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Chadaeva I, Kozhemyakina R, Shikhevich S, Bogomolov A, Kondratyuk E, Oshchepkov D, Orlov YL, Markel AL. A Principal Components Analysis and Functional Annotation of Differentially Expressed Genes in Brain Regions of Gray Rats Selected for Tame or Aggressive Behavior. Int J Mol Sci 2024; 25:4613. [PMID: 38731836 PMCID: PMC11083694 DOI: 10.3390/ijms25094613] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 05/13/2024] Open
Abstract
The process of domestication, despite its short duration as it compared with the time scale of the natural evolutionary process, has caused rapid and substantial changes in the phenotype of domestic animal species. Nonetheless, the genetic mechanisms underlying these changes remain poorly understood. The present study deals with an analysis of the transcriptomes from four brain regions of gray rats (Rattus norvegicus), serving as an experimental model object of domestication. We compared gene expression profiles in the hypothalamus, hippocampus, periaqueductal gray matter, and the midbrain tegmental region between tame domesticated and aggressive gray rats and revealed subdivisions of differentially expressed genes by principal components analysis that explain the main part of differentially gene expression variance. Functional analysis (in the DAVID (Database for Annotation, Visualization and Integrated Discovery) Bioinformatics Resources database) of the differentially expressed genes allowed us to identify and describe the key biological processes that can participate in the formation of the different behavioral patterns seen in the two groups of gray rats. Using the STRING- DB (search tool for recurring instances of neighboring genes) web service, we built a gene association network. The genes engaged in broad network interactions have been identified. Our study offers data on the genes whose expression levels change in response to artificial selection for behavior during animal domestication.
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Affiliation(s)
- Irina Chadaeva
- Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
| | | | | | - Anton Bogomolov
- Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Ekaterina Kondratyuk
- Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
- Siberian Federal Scientific Centre of Agro-BioTechnologies, Russian Academy of Sciences, Krasnoobsk 630501, Russia
- Research Institute of Clinical and Experimental Lymphology-Branch of Institute of Cytology and Genetics, Novosibirsk 630117, Russia
| | - Dmitry Oshchepkov
- Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Yuriy L Orlov
- Institute of Biodesign and Complex Systems Modeling, Sechenov First Moscow State Medical University (Sechenov University), Moscow 119991, Russia
- Agrarian and Technological Institute, Peoples' Friendship University of Russia, Moscow 117198, Russia
| | - Arcady L Markel
- Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
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Shikhevich S, Chadaeva I, Khandaev B, Kozhemyakina R, Zolotareva K, Kazachek A, Oshchepkov D, Bogomolov A, Klimova NV, Ivanisenko VA, Demenkov P, Mustafin Z, Markel A, Savinkova L, Kolchanov NA, Kozlov V, Ponomarenko M. Differentially Expressed Genes and Molecular Susceptibility to Human Age-Related Diseases. Int J Mol Sci 2023; 24:ijms24043996. [PMID: 36835409 PMCID: PMC9966505 DOI: 10.3390/ijms24043996] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/02/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Mainstream transcriptome profiling of susceptibility versus resistance to age-related diseases (ARDs) is focused on differentially expressed genes (DEGs) specific to gender, age, and pathogeneses. This approach fits in well with predictive, preventive, personalized, participatory medicine and helps understand how, why, when, and what ARDs one can develop depending on their genetic background. Within this mainstream paradigm, we wanted to find out whether the known ARD-linked DEGs available in PubMed can reveal a molecular marker that will serve the purpose in anyone's any tissue at any time. We sequenced the periaqueductal gray (PAG) transcriptome of tame versus aggressive rats, identified rat-behavior-related DEGs, and compared them with their known homologous animal ARD-linked DEGs. This analysis yielded statistically significant correlations between behavior-related and ARD-susceptibility-related fold changes (log2 values) in the expression of these DEG homologs. We found principal components, PC1 and PC2, corresponding to the half-sum and the half-difference of these log2 values, respectively. With the DEGs linked to ARD susceptibility and ARD resistance in humans used as controls, we verified these principal components. This yielded only one statistically significant common molecular marker for ARDs: an excess of Fcγ receptor IIb suppressing immune cell hyperactivation.
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Affiliation(s)
- Svetlana Shikhevich
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Irina Chadaeva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Bato Khandaev
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Rimma Kozhemyakina
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Karina Zolotareva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Anna Kazachek
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Dmitry Oshchepkov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Anton Bogomolov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Natalya V. Klimova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Vladimir A. Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Pavel Demenkov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Zakhar Mustafin
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Arcady Markel
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Ludmila Savinkova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Nikolay A. Kolchanov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Vladimir Kozlov
- Research Institute of Fundamental and Clinical Immunology (RIFCI) SB RAS, Novosibirsk 630099, Russia
| | - Mikhail Ponomarenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- Correspondence: ; Tel.: +7-(383)-363-4963 (ext. 1311)
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Chadaeva I, Ponomarenko P, Kozhemyakina R, Suslov V, Bogomolov A, Klimova N, Shikhevich S, Savinkova L, Oshchepkov D, Kolchanov NA, Markel A, Ponomarenko M. Domestication Explains Two-Thirds of Differential-Gene-Expression Variance between Domestic and Wild Animals; The Remaining One-Third Reflects Intraspecific and Interspecific Variation. Animals (Basel) 2021; 11:2667. [PMID: 34573632 PMCID: PMC8465180 DOI: 10.3390/ani11092667] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/04/2021] [Accepted: 09/06/2021] [Indexed: 12/19/2022] Open
Abstract
Belyaev's concept of destabilizing selection during domestication was a major achievement in the XX century. Its practical value has been realized in commercial colors of the domesticated fox that never occur in the wild and has been confirmed in a wide variety of pet breeds. Many human disease models involving animals allow to test drugs before human testing. Perhaps this is why investigators doing transcriptomic profiling of domestic versus wild animals have searched for breed-specific patterns. Here we sequenced hypothalamic transcriptomes of tame and aggressive rats, identified their differentially expressed genes (DEGs), and, for the first time, applied principal component analysis to compare them with all the known DEGs of domestic versus wild animals that we could find. Two principal components, PC1 and PC2, respectively explained 67% and 33% of differential-gene-expression variance (hereinafter: log2 value) between domestic and wild animals. PC1 corresponded to multiple orthologous DEGs supported by homologs; these DEGs kept the log2 value sign from species to species and from tissue to tissue (i.e., a common domestication pattern). PC2 represented stand-alone homologous DEG pairs reversing the log2 value sign from one species to another and from tissue to tissue (i.e., representing intraspecific and interspecific variation).
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Mikhail Ponomarenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (P.P.); (R.K.); (V.S.); (A.B.); (N.K.); (S.S.); (L.S.); (D.O.); (N.A.K.); (A.M.)
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Oshchepkov D, Ponomarenko M, Klimova N, Chadaeva I, Bragin A, Sharypova E, Shikhevich S, Kozhemyakina R. A Rat Model of Human Behavior Provides Evidence of Natural Selection Against Underexpression of Aggressiveness-Related Genes in Humans. Front Genet 2019; 10:1267. [PMID: 31921305 PMCID: PMC6923764 DOI: 10.3389/fgene.2019.01267] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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] [Received: 10/15/2018] [Accepted: 11/18/2019] [Indexed: 01/17/2023] Open
Abstract
Aggressiveness is a hereditary behavioral pattern that forms a social hierarchy and affects the individual social rank and accordingly quality and duration of life. Thus, genome-wide studies of human aggressiveness are important. Nonetheless, the aggressiveness-related genome-wide studies have been conducted on animals rather than humans. Recently, in our genome-wide study, we uncovered natural selection against underexpression of human aggressiveness-related genes and proved it using F1 hybrid mice. Simultaneously, this natural selection equally supports two opposing traits in humans (dominance and subordination) as if self-domestication could have happened with its disruptive natural selection. Because there is still not enough scientific evidence that this could happen, here, we verified this natural selection pattern using quantitative PCR and two outbred rat lines (70 generations of artificial selection for aggressiveness or tameness, hereinafter: domestication). We chose seven genes—Cacna2d3, Gad2, Gria2, Mapk1, Nos1, Pomc, and Syn1—over- or underexpression of which corresponds to aggressive or domesticated behavior (in humans or mice) that has the same direction as natural selection. Comparing aggressive male rats with domesticated ones, we found that these genes are overexpressed statistically significantly in the hypothalamus (as a universal behavior regulator), not in the periaqueductal gray, where there was no aggressiveness-related expression of the genes in males. Database STRING showed statistically significant associations of the human genes homologous to these rat genes with long-term depression, circadian entrainment, Alzheimer’s disease, and the central nervous system disorders during chronic IL-6 overexpression. This finding more likely supports positive perspectives of further studies on self-domestication syndromes.
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Affiliation(s)
- Dmitry Oshchepkov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Mikhail Ponomarenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia.,Natural Science Department, Novosibirsk State University, Novosibirsk, Russia
| | - Natalya Klimova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Irina Chadaeva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia.,Natural Science Department, Novosibirsk State University, Novosibirsk, Russia
| | - Anatoly Bragin
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Ekaterina Sharypova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia.,Natural Science Department, Novosibirsk State University, Novosibirsk, Russia
| | - Svetlana Shikhevich
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Rimma Kozhemyakina
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia.,Natural Science Department, Novosibirsk State University, Novosibirsk, Russia
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Wiedenhoeft J, Cagan A, Kozhemyakina R, Gulevich R, Schliep A. Bayesian localization of CNV candidates in WGS data within minutes. Algorithms Mol Biol 2019; 14:20. [PMID: 31572486 PMCID: PMC6757390 DOI: 10.1186/s13015-019-0154-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 08/08/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Full Bayesian inference for detecting copy number variants (CNV) from whole-genome sequencing (WGS) data is still largely infeasible due to computational demands. A recently introduced approach to perform Forward-Backward Gibbs sampling using dynamic Haar wavelet compression has alleviated issues of convergence and, to some extent, speed. Yet, the problem remains challenging in practice. RESULTS In this paper, we propose an improved algorithmic framework for this approach. We provide new space-efficient data structures to query sufficient statistics in logarithmic time, based on a linear-time, in-place transform of the data, which also improves on the compression ratio. We also propose a new approach to efficiently store and update marginal state counts obtained from the Gibbs sampler. CONCLUSIONS Using this approach, we discover several CNV candidates in two rat populations divergently selected for tame and aggressive behavior, consistent with earlier results concerning the domestication syndrome as well as experimental observations. Computationally, we observe a 29.5-fold decrease in memory, an average 5.8-fold speedup, as well as a 191-fold decrease in minor page faults. We also observe that metrics varied greatly in the old implementation, but not the new one. We conjecture that this is due to the better compression scheme. The fully Bayesian segmentation of the entire WGS data set required 3.5 min and 1.24 GB of memory, and can hence be performed on a commodity laptop.
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Tsybko A, Ilchibaeva T, Kozhemyakina R, Eremin D, Naumenko V. Nigrostriatal dopamine system is implicated in the regulation of genetically-defined aggressive behavior in rats. IBRO Rep 2019. [DOI: 10.1016/j.ibror.2019.07.189] [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: 11/28/2022] Open
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Kulikov A, Moskaliuk V, Kozhemyakina R, Bazovkina D, Terenina E, Volcho K, Naumenko V, Kulikova E. Effects of drug TC-2153 on the behavior and striatal-enriched tyrosine protein phosphatase in the brain of rats selectively bred for high and low aggression towards humans. IBRO Rep 2019. [DOI: 10.1016/j.ibror.2019.07.368] [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: 11/25/2022] Open
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Gulevich R, Kozhemyakina R, Shikhevich S, Konoshenko M, Herbeck Y. Aggressive behavior and stress response after oxytocin administration in male Norway rats selected for different attitudes to humans. Physiol Behav 2018; 199:210-218. [PMID: 30472394 DOI: 10.1016/j.physbeh.2018.11.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 08/31/2018] [Revised: 11/20/2018] [Accepted: 11/21/2018] [Indexed: 11/15/2022]
Abstract
Oxytocin (OXT) is known to influence on social behaviors, including intermale aggression and hypothalamic-pituitary-adrenal (HPA) axis activity. However, there are no data on the effects of oxytocin on intermale aggression and HPA axis activity in rats selected for elimination and enhancement of aggressiveness towards humans. The aim of this study is to elucidate the role of oxytocin in expression of aggressive behavior and stress response in Norway rats selected for elimination (tame) and enhancement (aggressive) of an aggressive-defensive reaction to humans. Oxytocin was administered to males via nasal applications once or for 5 days (daily). Resident-intruder test showed that in aggressive males, single oxytocin administration caused an increase in the latent period of aggressive interactions and a decrease in the percentage of direct aggression time (not including the time of lateral threat postures) as compared to the control aggressive rats administered with saline. After a 5-day oxytocin administration, aggressive animals demonstrated shorter time of aggressive interactions compared to the control rats. Resident-intruder test revealed no significant changes in behavior of tame rats after single oxytocin administration, while multiple administration caused an increase in aggressive behavior in tame rats. Oxytocin applications caused an elevation of corticosterone level after restriction in aggressive males, but did not affect expression of Crh, Crh1 and Crhr2 genes in hypothalamus in either tame or aggressive rats. The data obtained indicate significant role of oxytocinergic system in the behavior formed in the process of selection by reaction to humans.
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Affiliation(s)
- Rimma Gulevich
- Federal Research Center, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
| | - Rimma Kozhemyakina
- Federal Research Center, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
| | - Svetlana Shikhevich
- Federal Research Center, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
| | - Maria Konoshenko
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia.
| | - Yury Herbeck
- Federal Research Center, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
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Idova G, Alperina E, Plyusnina I, Gevorgyan M, Zhukova E, Konoshenko M, Kozhemyakina R, Shui-Wu W. Immune reactivity in rats selected for the enhancement or elimination of aggressiveness towards humans. Neurosci Lett 2015; 609:103-8. [PMID: 26475956 DOI: 10.1016/j.neulet.2015.10.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [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: 08/10/2015] [Revised: 09/22/2015] [Accepted: 10/09/2015] [Indexed: 11/15/2022]
Abstract
This study analyzes immune reactivity in two lines of rats selected for the enhancement or elimination of aggressiveness toward humans. Compared to nonaggressive line, aggressive rats showed increased blood ratio of CD4(+) and CD8(+)T lymphocytes, monocyte chemoattractant protein (MCP)-1 level both before and after immunization with sheep red blood cells (SRBC), enhanced IgM-immune response, as well as decreased level of interleukin (IL)-1α before immunization. However, antigen administration produced IL-1α increase in aggressive rats and its decrease in nonaggressive rats compared to non-immunized rats of the same lines. In addition, line-dependent alterations of T lymphocyte distribution in response to immune activation have been found only in the spleen. It is suggested that genetic differences in aggressive behavior may contribute to differences in immune function.
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Affiliation(s)
- Galina Idova
- Federal State Budgetary Scientific Institution "Scientific Research Institute of Physiology and Basic Medicine", Timakova Street, 4, Novosibirsk, Russia; Novosibirsk State University, Pirogova Street, 2, 630090 Novosibirsk, Russia.
| | - Elizaveta Alperina
- Federal State Budgetary Scientific Institution "Scientific Research Institute of Physiology and Basic Medicine", Timakova Street, 4, Novosibirsk, Russia
| | - Irina Plyusnina
- Federal Research Center "Institute of Cytology and Genetics", Siberian Branch of the Russian Academy of Sciences, Lavrentyev Avenue, 10, 630090 Novosibirsk, Russia; Novosibirsk State University, Pirogova Street, 2, 630090 Novosibirsk, Russia
| | - Margarita Gevorgyan
- Federal State Budgetary Scientific Institution "Scientific Research Institute of Physiology and Basic Medicine", Timakova Street, 4, Novosibirsk, Russia
| | - Elena Zhukova
- Federal State Budgetary Scientific Institution "Scientific Research Institute of Physiology and Basic Medicine", Timakova Street, 4, Novosibirsk, Russia
| | - Maria Konoshenko
- Novosibirsk State University, Pirogova Street, 2, 630090 Novosibirsk, Russia
| | - Rimma Kozhemyakina
- Federal Research Center "Institute of Cytology and Genetics", Siberian Branch of the Russian Academy of Sciences, Lavrentyev Avenue, 10, 630090 Novosibirsk, Russia; Novosibirsk State University, Pirogova Street, 2, 630090 Novosibirsk, Russia
| | - Wang Shui-Wu
- College of Medicine, Chang-Gung University, N. 259, Wen-Hwa1st Road, Kwei-Shan, Taoyuan City 333, Taiwan, ROC
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