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Goncharenko AV, Silkin VM, Chang YC. Nonlinearity vs nonlocality with emphasis on bandwidth broadening in semiconductor-based 1d metamaterials. Opt Express 2024; 32:12551-12568. [PMID: 38571075 DOI: 10.1364/oe.512215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/06/2024] [Indexed: 04/05/2024]
Abstract
The physics of nonlinear optical materials is incredibly versatile, with the design of novel materials and structures offering numerous degrees of freedom. Nevertheless, weak inherent nonlinearity of conventional optical materials continues to hinder the progress of a number of important applications. In this study, we delve into the realm of broadband enhancement of nonlinearity within one-dimensional (1d) plasmonic metamaterials, exploring its intricate connection with nonlocality. Specifically, we introduce a phenomenological framework for quantifying the effective third-order nonlinear susceptibility of 1d multiphase plasmonic nanostructures, utilizing heavily doped semiconductors, and subsequently applying this approach using realistic material parameters. Both direct and inverse problems of nonlinearity enhancement have been addressed. Our findings demonstrate a remarkable capability to significantly augment the third-order nonlinear susceptibility across a defined frequency range, while concurrently gauging the impact of nonlocality on this enhancement.
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2
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Shchulkin AV, Erokhina PD, Goncharenko AV, Mylnikov PY, Chernykh IV, Abalenikhina YV, Kotliarova MS, Yakusheva EN. Ethylmethylhydroxypyridine Succinate Is an Inhibitor but Not a Substrate of ABCB1 and SLCO1B1. Pharmaceuticals (Basel) 2023; 16:1529. [PMID: 38004395 PMCID: PMC10674565 DOI: 10.3390/ph16111529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/26/2023] Open
Abstract
2-Ethyl-6-methyl-3-hydroxypyridine succinate (EMHPS, Mexidol) is an original antioxidant and an anti-ischemic drug with the possibility of wide applications in the complex therapy of diseases, accompanied by the development of oxidative stress and ischemia; for example, ischemic stroke, chronic cerebral ischemia, and chronic heart failure. The use of EMHPS in the complex therapy of the above diseases may cause the development of drug-drug interactions, particularly pharmacokinetic interactions at the level of transporter proteins. In the present study, we evaluated the interaction of EMHPS with ABCB1 and SLCO1B1. In Caco-2 cells, it was shown that EMHPS is not a substrate of ABCB1 and that it does not affect its expression, but at the same time, it inhibits the activity of this transporter. Its inhibitory activity was inferior to verapamil-a classic inhibitor of ABCB1. In HEK293 and HEK293-SLCO1B1 cells, it was shown that EMHPS is not a substrate of SLCO1B1 either, but that it inhibited the activity of the transporter. However, its inhibitory activity was inferior to the classic inhibitor of SLCO1B1-rifampicin. Furthermore, it was found out that EMHPS does not affect SLCO1B1 expression in HepG2 cells. The approach proposed by the FDA (2020) and the International Transporter Consortium (2010) was used to assess the clinical significance of the study results. The effect of EMHPS on SLCO1B1 and the systemic inhibition of ABCB1 by EMPHS are not clinically significant, but ABCB1 inhibition by EMHPS in the gastrointestinal tract should be tested in vivo through clinical trials.
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Affiliation(s)
- Aleksey V. Shchulkin
- Department of Pharmacology, Ryazan State Medical University, 390026 Ryazan, Russia
| | - Pelageya D. Erokhina
- Department of Pharmacology, Ryazan State Medical University, 390026 Ryazan, Russia
| | - Anna V. Goncharenko
- Bach Institute of Biochemistry, Federal Research Centre “Fundamentals of Biotechnology”, Russian Academy of Sciences, 119071 Moscow, Russia; (A.V.G.)
| | - Pavel Yu. Mylnikov
- Department of Pharmacology, Ryazan State Medical University, 390026 Ryazan, Russia
| | - Ivan V. Chernykh
- Department of Pharmacology, Ryazan State Medical University, 390026 Ryazan, Russia
| | | | - Maria S. Kotliarova
- Bach Institute of Biochemistry, Federal Research Centre “Fundamentals of Biotechnology”, Russian Academy of Sciences, 119071 Moscow, Russia; (A.V.G.)
| | - Elena N. Yakusheva
- Department of Pharmacology, Ryazan State Medical University, 390026 Ryazan, Russia
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3
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Kotliarova MS, Shchulkin AV, Erokhina PD, Mylnikov PY, Yakusheva EN, Nadolinskaia NI, Zamakhaev MV, Goncharenko AV. Generation of a Cell Line Selectively Producing Functionally Active OATP1B1 Transporter. Biochemistry (Mosc) 2023; 88:1267-1273. [PMID: 37770393 DOI: 10.1134/s0006297923090067] [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: 05/25/2023] [Revised: 06/30/2023] [Accepted: 08/23/2023] [Indexed: 09/30/2023]
Abstract
The solute carrier organic anion transporter family member, OATP1B1, is one of the most important transporter proteins, which mediate penetration of many endogenous substances and xenobiotics into hepatocytes. A model system providing expression of the functional protein is needed to assess interaction of OATP1B1 with various substances. Based on the HEK293 cells, we obtained the HEK293-OATP1B1 cell line, constitutively expressing the SLCO1B1 gene encoding the OATP1B1 transporter. Expression of the SLCO1B1 gene was confirmed by real-time PCR analysis and Western blotting. Functionality of the transporter was assessed by the transport of atorvastatin, which is a substrate of OATP1B1. Cells of the resulting cell line, which selectively express the functionally active recombinant OATP1B1 transporter, can be used to study functions of the protein and to test drugs for being substrates, inducers, and inhibitors of OATP1B1, and to assess the risks of drug interactions.
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Affiliation(s)
- Mariia S Kotliarova
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071, Russia
| | | | | | | | | | - Nonna I Nadolinskaia
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071, Russia
| | - Mikhail V Zamakhaev
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071, Russia
| | - Anna V Goncharenko
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071, Russia.
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4
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Jamgochian HH, Zamakhaev MV, Sluchanko NN, Goncharenko AV, Shumkov MS. Development of Heterologous Expression System and Optimization of the Method of Cholera Toxin β-Subunit Production in E. coli. Biochemistry (Mosc) 2023; 88:1304-1317. [PMID: 37770397 DOI: 10.1134/s0006297923090109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 09/30/2023]
Abstract
Cholera is a deadly infection disease, which is usually associated with low hygiene levels and limited access to high-quality drinking water. An effective way to prevent cholera is the use of vaccines. Among active vaccine components there is the CtxB protein (cholera toxin β-subunit). In the current work, we have developed a genetic system for production of the recombinant CtxB in E. coli cells and studied conditions for synthesis and purification of the target product at the laboratory scale. It has been found that the optimal algorithm for isolation of the recombinant protein is to grow E. coli culture in the synthetic M9 medium with glycerol, followed by CtxB purification out of the spent culture medium using Ni2+-chelate affinity chromatography techniques. Forty-eight hours after induction of CtxB expression, concentration of the target product could be up to 50 mg/liter in the culture medium. The CtxB protein retains its pentameric structure during expression and through purification. The latter makes it possible to consider the developed system as a promising tool for the industrial-level production of recombinant CtxB for medical and research purposes.
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Affiliation(s)
- Hamesd H Jamgochian
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Mikhail V Zamakhaev
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Nikolai N Sluchanko
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Anna V Goncharenko
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia.
| | - Mikhail S Shumkov
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
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5
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Kurishev AO, Karpov DS, Nadolinskaia NI, Goncharenko AV, Golimbet VE. CRISPR/Cas-Based Approaches to Study Schizophrenia and Other Neurodevelopmental Disorders. Int J Mol Sci 2022; 24:ijms24010241. [PMID: 36613684 PMCID: PMC9820593 DOI: 10.3390/ijms24010241] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022] Open
Abstract
The study of diseases of the central nervous system (CNS) at the molecular level is challenging because of the complexity of neural circuits and the huge number of specialized cell types. Moreover, genomic association studies have revealed the complex genetic architecture of schizophrenia and other genetically determined mental disorders. Investigating such complex genetic architecture to decipher the molecular basis of CNS pathologies requires the use of high-throughput models such as cells and their derivatives. The time is coming for high-throughput genetic technologies based on CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat)/Cas systems to manipulate multiple genomic targets. CRISPR/Cas systems provide the desired complexity, versatility, and flexibility to create novel genetic tools capable of both altering the DNA sequence and affecting its function at higher levels of genetic information flow. CRISPR/Cas tools make it possible to find and investigate the intricate relationship between the genotype and phenotype of neuronal cells. The purpose of this review is to discuss innovative CRISPR-based approaches for studying the molecular mechanisms of CNS pathologies using cellular models.
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Affiliation(s)
| | - Dmitry S. Karpov
- Mental Health Research Center, Kashirskoe sh. 34, 115522 Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, 119991 Moscow, Russia
| | - Nonna I. Nadolinskaia
- Bach Institute of Biochemistry, Fundamentals of Biotechnology Federal Research Center, Russian Academy of Sciences, 119071 Moscow, Russia
| | - Anna V. Goncharenko
- Bach Institute of Biochemistry, Fundamentals of Biotechnology Federal Research Center, Russian Academy of Sciences, 119071 Moscow, Russia
| | - Vera E. Golimbet
- Mental Health Research Center, Kashirskoe sh. 34, 115522 Moscow, Russia
- Correspondence:
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Nadolinskaia NI, Kotliarova MS, Goncharenko AV. Fighting Tuberculosis: In Search of a BCG Replacement. Microorganisms 2022; 11:microorganisms11010051. [PMID: 36677343 PMCID: PMC9863999 DOI: 10.3390/microorganisms11010051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Tuberculosis is one of the most threatening infectious diseases and represents an important and significant reason for mortality in high-burden regions. The only licensed vaccine, BCG, is hardly capable of establishing long-term tuberculosis protection and is highly variable in its effectiveness. Even after 100 years of BCG use and research, we still cannot unequivocally answer the question of which immune correlates of protection are crucial to prevent Mycobacterium tuberculosis (Mtb) infection or the progression of the disease. The development of a new vaccine against tuberculosis arises a nontrivial scientific challenge caused by several specific features of the intracellular lifestyle of Mtb and the ability of the pathogen to manipulate host immunity. The purpose of this review is to discuss promising strategies and the possibilities of creating a new vaccine that could replace BCG and provide greater protection. The considered approaches include supplementing mycobacterial strains with immunodominant antigens and genetic engineering aimed at altering the interaction between the bacterium and the host cell, such as the exit from the phagosome. Improved new vaccine strains based on BCG and Mtb undergoing clinical evaluation are also overviewed.
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7
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Armianinova DK, Karpov DS, Kotliarova MS, Goncharenko AV. [Genetic Engineering in Mycobacteria]. Mol Biol (Mosk) 2022; 56:900-913. [PMID: 36475477 DOI: 10.31857/s0026898422060040] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 04/28/2022] [Indexed: 06/17/2023]
Abstract
Genetic tools for targeted modification of the mycobacterial genome contribute to the understanding of the physiology and virulence mechanisms of mycobacteria. Human and animal pathogens, such as the Mycobacterium tuberculosis complex, which causes tuberculosis, and M. leprae, which causes leprosy, are of particular importance. Genetic research opens up novel opportunities to identify and validate new targets for antibacterial drugs and to develop improved vaccines. Although mycobacteria are difficult to work with due to their slow growth rate and a limited possibility to transfer genetic information, significant progress has been made in developing genetic engineering methods for mycobacteria. The review considers the main approaches to changing the mycobacterial genome in a targeted manner, including homologous and site-specific recombination and use of the CRISPR/Cas system.
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Affiliation(s)
- D K Armianinova
- Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071 Russia
| | - D S Karpov
- Center of Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - M S Kotliarova
- Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071 Russia
| | - A V Goncharenko
- Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071 Russia
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8
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Nadolinskaia NI, Goncharenko AV. [CRISPR Interference in Regulation of Bacterial Gene Expression]. Mol Biol (Mosk) 2022; 56:892-899. [PMID: 36475476 DOI: 10.31857/s0026898422060167] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 04/15/2022] [Indexed: 06/17/2023]
Abstract
The review is devoted to the use of the CRISPR/Cas system for obtaining knockdowns of target bacterial genes by CRISPR-mediated interference (CRISPRi). CRISPRi is based on the preservation of the ability of the inactivated dCas nuclease in complex with guide RNA to bind a target, which leads to reversible repression of the selected genes. The review describes the principle of operation of CRISPR/Cas and CRIS-PRi/dCas and provides examples of various approaches to the use of CRISPRi with the most popular inactivated nucleases dCas9 and dCas12a. Also, attention is paid to the use of CRISPRi screening for genome-wide studies and the modular system for identifying many important patterns at the Mobile-CRISPRi genome level. In addition, we discuss the use of CRISPRi to optimize biotechnological production, such as the synthesis of malonyl-CoA, L-lysine, L-glutamate, and other significant products.
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Affiliation(s)
- N I Nadolinskaia
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology," Russian Academy of Sciences, Moscow, 119071 Russia
| | - A V Goncharenko
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology," Russian Academy of Sciences, Moscow, 119071 Russia
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9
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Goncharenko AV, Fitio V, Silkin V. Broadening the absorption bandwidth based on heavily doped semiconductor nanostructures. Opt Express 2022; 30:36622-36631. [PMID: 36258586 DOI: 10.1364/oe.472788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 08/31/2022] [Indexed: 06/16/2023]
Abstract
Broadband light absorption is a basis for the proper functionality of various materials, microstructures, and devices. Despite numerous studies, however, many aspects of broadband absorption remain uncovered. In this paper, we demonstrate an inverse-problem approach to designing nanostructures with a very low optical reflection and high absorption through a frequency band. Particular emphasis is made on a subwavelength transparent film as a top layer and anisotropic substrate. The polarization-dependent metamaterial absorber based on a subwavelenth semiconductor multicomponent multilayer structure is proposed and numerically investigated. For an illustration, we consider a four-component heavily doped silicon lattice with a thin undoped silicon top layer. The dielectric response of the structure is engineered by controlling the free carrier density and filling factor of each layer. A simulation study reveals a power law dependence of the bandwidth on the maximum reflectivity within the band.
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10
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Karpov DS, Goncharenko AV, Usachev EV, Vasina DV, Divisenko EV, Chalenko YM, Pochtovyi AA, Ovchinnikov RS, Makarov VV, Yudin SM, Tkachuk AP, Gushchin VA. A Strategy for the Rapid Development of a Safe Vibrio cholerae Candidate Vaccine Strain. Int J Mol Sci 2021; 22:ijms222111657. [PMID: 34769085 PMCID: PMC8583953 DOI: 10.3390/ijms222111657] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 12/01/2022] Open
Abstract
Approximately 1/6 of humanity is at high risk of experiencing cholera epidemics. The development of effective and safe vaccines against Vibrio cholerae, the primary cause of cholera, is part of the public health measures to prevent cholera epidemics. Natural nontoxigenic V. cholerae isolates represent a source of new genetically improved and relatively safe vaccine strains. However, the genomic engineering of wild-type V. cholerae strains is difficult, and these strains are genetically unstable due to their high homologous recombination activity. We comprehensively characterized two V. cholerae isolates using genome sequencing, bioinformatic analysis, and microscopic, physiological, and biochemical tests. Genetic constructs were Gibson assembled and electrotransformed into V. cholerae. Bacterial colonies were assessed using standard microbiological and immunological techniques. As a result, we created a synthetic chromoprotein-expressing reporter operon. This operon was used to improve the V. cholerae genome engineering approach and monitor the stability of the genetic constructs. Finally, we created a stable candidate V. cholerae vaccine strain bearing a recA deletion and expressing the β-subunit of cholera toxin. Thus, we developed a strategy for the rapid creation of genetically stable and relatively safe candidate vaccine strains. This strategy can be applied not only to V. cholerae but also to other important human bacterial pathogens.
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Affiliation(s)
- Dmitry S. Karpov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str., 32, 119991 Moscow, Russia
- Bach Institute of Biochemistry, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.V.G.); (E.V.U.); (D.V.V.); (A.P.T.); (V.A.G.)
- Correspondence: ; Tel.: +7-(499)-135-98-01
| | - Anna V. Goncharenko
- Bach Institute of Biochemistry, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.V.G.); (E.V.U.); (D.V.V.); (A.P.T.); (V.A.G.)
| | - Evgenii V. Usachev
- Bach Institute of Biochemistry, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.V.G.); (E.V.U.); (D.V.V.); (A.P.T.); (V.A.G.)
- N.F. Gamaleya Federal Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Gamaleya str., 18, 123098 Moscow, Russia; (E.V.D.); (Y.M.C.); (A.A.P.); (R.S.O.)
| | - Daria V. Vasina
- Bach Institute of Biochemistry, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.V.G.); (E.V.U.); (D.V.V.); (A.P.T.); (V.A.G.)
- N.F. Gamaleya Federal Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Gamaleya str., 18, 123098 Moscow, Russia; (E.V.D.); (Y.M.C.); (A.A.P.); (R.S.O.)
| | - Elizaveta V. Divisenko
- N.F. Gamaleya Federal Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Gamaleya str., 18, 123098 Moscow, Russia; (E.V.D.); (Y.M.C.); (A.A.P.); (R.S.O.)
| | - Yaroslava M. Chalenko
- N.F. Gamaleya Federal Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Gamaleya str., 18, 123098 Moscow, Russia; (E.V.D.); (Y.M.C.); (A.A.P.); (R.S.O.)
| | - Andrei A. Pochtovyi
- N.F. Gamaleya Federal Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Gamaleya str., 18, 123098 Moscow, Russia; (E.V.D.); (Y.M.C.); (A.A.P.); (R.S.O.)
- Department of Virology, Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Roman S. Ovchinnikov
- N.F. Gamaleya Federal Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Gamaleya str., 18, 123098 Moscow, Russia; (E.V.D.); (Y.M.C.); (A.A.P.); (R.S.O.)
| | - Valentin V. Makarov
- Centre for Strategic Planning of FMBA of Russia, 119121 Moscow, Russia; (V.V.M.); (S.M.Y.)
| | - Sergei M. Yudin
- Centre for Strategic Planning of FMBA of Russia, 119121 Moscow, Russia; (V.V.M.); (S.M.Y.)
| | - Artem P. Tkachuk
- Bach Institute of Biochemistry, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.V.G.); (E.V.U.); (D.V.V.); (A.P.T.); (V.A.G.)
- N.F. Gamaleya Federal Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Gamaleya str., 18, 123098 Moscow, Russia; (E.V.D.); (Y.M.C.); (A.A.P.); (R.S.O.)
| | - Vladimir A. Gushchin
- Bach Institute of Biochemistry, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.V.G.); (E.V.U.); (D.V.V.); (A.P.T.); (V.A.G.)
- N.F. Gamaleya Federal Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Gamaleya str., 18, 123098 Moscow, Russia; (E.V.D.); (Y.M.C.); (A.A.P.); (R.S.O.)
- Department of Virology, Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia
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11
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Nadolinskaia NI, Zamakhaev MV, Shumkov MS, Armianinova DK, Karpov DS, Goncharenko AV. CRISPR Interference of Adenylate Cyclases from Mycobacterium tuberculosis. APPL BIOCHEM MICRO+ 2021; 57:421-425. [PMID: 34334794 PMCID: PMC8315726 DOI: 10.1134/s0003683821040128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 01/20/2021] [Accepted: 02/22/2021] [Indexed: 11/25/2022]
Abstract
This work describes a modification of the pRH2521 vector of the pRH2502/pRH2521 system for CRISPR-dCas9-mediated RNA interference. The modification enabled an increase in the cloning efficiency of guide RNA spacers. The ability of the modified pRH2502/pRH2521 system to suppress the transcription of certain genes was evaluated with the use of genes of Mycobacterium tuberculosis adenylate cyclases. The results revealed the limitations of the pRH2502/pRH2521 system for CRISPR interference associated with the probability of the detection of a protospacer adjacent motif (PAM) in the gene promoter region.
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Affiliation(s)
- N I Nadolinskaia
- Bach Institute of Biochemistry, Fundamentals of Biotechnology Federal Research Center, Russian Academy of Sciences, 119071 Moscow, Russia
| | - M V Zamakhaev
- Bach Institute of Biochemistry, Fundamentals of Biotechnology Federal Research Center, Russian Academy of Sciences, 119071 Moscow, Russia
| | - M S Shumkov
- Bach Institute of Biochemistry, Fundamentals of Biotechnology Federal Research Center, Russian Academy of Sciences, 119071 Moscow, Russia
| | - D K Armianinova
- Bach Institute of Biochemistry, Fundamentals of Biotechnology Federal Research Center, Russian Academy of Sciences, 119071 Moscow, Russia
| | - D S Karpov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - A V Goncharenko
- Bach Institute of Biochemistry, Fundamentals of Biotechnology Federal Research Center, Russian Academy of Sciences, 119071 Moscow, Russia
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12
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Nadolinskaia NI, Karpov DS, Goncharenko AV. Vaccines Against Tuberculosis: Problems and Prospects (Review). APPL BIOCHEM MICRO+ 2020; 56:497-504. [PMID: 32981943 PMCID: PMC7508421 DOI: 10.1134/s0003683820050129] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/13/2020] [Accepted: 04/22/2020] [Indexed: 12/12/2022]
Abstract
Despite the efforts of the global medical and scientific community, tuberculosis remains the leading cause of death from infectious diseases. The expectation of success associated with the development of new anti-TB drugs was not justified, and the attention of researchers was largely drawn to the creation of new mycobacterial strains for vaccination against tuberculosis. The proposed review contains current information on the existing vaccine strains and the development of new, genetically engineered strains for the prevention of tuberculosis and the prevention and treatment of other diseases. The review includes relevant information on the correlation between BCG vaccination and the frequency and severity of COVID-19 infection.
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Affiliation(s)
- N I Nadolinskaia
- Bach Institute of Biochemistry, Federal Research Center Fundamentals of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
| | - D S Karpov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - A V Goncharenko
- Bach Institute of Biochemistry, Federal Research Center Fundamentals of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
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13
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Karpov DS, Domashin AI, Kotlov MI, Osipova PG, Kiseleva SV, Seregina TA, Goncharenko AV, Mironov AS, Karpov VL, Poddubko SV. [Biotechnological Potential of the Bacillus subtilis 20 Strain]. Mol Biol (Mosk) 2020; 54:137-145. [PMID: 32163397 DOI: 10.31857/s0026898420010085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 06/25/2019] [Indexed: 11/24/2022]
Abstract
Bacillus subtilis bacteria play an important role in veterinary medicine, medicine, and biotechnology, and the permanently growing demand for biotechnological products fuels the improvement of the properties of biotechnological strains. B. subtilis strains with improved characteristics maybe obtained by rational design and the directed evolution technologies, or be found among newly described strains. In the course of the long-term microbiome composition studies in the Russian segment of the International Space Station, the B. subtilis 20 strain was isolated, this strain shows the capacity for rapid growth and considerable biomass accumulation, as well as increased resistance to acidification of the environment in comparison to the "terrestrial" B. subtilis 168 strain. What is more, B. subtilis 20 is hyperresistant to the DNA and protein damaging factors that are linked to the overexpression of the genes controlling DNA repair, hydrogen sulfide production, and reactive oxygen species neutralization. The described properties of B. subtilis 20 are indicative of its considerable potential as a promising producer of biologically active compounds.
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Affiliation(s)
- D S Karpov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia.,
| | - A I Domashin
- Institute of Medical and Biological Problems, Russian Academy of Sciences, Moscow, 123007 Russia
| | - M I Kotlov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - P G Osipova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - S V Kiseleva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - T A Seregina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - A V Goncharenko
- Fundamentals of Biotechnology Federal Research Centre, Russian Academy of Sciences, Moscow, 119071 Russia
| | - A S Mironov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - V L Karpov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - S V Poddubko
- Institute of Medical and Biological Problems, Russian Academy of Sciences, Moscow, 123007 Russia
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14
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Goncharenko AV, Kotlyarova MS, Moisenovich AM, Arkhipova AY, Kulikov DA, Konkov AS, Kulikov AV, Mashkov AE, Agapov II, Moisenovich MM, Kirpichnikov MP. Osteogenic differentiation of mouse bone marrow stromal cells on fibroin microcarriers. DOKL BIOCHEM BIOPHYS 2018; 477:345-348. [PMID: 29297117 DOI: 10.1134/s1607672917060011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Indexed: 12/12/2022]
Abstract
We investigated the proliferation and osteogenic differentiation of mesenchymal stem cells cultured on fibroin microcarriers. Effective cell proliferation on the surface of the microcarriers, determined by the large surface area, and the contribution of microcarrier mineralization to the stimulation of the osteogenic differentiation of mesenchymal stem cells was revealed.
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Affiliation(s)
- A V Goncharenko
- Biological Faculty, Moscow State University, Moscow, 119992, Russia
| | - M S Kotlyarova
- Biological Faculty, Moscow State University, Moscow, 119992, Russia
| | - A M Moisenovich
- Biological Faculty, Moscow State University, Moscow, 119992, Russia
| | - A Y Arkhipova
- Biological Faculty, Moscow State University, Moscow, 119992, Russia
| | - D A Kulikov
- Vladimirskii Moscow Regional Research Clinical Institute, ul. Shchepkina 61/2, Moscow, 129110, Russia
| | - A S Konkov
- Biological Faculty, Moscow State University, Moscow, 119992, Russia
| | - A V Kulikov
- Institute of Theoretical and Experimental Biophysics, Pushchino Branch, Russian Academy of Sciences, Pushchino, Moscow oblast, 142292, Russia
| | - A E Mashkov
- Vladimirskii Moscow Regional Research Clinical Institute, ul. Shchepkina 61/2, Moscow, 129110, Russia
| | - I I Agapov
- Shumakov Research Institute of Transplantation and Artificial Organs, Russian Ministry of Health, Moscow, 113182, Russia
| | - M M Moisenovich
- Biological Faculty, Moscow State University, Moscow, 119992, Russia.
| | - M P Kirpichnikov
- Biological Faculty, Moscow State University, Moscow, 119992, Russia
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15
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Shleeva MO, Kondratieva TK, Demina GR, Rubakova EI, Goncharenko AV, Apt AS, Kaprelyants AS. Overexpression of Adenylyl Cyclase Encoded by the Mycobacterium tuberculosis Rv2212 Gene Confers Improved Fitness, Accelerated Recovery from Dormancy and Enhanced Virulence in Mice. Front Cell Infect Microbiol 2017; 7:370. [PMID: 28861399 PMCID: PMC5562752 DOI: 10.3389/fcimb.2017.00370] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 08/02/2017] [Indexed: 01/21/2023] Open
Abstract
Earlier we demonstrated that the adenylyl cyclase (AC) encoded by the MSMEG_4279 gene plays a key role in the resuscitation and growth of dormant Mycobacterium smegmatis and that overexpression of this gene leads to an increase in intracellular cAMP concentration and prevents the transition of M. smegmatis from active growth to dormancy in an extended stationary phase accompanied by medium acidification. We surmised that the homologous Rv2212 gene of M. tuberculosis (Mtb), the main cAMP producer, plays similar physiological roles by supporting, under these conditions, the active state and reactivation of dormant bacteria. To test this hypothesis, we established Mtb strain overexpressing Rv2212 and compared its in vitro and in vivo growth characteristics with a control strain. In vitro, the AC-overexpressing pMindRv2212 strain demonstrated faster growth in a liquid medium, prolonged capacity to form CFUs and a significant delay or even prevention of transition toward dormancy. AC-overexpressing cells exhibited easier recovery from dormancy. In vivo, AC-overexpressing bacteria demonstrated significantly higher growth rates (virulence) in the lungs and spleens of infected mice compared to the control strain, and, unlike the latter, killed mice in the TB-resistant strain before month 8 of infection. Even in the absence of selecting hygromycin B, all pMindRv2212 CFUs retained the Rv2212 insert during in vivo growth, strongly suggesting that AC overexpression is beneficial for bacteria. Taken together, our results indicate that cAMP supports the maintenance of Mtb cells vitality under unfavorable conditions in vitro and their virulence in vivo.
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Affiliation(s)
- Margarita O Shleeva
- Federal Research Centre 'Fundamentals of Biotechnology' of the Russian Academy of Sciences, A. N. Bach Institute of BiochemistryMoscow, Russia
| | - Tatyana K Kondratieva
- Department of Immunology, Laboratory for Immunogenetics, Central Institute for TuberculosisMoscow, Russia
| | - Galina R Demina
- Federal Research Centre 'Fundamentals of Biotechnology' of the Russian Academy of Sciences, A. N. Bach Institute of BiochemistryMoscow, Russia
| | - Elvira I Rubakova
- Department of Immunology, Laboratory for Immunogenetics, Central Institute for TuberculosisMoscow, Russia
| | - Anna V Goncharenko
- Federal Research Centre 'Fundamentals of Biotechnology' of the Russian Academy of Sciences, A. N. Bach Institute of BiochemistryMoscow, Russia
| | - Alexander S Apt
- Department of Immunology, Laboratory for Immunogenetics, Central Institute for TuberculosisMoscow, Russia.,Department of Immunology, School of Biology, Lomonosov Moscow State UniversityMoscow, Russia
| | - Arseny S Kaprelyants
- Department of Immunology, Laboratory for Immunogenetics, Central Institute for TuberculosisMoscow, Russia
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16
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Moisenovich MM, Kulikov DA, Goncharenko AV, Arkhipova AY, Vasiljeva TV, Filyushkin YN, Arkhipova LV, Kotlyarova MS, Kulikov AV, Mashkov AE, Agapov II, Kirpichnikov MP. Regeneration of jejunal wall defect using an implant based on silk fibroin fibers. DOKL BIOCHEM BIOPHYS 2017; 472:12-14. [PMID: 28421432 DOI: 10.1134/s1607672917010045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Indexed: 02/04/2023]
Abstract
Regenerative properties of fibroin implant vitalized with allogeneic bone marrow cells were assessed. The study was performed using the experimental model of rat jejunum wall damage. Three weeks after surgery, we observed recovery of all layers of the jejunum wall at the site of injury and complete degradation of the implant material.
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Affiliation(s)
- M M Moisenovich
- Biological Faculty, Moscow State University, Moscow, 119234, Russia.
| | - D A Kulikov
- Vladimirskii Moscow Regional Research Clinical Institute, Moscow, 129110, Russia
| | - A V Goncharenko
- Biological Faculty, Moscow State University, Moscow, 119234, Russia
| | - A Y Arkhipova
- Biological Faculty, Moscow State University, Moscow, 119234, Russia
| | - T V Vasiljeva
- Biological Faculty, Moscow State University, Moscow, 119234, Russia
| | - Yu N Filyushkin
- Vladimirskii Moscow Regional Research Clinical Institute, Moscow, 129110, Russia
| | - L V Arkhipova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow oblast, 142290, Russia
| | - M S Kotlyarova
- Biological Faculty, Moscow State University, Moscow, 119234, Russia
| | - A V Kulikov
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow oblast, 142290, Russia
| | - A E Mashkov
- Vladimirskii Moscow Regional Research Clinical Institute, Moscow, 129110, Russia
| | - I I Agapov
- Shumakov Federal Research Center of Transplantation and Artificial Organs, Ministry of Healthcare of the Russian Federation, Moscow, 113182, Russia
| | - M P Kirpichnikov
- Biological Faculty, Moscow State University, Moscow, 119234, Russia
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17
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Moisenovich MM, Malyuchenko NV, Arkhipova AY, Kotlyarova MS, Davydova LI, Goncharenko AV, Agapova OI, Drutskaya MS, Bogush VG, Agapov II, Debabov VG, Kirpichnikov MP. Novel 3D-microcarriers from recombinant spidroin for regenerative medicine. DOKL BIOCHEM BIOPHYS 2015; 463:232-5. [PMID: 26335819 DOI: 10.1134/s1607672915040109] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Indexed: 12/12/2022]
Abstract
Microcarriers generated from recombinant spidroin 1F9 are suitable for use as an injection material. The microcarriers were a heterogeneous mixture of microgel particles ranging from 50 to 300 µm in size with the predominance of particles of 50-150 µm. The surface of these microparticles had a complex topography and ensured efficient cultivation of primary and immortalized fibroblasts. Intradermal injections of microgel suspensions into the area of full-thickness skin wounds did not lead to the development of acute inflammation in mice; instead, they accelerated the recovery of skin tissue and stimulated neurogenesis and angiogenesis.
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18
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Goncharenko AV, Nazarov VU. Giant nonlocal lossless permittivity at optical frequencies. Opt Express 2015; 23:20439-20449. [PMID: 26367898 DOI: 10.1364/oe.23.020439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We show how to achieve a giant permittivity combined with negligible losses in both the visible and the near-IR for composites made of alternating layers of plasmonic and gain materials as the electric field is directed normally to the layers. The effects of nonlocality are taken into account that makes the method quite realistic. Solving the dispersion equation for eigenmodes of an infinite layered composite, we show that both propagating and nonpropagating modes can be excited, that leads to the realization of a giant nonlocal permittivity. Both phase and group velocities for the propagating eigenmode have been calculated showing that slow light can be achieved in the system under study. The results obtained open new possibilities for designing nanolaser, slow-light, superresolution imaging devices, etc.
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19
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Demidenok OI, Kaprelyants AS, Goncharenko AV. Toxin-antitoxinvapBClocus participates in formation of the dormant state inMycobacterium smegmatis. FEMS Microbiol Lett 2014; 352:69-77. [DOI: 10.1111/1574-6968.12380] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 12/31/2013] [Accepted: 12/31/2013] [Indexed: 01/01/2023] Open
Affiliation(s)
- Oksana I. Demidenok
- Laboratory of Biochemistry of Stresses in Microorganisms; A.N. Bach Institute of Biochemistry Russian Academy of Sciences; Moscow Russia
| | - Arseny S. Kaprelyants
- Laboratory of Biochemistry of Stresses in Microorganisms; A.N. Bach Institute of Biochemistry Russian Academy of Sciences; Moscow Russia
| | - Anna V. Goncharenko
- Laboratory of Biochemistry of Stresses in Microorganisms; A.N. Bach Institute of Biochemistry Russian Academy of Sciences; Moscow Russia
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20
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Goncharenko AV, Venger EF, Pinchuk AO. Homogenization of quasi-1d metamaterials and the problem of extended bandwidth. Opt Express 2014; 22:2429-2442. [PMID: 24663534 DOI: 10.1364/oe.22.002429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We derive approximate analytical expressions for the effective permittivity tensor of two-phase metamaterials whose geometry is close to one-dimensional (quasi-one-dimensional metamaterials). Specifically, we consider the metamaterial made of parallel slabs with width given by a linear or parabolic function. Using our approach, the design of epsilon-near-zero, ultra-low and high refractive index metallodielectric metamaterials with extended bandwidth has been demonstrated. In addition, generalizations to the three-dimensional case and some limitations of the presented technique are briefly considered.
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21
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Demidenok OI, Goncharenko AV. [Bacterial toxin-antitoxin systems and perspectives for their application in medicine: a review]. Prikl Biokhim Mikrobiol 2013; 49:539-546. [PMID: 25434177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The structure of various toxin-antitoxin (TA) families and the principles of their action are reviewed. TA loci are widely distributed in the genomes of eubacteria and archaea. Most TA systems are two-component and function in a similar way: a stable toxin alters vitally important cell functions and can be inactivated by a labile antitoxin.
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22
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Artsatbanov VY, Vostroknutova GN, Shleeva MO, Goncharenko AV, Zinin AI, Ostrovsky DN, Kapreliants AS. Influence of oxidative and nitrosative stress on accumulation of diphosphate intermediates of the non-mevalonate pathway of isoprenoid biosynthesis in corynebacteria and mycobacteria. Biochemistry (Mosc) 2012; 77:362-71. [PMID: 22809155 DOI: 10.1134/s0006297912040074] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Artificial generation of oxygen superoxide radicals in actively growing cultures of Mycobacterium tuberculosis, Myc. smegmatis, and Corynebacterium ammoniagenes is followed by accumulation in the bacterial cells of substantial amounts of 2-C-methyl-D-erythritol-2,4-cyclodiphosphate (MEcDP) - an intermediate of the non-mevalonate pathway of isoprenoid biosynthesis (MEP) - most possibly due to the interaction of the oxygen radicals with the 4Fe-4S group in the active center and inhibition of the enzyme (E)-4-oxy-3-methylbut-2-enyl diphosphate synthase (IspG). Cadmium ions known to inhibit IspG enzyme in chloroplasts (Rivasseau, C., Seemann, M., Boisson, A. M., Streb, P., Gout, E., Douce, R., Rohmer, M., and Bligny, R. (2009) Plant Cell Environ., 32, 82-92), when added to culture of Myc. smegmatis, substantially increase accumulation of MEcDP induced by oxidative stress with no accumulation of other organic phosphate intermediates in the cell. Corynebacterium ammoniagenes'', well-known for its ability to synthesize large amounts of MEcDP, was also shown to accumulate this unique cyclodiphosphate in actively growing culture when NO at low concentration is artificially generated in the medium. A possible role of the MEP-pathway of isoprenoid biosynthesis and a role of its central intermediate MEcDP in bacterial response to nitrosative and oxidative stress is discussed.
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Affiliation(s)
- V Yu Artsatbanov
- Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky pr. 33, 119071 Moscow, Russia
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23
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Anuchin AM, Goncharenko AV, Demidenok OI, Kaprel'iants AS. [Histone-like proteins of bacteria (review)]. Prikl Biokhim Mikrobiol 2011; 47:635-641. [PMID: 22288191] [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: 05/31/2023]
Abstract
Four major families of bacterial histone-like proteins (HU, IHF, H-NS, FIS), united on the basis of structural similarity and performing specific structural and regulatory functions in the cell, are discussed. Histone-like proteins perform topological modification of the chromosome (twisting, bending, and folding) and directly regulate the functioning of promoters of individual operons. Histone-like proteins are critical for the regulation of cell metabolism, are involved in the response to environmental changes, and play a key role in the transition to and maintenance of the quiescent state of bacteria.
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Anuchin AM, Goncharenko AV, Galon IV, Demidenok OI, Kudykina IK, Moĭsenovich MM, Muliukin AL, Kaprel'iants AS. [The model of resting forms of mycobacteria for testing of drugs for latent forms of tuberculosis]. Prikl Biokhim Mikrobiol 2010; 46:308-314. [PMID: 20586283] [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: 05/29/2023]
Abstract
The new model of obtaining of ovoid resting forms Mycobacterium smegmatis, which are morphologically different from vegetative (rod-like) cells, was developed. Ovoid forms were characterized by a drastically decreased level of metabolic activity, an increased stability to heat processing and antibiotics action, and also by prolonged (more than 2 months) storage time preserving colony-forming ability. Obtained resting forms of mycobacteria may be used in test-systems for checking efficiency of new medical agents against latent forms of tuberculosis and determination of role of these of those genes in entering rest state.
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Anuchin AM, Goncharenko AV, Demina GR, Mulyukin AL, Ostrovsky DN, Kaprelyants AS. The role of histone-like protein, Hlp, in Mycobacterium smegmatis dormancy. FEMS Microbiol Lett 2010; 308:101-7. [PMID: 20497227 DOI: 10.1111/j.1574-6968.2010.01988.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The role of histone-like protein (Hlp) in the development of a dormant state in long-incubated stationary-phase Mycobacterium smegmatis cells was studied in two models: (1) adoption of 'nonculturable' (NC) state, which is reversible due to resuscitation with proteinaceous resuscitation-promoting factor (Rpf) and (2) the formation of morphologically distinct, ovoid resting forms. In the first model, inactivation of the hlp gene resulted in prolongation of culturability of starved cells followed by irreversible nonculturability when mycobacterial cells were unresponsive to resuscitation with Rpf. In the second model, M. smegmatis strain with the inactivated hlp gene was able to form dormant ovoid cells, but they were less resistant to heating and UV radiation than those of wild-type strain. The susceptibility of ovoid cells produced by Delta hlp mutant to these damaging factors was probably due to a less condensed state of DNA, as revealed by fluorescent microscopy and DAPI staining. Evidently, Hlp is essential for cell viability at a later stage of NC dormancy or provides a greater stability of specialized dormant forms.
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Affiliation(s)
- Aleksey M Anuchin
- Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, Russia.
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Koltunov V, Greenblatt CL, Goncharenko AV, Demina GR, Klein BY, Young M, Kaprelyants AS. Structural changes and cellular localization of resuscitation-promoting factor in environmental isolates of Micrococcus luteus. Microb Ecol 2010; 59:296-310. [PMID: 19730766 DOI: 10.1007/s00248-009-9573-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Accepted: 07/31/2009] [Indexed: 05/28/2023]
Abstract
Dormancy among nonsporulating actinobacteria is now a widely accepted phenomenon. In Micrococcus luteus, the resuscitation of dormant cells is caused by a small secreted protein (resuscitation-promoting factor, or Rpf) that is found in "spent culture medium." Rpf is encoded by a single essential gene in M. luteus. Homologs of Rpf are widespread among the high G + C Gram-positive bacteria, including mycobacteria and streptomycetes, and most organisms make several functionally redundant proteins. M. luteus Rpf comprises a lysozyme-like domain that is necessary and sufficient for activity connected through a short linker region to a LysM motif, which is present in a number of cell-wall-associated enzymes. Muralytic activity is responsible for resuscitation. In this report, we characterized a number of environmental isolates of M. luteus, including several recovered from amber. There was substantial variation in the predicted rpf gene product. While the lysozyme-like and LysM domains showed little variation, the linker region was elongated from ten amino acid residues in the laboratory strains to as many as 120 residues in one isolate. The genes encoding these Rpf proteins have been characterized, and a possible role for the Rpf linker in environmental adaptation is proposed. The environmental isolates show enhanced resistance to lysozyme as compared with the laboratory strains and this correlates with increased peptidoglycan acetylation. In strains that make a protein with an elongated linker, Rpf was bound to the cell wall, rather than being released to the growth medium, as occurs in reference strains. This rpf gene was introduced into a lysozyme-sensitive reference strain. Both rpf genes were expressed in transformants which showed a slight but statistically significant increase in lysozyme resistance.
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Affiliation(s)
- Viktoria Koltunov
- Kuvin Centre and Department of Microbiology and Molecular Genetics, Hebrew University, Jerusalem 91120, Israel
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Demina GR, Makarov VA, Nikitushkin VD, Ryabova OB, Vostroknutova GN, Salina EG, Shleeva MO, Goncharenko AV, Kaprelyants AS. Finding of the low molecular weight inhibitors of resuscitation promoting factor enzymatic and resuscitation activity. PLoS One 2009; 4:e8174. [PMID: 20016836 PMCID: PMC2790607 DOI: 10.1371/journal.pone.0008174] [Citation(s) in RCA: 29] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Accepted: 11/08/2009] [Indexed: 11/19/2022] Open
Abstract
Background Resuscitation promoting factors (RPF) are secreted proteins involved in reactivation of dormant actinobacteria, including Mycobacterium tuberculosis. They have been considered as prospective targets for the development of new anti-tuberculosis drugs preventing reactivation of dormant tubercle bacilli, generally associated with latent tuberculosis. However, no inhibitors of Rpf activity have been reported so far. The goal of this study was to find low molecular weight compounds inhibiting the enzymatic and biological activities of Rpfs. Methodology/Principal Findings Here we describe a novel class of 2-nitrophenylthiocyanates (NPT) compounds that inhibit muralytic activity of Rpfs with IC50 1–7 µg/ml. Fluorescence studies revealed interaction of active NPTs with the internal regions of the Rpf molecule. Candidate inhibitors of Rpf enzymatic activity showed a bacteriostatic effect on growth of Micrococcus luteus (in which Rpf is essential for growth protein) at concentrations close to IC50. The candidate compounds suppressed resuscitation of dormant (“non-culturable”) cells of M. smegmatis at 1 µg/ml or delayed resuscitation of dormant M. tuberculosis obtained in laboratory conditions at 10 µg/ml. However, they did not inhibit growth of active mycobacteria under these concentrations. Conclusions/Significance NPT are the first example of low molecular weight compounds that inhibit the enzymatic and biological activities of Rpf proteins.
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Goncharenko AV, Chang YC. Effect of the incident angle on the electric near field of a conical probe for plane wave and Gaussian beam illumination. Opt Express 2007; 15:11517-11529. [PMID: 19547509 DOI: 10.1364/oe.15.011517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We consider a simple analytical model for the electric near field of a semi-infinite conical probe and apply it to study the incident angle dependence of the field for the case of side illumination by both the plane wave and the Gaussian beam. The electric near field is shown to peak when approaching the grazing incidence. In some cases, a peak can also occur at an incident angle somewhat below 90 degrees . The results obtained are in qualitative agreement with those for a thin semi-infinite wire and previously published results for the finite-size conical probes.
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29
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Goncharenko AV, Ershov IV, Salina EG, Wiesner J, Vostroknutova GN, Sandanov AA, Kapel'iants AS, Ostrovskiĭ DN. [The role of 2-C-methylerythritol-2,4-cyclopyrophosphate in the resuscitation of the "nonculturable" forms of Mycobacterium smegmatis]. Mikrobiologiia 2007; 76:172-8. [PMID: 17583212] [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: 05/15/2023]
Abstract
2-C-Methyl-D-erythritol-2,4-cyclopyrophosphate (MEC), an intermediate of the biosynthesis of isoprenoid compounds in bacteria, was found to be capable of exerting a resuscitating effect on resting Mycobacterium smegmatis cells. The introduction of an additional copy of the ispE gene encoding cytidyl-methylerythritol kinase, an enzyme involved in MEC synthesis in M. smegmatis, resulted in the emergence of a capacity for spontaneous reactivation of "nonculturable" M. smegmatis cells, which is not characteristic of the wild-type cells of this species. The involvement of MEC in the transition from the "nonculturable" state to the state of active growth is indicative of a previously unknown function of MEC, assumed to consist in regulation of the bacterial genome activity.
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Goncharenko AV, Chang HC, Wang JK. Electric near-field enhancing properties of a finite-size metal conical nano-tip. Ultramicroscopy 2007; 107:151-7. [PMID: 16876947 DOI: 10.1016/j.ultramic.2006.06.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2005] [Revised: 06/05/2006] [Accepted: 06/16/2006] [Indexed: 11/29/2022]
Abstract
Finite-difference time-domain (FDTD) technique simulations are performed to study the near-field resonance properties of a silver conical nano-tip with a rounded end. Varying the tip geometry, we have computed the electric field distribution, as well as the electric field enhancement factor in the immediate vicinity of the tip apex. The aim of this study is to find optimal geometric parameters of the conical tip, such as its angle and length, in order to maximize the electric field enhancement factor. The increase of the tip length is shown to result in a redshift of the tip resonance wavelength. In addition, some subsidiary (non-dipole) peaks appear for relatively long tips. The peak enhancement values for the small-angle tips increase with the tip length while those for the large-angle ones decrease with it. At the same time, the dependencies of the field enhancement on the cone angle exhibit non-monotonic behavior. In other words, an optimal angle exists allowing one to maximize the electric near field. Finally, the effect of the supporting dielectric medium on the electric field near the tip apex is discussed. In the approximation used, the effect is shown to leave the main conclusions unchanged.
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Affiliation(s)
- A V Goncharenko
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan 106, ROC.
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Telkov MV, Demina GR, Voloshin SA, Salina EG, Dudik TV, Stekhanova TN, Mukamolova GV, Kazaryan KA, Goncharenko AV, Young M, Kaprelyants AS. Proteins of the Rpf (resuscitation promoting factor) family are peptidoglycan hydrolases. Biochemistry (Moscow) 2006; 71:414-22. [PMID: 16615861 DOI: 10.1134/s0006297906040092] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The secreted Micrococcus luteus protein, Rpf, is required for successful resuscitation of dormant "non-culturable" M. luteus cells and for growth stimulation in poor media. The biochemical mechanism of Rpf action remained unknown. Theoretical predictions of Rpf domain architecture and organization, together with a recent NMR analysis of the protein structure, indicate that the conserved Rpf domain has a lysozyme-like fold. In the present study, we found that both the secreted native protein and the recombinant protein lyse crude preparations of M. luteus cell walls. They also hydrolyze 4-methylumbelliferyl-beta-D-N,N',N''-triacetylchitotrioside, a synthetic substrate for peptidoglycan muramidases, with optimum activity at pH 6. The Rpf protein also has weak proteolytic activity against N-CBZ-Gly-Gly-Arg-beta-naphthylamide, a substrate for trypsin-like enzymes. Rpf activity towards 4-methylumbelliferyl-beta-D-N,N',N''-triacetylchitotrioside was reduced when the glutamate residue at position 54, invariant for all Rpf family proteins and presumably involved in catalysis, was altered. The same amino acid substitution resulted in impaired resuscitation activity of Rpf. The data indicate that Rpf is a peptidoglycan-hydrolyzing enzyme, and strongly suggest that this specific activity is responsible for its growth promotion and resuscitation activity. A possible mechanism of Rpf-mediated resuscitation is discussed.
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Affiliation(s)
- M V Telkov
- Bach Institute of Biochemistry, Russian Academy of Sciences, 119071 Moscow, Russia
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Abstract
Using thermal deposition technique, we have prepared Au/Teflon thin films on glass substrates. To control the film microstructure, both TEM and AFM characterization have been carried out. The visible optical transmission spectra have been measured in-situ. The peak positions and linewidths in the spectra have been identified in terms of the gold nanoparticle shape, size, and arrangement. The results obtained provide evidence for formation of both sphere-like and cylinder-like gold nanoparticles in the films. The fraction of each kind of the particles depends on whether the plasma treatment has been used. The treatment is shown to enhance the fraction of the cylinder-like particles.
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Affiliation(s)
- A V Goncharenko
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei, Taiwan 106, Republic of China
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Goncharenko AV, Venger EF. Percolation threshold for Bruggeman composites. Phys Rev E Stat Nonlin Soft Matter Phys 2004; 70:057102. [PMID: 15600798 DOI: 10.1103/physreve.70.057102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2004] [Indexed: 05/24/2023]
Abstract
Using a simple phenomenological approach, we calculate the percolation threshold for Bruggeman composites having microgeometry of two kinds. Both kinds of composites consist of spheroids whose shape follows the Beta distribution. At the same time, the first one is a mixture of spheroids equally oriented along their revolution axis. In this case the percolation threshold is shown to be the same as for an assembly of equally oriented identical spheroids whose shape corresponds to the most probable shape of the distribution. For such composites the percolation threshold can vary between 0 and 1. The second one is a random mixture of the spheroids. In this case the percolation threshold is expressed in terms of the Gauss hypergeometric function; it is shown to vary between 0 and 1/3. The derived analytical results are supplemented with numerical calculations carried out for different values of the Beta distribution parameters.
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Affiliation(s)
- A V Goncharenko
- Institute of Semiconductor Physics, National Academy of Sciences of Ukraine, 41 Nauki avenue, 03028 Kyiv, Ukraine.
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Ostrovskiĭ DN, Demina GP, Deriabina II, Goncharenko AV, Eberl M, Shumaev KB, Shashkov AS. [Properties of 2-C-methyl-D-erythritol 2,4-cyclopyrophosphate--an intermediate in the non-mevalonate isoprenoid biosynthesis]. Prikl Biokhim Mikrobiol 2003; 39:565-70. [PMID: 14593871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
Extraction and purification from the biomass of Corynebacterium ammoniagenes of 2-C-methyl-D-erhythritol 2,4-cyclopyrophosphate (MEC) was associated with its spontaneous transformation into a number of derivatives (which was due to pyrophosphate bond lability and the formation of complexes with metals). These derivatives included 1,2-cyclophospho-4-phosphate, 2,4-diphosphate, 2,3-cyclophosphate, 1,4-diphosphate, and 3,5-diphosphate (identified by 1H, 31P, and 13C NMR spectroscopy) and accounted for about 10% MEC. When added to a solution of DNA in the presence of the Fenton reagent, MEC prevented DNA decomposition. In addition, MEC slowed down the interaction of the reagent with tempol radicals, which indicates that complexation of ferrous ions by MEC attenuates their ability to catalyze the formation of hydroxyl radicals from hydrogen peroxide. In the presence of 0.23 mM MEC, the rate of respiration of rat liver mitochondria increased 1.8 times. At 0.1-1.0 mM, MEC activated in vitro proliferation of human Vgamma9 T-cells. It is suggested that MEC acts as an endogenous stabilizing agent for bacterial cells subjected to oxidative stress and as an immunomodulator for eukaryotic hosts.
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Affiliation(s)
- D N Ostrovskiĭ
- Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, 119071 Russia.
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Goncharenko AV, Filatova TN, Padiukov LN, Baturo AP. [Common epitopes of protein antigens in Neisseria and Moraxella]. Zh Mikrobiol Epidemiol Immunobiol 2000:15-9. [PMID: 11220956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Cross reactions between N. meningitidis and M. catarrhalis proteins were studied with the use of a panel of monoclonal antibodies to M. catarrhalis protein antigens. All antigenic preparations under study were shown to give cross reactions between N. meningitidis serotype porin of 39 kD (strain B125) and M. catarrhalis proteins of 40-41 kD. These M. catarrhalis proteins belonged to main proteins of class F and had the function of porins in the cell. In addition, the epitope of 41-kD antigen, detected by monoclonal antibodies 3E10, is common for both N. meningitidis porin and N. meningitidis iron-regulated proteins of 70 and 50 kD. The epitope of M. catarrhalis protein of 67 kD, detected by monoclonal antibodies 1G6, is common for N. meningitidis porin and N. meningitidis iron-regulated proteins of 50 and 55 kD.
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Affiliation(s)
- A V Goncharenko
- Mechnikov Research Institute for Vaccines and Sera, Moscow, Russia
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Goncharenko AV, Filatova TN, Padiukov LN. [Protein antigens of Branhamella (Moraxella) catarrhalis and Neisseria meningitidis]. Zh Mikrobiol Epidemiol Immunobiol 1998:98-102. [PMID: 9949519] [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] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Affiliation(s)
- A V Goncharenko
- Mechnikov Research Institute for Vaccines and Sera, Moscow, Russia
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Shaposhnikov AV, Goncharenko AV. [Leukocytic index of intoxication in acute surgical diseases of the abdominal organs]. Klin Khir (1962) 1985:66. [PMID: 4021353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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