The nitrogen-fixation island insertion site is conserved in diazotrophic Pseudomonas stutzeri and Pseudomonas sp. isolated from distal and close geographical regions.
Identifieur interne : 000594 ( Main/Exploration ); précédent : 000593; suivant : 000595The nitrogen-fixation island insertion site is conserved in diazotrophic Pseudomonas stutzeri and Pseudomonas sp. isolated from distal and close geographical regions.
Auteurs : Anastasia Venieraki [Grèce] ; Maria Dimou [Grèce] ; Eleni Vezyri [Grèce] ; Alexandros Vamvakas [Grèce] ; Pagona-Artemis Katinaki [Grèce] ; Iordanis Chatzipavlidis [Grèce] ; Anastasia Tampakaki [Grèce] ; Panagiotis Katinakis [Grèce]Source :
- PloS one [ 1932-6203 ] ; 2014.
Descripteurs français
- KwdFr :
- ADN bactérien (composition chimique), ADN bactérien (génétique), ARN ribosomique 16S (génétique), Allemagne (MeSH), Analyse de séquence d'ADN (MeSH), Chine (MeSH), Données de séquences moléculaires (MeSH), Fixation de l'azote (génétique), Grèce (MeSH), Géographie (MeSH), Ilots génomiques (génétique), Modèles génétiques (MeSH), Phylogenèse (MeSH), Protéines bactériennes (génétique), Pseudomonas (classification), Pseudomonas (génétique), Pseudomonas stutzeri (génétique), Similitude de séquences d'acides nucléiques (MeSH), Spécificité d'espèce (MeSH), Séquence nucléotidique (MeSH), Séquences répétées d'acides nucléiques (génétique), Variation génétique (MeSH), Évolution moléculaire (MeSH).
- MESH :
- composition chimique : ADN bactérien, Pseudomonas.
- génétique : ADN bactérien, ARN ribosomique 16S, Fixation de l'azote, Ilots génomiques, Protéines bactériennes, Pseudomonas, Pseudomonas stutzeri, Séquences répétées d'acides nucléiques.
- Allemagne, Analyse de séquence d'ADN, Chine, Données de séquences moléculaires, Grèce, Géographie, Modèles génétiques, Phylogenèse, Similitude de séquences d'acides nucléiques, Spécificité d'espèce, Séquence nucléotidique, Variation génétique, Évolution moléculaire.
- Wicri :
- geographic : République populaire de Chine, Allemagne, Grèce.
English descriptors
- KwdEn :
- Bacterial Proteins (genetics), Base Sequence (MeSH), China (MeSH), DNA, Bacterial (chemistry), DNA, Bacterial (genetics), Evolution, Molecular (MeSH), Genetic Variation (MeSH), Genomic Islands (genetics), Geography (MeSH), Germany (MeSH), Greece (MeSH), Models, Genetic (MeSH), Molecular Sequence Data (MeSH), Nitrogen Fixation (genetics), Phylogeny (MeSH), Pseudomonas (classification), Pseudomonas (genetics), Pseudomonas stutzeri (genetics), RNA, Ribosomal, 16S (genetics), Repetitive Sequences, Nucleic Acid (genetics), Sequence Analysis, DNA (MeSH), Sequence Homology, Nucleic Acid (MeSH), Species Specificity (MeSH).
- MESH :
- chemical , chemistry : DNA, Bacterial.
- chemical , genetics : Bacterial Proteins, DNA, Bacterial, RNA, Ribosomal, 16S.
- geographic : China, Germany, Greece.
- classification : Pseudomonas.
- genetics : Genomic Islands, Nitrogen Fixation, Pseudomonas, Pseudomonas stutzeri, Repetitive Sequences, Nucleic Acid.
- Base Sequence, Evolution, Molecular, Genetic Variation, Geography, Models, Genetic, Molecular Sequence Data, Phylogeny, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Species Specificity.
Abstract
The presence of nitrogen fixers within the genus Pseudomonas has been established and so far most isolated strains are phylogenetically affiliated to Pseudomonas stutzeri. A gene ortholog neighborhood analysis of the nitrogen fixation island (NFI) in four diazotrophic P. stutzeri strains and Pseudomonas azotifigens revealed that all are flanked by genes coding for cobalamin synthase (cobS) and glutathione peroxidise (gshP). The putative NFIs lack all the features characterizing a mobilizable genomic island. Nevertheless, bioinformatic analysis P. stutzeri DSM 4166 NFI demonstrated the presence of short inverted and/or direct repeats within both flanking regions. The other P. stutzeri strains carry only one set of repeats. The genetic diversity of eleven diazotrophic Pseudomonas isolates was also investigated. Multilocus sequence typing grouped nine isolates along with P. stutzeri and two isolates are grouped in a separate clade. A Rep-PCR fingerprinting analysis grouped the eleven isolates into four distinct genotypes. We also provided evidence that the putative NFI in our diazotrophic Pseudomonas isolates is flanked by cobS and gshP genes. Furthermore, we demonstrated that the putative NFI of Pseudomonas sp. Gr65 is flanked by inverted repeats identical to those found in P. stutzeri DSM 4166 and while the other P. stutzeri isolates harbor the repeats located in the intergenic region between cobS and glutaredoxin genes as in the case of P. stutzeri A1501. Taken together these data suggest that all putative NFIs of diazotrophic Pseudomonas isolates are anchored in an intergenic region between cobS and gshP genes and their flanking regions are designated by distinct repeats patterns. Moreover, the presence of almost identical NFIs in diazotrophic Pseudomonas strains isolated from distal geographical locations around the world suggested that this horizontal gene transfer event may have taken place early in the evolution.
DOI: 10.1371/journal.pone.0105837
PubMed: 25251496
PubMed Central: PMC4174501
Affiliations:
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Greece.</nlm:affiliation><country xml:lang="fr">Grèce</country><wicri:regionArea>Department of Crop Science, Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens</wicri:regionArea><placeName><settlement type="city">Athènes</settlement><region nuts="2" type="region">Attique (région)</region></placeName></affiliation></author><author><name sortKey="Dimou, Maria" sort="Dimou, Maria" uniqKey="Dimou M" first="Maria" last="Dimou">Maria Dimou</name><affiliation wicri:level="3"><nlm:affiliation>Department of Crop Science, Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens, Greece.</nlm:affiliation><country xml:lang="fr">Grèce</country><wicri:regionArea>Department of Crop Science, Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens</wicri:regionArea><placeName><settlement type="city">Athènes</settlement><region nuts="2" type="region">Attique (région)</region></placeName></affiliation></author><author><name sortKey="Vezyri, Eleni" sort="Vezyri, Eleni" uniqKey="Vezyri E" first="Eleni" last="Vezyri">Eleni Vezyri</name><affiliation wicri:level="3"><nlm:affiliation>Department of Crop Science, Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens, Greece.</nlm:affiliation><country xml:lang="fr">Grèce</country><wicri:regionArea>Department of Crop Science, Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens</wicri:regionArea><placeName><settlement type="city">Athènes</settlement><region nuts="2" type="region">Attique (région)</region></placeName></affiliation></author><author><name sortKey="Vamvakas, Alexandros" sort="Vamvakas, Alexandros" uniqKey="Vamvakas A" first="Alexandros" last="Vamvakas">Alexandros Vamvakas</name><affiliation wicri:level="3"><nlm:affiliation>Department of Crop Science, Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens, Greece.</nlm:affiliation><country xml:lang="fr">Grèce</country><wicri:regionArea>Department of Crop Science, Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens</wicri:regionArea><placeName><settlement type="city">Athènes</settlement><region nuts="2" type="region">Attique (région)</region></placeName></affiliation></author><author><name sortKey="Katinaki, Pagona Artemis" sort="Katinaki, Pagona Artemis" uniqKey="Katinaki P" first="Pagona-Artemis" last="Katinaki">Pagona-Artemis Katinaki</name><affiliation wicri:level="3"><nlm:affiliation>Department of Crop Science, Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens, Greece.</nlm:affiliation><country xml:lang="fr">Grèce</country><wicri:regionArea>Department of Crop Science, Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens</wicri:regionArea><placeName><settlement type="city">Athènes</settlement><region nuts="2" type="region">Attique (région)</region></placeName></affiliation></author><author><name sortKey="Chatzipavlidis, Iordanis" sort="Chatzipavlidis, Iordanis" uniqKey="Chatzipavlidis I" first="Iordanis" last="Chatzipavlidis">Iordanis Chatzipavlidis</name><affiliation wicri:level="3"><nlm:affiliation>Department of Crop Science, Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens, Greece.</nlm:affiliation><country xml:lang="fr">Grèce</country><wicri:regionArea>Department of Crop Science, Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens</wicri:regionArea><placeName><settlement type="city">Athènes</settlement><region nuts="2" type="region">Attique (région)</region></placeName></affiliation></author><author><name sortKey="Tampakaki, Anastasia" sort="Tampakaki, Anastasia" uniqKey="Tampakaki A" first="Anastasia" last="Tampakaki">Anastasia Tampakaki</name><affiliation wicri:level="3"><nlm:affiliation>Department of Crop Science, Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens, Greece.</nlm:affiliation><country xml:lang="fr">Grèce</country><wicri:regionArea>Department of Crop Science, Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens</wicri:regionArea><placeName><settlement type="city">Athènes</settlement><region nuts="2" type="region">Attique (région)</region></placeName></affiliation></author><author><name sortKey="Katinakis, Panagiotis" sort="Katinakis, Panagiotis" uniqKey="Katinakis P" first="Panagiotis" last="Katinakis">Panagiotis Katinakis</name><affiliation wicri:level="3"><nlm:affiliation>Department of Crop Science, Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens, Greece.</nlm:affiliation><country xml:lang="fr">Grèce</country><wicri:regionArea>Department of Crop Science, Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens</wicri:regionArea><placeName><settlement type="city">Athènes</settlement><region nuts="2" type="region">Attique (région)</region></placeName></affiliation></author></analytic><series><title level="j">PloS one</title><idno type="eISSN">1932-6203</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Bacterial Proteins (genetics)</term><term>Base Sequence (MeSH)</term><term>China (MeSH)</term><term>DNA, Bacterial (chemistry)</term><term>DNA, Bacterial (genetics)</term><term>Evolution, Molecular (MeSH)</term><term>Genetic Variation (MeSH)</term><term>Genomic Islands (genetics)</term><term>Geography (MeSH)</term><term>Germany (MeSH)</term><term>Greece (MeSH)</term><term>Models, Genetic (MeSH)</term><term>Molecular Sequence Data (MeSH)</term><term>Nitrogen Fixation (genetics)</term><term>Phylogeny (MeSH)</term><term>Pseudomonas (classification)</term><term>Pseudomonas (genetics)</term><term>Pseudomonas stutzeri (genetics)</term><term>RNA, Ribosomal, 16S (genetics)</term><term>Repetitive Sequences, Nucleic Acid (genetics)</term><term>Sequence Analysis, DNA (MeSH)</term><term>Sequence Homology, Nucleic Acid (MeSH)</term><term>Species Specificity (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN bactérien (composition chimique)</term><term>ADN bactérien (génétique)</term><term>ARN ribosomique 16S (génétique)</term><term>Allemagne (MeSH)</term><term>Analyse de séquence d'ADN (MeSH)</term><term>Chine (MeSH)</term><term>Données de séquences moléculaires (MeSH)</term><term>Fixation de l'azote (génétique)</term><term>Grèce (MeSH)</term><term>Géographie (MeSH)</term><term>Ilots génomiques (génétique)</term><term>Modèles génétiques (MeSH)</term><term>Phylogenèse (MeSH)</term><term>Protéines bactériennes (génétique)</term><term>Pseudomonas (classification)</term><term>Pseudomonas (génétique)</term><term>Pseudomonas stutzeri (génétique)</term><term>Similitude de séquences d'acides nucléiques (MeSH)</term><term>Spécificité d'espèce (MeSH)</term><term>Séquence nucléotidique (MeSH)</term><term>Séquences répétées d'acides nucléiques (génétique)</term><term>Variation génétique (MeSH)</term><term>Évolution moléculaire (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA, Bacterial</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Bacterial Proteins</term><term>DNA, Bacterial</term><term>RNA, Ribosomal, 16S</term></keywords><keywords scheme="MESH" type="geographic" xml:lang="en"><term>China</term><term>Germany</term><term>Greece</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Pseudomonas</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>ADN bactérien</term><term>Pseudomonas</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Genomic Islands</term><term>Nitrogen Fixation</term><term>Pseudomonas</term><term>Pseudomonas stutzeri</term><term>Repetitive Sequences, Nucleic Acid</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN bactérien</term><term>ARN ribosomique 16S</term><term>Fixation de l'azote</term><term>Ilots génomiques</term><term>Protéines bactériennes</term><term>Pseudomonas</term><term>Pseudomonas stutzeri</term><term>Séquences répétées d'acides nucléiques</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Evolution, Molecular</term><term>Genetic Variation</term><term>Geography</term><term>Models, Genetic</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Sequence Analysis, DNA</term><term>Sequence Homology, Nucleic Acid</term><term>Species Specificity</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Allemagne</term><term>Analyse de séquence d'ADN</term><term>Chine</term><term>Données de séquences moléculaires</term><term>Grèce</term><term>Géographie</term><term>Modèles génétiques</term><term>Phylogenèse</term><term>Similitude de séquences d'acides nucléiques</term><term>Spécificité d'espèce</term><term>Séquence nucléotidique</term><term>Variation génétique</term><term>Évolution moléculaire</term></keywords><keywords scheme="Wicri" type="geographic" xml:lang="fr"><term>République populaire de Chine</term><term>Allemagne</term><term>Grèce</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The presence of nitrogen fixers within the genus Pseudomonas has been established and so far most isolated strains are phylogenetically affiliated to Pseudomonas stutzeri. A gene ortholog neighborhood analysis of the nitrogen fixation island (NFI) in four diazotrophic P. stutzeri strains and Pseudomonas azotifigens revealed that all are flanked by genes coding for cobalamin synthase (cobS) and glutathione peroxidise (gshP). The putative NFIs lack all the features characterizing a mobilizable genomic island. Nevertheless, bioinformatic analysis P. stutzeri DSM 4166 NFI demonstrated the presence of short inverted and/or direct repeats within both flanking regions. The other P. stutzeri strains carry only one set of repeats. The genetic diversity of eleven diazotrophic Pseudomonas isolates was also investigated. Multilocus sequence typing grouped nine isolates along with P. stutzeri and two isolates are grouped in a separate clade. A Rep-PCR fingerprinting analysis grouped the eleven isolates into four distinct genotypes. We also provided evidence that the putative NFI in our diazotrophic Pseudomonas isolates is flanked by cobS and gshP genes. Furthermore, we demonstrated that the putative NFI of Pseudomonas sp. Gr65 is flanked by inverted repeats identical to those found in P. stutzeri DSM 4166 and while the other P. stutzeri isolates harbor the repeats located in the intergenic region between cobS and glutaredoxin genes as in the case of P. stutzeri A1501. Taken together these data suggest that all putative NFIs of diazotrophic Pseudomonas isolates are anchored in an intergenic region between cobS and gshP genes and their flanking regions are designated by distinct repeats patterns. Moreover, the presence of almost identical NFIs in diazotrophic Pseudomonas strains isolated from distal geographical locations around the world suggested that this horizontal gene transfer event may have taken place early in the evolution. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25251496</PMID><DateCompleted><Year>2015</Year><Month>06</Month><Day>23</Day></DateCompleted><DateRevised><Year>2020</Year><Month>03</Month><Day>06</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>9</Volume><Issue>9</Issue><PubDate><Year>2014</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS One</ISOAbbreviation></Journal><ArticleTitle>The nitrogen-fixation island insertion site is conserved in diazotrophic Pseudomonas stutzeri and Pseudomonas sp. isolated from distal and close geographical regions.</ArticleTitle><Pagination><MedlinePgn>e105837</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0105837</ELocationID><Abstract><AbstractText>The presence of nitrogen fixers within the genus Pseudomonas has been established and so far most isolated strains are phylogenetically affiliated to Pseudomonas stutzeri. A gene ortholog neighborhood analysis of the nitrogen fixation island (NFI) in four diazotrophic P. stutzeri strains and Pseudomonas azotifigens revealed that all are flanked by genes coding for cobalamin synthase (cobS) and glutathione peroxidise (gshP). The putative NFIs lack all the features characterizing a mobilizable genomic island. Nevertheless, bioinformatic analysis P. stutzeri DSM 4166 NFI demonstrated the presence of short inverted and/or direct repeats within both flanking regions. The other P. stutzeri strains carry only one set of repeats. The genetic diversity of eleven diazotrophic Pseudomonas isolates was also investigated. Multilocus sequence typing grouped nine isolates along with P. stutzeri and two isolates are grouped in a separate clade. A Rep-PCR fingerprinting analysis grouped the eleven isolates into four distinct genotypes. We also provided evidence that the putative NFI in our diazotrophic Pseudomonas isolates is flanked by cobS and gshP genes. Furthermore, we demonstrated that the putative NFI of Pseudomonas sp. Gr65 is flanked by inverted repeats identical to those found in P. stutzeri DSM 4166 and while the other P. stutzeri isolates harbor the repeats located in the intergenic region between cobS and glutaredoxin genes as in the case of P. stutzeri A1501. Taken together these data suggest that all putative NFIs of diazotrophic Pseudomonas isolates are anchored in an intergenic region between cobS and gshP genes and their flanking regions are designated by distinct repeats patterns. Moreover, the presence of almost identical NFIs in diazotrophic Pseudomonas strains isolated from distal geographical locations around the world suggested that this horizontal gene transfer event may have taken place early in the evolution. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Venieraki</LastName><ForeName>Anastasia</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Crop Science, Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens, Greece.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Dimou</LastName><ForeName>Maria</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Crop Science, Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens, Greece.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Vezyri</LastName><ForeName>Eleni</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>Department of Crop Science, Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens, Greece.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Vamvakas</LastName><ForeName>Alexandros</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Crop Science, Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens, Greece.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Katinaki</LastName><ForeName>Pagona-Artemis</ForeName><Initials>PA</Initials><AffiliationInfo><Affiliation>Department of Crop Science, Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens, Greece.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chatzipavlidis</LastName><ForeName>Iordanis</ForeName><Initials>I</Initials><AffiliationInfo><Affiliation>Department of Crop Science, Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens, Greece.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tampakaki</LastName><ForeName>Anastasia</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Crop Science, Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens, Greece.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Katinakis</LastName><ForeName>Panagiotis</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Department of Crop Science, Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens, Greece.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><DataBankList 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(région)</li></region><settlement><li>Athènes</li></settlement></list><tree><country name="Grèce"><region name="Attique (région)"><name sortKey="Venieraki, Anastasia" sort="Venieraki, Anastasia" uniqKey="Venieraki A" first="Anastasia" last="Venieraki">Anastasia Venieraki</name></region><name sortKey="Chatzipavlidis, Iordanis" sort="Chatzipavlidis, Iordanis" uniqKey="Chatzipavlidis I" first="Iordanis" last="Chatzipavlidis">Iordanis Chatzipavlidis</name><name sortKey="Dimou, Maria" sort="Dimou, Maria" uniqKey="Dimou M" first="Maria" last="Dimou">Maria Dimou</name><name sortKey="Katinaki, Pagona Artemis" sort="Katinaki, Pagona Artemis" uniqKey="Katinaki P" first="Pagona-Artemis" last="Katinaki">Pagona-Artemis Katinaki</name><name sortKey="Katinakis, Panagiotis" sort="Katinakis, Panagiotis" uniqKey="Katinakis P" first="Panagiotis" last="Katinakis">Panagiotis Katinakis</name><name sortKey="Tampakaki, Anastasia" sort="Tampakaki, Anastasia" uniqKey="Tampakaki A" first="Anastasia" last="Tampakaki">Anastasia Tampakaki</name><name sortKey="Vamvakas, Alexandros" sort="Vamvakas, Alexandros" uniqKey="Vamvakas A" first="Alexandros" last="Vamvakas">Alexandros Vamvakas</name><name sortKey="Vezyri, Eleni" sort="Vezyri, Eleni" uniqKey="Vezyri E" first="Eleni" last="Vezyri">Eleni Vezyri</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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