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Abstract
Recent progress with techniques for monitoring RNA structure in cells such as ‘DMS-Seq’ and ‘Structure-Seq’ suggests that a new era of RNA structure-function exploration is on the horizon. This will also include systematic investigation of the factors required for the structural integrity of RNA. In this context, much evidence accumulated over 50 years suggests that polyamines play important roles as modulators of RNA structure. Here, we summarize and discuss recent literature relating to the roles of these small endogenous molecules in RNA function. We have included studies directed at understanding the binding interactions of polyamines with polynucleotides, tRNA, rRNA, mRNA and ribozymes using chemical, biochemical and spectroscopic tools. In brief, polyamines bind RNA in a sequence-selective fashion and induce changes in RNA structure in context-dependent manners. In some cases the functional consequences of these interactions have been observed in cells. Most notably, polyamine-mediated effects on RNA are frequently distinct from those of divalent cations (i.e. Mg2+) confirming their roles as independent molecular entities which help drive RNA-mediated processes.
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Affiliation(s)
- Helen L Lightfoot
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Jonathan Hall
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, CH-8093, Zürich, Switzerland
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Xaplanteri MA, Petropoulos AD, Dinos GP, Kalpaxis DL. Localization of spermine binding sites in 23S rRNA by photoaffinity labeling: parsing the spermine contribution to ribosomal 50S subunit functions. Nucleic Acids Res 2005; 33:2792-805. [PMID: 15897324 PMCID: PMC1129027 DOI: 10.1093/nar/gki557] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Polyamine binding to 23S rRNA was investigated, using a photoaffinity labeling approach. This was based on the covalent binding of a photoreactive analog of spermine, N1-azidobenzamidino (ABA)-spermine, to Escherichia coli ribosomes or naked 23S rRNA under mild irradiation conditions. The cross-linking sites of ABA-spermine in 23S rRNA were determined by RNase H digestion and primer-extension analysis. Domains I, II, IV and V in naked 23S rRNA were identified as discrete regions of preferred cross-linking. When 50S ribosomal subunits were targeted, the interaction of the photoprobe with the above 23S rRNA domains was elevated, except for helix H38 in domain II whose susceptibility to cross-linking was greatly reduced. In addition, cross-linking sites were identified in domains III and VI. Association of 30S with 50S subunits, poly(U), tRNAPhe and AcPhe-tRNA to form a post-translocation complex further altered the cross-linking, in particular to helices H11–H13, H21, H63, H80, H84, H90 and H97. Poly(U)-programmed 70S ribosomes, reconstituted from photolabeled 50S subunits and untreated 30S subunits, bound AcPhe-tRNA in a similar fashion to native ribosomes. However, they exhibited higher reactivity toward puromycin and enhanced tRNA-translocation efficiency. These results suggest an essential role for polyamines in the structural and functional integrity of the large ribosomal subunit.
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Affiliation(s)
| | | | | | - Dimitrios L. Kalpaxis
- To whom correspondence should be addressed. Tel: +30 2610 996124; Fax: +30 2610 997690;
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Amarantos I, Zarkadis IK, Kalpaxis DL. The identification of spermine binding sites in 16S rRNA allows interpretation of the spermine effect on ribosomal 30S subunit functions. Nucleic Acids Res 2002; 30:2832-43. [PMID: 12087167 PMCID: PMC117059 DOI: 10.1093/nar/gkf404] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A photoreactive analogue of spermine, N1-azidobenzamidino (ABA)-spermine, was covalently attached after irradiation to Escherichia coli 30S ribosomal subunits or naked 16S rRNA. By means of RNase H digestion and primer extension, the cross-linking sites of ABA-spermine in naked 16S rRNA were characterised and compared with those identified in 30S subunits. The 5' domain, the internal and terminal loops of helix H24, as well as the upper part of helix H44 in naked 16S rRNA, were found to be preferable binding sites for polyamines. Association of 16S rRNA with ribosomal proteins facilitated its interaction with photoprobe, except for 530 stem-loop nt, whose modification by ABA-spermine was abolished. Association of 30S with 50S subunits, poly(U) and AcPhe-tRNA (complex C) further altered the susceptibility of ABA-spermine cross-linking to 16S rRNA. Complex C, modified in its 30S subunit by ABA-spermine, reacted with puromycin similarly to non-photolabelled complex. On the contrary, poly(U)-programmed 70S ribosomes reconstituted from photolabelled 30S subunits and untreated 50S subunits bound AcPhe-tRNA more efficiently than untreated ribosomes, but were less able to recognise and reject near cognate aminoacyl-tRNA. The above can be interpreted in terms of conformational changes in 16S rRNA, induced by the incorporation of ABA-spermine.
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MESH Headings
- Azides/chemistry
- Azides/metabolism
- Azides/pharmacology
- Binding Sites/genetics
- Cross-Linking Reagents
- Kinetics
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA, Transfer, Amino Acyl/metabolism
- RNA, Transfer, Phe/metabolism
- Ribonuclease H/metabolism
- Ribosomes/drug effects
- Ribosomes/metabolism
- Spermine/analogs & derivatives
- Spermine/chemistry
- Spermine/metabolism
- Spermine/pharmacology
- Tritium
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Affiliation(s)
- Ioannis Amarantos
- Laboratory of Biochemistry and Laboratory of Biology, School of Medicine, University of Patras, GR-26500 Patras, Greece
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4
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Amarantos I, Xaplanteri MA, Choli-Papadopoulou T, Kalpaxis DL. Effects of two photoreactive spermine analogues on peptide bond formation and their application for labeling proteins in Escherichia coli functional ribosomal complexes. Biochemistry 2001; 40:7641-50. [PMID: 11412118 DOI: 10.1021/bi010010s] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The effect of two photoreactive analogues of spermine, N(1)-azidobenzamidino- (ABA-) spermine and N(1)-azidonitrobenzoyl- (ANB-) spermine, on ribosomal functions was studied in a cell-free system derived from Escherichia coli. In the dark, both analogues stimulated the binding of AcPhe-tRNA to poly(U)-programmed ribosomes, enhanced the stability of the ternary complex AcPhe-tRNA.poly(U).ribosome (complex C), and caused stimulatory and inhibitory effects on peptidyltransferase activity. ABA-spermine exhibited more pronounced effects than ANB-spermine. Each photoprobe was covalently attached after irradiation to both ribosomal subunits and also to free rRNA isolated from 70S ribosomes. Photolabeled complex C showed a reactivity toward puromycin, similar to that exhibited by complex C reacting reversibly with photoprobes free in solution. The distribution of the incorporated radioactivity among the ribosomal components was determined under two experimental conditions, one stimulating and the other inhibiting peptidyltransferase activity. Under both conditions, ABA-spermine was the strongest cross-linker. Upon stimulatory conditions, 14% of ABA-[(14)C]spermine cross-linked to complex C was bound to the protein fraction. The proteins primarily labeled were identified as S3, S4, L2, L3, L6, L15, L17, and L18. Upon inhibitory conditions, a higher percent of the incorporated radioactivity was found in ribosomal proteins, while the pattern of protein labeling was characterized by a remarkable decrease of cross-linked proteins L2, L3, L6, L15, L17. and L18 and by an increase of cross-linked proteins S9, S18, L1, L16, L22, L23, and L27. On the basis of these results and literature data, the involvement of spermine in the conformation and important functions of ribosomes is discussed.
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Affiliation(s)
- I Amarantos
- Laboratory of Biochemistry, School of Medicine, University of Patras, GR-26500 Patras, Greece
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Fujiwara K, Bai G, Kitagawa T, Tsuru D. Immunoelectron microscopic study for polyamines. J Histochem Cytochem 1998; 46:1321-8. [PMID: 9774631 DOI: 10.1177/002215549804601112] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The polyamines (PAs) are ubiquitous polycationic metabolites in eukaryotic and prokaryotic cells and are believed to be intimately involved in the regulation of DNA, RNA, and protein biosynthesis, the exact function of which remains unclear, mainly because of a lack of knowledge of PA subcellular localization. In this study, using immunoelectron microscopy, we have demonstrated that PAs are predominantly located on free and attached ribosomes of the rough endoplasmic reticulum in the neurons of the lateral reticular nucleus of rat medulla oblongata. The nuclei, axons, and nerve endings were devoid of PA. This suggests that PAs are one of the components of biologically active ribosomes, being closely involved in the translation processes of protein biosynthesis.
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Affiliation(s)
- K Fujiwara
- Faculty of Pharmaceutical Sciences, Nagasaki University, Nagasaki, Japan
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Kakegawa T, Sato E, Hirose S, Igarashi K. Polyamine binding sites on Escherichia coli ribosomes. Arch Biochem Biophys 1986; 251:413-20. [PMID: 3541786 DOI: 10.1016/0003-9861(86)90347-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
To determine the binding sites of polyamines on Escherichia coli ribosomes, ribosomal proteins crosslinked with polyamines through bifunctional reagents were analyzed. When 1,5-difluoro-2,4-dinitrobenzene was used as a crosslinking reagent, spermine was bound to S3, S8, S9, L1, L2, L3, L5, L6, L13, L18, L24, and L27 proteins. When dimethyl suberimidate was used, spermine was bound to S1, S3, S4, S5, S7, S8, S9, S15, L1, L2, L3, L6, L18, and L24 proteins. In addition to crosslinking with the above proteins, spermidine, when crosslinked with dimethyl suberimidate, bound to S2, S14, S20, L4, L5, L9, L13, and L16 proteins. The relationship between the binding site(s) of polyamines on ribosomes and the function of polyamines is discussed.
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Burma DP, Srivastava AK, Srivastava S, Tewari DS, Dash D, Sengupta SK. Differences in physical and biological properties of 50S ribosomes and 23S RNAs derived from tight and loose couple 70S ribosomes. Biochem Biophys Res Commun 1984; 124:970-8. [PMID: 6508789 DOI: 10.1016/0006-291x(84)91053-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Tight couple (TC) 50S ribosomes on treatment with kethoxal lose their capacity to associate with 30S ribosomes whereas loose couple (LC) 50S ribosomes on such treatment fully retain their association capacity. The same is true for 23S RNAs isolated from treated 50S ribosomes or isolated 23S RNAs directly treated with kethoxal, so far as their capacity to associate with 16S RNA is concerned. At certain Mg++ concentrations TC 23S RNA is highly susceptible to the nucleolytic action of single-strand specific enzyme RNase I; LC 23S RNA is quite resistant. The Mg++-dependencies of the two species of 23S RNAs for association with 16S RNA are also quite different. The fluorescence enhancement of ethidium bromide due to binding to TC 23S RNA is slightly less than LC 23S RNA. The hyperchromicity of LC 23S RNA due to thermal denaturation is somewhat more than TC 23S RNA. LC 23S RNA has slightly more elliptic CD spectrum than TC 23S RNA. These results clearly show that 23S RNAs present in TC and LC 50S ribosomes are distinct from each other. It has been recently demonstrated in this laboratory that they can be interconverted by the agents involved in translocation and thus appear to be conformomers.
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Igarashi K, Sakamoto I, Goto N, Kashiwagi K, Honma R, Hirose S. Interaction between polyamines and nucleic acids or phospholipids. Arch Biochem Biophys 1982; 219:438-43. [PMID: 6187285 DOI: 10.1016/0003-9861(82)90175-8] [Citation(s) in RCA: 91] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Burma DP. Structural alteration of rRNA in the L7/L12 region of 50s ribosome on removal of L7/L12 proteins. Biochem Biophys Res Commun 1982; 104:99-104. [PMID: 6280693 DOI: 10.1016/0006-291x(82)91945-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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10
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Effects of ethidium bromide and berenil on protein synthesis. J Biosci 1979. [DOI: 10.1007/bf02706329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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Reyes R, Vazquez D, Ballesta JP. Structure of the yeast ribosomes. Proteins associated with the rRNA. BIOCHIMICA ET BIOPHYSICA ACTA 1978; 521:229-34. [PMID: 363157 DOI: 10.1016/0005-2787(78)90265-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Polyamines have been shown to bind to doubled stranded regions of rRNA [3]. Therefore, ribosomal proteins that can be cross linked to these molecules in the ribosomes structure must be bound to or located in the vicinity of the RNA. This technique is the first to yield results on the proteins associated with the rRNA in the eukaryotic ribosome where the lack of purified ribosomal proteins does not allow the use of direct binding studies as in bacterial systems. Proteins S7, S10, S13, S21, S22 and S27 in the small subunit and L2/3, L5, L10/12, L19/20, L22, L23, L36/37, L42 and L43' in the large subunit are labelled when cross linked to [14C]spermidine using 1,5-difluoro 2,4-dinitrobenzene and are good candidates to be RNA-binding proteins in ribosomes from Saccharomyces cerevisiae.
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Igarashi K, Tanaka M, Eguchi K, Hirose S. Polyamine prevention of inhibition of rat liver isoleucyl-tRNA formation by poly(G), poly(I) or ribosomes. Biochem Biophys Res Commun 1978; 83:274-80. [PMID: 358977 DOI: 10.1016/0006-291x(78)90427-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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14
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Bernabeu C, Vazquez D, Ballesta JP. Proteins associated with rRNA in the Escherichia coli ribosome. BIOCHIMICA ET BIOPHYSICA ACTA 1978; 518:290-7. [PMID: 350280 DOI: 10.1016/0005-2787(78)90185-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Ribosomal proteins located near the rRNA have been identified by cross linking to [14C]spermine with 1,5-difluoro-2,4-dinitrobenzene. The polyamine binds to double-stranded rRNA; those proteins showing radioactivity covalently bound after treatment with the bifunctional reagent should therefore be located in the vicinity of these regions of rRNA. Six proteins from the small subunit, S4, S5, S9, S18, S19 and S20 and ten proteins from the large subunit L2, L6, L13, L14, L16, L17, L18, L19, L22 and L27 preferentially take up the label. The results obtained with three proteins from the large subunit, L6, L16 and L27, show a high degree of variability that could reflect differences of conformation in the subunit population. Several proteins were drastically modified by the cross-linking agent but were not detected in the two-dimensional gel electrophoresis (e.g., S1, S11, S21, L7, L8 and L12) and therefore could not be studied.
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Karpetsky TP, Hieter PA, Frank JJ, Levy CC. Polyamines, ribonucleases, and the stability of RNA. Mol Cell Biochem 1977; 17:89-99. [PMID: 333273 DOI: 10.1007/bf01743432] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Ballesta JP, Waring MJ, Vázquez D. Specific release of ribosomal proteins by nucleic acid-intercalating agents. Nucleic Acids Res 1976; 3:1307-22. [PMID: 781624 PMCID: PMC342988 DOI: 10.1093/nar/3.5.1307] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Increasing concentrations of ethidium bromide cause progressive inactivation of ribosomes, apparently by binding to double-stranded regions of the rRNA. At low drug concentrations (10(-4)M) the partial inhibition detected is due to specific release of proteins L7 and L12; activity can be restored by addition of an excess of these two proteins. At higher concentrations the inactivation is not reversed by supplementation with released proteins. The presence of ethanol affects the extent of ethidium binding and also the release of ribosomal proteins. In all tests the proteins most sensitive to the presence of the drug are L7 and L12, followed by L8/9, L11, L27, L28, L29 and L30. Despite the fact that L7 and L12 are the first two proteins released by ethidium they are never totally missing from drug-treated ribosomes, though the other proteins can be displaced completely. About 50% of proteins L7 and L12 remain on the ribosomes at the highest drug concentrations tested, possibly indicating heterogeneity in the binding sites for the several copies present in the ribosome.
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Igarashi K, Watanabe Y, Hirose S. Dependency of spermidine stimulation of polypeptide synthesis on the uracil content of messenger ribonucleic acid. Biochem Biophys Res Commun 1975; 67:407-13. [PMID: 1106408 DOI: 10.1016/0006-291x(75)90330-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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18
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Suryanarayana T, Burma DP. Effects of intercalating agents on the structure of the ribosome. Biochem Biophys Res Commun 1975; 65:708-13. [PMID: 1096896 DOI: 10.1016/s0006-291x(75)80203-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Igarashi K, Sugawara K, Izumi I, Nagayama C, Hirose S. Effect of polyamines of polyphenylalanine synthesis by Escherichia coli and rat-liver ribosomes. EUROPEAN JOURNAL OF BIOCHEMISTRY 1974; 48:495-502. [PMID: 4614977 DOI: 10.1111/j.1432-1033.1974.tb03790.x] [Citation(s) in RCA: 108] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Abstract
Putrescine uptake was studied in cultures of Escherichia coli K-12 grown in media of high or low osmolarity. When grown in high osmolarity medium, a transport system of low K(m) and low V(max) was found. For cultures grown in a medium of low osmolarity, the kinetics of putrescine uptake was more complex and consistent with the existence of an additional transport system of higher K(m) and V(max). This conclusion is supported by the isolation of mutants in which one or the other system appears to be defective and by the ability of chloramphenicol to block the expression of the second transport system. Both systems appear to prefer putrescine over other compounds, since several basic amino acids and other polyamines competed only weakly for transport. The action of both uptake systems was shown to cause significant displacement of intracellular putrescine. Both systems also are at least partially energy dependent.
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Teraoka H, Tanaka K. Effect of polyamines on the binding of dihydrostreptomycin and N-acetylphenylalanyl-tRNA to ribosomes from Escherichia coli. EUROPEAN JOURNAL OF BIOCHEMISTRY 1973; 40:423-9. [PMID: 4131255 DOI: 10.1111/j.1432-1033.1973.tb03211.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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