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Pobeguts OV, Galaymina MA, Sikamov KV, Urazaeva DR, Avshalumov AS, Mikhailycheva MV, Babenko VV, Smirnov IP, Gorbachev AY. Unraveling the adaptive strategies of Mycoplasma hominis through proteogenomic profiling of clinical isolates. Front Cell Infect Microbiol 2024; 14:1398706. [PMID: 38756231 PMCID: PMC11096450 DOI: 10.3389/fcimb.2024.1398706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 04/19/2024] [Indexed: 05/18/2024] Open
Abstract
Introduction Mycoplasma hominis (M. hominis) belongs to the class Mollicutes, characterized by a very small genome size, reduction of metabolic pathways, including transcription factors, and the absence of a cell wall. Despite this, they adapt well not only to specific niches within the host organism but can also spread throughout the body, colonizing various organs and tissues. The adaptation mechanisms of M. hominis, as well as their regulatory pathways, are poorly understood. It is known that, when adapting to adverse conditions, Mycoplasmas can undergo phenotypic switches that may persist for several generations. Methods To investigate the adaptive properties of M. hominis related to survival in the host, we conducted a comparative phenotypic and proteogenomic analysis of eight clinical isolates of M. hominis obtained from patients with urogenital infections and the laboratory strain H-34. Results We have shown that clinical isolates differ in phenotypic features from the laboratory strain, form biofilms more effectively and show resistance to ofloxacin. The comparative proteogenomic analysis revealed that, unlike the laboratory strain, the clinical isolates possess several features related to stress survival: they switch carbon metabolism, activating the energetically least advantageous pathway of nucleoside utilization, which allows slowing down cellular processes and transitioning to a starvation state; they reconfigure the repertoire of membrane proteins; they have integrative conjugative elements in their genomes, which are key mediators of horizontal gene transfer. The upregulation of the methylating subunit of the restriction-modification (RM) system type I and the additional components of RM systems found in clinical isolates suggest that DNA methylation may play a role in regulating the adaptation mechanisms of M. hominis in the host organism. It has been shown that based on the proteogenomic profile, namely the genome sequence, protein content, composition of the RM systems and additional subunits HsdM, HsdS and HsdR, composition and number of transposable elements, as well as the sequence of the main variable antigen Vaa, we can divide clinical isolates into two phenotypes: typical colonies (TC), which have a high growth rate, and atypical (aTC) mini-colonies, which have a slow growth rate and exhibit properties similar to persisters. Discussion We believe that the key mechanism of adaptation of M. hominis in the host is phenotypic restructuring, leading to a slowing down cellular processes and the formation of small atypical colonies. This is due to a switch in carbon metabolism and activation the pathway of nucleoside utilization. We hypothesize that DNA methylation may play a role in regulating this switch.
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Affiliation(s)
- Olga V. Pobeguts
- Department of Molecular Biology and Genetics, Federal State Budgetary Institution Lopukhin Federal Research and Clinical Center of Physical-chemical Medicine Federal Medical Biological Agency, Moscow, Russia
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Galyamina MA, Sikamov KV, Urazaeva DR, Avshalumov AS, Mikhaylycheva MV, Pobeguts OV, Gorbachev AY. Correlation between the Colony Phenotype and Amino Acid Sequence of the Variable Vaa Antigen in Clinical Isolates of Mycoplasma hominis. Bull Exp Biol Med 2024; 177:79-83. [PMID: 38960955 DOI: 10.1007/s10517-024-06135-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Indexed: 07/05/2024]
Abstract
A new Mycoplasma hominis phenotype forming mini-colonies (MC) on agar and distinct from the phenotype forming typical colonies (TC) not only in size, but also in morphology, growth rate, and resistance to adverse factors, has been previously identified. In this study, the phenotype of colonies was determined and a comparative analysis of the amino acid sequence of the main variable antigen Vaa of the laboratory strain N-34 and seven clinical isolates of M. hominis was performed. It is demonstrated that the amino acid sequence of Vaa in clinical isolates forming TC (similar to the laboratory strain N-34) is entirely analogous to that of laboratory strain. Clinical isolates forming MC carry amino acid substitutions in the variable C-terminal region of Vaa, which can contribute to adhesion to eukaryotic cells and immune evasion. The connection between colony phenotype and amino acid sequence of Vaa is established.
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Affiliation(s)
- M A Galyamina
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia.
| | - K V Sikamov
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - D R Urazaeva
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - A S Avshalumov
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - M V Mikhaylycheva
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - O V Pobeguts
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - A Yu Gorbachev
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
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Bragina E, Sorokina T, Chogovadze A, Shevchenko Y, Chernykh V, Barkhatova O, Rakovskaya I. Detection and evaluation of different morphological forms of Mycoplasma hominis in human semen. Asian J Androl 2024; 26:71-76. [PMID: 37738137 PMCID: PMC10846820 DOI: 10.4103/aja202333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 06/18/2023] [Indexed: 09/24/2023] Open
Abstract
Recently discovered microcolonial forms of Mycoplasma hominis ( M. hominis ) and their impact on human spermatogenesis are studied. The spermatozoa of 125 fertile men (sperm donors; from Reprobank [Reproductive Tissue Bank, Moscow, Russia]) and of 93 patients with fertility problems (from the Federal State Budgetary Institution "Research Centre for Medical Genetics [RCMG]", Moscow, Russia) were used. Classical colonies of M. hominis and microcolonies were detected by molecular biological methods, culture of bacteria, and transmission electron microscopy. The unique structure of microcolonial cells, in which the cytoplasmic cylinder is surrounded by concentric electron-dense and electron-light layers with a periodicity of 12-14 nm, and the ability of microcolonial cells to attach to spermatozoa are shown. In patients with lower sperm quality, microcolonies of M. hominis were detected 2.5 times more frequently than classical colonies. The detection of microcolonies in the ejaculate and the frequent isolation of microcolonies from sperm samples of patients with fertility problems suggest that microcolonial cells may be one cause of infertility.
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Affiliation(s)
- Elizaveta Bragina
- Research Centre for Medical Genetics, Moscow 115522, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology Lomonosov Moscow State University, Moscow 119992, Russia
| | | | | | | | - Vyacheslav Chernykh
- Research Centre for Medical Genetics, Moscow 115522, Russia
- N.I. Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Olga Barkhatova
- Federal Government Budgetary Institution “National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation”, Moscow 123098, Russia
| | - Irina Rakovskaya
- Federal Government Budgetary Institution “National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation”, Moscow 123098, Russia
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Gorina LG, Krylova NA, Rakovskaya IV, Geppe NA, Gamova NA, Barkhatova OI. Mechanisms of Long-Term Persistence of Mycoplasmas in Children with Asthma. Microorganisms 2023; 11:1683. [PMID: 37512855 PMCID: PMC10383847 DOI: 10.3390/microorganisms11071683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 06/25/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Improving the management of children with asthma associated with mycoplasma infection is important. Aim: To study the duration of the persistence of antigens, and DNA in a free state, in the structures of circulating immune complexes (CICs) and living cells of Mycoplasma pneumoniae (Mpn) and Mycoplasma hominis (Mh) in children with asthma. In total, 205 children with asthma from 1 to 14 years were observed. The reaction of aggregate-hemagglutination (AHAA), the direct immunofluorescence reaction (DIF), the reaction of the polymerase chain reaction (PCR), and the culture method were used. In addition, 47 children were re-examined 1.5 months after the treatment of mycoplasma infection with azithromycin. The number of samples positive for antigens and DNA in the free state and in the structures of CICs significantly decreased. Then, 50 blood serum samples containing Mh antigens, and 50 samples containing Mpn antigens were analyzed by culture method. Mh was isolated in 21 (65.5%) of 32 samples containing DNA. Mpn was isolated from antigen-positive samples in nine cases. The presented data indicate the long-term persistence of antigens, and DNA of mycoplasma cells in the free state, in the structure of CICs, as well as in the form of "microcolonies". A high level of CICs can be used to predict the course of the disease and the response to therapy.
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Affiliation(s)
- Luisa G Gorina
- Gamaleya National Research Center of Epidemiology and Microbiology, 123098 Moscow, Russia
| | - Natalya A Krylova
- Department of Childhood Diseases Sechenov, First Moscow State Medical University (Sechenov University), 119435 Moscow, Russia
| | - Irina V Rakovskaya
- Gamaleya National Research Center of Epidemiology and Microbiology, 123098 Moscow, Russia
| | - Natalia A Geppe
- Department of Childhood Diseases Sechenov, First Moscow State Medical University (Sechenov University), 119435 Moscow, Russia
| | - Natalia A Gamova
- Gamaleya National Research Center of Epidemiology and Microbiology, 123098 Moscow, Russia
| | - Olga I Barkhatova
- Gamaleya National Research Center of Epidemiology and Microbiology, 123098 Moscow, Russia
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Pachunka J, Hankins R. Mycoplasma hominis necrotising pneumonia in an immunocompetent adult male. BMJ Case Rep 2023; 16:e250107. [PMID: 37339824 DOI: 10.1136/bcr-2022-250107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023] Open
Abstract
Mycoplasma hominis, a common coloniser of the urogenital tract, is a rare cause of respiratory infections in an immunocompetent patient. M. hominis lacks a cell wall and can be difficult to identify with standard culture methods posing difficulties in diagnosis and treatment. We describe a case of M. hominis pneumonia in an immunocompetent man in his early 40s without any risk factors presenting with a cavitary lesion who developed empyema and necrotising pneumonia requiring surgical debridement. Identification of M. hominis and subsequent modification of antibiotic therapy led to favourable outcome. M. hominis should be considered in the differential diagnosis of patients with treatment resistant pneumonia especially in patients with trauma, intracranial injury, lung transplant or if immunocompromised. While M. Hominis is naturally resistant to all antibiotics that target cell wall synthesis, we recommend levofloxacin or other fluoroquinolone to most effectively treat with doxycycline as a potential alternative.
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Affiliation(s)
- Joseph Pachunka
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Richard Hankins
- Department of Internal Medicine, Division of Infectious Diseases, University of Nebraska Medical Center, Omaha, Nebraska, USA
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Galyamina MA, Ladygina VG, Pobeguts OV, Rakovskaya IV. Analysis of the Adhesive-Invasive Potential of Two Morphologically Different Types of Mycoplasma hominis Colonies. Bull Exp Biol Med 2022; 173:437-440. [DOI: 10.1007/s10517-022-05582-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Indexed: 10/14/2022]
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Fisunov GY, Pobeguts OV, Ladygina VG, Zubov AI, Galyamina MA, Kovalchuk SI, Ziganshin RK, Evsyutina DV, Matyushkina DS, Butenko IO, Bukato ON, Veselovsky VA, Semashko TA, Klimina KM, Levina GA, Barhatova OI, Rakovskaya IV. Thymidine utilisation pathway is a novel phenotypic switch of Mycoplasma hominis. J Med Microbiol 2022; 71. [PMID: 35037614 PMCID: PMC8895549 DOI: 10.1099/jmm.0.001468] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Introduction. Mycoplasma hominis is a bacterium belonging to the class Mollicutes. It causes acute and chronic infections of the urogenital tract. The main features of this bacterium are an absence of cell wall and a reduced genome size (517-622 protein-encoding genes). Previously, we have isolated morphologically unknown M. hominis colonies called micro-colonies (MCs) from the serum of patients with inflammatory urogenital tract infection.Hypothesis. MCs are functionally different from the typical colonies (TCs) in terms of metabolism and cell division.Aim. To determine the physiological differences between MCs and TCs of M. hominis and elucidate the pathways of formation and growth of MCs by a comparative proteomic analysis of these two morphological forms.Methodology. LC-MS proteomic analysis of TCs and MCs using an Ultimate 3000 RSLC nanoHPLC system connected to a QExactive Plus mass spectrometer.Results. The study of the proteomic profiles of M. hominis colonies allowed us to reconstruct their energy metabolism pathways. In addition to the already known pentose phosphate and arginine deamination pathways, M. hominis can utilise ribose phosphate and deoxyribose phosphate formed by nucleoside catabolism as energy sources. Comparative proteomic HPLC-MS analysis revealed that the proteomic profiles of TCs and MCs were different. We assume that MC cells preferably utilised deoxyribonucleosides, particularly thymidine, as an energy source rather than arginine or ribonucleosides. Utilisation of deoxyribonucleosides is less efficient as compared with that of ribonucleosides and arginine in terms of energy production. Thymidine phosphorylase DeoA is one of the key enzymes of deoxyribonucleosides utilisation. We obtained a DeoA overexpressing mutant that exhibited a phenotype similar to that of MCs, which confirmed our hypothesis.Conclusion. In addition to the two known pathways for energy production (arginine deamination and the pentose phosphate pathway) M. hominis can use deoxyribonucleosides and ribonucleosides. MC cells demonstrate a reorganisation of energy metabolism: unlike TC cells, they preferably utilise deoxyribonucleosides, particularly thymidine, as an energy source rather than arginine or ribonucleosides. Thus MC cells enter a state of energy starvation, which helps them to survive under stress, and in particular, to be resistant to antibiotics.
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Affiliation(s)
- Gleb Yu Fisunov
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Olga V Pobeguts
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Valentina G Ladygina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Alexandr I Zubov
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Mariya A Galyamina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Sergey I Kovalchuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Rustam K Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Daria V Evsyutina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Daria S Matyushkina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Ivan O Butenko
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Olga N Bukato
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Vladimir A Veselovsky
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Tatiana A Semashko
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Ksenia M Klimina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia.,Department of Biotechnology, Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia
| | - Galina A Levina
- Gamaleya National Research Center of Epidemiology and Microbiology, Moscow, Russia
| | - Olga I Barhatova
- Gamaleya National Research Center of Epidemiology and Microbiology, Moscow, Russia
| | - Irina V Rakovskaya
- Gamaleya National Research Center of Epidemiology and Microbiology, Moscow, Russia
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Medvedeva ES, Mouzykantov AA, Kostenko VV, Baranova NB, Markelova MI, Sabouni RG, Khusnutdinova DR, Chernova OA, Chernov VM. Adaptation to Antimicrobials and Pathogenicity in Mycoplasmas: Development of Ciprofloxacin-Resistance and Evolution of Virulence in Acholeplasma laidlawii. DOKL BIOCHEM BIOPHYS 2021; 501:444-448. [PMID: 34966969 DOI: 10.1134/s1607672921060028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 11/22/2022]
Abstract
For the first time it was shown that the development of resistance to ciprofloxacin in vitro in Acholeplasma laidlawii, a mycoplasma which is widely spread in nature and which is the main contaminant of cell cultures and vaccines, is associated with diverse pathways of virulence evolution: virulome and virulence differ significantly between ciprofloxacin-resistant strains, including those with the same level of antimicrobial resistance.
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Affiliation(s)
- E S Medvedeva
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Science Center, Russian Academy of Sciences, Kazan, Russia
| | - A A Mouzykantov
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Science Center, Russian Academy of Sciences, Kazan, Russia.
| | - V V Kostenko
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Science Center, Russian Academy of Sciences, Kazan, Russia
- Kazan (Volga Region) Federal University, Kazan, Russia
| | - N B Baranova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Science Center, Russian Academy of Sciences, Kazan, Russia
| | - M I Markelova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Science Center, Russian Academy of Sciences, Kazan, Russia
- Kazan (Volga Region) Federal University, Kazan, Russia
| | - R G Sabouni
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Science Center, Russian Academy of Sciences, Kazan, Russia
- Kazan (Volga Region) Federal University, Kazan, Russia
| | - D R Khusnutdinova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Science Center, Russian Academy of Sciences, Kazan, Russia
- Kazan (Volga Region) Federal University, Kazan, Russia
| | - O A Chernova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Science Center, Russian Academy of Sciences, Kazan, Russia
| | - V M Chernov
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Science Center, Russian Academy of Sciences, Kazan, Russia
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Chernova OA, Chernov VM, Mouzykantov AA, Baranova NB, Edelstein IA, Aminov RI. Antimicrobial drug resistance mechanisms among Mollicutes. Int J Antimicrob Agents 2020; 57:106253. [PMID: 33264670 DOI: 10.1016/j.ijantimicag.2020.106253] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 07/08/2020] [Accepted: 11/22/2020] [Indexed: 12/11/2022]
Abstract
Representatives of the Mollicutes class are the smallest, wall-less bacteria capable of independent reproduction. They are widespread in nature, most are commensals, and some are pathogens of humans, animals and plants. They are also the main contaminants of cell cultures and vaccine preparations. Despite limited biosynthetic capabilities, they are highly adaptable and capable of surviving under various stress and extreme conditions, including antimicrobial selective pressure. This review describes current understanding of antibiotic resistance (ABR) mechanisms in Mollicutes. Protective mechanisms in these bacteria include point mutations, which may include non-target genes, and unique gene exchange mechanisms, contributing to transfer of ABR genes. Better understanding of the mechanisms of emergence and dissemination of ABR in Mollicutes is crucial to control these hypermutable bacteria and prevent the occurrence of highly ABR strains.
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Affiliation(s)
- Olga A Chernova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Centre of RAS, Kazan, Russian Federation
| | - Vladislav M Chernov
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Centre of RAS, Kazan, Russian Federation
| | - Alexey A Mouzykantov
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Centre of RAS, Kazan, Russian Federation
| | - Natalya B Baranova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Centre of RAS, Kazan, Russian Federation
| | - Inna A Edelstein
- Smolensk State Medical University, Ministry of Health of Russian Federation, Smolensk, Russian Federation
| | - Rustam I Aminov
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK; Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation.
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