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Ivanov YD, Ableev AN, Shumov ID, Ivanova IA, Vaulin NV, Lebedev DV, Bukatin AS, Mukhin IS, Archakov AI. Registration of Functioning of a Single Horseradish Peroxidase Macromolecule with a Solid-State Nanopore. Int J Mol Sci 2023; 24:15636. [PMID: 37958620 PMCID: PMC10647385 DOI: 10.3390/ijms242115636] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 11/15/2023] Open
Abstract
Currently, nanopore-based technology for the determination of the functional activity of single enzyme molecules continues its development. The use of natural nanopores for studying single enzyme molecules is known. At that, the approach utilizing artificial solid-state nanopores is also promising but still understudied. Herein, we demonstrate the use of a nanotechnology-based approach for the investigation of the enzymatic activity of a single molecule of horseradish peroxidase with a solid-state nanopore. The artificial 5 nm solid-state nanopore has been formed in a 40 nm thick silicon nitride structure. A single molecule of HRP has been entrapped into the nanopore. The activity of the horseradish peroxidase (HRP) enzyme molecule inserted in the nanopore has been monitored by recording the time dependence of the ion current through the nanopore in the course of the reaction of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonate) (ABTS) oxidation reaction. We have found that in the process of ABTS oxidation in the presence of 2.5 mM hydrogen peroxide, individual HRP enzyme molecules are able to retain activity for approximately 700 s before a decrease in the ion current through the nanopore, which can be explained by structural changes of the enzyme.
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Affiliation(s)
- Yuri D. Ivanov
- Institute of Biomedical Chemistry, 10, Pogodinskaya St., Moscow 119121, Russia; (A.N.A.); (I.D.S.); (I.A.I.); (A.I.A.)
| | - Alexander N. Ableev
- Institute of Biomedical Chemistry, 10, Pogodinskaya St., Moscow 119121, Russia; (A.N.A.); (I.D.S.); (I.A.I.); (A.I.A.)
| | - Ivan D. Shumov
- Institute of Biomedical Chemistry, 10, Pogodinskaya St., Moscow 119121, Russia; (A.N.A.); (I.D.S.); (I.A.I.); (A.I.A.)
| | - Irina A. Ivanova
- Institute of Biomedical Chemistry, 10, Pogodinskaya St., Moscow 119121, Russia; (A.N.A.); (I.D.S.); (I.A.I.); (A.I.A.)
| | - Nikita V. Vaulin
- Laboratory of Renewable Energy Sources, St. Petersburg Academic University, 8/3, Khlopina st., St. Petersburg 194021, Russia; (N.V.V.); (D.V.L.); (A.S.B.); (I.S.M.)
- Institute for Analytical Instrumentation RAS, 31-33 Lit. A, Ivana Chernykh St., St. Petersburg 198095, Russia
| | - Denis V. Lebedev
- Laboratory of Renewable Energy Sources, St. Petersburg Academic University, 8/3, Khlopina st., St. Petersburg 194021, Russia; (N.V.V.); (D.V.L.); (A.S.B.); (I.S.M.)
- Institute for Analytical Instrumentation RAS, 31-33 Lit. A, Ivana Chernykh St., St. Petersburg 198095, Russia
- Institute of Chemistry, Saint Petersburg State University, 7/9, Universitetskaya Nab., St. Petersburg 199034, Russia
| | - Anton S. Bukatin
- Laboratory of Renewable Energy Sources, St. Petersburg Academic University, 8/3, Khlopina st., St. Petersburg 194021, Russia; (N.V.V.); (D.V.L.); (A.S.B.); (I.S.M.)
- Institute for Analytical Instrumentation RAS, 31-33 Lit. A, Ivana Chernykh St., St. Petersburg 198095, Russia
| | - Ivan S. Mukhin
- Laboratory of Renewable Energy Sources, St. Petersburg Academic University, 8/3, Khlopina st., St. Petersburg 194021, Russia; (N.V.V.); (D.V.L.); (A.S.B.); (I.S.M.)
- Higher School of Engineering Physics, Peter the Great Polytechnic University, 26, Polytehnicheskaya St., St. Petersburg 194021, Russia
| | - Alexander I. Archakov
- Institute of Biomedical Chemistry, 10, Pogodinskaya St., Moscow 119121, Russia; (A.N.A.); (I.D.S.); (I.A.I.); (A.I.A.)
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Lebedev DV, Solomonov NA, Dvoretckaia LN, Shkoldin VA, Permyakov DV, Arkhipov AV, Mozharov AM, Pavlov DV, Kuchmizhak AA, Mukhin IS. Femtosecond Laser-Printed Gold Nanoantennas for Electrically Driven and Bias-Tuned Nanoscale Light Sources Operating in Visible and Infrared Spectral Ranges. J Phys Chem Lett 2023:5134-5140. [PMID: 37252711 DOI: 10.1021/acs.jpclett.3c00650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Nanoscale electrically driven light-emitting sources with tunable wavelength represent a milestone for implementation of integrated optoelectronic chips. Plasmonic nanoantennas exhibiting an enhanced local density of optical states (LDOS) and strong Purcell effect hold promise for fabrication of bright nanoscale light emitters. Here, we justify gold parabola-shaped nanobumps and their ordered arrays produced by direct ablation-free femtosecond laser printing as broadband plasmonic light sources electrically excited by a probe of scanning tunneling microscope (STM). I-V curves of the probe-nanoantenna tunnel junction reveal characteristic bias voltages correlating with visible-range localized (0.55 and 0.85 μm) and near-IR (1.65 and 1.87 μm) collective plasmonic modes of these nanoantennas. These multiband resonances confirmed by optical spectroscopy and full-wave simulations provide enhanced LDOS for efficient electrically driven and bias-tuned light emission. Additionally, our studies confirm remarkable applicability of STM for accurate study of optical modes supported by the plasmonic nanoantennas at nanoscale spatial resolution.
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Affiliation(s)
- Denis V Lebedev
- Saint Petersburg Academic University, St. Petersburg, 194021 Russia
- Saint Petersburg State University, St. Petersburg, 199034, Russia
- Institute for Analytical Instrumentation RAS, St. Petersburg, 190103, Russia
| | | | | | - Vitaliy A Shkoldin
- Saint Petersburg Academic University, St. Petersburg, 194021 Russia
- ITMO University, St. Petersburg, 197101, Russia
| | | | - Alexander V Arkhipov
- Peter the Great Saint Petersburg Polytechnic University, St. Petersburg, 195251, Russia
| | | | - Dmitry V Pavlov
- Institute for Automation and Control Processes, FEB RAS, Vladivostok, 690041, Russia
| | - Aleksandr A Kuchmizhak
- Institute for Automation and Control Processes, FEB RAS, Vladivostok, 690041, Russia
- Pacific Quantum Center, Far Eastern Federal University, Vladivostok, 690922, Russia
| | - Ivan S Mukhin
- Saint Petersburg Academic University, St. Petersburg, 194021 Russia
- ITMO University, St. Petersburg, 197101, Russia
- Peter the Great Saint Petersburg Polytechnic University, St. Petersburg, 195251, Russia
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Lebedev DV, Shkoldin VA, Mozharov AM, Larin AO, Permyakov DV, Samusev AK, Petukhov AE, Golubok AO, Arkhipov AV, Mukhin IS. Nanoscale Electrically Driven Light Source Based on Hybrid Semiconductor/Metal Nanoantenna. J Phys Chem Lett 2022; 13:4612-4620. [PMID: 35588008 DOI: 10.1021/acs.jpclett.2c00986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A micro- or nanosized electrically controlled source of optical radiation is one of the key elements in optoelectronic systems. The phenomenon of light emission via inelastic tunneling (LEIT) of electrons through potential barriers or junctions opens up new possibilities for development of such sources. In this work, we present a simple approach for fabrication of nanoscale electrically driven light sources based on LEIT. We employ STM lithography to locally modify the surface of a Si/Au film stack via heating, which is enabled by a high-density tunnel current. Using the proposed technique, hybrid Si/Au nanoantennas with a minimum diameter of 60 nm were formed. Studying both electronic and optical properties of the obtained nanoantennas, we confirm that the resulting structures can efficiently emit photons in the visible range because of inelastic scattering of electrons. The proposed approach allows for fabrication of nanosized hybrid nanoantennas and studying their properties using STM.
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Affiliation(s)
- Denis V Lebedev
- St. Petersburg Academic University, 8/3 Khlopina str., St. Petersburg 194021, Russia
- Saint Petersburg State University, 7/9 Universitetskaya nab., St. Petersburg 199034, Russia
- Institute for Analytical Instrumentation RAS, 26 Rizhskii pr., St. Petersburg 190103, Russia
| | - Vitaly A Shkoldin
- St. Petersburg Academic University, 8/3 Khlopina str., St. Petersburg 194021, Russia
- ITMO University, 9 Kronverksky pr., St. Petersburg 197101, Russia
| | - Alexey M Mozharov
- Saint Petersburg State University, 7/9 Universitetskaya nab., St. Petersburg 199034, Russia
| | - Artem O Larin
- ITMO University, 9 Kronverksky pr., St. Petersburg 197101, Russia
| | | | - Anton K Samusev
- ITMO University, 9 Kronverksky pr., St. Petersburg 197101, Russia
| | - Anatoly E Petukhov
- Saint Petersburg State University, 7/9 Universitetskaya nab., St. Petersburg 199034, Russia
| | - Alexander O Golubok
- Institute for Analytical Instrumentation RAS, 26 Rizhskii pr., St. Petersburg 190103, Russia
| | - Alexander V Arkhipov
- Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya, 29, St. Petersburg 195251, Russia
| | - Ivan S Mukhin
- St. Petersburg Academic University, 8/3 Khlopina str., St. Petersburg 194021, Russia
- Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya, 29, St. Petersburg 195251, Russia
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4
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Lebedev DV, Shkoldin VA, Mozharov AM, Permyakov DV, Dvoretckaia LN, Bogdanov AA, Samusev AK, Golubok AO, Mukhin IS. Scanning Tunneling Microscopy-Induced Light Emission and I( V) Study of Optical Near-Field Properties of Single Plasmonic Nanoantennas. J Phys Chem Lett 2021; 12:501-507. [PMID: 33373245 DOI: 10.1021/acs.jpclett.0c03039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Electrically driven plasmonic nanoantennas can be integrated as a local source of the optical signal of advanced photonic schemes for on-chip data processing. The inelastic electron tunneling provides the photon generation or launch of surface plasmon waves. This process can be enhanced by the local density of optical states of nanoantennas. In this paper, we used scanning tunnel microscopy-induced light emission to probe the local optoelectronic properties of single gold nanodiscs. The electromagnetic field distribution in the vicinity of plasmonic structures was investigated with high spatial resolution. The obtained photon maps reveal the nonuniform distribution of electromagnetic near-fields, which is consistent with nanoantenna optical modes. Also, the analysis of derived I(V) curves showed a direct correlation between the nanoantenna optical states and the appearance of features on current-voltage characteristics.
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Affiliation(s)
- Denis V Lebedev
- Saint Petersburg State University, 7/9 Universitetskaya nab., St. Petersburg 199034, Russia
- Institute for Analytical Instrumentation RAS, 26 Rizhskii pr., St. Petersburg 190103, Russia
- St. Petersburg Academic University, 8/3 Khlopina str., St. Petersburg 194021, Russia
| | - Vitaliy A Shkoldin
- St. Petersburg Academic University, 8/3 Khlopina str., St. Petersburg 194021, Russia
- ITMO University, 9 Kronverksky pr., St. Petersburg 197101, Russia
| | - Alexey M Mozharov
- St. Petersburg Academic University, 8/3 Khlopina str., St. Petersburg 194021, Russia
| | | | - Lilia N Dvoretckaia
- St. Petersburg Academic University, 8/3 Khlopina str., St. Petersburg 194021, Russia
| | | | - Anton K Samusev
- ITMO University, 9 Kronverksky pr., St. Petersburg 197101, Russia
| | - Alexander O Golubok
- Institute for Analytical Instrumentation RAS, 26 Rizhskii pr., St. Petersburg 190103, Russia
| | - Ivan S Mukhin
- St. Petersburg Academic University, 8/3 Khlopina str., St. Petersburg 194021, Russia
- ITMO University, 9 Kronverksky pr., St. Petersburg 197101, Russia
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5
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Shvetsov AV, Lebedev DV, Zabrodskaya YA, Shaldzhyan AA, Egorova MA, Vinogradova DS, Konevega AL, Gorshkov AN, Ramsay ES, Radulescu A, Sergeeva MV, Plotnikova MA, Komissarov AB, Taraskin AS, Lebedev KI, Garmay YP, Kuznetsov VV, Isaev-Ivanov VV, Vasin AV, Tsybalova LM, Egorov VV. Cold and distant: structural features of the nucleoprotein complex of a cold-adapted influenza A virus strain. J Biomol Struct Dyn 2020; 39:4375-4384. [PMID: 32490728 DOI: 10.1080/07391102.2020.1776636] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Two influenza A nucleoprotein variants (wild-type: G102R; and mutant: G102R and E292G) were studied with regard to macro-molecular interactions in oligomeric form (24-mers). The E292G mutation has been previously shown to provide cold adaptation. Molecular dynamics simulations of these complexes and trajectory analysis showed that the most significant difference between the obtained models was distance between nucleoprotein complex strands. The isolated complexes of two ribonucleoprotein variants were characterized by transmission electron microscopy and differential scanning fluorimetry (DSF). Presence of the E292G substitution was shown by DSF to affect nucleoprotein complex melting temperature. In the filament interface peptide model, it was shown that the peptide corresponding in primary structure to the wild-type NP (SGYDFEREGYS) is prone to temperature-dependent self-association, unlike the peptide corresponding to E292G substitution (SGYDFGREGYS). It was also shown that the SGYDFEREGYS peptide is capable of interacting with a monomeric nucleoprotein (wild type); this interaction's equilibrium dissociation constant is five orders of magnitude lower than for the SGYDFGREGYS peptide. Using small-angle neutron scattering (SANS), the supramolecular structures of isolated complexes of these proteins were studied at temperatures of 15, 32, and 37 °C. SANS data show that the structures of the studied complexes at elevated temperature differ from the rod-like particle model and react differently to temperature changes. The data suggest that the mechanism behind cold adaptation with E292G is associated with a weakening of the interaction between strands of the ribonucleoprotein complex and, as a result, the appearance of inter-chain interface flexibility necessary for complex function at low temperature.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- A V Shvetsov
- Petersburg Nuclear Physics Institute named by B. P, Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia.,Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia.,National Research Centre Kurchatov Institute, Moscow, Russia
| | - D V Lebedev
- Petersburg Nuclear Physics Institute named by B. P, Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia.,National Research Centre Kurchatov Institute, Moscow, Russia
| | - Y A Zabrodskaya
- Petersburg Nuclear Physics Institute named by B. P, Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia.,Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia.,National Research Centre Kurchatov Institute, Moscow, Russia.,Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia
| | - A A Shaldzhyan
- Petersburg Nuclear Physics Institute named by B. P, Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia.,Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia
| | - M A Egorova
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia
| | - D S Vinogradova
- Petersburg Nuclear Physics Institute named by B. P, Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia.,NanoTemper Technologies Rus, St. Petersburg, Russia
| | - A L Konevega
- Petersburg Nuclear Physics Institute named by B. P, Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia.,Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia.,National Research Centre Kurchatov Institute, Moscow, Russia
| | - A N Gorshkov
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia
| | - E S Ramsay
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia
| | - A Radulescu
- Jülich Centre, Neutron Science at Heinz Maier-Leibnitz Zentrum, Garching, Munich, Germany
| | - M V Sergeeva
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia
| | - M A Plotnikova
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia
| | - A B Komissarov
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia
| | - A S Taraskin
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia
| | - K I Lebedev
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia.,Pavlov First Saint Petersburg State Medical University, St. Petersburg, Russia
| | - Yu P Garmay
- Petersburg Nuclear Physics Institute named by B. P, Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia
| | - V V Kuznetsov
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia
| | - V V Isaev-Ivanov
- Petersburg Nuclear Physics Institute named by B. P, Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia
| | - A V Vasin
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia.,Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia.,St. Petersburg State Chemical-Pharmaceutical Academy, St. Petersburg, Russia
| | - L M Tsybalova
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia
| | - V V Egorov
- Petersburg Nuclear Physics Institute named by B. P, Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia.,National Research Centre Kurchatov Institute, Moscow, Russia.,Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia.,Federal State Budgetary Scientific Institution "Institute of Experimental Medicine", St. Petersburg, Russia
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Ryzhkov II, Lebedev DV, Solodovnichenko VS, Minakov AV, Simunin MM. On the origin of membrane potential in membranes with polarizable nanopores. J Memb Sci 2018. [DOI: 10.1016/j.memsci.2017.11.073] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Ryzhkov II, Lebedev DV, Solodovnichenko VS, Shiverskiy AV, Simunin MM. Induced-Charge Enhancement of the Diffusion Potential in Membranes with Polarizable Nanopores. Phys Rev Lett 2017; 119:226001. [PMID: 29286816 DOI: 10.1103/physrevlett.119.226001] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Indexed: 06/07/2023]
Abstract
When a charged membrane separates two salt solutions of different concentrations, a potential difference appears due to interfacial Donnan equilibrium and the diffusion junction. Here, we report a new mechanism for the generation of a membrane potential in polarizable conductive membranes via an induced surface charge. It results from an electric field generated by the diffusion of ions with different mobilities. For uncharged membranes, this effect strongly enhances the diffusion potential and makes it highly sensitive to the ion mobilities ratio, electrolyte concentration, and pore size. Theoretical predictions on the basis of the space-charge model extended to polarizable nanopores fully agree with experimental measurements in KCl and NaCl aqueous solutions.
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Affiliation(s)
- I I Ryzhkov
- Institute of Computational Modelling SB RAS, Federal Research Center KSC SB RAS, Akademgorodok 50, 660036 Krasnoyarsk, Russia
- Siberian Federal University, Svobodny 79, 660041 Krasnoyarsk, Russia
| | - D V Lebedev
- Institute of Computational Modelling SB RAS, Federal Research Center KSC SB RAS, Akademgorodok 50, 660036 Krasnoyarsk, Russia
| | - V S Solodovnichenko
- Institute of Computational Modelling SB RAS, Federal Research Center KSC SB RAS, Akademgorodok 50, 660036 Krasnoyarsk, Russia
| | - A V Shiverskiy
- Institute of Computational Modelling SB RAS, Federal Research Center KSC SB RAS, Akademgorodok 50, 660036 Krasnoyarsk, Russia
| | - M M Simunin
- Siberian Federal University, Svobodny 79, 660041 Krasnoyarsk, Russia
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Egorov VV, Zabrodskaya YA, Lebedev DV, Gorshkov AN, Kuklin AI. Structural features of the ionic self-complementary amyloidogenic peptide. ACTA ACUST UNITED AC 2017. [DOI: 10.1088/1742-6596/848/1/012022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Ilatovskiĭ AV, Lebedev DV, Filatov MV, Petukhov MG, Isaev-Ivanov VV. [Current insights into chromatin structure organization]. Tsitologiia 2012; 54:298-306. [PMID: 22724366] [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: 06/01/2023]
Abstract
This review summarizes current insights into organization of chromatin structure at different levels of DNA compaction. Analysis of available experimental data allowed concluding that only nucleosomal level of structural organization was sufficiently investigated, whereas structure of a 30-nm chromatin fiber remains an open issue. The data on the chromatin structure obtained at the level of the nucleus speak in favor of a biphasic fractal organization of chromatin.
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Chervinets IV, Botina SG, Glazova AA, Koroban NV, Chervinets VM, Samoukina AM, Gavrilova OA, Lebedev DV, Mironov AI. [Genetic identification and study of the ability of lactobacilli isolated from the oral cavity of healthy individuals to form biofilms]. Klin Lab Diagn 2011:44-46. [PMID: 21506386] [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
The highly antagonistic lactobacillus strains isolated from the oral cavity of human individuals were genetically passported as L. fermentum 39, L. rhamnosus 50, and L. rhamnosus 24, by applying the RAPD-PCR technique with two types of primers (M13, MSP). These lactobacillus strains showed high degrees of autoaggregation, surface hydrophobicity, coaggregation, and adhesion. These characteristics determine the obvious capacity of lactobacilli to form biofilms, which may be used to design new probiotic agents.
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Botina SG, Chervinets IV, Klimina KM, Koroban NV, Chervinets VM, Gavrilova OA, Lebedev DV, Mironov AI. [Genetic identification of antagonistically active lactobacillus strains isolated from the oral cavity of healthy individuals]. Klin Lab Diagn 2010:43-46. [PMID: 21313755] [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
Examination of dental deposits from 45 healthy individuals detected 3 lactobacillus strains showing a high antagonism toward test cultures. The api 50 CH "bio Merieux" test systems were employed to identify strains as Lactobacillus fermentum 39, Lactobacillus rhamnosus 24 and Lactobacillus paracasei 50. The results of analyzing the sequences of the 16S rRNA genes of the test strains confirmed this identification, except for the latter strain. The taxonomic status of the third strain L. rhamnosus 50 was determined by the bioinformative analysis of the nucleotide sequence of the 16S rRNA genes.
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Chervinets IV, Samoukina AM, Chervinets VM, Mikhaĭlova ES, Lebedev DV, Bondarenko VM. [Ability of human oral cavity indigenous lactobacilli to form biofilms]. Zh Mikrobiol Epidemiol Immunobiol 2010:80-83. [PMID: 21384592] [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: 05/30/2023]
Abstract
AIM To determine ability of lactobacilli strains indigenous for oral cavity of healthy persons to adhesion, autoaggregation, surface hydrophobicity, coaggregation and formation of biofilms. MATERIALS AND METHODS Twenty-three anatagonistically active isolates of lactobacilli, including 5 strains of Lactobacillus plantarum, 6--L. rhamnosus, 4--L. paracasei, and 8--L. fermentum, were studied. Characteristics of lactobacilli associated with adhesion, autoaggregation, surface hydrophobicity, coaggregation, and formation of biofilms were determined. RESULTS Bacteria were characterized by high and intermediate level of adhesion, autoaggregation, surface hydrophobicity, expressed ability to form biofilms and different coaggregation activity relative to test-strains Staphylococcus aureus, Escherichia coli, Candida albicans, Pseudomonas aeruginosa, and Bacillus subtilis. CONCLUSION Studied characteristics of lactobacilli could be used for development of new probiotics aimed at stabilization of oral cavity normoflora.
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Ogneva IV, Lebedev DV, Shenkman BS. [Lateral mechanics of muscle fibres and its role in signaling]. Biofizika 2009; 54:522-528. [PMID: 19569516] [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: 05/28/2023]
Abstract
Different aspects of the lateral mechanics of muscle fibres have been considered. The current data on the transverse stiffness of intact muscle cells, demenbranized muscle fibres, and isolated myofibrils under various conditions and at different stages of the differentiation of myofibers. The signaling role of cytoskeleton proteins and possible mechanisms of their involvement in the structural basis of transverse stiffness are dissussed.
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Davydov BN, Gavrilova OA, Chervinets VM, Chervinets IV, Lebedev DV. [Oral cavity microbiocenose in healthy teenagers and patients with chronic gastritis and gastroduodenitis]. Stomatologiia (Mosk) 2009; 88:23-26. [PMID: 19491778] [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: 05/27/2023]
Abstract
Microbial association distinctive features and colonization degree of different oral cavity biotope were established in healthy teenagers and patients with chronic gastritis and gastroduodenitis. There were studied mucous membrane surfaces of cheek, tongue, content of gingival crevice, oral fluid and dental plaque of 24 healthy persons of the age 12-17 years and 29 patients of the same age with gastritis and gastroduodenitis. On the mucous membranes of the ill teenagers there were found Porphiromonas type bacteria, 20% more Staphylococcus, 90% less Peptostreptococcus, 30% less Lactobacillus, 20% less Veillonella and Stomatococcus. In saliva anaerobic Peptostreptococcus and facultative anaerobic Streptococcus (7 lg COE/ml); Porphiromonas, Veillonella, Peptococcus and Staphylococcus (6 lg COE/ml); Neisseria (5 lg COE/ml); Stomatococcus, Enterobacteriaceae and Bacillus (4.6 lg COE/ml); Lactobacillus and Candida (4 lg COE/ml) predominated. In patients with chronic pathology in all tested biotopes there was found the increase of the whole microbiota spectra (representatives of opportunistic pathogenic microfiora were detected more often) as well as the bacteria number if compared with healthy teenagers.
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Ogneva IV, Lebedev DV, Isaev-Ivanov VV, Shenkman BS. [Spatial distribution of transverse stiffness of relaxed and activated rat soleus myofibers]. Biofizika 2008; 53:1073-1077. [PMID: 19137695] [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: 05/27/2023]
Abstract
The transverse stiffness of isolated glycerinated and demembranized muscle fibers from soleus muscle of Wistar rat were measured in different functional states by atomic force microscopy. It was shown that transverse stiffness of relaxed fibers near the Z-disk projection is approximately twice as high as near the M-line. The transverse stiffness of demembranized fibers is much higher than that of glycerinated fibers for both the Z-disk and M-line. The activation of the fiber resulted in a significant increase in transverse stiffness. However, while the stiffness of activated glycerinated fibers near the Z-disk increased about twofold, demembranized fibers showed a more than fourfold increase in transverse stiffness compared to relaxed fibers. The stiffness of both glycerinated and demembranized fibers near the M-line increased approximately threefold.
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16
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Gavrilova OA, Chervinets IV, Bondarenko VM, Chervinets VM, Samoukina AM, Lebedev DV. [Oral cavity microbiocenosis in healthy adolescents and patients with chronic gastroduodenitis]. Zh Mikrobiol Epidemiol Immunobiol 2008:59-63. [PMID: 19186547] [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: 05/27/2023]
Abstract
AIM To determine characteristics of microbial associations and degree of oral cavity colonization by different biotopes in healthy adolescents and patients with chronic gastroduodenitis. MATERIALS AND METHODS Saliva, dental deposit, content of tooth-gingival cavity and material from buccal and lingual mucous surfaces of 24 healthy adolescents and 29 patients of the same age with gastroduodenitis were used for bacteriological analysis. Inoculation were made on the following growth media: yolk-salt agar, Endo, Saburo, MRS as well as on Columbia and Saedler blood agars. RESULTS It was shown that rate of isolation of peptostreptococci from oral cavity of patients was 90% lower compared with controls; rate of isolation of lactobacilli, Veillonella, and stomatococci was 30% lower, whereas hemolytic Porphyromonas, staphylococci and streptococci were isolated 20% more frequently. Concentration of peptostreptococci and streptococci was 7.0 lg CFU/ml, whereas concentration of Porphyromonas, Veillonella, peptococci and staphylococci was 6.0 lg CFU/ml, Neisseria--5.0 lg CFU/ml, stomatococci, bacilli and Candida fungi --4.5 lg CFU/ml. Decrease of concentration of lactobacilli to 4.0 lg CFU/ml was noted. CONCLUSION Compared with healthy group of children, widened spectrum of microorganisms in all studied biotopes of oral cavity was observed in patients with chronic gastroduodenitis; species belonging to pathogenic microflora were detected in patients more frequently and in more quantities.
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Ogneva IV, Lebedev DV, Shenkman BS. [Transverse stiffness of muscular fibers. Methods of measuring and physiological foundations]. Aviakosm Ekolog Med 2008; 42:69-74. [PMID: 19055017] [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: 05/27/2023]
Abstract
The article contains the data about transverse stiffness of both native and demembraned fibers of different muscles. Under consideration is atomic force microscopy as the most promising method of investigating the cell and molecular mechanic properties of living objects.
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Lebedev DV, Monkenbusch M, Shalguev VI, Lantsov VA, Isaev-Ivanov VV. [Dynamic properties of recA protein filaments from E. coli and P. aeruginosa investigated by neutron spin-echo]. Biofizika 2007; 52:799-803. [PMID: 17969911] [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: 05/25/2023]
Abstract
Bacterial RecA protein is the key enzyme in the processes of homologous recombination, post-replication repair and induction of SOS-repair functions. While a significant amount of data on the structure of RecA protein and its functional analogs has been obtained, there is little information about the molecular dynamics of this protein. In this work we present the results of neutron spin-echo measurements of the relaxation kinetics of filaments formed by RecA proteins from E. coli and P. aeruginosa. The results suggest that the protein filaments exhibit both diffusion and internal relaxation modes, which change during the formation of complexes of these proteins with ATP and single-stranded DNA.
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Egorov VV, Solovyov KV, Grudinina NA, Lebedev DV, Isaev-Ivanov VV, Kiselev OI, Shawlovsky MM. Atomic Force Microscopy Study of Peptides Homologous to Beta-Domain of Alpha-Lactalbumins. Protein Pept Lett 2007; 14:471-4. [PMID: 17584173 DOI: 10.2174/092986607780782858] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Symmetrical peptide GYDTQAIVENNESTEYG (WT, Wild Type) identical to 35-51 aminoacid residues of human alpha-lactalbumin (HLA) and peptide GYDTQTVVNNNGHTDYG (ID, IDeal symmetry) homologous to beta-domain of mammalian alpha-lactalbumins can form amyloid-like fibrils in conditions required for fibrillogenesis of HLA. The latter peptide can also form fibrils in deionized water. Fibrils formed by these peptides can cause forming of HLA amyloid-like aggregates in physiological conditions. These results provide an evidence for presence of amyloidogenic determinant in beta-domain of alpha-lactalbumin. Thus, symmetry in the primary structure may play the role in fibrillogenesis of proteins.
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Affiliation(s)
- V V Egorov
- Institute for Experimental Medicine RAMS, 12, Akad. Pavlova St., Saint Petersburg, Russia.
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20
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Mazo EB, Sergeeva NA, Grigor'ev ME, Lebedev DV, Solov'eva EV, Konorev VA, Krovets AA. [Comparative value of molecular forms of prostate-specific antigen in diagnosis of prostatic cancer]. Urologiia 2006:21-4. [PMID: 16889084] [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: 05/11/2023]
Abstract
The aim of the study was to compare diagnostic significance of free PSA (fPSA)/total PSA (tPSA) versus PSA complex with alpha1-antichymotrypsin (cPSA) in tPSA level within 4-10 ng/ml in differential diagnosis of prostatic cancer (PC). A complete urological examination (digital rectal test, transrectal ultrasound investigation, serum assay for fPSA and tPSA, multifocal transperineal prostatic biopsy) was made in 108 patients with tPSA blood level 4-10 ng/ ml. Prostatic adenoma (PA) was histologically verified in 61 of 108 patients, fPSA/tPSA was normal. In the other 39 of 108 patients fPSA/tPSA was under 15% while cPSA was in the range 3.8-9.6 ng/ml. A course of etiotropic therapy of chronic prostatic inflammation produced no significant changes in fPSA/tPSA and cPSA in 28 out of 39 patients. Histologically, these 28 patients had PC. In the rest 11 of 39 patients chronic prostatitis treatment fPSA/tPSA significantly rose to 18.2%, on the average. CPSA decreased to 2.4 ng/ml. These 11 patients were found histologically to have PA and signs of chronic inflammation. In 8 of 108 patients fPSA/tPSA was not indicative of PC being 18,2% on the average while cPSA indicated the presence of PC and was 4.2 ng.ml, on the average. PC was verified histologically in these 8 patients. Thus, cPSA in PC suspects is more informative than fPSA/tPSA in PC diagnosis. CPSA in the serum depends on prostatic inflammation making difficult differential diagnosis of PC in interpretation of tPSA, fPSA/tPSA and cPSA. Therefore, estimation of PSA variants and molecular forms in PC suspects and prostatic inflammation should be made after etiotropic therapy.
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21
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Lebedev DV, Filatov MV, Kuklin AI, Islamov AK, Kentzinger E, Pantina R, Toperverg BP, Isaev-Ivanov VV. Fractal nature of chromatin organization in interphase chicken erythrocyte nuclei: DNA structure exhibits biphasic fractal properties. FEBS Lett 2005; 579:1465-8. [PMID: 15733858 DOI: 10.1016/j.febslet.2005.01.052] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2004] [Revised: 12/29/2004] [Accepted: 01/14/2005] [Indexed: 10/25/2022]
Abstract
Arrangement of chromatin in intact chicken erythrocyte nuclei was investigated by small angle neutron scattering. The scattering spectra have revealed that on the scales between 15 nm and 1.5 microm the interior of the nucleus exhibited properties of a mass fractal. The fractal dimension of the protein component of cell nucleus held constant at approximately 2.5, while the DNA organization was biphasic, with the fractal dimension slightly higher than 2 on the scales smaller than 300 nm and approaching 3 on the larger scales.
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Affiliation(s)
- D V Lebedev
- Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina, Russia
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22
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Lebedev DV, Baitin DM, Islamov AK, Kuklin AI, Shalguev VK, Lanzov VA, Isaev-Ivanov VV. Analytical model for determination of parameters of helical structures in solution by small angle scattering: comparison of RecA structures by SANS. FEBS Lett 2003; 537:182-6. [PMID: 12606054 DOI: 10.1016/s0014-5793(03)00107-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [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] [Indexed: 11/23/2022]
Abstract
The filament structures of the self-polymers of RecA proteins from Escherichia coli and Pseudomonas aeruginosa, their complexes with ATPgammaS, phage M13 single-stranded DNA (ssDNA) and the tertiary complexes RecA::ATPgammaS::ssDNA were compared by small angle neutron scattering. A model was developed that allowed for an analytical solution for small angle scattering on a long helical filament, making it possible to obtain the helical pitch and the mean diameter of the protein filament from the scattering curves. The results suggest that the structure of the filaments formed by these two RecA proteins, and particularly their complexes with ATPgammaS, is conservative.
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Affiliation(s)
- D V Lebedev
- Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina, Russia
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Mazo EB, Grigor'ev ME, Stepenskiĭ AB, Lebedev DV. [Diagnostic and prognostic value of quantitative monitoring of prostate specific antigen in blood serum and urine from patients with prostate cancer after radical prostatectomy]. TERAPEVT ARKH 2003; 74:65-7. [PMID: 12469637] [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: 02/27/2023]
Abstract
AIM To study values of prostate-specific antigen (PSA) in the blood serum and urine before and after massage of the prostatic bed in patients with prostatic cancer (PC) after radical prostatectomy. MATERIAL AND METHODS Changes in serum and urine PSA concentrations were followed up in 17 patients with PC (T2-3N0M0) 14 months (4-24 mon) after radical prostatectomy. Control examinations were made once a month. MRT or CT and osteoscintigraphy were made in suspected recurrence and/or metastases of PC. RESULTS There were no changes in PSA consentrations in the serum and urine before and after the massage of prostatic bed in 10 of 17 patients. In 3 patients PSA concentrations in blood and serum increased after the massage, in one of them blood levels of PSA after the massage went up 5 months after PSA increase in the urine. In 4 of 17 patients urine PSA levels increased after the massage, the blood levels remaining the same. CONCLUSION Follow-up measurements of blood and urinary levels in PC patients after radical prostatectomy before and following massage of the prostatic bed allow detection of prostatic PSA-positive cells which were not removed at surgery. We suggest that these cells may be the basis of recurrent disease.
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Grigor'ev ME, Stepenskiĭ AB, Lebedev DV. [Specific antigens in screening and monitoring patients with prostate cancer]. Urologiia 2002:50-4. [PMID: 12077825] [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: 02/25/2023]
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Chekhonin VP, Grigor'ev ME, Zhirkov IA, Lebedev DV. [Prostate-specific membrane antigen and its role in diagnosis of prostate cancer]. Vopr Med Khim 2002; 48:31-43. [PMID: 12068496] [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: 02/25/2023]
Abstract
This paper reviews recent achievements of the employment of prostate specific membrane antigen in the diagnostics of prostate cancer.
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Affiliation(s)
- V P Chekhonin
- Serbsky National Research Center for Social & Forensic Psychiatry, 23 Kropotkinsky Per., Moscow, Russia
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Basavappa S, Huang CC, Mangel AW, Lebedev DV, Knauf PA, Ellory JC. Swelling-activated amino acid efflux in the human neuroblastoma cell line CHP-100. J Neurophysiol 1996; 76:764-9. [PMID: 8871197 DOI: 10.1152/jn.1996.76.2.764] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [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] [Indexed: 02/02/2023] Open
Abstract
1. The effects of hypoosmotic stress on cell volume and amino acid efflux were evaluated in the human neuroblastoma cell line CHP-100 with the Coulter Counter Multisizer and radiolabeled amino acid efflux, respectively. 2. CHP-100 cells swelled by approximately 35 +/- 5% (means +/- SE) when the osmolarity of the solution was decreased from 290 to 190 mOsm/kg H2O. The rapid swelling was followed by a biphasic regulatory volume decrease (RVD). 3. In cells loaded with 14C-taurine, hypoosmotic stress induced a 300 +/- 22% (n = 23, P < 0.05) increase in taurine efflux compared with controls. This efflux was inhibited by the chloride channel blockers 5-nitro-2-(3-phenylpropylamino)-benzoic acid (NPPB), 4,4'-diisothio-cyanostilbene-2,2'-disulfonic acid (DIDS), niflumic acid and by the volume-activated anion channel blocker tamoxifen. In addition, the swelling-activated taurine efflux was dependent upon extracellular calcium. 4. Similarly, in cells loaded with 14C-glycine, hypoosmotic stress significantly increased glycine efflux, which was also sensitive to NPPB. In contrast, efflux of 3H-glutamate was not significantly altered after hypoosmotic stress. 5. With the use of patch clamp recording techniques, Cl- channels were activated in cell attached patches after exposure to hypoosmotic solutions. 6. In nystatin perforated patches, permeability of the hypoosmotically activated anion channel was observed to be SCN- > I- > Br- > Cl- >> Glutamate. 7. It is concluded that in CHP-100 cells, anion channels are activated during hypoosmotic stress and these channels represent a pathway for efflux of amino acids.
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Affiliation(s)
- S Basavappa
- University Laboratory of Physiology, University of Oxford, United Kingdom
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Karpel' GG, Lebedev DV, Iastrebov II. [Hemangioendothelioma of the liver as the cause of sudden death]. Sud Med Ekspert 1990; 33:57-8. [PMID: 2087762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Lebedev DV. [Not Available]. Vopr Istor Estestvozn Tekh 1987:113-24. [PMID: 11636234] [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: 04/17/2023]
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