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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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Smirnov DN, Shekhovtsov SV, Shipova AA, Gazizova GR, Shagimardanova EI, Bulakhova NA, Meshcheryakova EN, Poluboyarova TV, Khrameeva EE, Peltek SE, Berman DI. De novo assembly and analysis of the transcriptome of the Siberian wood frog Rana amurensis. Vavilovskii Zhurnal Genet Selektsii 2022; 26:109-116. [PMID: 35342853 PMCID: PMC8894097 DOI: 10.18699/vjgb-22-07] [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: 08/10/2021] [Revised: 11/02/2021] [Accepted: 11/02/2021] [Indexed: 11/30/2022] Open
Abstract
The Siberian wood frog Rana amurensis Boulenger, 1886 is the most hypoxia-tolerant amphibian. It can survive for several months in an almost complete absence of oxygen. Little is known about the mechanisms of this remarkable resilience, in part because studies of amphibian genomes are impeded by their large size. To make the Siberian wood frog more amenable for genetic analysis, we performed transcriptome sequencing and de novo assembly for the R. amurensis brain under hypoxia and normoxia, as well as for the normoxic heart. In order to build a de novo transcriptome assembly of R. amurensis, we utilized 125-bp paired-end reads obtained from the brain under normoxia and hypoxia conditions, and from the heart under normoxia. In the transcriptome assembled from about 100,000,000 reads, 81.5 % of transcripts were annotated as complete, 5.3 % as fragmented, and 13.2 % as missing. We detected 59,078 known transcripts that clustered into 22,251 genes; 11,482 of them were assigned to specific GO categories. Among them, we found 6696 genes involved in protein binding, 3531 genes involved in catalytic activity, and 576 genes associated with transporter activity. A search for genes encoding receptors of the most important neurotransmitters, which may participate in the response to hypoxia, resulted in a set of expressed receptors of dopamine, serotonin, GABA, glutamate, acetylcholine, and norepinephrine. Unexpectedly, no transcripts for histamine receptors were found. The data obtained in this study create a valuable resource for studying the mechanisms of hypoxia tolerance in the Siberian wood frog, as well as for amphibian studies in general.
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Affiliation(s)
- D. N. Smirnov
- Center of Life Sciences, Skolkovo Institute of Science and Technology; Ben-Gurion University of the Negev, Department of Life Sciences
| | - S. V. Shekhovtsov
- Institute of the Biological Problems of the North of the Far-Eastern Branch of the Russian Academy of Sciences; Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - A. A. Shipova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - G. R. Gazizova
- Institute of Fundamental Medicine and Biology, Kazan Federal University
| | | | - N. A. Bulakhova
- Institute of the Biological Problems of the North of the Far-Eastern Branch of the Russian Academy of Sciences
| | - E. N. Meshcheryakova
- Institute of the Biological Problems of the North of the Far-Eastern Branch of the Russian Academy of Sciences
| | - T. V. Poluboyarova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - E. E. Khrameeva
- Center of Life Sciences, Skolkovo Institute of Science and Technology
| | - S. E. Peltek
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - D. I. Berman
- Institute of the Biological Problems of the North of the Far-Eastern Branch of the Russian Academy of Sciences
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Beklemishev AB, Pykhtina MB, Kulikov YM, Goryachkovskaya TN, Bochkov DV, Sergeeva SV, Vasileva AR, Romanov VP, Novikova DS, Peltek SE. Creation of a recombinant Komagataella phaffii strain, a producer of proteinase K from Tritirachium album. Vavilovskii Zhurnal Genet Selektsii 2022; 25:882-888. [PMID: 35083407 PMCID: PMC8755523 DOI: 10.18699/vj21.102] [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: 11/16/2021] [Revised: 11/29/2021] [Accepted: 11/29/2021] [Indexed: 11/19/2022] Open
Abstract
The objects of the study were recombinant clones of Komagataella phaffii K51 carrying the heterologous proteinase K (PK-w) gene from Tritirachium album integrated into their genome as well as samples of recombinant proteinase K isolated from these clones. The aims of this work were i) to determine whether it is possible to create recombinant K. phaffii K51 clones overexpressing functionally active proteinase K from T. album and ii) to analyze the enzymatic activity of the resulting recombinant enzyme. The following methods were used: computational analysis of primary structure of the proteinase K gene, molecular biological methods (PCR, electrophoresis of DNA in an agarose gel, electrophoresis of proteins in an SDS polyacrylamide gel under denaturing conditions, spectrophotometry, and quantitative assays of protease activity), and genetic engineering techniques (cloning and selection of genes in bacterial cells Escherichia coli TOP10 and in the methylotrophic yeast K. phaffii K51). The gene encoding natural proteinase K (PK-w) was designed and optimized for expression in K. phaffii K51. The proteinase K gene was synthesized and cloned within the plasmid pPICZα-A vector in E. coli TOP10 cells. The proteinase K gene was inserted into pPICZα-A in such a way that – at a subsequent stage of transfection into yeast cells – it was efficiently expressed under the control of the promoter and terminator of the AOX1 gene, and the product of the exogenous gene contained the signal peptide of the Saccharomyces cerevisiae a-factor to ensure the protein’s secretion into the culture medium. The resultant recombinant plasmid (pPICZα-A/PK-w) was transfected into K. phaffii K51 cells. A recombinant K. phaffii K51 clone was obtained that carried the synthetic proteinase K gene and ensured its effective expression and secretion into the culture medium. An approximate productivity of the yeast recombinant clones for recombinant proteinase K was 25 μg/ mL after 4 days of cultivation. The resulting recombinant protease has a high specific proteolytic activity: ~5000 U/mg.
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Affiliation(s)
- A. B. Beklemishev
- Federal Research Center of Fundamental and Translational Medicine; Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - M. B. Pykhtina
- Federal Research Center of Fundamental and Translational Medicine; Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - Ya. M. Kulikov
- Federal Research Center of Fundamental and Translational Medicine; Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - T. N. Goryachkovskaya
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - D. V. Bochkov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - S. V. Sergeeva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - A. R. Vasileva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - V. P. Romanov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | | | - S. E. Peltek
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
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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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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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Rozanov AS, Pershina EG, Bogacheva NV, Shlyakhtun V, Sychev AA, Peltek SE. Diversity and occurrence of methylotrophic yeasts used in genetic engineering. Vavilovskii Zhurnal Genet Selektsii 2020; 24:149-157. [PMID: 33659794 PMCID: PMC7716571 DOI: 10.18699/vj20.602] [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
Methylotrophic yeasts have been used as the platform for expression of heterologous proteins since the
1980’s. They are highly productive and allow producing eukaryotic proteins with an acceptable glycosylation level.
The first Pichia pastoris-based system for expression of recombinant protein was developed on the basis of the treeexudate-
derived strain obtained in the US southwest. Being distributed free of charge for scientific purposes, this system
has become popular around the world. As methylotrophic yeasts were classified in accordance with biomolecular
markers, strains used for production of recombinant protein were reclassified as Komagataella phaffii. Although patent
legislation suggests free access to these yeasts, they have been distributed on a contract basis. Whereas their status
for commercial use is undetermined, the search for alternative stains for expression of recombinant protein continues.
Strains of other species of methylotrophic yeasts have been adapted, among which the genus Ogataea representatives
prevail. Despite the phylogenetic gap between the genus Ogataea and the genus Komagataella representatives,
it turned out possible to use classic vectors and promoters for expression of recombinant protein in all cases. There
exist expression systems based on other strains of the genus Komagataella as well as the genus Candida. The potential
of these microorganisms for genetic engineering is far from exhausted. Both improvement of existing expression systems
and development of new ones on the basis of strains obtained from nature are advantageous. Historically, strains
obtained on the southwest of the USA were used as expression systems up to 2009. Currently, expression systems
based on strains obtained in Thailand are gaining popularity. Since this group of microorganisms is widely represented
around the world both in nature and in urban environments, it may reasonably be expected that new expression systems
for recombinant proteins based on strains obtained in other regions of the globe will appear.
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Affiliation(s)
- A S Rozanov
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E G Pershina
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - N V Bogacheva
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - V Shlyakhtun
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A A Sychev
- Innovation Centre Biruch-NT, Belgorod region, Russia
| | - S E Peltek
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 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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Slynko NM, Burmakina NV, Potseluyev OM, Kapustyanchik SY, Galitsin GY, Goryachkovskaya TN, Kuybida LV, Shekhovtsov SV, Peltek SE, Shumny VK. Gas chromatography-mass spectrometry in the taxonomy of Miscanthus. Vavilovskii Zhurnal Genet Selektsii 2020. [DOI: 10.18699/vj19.583] [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: 11/19/2022] Open
Abstract
Chemotaxonomy as a system approach deals with intra- and interspecific polymorphism of a group of taxa in order to clarify their taxonomic positions or to select material for selection or introduction. In this study we performed chemotaxonomic analysis of specimens of Miscanthus sinensis and M. sacchariflorus collected in the Russian Far East and of hybrid plants of both natural and artificial origin. We found 153 substances and identified 143 of them in extracts of eleven Miscanthus plants by gas chromatography-mass spectrometry (GC-MS). These substances can be grouped into alkanes (20 compounds), fatty acids (34), phenols (13), sterols (18) toсopherols (8), norterpenoids (12), and phytols (13), as well as their derivatives. The main components of the extracts of miscanthus samples are fatty acids and their derivatives (total content 19.94–41.02 %), dominated by palmitic and linolenic acids, and sterols (mainly β-sitosterol, stigmasterol, and α-amyrin), which constitute 17.15–31.73 %. The values of the CPI “oddness index” for the alkane components of the extracts were within 1.55–7.18, with extracts from leaves of the Far Eastern samples characterized by the lower half of this range (1.55–2.74), while extracts from leaves of hybrids fell to the upper half (5.78–7.18). Principal component analysis of extraction profiles allowed us to separate three distinct clusters: M. sinensis, M. sachariflorus, and their hybrids, as well as to verify the origin of one of the natural hybrids. The results of chemotaxonomic analysis mostly matched those of DNA sequencing of a fragment of the plastid genome, which, moreover, allowed us to identify the species nature of the maternal plants used to obtain these hybrids. Chemotaxonomic analysis using GC-MS was found to be an efficient additional technique to delimit various morphological forms of M. sinensis, M. sachariflorus, and their hybrids.
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Affiliation(s)
| | | | | | | | | | | | - L. V. Kuybida
- Voevodsky Institute of Chemical Kinetics and Combustion, SB RAS
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Kazantsev FV, Smirnova AA, Rozanov AS, Uvarova YE, Afonnikov DA, Peltek SE, Lashin SA. Information system on microbial collections as a part of bioresource collections portal for Russia’s FASO organizations: a working protocol. Vavilovskii Zhurnal Genet Selektsii 2018. [DOI: 10.18699/vj18.361] [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: 11/19/2022] Open
Abstract
Nowadays, many scientific organizations of Russia own collections of microorganisms on which large volumes of information have been generated. These data represent the descriptions of objects of diverse nature (bacteria, archaea, fungi, protists) and their properties, which have been carefully collected and cataloged by generations of researchers. Not every organization that has such collections has an open access electronic catalog, which not only complicates work with these unique materials, but also even hides the fact of the existence of such collections. This state of affairs requires the development of electronic resources for presenting these materials to the scientific community. To put together the information on microorganism collections, we have developed an internet portal (http://www.biores.cytogen.ru/microbes/) of microbial bioresource collections of FASO organizations in the Russian Federation. The portal was created under the project developing the information system for bioresource collections of FASO institutes. It is a platform where collection organizations can place information about the storage units of their collections, as well as other information on collections, including links to their own catalogs. In this paper, we describe the principles of working with the portal. The portal’s graphical interface allows users, both registered and unregistered, to receive the following information about collections of microorganisms: a list of collections represented in the database, contact details of the organization and information about the curator of the collection, summary statistics for each collection, as well as information on storage units. Registered users – owners of collections – have the opportunity to create and modify records about the storage units of their collections, and to update their description. To automate work with the portal, software access to the database through the REST API has been implemented (http://api.biores.cytogen.ru/ microbes/). At present, the portal is still being filled, but it already contains a description of more than 13,000 items of storage (of which 3500 are in the microorganisms’ part) of 65 bioresource collections in Russia’s FASO organizations. Of these collections, 12 with microorganisms have a total diversity of funds of about 50,000 strains).
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Affiliation(s)
- F. V. Kazantsev
- Institute of Cytology and Genetics SB RAS; Novosibirsk State University
| | | | | | | | - D. A. Afonnikov
- Institute of Cytology and Genetics SB RAS; Novosibirsk State University
| | | | - S. A. Lashin
- Institute of Cytology and Genetics SB RAS; Novosibirsk State University
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Shekhovtsov SV, Sundukov YN, Blakemore RJ, Gongalsky KB, Peltek SE. Identifying earthworms (Oligochaeta, Megadrili) of the Southern Kuril Islands using DNA barcodes. Anim Biodiv Conserv 2018. [DOI: 10.32800/abc.2018.41.0009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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12
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Shekhovtsov SV, Berman DI, Bulakhova NA, Vinokurov NN, Peltek SE. Phylogeography of Eisenia nordenskioldi nordenskioldi (Lumbricidae, Oligochaeta) from the north of Asia. Polar Biol 2017. [DOI: 10.1007/s00300-017-2184-2] [Citation(s) in RCA: 4] [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: 10/19/2022]
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13
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Stakhneva EM, Meshcheryakova IA, Demidov EA, Starostin KV, Ragino YI, Peltek SE, Voevoda MI. Proteomic Study of Blood Serum in Coronary Atherosclerosis. Bull Exp Biol Med 2017; 162:343-345. [PMID: 28091899 DOI: 10.1007/s10517-017-3611-7] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Indexed: 11/28/2022]
Abstract
Changes in the blood serum proteins were assessed in men with coronary atherosclerosis and without coronary heart disease. Proteins were separated by 2D-electrophoresis, protein fractions were identified by their peptide fingerprint by MALDI method; fractions with more than twofold increase in protein level were determined. In blood serum of patients with coronary atherosclerosis, the content of C4 complement protein increased and ceruloplasmin level decreased, which is typical of heart failure and coronary heart disease.
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Affiliation(s)
- E M Stakhneva
- Research Institute of Internal and Preventive Medicine, Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia.
| | - I A Meshcheryakova
- Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E A Demidov
- Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - K V Starostin
- Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Yu I Ragino
- Research Institute of Internal and Preventive Medicine, Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - S E Peltek
- Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - M I Voevoda
- Research Institute of Internal and Preventive Medicine, Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
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14
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Shekhovtsov SV, Berman DI, Golovanova EV, Peltek SE. Genetic diversity of the earthworm Eisenia nordenskioldi (Lumbricidae, Annelida). Vavilovskii Zhurnal Genet Selektsii 2017. [DOI: 10.18699/vj17.24-o] [Citation(s) in RCA: 7] [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: 11/19/2022] Open
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15
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Bryanskaya AV, Uvarova YE, Rozanov AS, Slynko NM, Shlyakhtun VN, Starostin KV, Demidov EA, Lazareva EV, Taran OP, Peltek SE. Collection of microorganisms of ICG SB RAS as a genetic resource for biotechnology. Vavilovskii Zhurnal Genet Selektsii 2017. [DOI: 10.18699/vj17.279] [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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16
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Shekhovtsov SV, Golovanova EV, Bazarova NE, Belova YN, Berman DI, Derzhinsky EA, Shashkov MP, Peltek SE. Genetic diversity of the Aporrectodea caliginosa complex in Russia. Vavilovskii Zhurnal Genet Selektsii 2017. [DOI: 10.18699/vj17.255] [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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17
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Rozanov AS, Shlyahtun VN, Tekutieva LA, Son OM, Sizova SV, Peltek SE. Methods of yeast genome editing. Vavilovskii Zhurnal Genet Selektsii 2017. [DOI: 10.18699/vj17.321] [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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18
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Samoylova YV, Piligaev AV, Sorokina KN, Rozanov AS, Peltek SE, Novikov AA, Almyasheva NR, Parmon VN. Application of the immobilized bacterial recombinant lipase from Geobacillus stearothermophilus G3 for the production of fatty acid methyl esters. Catal Ind 2016. [DOI: 10.1134/s2070050416020082] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [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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19
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Shekhovtsov SV, Bazarova NE, Berman DI, Bulakhova NA, Golovanova EV, Konyaev SV, Krugova TM, Lyubechanskii II, Peltek SE. DNA barcoding: how many earthworm species are there in the south of West Siberia? Vavilovskii Zhurnal Genet Selektsii 2016. [DOI: 10.18699/vj15.110] [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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20
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Peltek SE, Demidova EV, Popik VM, Goryachkovskaya TN. Escherichia coli stress response systems and their reaction to terahertz radiation. Vavilovskii Zhurnal Genet Selektsii 2016. [DOI: 10.18699/vj16.206] [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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21
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Goryachkovskaya TN, Konstantinova SH, Meshcheriakova IA, Bannikova SV, Demidov EA, Bryanskaya AV, Scheglov MA, Semenov AI, Oshchepkov DY, Popik VM, Peltek SE. The impact of terahertz radiation on an extremophilic archaean Halorubrum saccharovorum proteome. Vavilovskii Zhurnal Genet Selektsii 2016. [DOI: 10.18699/vj16.205] [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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22
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Shekhovtsov SV, Golovanova EV, Peltek SE. Different dispersal histories of lineages of the earthworm Aporrectodea caliginosa (Lumbricidae, Annelida) in the Palearctic. Biol Invasions 2015. [DOI: 10.1007/s10530-015-1045-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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23
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Krestina MS, Shevelev OB, Koptyug IV, Gerlinskaya LA, Peltek SE, Akulov AE. NMR metabolic profiling of the liver following administrationof alcohol andthemushroom Ganoderma lucidum in rats. Vavilovskii Zhurnal Genet Selektsii 2015. [DOI: 10.18699/vj15.067] [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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24
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Bryanskaya AV, Uvarova YE, Slynko NM, Demidov EA, Rozanov AS, Peltek SE. Theoretical and practical issues of hydrocarbon biological oxidation by microorganisms. ACTA ACUST UNITED AC 2015. [DOI: 10.1134/s2079059715040036] [Citation(s) in RCA: 3] [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: 11/23/2022]
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25
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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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26
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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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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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29
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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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30
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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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31
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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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32
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Peltek SE, Goryachkovskaya TN, Popik VM, Pindyurin VF, Eliseev VS, Gol’denberg BG, Shcheglov MA, Tikunova NV, Khlebodarova TM, Rubtsov NB, Kulipanov GN, Kolchanov NA. Microfluidics in biology and genosensor construction. ACTA ACUST UNITED AC 2008. [DOI: 10.1134/s1995078008090127] [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: 01/09/2023]
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33
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Peltek SE, Frumin LL, Chasovskikh VV. Nonlinear pulsed-field gel electrophoresis of polymeric DNA chains. DOKL BIOCHEM BIOPHYS 2006; 404:368-72. [PMID: 16392759 DOI: 10.1007/s10628-005-0116-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- S E Peltek
- Institute of Cytology and Genetics, Siberian Division, Russian Academy of Sciences, pr. Akademika Lavrent'eva 10, Novosibirsk, 630090 Russia
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34
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Peltek SE, Frumin LL, Chasovskikh VV. Rapid separation of large DNA fragments. DOKL BIOCHEM BIOPHYS 2005; 403:272-4. [PMID: 16229140 DOI: 10.1007/s10628-005-0090-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- S E Peltek
- Institute of Cytology and Genetics, Siberian Division, Russian Academy of Sciences, pr. Akademica Lavrent'eva 10, Novosibirsk, 630090 Russia
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35
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Petrov AK, Kozlov AS, Taraban MB, Goryachkovskaya TN, Malyshkin SB, Popik VM, Peltek SE. Soft Ablation of Biological Objects Caused by Free-Electron Laser Submillimeter Radiation. DOKL BIOCHEM BIOPHYS 2005; 404:357-9. [PMID: 16392756 DOI: 10.1007/s10628-005-0113-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- A K Petrov
- Institute of Chemical Kinetics of Combustion, Siberian Division, Russian Academy of Sciences, Novosibirsk, Russia
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36
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Goncharov NP, Bannikova SV, Peltek SE. Cultivar Identification of a Monosomic Common Wheat Series. RUSS J GENET+ 2003. [DOI: 10.1023/b:ruge.0000009165.87364.4d] [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]
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37
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Chasovskikh VV, Frumin LL, Peltek SE, Zilberstein GV. A model of the motion of a long DNA chain in a pulsed electric field. Phys Chem Chem Phys 2002. [DOI: 10.1039/b110042d] [Citation(s) in RCA: 2] [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: 11/21/2022]
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Abstract
A comparatively new procedure is described for the nonlinear electrophoresis of proteins. Movement and separation of complexes formed by proteins and ionic detergents is first experimentally demonstrated for SDS rainbow colored protein molecular weight markers (Amersham). This result was revealed by SDS-PAGE in an asymmetric zero average pulsed electric field with a peak amplitude of up to 300 V cm(-1) and a frequency of 100 Hz. The highest molecular weight fractions were found to have the highest nonlinear drift velocity. A two-dimensional map of distribution of the protein complexes developed using nonlinear electrophoresis followed by SDS gel electrophoresis in an orthogonal direction, reveals nonuniform distribution of the fractions. Nonlinear electrophoresis can be run without electrode chambers, since the buffer electrolyte is not used up in alternating electric fields. Thus, this new type of electrophoresis can have advantages in microfluidic systems and biochips. Also possible uses are discussed of nonlinear electrophoresis via nonlinear focusing of protein-detergent complexes for further improvement of the SDS-PAGE technique for the separation and examination of these large hydrophobic complexes.
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Affiliation(s)
- S E Peltek
- Proteologics (Israel) Ltd, Weizmann Science Park, Rehovot
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Frumin LL, Peltek SE, Zilberstein GV. Nonlinear focusing of DNA macromolecules. Phys Rev E Stat Nonlin Soft Matter Phys 2001; 64:021902. [PMID: 11497615 DOI: 10.1103/physreve.64.021902] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2000] [Revised: 03/01/2001] [Indexed: 11/07/2022]
Abstract
The present paper reports the nonlinear electrophoretic focusing techniques developed after an original idea by Chacron and Slater [Phys. Rev. E 56, 3436 (1997)]. Focusing of DNA molecules is achieved in an alternating nonuniform electric field, created in a wedge gel with hyperbolic boundaries. The fractions separated on such a wedge retained their rectilinear shape during the electrophoresis. Experiments with gel electrophoresis confirm the possibility of a noticeable nonlinear focusing of DNA molecules.
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Affiliation(s)
- L L Frumin
- Proteologics (Israel) Ltd., Weizmann Science Park, Building Lev HaPark, 5 Oppenheimer Street, Rehovot, 76701, Israel
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40
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Frumin LL, Peltek SE, Zilberstein GV. Rapid separation of large DNA fragments. Anal Biochem 2001; 293:288-91. [PMID: 11399045 DOI: 10.1006/abio.2001.5123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- L L Frumin
- Proteologics (Israel) Ltd., Weizmann Science Park, 5 Oppenhaimer Street, Rehovot, 76701, Israel
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41
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Abstract
Effects of nonlinear dependence drift velocity of (double-stranded) DNA vs. electric field strength were investigated. In comparatively weak fields, the molecular drift velocity is proportional to the external electric field, while in strong fields there is additional nonlinear component. This effect offers possibilities to manipulate the total drift velocity at will-the macromolecules of different size can be made to move in opposite directions in pulsed field gel electrophoresis.A new approach for focusing DNA molecules based on nonlinear electrophoresis and geometric trapping in electric fields is proposed. The focusing is carried out in an alternating nonuniform electric field, created by using a wedge gel with hyperbolic boundaries. It is shown that the fractions separated in such wedge retain their rectilinear shape. Gel electrophoresis experiments supported the possibility of a pronounced nonlinear focusing of DNA molecules. This nonlinear separation technique presents encouraging prospects for micromanipulating systems and also for preparative isolation of long DNA fragments and development of new separation methods for bacterial fingerprinting.
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Affiliation(s)
- L L Frumin
- Proteologics (Israel) Ltd., Weizmann Science Park, Bld. Lev HaPark, Str. Oppenhaimer 5, 76701, Rehovot, Israel
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42
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Abstract
A new approach to focusing DNA molecules in a nonuniform electric field based on nonlinear mobility (L. L. Frumin, S. E. Peltek, S. Bukshpan, V. V. Chasovskikh and G. V. Zilberstein, PhysChemComm, 2000, 11) is proposed. The focusing is carried out in an alternating nonuniform electric field, created by using a wedge gel with hyperbolic boundaries. Methods of the theory of analytical functions were used to demonstrate that the fractions separated electrophoretically in such a wedge retain their rectilinear shape. Solutions for the focusing points for the case of mere velocity cubic nonlinearity were obtained as well as for the square velocity nonlinearity, suggested in a number of modern approaches. Gel electrophoresis experiments supported the possibility of a pronounced nonlinear focusing of DNA molecules. This nonlinear separation technique presents encouraging prospects for preparative isolation of long DNA fragments and development of new separation methods for bacterial fingerprinting.
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Affiliation(s)
- L L Frumin
- Proteologics (Israel) Ltd, Weizmann Science Park, 5 Oppenhaimer St., Rohovot 76701, Israel
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43
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Abstract
The focusing problem under isoelectric focusing has been solved analytically precisely. The solutions determine the law of the fraction moving and narrowing in the instant electric field gradient. This is especially actually because of developing the calculation methods in electrophoretical experiment.
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Affiliation(s)
- L L Frumin
- Proteologics (Israel) Ltd, 4 Pekeris Street, 76702, Rehovot, Israel.
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