NA, Voevoda MI. Changes induced in mouse lipid metabolism by simultaneous impact of antisense oligonucleotide derivatives to <i>apoB</i>, <i>PCSK9</i>, and <i>apoCIII</i> mRNAs. Vavilovskii Zhurnal Genet Selektsii 2020. [DOI: 10.18699/vj19.579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
| | | | | | | | | | | | - N. A. Popova
- Institute of Cytology and Genetics, SB RAS; Novosibirsk State University
| | | | - M. I. Voevoda
- Institute of Cytology and Genetics, SB RAS; Novosibirsk State University; Federal Research Center of Fundamental and Translational Medicine
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Ponomarenko MP, Rasskazov DA, Chadaeva IV, Sharypova EB, Drachkova IA, Ponomarenko PM, Oshchepkova EA, Savinkova LK, Kolchanov NA. Candidate SNP Markers of Atherosclerosis That May Significantly Change the Affinity of the TATA-Binding Protein for the Human Gene Promoters. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419090114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Demenkov PS, Saik OV, Ivanisenko TV, Kolchanov NA, Kochetov AV, Ivanisenko VA. Prioritization of potato genes involved in the formation of agronomically valuable traits using the SOLANUM TUBEROSUM knowledge base. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The development of highly efficient technologies in genomics, transcriptomics, proteomics and metabolomics, as well as new technologies in agriculture has led to an “information explosion” in plant biology and crop production, including potato production. Only a small part of the information reaches formalized databases (for example, Uniprot, NCBI Gene, BioGRID, IntAct, etc.). One of the main sources of reliable biological data is the scientific literature. The well-known PubMed database contains more than 18 thousand abstracts of articles on potato. The effective use of knowledge presented in such a number of non-formalized documents in natural language requires the use of modern intellectual methods of analysis. However, in the literature, there is no evidence of a widespread use of intelligent methods for automatically extracting knowledge from scientific publications on cultures such as potatoes. Earlier we developed the SOLANUM TUBEROSUM knowledge base (http://www-bionet.sysbio.cytogen. ru/and/plant/). Integrated into the knowledge base information about the molecular genetic mechanisms underlying the selection of significant traits helps to accelerate the identification of candidate genes for the breeding characteristics of potatoes and the development of diagnostic markers for breeding. The article searches for new potential participants of the molecular genetic mechanisms of resistance to adverse factors in plants. Prioritizing candidate genes has shown that the PHYA, GF14, CNIH1, RCI1A, ABI5, CPK1, RGS1, NHL3, GRF8, and CYP21-4 genes are the most promising for further testing of their relationships with resistance to adverse factors. As a result of the analysis, it was shown that the molecular genetic relationships responsible for the formation of significant agricultural traits are complex and include many direct and indirect interactions. The construction of associative gene networks and their analysis using the SOLANUM TUBEROSUM knowledge base is the basis for searching for target genes for targeted mutagenesis and marker-oriented selection of potato varieties with valuable agricultural characteristics.
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Affiliation(s)
- P. S. Demenkov
- Institute of Cytology and Genetics, SB RAS; Novosibirsk State University
| | - O. V. Saik
- Institute of Cytology and Genetics, SB RAS
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Turnaev II, Rasskazov DA, Arkova OV, Ponomarenko MP, Ponomarenko PM, Savinkova LK, Kolchanov NA. [Hypothetical SNP Markers That Significantly Affect the Affinity of the TATA-Binding Protein to VEGFA, ERBB2, IGF1R, FLT1, KDR, and MET Oncogene Promoters as Chemotherapy Targets]. Mol Biol (Mosk) 2018; 50:161-73. [PMID: 27028822 DOI: 10.7868/s0026898416010201] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 06/08/2015] [Indexed: 11/23/2022]
Abstract
The following hypothesis has been proposed: IF an SNP can significantly increase the expression of an oncogene by increasing the affinity of the TATA-binding protein (TBP) to its promoter, THEN this SNP can also reduce the apparent bioactivity of inhibitors of this oncogene during antitumor chemotherapy and vice versa. In the context of this hypothesis, the previously proposed method (http://beehive.bionet.nsc. ru/cgi-bin/mgs/tatascan/start.pl) was applied to analyze all SNPs found within the [-70; -20] regions (which harbor all proven TBP-binding sites) of the promoters of VEGFA, EGFR, ERBB2, IGF1R, FLT1, KDR, and MET oncogenes according to the human reference genome, hg19. For 83% of these SNPs, their effect on TBP affinity to the oncogene promoters required for assembly of preinitiation complexes was not significant. rs36208385, rs36208384, rs370995111, rs372731987, rs111811434, rs369547510, rs76407893, rs369728300, and rs72001900 can potentially serve as SNP markers to reduce the apparent bioactivity of oncogene inhibitors, while rs141092704, rs184083669, rs145139616, rs200697953, rs187746433, rs199730913, rs377370642, rs114484350, rs374921120, rs146790957, rs376727645, and rs72001900 can be the markers for enhancing this activity.
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Affiliation(s)
- I I Turnaev
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - D A Rasskazov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - O V Arkova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - M P Ponomarenko
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia.,Novosibirsk State University, Novosibirsk, 630090 Russia.,
| | - P M Ponomarenko
- Children's Hospital Los Angeles, University of Southern California, CA 90027, USA
| | - L K Savinkova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - N A Kolchanov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia.,Novosibirsk State University, Novosibirsk, 630090 Russia
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11
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Lashin SA, Afonnikov DA, Genaev MA, Kazantsev FV, Komyshev EG, Oschepkova EA, Petrov АV, Rasskazov DA, Smirnova AA, Kolchanov NA. AN INTEGRATED INFORMATION SYSTEM ON BIORESOURCE COLLECTIONS OF THE FASO OF RUSSIA. Vavilovskii Zhurnal Genet Selektsii 2018. [DOI: 10.18699/vj18.360] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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12
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Yudin NS, Lukyanov KI, Voevoda MI, Kolchanov NA. Application of reproductive technologies to improve dairy cattle genomic selection. ACTA ACUST UNITED AC 2016. [DOI: 10.1134/s207905971603014x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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13
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Turnaev II, Rasskazov DA, Arkova OV, Ponomarenko MP, Ponomarenko PM, Savinkova LK, Kolchanov NA. Hypothetical SNP markers that significantly affect the affinity of the TATA-binding protein to VEGFA, ERBB2, IGF1R, FLT1, KDR, and MET oncogene promoters as chemotherapy targets. Mol Biol 2016. [DOI: 10.1134/s0026893316010209] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Potter EA, Dolgova EV, Minkevich AM, Nikolin VP, Popova NA, Efremov YR, Baiborodin SI, Rogachev VA, Proskurina AS, Kozel AV, Taranov OS, Omigov VV, Vereschagin EI, Petrov DB, Ostanin AA, Chernykh ER, Kolchanov NA, Bogachev SS. Analysis of different therapeutic schemes combining cyclophosphamide and doublestranded DNA preparation for eradication of Krebs-2 primary ascites in mice. Vavilovskii Zhurnal Genet Selektsii 2016. [DOI: 10.18699/vj15.117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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15
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Potter EA, Dolgova EV, Minkevich AM, Efremov YR, Taranov OS, Omigov VV, Nikolin VP, Popova NA, Proskurina AS, Vereschagin EI, Kozel AV, Rogachev VA, Petrov DB, Ostanin AA, Chernykh ER, Kolchanov NA, Bogachev SS. Therapeutic effects of cyclophosphamide, dsDNA preparations and combinations thereof against Krebs-2 ascites cancer cells and various cancer transplants. Vavilovskii Zhurnal Genet Selektsii 2016. [DOI: 10.18699/vj15.116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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16
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Arkova OV, Drachkova IA, Arshinova TV, Rasskazov DA, Suslov VV, Ponomarenko PM, Ponomarenko MP, Kolchanov NA, Savinkova LK. Prediction and verification of the influence of the rs367781716 SN P on the interaction of ТАТА -binding protein with the promoter of the human АВСА9 gene. Vavilovskii Zhurnal Genet Selektsii 2016. [DOI: 10.18699/vj15.085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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17
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Potter EA, Dolgova EV, Proskurina AS, Efremov YR, Taranov OS, Nikolin VP, Popova NA, Dubatolova TD, Petrova DD, Vereschagin EI, Minkevich AM, Andrushkevich OM, Baiborodin SI, Rogachev VA, Ostanin AA, Chernykh ER, Kolchanov NA, Bogachev SS. Development of the therapeutic regimen based on the synergistic activity of cyclophosphamide and double-stranded DNA preparation which results in complete cure of mice engrafted with Krebs-2 ascites. Vavilovskii Zhurnal Genet Selektsii 2016. [DOI: 10.18699/vj16.162] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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18
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Potter EA, Dolgova EV, Minkevich AM, Nikolin VP, Popova NA, Efremov YR, Baiborodin SI, Rogachev VA, Proskurina AS, Taranov OS, Vereschagin EI, Ostanin AA, Chernykh ER, Kolchanov NA, Bogachev SS. Eradication of Krebs-2 primary ascites via a single-injection regimen of cyclophosphamide and double-stranded DNA. Vavilovskii Zhurnal Genet Selektsii 2016. [DOI: 10.18699/vj16.161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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19
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Oshchepkova EA, Omelyanchuk NA, Savina MS, Pasternak T, Kolchanov NA, Zemlyanskaya EV. Systems biology analysis of the WOX5 gene and its functions in the root stem cell niche. Vavilovskii Zhurnal Genet Selektsii 2016. [DOI: 10.18699/vj16.173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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20
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Saik OV, Konovalova NA, Demenkov PS, Ivanisenko NV, Ivanisenko TV, Ivanoshchuk DE, Konovalova OS, Podkolodnaya OA, Lavrik IN, Kolchanov NA, Ivanisenko VA. Molecular-genetic mechanisms of the interaction between processes of cell response to mechanical stress and neuronal apoptosis in primary open-angle glaucoma. Vavilovskii Zhurnal Genet Selektsii 2016. [DOI: 10.18699/vj16.200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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21
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Yudin NS, Lukyanov KI, Voevoda MI, Kolchanov NA. Application of reproductive technologies to the improvement of dairy cattle genomic selection. Vavilovskii Zhurnal Genet Selektsii 2015. [DOI: 10.18699/vj15.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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22
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Moshkin MP, Petrovski DV, Akulov AE, Romashchenko AV, Gerlinskaya LA, Ganimedov VL, Muchnaya MI, Sadovsky AS, Koptyug IV, Savelov AA, Yu Troitsky S, Moshkin YM, Bukhtiyarov VI, Kolchanov NA, Sagdeev RZ, Fomin VM. Correction to ‘Nasal aerodynamics protects brain and lung from inhaled dust in subterranean diggers,
Ellobius talpinus
’. Proc Biol Sci 2015; 282:20152308. [DOI: 10.1098/rspb.2015.2308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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23
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Goryachkovskaya TN, Kozlov AS, Popik VM, Kolchanov NA, Peltek SE. Dependence of a DNA globule size in a gas phase on the chain length. ACTA ACUST UNITED AC 2015. [DOI: 10.1134/s2079059715040061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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Tregubchak TV, Shekhovtsov SV, Nepomnyashchikh TS, Peltek SE, Kolchanov NA, Shchelkunov SN. TNF-Binding domain of the variola virus CrmB protein synthesized in Escherichia coli cells effectively interacts with human TNF. DOKL BIOCHEM BIOPHYS 2015; 462:176-80. [PMID: 26163214 DOI: 10.1134/s1607672915030102] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Indexed: 11/23/2022]
Affiliation(s)
- T V Tregubchak
- State Research Center of Virology and Biotechnology Vector, Kol'tsovo, Novosibirsk oblast, 633159, Russia
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25
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Moshkin MP, Petrovski DV, Akulov AE, Romashchenko AV, Gerlinskaya LA, Ganimedov VL, Muchnaya MI, Sadovsky AS, Koptyug IV, Savelov AA, Troitsky SY, Moshkn YM, Bukhtiyarov VI, Kolchanov NA, Sagdeev RZ, Fomin VM. Nasal aerodynamics protects brain and lung from inhaled dust in subterranean diggers, Ellobius talpinus. Proc Biol Sci 2015; 281:rspb.2014.0919. [PMID: 25143031 DOI: 10.1098/rspb.2014.0919] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Inhalation of air-dispersed sub-micrometre and nano-sized particles presents a risk factor for animal and human health. Here, we show that nasal aerodynamics plays a pivotal role in the protection of the subterranean mole vole Ellobius talpinus from an increased exposure to nano-aerosols. Quantitative simulation of particle flow has shown that their deposition on the total surface of the nasal cavity is higher in the mole vole than in a terrestrial rodent Mus musculus (mouse), but lower on the olfactory epithelium. In agreement with simulation results, we found a reduced accumulation of manganese in olfactory bulbs of mole voles in comparison with mice after the inhalation of nano-sized MnCl2 aerosols. We ruled out the possibility that this reduction is owing to a lower transportation from epithelium to brain in the mole vole as intranasal instillations of MnCl2 solution and hydrated nanoparticles of manganese oxide MnO · (H2O)x revealed similar uptake rates for both species. Together, we conclude that nasal geometry contributes to the protection of brain and lung from accumulation of air-dispersed particles in mole voles.
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Affiliation(s)
- M P Moshkin
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk 630090, Russia Department of Physiology, Novosibirsk State University, Novosibirsk 630090, Russia Department of Zoology and Animal Ecology, Tomsk State University, Tomsk 634050, Russia
| | - D V Petrovski
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk 630090, Russia
| | - A E Akulov
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk 630090, Russia
| | - A V Romashchenko
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk 630090, Russia Design Technological Institute of Digital Techniques, Siberian Branch of RAS, Novosibirsk 630090, Russia
| | - L A Gerlinskaya
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk 630090, Russia
| | - V L Ganimedov
- Khristianovich Institute of Theoretical and Applied Mechanics, Siberian Branch of RAS, Novosibirsk 630090, Russia
| | - M I Muchnaya
- Khristianovich Institute of Theoretical and Applied Mechanics, Siberian Branch of RAS, Novosibirsk 630090, Russia
| | - A S Sadovsky
- Khristianovich Institute of Theoretical and Applied Mechanics, Siberian Branch of RAS, Novosibirsk 630090, Russia
| | - I V Koptyug
- International Tomographic Center, Siberian Branch of RAS, Novosibirsk 630090, Russia
| | - A A Savelov
- International Tomographic Center, Siberian Branch of RAS, Novosibirsk 630090, Russia
| | - S Yu Troitsky
- Boreskov Institute of Catalysis, Siberian Branch of RAS, Novosibirsk 630090, Russia
| | - Y M Moshkn
- Department of Biochemistry, Erasmus Medical Center, Dr. Molewaterplein 50, Rotterdam 3015GE, The Netherlands
| | - V I Bukhtiyarov
- Boreskov Institute of Catalysis, Siberian Branch of RAS, Novosibirsk 630090, Russia
| | - N A Kolchanov
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk 630090, Russia Department of Physiology, Novosibirsk State University, Novosibirsk 630090, Russia
| | - R Z Sagdeev
- International Tomographic Center, Siberian Branch of RAS, Novosibirsk 630090, Russia
| | - V M Fomin
- Khristianovich Institute of Theoretical and Applied Mechanics, Siberian Branch of RAS, Novosibirsk 630090, Russia
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26
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Ignatieva EV, Podkolodnaya OA, Orlov YL, Vasiliev GV, Kolchanov NA. Regulatory genomics: Combined experimental and computational approaches. RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415040067] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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27
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Ignatieva EV, Podkolodnaya OA, Orlov YL, Vasiliev GV, Kolchanov NA. [Regulatory Genomics: Integrated Experimental and Computer Approaches]. Genetika 2015; 51:409-429. [PMID: 26087618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The review describes integrated experimental and computer approaches to the investigation of the mechanisms of transcriptional regulation of the organization of eukaryotic genes and transcription regulatory regions. These include (a) an analysis of the factors affecting the affinity of TBP (TATA-binding protein) for the TATA box; (b) research on the patterns of chromatin mark distributions and their role in the regulation of gene expression; (c) a study of 3D chromatin organization; (d) an estimation of the effects of polymorphisms on gene expression via high-resolution Chip-seq and DNase-seq techniques. It was demonstrated that integrated experimental and computer approaches are very important for the current understanding of transcription regulatory mechanisms and the structural and functional organization of the regulatory regions controlling transcription.
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Bogomazova AN, Vassina EM, Goryachkovskaya TN, Popik VM, Sokolov AS, Kolchanov NA, Lagarkova MA, Kiselev SL, Peltek SE. No DNA damage response and negligible genome-wide transcriptional changes in human embryonic stem cells exposed to terahertz radiation. Sci Rep 2015; 5:7749. [PMID: 25582954 PMCID: PMC4291560 DOI: 10.1038/srep07749] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 12/08/2014] [Indexed: 02/07/2023] Open
Abstract
Terahertz (THz) radiation was proposed recently for use in various applications, including medical imaging and security scanners. However, there are concerns regarding the possible biological effects of non-ionising electromagnetic radiation in the THz range on cells. Human embryonic stem cells (hESCs) are extremely sensitive to environmental stimuli, and we therefore utilised this cell model to investigate the non-thermal effects of THz irradiation. We studied DNA damage and transcriptome responses in hESCs exposed to narrow-band THz radiation (2.3 THz) under strict temperature control. The transcription of approximately 1% of genes was subtly increased following THz irradiation. Functional annotation enrichment analysis of differentially expressed genes revealed 15 functional classes, which were mostly related to mitochondria. Terahertz irradiation did not induce the formation of γH2AX foci or structural chromosomal aberrations in hESCs. We did not observe any effect on the mitotic index or morphology of the hESCs following THz exposure.
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Affiliation(s)
- A. N. Bogomazova
- Vavilov Institute of General Genetics RAS, Moscow, Russia
- Skoltech Center for Stem Cell Research, Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region, Russia
| | - E. M. Vassina
- Vavilov Institute of General Genetics RAS, Moscow, Russia
- Skoltech Center for Stem Cell Research, Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region, Russia
| | | | - V. M. Popik
- Budker Institute of Nucleic Physics SB RAS, Novosibirsk, Russia
| | | | | | - M. A. Lagarkova
- Vavilov Institute of General Genetics RAS, Moscow, Russia
- Scientific Research Institute of Physical-Chemical Medicine, Moscow, Russia
- Skoltech Center for Stem Cell Research, Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region, Russia
| | - S. L. Kiselev
- Vavilov Institute of General Genetics RAS, Moscow, Russia
- Skoltech Center for Stem Cell Research, Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region, Russia
| | - S. E. Peltek
- Institute of Cytology and Genetics RAS, Novosibirsk, Russia
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Arkova OV, Kuznetsov NA, Fedorova OS, Kolchanov NA, Savinkova LK. Real-Time Interaction between TVR and the TATA Box of the Human Triosephosphate Isomerase Gene Promoter in the Norm and Pathology. Acta Naturae 2014. [DOI: 10.32607/20758251-2014-6-2-36-40] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The TATA-binding protein (ТВР) is a key part of the transcription complex of RNA polymerase II. Alone or as a part of the basal transcription factor TFIID, TBP binds the TATA box located in the core region of the TATA-containing promoters of class II genes. Previously, we studied the effects of single nucleotide polymorphisms (SNPs) on ТВР/ТАТА-box interactions using gel retardation assay. It was demonstrated that most SNPs in the ТАТА boxes of some human gene promoters cause a 2- to 4-fold decrease in ТВР/ТАТА affinity, which is associated with an increased risk of hereditary diseases, such as thalassemias of diverse severity, hemophilia B Leyden, myocardial infarction, thrombophlebitis, lung cancer, etc. In this work, the process of ТВР/ТАТА complex formation has been studied in real time by a stopped-flow technique using recombinant human TBP and duplexes, which were identical to the TATA box of the wild-type and a SNP-containing triosephosphate isomerase gene promoter and were fluorescently labeled by the Cy3/Cy5 FRET pair. It has been demonstrated for the first time that real-time binding of ТВР to the TATA box of the TPI gene promoter is complete within 10 s and is described by a single-stage kinetic model. The complex formation of ТВР with the wild-type TATA box occurs 5.5 times faster and the complex dissociation occurs 31 times slower compared with the SNPcontaining TATA box. Within the first seconds of the interaction, ТВР binds to and simultaneously bends the TATA box. Importantly, the TATA box of the wild-type TPI gene promoter requires lower TBP concentrations compared to the TATA box containing the -24Т G SNP, which is associated with neurological and muscular disorders, cardiomyopathy, and other diseases.
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Moshkin MP, Petrovskiĭ DV, Akulov AE, Romashchenko AV, Gerlinskaia LA, Muchnaia MI, Ganimedov VL, Sadovskiĭ AS, Savelov AA, Koptiug IV, Troitskiĭ SI, Bukhtiiarov VI, Kolchanov NA, Sagdeev RZ, Fomin VM. [Aerosol deposition in nasal passages of burrowing and ground rodents when breathing dust-laden air]. Zh Obshch Biol 2014; 75:214-225. [PMID: 25771679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In subterranean rodents, which dig down the passages with frontal teeth, adaptation to the underground mode of life presumes forming of mechanisms that provide protection against inhaling dust particles of different size when digging. One of such mechanisms can be specific pattern of air flow organization in the nasal cavity. To test this assumption, comparative study of geometry and aerodynamics of nasal passages has been conducted with regard to typical representative of subterranean rodents, the mole vole, and a representative of ground rodents, the house mouse. Numerical modeling of air flows and deposition of micro- and nanoparticle aerosols indicates that sedimentation of model particles over the whole surface of nasal cavity is higher in mole vole than in house mouse. On the contrary, particles deposition on the surface of olfactory epithelium turns out to be substantially less in the burrowing rodent as compared to the ground one. Adaptive significance of the latter observation has been substantiated by experimental study on the uptake ofnanoparticles of hydrated manganese oxide MnO x (H2O)x and Mn ions from nasal cavity into brain. It has been shown with use of magnetic resonance tomography method that there is no difference between studied species with respect to intake of particles or ions by olfactory bulb when they are introduced intranasally. Meanwhile, when inhaling nanoparticle aerosol of MnCl2, deposition of Mn in mouse's olfactory bulbs surpasses markedly that in vole's bulbs. Thereby, the morphology of nasal passages as a factor determining the aerodynamics of upper respiratory tract ensures for burrowing rodents more efficient protection of both lungs and brain against inhaled aerosols than for ground ones.
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Ivanisenko NV, Mishchenko EL, Akberdin IR, Demenkov PS, Likhoshvai VA, Kozlov KN, Todorov DI, Samsonova MG, Samsonov AM, Kolchanov NA, Ivanisenko VA. Replication of the subgenomic hepatitis C virus replicon in the presence of the NS3 protease inhibitors: a stochastic model. Biophysics (Nagoya-shi) 2014. [DOI: 10.1134/s0006350913050059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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Pastushkova LK, Kireev KS, Kononikhin AS, Tiys ES, Popov IA, Dobrokhotov IV, Custaud MA, Ivanisenko VA, Kolchanov NA, Nikolaev EN, Pochuev VI, Larina IM. [Permanent proteins in healthy human's urine in the experiment with 520-day isolation]. Aviakosm Ekolog Med 2014; 48:48-54. [PMID: 25033613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Purpose of the study was to track permanent proteins of urine proteome in the 520-day isolation experiment at the IBMP Ground-Based Test Facility with controlled environmental parameters. Object of the investigation was urine sampled from 6 normal male subjects at the age of 25 to 37 years. Second morning aliquots were gathered during baseline data collection, on days 50, 93, 124, 153, 180, 251, 274, 303, 330, 371, 400 and 427 of isolation, and in 7 days after its completion. Samples were subject to chromatography-mass spectrometry; results were analyzed with the help of bioinformatics resources. The following 7 permanent proteins were observed in urine over the entire length of the investigation: epidermal growth factor, polymer immunoglobulin receptor, plasma serine protease inhibitor, protein AMBP, keratin, type II cytoskeletal 1, collagen alpha-1 (vi) chain, serum albumin.
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Nikolaev SV, Zubairova US, Penenko AV, Mjolsness ED, Shapiro BE, Kolchanov NA. Model of structuring the stem cell niche in shoot apical meristem of Arabidopsis thaliana. Dokl Biol Sci 2013; 452:316-9. [PMID: 24150656 DOI: 10.1134/s0012496613050104] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Indexed: 01/21/2023]
Affiliation(s)
- S V Nikolaev
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
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Ivanisenko NV, Mishchenko EL, Akberdin IR, Demenkov PS, Likhoshvai VA, Kozlov KN, Todorov DI, Samsonova MG, Samsonov AM, Kolchanov NA, Ivanisenko VA. [Replication of the subgenomic hepatitis C virus replicon in the presence of the NS3 protease inhibitors: a stochastic model]. Biofizika 2013; 58:758-774. [PMID: 25481944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The hepatitis C virus (HCV) belongs to Flaviviridae family and causes hazardous liver diseases leading frequently to cirrhosis and hepatocellular carcinoma. HCV is able to rapidly acquire drug resistance and for this reason there is currently no effective anti-HCV therapy in spite of appearance of new potential drugs. Mathematical models are relevant to predict the efficacy of potential drugs against virus or host targets. One of the promising targets for development of new drugs is the viral NS3 protease. Here we developed a stochastic model of the subgenomic HCV replicon replication in Huh-7 cells and in the presence of the NS3 protease inhibitors. Along with consideration of the stochastic nature of the subgenomic HCV replicon replication the model takes into account the existence and generation of main NS3 protease drug resistant mutants, namely BILN-2061 (A156T, D168V, R155Q), VX-950 (A156S, A156T, T54A) and SCH-503034 (A156T, A156S, T54A). The model reproduces well the viral RNA kinetics in the cell from the moment of the subgenomic HCV replicon transfection to steady state, as well as the viral RNA suppression kinetics in the presence of NS3 protease inhibitors BILN-2061, VX-950 and SCH-503034. We showed that the resistant mutants should be taken into account for the correct description of biphasic kinetics of the viral RNA suppression. The mutants selected in the presence of different inhibitor concentrations have maximal replication capacity in the given inhibitor concentration range. Our model can be used to interpret the results of the new anti-HCV drug testing in replicon systems, as well as to predict the efficacy of new potential drugs and optimize the regimen of their use.
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35
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Tkacheva NI, Morozov SV, Grigor’ev IA, Mognonov DM, Kolchanov NA. Modification of cellulose as a promising direction in the design of new materials. Polym Sci Ser B 2013. [DOI: 10.1134/s1560090413070063] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Demenkov PS, Ivanisenko TV, Kolchanov NA, Ivanisenko VA. ANDVisio: a new tool for graphic visualization and analysis of literature mined associative gene networks in the ANDSystem. In Silico Biol 2013; 11:149-61. [PMID: 22935968 DOI: 10.3233/isb-2012-0449] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The ANDVisio tool is designed to reconstruct and analyze associative gene networks in the earlier developed Associative Network Discovery System (ANDSystem) software package. The ANDSystem incorporates utilities for automated extraction of knowledge from Pubmed published scientific texts, analysis of factographic databases, also the ANDCell database containing information on molecular-genetic events retrieved from texts and databases. ANDVisio is a new user's interface to the ANDCell database stored in a remote server. ANDVisio provides graphic visualization, editing, search, also saving of associative gene networks in different formats resulting from user's request. The associative gene networks describe semantic relationships between molecular-genetic objects (proteins, genes, metabolites and others), biological processes, and diseases. ANDVisio is provided with various tools to support filtering by object types, relationships between objects and information sources; graph layout; search of the shortest pathway; cycles in graphs.
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Affiliation(s)
- P S Demenkov
- Computer Proteomics Laboratory, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
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Vtyurina NN, Grohovsky SL, Vasiliev AB, Titov II, Ponomarenko PM, Ponomarenko MP, Peltek SE, Nechipurenko YD, Kolchanov NA. Contextual DNA features significant for the DNA damage by the 193-nm ultraviolet laser beam. DOKL BIOCHEM BIOPHYS 2013; 447:267-72. [DOI: 10.1134/s1607672912060038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2012] [Indexed: 11/23/2022]
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Abstract
Key aspects of gene transcription regulation in multicellular organisms, including the characteristics of their promoters, transcription-factor binding sites, and composition elements are reviewed. The functional role of transcription regulatory proteins (basal factors and regulatory transcription factors), and the mechanisms responsible for regulation of their activity are also discussed. Furthermore, we describe the importance of DNA-encoded nucleosome organization and chromatin modifications in the course of transcription regulation, as well as some mechanisms that regulate the activity of transcription factors associated with genetic networks. The current outlook on regulatory gene expression codes in eukaryotes is presented.
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Affiliation(s)
- T I Merkulova
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, Russia
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Sorokina KN, Yakovlev VA, Piligaev AV, Kukushkin RG, Pel’tek SE, Kolchanov NA, Parmon VN. Potential of microalgae as a source of bioenergy. Catal Ind 2012. [DOI: 10.1134/s2070050412030117] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Podkolodnaya OA, Ignatieva EV, Podkolodnyy NL, Kolchanov NA. Routes of nanoparticle uptake into mammalian organisms, their biocompatibility and cellular effects. ACTA ACUST UNITED AC 2012. [DOI: 10.1134/s2079086412040068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Matushkin YG, Levitsky VG, Orlov YL, Likhoshvai VA, Kolchanov NA. Translation efficiency in yeasts correlates with nucleosome formation in promoters. J Biomol Struct Dyn 2012; 31:96-102. [PMID: 22803765 DOI: 10.1080/07391102.2012.691366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Elongation efficiency index (EEI) was suggested earlier to estimate gene expression efficiency by nucleotide context of coding sequence in unicellular organisms. We have analyzed association between EEI and nucleosome formation potential (NFP) in 5' regulatory regions upstream translation initiation site (TIS) from two yeast species. Theoretical estimations of NFP based on DNA sequence were obtained by Recon method. Experimental estimation of nucleosome occupancy was obtained by high-throughput sequencing data of nucleosomal DNA in Saccharomyces cerevisiae . For the sample of all genes correlation coefficient was calculated between two vectors: vector of NFP values for fixed position relative to TIS and vector of EEI values. Profiles of correlation coefficients of NFP and EEI were counted in (-600; +600) regions relative to TIS for gene sequences extracted from GenBank. We found regions of strong negative dependence between NFP and EEI for all genes as well as for 10% highly expressed genes in Schizosaccharomyces pombe (10% of EEI-highest genes). At the same time, we found positive dependence between NFP and EEI for all genes and for low expressed genes in S. cerevisiae (10% of EEI-lowest genes). The association between NFP and EEI could be explained by evolutionary selection of context characteristics of nucleotide sequences for gene expression optimization.
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Affiliation(s)
- Yu G Matushkin
- Institute of Cytology and Genetics SB RAS, Lavrentiev ave. 10, Novosibirsk, 630090, Russia.
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Pintus SS, Ivanisenko NV, Demenkov PS, Ivanisenko TV, Ramachandran S, Kolchanov NA, Ivanisenko VA. The substitutions G245C and G245D in the Zn(2+)-binding pocket of the p53 protein result in differences of conformational flexibility of the DNA-binding domain. J Biomol Struct Dyn 2012; 31:78-86. [PMID: 22803791 DOI: 10.1080/07391102.2012.691364] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Transcription activation of the proapoptotic target genes is a means by which the p53 protein implements its function of tumor suppression. Zn(2+) is a known regulator of p53 binding to the target genes. We have previously obtained an evidence that amino acid substitutions in the p53 Zn(2+)-binding pocket can presumably exert an influence on Zn(2+) position in the Zn(2+)-p53 complex and thereby affect p53 binding to DNA. With these background considerations, our aim was to estimate the effect of the putative changes in the Zn(2+) position in its binding pocket due to the G245C and G245D substitutions on the conformation of the p53 DNA-binding motif. Statistical analysis of the molecular dynamics (MD) trajectories of the mutant p53-Zn(2+) complexes was used to detect significant deviations in conformation of the mutant p53 forms. MD simulations demonstrated that (1) the two substitutions in the Zn(2+)-binding pocket caused changes in the conformation of the p53 DNA-binding motif, as compared with the wild-type (WT) p53; (2) binding of Zn(2+) to the p53 mutant forms reduced the effect of the substitutions on conformational change; and (3) Zn(2+) binding in the normal position compensated the effect of the mutations on the conformation in comparison to the altered Zn(2+) position.
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Affiliation(s)
- S S Pintus
- Laboratory of Computational Proteomics, Institute of Cytology and Genetics SB RAS, Lavrentyev av. 10, Novosibirsk, 630090, Russia.
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Mironova VV, Omelyanchuk NA, Novoselova ES, Doroshkov AV, Kazantsev FV, Kochetov AV, Kolchanov NA, Mjolsness E, Likhoshvai VA. Combined in silico/in vivo analysis of mechanisms providing for root apical meristem self-organization and maintenance. Ann Bot 2012; 110:349-60. [PMID: 22510326 PMCID: PMC3394645 DOI: 10.1093/aob/mcs069] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Accepted: 02/14/2012] [Indexed: 05/21/2023]
Abstract
BACKGROUND AND AIMS The root apical meristem (RAM) is the plant stem cell niche which provides for the formation and continuous development of the root. Auxin is the main regulator of RAM functioning, and auxin maxima coincide with the sites of RAM initiation and maintenance. Auxin gradients are formed due to local auxin biosynthesis and polar auxin transport. The PIN family of auxin transporters plays a critical role in polar auxin transport, and two mechanisms of auxin maximum formation in the RAM based on PIN-mediated auxin transport have been proposed to date: the reverse fountain and the reflected flow mechanisms. METHODS The two mechanisms are combined here in in silico studies of auxin distribution in intact roots and roots cut into two pieces in the proximal meristem region. In parallel, corresponding experiments were performed in vivo using DR5::GFP Arabidopsis plants. KEY RESULTS The reverse fountain and the reflected flow mechanism naturally cooperate for RAM patterning and maintenance in intact root. Regeneration of the RAM in decapitated roots is provided by the reflected flow mechanism. In the excised root tips local auxin biosynthesis either alone or in cooperation with the reverse fountain enables RAM maintenance. CONCLUSIONS The efficiency of a dual-mechanism model in guiding biological experiments on RAM regeneration and maintenance is demonstrated. The model also allows estimation of the concentrations of auxin and PINs in root cells during development and under various treatments. The dual-mechanism model proposed here can be a powerful tool for the study of several different aspects of auxin function in root.
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Affiliation(s)
- V V Mironova
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia.
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Larina IM, Kolchanov NA, Dobrokhotov IV, Ivanisenko VA, Demenkov PS, Tiĭs ES, Valeeva OA, Pastushkova LK, Nikolaev EN. [Reconstruction of associative protein networks connected with processes of sodium exchange' regulation and sodium deposition in healthy volunteers by urine proteome analysis]. Fiziol Cheloveka 2012; 38:107-115. [PMID: 22830250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The study was conducted during the experiment with 105-day isolation in experimental complex. In the present investigation we collected urine samples from 6 healthy volunteers. The physical activity, diurnal rhythm, temperature parameters and level of oxygen and carbon dioxide were controlled during the experiment. According to the program, food intake (electrolytes, water, calories, fat, carbohydrates, protein, vitamins, etc.) on each stage of experiment was normalized. All samples were analyzed using mass spectrometer of an ionic cyclotron resonance with transformation of Fure LTQ FT MS (Thermo) on the basis of the AMT-tags (accurate mass and time tags) approach. Among more than 20 000 we found out 690 proteotypical proteins and we identified about 600 urine proteins. For physiological interpretation of the proteome data we used computer systems ANDCell and ANDVisio. Clustering of proteins and application of these systems revealed proteins that are most closely associated with the regime of sodium intake, as well as build the network of their interactions.
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Ivanisenko VA, Demenkov PS, Pintus SS, Ivanisenko TV, Podkolodny NL, Ivanisenko LN, Rozanov AS, Bryanskaya AV, Kostrjukova ES, Levizkiy SA, Selezneva OV, Chukin MM, Larin AK, Kondratov IG, Lazarev VN, Peltek SE, Govorun VM, Kolchanov NA. Computer analysis of metagenomic data—Pediction of quantitative value of specific activity of proteins. DOKL BIOCHEM BIOPHYS 2012; 443:76-80. [DOI: 10.1134/s1607672912020056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Indexed: 11/23/2022]
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Lashin SA, Matushkin YG, Suslov VV, Kolchanov NA. Evolutionary trends in the prokaryotic community and prokaryotic community-phage systems. RUSS J GENET+ 2011. [DOI: 10.1134/s1022795411110123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Lashin SA, Matushkin IG, Suslov VV, Kolchanov NA. [Evolutionary trends in the prokaryotic community and prokaryotic community-phage systems]. Genetika 2011; 47:1676-1685. [PMID: 22384696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The Evolutionary Constructor software has been used for computer simulation of the life and evolution of communities of unicellular haploid organisms (prokaryotic cells). Opposite trends of the community evolution (simplification and complication of the genome) have been studied. It has been demonstrated that species with reduced genomes tend to replace genetically and metabolically rich species under highly favorable environmental conditions. Under unfavorable conditions, the opposite tendency is observed. It has also been shown that introduction of phages capable of killing the cells into the system may radically change the current evolutionary trend.
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Affiliation(s)
- S A Lashin
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia.
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Afonnikov DA, Medvedev KE, Gunbin KV, Kolchanov NA. Important role of hydrophobic interactions in high-pressure adaptation of proteins. DOKL BIOCHEM BIOPHYS 2011; 438:113-6. [PMID: 21725885 DOI: 10.1134/s160767291103001x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Indexed: 11/23/2022]
Affiliation(s)
- D A Afonnikov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
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Ivanisenko VA, Demenkov PS, Ivanisenko TV, Kolchanov NA. [Protein Structure Discovery: software package to perform computational proteomics tasks]. Bioorg Khim 2011; 37:22-35. [PMID: 21460878 DOI: 10.1134/s1068162011010080] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Software-information system Protein Structure Discovery was developed. The system can be used for the wide range of tasks in the field of computer proteomics including prediction of function, structure and immunological properties of proteins. A specially created section of the system allows evaluating the quantitative and qualitative effects of mutations on the structural and functional properties of proteins. There are 19 of different programs integrated into the system, including the database of protein functional sites PDBSite, a PDBSiteScan program for the prediction of functional sites in three-dimensional structures of proteins, and WebProAnalyst program for the quantitative analysis of the structure-activity relationship of proteins. Protein Structure Discovery program has a Web interface and is available for users through the Internet (http://www-bionet.sscc.ru/psd/). For example, binding sites of zinc ion and ADP showed high stability of the method to errors PDBSiteScan reconstruction of spatial structures of proteins in the recognition of functional sites in model structures.
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