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Kuntz M, Keller M, Crouse EJ, Burkard G, Weil JH. Fractionation and identification of Euglena gracilis cytoplasmic and chloroplastic tRNAs and mapping of tRNA genes on chloroplast DNA. Curr Genet 2013; 6:63-9. [PMID: 24186373 DOI: 10.1007/bf00397643] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/1982] [Indexed: 11/26/2022]
Abstract
The cytoplasmic and chloroplast tRNAs of Euglena gracilis Z strain were fractionated by two-dimensional gel electrophoresis and identified by aminoacylation. Purified chloroplast tRNAs, labeled in vitro with |(32)P|, were hybridized to endonuclease restriction fragments of chloroplast DNA, allowing the corresponding tRNA genes to be localized on the physical map of Euglena chloroplast DNA.
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Affiliation(s)
- M Kuntz
- Institut de Biologie Moléculaire et Cellulaire du CNRS, Université Louis Pasteur, 15 rue Descartes, 67084, Strasbourg, France
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Greenwood SJ, Schnare MN, Cook JR, Gray MW. Analysis of intergenic spacer transcripts suggests 'read-around' transcription of the extrachromosomal circular rDNA in Euglena gracilis. Nucleic Acids Res 2001; 29:2191-8. [PMID: 11353089 PMCID: PMC55454 DOI: 10.1093/nar/29.10.2191] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2001] [Accepted: 03/21/2001] [Indexed: 11/14/2022] Open
Abstract
We report here the sequence of the 1743 bp intergenic spacer (IGS) that separates the 3'-end of the large subunit ribosomal RNA (rRNA) gene from the 5'-end of the small subunit (SSU) rRNA gene in the circular, extrachromosomal ribosomal DNA (rDNA) of Euglena gracilis. The IGS contains a 277 nt stretch of sequence that is related to a sequence found in ITS 1, an internal transcribed spacer between the SSU and 5.8S rRNA genes. Primer extension analysis of IGS transcripts identified three abundant reverse transcriptase stops that may be analogous to the transcription initiation site (TIS) and two processing sites (A' and A0) that are found in this region in other eukaryotes. Features that could influence processing at these sites include an imperfect palindrome near site A0 and a sequence near site A' that could potentially base pair with U3 small nucleolar RNA. Our identification of the TIS (verified by mung bean nuclease analysis) is considered tentative because we also detected low-abundance transcripts upstream of this site throughout the entire IGS. This result suggests the possibility of 'read-around' transcription, i.e. transcription that proceeds multiple times around the rDNA circle without termination.
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MESH Headings
- Animals
- Base Pairing
- Base Sequence
- Conserved Sequence/genetics
- DNA, Circular/genetics
- DNA, Intergenic/genetics
- DNA, Ribosomal/genetics
- Euglena/genetics
- Molecular Sequence Data
- Nuclease Protection Assays
- RNA Processing, Post-Transcriptional
- RNA, Ribosomal/biosynthesis
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Small Nucleolar/metabolism
- Regulatory Sequences, Nucleic Acid/genetics
- Repetitive Sequences, Nucleic Acid/genetics
- Sequence Alignment
- Single-Strand Specific DNA and RNA Endonucleases/metabolism
- Transcription, Genetic/genetics
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Affiliation(s)
- S J Greenwood
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
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Ravel-Chapuis P. Nuclear rDNA in Euglena gracilis: paucity of chromosomal units and replication of extrachromosomal units. Nucleic Acids Res 1988; 16:4801-10. [PMID: 3133636 PMCID: PMC336697 DOI: 10.1093/nar/16.11.4801] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Copy number of chromosomal rDNA units was investigated in two Euglena gracilis wild-type strains. It was established by dot blot analysis that these strains possess about four integrated units per haploid genome. This is the first example of a photosynthetic cell with only a few chromosomal ribosomal genes. In addition to these units, Euglena has 800 to 4000 extrachromosomal rDNA units. Electron microscopy revealed that these free rDNA circles bear a replication origin, and intermediates of replication show a D-loop structure.
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Affiliation(s)
- P Ravel-Chapuis
- Université Lyon I, Laboratoire de Biologie Cellulaire, UA CNRS 92, Villeurbanne, France
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Ravel-Chapuis P, Nicolas P, Nigon V, Neyret O, Freyssinet G. Extrachromosomal circular nuclear rDNA in Euglena gracilis. Nucleic Acids Res 1985; 13:7529-37. [PMID: 3932973 PMCID: PMC322060 DOI: 10.1093/nar/13.20.7529] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The presence of extrachromosomal nuclear ribosomal DNA (rDNA) in the unicellular alga Euglena gracilis has been established. This rDNA is circular. Each circle is 3.8 micron long and contains one rDNA unit. Oligomers are rare. Extrachromosomal rDNA is present in large amounts during the exponential phase of growth and appears less abundant during the stationary phase. It was found in all wild-type and mutant strains of Euglena examined. Our estimations suggest that rDNA in Euglena is mainly extrachromosomal. Research of extrachromosomal rDNA in spinach and Petunia was negative.
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Keus RJ, Stam NJ, Zwiers T, de Heij HT, Groot GS. The nucleotide sequences of the genes coding for tRNAArgUCU, tRNAArgACG and tRNAAsnGUU on Spirodela oligorhiza chloroplast DNA. Nucleic Acids Res 1984; 12:5639-46. [PMID: 6462915 PMCID: PMC320020 DOI: 10.1093/nar/12.14.5639] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The nucleotide sequences of the genes coding for tRNAArgUCU, tRNAArgACG and tRNAAsnGUU on chloroplast DNA of Spirodela oligorhiza have been determined. All three genes are expressed. 5' Proximal to these genes sequences are found homologous to prokaryotic promoter sequences, which might be involved as transcriptional start motifs.
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Karabin GD, Narita JO, Dodd JR, Hallick RB. Euglena gracilis chloroplast ribosomal RNA transcription units. Nucleotide sequence polymorphism in 5 S rRNA genes and 5 S rRNAs. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(17)43730-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Karabin GD, Hallick RB. Euglena gracilis chloroplast transfer RNA transcription units. Nucleotide sequence analysis of a tRNAThr-tRNAGly-tRNAMet-tRNASer-tRNAGln gene cluster. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(20)81920-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Selden RF, Steinmetz A, McIntosh L, Bogorad L, Burkard G, Mubumbila M, Kuntz M, Crouse EJ, Weil JH. Transfer RNA genes ofZea mays chloroplast DNA. PLANT MOLECULAR BIOLOGY 1983; 2:141-153. [PMID: 24318208 DOI: 10.1007/bf01578514] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/1983] [Revised: 07/07/1983] [Accepted: 07/07/1983] [Indexed: 06/02/2023]
Abstract
A minimum of 37 genes corresponding to tRNAs for 17 different amino acids have been localized on the restriction endonuclease cleavage site map of theZea mays chloroplast DNA molecule. Of these, 14 genes corresponding to tRNAs for 11 amino acids are located in the larger of the two single-copy regions which separate the two inverted copies of the repeat region. One tRNA gene is in the smaller single-copy region. Each copy of the large repeated sequence contains, in addition to the ribosomal RNA genes, 11 tRNA genes corresponding to tRNAs for 8 amino acids. The genes for tRNA2 (Ile) and tRNA(Ala) map in the ribosomal spacer sequence separating the 16S and 23S ribosomal RNA genes. The three isoaccepting species for the tRNAs(Leu) and the three for tRNAs(Ser), as well as the two isoaccepting species for tRNA(Asn), tRNA(Gly), tRNAs(Ile), tRNAs(Met), tRNAs(Thr), are shown to be encoded at different loci.Two independent methods have been used for the localization of tRNA genes on the physical map of the maize chloroplast DNA molecule: (a) cloned chloroplast DNA fragments were hybridized with radioactively-labelled total 4S RNAs, the hybridized RNAs were then eluted, and identified by two-dimensional polyacrylamide gel electrophoresis, and (b) individual tRNAs were(32)P-labelledin vitro and hybridized to DNA fragments generated by digestion of maize chloroplast DNA with various restriction endonucleases.
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Affiliation(s)
- R F Selden
- The Biological Laboratories, Harvard University, Cambridge, Massachusetts, USA
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Villalba E, Ramírez JL. Ribosomal DNA of Leishmania brasiliensis: number of ribosomal copies and gene isolation. THE JOURNAL OF PROTOZOOLOGY 1982; 29:438-41. [PMID: 7131353 DOI: 10.1111/j.1550-7408.1982.tb05428.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The DNA content of the hemoflagellate Leishmania brasiliensis, strain Y, has been determined by colorimetric reactions and found to be nearly 0.226 pg/cell. When this DNA is bound to filters and hybridized with labeled rRNA from the same organism, saturation is reached at 0.47% of the DNA, corresponding to an estimated 160 ribosomal gene copies. When the DNA is sheared and centrifuged to equilibrium in CsCl gradients, two major satellites of the main band (rho = 1.712 g/cm3) are observed: a heavy one (1.720 g/cm3), which hybridizes with labeled rRNA, and a light one (1.699 g/cm3) with the electron microscopic characteristics of the kinetoplast DNA network.
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Orozco EM, Hallick RB. Euglena gracilis chloroplast transfer RNA transcription units. I. Physical map of the transfer RNA gene loci. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(19)81104-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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PHOTOCONTROL OF CHLOROPLAST DEVELOPMENT IN EUGLENA. Physiology (Bethesda) 1982. [DOI: 10.1016/b978-0-12-139903-0.50015-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023] Open
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13
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A map of specific cleavage sites and tRNA genes in the chloroplast genome of Euglena gracilis bacillaris. ACTA ACUST UNITED AC 1981. [DOI: 10.1007/bf00425601] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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14
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Mubumbila M, Burkard G, Keller M, Steinmetz A, Crouse E, Weil JH. Hybridization of bean, spinach, maize and Euglena chloroplast transfer RNAs with homologous and heterologous chloroplast DNAs. An approach to the study of homology between chloroplast tRNAs from various species. BIOCHIMICA ET BIOPHYSICA ACTA 1980; 609:31-9. [PMID: 7407185 DOI: 10.1016/0005-2787(80)90198-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Chloroplast tRNAs from two dicotyledons (spinach and bean), a monocotyledon (maize) and a green alga (Euglena) have been fractionated by two-dimensional gel electrophoresis. The individual tRNAs have been identified, albeled with 125I or 32P, and used in tRNA-DNA hybridization experiments. Spinach chloroplast tRNAs hybridize as well, and maize chloroplast tRNAs almost as well as bean chloroplast tRNAs to bean chloroplast DNA, thus suggesting a high degree of homology between the chloroplast tRNAs from the two dicotyledons and between the tRNAs from the two dicotyledons and those of the monocotyledon. But Euglena total chloroplast tRNA hybridizes very poorly to bean chloroplast DNA, and among the 14 individual tRNAs tested, only one, Euglena chloroplast tRNAPhe, hybridizes to both maize and bean chloroplast DNAs, which is in good agreement with the fact that Euglena and bean chloroplast tRNAsPhe have almost identical primary structures.
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Keller M, Burkard G, Bohnert HJ, Mubumbila M, Gordon K, Steinmetz A, Heiser D, Crouse EJ, Weil JH. Transfer RNA genes associated with the 16S and 23S rRNA genes of Euglena chloroplast DNA. Biochem Biophys Res Commun 1980; 95:47-54. [PMID: 6774711 DOI: 10.1016/0006-291x(80)90702-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Driesel AJ, Crouse EJ, Gordon K, Bohnert HJ, Herrmann RG, Steinmetz A, Mubumbila M, Keller M, Burkard G, Weil JH. Fractionation and identification of spinach chloroplast transfer RNAs and mapping of their genes on the restriction map of chloroplast DNA. Gene 1979; 6:285-306. [PMID: 499808 DOI: 10.1016/0378-1119(79)90070-2] [Citation(s) in RCA: 117] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Spinach chloroplast 4S RNAs has been separated by two-dimensional polyacrylamide gel electrophoresis into about 35 species. After extraction from the gel, 27 of these RNA species were identified by aminoacylation as tRNAs specific for 16 amino acids. Individual tRNAs were labeled in vitro with 125I and hybridized to DNA fragments obtained by digestion of spinach chloroplast DNA with KpnI, PstI, SalI and XmaI restriction endonucleases. A minimum of 21 genes corresponding to tRNAs for 14 different amino acids have been localized on the restriction endonuclease cleavage site map of the DNA molecule. Of these, 15 genes corresponding to tRNAs for 12 amino acids are located in the larger of the two single-copy regions which separate the two inverted copies of the repeat region. Each copy of this repeat region contains a set of genes for the ribosomal RNAs and a gene for tRNA2Ile in the "spacer" sequence between the 16S and 23S ribosomal RNAs. The genes for tRNA1Ile, tRNA2Leu and tRNA3Leu also map in the repeat region, but outside the ribosomal DNA unit. At present, two more chloroplast tRNAs (for Pro and Lys) have been identified, but not mapped, while 4 unidentified 4S RNAs have been mapped in the large single-copy region of the DNA molecule. Evidence is presented that isoaccepting tRNA species can be transcripts from different loci.
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SCHWARTZBACH STEVEND, BARNETT WEDGAR, HECKER LANNYI. Evidence that Euglena chloroplasts do not export tRNAs. Nature 1979. [DOI: 10.1038/280086a0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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19
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Imbault P, Sarantoglou V, Weil JH. Purification of the chloroplastic valyl-tRNA synthetase from Euglena gracilis. Biochem Biophys Res Commun 1979; 88:75-84. [PMID: 110330 DOI: 10.1016/0006-291x(79)91698-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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20
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Verdier G. Poly(adenylic acid)-containing RNA of Euglena gracilis during chloroplast development. 2. Transcriptional origin of the different RNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1979; 93:581-6. [PMID: 105905 DOI: 10.1111/j.1432-1033.1979.tb12858.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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21
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Helling RB, El-Gewely MR, Lomax MI, Baumgartner JE, Schwartzbach SD, Barnett WE. Organization of the chloroplast ribosomal RNA genes of Euglena gracilis bacillaris. ACTA ACUST UNITED AC 1979. [DOI: 10.1007/bf00433298] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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22
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Selsky MI. Reversed phase chromatographic analysis of Nostoc and Euglena isoleucyl-tRNAs aminoacylated in vitro in homologous and heterologous systems. BIOCHIMICA ET BIOPHYSICA ACTA 1978; 520:555-67. [PMID: 102350 DOI: 10.1016/0005-2787(78)90141-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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23
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Nigon V, Heizmann P. Morphology, Biochemistry, and Genetics of Plastid Development in Euglena gracilis. INTERNATIONAL REVIEW OF CYTOLOGY 1978. [DOI: 10.1016/s0074-7696(08)62243-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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24
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Barnett WE, Schwartzbach SD, Hecker LI. The transfer RNAs of eukaryotic organelles. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1978; 21:143-79. [PMID: 358277 DOI: 10.1016/s0079-6603(08)60269-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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25
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Lomax MI, Helling RB, Hecker LI, Schwartzbach SD, Barnett WE. Cloned ribosomal RNA genes from chloroplasts of Euglena gracilis. Science 1977; 196:202-5. [PMID: 403604 DOI: 10.1126/science.403604] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Fragments of Euglena chloroplast DNA generated by endonuclease R-Eco RI were separated by agarose-gel electrophoresis into 24 distinct bands. At least five fragments contain sequences complementary to chloroplast ribosomal RNA, Most of the Eco RI fragments have been cloned in a plasmid of Escherichia coli. Three of the cloned fragments were shown to contain chloroplast ribosomal RNA sequences by DNA-RNA hybridization.
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