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Shekhovtsov SV, Vorontsova YL, Slepneva IA, Smirnov DN, Khrameeva EE, Shatunov A, Poluboyarova TV, Bulakhova NA, Meshcheryakova EN, Berman DI, Glupov VV. The Impact of Long-Term Hypoxia on the Antioxidant Defense System in the Siberian Frog Rana amurensis. Biochemistry (Mosc) 2024; 89:441-450. [PMID: 38648764 DOI: 10.1134/s0006297924030052] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/16/2023] [Accepted: 12/29/2023] [Indexed: 04/25/2024]
Abstract
The Siberian frog Rana amurensis has a uniquely high tolerance to hypoxia among amphibians, as it is able to withstand several months underwater with almost no oxygen (0.2 mg/liter) vs. several days for other studied species. Since it was hypothesized that hypoxia actives the antioxidant defense system in hypoxia-tolerant animals, one would expect similar response in R. amurensis. Here, we studied the effect of hypoxia in the Siberian frog based on the transcriptomic data, activities of antioxidant enzyme, and content of low-molecular-weight antioxidants. Exposure to hypoxia upregulated expression of three relevant transcripts (catalase in the brain and two aldo-keto reductases in the liver). The activities of peroxidase in the blood and catalase in the liver were significantly increased, while the activity of glutathione S-transferase in the liver was reduced. The content of low-molecular-weight antioxidants (thiols and ascorbate) in the heart and liver was unaffected. In general, only a few components of the antioxidant defense system were affected by hypoxia, while most remained unchanged. Comparison to other hypoxia-tolerant species suggests species-specific adaptations to hypoxia-related ROS stress.
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Affiliation(s)
- Sergei V Shekhovtsov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
- Institute of Biological Problems of the North, Far East Branch of the Russian Academy of Sciences, Magadan, 630058, Russia
| | - Yana L Vorontsova
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630091, Russia
| | - Irina A Slepneva
- Voevodsky Institute of Chemical Kinetics and Combustion, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Dmitry N Smirnov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
- Department of Life Sciences, Ben-Gurion University of the Negev, 8410501 Beer Sheva, Israel
| | - Ekaterina E Khrameeva
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
| | - Alexey Shatunov
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0QQ, United Kingdom
| | - Tatiana V Poluboyarova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Nina A Bulakhova
- Institute of Biological Problems of the North, Far East Branch of the Russian Academy of Sciences, Magadan, 630058, Russia
| | - Ekaterina N Meshcheryakova
- Institute of Biological Problems of the North, Far East Branch of the Russian Academy of Sciences, Magadan, 630058, Russia
| | - Daniil I Berman
- Institute of Biological Problems of the North, Far East Branch of the Russian Academy of Sciences, Magadan, 630058, Russia
| | - Viktor V Glupov
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630091, Russia
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Shekhovtsov SV, Bulakhova NA, Tsentalovich YP, Zelentsova EA, Osik NA, Meshcheryakova EN, Poluboyarova TV, Berman DI. Metabolomic Profiling Reveals Differences in Hypoxia Response between Far Eastern and Siberian Frogs. Animals (Basel) 2023; 13:3349. [PMID: 37958105 PMCID: PMC10647746 DOI: 10.3390/ani13213349] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/08/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023] Open
Abstract
Anoxia is a significant challenge for most animals, as it can lead to tissue damage and death. Among amphibians, the Siberian frog Rana amurensis is the only known species capable of surviving near-zero levels of oxygen in water for a prolonged period. In this study, we aimed to compare metabolomic profiles of the liver, brain, and heart of the Siberian frog exposed to long-term oxygen deprivation (approximately 0.2 mg/L water) with those of the susceptible Far Eastern frog (Rana dybowskii) subjected to short-term hypoxia to the limits of its tolerance. One of the most pronounced features was that the organs of the Far Eastern frog contained more lactate than those of the Siberian frog despite a much shorter exposure time. The amounts of succinate were similar between the two species. Interestingly, glycerol and 2,3-butanediol were found to be significantly accumulated under hypoxia in the Siberian frog, but not in the Far Eastern frog. The role and biosynthesis of these substances are still unclear, but they are most likely formed in certain side pathways of glycolysis. Based on the obtained data, we suggest a pathway for metabolic changes in the Siberian frog under anoxia.
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Affiliation(s)
- Sergei V. Shekhovtsov
- Institute of Cytology and Genetics SB RAS, Lavrentieva av. 10, 630090 Novosibirsk, Russia;
- Institute of the Biological Problems of the North FEB RAS, Portovaya 18, 685000 Magadan, Russia; (N.A.B.); (E.N.M.); (D.I.B.)
| | - Nina A. Bulakhova
- Institute of the Biological Problems of the North FEB RAS, Portovaya 18, 685000 Magadan, Russia; (N.A.B.); (E.N.M.); (D.I.B.)
| | - Yuri P. Tsentalovich
- International Tomography Center SB RAS, Institutskaya 3a, 630090 Novosibirsk, Russia; (Y.P.T.); (E.A.Z.); (N.A.O.)
| | - Ekaterina A. Zelentsova
- International Tomography Center SB RAS, Institutskaya 3a, 630090 Novosibirsk, Russia; (Y.P.T.); (E.A.Z.); (N.A.O.)
| | - Nataliya A. Osik
- International Tomography Center SB RAS, Institutskaya 3a, 630090 Novosibirsk, Russia; (Y.P.T.); (E.A.Z.); (N.A.O.)
| | - Ekaterina N. Meshcheryakova
- Institute of the Biological Problems of the North FEB RAS, Portovaya 18, 685000 Magadan, Russia; (N.A.B.); (E.N.M.); (D.I.B.)
| | | | - Daniil I. Berman
- Institute of the Biological Problems of the North FEB RAS, Portovaya 18, 685000 Magadan, Russia; (N.A.B.); (E.N.M.); (D.I.B.)
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Shekhovtsov SV, Zelentsova EA, Bulakhova NA, Meshcheryakova EN, Shishikina KI, Tsentalovich YP, Berman DI. Biochemical response of two earthworm taxa exposed to freezing. J Comp Physiol B 2023:10.1007/s00360-023-01500-w. [PMID: 37266592 DOI: 10.1007/s00360-023-01500-w] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 05/12/2023] [Accepted: 05/23/2023] [Indexed: 06/03/2023]
Abstract
Several earthworm species are known to be able to withstand freezing. At the biochemical level, this ability is based on cryoprotectant accumulation as well as several other mechanisms. In this study, we used 1H NMR to investigate metabolomic changes in two freeze-tolerant earthworm taxa, Dendrobaena octaedra and one of the genetic lineages of Eisenia sp. aff. nordenskioldi f. pallida. A total of 45 metabolites were quantified. High concentrations of glucose were present in frozen tissues of both taxa. No other putative cryoprotectants were found. We detected high levels of glycolysis end products and succinate in frozen animals, indicating the activation of glycolysis. Concentrations of many other substances also significantly increased. On the whole, metabolic change in response to freezing was much more pronounced in the specimens of Eisenia sp. aff. nordenskioldi f. pallida, including signs of nucleotide degradation.
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Affiliation(s)
- Sergei V Shekhovtsov
- Institute of the Biological Problems of the North FEB RAS, Magadan, 685000, Russia.
- Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia.
| | - Ekaterina A Zelentsova
- International Tomography Center SB RAS, Novosibirsk, 630090, Russia
- Department of Chemical and Biological Physics, Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Nina A Bulakhova
- Institute of the Biological Problems of the North FEB RAS, Magadan, 685000, Russia
| | | | - Ksenia I Shishikina
- Institute of the Biological Problems of the North FEB RAS, Magadan, 685000, Russia
| | | | - Daniil I Berman
- Institute of the Biological Problems of the North FEB RAS, Magadan, 685000, Russia
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Shekhovtsov SV, Vasiliev GV, Latif R, Poluboyarova TV, Peltek SE, Rapoport IB. The mitochondrial genome of Dendrobaena tellermanica Perel, 1966 (Annelida: Lumbricidae) and its phylogenetic position. Vavilovskii Zhurnal Genet Selektsii 2023; 27:146-152. [PMID: 37063518 PMCID: PMC10090101 DOI: 10.18699/vjgb-23-20] [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: 07/29/2022] [Revised: 09/30/2022] [Accepted: 09/30/2022] [Indexed: 04/18/2023] Open
Abstract
Earthworms are an important ecological group that has a significant impact on soil fauna as well as plant communities. Despite their importance, genetic diversity and phylogeny of earthworms are still insufficiently studied. Most studies on earthworm genetic diversity are currently based on a few mitochondrial and nuclear genes. Mitochondrial genomes are becoming a promising target for phylogeny reconstruction in earthworms. However, most studies on earthworm mitochondrial genomes were made on West European and East Asian species, with much less sampling from other regions. In this study, we performed sequencing, assembly, and analysis of the mitochondrial genome of Dendrobaena tellermanica Perel, 1966 from the Northern Caucasus. This species was earlier included into D. schmidti (Michaelsen, 1907), a polytypic species with many subspecies. The genome was assembled as a single contig 15,298 bp long which contained a typical gene set: 13 protein-coding genes (three subunits of cytochrome c oxidase, seven subunits of NADH dehydrogenase, two subunits of ATP synthetase, and cytochrome b), 12S and 16S ribosomal RNA genes, and 22 tRNA genes. All genes were located on one DNA strand. The assembled part of the control region, located between the tRNA-Arg and tRNA-His genes, was 727 bp long. The control region contained multiple hairpins, as well as tandem repeats of the AACGCTT monomer. Phylogenetic analysis based on the complete mitochondrial genomes indicated that the genus Dendrobaena occupied the basal position within Lumbricidae. D. tellermanica was a rather distant relative of the cosmopolitan D. octaedra, suggesting high genetic diversity in this genus. D. schmidti turned out to be paraphyletic with respect to D. tellermanica. Since D. schmidti is known to contain very high genetic diversity, these results may indicate that it may be split into several species.
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Affiliation(s)
- S V Shekhovtsov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Institute of Biological Problems of the North of the Far Eastern Branch of the Russian Academy of Sciences, Magadan, Russia
| | - G V Vasiliev
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - R Latif
- Semnan University, Semnan, Iran
| | - T V Poluboyarova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - S E Peltek
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - I B Rapoport
- Tembotov Institute of Ecology of Mountain Territories of Russian Academy of Sciences, Nalchik, Russia
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Shekhovtsov SV, Bulakhova NA, Tsentalovich YP, Zelentsova EA, Meshcheryakova EN, Poluboyarova TV, Berman DI. Metabolomic Analysis Reveals That the Moor Frog Rana arvalis Uses Both Glucose and Glycerol as Cryoprotectants. Animals (Basel) 2022; 12:ani12101286. [PMID: 35625132 PMCID: PMC9137551 DOI: 10.3390/ani12101286] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 11/27/2022] Open
Abstract
Simple Summary The moor frog Rana arvalis can tolerate freezing to low temperatures, up to −16 °C. We performed metabolomic analysis of the liver and hindlimb muscles of frozen and control R. arvalis. We found that the moor frog synthesizes glucose and glycerol in similar concentrations as low molecular weight cryoprotectants. This is the first such case reported for the genus Rana, which was believed to use glucose only. We found that freezing upregulates glycolysis, with the accumulation of several end products: lactate, alanine, ethanol, and, possibly, 2,3-butanediol. To our knowledge, this is also the first report of ethanol as an end product of glycolysis in terrestrial vertebrates. We observed highly increased concentrations of nucleotide degradation products, implying high level of stress. We found almost no signs of adaptations to reoxygenation stress, with overall low levels of antioxidants. We also performed metabolomics analysis of subcutaneous ice that was found to contain glucose, glycerol, and several other substances. Abstract The moor frog Rana arvalis is one of a few amphibians that can tolerate freezing to low temperatures, up to −16 °C. In this study, we performed metabolomic analysis of the liver and hindlimb muscles of frozen and control R. arvalis. We found that the moor frog synthesizes glucose and glycerol in similar concentrations as low molecular weight cryoprotectants. This is the first such case reported for the genus Rana, which was believed to use glucose only. We found that freezing upregulates glycolysis, with the accumulation of several end products: lactate, alanine, ethanol, and, possibly, 2,3-butanediol. To our knowledge, this is also the first report of ethanol as an end product of glycolysis in terrestrial vertebrates. We observed highly increased concentrations of nucleotide degradation products, implying high level of stress. The Krebs cycle arrest resulted in high concentrations of succinate, which is common for animals. However, we found almost no signs of adaptations to reoxygenation stress, with overall low levels of antioxidants. We also performed metabolomics analysis of subcutaneous ice that was found to contain glucose, glycerol, and several other substances.
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Affiliation(s)
- Sergei V. Shekhovtsov
- Institute of the Biological Problems of the North FEB RAS, 685000 Magadan, Russia; (N.A.B.); (E.N.M.); (D.I.B.)
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia;
- Correspondence:
| | - Nina A. Bulakhova
- Institute of the Biological Problems of the North FEB RAS, 685000 Magadan, Russia; (N.A.B.); (E.N.M.); (D.I.B.)
| | - Yuri P. Tsentalovich
- International Tomography Center SB RAS, 630090 Novosibirsk, Russia; (Y.P.T.); (E.A.Z.)
| | - Ekaterina A. Zelentsova
- International Tomography Center SB RAS, 630090 Novosibirsk, Russia; (Y.P.T.); (E.A.Z.)
- Department of Chemical and Biological Physics, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Ekaterina N. Meshcheryakova
- Institute of the Biological Problems of the North FEB RAS, 685000 Magadan, Russia; (N.A.B.); (E.N.M.); (D.I.B.)
| | | | - Daniil I. Berman
- Institute of the Biological Problems of the North FEB RAS, 685000 Magadan, Russia; (N.A.B.); (E.N.M.); (D.I.B.)
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Rozanov AS, Shekhovtsov SV, Bogacheva NV, Pershina EG, Ryapolova AV, Bytyak DS, S E Peltek. Production of subtilisin proteases in bacteria and yeast. Vavilovskii Zhurnal Genet Selektsii 2021; 25:125-134. [PMID: 34901710 PMCID: PMC8629363 DOI: 10.18699/vj21.015] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 11/19/2022] Open
Abstract
In this review, we discuss the progress in the study and modification of subtilisin proteases. Despite longstanding applications of microbial proteases and a large number of research papers, the search for new protease genes, the construction of producer strains, and the development of methods for their practical application are still relevant and important, judging by the number of citations of the research articles on proteases and their microbial producers. This enzyme class represents the largest share of the industrial production of proteins worldwide. This situation can explain the high level of interest in these enzymes and points to the high importance of designing domestic technologies for their manufacture. The review covers subtilisin classification, the history of their discovery, and subsequent research on the optimization of their properties. An overview of the classes of subtilisin proteases and related enzymes is provided too. There is a discussion about the problems with the search for (and selection of) subtilases from natural strains of various microorganisms, approaches to (and specifics of) their modification, as well as the relevant genetic engineering techniques. Details are provided on the methods for expression optimization of industrial subtilases of various strains: the details of the most important parameters of cultivation, i.e., composition of the media, culture duration, and the influence of temperature and pH. Also presented are the results of the latest studies on cultivation techniques: submerged and solid-state fermentation. From the literature data reviewed, we can conclude that native enzymes (i.e., those obtained from natural sources) currently hardly have any practical applications because of the decisive advantages of the enzymes modified by genetic engineering and having better properties: e.g., thermal stability, general resistance to detergents and specific resistance to various oxidants, high activity in various temperature ranges, independence from metal ions, and stability in the absence of calcium. The vast majority of subtilisin proteases are expressed in producer strains belonging to different species of the genus Bacillus. Meanwhile, there is an effort to adapt the expression of these enzymes to other microbes, in particular species of the yeast Pichia pastoris.
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Affiliation(s)
- A S Rozanov
- Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Laboratory of Molecular Biotechnologies, Novosibirsk, Russia
| | - S V Shekhovtsov
- Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Laboratory of Molecular Biotechnologies, Novosibirsk, Russia
| | - N V Bogacheva
- Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Laboratory of Molecular Biotechnologies, Novosibirsk, Russia
| | - E G Pershina
- Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Laboratory of Molecular Biotechnologies, Novosibirsk, Russia
| | - A V Ryapolova
- Innovation Centre "Biruch-NT", Malobykovo village, Belgorod region, Russia
| | - D S Bytyak
- Innovation Centre "Biruch-NT", Malobykovo village, Belgorod region, Russia
| | - S E Peltek
- Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Laboratory of Molecular Biotechnologies, Novosibirsk, Russia
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Shekhovtsov SV, Efremov YR, Poluboyarova TV, Peltek SE. Variation in nuclear genome size within the Eisenia nordenskioldi complex (Lumbricidae, Annelida). Vavilovskii Zhurnal Genet Selektsii 2021; 25:647-651. [PMID: 34782884 PMCID: PMC8558923 DOI: 10.18699/vj21.073] [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] [Received: 02/19/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 11/19/2022] Open
Abstract
The size of the nuclear genome in eukaryotes is mostly determined by mobile elements and noncoding
sequences and may vary within wide limits. It can differ signif icantly both among higher-order taxa and closely
related species within a genus; genome size is known to be uncorrelated with organism complexity (the so-called
C-paradox). Less is known about intraspecif ic variation of this parameter. Typically, genome size is stable within a
species, and the known exceptions turn out be cryptic taxa. The Eisenia nordenskioldi complex encompasses several
closely related earthworm species. They are widely distributed in the Urals, Siberia, and the Russian Far East, as
well as adjacent regions. This complex is characterized by signif icant morphological, chromosomal, ecological, and
genetic variation. The aim of our study was to estimate the nuclear genome size in several genetic lineages of the
E. nordenskioldi complex using f low cytometry. The genome size in different genetic lineages differed strongly,
which supports the hypothesis that they are separate species. We found two groups of lineages, with small
(250–500 Mbp) and large (2300–3500 Mbp) genomes. Moreover, different populations within one lineage also
demonstrated variation in genome size (15–25 %). We compared the obtained data to phylogenetic trees based
on transcriptome data. Genome size in ancestral population was more likely to be big. It increased or decreased
independently in different lineages, and these processes could be associated with changes in genome size and/or
transition to endogeic lifestyle.
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Affiliation(s)
| | - Ya R Efremov
- Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | | | - S E Peltek
- Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
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Rozanov AS, Korzhuk AV, Shekhovtsov SV, Vasiliev GV, Peltek SE. Microorganisms of Two Thermal Pools on Kunashir Island, Russia. Biology (Basel) 2021; 10:924. [PMID: 34571800 PMCID: PMC8468003 DOI: 10.3390/biology10090924] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 11/18/2022]
Abstract
The Kuril Archipelago is a part of the Circum-Pacific Belt (Ring of Fire). These islands have numerous thermal springs. There are very few studies on these microbial communities, and none of them have been conducted by modern molecular biological methods. Here we performed the first metagenomic study on two thermophilic microbial communities of Kunashir Island. Faust Lake is hot (48 °C) and highly acidic (pH 2.0). We constructed 28 metagenome-assembled genomes as well as 17 16S ribosomal RNA sequences. We found that bottom sediments of Faust Lake are dominated by a single species of red algae belonging to the Cyanidiaceae family. Archaeans in Faust Lake are more diverse than bacteria but less abundant. The Tretyakovsky Thermal Spring is also hot (52 °C) but only weakly acidic (pH 6.0). It has much higher microbial diversity (233 metagenome-assembled genomes; 93 16S ribosomal RNAs) and is dominated by bacteria, with only several archaeans and one fungus. Despite their geographic proximity, these two thermal springs were found to not share any species. A comparison of these two lakes with other thermal springs of the Circum-Pacific Belt revealed that only a few members of the communities are shared among different locations.
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Affiliation(s)
- Aleksei S. Rozanov
- Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences (ICG SB RAS), 630090 Novosibirsk, Russia; (S.V.S.); (G.V.V.); (S.E.P.)
| | - Anton V. Korzhuk
- Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences (ICG SB RAS), 630090 Novosibirsk, Russia; (S.V.S.); (G.V.V.); (S.E.P.)
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Sergei V. Shekhovtsov
- Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences (ICG SB RAS), 630090 Novosibirsk, Russia; (S.V.S.); (G.V.V.); (S.E.P.)
| | - Gennady V. Vasiliev
- Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences (ICG SB RAS), 630090 Novosibirsk, Russia; (S.V.S.); (G.V.V.); (S.E.P.)
| | - Sergei E. Peltek
- Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences (ICG SB RAS), 630090 Novosibirsk, Russia; (S.V.S.); (G.V.V.); (S.E.P.)
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Shekhovtsov SV, Ermolov SA, Poluboyarova TV, Kim-Kashmenskaya MN, Derzhinsky YA, Peltek SE. Morphological differences between genetic lineages of the peregrine earthworm : Aporrectodea caliginosa (Savigny, 1826). ACTA ZOOL ACAD SCI H 2021. [DOI: 10.17109/azh.67.3.235.2021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Aporrectodea caliginosa is a universally distributed and highly abundant peregrine earthworm that is the object of many ecological and ecotoxicological studies. Molecular phylogenetic analysis suggested that A. caliginosa consists of three highly diverged genetic lineages. In this study, we investigated morphological diversity within a sample of these three lineages from Belarus. We detected a variety of forms with different degrees of pigmentation and a shift in the clitellum position. The three genetic lineages of A. caliginosa demonstrated different propensity to particular morphological variants, including size, colour, and the clitellum position, yet no character could be used to distinguish among the lineages with sufficient accuracy. Thus, our results suggest that identification of the genetic lineage should be recommended for ecological studies involving A. caliginosa to account for possible differences between them.
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Uvarova YE, Bryanskaya AV, Rozanov AS, Shlyakhtun VN, Demidov EA, Starostin KV, Goryachkovskaya TN, Shekhovtsov SV, Slynko NM, Peltek SE. An integrated method for taxonomic identification of microorganisms. Vavilovskii Zhurnal Genet Selektsii 2021; 24:376-382. [PMID: 33659820 PMCID: PMC7716526 DOI: 10.18699/vj20.630] [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
For accurate species-level identification of microorganisms, researchers today increasingly use a
combination of standard microbiological cultivation and visual observation methods with molecular biological and genetic techniques that help distinguish between species and strains of microorganisms at the level
of DNA or RNA molecules. The aim of this work was to identify microorganisms from the ICG SB RAS Collection
using an integrated approach that involves a combination of various phenotypic and genotypic characteristics. Key molecular-genetic and phenotypic characteristics were determined for 93 microbial strains from the
ICG SB RAS Collection. The strains were characterized by means of morphological, physiological, moleculargenetic, and mass-spectrometric parameters. Specific features of the growth of the strains on different media
were determined, and cell morphology was evaluated. The strains were tested for the ability to utilize various
substrates. The strains studied were found to significantly differ in their biochemical characteristics. Physiological characteristics of the strains from the collection were identified too, e.g., the relationship with oxygen,
type of nutrition, suitable temperature and pH ranges, and NaCl tolerance. In this work, the microorganisms
analyzed were combined into separate groups based on the similarities of their phenotypic characteristics.
This categorization, after further refinement and expansion of the spectrum of taxa and their metabolic maps,
may serve as the basis for the creation of an “artificial” classification that can be used as a key for simplified and
quicker identification and recognition of microorganisms within both the ICG SB RAS Collection and other
collections
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Affiliation(s)
- Yu E Uvarova
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A V Bryanskaya
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A S Rozanov
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - V N Shlyakhtun
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E A Demidov
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - K V Starostin
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - T N Goryachkovskaya
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - S V Shekhovtsov
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - N M Slynko
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - S E Peltek
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Shekhovtsov SV, Shipova AA, Poluboyarova TV, Vasiliev GV, Golovanova EV, Geraskina AP, Bulakhova NA, Szederjesi T, Peltek SE. Species Delimitation of the Eisenia nordenskioldi Complex (Oligochaeta, Lumbricidae) Using Transcriptomic Data. Front Genet 2020; 11:598196. [PMID: 33365049 PMCID: PMC7750196 DOI: 10.3389/fgene.2020.598196] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 08/27/2020] [Accepted: 11/09/2020] [Indexed: 01/22/2023] Open
Abstract
Eisenia nordenskioldi (Eisen, 1879) is the only autochthonous Siberian earthworm with a large distribution that ranges from tundra to steppe and broadleaved forests. This species has a very high morphological, ecological, karyological, and genetic diversity, so it was proposed that E. nordenskioldi should be split into several species. However, the phylogeny of the complex was unclear due to the low resolution of the methods used and the high diversity that should have been taken into account. We investigated this question by (1) studying the diversity of the COI gene of E. nordenskioldi throughout its range and (2) sequencing transcriptomes of different genetic lineages to infer its phylogeny. We found that E. nordenskioldi is monophyletic and is split into two clades. The first one includes the pigmented genetic lineages widespread in the northern and western parts of the distribution, and the second one originating from the southern and southeastern part of the species' range and representing both pigmented and non-pigmented forms. We propose to split the E. nordenskioldi complex into two species, E. nordenskioldi and Eisenia sp. 1 (aff. E. nordenskioldi), corresponding to these two clades. The currently recognized non-pigmented subspecies E. n. pallida will be abolished as a polyphyletic and thus a non-natural taxon, while Eisenia sp. 1 will be expanded to include several lineages earlier recognized as E. n. nordenskioldi and E. n. pallida.
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Affiliation(s)
- Sergei V Shekhovtsov
- Department of Molecular Biotechnology, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Kurchatov Genomic Center, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Laboratory of Biocenology, Institute of Biological Problems of the North of the Far Eastern Branch of the Russian Academy of Sciences, Magadan, Russia
| | - Aleksandra A Shipova
- Department of Molecular Biotechnology, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Kurchatov Genomic Center, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Tatiana V Poluboyarova
- Department of Molecular Biotechnology, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Kurchatov Genomic Center, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Laboratory of Biocenology, Institute of Biological Problems of the North of the Far Eastern Branch of the Russian Academy of Sciences, Magadan, Russia
| | - Gennady V Vasiliev
- Department of Molecular Biotechnology, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Elena V Golovanova
- Laboratory of Systematics and Ecology of Invertebrates, Omsk State Pedagogical University, Omsk, Russia
| | - Anna P Geraskina
- Center for Forest Ecology and Productivity of the Russian Academy of Sciences, Moscow, Russia
| | - Nina A Bulakhova
- Laboratory of Biocenology, Institute of Biological Problems of the North of the Far Eastern Branch of the Russian Academy of Sciences, Magadan, Russia.,Laboratory of Biodiversity and Ecology, Tomsk State University, Tomsk, Russia
| | - Tímea Szederjesi
- Department of Zoology, Hungarian Natural History Museum, Budapest, Hungary
| | - Sergei E Peltek
- Department of Molecular Biotechnology, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Kurchatov Genomic Center, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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12
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Shekhovtsov SV, Bulakhova NA, Tsentalovich YP, Zelentsova EA, Yanshole LV, Meshcheryakova EN, Berman DI. Metabolic response of the Siberian wood frog Rana amurensis to extreme hypoxia. Sci Rep 2020; 10:14604. [PMID: 32884088 PMCID: PMC7471963 DOI: 10.1038/s41598-020-71616-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 08/17/2020] [Indexed: 11/19/2022] Open
Abstract
The Siberian wood frog Rana amurensis is a recently discovered example of extreme hypoxia tolerance that is able to survive several months without oxygen. We studied metabolomic profiles of heart and liver of R. amurensis exposed to 17 days of extreme hypoxia. Without oxygen, the studied tissues experience considerable stress with a drastic decrease of ATP, phosphocreatine, and NAD+ concentrations, and concomitant increase of AMP, creatine, and NADH. Heart and liver switch to different pathways of glycolysis with differential accumulation of lactate, alanine, succinate, as well as 2,3-butanediol (previously not reported for vertebrates as an end product of glycolysis) and depletion of aspartate. We also observed statistically significant changes in concentrations of certain osmolytes and choline-related compounds. Low succinate/fumarate ratio and high glutathione levels indicate adaptations to reoxygenation stress. Our data suggest that maintenance of the ATP/ADP pool is not required for survival of R. amurensis, in contrast to anoxia-tolerant turtles.
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Affiliation(s)
- Sergei V Shekhovtsov
- Institute of the Biological Problems of the North FEB RAS, Magadan, Russia.
- Kurchatov Genomic Center, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
| | - Nina A Bulakhova
- Institute of the Biological Problems of the North FEB RAS, Magadan, Russia
- Tomsk State University, Tomsk, Russia
| | | | - Ekaterina A Zelentsova
- International Tomography Center SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | | | | | - Daniil I Berman
- Institute of the Biological Problems of the North FEB RAS, Magadan, Russia
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Shekhovtsov SV, Rapoport IB, Poluboyarova TV, Geraskina AP, Golovanova EV, Peltek SE. Morphotypes and genetic diversity of Dendrobaena schmidti (Lumbricidae, Annelida). Vavilovskii Zhurnal Genet Selektsii 2020; 24:48-54. [PMID: 33659780 PMCID: PMC7716558 DOI: 10.18699/vj20.594] [Citation(s) in RCA: 3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Dendrobaena schmidti (Michaelsen, 1907) is a polymorphic earthworm species from the Caucasus and adjacent regions. Adult D. schmidti individuals have highly variable body size (from 1.5 to well over 10 cm) and color (from dark purple to total lack of pigmentation), so a lot of subspecies of D. schmidti have been described; however, the existence of most of them is currently under dispute. We studied the genetic diversity of D. schmidti from seven locations from the Western Caucasus using mitochondrial (a fragment of the cytochrome oxidase I gene) and nuclear (internal ribosomal transcribed spacer 2) DNA. For both genes studied, we found that our sample was split into two groups. The first group included somewhat bigger (3–7.5 cm) individuals that were only slightly pigmented or totally unpigmented (when fixed by ethanol). The second group contained small (1.7–3.5 cm) specimens with dark purple pigmentation. In one of the studied locations these two groups were found in sympatry. However, there were no absolute differences either in general appearance (pigmented/unpigmented, small/big) or among diagnostic characters. Although the two groups differed in size (the majority of individuals from the first group were 5–6 cm long, and of the second one, 2–3 cm), the studied samples overlapped to a certain degree. Pigmentation, despite apparent differences, was also unreliable, since it was heavily affected by fixation of the specimens. Thus, based on the obtained data we can conclude that D. schmidti consists of at least two species that have identical states of diagnostic characters, but differ in general appearance.
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Affiliation(s)
- S V Shekhovtsov
- Institute of Cytology and Genetics of Suberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Institute of Biological Problems of the North of Far Eastern Branch of the Russian Academy of Sciences, Magadan, Russia Novosibirsk State University, Novosibirsk, Russia
| | - I B Rapoport
- Tembotov Institute of Ecology of Mountain Territories of the Russian Academy of Sciences, Nalchik, Russia
| | - T V Poluboyarova
- Institute of Cytology and Genetics of Suberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Institute of Biological Problems of the North of Far Eastern Branch of the Russian Academy of Sciences, Magadan, Russia
| | - A P Geraskina
- Center for Forest Ecology and Productivity of the Russian Academy of Sciences, Moscow, Russia
| | | | - S E Peltek
- Institute of Cytology and Genetics of Suberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Slynko NM, Burmakina NV, Potseluyev OM, Kapustyanchik SY, Galitsin GY, Goryachkovskaya TN, Kuybida LV, Shekhovtsov SV, Peltek SE, Shumny VK. Erratum to: “Gas chromatography-mass spectrometry in the taxonomy of Miscanthus”. Vavilovskii Zhurnal Genet Selektsii 2020; 24:109. [PMID: 33659789 PMCID: PMC7716577 DOI: 10.18699/vj20.603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Vavilovskii Zhurnal Genetiki i Selektsii = Vavilov Journal of Genetics and Breeding. 2019;23(8):1076-1081 (in Russian)
Page 1081, in Acknowledgements instead of
This work was supported by State Budgeted Project АААА-А17-117092070032-4.
should read
This work was supported by State Budgeted Project 0259-2019-0011.
The original article can be found under DOI 10.18699/VJ19.583
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Affiliation(s)
- Sergei V. Shekhovtsov
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Institute of Biological Problems of the North FEB RAS, Magadan, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
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Abstract
BACKGROUND Many earthworm species demonstrate significant cryptic diversity, with several highly diverged mitochondrial lineages found within most of the taxa studied to date. The status of differences between these lineages on the nuclear level is still unclear. Because of widespread polyploidy in earthworms, most studies were limited to two nuclear loci, the ribosomal and the histone clusters. Here we attempted to elucidate the status of a set of genetic lineages within Eisenia nordenskioldi nordenskioldi, an earthworm species from Northern Asia with high intraspecific diversity. We performed RNA-seq on an IonTorrent platform for five specimens of this species belonging to five genetic lineages, as well as two outgroups from the family Lumbricidae, the congenetic E. andrei, and Lumbricus rubellus. RESULTS We de novo assembled transcriptomes and constructed datasets of genes present in all seven specimens using broad (ProteinOrtho; 809 genes) and narrow (HaMStR; 203 genes) ortholog assignment. The majority of orthologs had identical amino acid sequences in all studied specimens, which we believe was due to strong bias towards the most conserved genes. However, for the rest of genes the differences among the lineages were lower than those between them and the congeneric E. andrei. Both datasets yielded phylogenetic trees with the same topology. E. n. nordenskioldi was found to be monophyletic. The differences on the genetic level had no concordance with geography, implying complex history of dispersal. CONCLUSIONS We found that genetic lineages of E. n. nordenskioldi are genetically distinct on nuclear level and probably diverged long ago. Current data implies that they might even represent distinct species within the E. nordenskioldi species complex.
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Affiliation(s)
- Sergei V. Shekhovtsov
- Institute of Cytology and Genetics SB RAS, Pr. Lavrientieva 10, Novosibirsk, 630090 Russia
- Institute of Biological Problems of the North FEB RAS, Portovaya St. 18, Magadan, 685000 Russia
| | - Nikita I. Ershov
- Institute of Cytology and Genetics SB RAS, Pr. Lavrientieva 10, Novosibirsk, 630090 Russia
| | - Gennady V. Vasiliev
- Institute of Cytology and Genetics SB RAS, Pr. Lavrientieva 10, Novosibirsk, 630090 Russia
| | - Sergey E. Peltek
- Institute of Cytology and Genetics SB RAS, Pr. Lavrientieva 10, Novosibirsk, 630090 Russia
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Shekhovtsov SV, Golovanova EV, Peltek SE. Mitochondrial DNA variation in Eisenia n. nordenskioldi (Lumbricidae) in Europe and Southern Urals. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4643-4645. [PMID: 26644175 DOI: 10.3109/19401736.2015.1101594] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [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: 11/13/2022]
Abstract
There are many peregrine European earthworm species that are found in Siberia. In contrast, it is generally considered that the only Siberian species, E. n. nordenskioldi, was capable to disperse in the reverse direction, from Siberia into Europe. We studied genetic diversity of E. n. nordenskioldi in Southern Urals and Eastern Europe using the mitochondrial cox1 gene. We found that E. n. nordenskioldi from that region represents a new genetic lineage distinct from the previously known populations of this species from Siberia. Molecular clock estimates suggest that this newly found lineage separated from the rest of the species in Lower Pleistocene. Within the studied sample, we detected two geographically restricted groups, which also diverged long before the Holocene, one found in the East European Plain and the other restricted to the Urals. Those two groups were found in sympatry in only one population. Therefore, our results do not support the traditional viewpoint, suggesting that E. n. nordenskioldi is definitely not a recent invader in Europe.
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Affiliation(s)
- Sergei V Shekhovtsov
- a Laboratory of Molecular Biotechnology , Institute of Cytology and Genetics SB RAS , Novosibirsk , Russia and
| | - Elena V Golovanova
- b Department of Zoology and Physiology , Omsk State Pedagogical University , Omsk , Russia
| | - Sergei E Peltek
- a Laboratory of Molecular Biotechnology , Institute of Cytology and Genetics SB RAS , Novosibirsk , Russia and
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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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Shekhovtsov SV, Berman DI, Peltek SE. Phylogeography of the earthworm Eisenia nordenskioldi nordenskioldi (Lumbricidae, Oligochaeta) in northeastern Eurasia. Dokl Biol Sci 2015; 461:85-8. [PMID: 25937328 DOI: 10.1134/s0012496615020039] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Indexed: 11/22/2022]
Affiliation(s)
- S V Shekhovtsov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russia,
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Kruchinina MV, Kurilovich SA, Voevoda MI, Gromov AA, Nemtsova EG, Generalov VM, Safatov AS, Generalov KV, Buryak GA, Kruchinin VN, Rykhlitsky SV, Spesivtsev EV, Volodin VA, Mogilnikov KP, Antsygin VD, Peltek SE, Shekhovtsov SV. [MODERN METHODS OF PHYSICAL-CHEMICAL RESEARCH IN GASTROENTEROLOGY PRACTICE: THE EXPERIENCE OF INTERACTION]. Eksp Klin Gastroenterol 2015:74-82. [PMID: 26281181] [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
UNLABELLED The aim of this work was to assess the potential of some physical and chemical methods for studying erythrocytes and blood serum in gastroenterological practice by the example of colorectal cancer (CC). MATERIALS AND METHODS A total of 26 persons with various stages of colorectal cancer and 16 healthy (control group) were examined. Parameters of erythrocytes and blood serum were investigated by light microscopy, dielectrophoresis in a non-uniform alternating electric field (DEF in NUAEF), terahertz spectroscopy, ellipsometry, Raman-spectroscopy. RESULTS Polymorphism of erythrocytes, rigidity, viscosity, indexes of aggregation and destruction were significantly higher in patients with CC and polarizability, amplitude of erythrocyte deformation in NUAEF being lower than those in the controls. The study of erythrocytes by terahertz spectroscopy revealed the low levels of amplitude transmittance over the whole frequency range in CC patients compared to the controls. The increasing of refractive index, degree of heterogeneity of thin films obtained from the serum in CC patients were observed in considering the ellipsometric parameters. We found a significant increasing of the concentration of antigens to CD24 at the early stage of the disease. The areas of some peaks in Raman spectra were significantly lower in patients with CC compared to the healthy ones, it is possible due to a carotin deficiency. Most of the studied parameters were correlated with the stage of the disease. A set of optical methods for studying blood serum compared with those of histology and radiological methods of diagnosis showed their high sensitivity and specificity, positive and negative predictive value (80 % and above). CONCLUSION The obtained results of the pilot study demonstrate the prospects of using physical and chemical methods of research of erythrocytes and blood serum for early diagnosis, stage of disease and monitoring the effectiveness of treatment of CC.
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Brusentsov II, Katokhin AV, Brusentsova IV, Shekhovtsov SV, Borovikov SN, Goncharenko GG, Lider LA, Romashov BV, Rusinek OT, Shibitov SK, Suleymanov MM, Yevtushenko AV, Mordvinov VA. Low genetic diversity in wide-spread Eurasian liver fluke Opisthorchis felineus suggests special demographic history of this trematode species. PLoS One 2013; 8:e62453. [PMID: 23634228 PMCID: PMC3636034 DOI: 10.1371/journal.pone.0062453] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [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: 12/04/2012] [Accepted: 03/21/2013] [Indexed: 01/09/2023] Open
Abstract
Opisthorchis felineus or Siberian liver fluke is a trematode parasite (Opisthorchiidae) that infects the hepato-biliary system of humans and other mammals. Despite its public health significance, this wide-spread Eurasian species is one of the most poorly studied human liver flukes and nothing is known about its population genetic structure and demographic history. In this paper, we attempt to fill this gap for the first time and to explore the genetic diversity in O. felineus populations from Eastern Europe (Ukraine, European part of Russia), Northern Asia (Siberia) and Central Asia (Northern Kazakhstan). Analysis of marker DNA fragments from O. felineus mitochondrial cytochrome c oxidase subunit 1 and 3 (cox1, cox3) and nuclear rDNA internal transcribed spacer 1 (ITS1) sequences revealed that genetic diversity is very low across the large geographic range of this species. Microevolutionary processes in populations of trematodes may well be influenced by their peculiar biology. Nevertheless, we suggest that lack of population genetics structure observed in O. felineus can be primarily explained by the Pleistocene glacial events and subsequent sudden population growth from a very limited group of founders. Rapid range expansion of O. felineus through Asian and European territories after severe bottleneck points to a high dispersal potential of this trematode species.
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Affiliation(s)
- Ilja I. Brusentsov
- Laboratory of Molecular Mechanisms of Pathological Processes, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexey V. Katokhin
- Laboratory of Molecular Mechanisms of Pathological Processes, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Irina V. Brusentsova
- Laboratory of Molecular Mechanisms of Pathological Processes, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Sergei V. Shekhovtsov
- Laboratory of Molecular Biotechnology, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Sergei N. Borovikov
- Department of Animal Biotechnology, S.Seifullin Kazakh Agrotechnical University, Astana, Republic of Kazakhstan
| | | | - Lyudmila A. Lider
- Department of Veterinary Medicine, S.Seifullin Kazakh Agrotechnical University, Astana, Republic of Kazakhstan
| | - Boris V. Romashov
- Scientific Department, Voronezh State Biosphere Reserve, Voronezh, Russia
| | - Olga T. Rusinek
- Department of Parasitology, The Baikal Museum at the Irkutsk Scientific Center, Siberian Branch, Russian Academy of Sciences, Listvyanka, Irkutsk, Russia
| | - Samat K. Shibitov
- Department of Epizootological Problems, All-Russian K.I. Skryabin Institute of Helminthology, Moscow, Russia
| | - Marat M. Suleymanov
- Laboratory of Molecular Mechanisms of Pathological Processes, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Andrey V. Yevtushenko
- Department of Parasitology Ichthyopathology and Arachnology, National Scientific Center “Institute of Experimental and Clinical Veterinary Medicine”, Kharkov, Ukraine
| | - Viatcheslav A. Mordvinov
- Laboratory of Molecular Mechanisms of Pathological Processes, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
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Shekhovtsov SV, Katokhin AV, Kolchanov NA, Mordvinov VA. The complete mitochondrial genomes of the liver flukes Opisthorchis felineus and Clonorchis sinensis (Trematoda). Parasitol Int 2010; 59:100-3. [DOI: 10.1016/j.parint.2009.10.012] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Revised: 09/30/2009] [Accepted: 10/27/2009] [Indexed: 11/16/2022]
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Shekhovtsov SV, Katokhin AV, Romanov KV, Besprozvannykh VV, Fedorov KP, Yurlova NI, Serbina EA, Sithithaworn P, Kolchanov NA, Mordvinov VA. A novel nuclear marker, Pm-int9, for phylogenetic studies of Opisthorchis felineus, Opisthorchis viverrini, and Clonorchis sinensis (Opisthorchiidae, Trematoda). Parasitol Res 2009; 106:293-7. [PMID: 19777262 DOI: 10.1007/s00436-009-1628-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Accepted: 09/03/2009] [Indexed: 01/23/2023]
Abstract
Opisthorchis felineus, O. viverrini, and Clonorchis sinensis, the trematodes of the family Opisthorchiidae, are important human parasites. Two previous studies (Kang et al. Parasitol Int 57:191-197, 2008; Katokhin et al. Dokl Biochem Biophys 421:214-217, 2008) have provided evidence using ribosomal and mitochondrial sequences that O. viverrini, O. felineus, and C. sinensis are closely related. We developed a novel nuclear marker, Pm-int9, which included the ninth intron of the paramyosin gene and flanking exon sequences. Samples of O. felineus from four localities of West Siberia, C. sinensis from the Russian Far East, and O. viverrini from Thailand were genotyped by Pm-int9. Little variation was detected in exon sequences, however, intron sequences turned out to be more variable than ribosomal internal transcribed spacers. We can conclude that Pm-int9 is valuable for interspecific variation studies. Phylogenetic analysis based on Pm-int9 revealed that O. viverrini and C. sinensis were closer to each other than either of them to O. felineus, supporting the opinion that C. sinensis should be considered the sister species of Opisthorchis spp.
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Affiliation(s)
- Sergei V Shekhovtsov
- Institute of Cytology and Genetics, Prospect Lavrientieva 10, Novosibirsk, Russian Federation.
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Mordvinov VA, Mardanov AV, Ravin NV, Shekhovtsov SV, Demakov SA, Katokhin AV, Kolchanov NA, Skryabin KG. Complete Sequencing of the Mitochondrial Genome of Opisthorchis felineus , Causative Agent of Opisthorchiasis. Acta Naturae 2009. [DOI: 10.32607/20758251-2009-1-1-99-104] [Citation(s) in RCA: 3] [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: 11/20/2022] Open
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Mordvinov VA, Mardanov CACV, Ravin NV, Shekhovtsov SV, Demakov SА, Katokhin CACV, Kolchanov NА, Skryabin KG. Complete Sequencing of the Mitochondrial Genome of Opisthorchis felineus, Causative Agent of Opisthorchiasis. Acta Naturae 2009; 1:99-104. [PMID: 22649593 PMCID: PMC3347509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Opisthorchis felineus, a hepatic trematode, is the causative agent of opisthorchiasis, a dangerous disease in both human beings and animals. Opisthorchiasis is widespread in Russia, especially Western Siberia. The purpose of the present study was to determine the complete mitochondrial DNA sequence of this flatworm. Two parallel methods were employed: (1) capillary electrophoresis to sequence the mitochondrial genome fragments obtained through specific PCR amplification, and (2) high throughput sequencing of the DNA sample. Both methods made possible the determination of the complete nucleotide sequence of the O. felineus mitochondrial genome. The genome consists of a ring molecule 14,277 nt in length that contains 35 genes coding 2 rRNA, 22 tRNA, and 12 proteins: 3 subunits of cytochrome-C-oxidase, 7 subunits of NADH-dehydrogenase, B apocytochrome, and subunit 6 of ATP-synthetase.Like many other flatworms, O. felineus is characterized by the absence of the ATP-synthetase subunit 8 gene. Nineteen out of the 22 tRNAs have a typical "clover leaf" structure. The tRNA(AGC) and tRNA-Cys genes lack DHU-loops, while the tRNA-Ser(UCA) has 2 alternative structures: one with a DHU-loop, and one without it. Analyzing the results obtained from the high throughput sequencing revealed 45 single-nucleotide polymorphisms within the mitochondrial genome. The results obtained in this study may be used in the development of molecular diagnostic methods for opisthorchiasis. This study shows that high throughput sequencing is a fast and effective method for decoding the mitochondrial genome of animals.
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Affiliation(s)
- V A Mordvinov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Lavrentieva Ave, Novosibirsk, 630090, Russia
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Katokhin AV, Shekhovtsov SV, Konkow S, Yurlova NI, Serbina EA, Vodianitskai SN, Fedorov KP, Loktev VB, Muratov IV, Ohyama F, Makhnev TV, Pel'tek SE, Mordvinov VA. Assessment of the genetic distinctions of Opisthorchis felineus from O. viverrini and Clonorchis sinensis by ITS2 and CO1 sequences. DOKL BIOCHEM BIOPHYS 2008; 421:214-7. [PMID: 18853775 DOI: 10.1134/s1607672908040133] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- A V Katokhin
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, pr. Lavrent'eva 10, Novosibirsk, 630090 Russia
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