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Merkl PE, Schächner C, Pilsl M, Schwank K, Schmid C, Längst G, Milkereit P, Griesenbeck J, Tschochner H. Specialization of RNA Polymerase I in Comparison to Other Nuclear RNA Polymerases of Saccharomyces cerevisiae. Methods Mol Biol 2022; 2533:63-70. [PMID: 35796982 PMCID: PMC9761553 DOI: 10.1007/978-1-0716-2501-9_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In archaea and bacteria the major classes of RNAs are synthesized by one DNA-dependent RNA polymerase (RNAP). In contrast, most eukaryotes have three highly specialized RNAPs to transcribe the nuclear genome. RNAP I synthesizes almost exclusively ribosomal (r)RNA, RNAP II synthesizes mRNA as well as many noncoding RNAs involved in RNA processing or RNA silencing pathways and RNAP III synthesizes mainly tRNA and 5S rRNA. This review discusses functional differences of the three nuclear core RNAPs in the yeast S. cerevisiae with a particular focus on RNAP I transcription of nucleolar ribosomal (r)DNA chromatin.
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Affiliation(s)
- Philipp E Merkl
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
- TUM ForTe, Technische Universität München, Munich, Germany
| | - Christopher Schächner
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Michael Pilsl
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Katrin Schwank
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Catharina Schmid
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Gernot Längst
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Philipp Milkereit
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany.
| | - Joachim Griesenbeck
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Herbert Tschochner
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany.
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Schächner C, Merkl PE, Pilsl M, Schwank K, Hergert K, Kruse S, Milkereit P, Tschochner H, Griesenbeck J. Establishment and Maintenance of Open Ribosomal RNA Gene Chromatin States in Eukaryotes. Methods Mol Biol 2022; 2533:25-38. [PMID: 35796980 PMCID: PMC9761505 DOI: 10.1007/978-1-0716-2501-9_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In growing eukaryotic cells, nuclear ribosomal (r)RNA synthesis by RNA polymerase (RNAP) I accounts for the vast majority of cellular transcription. This high output is achieved by the presence of multiple copies of rRNA genes in eukaryotic genomes transcribed at a high rate. In contrast to most of the other transcribed genomic loci, actively transcribed rRNA genes are largely devoid of nucleosomes adapting a characteristic "open" chromatin state, whereas a significant fraction of rRNA genes resides in a transcriptionally inactive nucleosomal "closed" chromatin state. Here, we review our current knowledge about the nature of open rRNA gene chromatin and discuss how this state may be established.
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Affiliation(s)
- Christopher Schächner
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Philipp E Merkl
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
- TUM ForTe, Technische Universität München, Munich, Germany
| | - Michael Pilsl
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Katrin Schwank
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Kristin Hergert
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Sebastian Kruse
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Philipp Milkereit
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany.
| | - Herbert Tschochner
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany.
| | - Joachim Griesenbeck
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany.
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Omar A, Moon JH, Jung JH. Molecular phylogeny of a new gonostomatid ciliate revealing a discrepancy between interphasic and cell divisional patterns (Ciliophora, Hypotricha). Eur J Protistol 2021; 79:125794. [PMID: 33975056 DOI: 10.1016/j.ejop.2021.125794] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 03/07/2021] [Accepted: 04/06/2021] [Indexed: 10/21/2022]
Abstract
The morphology, ontogenesis, and molecular phylogeny of a new ciliate, Gonostomum koreanum n. sp., discovered in a terrestrial moss sample from South Korea, were investigated. Morphologically, it is characterized by a gonostomatid oral apparatus, two macronuclear nodules, six frontoventral rows, the two rightmost of which (frontoventral rows V and VI) extend posteriorly to near pretransverse and transverse cirri, and three dorsal kineties each with a single caudal cirrus posteriorly. The new species is easily confused with members of the genus Metagonostomum because of the long frontoterminal cirral row but differs mainly in the de novo (vs. intrakinetal) origin of anlage VI, a character found only in Gonostomum and Paragonostomum. To solve the discrepancy between the interphasic and ontogenetic patterns, we additionally performed morphological and multigene analyses on three gonostomatid species, namely Gonostomum koreanum n. sp. and its morphologically (M. gonostomoida) and ontogenetically (G. kuehnelti) most similar species. The multigene analyses show that the new species is closely related to G. kuehnelti and the core gonostomatids consists of five groups based on the origin of the frontoventral rows.
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Affiliation(s)
- Atef Omar
- Natural Science Research Institute, Gangneung-Wonju National University, Gangneung 25457, South Korea; Department of Zoology, Al Azhar University, Assiut 71524, Egypt
| | - Ji Hye Moon
- Department of Biology, Gangneung-Wonju National University, Gangneung 25457, South Korea
| | - Jae-Ho Jung
- Department of Biology, Gangneung-Wonju National University, Gangneung 25457, South Korea.
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Bozidis P, Sakkas H, Pertsalis A, Christodoulou A, Kalogeropoulos CD, Papadopoulou C. Molecular Analysis of Dirofilaria repens Isolates from Eye-Care Patients in Greece. Acta Parasitol 2021; 66:271-276. [PMID: 32780297 DOI: 10.1007/s11686-020-00257-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/28/2020] [Indexed: 11/24/2022]
Abstract
PURPOSE Human ocular dirofilariasis is a zoonotic disease caused by several species of filarioid helminths of the genus Dirofilaria. The aim of this study was to further re-examine five preserved specimens previously isolated from patients with ocular dirofilariasis by molecular means. METHODS Four of the examined helminths had been stored in unbuffered formaldehyde solution for more than eight years; whereas, the fifth helminth was stored in ethanol buffer for more than two years. For the four specimens stored in formaldehyde, different methods of DNA recovery and amplification were applied and investigated for their efficiency in DNA extraction and PCR amplification. However, the DNA extraction and PCR amplification were successful only for the ethanol-preserved helminth. RESULTS The genetic identification of the ethanol-preserved specimen as Dirofilaria repens (D. repens) and its phylogenetic position based on the analysis of mitochondrial 12S ribosomal RNA, nuclear 18S ribosomal RNA and mitochondrial cytochrome c oxidase subunit one sequences are reported in the present paper. To our knowledge, these are the only deposited sequences related to D. repens that have been isolated in Greece. CONCLUSIONS Routine laboratory diagnosis is based on phenotypic characteristics of the helminthic parasites, but more accurate diagnosis requires molecular identification. Although the specimens preserved in formalin buffers may be a potential source for the enrichment of parasite genome databases, the DNA recovery of such samples is a challenging task.
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Affiliation(s)
- Petros Bozidis
- Microbiology Department, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110, Ioannina, Greece.
| | - Hercules Sakkas
- Microbiology Department, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110, Ioannina, Greece
| | - Athanasios Pertsalis
- Microbiology Department, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110, Ioannina, Greece
| | | | - Chris D Kalogeropoulos
- Ophthalmology Department, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110, Ioannina, Greece
| | - Chrissanthy Papadopoulou
- Microbiology Department, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110, Ioannina, Greece
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Jung JH, Omar A, Kim KS, Kang SC, Kwak DY, Sun JH, Min GS. A study on the non-monophyletic genera Australothrix and Holostichides based on multigene and morphological analyses with a reexamination of type materials (Protozoa: Ciliophora). Mol Phylogenet Evol 2019; 139:106538. [PMID: 31220579 DOI: 10.1016/j.ympev.2019.106538] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 10/26/2022]
Abstract
In a study of ciliate diversity, we collected two new species of the genera Australothrix and Holostichides. Based on nuclear ribosomal genes, our study shows that these two genera are genetically non-monophyletic. To clarify the issues of the non-monophyly, we reexamined type material of H. heterotypicus, H. terrae, and Birojimia soyaensis. Based on multigene and morphometric analyses, Australothrix and Holostichides are clearly non-monophyletic even in mitochondrial CO1 gene trees. The multigene analyses show a clade composed of A. lineae sp. nov., H. terrae, and B. soyaensis, suggesting that a cytopharynx with argyrophilic structures might be their synapomorphy. A list of species with this type of cytopharynx is provided for further studies to either accept or reject this hypothesis. Based on the reexamination, we discriminate the morphologically nearly identical (cryptic/sibling) species H. obliquocirratus sp. nov. from H. heterotypicus and they show significant genetic dissimilarities in the multigene trees. They showed only few morphological (non-quantitative) differences and thus distinguishing them morphologically needs careful investigation.
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Affiliation(s)
- Jae-Ho Jung
- Department of Biology, Gangneung-Wonju National University, Gangneung 25457, Republic of Korea.
| | - Atef Omar
- Department of Biology, Gangneung-Wonju National University, Gangneung 25457, Republic of Korea; Department of Zoology, Al-Azhar University, Assiut 71524, Egypt
| | - Kang-San Kim
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Seung-Chae Kang
- Institute of Science-Gifted Education, Gangneung-Wonju National University, Gangneung 25457, Republic of Korea
| | - Dong-Yoon Kwak
- Institute of Science-Gifted Education, Gangneung-Wonju National University, Gangneung 25457, Republic of Korea
| | - Jun-Hyeok Sun
- Institute of Science-Gifted Education, Gangneung-Wonju National University, Gangneung 25457, Republic of Korea
| | - Gi-Sik Min
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
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Abstract
Background Although Tellinidae is one of the largest and most diverse families of bivalves, its taxonomy is utterly chaotic. This is mainly due to the morphological diversity and homoplasy displayed by their shells and to the scarcity of the molecular phylogenetic studies performed on them. A molecular cytogenetic analysis of four tellin shell species, Bosemprella incarnata, Macomangulus tenuis, Moerella donacina and Serratina serrata, was performed. To molecularly characterize the analyzed specimens, the sequence of a fragment of the mitochondrial cytochrome c oxidase subunit I (COI) was also studied. Results The karyotypes of the four species were composed of different amounts of bi-armed and telocentric chromosomes. The chromosomal mapping of 45S and 5S rDNA and H3 histone gene clusters by fluorescent in situ hybridization also revealed conspicuous differences on the distribution of these DNA sequences on their karyotypes. Vertebrate type telomeric sequences were located solely on both ends of each chromosome in all four tellin shells. Conclusion We present clear evidence of the valuable information provided by FISH signals in both analyzing chromosome evolution in Tellinidae and as a further tool in identifying tellin shell specimens for molecular phylogenies.
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Affiliation(s)
- Daniel García-Souto
- Departamento de Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, E-36310, Vigo, Spain
| | - Gonzalo Ríos
- Departamento de Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, E-36310, Vigo, Spain
| | - Juan J Pasantes
- Departamento de Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, E-36310, Vigo, Spain.
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Dimitrova AD, Georgiev O, Mishev K, Tzvetkov S, Ananiev ED, Karagyozov L. Mapping of unmethylated sites in rDNA repeats in barley NOR deletion line. J Plant Physiol 2016; 205:97-104. [PMID: 27649325 DOI: 10.1016/j.jplph.2016.07.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 07/20/2016] [Accepted: 07/21/2016] [Indexed: 06/06/2023]
Abstract
Extensive cytosine methylation is characteristic of plant rDNA. Evidence exists, however, that the active rRNA genes are less methylated. In this work we report on the mapping of unmethylated CCGG sites in Hordeum vulgare rDNA repeats by digestion with methylation sensitive restriction enzyme HpaII and indirect end-labeling of the generated fragments. For mapping we used genomic DNA from barley deletion line with a single NOR on chromosome 5H. This NOR is more active in order to compensate for the missing NOR 6H. The enhanced NOR 5H activity in the deletion mutant is not due to higher multiplicity of the rRNA genes or, as sequencing showed, to changes in the subunit structure of the intergenic spacer. The HpaII sites in barley rDNA are heavily methylated. Nevertheless, a fraction of the rDNA repeats is hypomethylated with unmethylated CCGG sites at various positions. One unmethylated CCGG sequence is close to the transcription start site, downstream of the 135bp subrepeats. Unmethylated sites are also present in the external transcribed spacer and in the genes coding mature rRNAs. The patterns of unmethylated sites in the barley deletion line and in lines with two NORs were compared. It is hypothesized that the occurrence of unmethylated sites on a fixed subset of rDNA repeats correlates with their transcriptional activity.
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Affiliation(s)
- Anna D Dimitrova
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 21, 1113 Sofia, Bulgaria.
| | - Oleg Georgiev
- Institute of Molecular Life Sciences, University Zurich-Irchel, Winterthurer Str. 190, CH-8057 Zurich, Switzerland
| | - Kiril Mishev
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 21, 1113 Sofia, Bulgaria
| | - Stefan Tzvetkov
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 21, 1113 Sofia, Bulgaria
| | - Evgueni D Ananiev
- Department of Plant Physiology, Faculty of Biology, St. Kl. Ohridsky University of Sofia, 8 Dragan Tsankov bld., 1164 Sofia, Bulgaria
| | - Luchezar Karagyozov
- Department of Plant Physiology, Faculty of Biology, St. Kl. Ohridsky University of Sofia, 8 Dragan Tsankov bld., 1164 Sofia, Bulgaria
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Koshel E, Galkina S, Saifitdinova A, Dyomin A, Deryusheva S, Gaginskaya E. Ribosomal RNA gene functioning in avian oogenesis. Cell Tissue Res 2016; 366:533-542. [PMID: 27339801 DOI: 10.1007/s00441-016-2444-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 05/18/2016] [Indexed: 12/18/2022]
Abstract
Despite long-term exploration into ribosomal RNA gene functioning during the oogenesis of various organisms, many intriguing problems remain unsolved. In this review, we describe nucleolus organizer region (NOR) activity in avian oocytes. Whereas oocytes from an adult avian ovary never reveal the formation of the nucleolus in the germinal vesicle (GV), an ovary from juvenile birds possesses both nucleolus-containing and non-nucleolus-containing oocytes. The evolutionary diversity of oocyte NOR functioning and the potential non-rRNA-related functions of the nucleolus in oocytes are also discussed.
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Affiliation(s)
- Elena Koshel
- Department of Cytology and Histology, Saint-Petersburg State University, Saint-Petersburg, 199034, Russia
| | - Svetlana Galkina
- Department of Cytology and Histology, Saint-Petersburg State University, Saint-Petersburg, 199034, Russia
| | - Alsu Saifitdinova
- Department of Cytology and Histology, Saint-Petersburg State University, Saint-Petersburg, 199034, Russia
| | - Alexandr Dyomin
- Department of Cytology and Histology, Saint-Petersburg State University, Saint-Petersburg, 199034, Russia
| | - Svetlana Deryusheva
- Department of Cytology and Histology, Saint-Petersburg State University, Saint-Petersburg, 199034, Russia.,Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA
| | - Elena Gaginskaya
- Department of Cytology and Histology, Saint-Petersburg State University, Saint-Petersburg, 199034, Russia.
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García-Souto D, Pérez-García C, Morán P, Pasantes JJ. Divergent evolutionary behavior of H3 histone gene and rDNA clusters in venerid clams. Mol Cytogenet 2015; 8:40. [PMID: 26106449 PMCID: PMC4477615 DOI: 10.1186/s13039-015-0150-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 06/09/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Histone H3 gene clusters have been described as highly conserved chromosomal markers in invertebrates. Surprisingly, in bivalves remarkable interspecific differences were found among the eight mussels and between the two clams in which histone H3 gene clusters have already been located. Although the family Veneridae comprises 10 % of the species of marine bivalves, their chromosomes are poorly studied. The clams belonging to this family present 2n = 38 chromosomes and similar karyotypes showing chromosome pairs gradually decreasing in length. In order to assess the evolutionary behavior of histone and rRNA multigene families in bivalves, we mapped histone H3 and ribosomal RNA probes to chromosomes of ten species of venerid clams. RESULTS In contrast with the reported conservation of histone H3 gene clusters and their intercalary location in invertebrates, these loci varied in number and were mostly subterminal in venerid clams. On the other hand, while a single 45S rDNA cluster, highly variable in location, was found in these organisms, 5S rDNA clusters showed interspecific differences in both number and location. The distribution patterns of these sequences were species-specific and mapped to different chromosomal positions in all clams but Ruditapes decussatus, in which one of the minor rDNA clusters and the major rDNA cluster co-located. CONCLUSION The diversity in the distribution patterns of histone H3 gene, 5S rDNA and 28S rDNA clusters found in venerid clams, together with their different evolutionary behaviors in other invertebrate taxa, strongly suggest that the control of the spreading of these multigene families in a group of organisms relies upon a combination of evolutionary forces that operate differently depending not only on the specific multigene family but also on the particular taxa. Our data also showed that H3 histone gene and rDNA clusters are useful landmarks to integrate nex-generation sequencing (NGS) and evolutionary genomic data in non-model species.
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Affiliation(s)
- Daniel García-Souto
- Departamento Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, E-36310 Vigo, Spain
| | | | - Paloma Morán
- Departamento Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, E-36310 Vigo, Spain
| | - Juan J Pasantes
- Departamento Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, E-36310 Vigo, Spain
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