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Noskov YA, Manasypov RM, Ermolaeva NI, Antonets DV, Shirokova LS, Pokrovsky OS. Environmental factors controlling seasonal and spatial variability of zooplankton in thermokarst lakes along a permafrost gradient of Western Siberia. Sci Total Environ 2024; 922:171284. [PMID: 38432389 DOI: 10.1016/j.scitotenv.2024.171284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 02/23/2024] [Accepted: 02/24/2024] [Indexed: 03/05/2024]
Abstract
Humic thermokarst lakes of permafrost peatlands in Western Siberia Lowland (WSL) are major environmental controllers of carbon and nutrient storage in inland waters and greenhouse gases emissions to the atmosphere in the subarctic. In contrast to sizable former research devoted to hydrochemical and hydrobiological (phytoplankton) composition, zooplankton communities of these thermokarst lakes and thaw ponds remain poorly understood, especially along the latitudinal gradient, which is a perfect predictor of permafrost zones. To fill this gap, 69 thermokarst lakes of the WSL were sampled using unprecedented spatial coverage, from continuous to sporadic permafrost zone, in order to assess zooplankton (Cladocera, Copepoda, Rotifera) diversity and abundance across three main open water physiological seasons (spring, summer and autumn). We aimed at assessing the relationship of environmental factors (water column hydrochemistry, nutrients, and phytoplankton parameters) with the abundance and diversity of zooplankton. A total of 74 zooplankton species and taxa were detected, with an average eight taxa per lake/pond. Species richness increased towards the north and reached the maximum in the continuous permafrost zone with 13 species found in this zone only. In contrast, the number of species per waterbody decreased towards the north, which was mainly associated with a decrease in the number of cladocerans. Abundance and diversity of specific zooplankton groups strongly varied across the seasons and permafrost zones. Among the main environmental controllers, Redundancy Analysis revealed that water temperature, lake area, depth, pH, Dissolved Inorganic and Organic Carbon and CO2 concentrations were closely related to zooplankton abundance. Cladocerans were positively related to water temperature during all seasons. Copepods were positively related to depth and lake water pH in all seasons. Rotifers were related to different factors in each season, but were most strongly associated with DOC, depth, CH4, phytoplankton and cladoceran abundance. Under climate warming scenario, considering water temperature increase and permafrost boundary shift northward, one can expect an increase in the diversity and abundance of cladocerans towards the north which can lead to partial disappearance of copepods, especially rare calanoid species.
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Affiliation(s)
- Yury A Noskov
- Biological Institute, BIO-GEO-CLIM Laboratory, Tomsk State University, 36 Lenin av., 634050 Tomsk, Russia; Institute of Systematics and Ecology of Animals SB RAS, 11 Frunze str., 630091 Novosibirsk, Russia.
| | - Rinat M Manasypov
- Biological Institute, BIO-GEO-CLIM Laboratory, Tomsk State University, 36 Lenin av., 634050 Tomsk, Russia
| | - Nadezhda I Ermolaeva
- Institute for Water and Environmental Problems SB RAS, 1 Molodezhnaya str., 656038 Barnaul, Russia
| | - Denis V Antonets
- MSU Institute for Artificial Intelligence, Lomonosov Moscow State University, 119192 Moscow, Russia
| | - Liudmila S Shirokova
- Federal Center for Integrated Arctic Research, Institute of Ecological Problem of the North, 23 Nab. Severnoi Dviny, 163000 Arkhangelsk, Russia
| | - Oleg S Pokrovsky
- GET UMR 5563 CNRS University of Toulouse (France), 14 Avenue Edouard Belin, 31400 Toulouse, France.
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Kisakov DN, Antonets DV, Shaburova EV, Kisakova LA, Tigeeva EV, Yakovlev VA, Starostina EV, Borgoyakova MB, Protopopova EV, Svyatchenko VA, Loktev VB, Rudometov AP, Ilyichev AA, Nepomnyashchikh TS, Karpenko LI. DNA Vaccine Encoding the Artificial T-Cell Polyepitope Immunogen of Tick-Borne Encephalitis Virus. Bull Exp Biol Med 2023; 176:72-76. [PMID: 38091143 DOI: 10.1007/s10517-023-05970-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Indexed: 12/19/2023]
Abstract
A promising approach to the development of new means for preventing infection caused by tick-borne encephalitis virus can be DNA vaccines encoding polyepitope T-cell immunogens. A DNA vaccine pVAX-AG4-ub encoding an artificial polyepitope immunogen that includes cytotoxic and T-helper epitopes from the NS1, NS3, NS5, and E proteins of the tick-borne encephalitis virus has been obtained. The developed construct ensured the synthesis of the corresponding mRNAs in transfected eukaryotic cells. Immunization of mice with pVAX-AG4-ub induced the formation of a virus-specific T-cell response providing 50% protection from lethal infection with the virus.
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Affiliation(s)
- D N Kisakov
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia.
| | - D V Antonets
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - E V Shaburova
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - L A Kisakova
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - E V Tigeeva
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - V A Yakovlev
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - E V Starostina
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - M B Borgoyakova
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - E V Protopopova
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - V A Svyatchenko
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - V B Loktev
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - A P Rudometov
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - A A Ilyichev
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - T S Nepomnyashchikh
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - L I Karpenko
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
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Karpenko LI, Apartsin EK, Dudko SG, Starostina EV, Kaplina ON, Antonets DV, Volosnikova EA, Zaitsev BN, Bakulina AY, Venyaminova AG, Ilyichev AA, Bazhan SI. Cationic Polymers for the Delivery of the Ebola DNA Vaccine Encoding Artificial T-Cell Immunogen. Vaccines (Basel) 2020; 8:vaccines8040718. [PMID: 33271964 PMCID: PMC7760684 DOI: 10.3390/vaccines8040718] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/23/2020] [Accepted: 11/27/2020] [Indexed: 11/16/2022] Open
Abstract
Background: According to current data, an effective Ebola virus vaccine should induce both humoral and T-cell immunity. In this work, we focused our efforts on methods for delivering artificial T-cell immunogen in the form of a DNA vaccine, using generation 4 polyamidoamine dendrimers (PAMAM G4) and a polyglucin:spermidine conjugate (PG). Methods: Optimal conditions were selected for obtaining complexes of previously developed DNA vaccines with cationic polymers. The sizes, mobility and surface charge of the complexes with PG and PAMAM 4G have been determined. The immunogenicity of the obtained vaccine constructs was investigated in BALB/c mice. Results: It was shown that packaging of DNA vaccine constructs both in the PG envelope and the PAMAM 4G envelope results in an increase in their immunogenicity as compared with the group of mice immunized with the of vector plasmid pcDNA3.1 (a negative control). The highest T-cell responses were shown in mice immunized with complexes of DNA vaccines with PG and these responses significantly exceeded those in the groups of animals immunized with both the combination of naked DNAs and the combination DNAs coated with PAMAM 4G. In the group of animals immunized with complexes of the DNA vaccines with PAMAM 4G, no statistical differences were found in the ability to induce T-cell responses, as compared with the group of mice immunized with the combination of naked DNAs. Conclusions: The PG conjugate can be considered as a promising and safe means to deliver DNA-based vaccines. The use of PAMAM requires further optimization.
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Affiliation(s)
- Larisa I. Karpenko
- State Research Center of Virology and Biotechnology “Vector”, Koltsovo, 630559 Novosibirsk Region, Russia; (S.G.D.); (E.V.S.); (O.N.K.); (D.V.A.); (E.A.V.); (B.N.Z.); (A.Y.B.); (A.A.I.)
- Correspondence: (L.I.K.); (S.I.B.); Tel.: +7-383-363-47-00 (ext. 2001) (L.I.K. & S.I.B.)
| | - Evgeny K. Apartsin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.K.A.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Laboratoire de Chimie de Coordination, CNRS, 31077 Toulouse, France
| | - Sergei G. Dudko
- State Research Center of Virology and Biotechnology “Vector”, Koltsovo, 630559 Novosibirsk Region, Russia; (S.G.D.); (E.V.S.); (O.N.K.); (D.V.A.); (E.A.V.); (B.N.Z.); (A.Y.B.); (A.A.I.)
| | - Ekaterina V. Starostina
- State Research Center of Virology and Biotechnology “Vector”, Koltsovo, 630559 Novosibirsk Region, Russia; (S.G.D.); (E.V.S.); (O.N.K.); (D.V.A.); (E.A.V.); (B.N.Z.); (A.Y.B.); (A.A.I.)
| | - Olga N. Kaplina
- State Research Center of Virology and Biotechnology “Vector”, Koltsovo, 630559 Novosibirsk Region, Russia; (S.G.D.); (E.V.S.); (O.N.K.); (D.V.A.); (E.A.V.); (B.N.Z.); (A.Y.B.); (A.A.I.)
| | - Denis V. Antonets
- State Research Center of Virology and Biotechnology “Vector”, Koltsovo, 630559 Novosibirsk Region, Russia; (S.G.D.); (E.V.S.); (O.N.K.); (D.V.A.); (E.A.V.); (B.N.Z.); (A.Y.B.); (A.A.I.)
| | - Ekaterina A. Volosnikova
- State Research Center of Virology and Biotechnology “Vector”, Koltsovo, 630559 Novosibirsk Region, Russia; (S.G.D.); (E.V.S.); (O.N.K.); (D.V.A.); (E.A.V.); (B.N.Z.); (A.Y.B.); (A.A.I.)
| | - Boris N. Zaitsev
- State Research Center of Virology and Biotechnology “Vector”, Koltsovo, 630559 Novosibirsk Region, Russia; (S.G.D.); (E.V.S.); (O.N.K.); (D.V.A.); (E.A.V.); (B.N.Z.); (A.Y.B.); (A.A.I.)
| | - Anastasiya Yu. Bakulina
- State Research Center of Virology and Biotechnology “Vector”, Koltsovo, 630559 Novosibirsk Region, Russia; (S.G.D.); (E.V.S.); (O.N.K.); (D.V.A.); (E.A.V.); (B.N.Z.); (A.Y.B.); (A.A.I.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Aliya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.K.A.); (A.G.V.)
| | - Alexander A. Ilyichev
- State Research Center of Virology and Biotechnology “Vector”, Koltsovo, 630559 Novosibirsk Region, Russia; (S.G.D.); (E.V.S.); (O.N.K.); (D.V.A.); (E.A.V.); (B.N.Z.); (A.Y.B.); (A.A.I.)
| | - Sergei I. Bazhan
- State Research Center of Virology and Biotechnology “Vector”, Koltsovo, 630559 Novosibirsk Region, Russia; (S.G.D.); (E.V.S.); (O.N.K.); (D.V.A.); (E.A.V.); (B.N.Z.); (A.Y.B.); (A.A.I.)
- Correspondence: (L.I.K.); (S.I.B.); Tel.: +7-383-363-47-00 (ext. 2001) (L.I.K. & S.I.B.)
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Bazhan SI, Antonets DV, Starostina EV, Ilyicheva TN, Kaplina ON, Marchenko VY, Volkova OY, Bakulina AY, Karpenko LI. In silico design of influenza a virus artificial epitope-based T-cell antigens and the evaluation of their immunogenicity in mice. J Biomol Struct Dyn 2020; 40:3196-3212. [PMID: 33222632 DOI: 10.1080/07391102.2020.1845978] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The polyepitope strategy is promising approach for successfully creating a broadly protective flu vaccine, which targets T-lymphocytes (both CD4+ and CD8+) to recognise the most conserved epitopes of viral proteins. In this study, we employed a computer-aided approach to develop several artificial antigens potentially capable of evoking immune responses to different virus subtypes. These antigens included conservative T-cell epitopes of different influenza A virus proteins. To design epitope-based antigens we used experimentally verified information regarding influenza virus T-cell epitopes from the Immune Epitope Database (IEDB) (http://www.iedb.org). We constructed two "human" and two "murine" variants of polyepitope antigens. Amino acid sequences of target polyepitope antigens were designed using our original TEpredict/PolyCTLDesigner software. Immunogenic and protective features of DNA constructs encoding "murine" target T-cell immunogens were studied in BALB/c mice. We showed that mice groups immunised with a combination of computer-generated "murine" DNA immunogens had a 37.5% survival rate after receiving a lethal dose of either A/California/4/2009 (H1N1) virus or A/Aichi/2/68 (H3N2) virus, while immunisation with live flu H1N1 and H3N2 vaccine strains provided protection against homologous viruses and failed to protect against heterologous viruses. These results demonstrate that mechanisms of cross-protective immunity may be associated with the stimulation of specific T-cell responses. This study demonstrates that our computer-aided approach may be successfully used for rational designing artificial polyepitope antigens capable of inducing virus-specific T-lymphocyte responses and providing partial protection against two different influenza virus subtypes.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sergei I Bazhan
- Theoretical Department, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
| | - Denis V Antonets
- Theoretical Department, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
| | - Ekaterina V Starostina
- Bioengineering Department, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
| | - Tatyana N Ilyicheva
- Department of zoonotic infections and Influenza, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
| | - Olga N Kaplina
- Bioengineering Department, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
| | - Vasiliy Yu Marchenko
- Department of zoonotic infections and Influenza, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
| | - Olga Yu Volkova
- Immunogenetics laboratory, Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anastasiya Yu Bakulina
- Theoretical Department, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia.,Laboratory of structural bioinformatics and molecular modeling, Novosibirsk State University, Novosibirsk, Russia
| | - Larisa I Karpenko
- Bioengineering Department, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
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5
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Rudometov AP, Chikaev AN, Rudometova NB, Antonets DV, Lomzov AA, Kaplina ON, Ilyichev AA, Karpenko LI. Artificial Anti-HIV-1 Immunogen Comprising Epitopes of Broadly Neutralizing Antibodies 2F5, 10E8, and a Peptide Mimic of VRC01 Discontinuous Epitope. Vaccines (Basel) 2019; 7:vaccines7030083. [PMID: 31390770 PMCID: PMC6789618 DOI: 10.3390/vaccines7030083] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 06/26/2019] [Revised: 07/24/2019] [Accepted: 07/30/2019] [Indexed: 01/05/2023] Open
Abstract
The construction of artificial proteins using conservative B-cell and T-cell epitopes is believed to be a promising approach for a vaccine design against diverse viral infections. This article describes the development of an artificial HIV-1 immunogen using a polyepitope immunogen design strategy. We developed a recombinant protein, referred to as nTBI, that contains epitopes recognized by broadly neutralizing HIV-1 antibodies (bNAbs) combined with Th-epitopes. This is a modified version of a previously designed artificial protein, TBI (T- and B-cell epitopes containing Immunogen), carrying four T- and five B-cell epitopes from HIV-1 Env and Gag proteins. To engineer the nTBI molecule, three B-cell epitopes of the TBI protein were replaced with the epitopes recognized by broadly neutralizing HIV-1 antibodies 10E8, 2F5, and a linear peptide mimic of VRC01 epitope. We showed that immunization of rabbits with the nTBI protein elicited antibodies that recognize HIV-1 proteins and were able to neutralize Env-pseudotyped SF162.LS HIV-1 strain (tier 1). Competition assay revealed that immunization of rabbits with nTBI induced mainly 10E8-like antibodies. Our findings support the use of nTBI protein as an immunogen with predefined favorable antigenic properties.
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Affiliation(s)
- Andrey P Rudometov
- State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region 630559, Russia.
| | - Anton N Chikaev
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, 8/2 Lavrentiev Avenue Novosibirsk, Novosibirsk 630090, Russia.
| | - Nadezhda B Rudometova
- State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region 630559, Russia
| | - Denis V Antonets
- State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region 630559, Russia
| | - Alexander A Lomzov
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Olga N Kaplina
- State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region 630559, Russia
| | - Alexander A Ilyichev
- State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region 630559, Russia
| | - Larisa I Karpenko
- State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region 630559, Russia.
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Ovchinnikov VY, Antonets DV, Gulyaeva LF. The search of CAR, AhR, ESRs binding sites in promoters of intronic and intergenic microRNAs. J Bioinform Comput Biol 2017; 16:1750029. [PMID: 29301444 DOI: 10.1142/s0219720017500299] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
MicroRNAs (miRNAs) play important roles in the regulation of gene expression at the post-transcriptional level. Many exogenous compounds or xenobiotics may affect microRNA expression. It is a well-established fact that xenobiotics with planar structure like TCDD, benzo(a)pyrene (BP) can bind aryl hydrocarbon receptor (AhR) followed by its nuclear translocation and transcriptional activation of target genes. Another chemically diverse group of xenobiotics including phenobarbital, DDT, can activate the nuclear receptor CAR and in some cases estrogen receptors ESR1 and ESR2. We hypothesized that such chemicals can affect miRNA expression through the activation of AHR, CAR, and ESRs. To prove this statement, we used in silico methods to find DRE, PBEM, ERE potential binding sites for these receptors, respectively. We have predicted AhR, CAR, and ESRs binding sites in 224 rat, 201 mouse, and 232 human promoters of miRNA-coding genes. In addition, we have identified a number of miRNAs with predicted AhR, CAR, and ESRs binding sites that are known as oncogenes and as tumor suppressors. Our results, obtained in silico, open a new strategy for ongoing experimental studies and will contribute to further investigation of epigenetic mechanisms of carcinogenesis.
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Affiliation(s)
- Vladimir Y Ovchinnikov
- 1 Laboratory of Molecular Mechanisms of Pathological Processes, The Federal Research Center Institute of Cytology and Genetics The Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russian Federation
| | - Denis V Antonets
- 2 Laboratory of Complex Systems Modeling, A.P. Ershov Institute of Informatics Systems, Prospekt Lavrentyeva 6, Novosibirsk 630090, Russian Federation.,3 AcademGene LLC, Prospekt Lavrentyeva 6, Novosibirsk 630090, Russian Federation
| | - Lyudmila F Gulyaeva
- 4 Laboratory of Molecular Mechanisms of Carcinogenesis, Research Institute of Molecular Biology and Biophysics, Timakov St., 2/12, Novosibirsk 630117, Russian Federation.,5 Natural Science Department, Novosibirsk State University, Pirogova St., 2, Novosibirsk 630090, Russian Federation
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Nepomnyashchikh TS, Antonets DV, Shchelkunov SN. [Gene therapy of arthritis]. Genetika 2016; 52:625-640. [PMID: 29368491] [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: 06/07/2023]
Abstract
Gene therapy can offer a new approach to arthritis treatment which acts at an inflammation site. Numerous studies show high efficacy of gene therapy in different models of arthritis in humans. Even a single injection of a recombinant vector results in a stable prolonged expression of a therapeutic gene and a longterm therapeutic effect. In contrast to biologic therapy involving numerous systemic injections of recombinant anti-inflammatory proteins, gene therapy does not produce systemic side effects. Vectors based on retroviruses, adenoviruses, adeno-associated viruses, and recombinant plasmids could provide delivery of target genes. Of significant importance is the development of noninvasive methods of gene therapy: intranasal and peroral. The current state of research in arthritis gene therapy is discussed in this review.
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8
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Nazarkina ZK, Kharkova MV, Antonets DV, Morozkin ES, Bazhan SI, Karpenko LI, Vlassov VV, Ilyichev AA, Laktionov PP. Erratum to: Design of Polyepitope DNA Vaccine against Breast Carcinoma Cells and Analysis of Its Expression in Dendritic Cells. Bull Exp Biol Med 2016; 160:727. [PMID: 27037926 DOI: 10.1007/s10517-016-3261-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Zh K Nazarkina
- Institute of Chemical Biology and Fundamental Medicine Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia. .,Meshalkin Novosibirsk State Research Institute of Circulation Pathology, Novosibirsk, Russia.
| | - M V Kharkova
- Institute of Chemical Biology and Fundamental Medicine Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - D V Antonets
- State Research Center of Virology and Biotechnology "Vector", Koltsovo, Russia
| | - E S Morozkin
- Institute of Chemical Biology and Fundamental Medicine Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - S I Bazhan
- State Research Center of Virology and Biotechnology "Vector", Koltsovo, Russia
| | - L I Karpenko
- State Research Center of Virology and Biotechnology "Vector", Koltsovo, Russia
| | - V V Vlassov
- Institute of Chemical Biology and Fundamental Medicine Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A A Ilyichev
- Institute of Chemical Biology and Fundamental Medicine Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia.,State Research Center of Virology and Biotechnology "Vector", Koltsovo, Russia
| | - P P Laktionov
- Institute of Chemical Biology and Fundamental Medicine Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia.,Meshalkin Novosibirsk State Research Institute of Circulation Pathology, Novosibirsk, Russia
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9
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Nazarkina ZK, Khar'kova MV, Antonets DV, Morozkin ES, Bazhan SI, Karpenko LI, Vlasov VV, Ilyichev AA, Laktionov PP. Design of Polyepitope DNA Vaccine against Breast Carcinoma Cells and Analysis of Its Expression in Dendritic Cells. Bull Exp Biol Med 2016; 160:486-90. [PMID: 26915653 DOI: 10.1007/s10517-016-3203-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [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: 06/26/2014] [Indexed: 01/07/2023]
Abstract
Polyepitope DNA vaccine inducing T-cell-mediated immune response against cancer-specific antigens is a promising tool for selective elimination of tumor cells. Breast cancer-specific polyepitope DNA vaccine was designed using TEpredict and PolyCTLDesigner software on the basis of immunogenic peptides of HER2 and Mammaglobin-1 (Mam) tumor antigens. LPS-free preparations of plasmid DNA encoding polyepitope T-cell antigen and full-length copies of HER2 and Mam antigens were obtained. TaqMan-PCR systems for evaluation of the expression of immunogens in cells were created. The protocol of vaccine DNA delivery into dendritic cells was optimized. Expression of the target immunogens in dendritic cells derived from human peripheral blood mononuclear fraction after transfection with plasmid DNA preparations is demonstrated.
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Affiliation(s)
- Zh K Nazarkina
- Institute of Chemical Biology and Basic Medicine, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia. .,E. N. Meshalkin Novosibirsk Research Institute of Circulation Pathology, Novosibirsk, Russia.
| | - M V Khar'kova
- Institute of Chemical Biology and Basic Medicine, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - D V Antonets
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Russia
| | - E S Morozkin
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Russia
| | - S I Bazhan
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Russia
| | - L I Karpenko
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Russia
| | - V V Vlasov
- Institute of Chemical Biology and Basic Medicine, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A A Ilyichev
- Institute of Chemical Biology and Basic Medicine, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia.,Vector State Research Center of Virology and Biotechnology, Koltsovo, Russia
| | - P P Laktionov
- Institute of Chemical Biology and Basic Medicine, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia.,Vector State Research Center of Virology and Biotechnology, Koltsovo, Russia
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Abstract
RV144 clinical trial was modestly effective in preventing HIV infection. New alternative approaches are needed to design improved HIV-1 vaccines and their delivery strategies. One of these approaches is construction of synthetic polyepitope HIV-1 immunogen using protective T- and B-cell epitopes that can induce broadly neutralizing antibodies and responses of cytotoxic (CD8(+) CTL) and helpers (CD4(+) Th) T-lymphocytes. This approach seems to be promising for designing of new generation of vaccines against HIV-1, enables in theory to cope with HIV-1 antigenic variability, focuses immune responses on protective determinants and enables to exclude from the vaccine compound that can induce autoantibodies or antibodies enhancing HIV-1 infectivity. Herein, the authors will focus on construction and rational design of polyepitope T-cell HIV-1 immunogens and their delivery, including: advantages and disadvantages of existing T-cell epitope prediction methods; features of organization of polyepitope immunogens, which can generate high-level CD8(+) and CD4(+) T-lymphocyte responses; the strategies to optimize efficient processing, presentation and immunogenicity of polyepitope constructs; original software to design polyepitope immunogens; and delivery vectors as well as mucosal strategies of vaccination. This new knowledge may bring us a one step closer to developing an effective T-cell vaccine against HIV-1, other chronic viral infections and cancer.
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Affiliation(s)
- Larisa I Karpenko
- State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk region, 630559, Russia
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11
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Antonets DV, Bazhan SI. PolyCTLDesigner: a computational tool for constructing polyepitope T-cell antigens. BMC Res Notes 2013; 6:407. [PMID: 24107711 PMCID: PMC3853014 DOI: 10.1186/1756-0500-6-407] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [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: 02/14/2013] [Accepted: 09/24/2013] [Indexed: 11/10/2022] Open
Abstract
Background Construction of artificial polyepitope antigens is one of the most promising strategies for developing more efficient and safer vaccines evoking T-cell immune responses. Epitope rearrangements and utilization of certain spacer sequences have been proven to greatly influence the immunogenicity of polyepitope constructs. However, despite numerous efforts towards constructing and evaluating artificial polyepitope immunogens as well as despite numerous computational methods elaborated to date for predicting T-cell epitopes, peptides binding to TAP and for antigen processing prediction, only a few computational tools were currently developed for rational design of polyepitope antigens. Findings Here we present a PolyCTLDesigner program that is intended for constructing polyepitope immunogens. Given a set of either known or predicted T-cell epitopes the program selects N-terminal flanking sequences for each epitope to optimize its binding to TAP (if necessary) and joins resulting oligopeptides into a polyepitope in a way providing efficient liberation of potential epitopes by proteasomal and/or immunoproteasomal processing. And it also tries to minimize the number of non-target junctional epitopes resulting from artificial juxtaposition of target epitopes within the polyepitope. For constructing polyepitopes, PolyCTLDesigner utilizes known amino acid patterns of TAP-binding and proteasomal/immunoproteasomal cleavage specificity together with genetic algorithm and graph theory approaches. The program was implemented using Python programming language and it can be used either interactively or through scripting, which allows users familiar with Python to create custom pipelines. Conclusions The developed software realizes a rational approach to designing poly-CTL-epitope antigens and can be used to develop new candidate polyepitope vaccines. The current version of PolyCTLDesigner is integrated with our TEpredict program for predicting T-cell epitopes, and thus it can be used not only for constructing the polyepitope antigens based on preselected sets of T-cell epitopes, but also for predicting cytotoxic and helper T-cell epitopes within selected protein antigens. PolyCTLDesigner is freely available from the project’s web site: http://tepredict.sourceforge.net/PolyCTLDesigner.html.
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Affiliation(s)
- Denis V Antonets
- State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russian Federation.
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12
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Nepomniashchikh TS, Antonets DV, Lebedev LR, Gileva IP, Shchelkunov SN. [Modeling spatial structures of variola and cowpox virus TNF-binding CrmB proteins bound to murine or human TNF]. Mol Biol (Mosk) 2010; 44:1054-1063. [PMID: 21290827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Orthopoxviruses bear in their genomes several genes coding for homologous secreted proteins able to bind tumor necrosis factor. Different species of the genus possess different sets of these tumor necrosis factor-binding proteins. Viriola virus encodes the only one of them named CrmB. Despite sharing high sequence identity, CrmB proteins belonging to distinct orthopoxviral species were shown to significantly differ by their physico-chemical and biological properties. We modeled spatial structures of tumor necrosis factor receptor domains of variola and cowpox virus CrmB proteins bound to either murine, or human or mutated human tumor necrosis factor. In the sequence of last the arginine residue at position 31 is substituted with glutamine that is characteristic for murine tumor necrosis factor. Theoretical analysis of modeled ligand-receptor complexes revealed that the least stable should be the complex of cowpox virus CrmB with human tumor necrosis factor, and that arginine to glutamine substitution at position 31 should significantly stabilize binding of corresponding human tumor necrosis factor mutant to cowpox virus CrmB. Experimental evaluation of recombinant variola and cowpox virus CrmB efficiencies in inhibiting cytotoxic effect of all these tumor necrosis factors have approved our predictions.
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13
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Antonets DV, Nepomnyashchikh TS, Shchelkunov SN. SECRET domain of variola virus CrmB protein can be a member of poxviral type II chemokine-binding proteins family. BMC Res Notes 2010; 3:271. [PMID: 20979600 PMCID: PMC2987869 DOI: 10.1186/1756-0500-3-271] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [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: 06/17/2010] [Accepted: 10/27/2010] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Variola virus (VARV) the causative agent of smallpox, eradicated in 1980, have wide spectrum of immunomodulatory proteins to evade host immunity. Recently additional biological activity was discovered for VARV CrmB protein, known to bind and inhibit tumour necrosis factor (TNF) through its N-terminal domain homologous to cellular TNF receptors. Besides binding TNF, this protein was also shown to bind with high affinity several chemokines which recruit B- and T-lymphocytes and dendritic cells to sites of viral entry and replication. Ability to bind chemokines was shown to be associated with unique C-terminal domain of CrmB protein. This domain named SECRET (Smallpox virus-Encoded Chemokine Receptor) is unrelated to the host proteins and lacks significant homology with other known viral chemokine-binding proteins or any other known protein. FINDINGS De novo modelling of VARV-CrmB SECRET domain spatial structure revealed its apparent structural homology with cowpox virus CC-chemokine binding protein (vCCI) and vaccinia virus A41 protein, despite low sequence identity between these three proteins. Potential ligand-binding surface of modelled VARV-CrmB SECRET domain was also predicted to bear prominent electronegative charge which is characteristic to known orthopoxviral chemokine-binding proteins. CONCLUSIONS Our results suggest that SECRET should be included into the family of poxviral type II chemokine-binding proteins and that it might have been evolved from the vCCI-like predecessor protein.
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Affiliation(s)
- Denis V Antonets
- State Research Center of Virology and Biotechnology "Vector" Rospotrebnadzor, Novosibirsk region, Koltsovo, Russian Federation.
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14
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Bazhan SI, Karpenko LI, Ilyicheva TN, Belavin PA, Seregin SV, Danilyuk NK, Antonets DV, Ilyichev AA. Rational design based synthetic polyepitope DNA vaccine for eliciting HIV-specific CD8+ T cell responses. Mol Immunol 2010; 47:1507-15. [PMID: 20189249 DOI: 10.1016/j.molimm.2010.01.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Revised: 01/05/2010] [Accepted: 01/24/2010] [Indexed: 11/30/2022]
Abstract
Advances in defining HIV-1 CD8+ T cell epitopes and understanding endogenous MHC class I antigen processing enable the rational design of polyepitope vaccines for eliciting broadly targeted CD8+ T cell responses to HIV-1. Here we describe the construction and comparison of experimental DNA vaccines consisting of ten selected HLA-A2 epitopes from the major HIV-1 antigens Env, Gag, Pol, Nef, and Vpr. The immunogenicity of designed gene constructs was assessed after double DNA prime, single vaccinia virus boost immunization of HLA-A2 transgenic mice. We compared a number of parameters including different strategies for fusing ubiquitin to the polyepitope and including spacer sequences between epitopes to optimize proteasome liberation and TAP transport. It was demonstrated that the vaccine construct that induced in vitro the largest number of [peptide-MHC class I] complexes was also the most immunogenic in the animal experiments. This most immunogenic vaccine construct contained the N-terminal ubiquitin for targeting the polyepitope to the proteasome and included both proteasome liberation and TAP transport optimized spacer sequences that flanked the epitopes within the polyepitope construct. The immunogenicity of determinants was strictly related to their affinities for HLA-A2. Our finding supports the concept of rational vaccine design based on detailed knowledge of antigen processing.
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Affiliation(s)
- S I Bazhan
- State Research Center of Virology and Biotechnology Vector, Koltsovo, Novosibirsk Region, 630559 Russia.
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15
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Antonets DV, Maksiutov AZ. [TEpredict: software for T-cell epitope prediction]. Mol Biol (Mosk) 2010; 44:130-139. [PMID: 20198867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A program named TEpredict was developed for T-cell epitope prediction. Original models for T-cell epitope prediction were constructed by means of Partial Least Squares regression method on the basis of data, extracted from the IEDB (Immune Epitope Database)--the most complete resource of experimental peptide-MHC binding data known to date. TEpredict is also able to predict proteasomal processing of protein antigens, and the ability of produced oligopeptides to bind to TAP (Tansporters Associated with Processing). TEpredict could exclude peptides, shearing local similarity with human proteins, from the set of predicted T-cell epitopes. It is also able to estimate expected population coverage by selected peptides, using known HLA allele genotypic frequencies data. The majority of produced models demonstrated high sensitivity of predictions (0.50-0.80) concurrent with high specificity (0.75-0.99). TEpredict was shown to be highly competitive or even superior in comparison with such programs as ProPred1, SVRMHC, SVMHC and SYFPEITHI. TEpredict demonstrated high quality of predictions and we expect that it could become a useful tool in the development ofpolyepitope vaccines against dangerous human pathogens, including HIV, influenza etc. The program and its source code could be freely downloaded from the project web-site: http://tepredict.sourceforge.net.
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16
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Antonets DV, Bakulina AY, Portnyagina OY, Sidorova OV, Novikova OD, Maksyutov AZ. Prediction of antigenically active regions in the OmpF-like porin of Yersinia pseudotuberculosis. DOKL BIOCHEM BIOPHYS 2007; 414:124-6. [PMID: 17695318 DOI: 10.1134/s160767290703009x] [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: 11/23/2022]
Affiliation(s)
- D V Antonets
- Vektor State Research Center of Virology and Biotechnology, p. Koltsovo, Novosibirsk oblast, 630559 Russia
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17
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Gileva IP, Nepomnyashchikh TS, Antonets DV, Lebedev LR, Kochneva GV, Grazhdantseva AV, Shchelkunov SN. Properties of the recombinant TNF-binding proteins from variola, monkeypox, and cowpox viruses are different. Biochim Biophys Acta 2006; 1764:1710-8. [PMID: 17070121 PMCID: PMC9628946 DOI: 10.1016/j.bbapap.2006.09.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2006] [Revised: 08/10/2006] [Accepted: 09/08/2006] [Indexed: 11/30/2022]
Abstract
Tumor necrosis factor (TNF), a potent proinflammatory and antiviral cytokine, is a critical extracellular immune regulator targeted by poxviruses through the activity of virus-encoded family of TNF-binding proteins (CrmB, CrmC, CrmD, and CrmE). The only TNF-binding protein from variola virus (VARV), the causative agent of smallpox, infecting exclusively humans, is CrmB. Here we have aligned the amino acid sequences of CrmB proteins from 10 VARV, 14 cowpox virus (CPXV), and 22 monkeypox virus (MPXV) strains. Sequence analyses demonstrated a high homology of these proteins. The regions homologous to cd00185 domain of the TNF receptor family, determining the specificity of ligand–receptor binding, were found in the sequences of CrmB proteins. In addition, a comparative analysis of the C-terminal SECRET domain sequences of CrmB proteins was performed. The differences in the amino acid sequences of these domains characteristic of each particular orthopoxvirus species were detected. It was assumed that the species-specific distinctions between the CrmB proteins might underlie the differences in these physicochemical and biological properties. The individual recombinant proteins VARV-CrmB, MPXV-CrmB, and CPXV-CrmB were synthesized in a baculovirus expression system in insect cells and isolated. Purified VARV-CrmB was detectable as a dimer with a molecular weight of 90 kDa, while MPXV- and CPXV-CrmBs, as monomers when fractioned by non-reducing SDS-PAGE. The CrmB proteins of VARV, MPXV, and CPXV differed in the efficiencies of inhibition of the cytotoxic effects of human, mouse, or rabbit TNFs in L929 mouse fibroblast cell line. Testing of CrmBs in the experimental model of LPS-induced shock using SPF BALB/c mice detected a pronounced protective effect of VARV-CrmB. Thus, our data demonstrated the difference in anti-TNF activities of VARV-, MPXV-, and CPXV-CrmBs and efficiency of VARV-CrmB rather than CPXV- or MPXV-CrmBs against LPS-induced mortality in mice.
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Affiliation(s)
- Irina P Gileva
- State Research Center of Virology and Biotechnology Vector, Koltsovo, Novosibirsk oblast, 630559 Russia
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