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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Dubovtseva I. Y., Aksenenko M. B., Nikolaeva E. D., Averchuk A. S., Moshev A. V., Savchenko A. A., Markova S. V., Ruksha T. G.
Заглавие : FOXC1-Mediated Effects of miR-204-5p on Melanoma Cell Proliferation
Место публикации : Mol Biol (Mosk): NLM (Medline), 2021. - Vol. 55, Is. 4. - С. 667-675. - ISSN 00268984 (ISSN), DOI 10.31857/S0026898421030058
Аннотация: MicroRNAs epigenetically regulate physiological and pathological processes. Previously, we found that miR-204-5p is expressed at low levels in melanoma cells, and an increase in its level leads to a change in proliferation, migration, and invasion of these cancer cells. Now, using bioinformatics analysis, it has been shown that the target of miR-204-5p is FOXC1 transcription factor, which is implicated in carcinogenesis. Using the luciferase reporter assay, it was found that miR-204-5p suppresses expression of the FOXC1 gene by binding to its 3' non-coding region. Transfection of small interfering RNA (siRNA) targeting FOXC1 into melanoma cells caused a decrease in miR-204-5p levels, which is consistent with the generally accepted concept of feedback regulation of miRNA expression by target genes. According to the results of the MTT test and fluorescence microscopy, the proliferation level of melanoma cells under the influence of siRNA to FOXC1 decreased 72 h after transfection. Changes in the ratio of cells by cell cycle phase were analyzed using flow cytometry. Regulatory relationships between FOXC1 and miR-204-5p, and an inhibitory effect of FOXC1 knockdown on melanoma cell proliferation were revealed. Based on the results, it can be assumed that miR-204-5p regulates proliferation of melanoma cells by affecting FOXC1 expression.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Wu Y. -T., Chiang P. -W., Tandon K., Rogozin D. Y., Degermendzhy A. G., Tang S. -L.
Заглавие : Single-cell genomics-based analysis reveals a vital ecological role of thiocapsa sp. LSW in the meromictic Lake Shunet, Siberia
Место публикации : Microb. Genomics: Microbiology Society, 2021. - Vol. 7, Is. 12. - Ст.000712. - ISSN 20575858 (ISSN), DOI 10.1099/mgen.0.000712
Аннотация: Meromictic lakes usually harbour certain prevailing anoxygenic phototrophic bacteria in their anoxic zone, such as the purple sulfur bacterium (PSB) Thiocapsa sp. LSW (hereafter LSW) in Lake Shunet, Siberia. PSBs have been suggested to play a vital role in carbon, nitrogen and sulfur cycling at the oxic–anoxic interface of stratified lakes; however, the ecological significance of PSBs in the lake remains poorly understood. In this study, we explored the potential ecological role of LSW using a deep-sequencing analysis of single-cell genomics associated with flow cytometry. An approximately 2.7 Mb draft genome was obtained based on the co-assembly of five single-cell genomes. LSW might grow photolithoautotrophically and could play putative roles not only as a carbon fixer and diazotroph, but also as a sulfate reducer/oxidizer in the lake. This study provides insights into the potential ecological role of Thiocapsa sp. in meromictic lakes. © 2021 The Authors.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Dubovtseva, I. Yu, Aksenenko M. B., Nikolaeva E. D., Averchuk A. S., Moshev, A., V, Savchenko A. A., Markova, S., V, Ruksha T. G.
Заглавие : FOXC1-Mediated Effects of miR-204-5p on Melanoma Cell Proliferation
Колич.характеристики :8 с
Место публикации : Mol. Biol.: PLEIADES PUBLISHING INC, 2021. - Vol. 55, Is. 4. - С. 610-617. - ISSN 0026-8933, DOI 10.1134/S0026893321020199. - ISSN 1608-3245(eISSN)
Примечания : Cited References:24
Предметные рубрики: FOXC1
Аннотация: MicroRNAs epigenetically regulate physiological and pathological processes. Previously, we found that miR-204-5p is expressed at low levels in melanoma cells, and an increase in its level leads to a change in proliferation, migration, and invasion of these cancer cells. Now, using bioinformatics analysis, it has been shown that the target of miR-204-5p is FOXC1 transcription factor, which is implicated in carcinogenesis. Using the luciferase reporter assay, it was found that miR-204-5p suppresses expression of the FOXC1 gene by binding to its 3' non-coding region. Transfection of small interfering RNA (siRNA) targeting FOXC1 into melanoma cells caused a decrease in miR-204-5p levels, which is consistent with the generally accepted concept of feedback regulation of miRNA expression by target genes. According to the results of the MTT test and fluorescence microscopy, the proliferation level of melanoma cells under the influence of siRNA to FOXC1 decreased 72 h after transfection. Changes in the ratio of cells by cell cycle phase were analyzed using flow cytometry. Regulatory relationships between FOXC1 and miR-204-5p, and an inhibitory effect of FOXC1 knockdown on melanoma cell proliferation were revealed. Based on the results, it can be assumed that miR-204-5p regulates proliferation of melanoma cells by affecting FOXC1 expression.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Prudnikova S. V., Evgrafova S. Y., Volova T. G.
Заглавие : Metabolic activity of cryogenic soils in the subarctic zone of Siberia towards “green” bioplastics
Место публикации : Chemosphere: Elsevier Ltd, 2021. - Vol. 263. - Ст.128180. - ISSN 00456535 (ISSN), DOI 10.1016/j.chemosphere.2020.128180
Аннотация: The present study investigates, for the first time, the structure of the microbial community of cryogenic soils in the subarctic region of Siberia and the ability of the soil microbial community to metabolize degradable microbial bioplastic – poly-3-hydroxybutyrate [P(3HB)]. When the soil thawed, with the soil temperature between 5-7 and 9–11 °C, the total biomass of microorganisms at a 10-20-cm depth was 226–234 mg g?1 soil and CO2 production was 20–46 mg g?1 day?1. The total abundance of microscopic fungi varied between (7.4 ± 2.3) ? 103 and (18.3 ± 2.2) ? 103 CFU/g soil depending on temperature; the abundance of bacteria was several orders of magnitude greater: (1.6 ± 0.1) ? 106 CFU g?1 soil. The microbial community in the biofilm formed on the surface of P(3HB) films differed from the background soil in concentrations and composition of microorganisms. The activity of microorganisms caused changes in the surface microstructure of polymer films, a decrease in molecular weight, and an increase in the degree of crystallinity of P(3HB), indicating polymer biodegradation due to metabolic activity of microorganisms. The clear-zone technique – plating of isolates on the mineral agar with polymer as sole carbon source – was used to identify P(3HB)-degrading microorganisms inhabiting cryogenic soil in Evenkia. Analysis of nucleotide sequences of rRNA genes was performed to identify the following P(3HB)-degrading species: Bacillus pumilus, Paraburkholderia sp., Pseudomonas sp., Rhodococcus sp., Stenotrophomonas rhizophila, Streptomyces prunicolor, and Variovorax paradoxus bacteria and the Penicillium thomii, P. arenicola, P. lanosum, Aspergillus fumigatus, and A. niger fungi. © 2020 Elsevier Ltd
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Rogozin D. Y., Bulkhin A. O., Zykov V. V., Ivanova E. A., Darin, A., V, Kalugin I. A., Baturina O. A., Kabilov M. R.
Заглавие : Long-Chain Alkenones in Saline Meromictic Lakes of the North Minusinsk Depression (Southern Siberia): First Knowledge and Possible Correlation with Water-Level Dynamics
Колич.характеристики :13 с
Коллективы : Russian Foundation for Basic ResearchRussian Foundation for Basic Research (RFBR) [19-05-00428, 18-45-243002 r_mol_a]; Government of Krasnoyarsk Krai [18-45-243002 r_mol_a]; Krasnoyarsk Krai Foundation of Science [18-45-243002 r_mol_a]
Место публикации : Contemp. Probl. Ecol.: MAIK NAUKA/INTERPERIODICA/SPRINGER, 2020. - Vol. 13, Is. 6. - С. 643-655. - ISSN 1995-4255, DOI 10.1134/S199542552006013X. - ISSN 1995-4263(eISSN)
Примечания : Cited References:37. - This work was supported by the Russian Foundation for Basic Research (project no. 19-05-00428) and was jointly funded by the Russian Foundation for Basic Research, Government of Krasnoyarsk Krai and Krasnoyarsk Krai Foundation of Science under the scientific project "Bottom Sediments of Lake Uchum (Krasnoyarsk Krai) as a Source of Information for the Paleoclimate and Prediction of Healing Properties of a Water Body," project no. 18-45-243002 r_mol_a.
Предметные рубрики: TEMPERATURE
SHIRA
PALEOTEMPERATURE
CALIBRATION
SEDIMENTS
ATLANTIC
Аннотация: Long-chain alkenones (LCAs)-lipides produced by some microalgae of the Haptophyta group in seas and continental water bodies-are promising paleomarkers of climate changes because they are well-preserved in bottom sediments. The hydrocarbon chain and the degree of unsaturation of double bonds of this class of lipides can vary depending on habitat conditions of their producers. For the first time, we have discovered LCAs in the bottom sediments of two saline meromictic lakes Shira and Uchum located in arid steppes of southern Siberia (the North Minusinsk Depression) and estimated the distribution of their total content, length, and the degree of unsaturation. The highly abundant population of producers of LCAs-haptophyte algae of the genus Isochrysis (Haptophyta)-is revealed in the water column of Lake Uchum. It is shown that the species composition of the haptophyte algae and composition of the LCAs in the lakes under study are similar to those in saline stratified lakes of North America (Saskatchewan, Canada) with a similar climate and salt composition. The abundance of the C37:4 alkenone in the bottom sediments in the last 100 years reflected the variations in lake salinity caused by the documented changes in the water level. In this way, it is shown that the LCAs may be used as a paleomarker of climate-driven changes in the water level of the saline lakes in southern Siberia.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Rogozin D. Y., Bulkhin A. O., Zykov V. V., Ivanova E. A., Darin A. V., Kalugin I. A., Baturina O. A., Kabilov M. R.
Заглавие : Long-Chain Alkenones in Saline Meromictic Lakes of the North Minusinsk Depression (Southern Siberia): First Knowledge and Possible Correlation with Water-Level Dynamics
Место публикации : Contemp. Probl. Ecol.: Pleiades journals, 2020. - Vol. 13, Is. 6. - С. 643-655. - ISSN 19954255 (ISSN), DOI 10.1134/S199542552006013X
Аннотация: Abstract: Long-chain alkenones (LCAs)—lipides produced by some microalgae of the Haptophyta group in seas and continental water bodies—are promising paleomarkers of climate changes because they are well-preserved in bottom sediments. The hydrocarbon chain and the degree of unsaturation of double bonds of this class of lipides can vary depending on habitat conditions of their producers. For the first time, we have discovered LCAs in the bottom sediments of two saline meromictic lakes Shira and Uchum located in arid steppes of southern Siberia (the North Minusinsk Depression) and estimated the distribution of their total content, length, and the degree of unsaturation. The highly abundant population of producers of LCAs—haptophyte algae of the genus Isochrysis (Haptophyta)—is revealed in the water column of Lake Uchum. It is shown that the species composition of the haptophyte algae and composition of the LCAs in the lakes under study are similar to those in saline stratified lakes of North America (Saskatchewan, Canada) with a similar climate and salt composition. The abundance of the С37:4 alkenone in the bottom sediments in the last 100 years reflected the variations in lake salinity caused by the documented changes in the water level. In this way, it is shown that the LCAs may be used as a paleomarker of climate-driven changes in the water level of the saline lakes in southern Siberia. © 2020, Pleiades Publishing, Ltd.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Krasitskaya V. V., Bashmakova E. E., Kudryavtsev A. N., Vorobjeva M. A., Shatunova E. A., Frank L. A.
Заглавие : The Hybrid Protein ZZ-OL as an Analytical Tool for Biotechnology Research
Колич.характеристики :7 с
Коллективы : Russian FederationRussian Federation [MK-772.2020.4]; Russian Science FoundationRussian Science Foundation (RSF) [16-14-10296]
Место публикации : Russ. J. Bioorg. Chem.: MAIK NAUKA/INTERPERIODICA/SPRINGER, 2020. - Vol. 46, Is. 6. - С. 1004-1010. - ISSN 1068-1620, DOI 10.1134/S106816202006014X. - ISSN 1608-330X(eISSN)
Примечания : Cited References:14. - The study was partially supported by a grant of the President of the Russian Federation for Young Scientists, the Candidates of Sciences (project MK-772.2020.4 in the part involving the synthesis and analysis of variants of proteins with melanoma-inhibiting activity) and a grant of the Russian Science Foundation (project no. 16-14-10296 in the part involving the bioluminescence analysis of binding of DNA aptamers to targets).
Аннотация: The gene of the hybrid protein that encodes the double synthetic fragment proZZ of the immunoglobulin-binding domain of protein A of Staphylococcus aureus and apo-obelin joined by a short linker has been cloned. The corresponding hybrid protein has been obtained by expression in Escherichia coli cells. The protein activated with a substrate (coelenterazine) possesses the bioluminescent Ca2+-dependent activity of the photoprotein close to that of recombinant wild-type obelin, and the immunoglobulin-binding ability of protein A. It has been shown that the hybrid can be used as a highly sensitive label to detect antibodies and estimate their affinity and interaction with recombinant proteins, as well as in investigations of other kinds.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Mitiouchkina, Tatiana, Mishin, Alexander S., Somermeyer, Louisa Gonzalez, Markina, Nadezhda M., Chepurnyh, Tatiana, V, Guglya, Elena B., Karataeva, Tatiana A., Palkina, Kseniia A., Shakhova, Ekaterina S., Fakhranurova, Liliia, I, Chekova, Sofia, V, Tsarkova, Aleksandra S., Golubev, Yaroslav, V, Negrebetsky, Vadim V., Dolgushin, Sergey A., Shalaev, Pavel, V, Shlykov, Dmitry, Melnik, Olesya A., Shipunova, Victoria O., Deyev, Sergey M., Bubyrev, Andrey, I, Pushin, Alexander S., Choob, Vladimir V., Dolgov, Sergey, V, Kondrashov, Fyodor A., Yampolsky, Ilia, V, Sarkisyan, Karen S.
Заглавие : Plants with genetically encoded autoluminescence
Колич.характеристики :7 с
Коллективы : Planta LLC; Skolkovo Innovation Centre; MRC London Institute of Medical Sciences [UKRI MC-A658-5QEA0]; Imperial College Research Fellowship; Institute of Bioorganic Chemistry of the Russian Academy of Sciences.ore Facility (CKP IBCH - Russian Ministry of Education and Science Grant) [RFMEFI62117X0018]; ERC grant [771209-CharFL]; European Union's Horizon 2020 Research and Innovation Programme under Marie Sklodowska-Curie Grant [665385]; Russian Science Foundation grantRussian Science Foundation (RSF) [19-74-10102, 17-14-01169p, 16-14-00052p]; Ministry of Science and Higher Education of the Russian Federation [075-15-2019-1789]; [075-15-2019-411]
Место публикации : Nat. Biotechnol.: NATURE PUBLISHING GROUP, 2020. - Article in press. - ISSN 1087-0156, DOI 10.1038/s41587-020-0500-9. - ISSN 1546-1696(eISSN)
Примечания : Cited References:17. - This study was designed, performed and funded by Planta LLC. We thank K. Wood for assisting in manuscript development. Planta acknowledges support from the Skolkovo Innovation Centre. We thank D. Bolotin and the Milaboratory (milaboratory. com) for access to computing and storage infrastructure. We thank S. Shakhov for providing photography equipment. The Synthetic Biology Group is funded by the MRC London Institute of Medical Sciences (UKRI MC-A658-5QEA0, K.S.S.). K.S.S. is supported by an Imperial College Research Fellowship. Experiments were partially carried out using equipment provided by the Institute of Bioorganic Chemistry of the Russian Academy of Sciences.ore Facility (CKP IBCH; supported by the Russian Ministry of Education and Science Grant RFMEFI62117X0018). The F.A.K. lab is supported by ERC grant agreement 771209-CharFL. This project received funding from the European Union's Horizon 2020 Research and Innovation Programme under Marie Sklodowska-Curie Grant Agreement 665385. K.S.S. acknowledges support by President's Grant 075-15-2019-411. Design and assembly of some of the plasmids was supported by Russian Science Foundation grant 19-74-10102. Imaging experiments were partially supported by Russian Science Foundation grant 17-14-01169p. LC-MS/MS analyses of extracts were supported by Russian Science Foundation grant 16-14-00052p. Design and assembly of plasmids was partially supported by grant 075-15-2019-1789 from the Ministry of Science and Higher Education of the Russian Federation allocated to the Center for Precision Genome Editing and Genetic Technologies for Biomedicine.
Предметные рубрики: METABOLISM
LIBRARY
Аннотация: Autoluminescent plants engineered to express a bacterial bioluminescence gene cluster in plastids have not been widely adopted because of low light output. We engineered tobacco plants with a fungal bioluminescence system that converts caffeic acid (present in all plants) into luciferin and report self-sustained luminescence that is visible to the naked eye. Our findings could underpin development of a suite of imaging tools for plants.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Bashmakova E. E., Kudryavtsev A. N., Frank L. A.
Заглавие : Development of the method to produce functionally active recombinant streptavidin in escherichia coli cells
Место публикации : J. Sib. Fed. Univ. - Biol.: Siberian Federal University, 2020. - Vol. 13, Is. 2. - С. 218-229. - ISSN 19971389 (ISSN), DOI 10.17516/1997-1389-0324
Аннотация: Streptavidin is a homotetrameric protein produced by Streptomyces avidinii, each subunit of which binds biotin (vitamin H), forming a stable complex (Kd = 10-15 M). Streptavidin-biotin coreaction is widely used in analytical systems, for targeted delivery of compounds, for affinity purification, etc. The aim of this study was to develop a rational technique to produce functionally active recombinant streptavidin. Recombinant Escherichia coli strains producing minimal core and full-sized streptavidin variants were obtained. The E. coli BL21 Codon Plus (DE3) RIPL, as host cells, and the pET19b plasmid carrying gene of minimally-sized core (miniSAV) or full-sized (SAV) streptavidin were used. Synthesis of miniSAV results in its localization as insoluble inclusion bodies. Denatured miniSAV yield was 130 mg per liter of E. coli c ulture. T he r enaturation g ives o nly 10- 15 % of the functionally active protein. Full-sized streptavidin localizes in the cytoplasm in a soluble state, but its toxicity causes low yield of the protein (10-13 mg per liter of the culture). The induction of SAV synthesis at the end of the logarithmic stage of cell growth was found to increase the yield of SAV approximately 2-fold. The yield of functionally active protein was 30 mg per liter culture. SAV was produced practically in individual state after affine chromatography on 2-iminobiotin agarose. One molecule of full-sized streptavidin bound 3.9 biotin molecules as was shown by colorimetric analysis using HABA (4-hydroxyazobenzene-2-carboxylic acid). Both streptavidins form sandwichtype complexes with biotinylated molecules in solid-phase microassay conditions. E. coli BL21 Codon Plus (DE3) RIPL/pET19bSAV strain was stable during storage with 20 % glycerol at -70 °C, which was shown by repeated two-year reseeding. The streptavidin producing strain (E. coli BL21 Codon Plus (DE3) RIPL/pET19bSAV) is deposited in the Collection for extremophile microorganisms and type cultures (Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk), No. 3505. The method for producing functionally active recombinant streptavidin developed in this study ensures its availability for biotechnological research. © Siberian Federal University. All rights reserved.
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10.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Volova, Tatiana, Sapozhnikova, Kristina, Zhila, Natalia
Заглавие : Cupriavidus necator B-10646 growth and polyhydroxyalkanoates production on different plant oils
Колич.характеристики :10 с
Коллективы : Project "Agropreparations of the new generation: a strategy of construction and realization" [074-02-2018-328]; Government of the Russian Federation; State assignment of the Ministry of Science and Higher Education of the Russian Federation [FSRZ-2020-0006]
Место публикации : Int. J. Biol. Macromol.: ELSEVIER, 2020. - Vol. 164. - С. 121-130. - ISSN 0141-8130, DOI 10.1016/j.ijbiomac.2020.07.095. - ISSN 1879-0003(eISSN)
Примечания : Cited References:52. - This studywas financially supported by Project "Agropreparations of the new generation: a strategy of construction and realization" (Agreement No 074-02-2018-328) in accordance with Resolution No 220 of the Government of the Russian Federation of April 9, 2010, "On measures designed to attract leading scientists to the Russian institutions of higher learning" (polymer synthesis fromplant oils), and by the State assignment of the Ministry of Science and Higher Education of the Russian Federation No. FSRZ-2020-0006 (polymer properties).
Предметные рубрики: FATTY-ACID-COMPOSITION
PHA SYNTHASE GENE
PALM KERNEL OIL
Аннотация: The study addresses the growth of the wild-type strain Cupriavidus necator B-10646 and synthesis of polyhydroxyalkanoates by this strain on media containing plant oils with different compositions of fatty acids: palm, Siberian oilseed, and refined and unrefined sunflower seed oils. The study showed that the best carbon substrate was palm oil. Comparison of fatty acid compositions of the starting oils and unutilized residual substrates showed that C. necator B-10646 cells consumed the fatty acids from palm oil evenly while in experiments with other oils, they utilized polyenoic fatty acids first. Higher production parameters of the culture were obtained by preparation of emulsified oil medium using Tween 80 and sodium cocoyl glutamate as emulsifiers. All polyhydroxyalkanoate specimens were terpolymers that contained 3-hydroxybutyrate as the major component and minor amounts of 3-hydroxyvalerate (0.9-1.9 mol%) and 3-hydroxyhexanoate (0.5-1.1 mol%). Molecular weight of polyhydroxyalkanoate specimens depended on the type of plant oil and emulsifier. (C) 2020 Elsevier B.V. All rights reserved.
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11.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Larionova M. D., Markova S. V., Tikunova N. V., Vysotski E. S.
Заглавие : The smallest isoform of Metridia longa luciferase as a fusion partner for hybrid proteins
Место публикации : Int. J. Mol. Sci.: MDPI AG, 2020. - Vol. 21, Is. 14. - Ст.4971. - С. 1-16. - ISSN 16616596 (ISSN), DOI 10.3390/ijms21144971
Аннотация: Bioluminescent proteins are widely used as reporter molecules in various in vitro and in vivo assays. The smallest isoform of Metridia luciferase (MLuc7) is a highly active, naturally secreted enzyme which, along with other luciferase isoforms, is responsible for the bright bioluminescence of marine copepod Metridia longa. In this study, we report the construction of two variants of a hybrid protein consisting of MLuc7 and 14D5a single-chain antibody to the surface glycoprotein E of tick-borne encephalitis virus as a model fusion partner. We demonstrate that, whereas fusion of a single-chain antibody to either N-or C-terminus of MLuc7 does not affect its bioluminescence properties, the binding site on the single-chain antibody influences its binding capacity. The affinity of 14D5a-MLuc7 hybrid protein (KD = 36.2 nM) where the C-terminus of the single-chain antibody was fused to the N-terminus of MLuc7, appeared to be 2.5-fold higher than that of the reverse, MLuc7-14D5a (KD = 87.6 nM). The detection limit of 14D5a-MLuc7 hybrid protein was estimated to be 45 pg of the recombinant glycoprotein E. Although the smallest isoform of M. longa luciferase was tested as a fusion partner only with a single-chain antibody, it is reasonable to suppose that MLuc7 can also be successfully used as a partner for genetic fusion with other proteins. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.
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12.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Artamonova V. S., Afanasyev S. A., Bardukov N. V., Golod V. M., Kokodiy S. V., Koulish A. V., Pashkov A. N., Pipoyan S. K., Reshetnikov S. I., Makhrov A. A.
Заглавие : The Center of Origin and Colonization Routes of Noble Salmons of the Genus Salmo (Salmonidae, Actinopterigii)
Место публикации : Doklad. Biochem. Biophys.: Pleiades Publishing, 2020. - Vol. 493, Is. 1. - С. 171-177. - ISSN 16076729 (ISSN), DOI 10.1134/S160767292004002X
Аннотация: Abstract: Genetic diversity and colonization routes of noble salmons were studied using a partial nucleotide sequence of the mitochondrial COI gene. The brown trout S. trutta, which is the most ancient species of the genus, was concluded to originate from the modern southeastern Pontic-Caspian area, which is currently inhabited by members of the subspecies S. trutta oxianus. Migrating westward while the Paratethys was in existence (5–34 million years ago), species of the genus colonized ancient water bodies in the modern Mediterranean basin and formed many isolated populations that survived desiccation of the Mediterranean Sea (5–6 million years ago). The Strait of Gibraltar mediated brown trout migrations to Northern Europe; the subspecies S. trutta trutta belongs to a relatively young phylogenetic lineage of the species. A separate brown trout lineage, currently classified as the subspecies S. trutta labrax, formed most likely in the area of the modern Danube basin, which was a relatively separate part of the Paratethys and was sometimes isolated as the Pannonian Lake. A highly divergent phylogenetic lineage of Atlantic salmon (S. salar) haplotypes originates from a haplotype of the brown trout that inhabited the area of the modern Strait of Gibraltar. © 2020, Pleiades Publishing, Ltd.
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13.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Chang, Dao, Liu, Yangkun, Chen, Yangyang, Hu, Xiaomin, Burov, Andrey, Puzyr, Alexey, Bondar, Vladimir, Yao, Lunguang
Заглавие : Study of the immunogenicity of the VP2 protein of canine parvovirus produced using an improved Baculovirus expression system
Колич.характеристики :9 с
Коллективы : National Natural Science Foundation of ChinaNational Natural Science Foundation of China [31870917]; program for Innovative Research Team of Science and Technology in University of Henan Province [20IRTSTHN024]; Key Scientific Research Projects of Colleges and Universities in Henan Province of China [18B230008]
Место публикации : BMC Vet. Res.: BMC, 2020. - Vol. 16, Is. 1. - Ст.202. - ISSN 1746-6148(eISSN), DOI 10.1186/s12917-020-02422-3
Примечания : Cited References:30. - This work was financially supported by the National Natural Science Foundation of China (No. 31870917), The program for Innovative Research Team of Science and Technology in University of Henan Province (No. 20IRTSTHN024) and Key Scientific Research Projects of Colleges and Universities in Henan Province of China (No. 18B230008). The funding bodies played no role in the design of the study, the collection, analysis, and interpretation of data and in writing the manuscript.
Предметные рубрики: VIRUS-LIKE PARTICLES
ESCHERICHIA-COLI
GENETIC-ANALYSIS
CPV-VP2
Аннотация: Background Canine parvovirus (CPV) is now recognized as a serious threat to the dog breeding industry worldwide. Currently used CPV vaccines all have their specific drawbacks, prompting a search for alternative safe and effective vaccination strategies such as subunit vaccine. VP2 protein is the major antigen targeted for developing CPV subunit vaccine, however, its production in baculovirus expression system remains challenging due to the insufficient yield. Therefore, our study aims to increase the VP2 protein production by using an improved baculovirus expression system and to evaluate the immunogenicity of the purified VP2 protein in mice. Results The results showed that high-level expression of the full length VP2 protein was achieved using our modified baculovirus expression system. The recombinant virus carrying two copies of VP2 gene showed the highest expression level, with a productivity of 186 mg/L, which is about 1.4-1.6 fold that of the recombinant viruses carrying only one copy. The purified protein reacted with Mouse anti-His tag monoclonal antibody and Rabbit anti-VP2 polyclonal antibody. BALB/c mice were intramuscularly immunized with purified VP2 protein twice at 2 week intervals. After vaccination, VP2 protein could induce the mice produce high level of hemagglutination inhibition antibodies. Conclusions Full length CPV VP2 protein was expressed at high level and purified efficiently. Moreover, it stimulated mice to produce high level of antibodies with hemmaglutination inhibition properties. The VP2 protein expressed in this study could be used as a putative economic and efficient subunit vaccine against CPV infection.
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14.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Shen, Y.a., Chen, Sheng-Chung, Lai, Mei-Chin, Huang, Hsing-Hua, Chiu, Hsiu-Hui, Tang, Sen-Lin, Rogozin, Denis Yu, Degermendzhy, Andrey G.
Заглавие : Methanolobus halotolerans sp. nov., isolated from the saline Lake Tus in Siberia
Колич.характеристики :8 с
Коллективы : Ministry of Education, Taiwan, ROC under the ATU planMinistry of Education, Taiwan; thematic project funding of Taiwan-Russian Joint Project [NSC99-2923-B-001-001-MY3, NSC102-2923-B-001-004]; Ministry of Science and Technology, TaiwanMinistry of Science and Technology, Taiwan [MOST103/104/105/106/107-3113-M-005-001]; Russian Foundation for Basic ResearchRussian Foundation for Basic Research (RFBR) [14-04-01060-a]
Место публикации : Int. J. Syst. Evol. Microbiol.: MICROBIOLOGY SOC, 2020. - Vol. 70, Is. 10. - С. 5586-5593. - ISSN 1466-5026, DOI 10.1099/ijsem.0.004453. - ISSN 1466-5034(eISSN)
Примечания : Cited References:38. - This work was supported by grants from the Ministry of Education, Taiwan, ROC under the ATU plan (to M.C.L.), by the thematic project funding of Taiwan-Russian Joint Project (NSC99-2923-B-001-001-MY3 and NSC102-2923-B-001-004 to S.L.T.), by the Ministry of Science and Technology (MOST103/104/105/106/107-3113-M-005-001 to M.C.L.), Taiwan and the Russian Foundation for Basic Research, Grant No. 14-04-01060-a (to D.Y.R. and A.G.D.).
Предметные рубрики: TAIWANENSIS SP NOV.
METHYLOTROPHIC METHANOGEN
SEDIMENTS
ACCURATE
DNA
Аннотация: A halotolerant, psychrotolerant and methylotrophic methanogen, strain SY-01(T), was isolated from the saline Lake Tus in Siberia. Cells of strain SY-01(T) were non-motile, cocci and 0.8-1.0 mu m in diameter. The only methanogenic substrate utilized by strain SY-01(T) was methanol. The temperature range of growth for strain SY-01(T) was from 4 to 40 degrees C and the optimal temperature for growth was 30 degrees C. The pH range of growth was from pH 7.2 to 9.0, with optimal growth at pH 8.0. The NaCl range of growth was 0-1.55 M with optimal growth at 0.51 M NaCl. The G+C content of the genome of strain SY-01(T) was 43.6 mol% as determined by genome sequencing. Phylogenetic analysis revealed that strain SY-01(T) was most closely related to Methanolobus zinderi SD1(T) (97.3% 16S rRNA gene sequence similarity), and had 95.5-97.2 % similarities to other Methanolobus species with valid names. Genome relatedness between strain SY-01(T) and DSM 21339(T) was computed using average nucleotide identity and digital DNA-DNA-hybridization, which yielded values of 79.7 and 21.7 %, respectively. Based on morphological, phenotypic, phylogenetic and genomic relatedness data presented here, it is evident that strain SY-01(T) represents a novel species of the genus Methanolobus, and the name Methanolobus halotolerans sp. nov. is proposed. The type strain is SY-01(T) (=BCRC AR10051(T)=NBRC 113166(T)=DSM 107642(T)).
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15.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Chang D., Liu Y., Chen Y., Hu X., Burov A., Puzyr A., Bondar V., Yao L.
Заглавие : Study of the immunogenicity of the VP2 protein of canine parvovirus produced using an improved Baculovirus expression system
Место публикации : BMC Vet. Res.: BioMed Central Ltd., 2020. - Vol. 16, Is. 1. - Ст.202. - ISSN 17466148 (ISSN), DOI 10.1186/s12917-020-02422-3
Аннотация: Background: Canine parvovirus (CPV) is now recognized as a serious threat to the dog breeding industry worldwide. Currently used CPV vaccines all have their specific drawbacks, prompting a search for alternative safe and effective vaccination strategies such as subunit vaccine. VP2 protein is the major antigen targeted for developing CPV subunit vaccine, however, its production in baculovirus expression system remains challenging due to the insufficient yield. Therefore, our study aims to increase the VP2 protein production by using an improved baculovirus expression system and to evaluate the immunogenicity of the purified VP2 protein in mice. Results: The results showed that high-level expression of the full length VP2 protein was achieved using our modified baculovirus expression system. The recombinant virus carrying two copies of VP2 gene showed the highest expression level, with a productivity of 186 mg/L, which is about 1.4-1.6 fold that of the recombinant viruses carrying only one copy. The purified protein reacted with Mouse anti-His tag monoclonal antibody and Rabbit anti-VP2 polyclonal antibody. BALB/c mice were intramuscularly immunized with purified VP2 protein twice at 2 week intervals. After vaccination, VP2 protein could induce the mice produce high level of hemagglutination inhibition antibodies. Conclusions: Full length CPV VP2 protein was expressed at high level and purified efficiently. Moreover, it stimulated mice to produce high level of antibodies with hemmaglutination inhibition properties. The VP2 protein expressed in this study could be used as a putative economic and efficient subunit vaccine against CPV infection. © 2020 The Author(s).
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16.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Deeva, Anna A., Zykova, Evgenia A., Nemtseva, Elena V., Kratasyuk, Valentina A.
Заглавие : Functional divergence between evolutionary-related LuxG and Fre oxidoreductases of luminous bacteria
Колич.характеристики :7 с
Коллективы : Russian Foundation for Basic Research [18-44-243009]; Ministry of Education and Science of the Russian Federation [0356-2019-0019, 6.7734.2017]; Krasnoyarsk Region Science and Technology [18-44-243009]
Место публикации : Proteins: WILEY, 2019. - Vol. 87, Is. 9. - С. 723-729. - ISSN 0887-3585, DOI 10.1002/prot.25696. - ISSN 1097-0134(eISSN)
Примечания : Cited References:39. - The Russian Foundation for Basic Research and Krasnoyarsk Region Science and Technology Support Fund, Grant/Award Number: 18-44-243009; Ministry of Education and Science of the Russian Federation, Grant/Award Numbers: 0356-2019-0019, 6.7734.2017
Предметные рубрики: ESCHERICHIA-COLI
FLAVIN OXIDOREDUCTASE
CRYSTAL-STRUCTURE
Аннотация: In luminous bacteria NAD(P)H:flavin-oxidoreductases LuxG and Fre, there are homologous enzymes that could provide a luciferase with reduced flavin. Although Fre functions as a housekeeping enzyme, LuxG appears to be a source of reduced flavin for bioluminescence as it is transcribed together with luciferase. This study is aimed at providing the basic conception of Fre and LuxG evolution and revealing the peculiarities of the active site structure resulted from a functional variation within the oxidoreductase family. A phylogenetic analysis has demonstrated that Fre and LuxG oxidoreductases have evolved separately after the gene duplication event, and consequently, they have acquired changes in the conservation of functionally related sites. Namely, different evolutionary rates have been observed at the site responsible for specificity to flavin substrate (Arg 46). Also, Tyr 72 forming a part of a mobile loop involved in FAD binding has been found to be conserved among Fre in contrast to LuxG oxidoreductases. The conservation of different amino acid types in NAD(P)H binding site has been defined for Fre (arginine) and LuxG (proline) oxidoreductases.
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17.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Bashmakova E. E., Krasitskaya V. V., Bondar A. A., Eremina E. N., Slepov E. V., Zukov R. A., Frank L. A.
Заглавие : Bioluminescent SNP genotyping technique: Development and application for detection of melanocortin 1 receptor gene polymorphisms
Место публикации : Talanta: Elsevier B.V., 2018. - Vol. 189. - С. 111-115. - ISSN 00399140 (ISSN) , DOI 10.1016/j.talanta.2018.06.057
Ключевые слова (''Своб.индексиров.''): ca2+-regulated photoprotein obelin--genotyping--melanocortin 1 receptor gene--single nucleotide polymorphisms (snp)--bioluminescence--clinical research--curricula--diagnosis--genes--oncology--biomedical research--clinical characteristics--development and applications--genotyping--healthy individuals--photoproteins--receptor genes--single-nucleotide polymorphisms--dermatology
Аннотация: SNP genotyping based on the reaction of specific primer extension with the following bioluminescent detection of its products was shown to be potentially applicable for biomedical exploration. The paper describes its elaboration and first application in extensive biomedical research concerning MC1R gene variants’ frequency and associations with clinical characteristics in melanoma patients of Eastern Siberia (Krasnoyarsk region, Russia). Polymorphisms rs 1805007 (R151C), rs 1805008 (R160W), and rs 1805009 (D294H) were detected in 174 DNA samples from patients with histologically proved diagnosis of cutaneous melanoma and in 200 samples from healthy individuals. All the results on bioluminescent SNP genotyping were confirmed by Sanger sequencing. Some features characteristic of the population were found, i.e. melanoma is mostly associated with R160W or R151C while variant D294H is extremely rare; simultaneous carriage of any two investigated variants is also strongly associated with melanoma; R151C is associated with ulceration and consequently the disease course is more aggressive, etc. The design of the technique allows fast evaluation of any known diagnostically important SNP frequencies and associations across population. © 2018 Elsevier B.V.
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18.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Wu, Yu-Ting, Yang, Cheng-Yu, Chiang, Pei-Wen, Tseng, Ching-Hung, Chiu, Hsiu-Hui, Saeed, Isaam, Baatar, Bayanmunkh, Rogozin, Denis, Halgamuge, Saman, Degermendzhi, Andrei, Tang, Sen-Lin
Заглавие : Comprehensive Insights Into Composition, Metabolic Potentials, and Interactions Among Archaeal, Bacterial, and Viral Assemblages in Meromictic Lake Shunet in Siberia
Колич.характеристики :21 с
Коллективы : Ministry of Science and Technology in Taiwan [NSC 99-2923-B-001-001-MY3, NSC 102-2923-B-001-004]; Russian Foundation for Basic Research [16-05-00091-a]; Russian Federation [NSh-9249.2016.5]
Место публикации : Front. Microbiol.: FRONTIERS MEDIA SA, 2018. - Vol. 9. - Ст.1763. - ISSN 1664-302X, DOI 10.3389/fmicb.2018.01763
Примечания : Cited References:103. - This research was supported by the Ministry of Science and Technology in Taiwan through the Taiwan-Russia Joint Project Grant NSC 99-2923-B-001-001-MY3 and NSC 102-2923-B-001-004 and the Russian Foundation for Basic Research, Grant No. 16-05-00091-a. The research was partially supported by the Council on grants from the President of the Russian Federation for support of leading scientific schools (grant NSh-9249.2016.5).
Предметные рубрики: BACTERIOPLANKTON COMMUNITY COMPOSITION
RIBOSOMAL-RNA GENES
ANTARCTIC
Ключевые слова (''Своб.индексиров.''): lake shunet--metagenomics--archaeal--bacterial and viral assemblages--meromictic lake
Аннотация: Microorganisms are critical to maintaining stratified biogeochemical characteristics in meromictic lakes; however, their community composition and potential roles in nutrient cycling are not thoroughly described. Both metagenomics and metaviromics were used to determine the composition and capacity of archaea, bacteria, and viruses along the water column in the landlocked meromictic Lake Shunet in Siberia. Deep sequencing of 265 Gb and high-quality assembly revealed a near-complete genome corresponding to Nonlabens sp. sh3vir. in a viral sample and 38 bacterial bins (0.2-5.3 Mb each). The mixolimnion (3.0 m) had the most diverse archaeal, bacterial, and viral communities, followed by the monimolimnion (5.5 m) and chemocline (5.0 m). The bacterial and archaeal communities were dominated by Thiocapsa and Methanococcoides, respectively, whereas the viral community was dominated by Siphoviridae. The archaeal and bacterial assemblages and the associated energy metabolism were significantly related to the various depths, in accordance with the stratification of physicochemical parameters. Reconstructed elemental nutrient cycles of the three layers were interconnected, including co-occurrence of denitrification and nitrogen fixation in each layer and involved unique processes due to specific biogeochemical properties at the respective depths. According to the gene annotation, several pre-dominant yet unknown and uncultured bacteria also play potentially important roles in nutrient cycling. Reciprocal BLAST analysis revealed that the viruses were specific to the host archaea and bacteria in the mixolimnion. This study provides insights into the bacterial, archaeal, and viral assemblages and the corresponding capacity potentials in Lake Shunet, one of the three meromictic lakes in central Asia. Lake Shunet was determined to harbor specific and diverse viral, bacterial, and archaeal communities that intimately interacted, revealing patterns shaped by indigenous physicochemical parameters.
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19.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Artamonova V. S., Kolmakova O. V., Kirillova E. A., Makhrov A. A.
Заглавие : Phylogeny of Salmonoid Fishes (Salmonoidei) Based on mtDNA COI Gene Sequences (Barcoding)
Колич.характеристики :15 с
Коллективы : Russian Science Foundation [16-14-10001]
Место публикации : Contemp. Probl. Ecol.: MAIK NAUKA/INTERPERIODICA/SPRINGER, 2018. - Vol. 11, Is. 3. - С. 271-285. - ISSN 1995-4255, DOI 10.1134/S1995425518030022. - ISSN 1995-4263(eISSN)
Примечания : Cited References:102. - We are very grateful to colleagues who helped collect samples: E.G. Berestovskii, I.N. Bolotov, E.A. Borovikova, I.V. Vikhrev, L.A. Glushchenko, V.V. Ignatenko, D.P. Karabanov, A.P. Novoselov, V.M. Spitsyn, V.A. Shirokov, and I.L. Shchurov; employees of Trout Hatchery "Adler", the Federal Breeding and Genetic Center for Fish Culture, and Vygsky and Kemsky fish hatcheries; and residents of Barabash-Levada, Len-lu, and Chupa settlements. We also thank S.S. Alekseev for identifying sharp-snouted and blunt-snouted lenoks. This work was supported by the Russian Science Foundation, project no. 16-14-10001.
Предметные рубрики: MOLECULAR DATING ANALYSIS
GROWTH-HORMONE INTRONS
SALMONIFORMES
Ключевые слова (''Своб.индексиров.''): evolution--network--molecular clock--amino acid sequence--reproductive--isolation--immobilization--fishes
Аннотация: We have analyzed the partial sequences of the mitochondrial COI gene along with the amino acid sequences of cytochrome oxidase subunit I, encoded by this gene region, in representatives of 11 genera of salmonoid fish. For amino acid sequences, two alternative networks are constructed with outgroups represented by either Esocoidei or Osmeroidei as the supposed ancestral groups. This way, Osmeroidei appear to be closer to the salmonoid fish than Esocoidei, and their presence in the network as an outgroup explains the available data on the morphology and karyology of salmonoids much better. A number of the results of this study are fundamentally new. In particular, the slowing down of the molecular evolution of the grayling (Thymallidae) is shown. We conclude that the charr (Salvelinus) is one of the modern genera of salmonoids closest to their ancestor. The hypothesis of the phylogenetic proximity of the genera Brachymystax, Hucho, and Salmo has been confirmed. We also discuss the possibility that it is namely the changes in the amino acid sequence of cytochrome oxidase subunit I that lead to postzygotic reproductive isolation between taxa.
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20.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Grodnitskaya I. D., Trusova M. Y., Syrtsov S. N., Koroban N. V.
Заглавие : Structure of microbial communities of peat soils in two bogs in Siberian tundra and forest zones
Место публикации : Microbiology: Maik Nauka Publishing / Springer SBM, 2018. - Vol. 87, Is. 1. - С. 89-102. - ISSN 00262617 (ISSN) , DOI 10.1134/S0026261718010083
Ключевые слова (''Своб.индексиров.''): 16s rrna gene--bacterial diversity--ch4 and co2 emission--cryogenic conditions--methanogenesis--methanotrophy--microbial biomass and chemoorganotroph respiration--oligo-mesotrophic and polygonal bogs--permafrost--subarctic tundra
Аннотация: The structure and functional activity of microbial complexes of a forest oligo-mesotrophic subshrub- grass-moss bog (OMB, Central Evenkiya) and a subshrub-sedge bog in the polygonal tundra (PB, Lena River Delta Samoylovsky Island) was studied. Soil of the forest bog (OMB) differed from that of the polygonal tundra bog (PB) in higher productivity (Corg, Ntotal, P, and K reserves), higher biomass of aerobic chemoorganotrophs (2.0 to 2.6 times), and twice the level of available organic matter. The contribution of microorganisms to the carbon pool was different, with the share of Cmic in Corg 1.4 to 2.5 times higher in PB compared to OMB. Qualitative composition of the methane cycle microorganisms in PB and OMB soils differed significantly. Methanogenic archaea (Euryarchaeota) in the shrub-sedge PB of tundra were more numerous and diverse than in the oligo-mesotrophic bog (OMB) and belonged to six families (Methanomassiliicoccaceae, Methanoregulaceae, Methanobacteriaceae, Methanomicrobiaceaee, Methanosarcinaceae, and Methanotrichaceae), while members of only four families (Methanosarcinacea, Methanobacteriaceae, Methanotrichaceae, and Methanomassiliicoccaceae) were revealed in OMB. In both bogs, methane-oxidizing bacteria belonged to Alphaproteobacteria (II) and Gammaproteobacteria (I). Methanotroph diversity was higher in OMB than in PB. Microbial communities of PB soils had higher potential activity of methanogenesis and methanotrophy compared to those of OMB. Methanogenic and methanotrophic activities in PB were 20 and 2.3 times higher, respectively, than in OMB. © 2018, Pleiades Publishing, Ltd.
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