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Thompson RM, Fox EM, Montero-Calasanz MDC. Draft genome sequences of five Mycobacterium strains, isolated from Alnus glutinosa root nodules. Microbiol Resour Announc 2024; 13:e0113223. [PMID: 38189310 PMCID: PMC10868193 DOI: 10.1128/mra.01132-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 12/15/2023] [Indexed: 01/09/2024] Open
Abstract
Mycobacterium is a clinically relevant genus of bacteria, with this paper reporting draft genomes of five Mycobacterium strains derived from Alnus glutinosa root nodules. The genome sizes of the isolates ranged from 6.1 to 6.9 Mbp, composed of 22-59 contigs. The N50 values ranged from 303,875 to 865,751 bp, presenting a GC% of 66.07%-66.96%.
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Affiliation(s)
- Ryan Michael Thompson
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Edward M. Fox
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Maria del Carmen Montero-Calasanz
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
- IFAPA Las Torres-Andalusian Institute of Agricultural and Fisheries Research and Training, Junta de Andalucía, Seville, Spain
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Thongboontho R, Petcharat K, Munkong N, Khonthun C, Boondech A, Phromnoi K, Thim-uam A. Effects of Pogonatherum paniceum (Lamk) Hack extract on anti-mitochondrial DNA mediated inflammation by attenuating Tlr9 expression in LPS-induced macrophages. Nutr Res Pract 2023; 17:827-843. [PMID: 37780212 PMCID: PMC10522809 DOI: 10.4162/nrp.2023.17.5.827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 05/10/2023] [Accepted: 05/19/2023] [Indexed: 10/03/2023] Open
Abstract
BACKGROUND/OBJECTIVES Mitochondrial DNA leakage leads to inflammatory responses via endosome activation. This study aims to evaluate whether the perennial grass water extract (Pogonatherum panicum) ameliorate mitochondrial DNA (mtDNA) leakage. MATERIALS/METHODS The major bioactive constituents of P. paniceum (PPW) were investigated by high-performance liquid chromatography, after which their antioxidant activities were assessed. In addition, RAW 264.7 macrophages were stimulated with lipopolysaccharide, resulting in mitochondrial damage. Quantitative polymerase chain reaction and enzyme-linked immunosorbent assay were used to examine the gene expression and cytokines. RESULTS Our results showed that PPW extract-treated activated cells significantly decrease reactive oxygen species and nitric oxide levels by reducing the p22phox and iNOS expression and lowering cytokine-encoding genes, including IL-6, TNF-α, IL-1β, PG-E2 and IFN-γ relative to the lipopolysaccharide (LPS)-activated macrophages. Furthermore, we observed that LPS enhanced the mtDNA leaked into the cytoplasm, increasing the transcription of Tlr9 and signaling both MyD88/Irf7-dependent interferon and MyD88/NF-κb p65-dependent inflammatory cytokine mRNA expression but which was alleviated in the presence of PPW extract. CONCLUSIONS Our data show that PPW extract has antioxidant and anti-inflammatory activities by facilitating mtDNA leakage and lowering the Tlr9 expression and signaling activation.
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Affiliation(s)
- Rungthip Thongboontho
- Division of Biochemistry, School of Medical Sciences, University of Phayao, Mae Ka 56000, Thailand
| | - Kanoktip Petcharat
- Division of Biochemistry, School of Medical Sciences, University of Phayao, Mae Ka 56000, Thailand
| | - Narongsuk Munkong
- Department of Pathology, School of Medicine, University of Phayao, Mae Ka 56000, Thailand
| | - Chakkraphong Khonthun
- Division of Biochemistry, School of Medical Sciences, University of Phayao, Mae Ka 56000, Thailand
| | - Atirada Boondech
- Biology Program, Faculty of Science and Technology, Kamphaeng Phet Rajabhat University, Nakhon Chum 65000, Thailand
| | - Kanokkarn Phromnoi
- Division of Biochemistry, School of Medical Sciences, University of Phayao, Mae Ka 56000, Thailand
| | - Arthid Thim-uam
- Division of Biochemistry, School of Medical Sciences, University of Phayao, Mae Ka 56000, Thailand
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Tamošiūnė I, Andriūnaitė E, Vinskienė J, Stanys V, Rugienius R, Baniulis D. Enduring Effect of Antibiotic Timentin Treatment on Tobacco In Vitro Shoot Growth and Microbiome Diversity. PLANTS (BASEL, SWITZERLAND) 2022; 11:832. [PMID: 35336713 PMCID: PMC8954828 DOI: 10.3390/plants11060832] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
Plant in vitro cultures initiated from surface-sterilized explants often harbor complex microbial communities. Antibiotics are commonly used to decontaminate plant tissue culture or during genetic transformation; however, the effect of antibiotic treatment on the diversity of indigenous microbial populations and the consequences on the performance of tissue culture is not completely understood. Therefore, the aim of this study was to assess the effect of antibiotic treatment on the growth and stress level of tobacco (Nicotiana tabacum L.) shoots in vitro as well as the composition of the plant-associated microbiome. The study revealed that shoot cultivation on a medium supplemented with 250 mg L-1 timentin resulted in 29 ± 4% reduced biomass accumulation and a 1.2-1.6-fold higher level of oxidative stress injury compared to the control samples. Moreover, the growth properties of shoots were only partially restored after transfer to a medium without the antibiotic. Microbiome analysis of the shoot samples using multivariable region-based 16S rRNA gene sequencing revealed a diverse microbial community in the control tobacco shoots, including 59 bacterial families; however, it was largely dominated by Mycobacteriaceae. Antibiotic treatment resulted in a decline in microbial diversity (the number of families was reduced 4.5-fold) and increased domination by the Mycobacteriaceae family. These results imply that the diversity of the plant-associated microbiome might represent a significant factor contributing to the efficient propagation of in vitro tissue culture.
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Pirttilä AM, Mohammad Parast Tabas H, Baruah N, Koskimäki JJ. Biofertilizers and Biocontrol Agents for Agriculture: How to Identify and Develop New Potent Microbial Strains and Traits. Microorganisms 2021; 9:817. [PMID: 33924411 PMCID: PMC8069042 DOI: 10.3390/microorganisms9040817] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/09/2021] [Accepted: 04/11/2021] [Indexed: 12/02/2022] Open
Abstract
Microbiological tools, biofertilizers, and biocontrol agents, which are bacteria and fungi capable of providing beneficial outcomes in crop plant growth and health, have been developed for several decades. Currently we have a selection of strains available as products for agriculture, predominantly based on plant-growth-promoting rhizobacteria (PGPR), soil, epiphytic, and mycorrhizal fungi, each having specific challenges in their production and use, with the main one being inconsistency of field performance. With the growing global concern about pollution, greenhouse gas accumulation, and increased need for plant-based foods, the demand for biofertilizers and biocontrol agents is expected to grow. What are the prospects of finding solutions to the challenges on existing tools? The inconsistent field performance could be overcome by using combinations of several different types of microbial strains, consisting various members of the full plant microbiome. However, a thorough understanding of each microbiological tool, microbial communities, and their mechanisms of action must precede the product development. In this review, we offer a brief overview of the available tools and consider various techniques and approaches that can produce information on new beneficial traits in biofertilizer and biocontrol strains. We also discuss innovative ideas on how and where to identify efficient new members for the biofertilizer and biocontrol strain family.
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Affiliation(s)
- Anna Maria Pirttilä
- Ecology and Genetics, University of Oulu, FIN-90014 Oulu, Finland; (H.M.P.T.); (N.B.); (J.J.K.)
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Tamošiūnė I, Gelvonauskienė D, Haimi P, Mildažienė V, Koga K, Shiratani M, Baniulis D. Cold Plasma Treatment of Sunflower Seeds Modulates Plant-Associated Microbiome and Stimulates Root and Lateral Organ Growth. FRONTIERS IN PLANT SCIENCE 2020; 11:568924. [PMID: 32983218 PMCID: PMC7485318 DOI: 10.3389/fpls.2020.568924] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 08/17/2020] [Indexed: 05/05/2023]
Abstract
Cold atmospheric pressure (CP) plasma irradiation of seeds has been shown to promote plant growth, but the molecular basis of this phenomenon is poorly understood. In our study, optimum irradiation of common sunflower seeds using a dielectric barrier discharge CP device stimulated growth of sunflower lateral organs and roots by 9-14% compared to the control. Metagenomic analysis revealed that the structure of plant-associated bacterial assembly was greatly modified upon CP treatment and could be attributed to the antimicrobial effect of CP-generated reactive species. The treatment resulted in the domination of spore forming Mycobacterium sp. in the above-ground tissues of the seedlings. While the overall bacterial diversity in the roots was barely affected, the CP-induced shift in microbial composition is the likely basis for the observed seedling root growth stimulation and the long-term effect on lateral organ growth and could be mediated by increase in water uptake and/or direct root signaling. Low amplitude protein abundance differences were detected in the roots of the emerging seedlings that are characteristic to low intensity stress stimuli response and could be linked to the changes in plant-associated microbiome upon CP treatment.
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Affiliation(s)
- Inga Tamošiūnė
- Institute of Horticulture, Lithuanian Research Centre for Agriculture and Forestry, Babtai, Lithuania
| | - Dalia Gelvonauskienė
- Institute of Horticulture, Lithuanian Research Centre for Agriculture and Forestry, Babtai, Lithuania
| | - Perttu Haimi
- Institute of Horticulture, Lithuanian Research Centre for Agriculture and Forestry, Babtai, Lithuania
| | - Vida Mildažienė
- Faculty of Natural Sciences, Vytautas Magnus University, Kaunas, Lithuania
| | - Kazunori Koga
- Faculty of Information Science and Electrical Engineering, Kyushu University, Fukuoka, Japan
- Center for Novel Science Initiatives, National Institutes of Natural Sciences, Tokyo, Japan
| | - Masaharu Shiratani
- Faculty of Information Science and Electrical Engineering, Kyushu University, Fukuoka, Japan
| | - Danas Baniulis
- Institute of Horticulture, Lithuanian Research Centre for Agriculture and Forestry, Babtai, Lithuania
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Pereira SG, Alarico S, Tiago I, Reis D, Nunes-Costa D, Cardoso O, Maranha A, Empadinhas N. Studies of antimicrobial resistance in rare mycobacteria from a nosocomial environment. BMC Microbiol 2019; 19:62. [PMID: 30890149 PMCID: PMC6425705 DOI: 10.1186/s12866-019-1428-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 02/26/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Nontuberculous mycobacteria (NTM) are ubiquitous in nature and recognized agents of opportunistic infection, which is often aggravated by their intrinsic resistance to antimicrobials, poorly defined therapeutic strategies and by the lack of new drugs. However, evaluation of their prevalence in anthropogenic environments and the associated antimicrobial resistance profiles have been neglected. In this work, we sought to determine minimal inhibitory concentrations of 25 antimicrobials against 5 NTM isolates recovered from a tertiary-care hospital surfaces. Antimicrobial susceptibilities of 5 other Corynebacterineae isolated from the same hospital were also determined for their potential clinical relevance. RESULTS Our phylogenetic study with each of the NTM isolates confirm they belong to Mycobacterium obuense, Mycobacterium mucogenicum and Mycobacterium paragordonae species, the latter initially misidentified as strains of M. gordonae, a species frequently isolated from patients with NTM disease in Portugal. In contrast to other strains, the M. obuense and M. mucogenicum examined here were resistant to several of the CLSI-recommended drugs, suggestive of multidrug-resistant profiles. Surprisingly, M. obuense was susceptible to vancomycin. Their genomes were sequenced allowing detection of gene erm (erythromycin resistance methylase) in M. obuense, explaining its resistance to clarithromycin. Remarkably, and unlike other strains of the genus, the Corynebacterium isolates were highly resistant to penicillin, ciprofloxacin and linezolid. CONCLUSIONS This study highlights the importance of implementing effective measures to screen, accurately identify and control viable NTM and closely related bacteria in hospital settings. Our report on the occurrence of rare NTM species with antibiotic susceptibility profiles that are distinct from those of the corresponding Type strains, along with unexpected resistance mechanisms detected seem to suggest that resistance may be more common than previously thought and also a potential threat to frail and otherwise vulnerable inpatients.
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Affiliation(s)
- Sónia Gonçalves Pereira
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
| | - Susana Alarico
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
- Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3030-789 Coimbra, Portugal
| | - Igor Tiago
- Centre for Functional Ecology (CFE), Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Diogo Reis
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
| | - Daniela Nunes-Costa
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
- PhD Program in Experimental Biology and Biomedicine (PDBEB), Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3030-789 Coimbra, Portugal
| | - Olga Cardoso
- Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
- Chemical Process Engineering and Forest Products Center (CIEPQPF), University of Coimbra, Coimbra, Portugal
| | - Ana Maranha
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
- Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3030-789 Coimbra, Portugal
| | - Nuno Empadinhas
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
- Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3030-789 Coimbra, Portugal
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Bouam A, Armstrong N, Levasseur A, Drancourt M. Mycobacterium terramassiliense, Mycobacterium rhizamassiliense and Mycobacterium numidiamassiliense sp. nov., three new Mycobacterium simiae complex species cultured from plant roots. Sci Rep 2018; 8:9309. [PMID: 29915369 PMCID: PMC6006331 DOI: 10.1038/s41598-018-27629-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 06/05/2018] [Indexed: 12/04/2022] Open
Abstract
Three slowly growing mycobacteria named strain AB308, strain AB215 and strain AB57 were isolated from the tomato plant roots. The 16S rRNA and rpoB gene sequence analyses suggested that each strain was representative of one hitherto unidentified slowly-growing Mycobacterium species of the Mycobacterium simiae complex. Genome sequencing indicated that each strain contained one chromosome of 6.015-6.029 Mbp. A total of 1,197, 1,239 and 1,175 proteins were found to be associated with virulence and 107, 76 and 82 proteins were associated with toxin/antitoxin systems for strains AB308, AB215 and AB57, respectively. The three genomes encode for secondary metabolites, with 38, 33 and 46 genes found to be associated with polyketide synthases/non-ribosomal peptide synthases and nine, seven and ten genes encoding for bacteriocins, respectively. The genome of strain AB308 encodes for one questionable prophage and three incomplete prophages, while only incomplete prophages were predicted in AB215 and AB57 genomes. Genetic and genomic data indicate that strains AB308, AB215 and AB57 are each representative of a new Mycobacterium species that we respectively named Mycobacterium terramassiliense, Mycobacterium numidiamassiliense and Mycobacterium rhizamassiliense.
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Affiliation(s)
- A Bouam
- Aix-Marseille Univ, IRD, MEPHI, IHU Méditerranée-Infection, Marseille, France
| | - N Armstrong
- Aix-Marseille Univ, IRD, MEPHI, IHU Méditerranée-Infection, Marseille, France
| | - A Levasseur
- Aix-Marseille Univ, IRD, MEPHI, IHU Méditerranée-Infection, Marseille, France
| | - M Drancourt
- Aix-Marseille Univ, IRD, MEPHI, IHU Méditerranée-Infection, Marseille, France.
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9
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Tejesvi MV, Picart P, Kajula M, Hautajärvi H, Ruddock L, Kristensen H, Tossi A, Sahl H, Ek S, Mattila S, Pirttilä AM. Identification of antibacterial peptides from endophytic microbiome. Appl Microbiol Biotechnol 2016; 100:9283-9293. [DOI: 10.1007/s00253-016-7765-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 06/26/2016] [Accepted: 07/20/2016] [Indexed: 01/22/2023]
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10
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Pirttilä AM. Commentary: Agroforestry leads to shifts within the gammaproteobacterial microbiome of banana plants cultivated in Central America. Front Microbiol 2016; 7:656. [PMID: 27199975 PMCID: PMC4858751 DOI: 10.3389/fmicb.2016.00656] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 04/20/2016] [Indexed: 12/18/2022] Open
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Quambusch M, Pirttilä AM, Tejesvi MV, Winkelmann T, Bartsch M. Endophytic bacteria in plant tissue culture: differences between easy- and difficult-to-propagate Prunus avium genotypes. TREE PHYSIOLOGY 2014; 34:524-33. [PMID: 24812040 DOI: 10.1093/treephys/tpu027] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The endophytic bacterial communities of six Prunus avium L. genotypes differing in their growth patterns during in vitro propagation were identified by culture-dependent and culture-independent methods. Five morphologically distinct isolates from tissue culture material were identified by 16S rDNA sequence analysis. To detect and analyze the uncultivable fraction of endophytic bacteria, a clone library was established from the amplified 16S rDNA of total plant extract. Bacterial diversity within the clone libraries was analyzed by amplified ribosomal rDNA restriction analysis and by sequencing a clone for each identified operational taxonomic unit. The most abundant bacterial group was Mycobacterium sp., which was identified in the clone libraries of all analyzed Prunus genotypes. Other dominant bacterial genera identified in the easy-to-propagate genotypes were Rhodopseudomonas sp. and Microbacterium sp. Thus, the community structures in the easy- and difficult-to-propagate cherry genotypes differed significantly. The bacterial genera, which were previously reported to have plant growth-promoting effects, were detected only in genotypes with high propagation success, indicating a possible positive impact of these bacteria on in vitro propagation of P. avium, which was proven in an inoculation experiment.
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Affiliation(s)
- Mona Quambusch
- Woody Plant and Propagation Physiology Section, Institute for Horticultural Production Systems, Leibniz Universitaet Hannover, Herrenhaeuser Strasse 2, 30419 Hannover, Germany
| | | | | | - Traud Winkelmann
- Woody Plant and Propagation Physiology Section, Institute for Horticultural Production Systems, Leibniz Universitaet Hannover, Herrenhaeuser Strasse 2, 30419 Hannover, Germany
| | - Melanie Bartsch
- Woody Plant and Propagation Physiology Section, Institute for Horticultural Production Systems, Leibniz Universitaet Hannover, Herrenhaeuser Strasse 2, 30419 Hannover, Germany
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Tan H, Deng Q, Cao L. Ruminant feces harbor diverse uncultured symbiotic actinobacteria. World J Microbiol Biotechnol 2013; 30:1093-100. [DOI: 10.1007/s11274-013-1529-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 10/15/2013] [Indexed: 11/29/2022]
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Kozyrovska NO. Crosstalk between endophytes and a plant host within information-processing networks. ACTA ACUST UNITED AC 2013. [DOI: 10.7124/bc.00081d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- N. O. Kozyrovska
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
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