Base de dados : MEDLINE
Pesquisa : B02.075.800 [Categoria DeCS]
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  1 / 9 MEDLINE  
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[PMID]:27130276
[Au] Autor:Jay ZJ; Beam JP; Kozubal MA; Jennings RD; Rusch DB; Inskeep WP
[Ad] Endereço:Department of Land Resources and Environmental Sciences and Thermal Biology Institute, Montana State University, Bozeman, MT, 59175-3120, USA.
[Ti] Título:The distribution, diversity and function of predominant Thermoproteales in high-temperature environments of Yellowstone National Park.
[So] Source:Environ Microbiol;18(12):4755-4769, 2016 Dec.
[Is] ISSN:1462-2920
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:High-temperature environments (> 70°C) contain diverse and abundant members of the crenarchaeal order Thermoproteales. However, a comprehensive study of the distribution and function of diverse members of this group across different habitat types has not been conducted. Consequently, the goals of this study were to determine the distribution of different Thermoproteales genera across geochemically distinct geothermal habitats of Yellowstone National Park, and to identify key functional attributes of major genera that correlate with environmental parameters. Curated sequence assemblies belonging to five genera were characterized in replicate samples of 11 high-temperature communities ranging in pH from 3 to 9. Thermocladium, Vulcanisaeta and Caldivirga spp. were the primary Thermoproteales populations present in low pH (pH < 5) habitats, whereas Thermoproteus populations were found in mildly-acidic (pH 5-6) sulfur sediments, and Pyrobaculum populations were confined to higher pH (pH > 6) sulfur sediments and/or filamentous 'streamer' communities. Metabolic reconstruction and comparative genomics among assemblies show that these populations are primarily chemoorganotrophs that utilize different electron acceptors depending on geochemical conditions. The presence of potential CO fixation pathways in some Thermoproteales populations appears to be linked with NiFe hydrogenases, which combined with high levels of H in many sulfidic systems, may provide the energy required to fix inorganic C.
[Mh] Termos MeSH primário: Fontes Termais/microbiologia
Parques Recreativos
Thermoproteales/fisiologia
[Mh] Termos MeSH secundário: Biodiversidade
Fontes Termais/química
Temperatura Alta
Filogenia
RNA Ribossômico 16S
Enxofre/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (RNA, Ribosomal, 16S); 70FD1KFU70 (Sulfur)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170821
[Lr] Data última revisão:
170821
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160501
[St] Status:MEDLINE
[do] DOI:10.1111/1462-2920.13366


  2 / 9 MEDLINE  
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[PMID]:26156036
[Au] Autor:Jay ZJ; Inskeep WP
[Ad] Endereço:Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA. zackary.jay@montana.edu.
[Ti] Título:The distribution, diversity, and importance of 16S rRNA gene introns in the order Thermoproteales.
[So] Source:Biol Direct;10:35, 2015 Jul 09.
[Is] ISSN:1745-6150
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Intron sequences are common in 16S rRNA genes of specific thermophilic lineages of Archaea, specifically the Thermoproteales (phylum Crenarchaeota). Environmental sequencing (16S rRNA gene and metagenome) from geothermal habitats in Yellowstone National Park (YNP) has expanded the available datasets for investigating 16S rRNA gene introns. The objectives of this study were to characterize and curate archaeal 16S rRNA gene introns from high-temperature habitats, evaluate the conservation and distribution of archaeal 16S rRNA introns in geothermal systems, and determine which "universal" archaeal 16S rRNA gene primers are impacted by the presence of intron sequences. RESULTS: Several new introns were identified and their insertion loci were constrained to thirteen locations across the 16S rRNA gene. Many of these introns encode homing endonucleases, although some introns were short or partial sequences. Pyrobaculum, Thermoproteus, and Caldivirga 16S rRNA genes contained the most abundant and diverse intron sequences. Phylogenetic analysis of introns revealed that sequences within the same locus are distributed biogeographically. The most diverse set of introns were observed in a high-temperature, circumneutral (pH 6) sulfur sediment environment, which also contained the greatest diversity of different Thermoproteales phylotypes. CONCLUSIONS: The widespread presence of introns in the Thermoproteales indicates a high probability of misalignments using different "universal" 16S rRNA primers employed in environmental microbial community analysis.
[Mh] Termos MeSH primário: DNA Arqueal/genética
Íntrons
RNA Ribossômico 16S/genética
Thermoproteales/genética
[Mh] Termos MeSH secundário: Fontes Termais
Filogenia
Análise de Sequência de DNA
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.
[Nm] Nome de substância:
0 (DNA, Archaeal); 0 (RNA, Ribosomal, 16S)
[Em] Mês de entrada:1604
[Cu] Atualização por classe:170220
[Lr] Data última revisão:
170220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:150710
[St] Status:MEDLINE
[do] DOI:10.1186/s13062-015-0065-6


  3 / 9 MEDLINE  
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[PMID]:23475616
[Au] Autor:Murphy CN; Dodsworth JA; Babbitt AB; Hedlund BP
[Ad] Endereço:School of Life Sciences, University of Nevada, Las Vegas, NV, USA.
[Ti] Título:Community microrespirometry and molecular analyses reveal a diverse energy economy in Great Boiling Spring and Sandy's Spring West in the U.S. Great Basin.
[So] Source:Appl Environ Microbiol;79(10):3306-10, 2013 May.
[Is] ISSN:1098-5336
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Microrespirometry showed that several organic and inorganic electron donors stimulated oxygen consumption in two ∼80°C springs. Sediment and planktonic communities were structurally and functionally distinct, and quantitative PCR revealed catabolically distinct subpopulations of Thermocrinis. This study suggests that a variety of chemolithotrophic metabolisms operate simultaneously in these springs.
[Mh] Termos MeSH primário: Biota
Metabolismo Energético
Sedimentos Geológicos/microbiologia
Fontes Termais/microbiologia
Microbiologia da Água
[Mh] Termos MeSH secundário: Bactérias Aeróbias/genética
Bactérias Aeróbias/crescimento & desenvolvimento
Bactérias Aeróbias/metabolismo
Técnicas Biossensoriais/métodos
Transporte de Elétrons
Genes de RNAr
Hidrogênio/metabolismo
Oxigênio/metabolismo
RNA Bacteriano/genética
Thermoproteales/genética
Thermoproteales/crescimento & desenvolvimento
Thermoproteales/metabolismo
Estados Unidos
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.
[Nm] Nome de substância:
0 (RNA, Bacterial); 7YNJ3PO35Z (Hydrogen); S88TT14065 (Oxygen)
[Em] Mês de entrada:1312
[Cu] Atualização por classe:170220
[Lr] Data última revisão:
170220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:130312
[St] Status:MEDLINE
[do] DOI:10.1128/AEM.00139-13


  4 / 9 MEDLINE  
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[PMID]:22106294
[Au] Autor:Paytubi S; McMahon SA; Graham S; Liu H; Botting CH; Makarova KS; Koonin EV; Naismith JH; White MF
[Ad] Endereço:Biomedical Sciences Research Complex, University of St Andrews, Fife KY16 9ST, United Kingdom.
[Ti] Título:Displacement of the canonical single-stranded DNA-binding protein in the Thermoproteales.
[So] Source:Proc Natl Acad Sci U S A;109(7):E398-405, 2012 Feb 14.
[Is] ISSN:1091-6490
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:ssDNA-binding proteins (SSBs) based on the oligonucleotide-binding fold are considered ubiquitous in nature and play a central role in many DNA transactions including replication, recombination, and repair. We demonstrate that the Thermoproteales, a clade of hyperthermophilic Crenarchaea, lack a canonical SSB. Instead, they encode a distinct ssDNA-binding protein that we term "ThermoDBP," exemplified by the protein Ttx1576 from Thermoproteus tenax. ThermoDBP binds specifically to ssDNA with low sequence specificity. The crystal structure of Ttx1576 reveals a unique fold and a mechanism for ssDNA binding, consisting of an extended cleft lined with hydrophobic phenylalanine residues and flanked by basic amino acids. Two ssDNA-binding domains are linked by a coiled-coil leucine zipper. ThermoDBP appears to have displaced the canonical SSB during the diversification of the Thermoproteales, a highly unusual example of the loss of a "ubiquitous" protein during evolution.
[Mh] Termos MeSH primário: Proteínas de Ligação a DNA/metabolismo
Thermoproteales/metabolismo
[Mh] Termos MeSH secundário: Clonagem Molecular
Cristalografia por Raios X
Proteínas de Ligação a DNA/química
Proteínas de Ligação a DNA/genética
Ligação Proteica
Dobramento de Proteína
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (DNA-Binding Proteins)
[Em] Mês de entrada:1204
[Cu] Atualização por classe:170922
[Lr] Data última revisão:
170922
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:111123
[St] Status:MEDLINE
[do] DOI:10.1073/pnas.1113277108


  5 / 9 MEDLINE  
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[PMID]:21398550
[Au] Autor:Gumerov VM; Mardanov AV; Beletsky AV; Prokofeva MI; Bonch-Osmolovskaya EA; Ravin NV; Skryabin KG
[Ad] Endereço:Centre Bioengineering, Russian Academy of Sciences, Prosp. 60-let Oktyabrya, Bld. 7-1, Moscow 117312, Russia.
[Ti] Título:Complete genome sequence of "Vulcanisaeta moutnovskia" strain 768-28, a novel member of the hyperthermophilic crenarchaeal genus Vulcanisaeta.
[So] Source:J Bacteriol;193(9):2355-6, 2011 May.
[Is] ISSN:1098-5530
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Strain 768-28 was isolated from a hot spring in Kamchatka, Russia, and represents a novel member of the Vulcanisaeta genus. The complete genome sequence of this thermoacidophilic anaerobic crenarchaeon reveals genes for protein and carbohydrate-active enzymes, the Embden-Meyerhof and Entner-Doudoroff pathways for glucose metabolism, the tricarboxylic acid cycle, beta-oxidation of fatty acids, and sulfate reduction.
[Mh] Termos MeSH primário: Genoma Arqueal
Thermoproteales/genética
[Mh] Termos MeSH secundário: Sequência de Bases
DNA Arqueal/genética
Regulação da Expressão Gênica em Archaea/fisiologia
Dados de Sequência Molecular
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (DNA, Archaeal)
[Em] Mês de entrada:1107
[Cu] Atualização por classe:170220
[Lr] Data última revisão:
170220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:110315
[St] Status:MEDLINE
[do] DOI:10.1128/JB.00237-11


  6 / 9 MEDLINE  
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[PMID]:20430862
[Au] Autor:Fujishima K; Sugahara J; Tomita M; Kanai A
[Ad] Endereço:Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.
[Ti] Título:Large-scale tRNA intron transposition in the archaeal order Thermoproteales represents a novel mechanism of intron gain.
[So] Source:Mol Biol Evol;27(10):2233-43, 2010 Oct.
[Is] ISSN:1537-1719
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Recently, diverse arrangements of transfer RNA (tRNA) genes have been found in the domain Archaea, in which the tRNA is interrupted by a maximum of three introns or is even fragmented into two or three genes. Whereas most of the eukaryotic tRNA introns are inserted strictly at the canonical nucleotide position (37/38), archaeal intron-containing tRNAs have a wide diversity of small tRNA introns, which differ in their numbers and locations. This feature is especially pronounced in the archaeal order Thermoproteales. In this study, we performed a comprehensive sequence comparison of 286 tRNA introns and their genes in seven Thermoproteales species to clarify how these introns have emerged and diversified during tRNA gene evolution. We identified 46 intron groups containing sets of highly similar sequences (>70%) and showed that 16 of them contain sequences from evolutionarily distinct tRNA genes. The phylogeny of these 16 intron groups indicates that transposition events have occurred at least seven times throughout the evolution of Thermoproteales. These findings suggest that frequent intron transposition occurs among the tRNA genes of Thermoproteales. Further computational analysis revealed limited insertion positions and corresponding amino acid types of tRNA genes. This has arisen because the bulge-helix-bulge splicing motif is required at the newly transposed position if the pre-tRNA is to be correctly processed. These results clearly demonstrate a newly identified mechanism that facilitates the late gain of short introns at various noncanonical positions in archaeal tRNAs.
[Mh] Termos MeSH primário: Evolução Molecular
Rearranjo Gênico/genética
Íntrons/genética
Filogenia
RNA de Transferência/genética
Thermoproteales/genética
[Mh] Termos MeSH secundário: Sequência de Bases
Análise por Conglomerados
Biologia Computacional
RNA de Transferência/classificação
Alinhamento de Sequência
Especificidade da Espécie
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
9014-25-9 (RNA, Transfer)
[Em] Mês de entrada:1101
[Cu] Atualização por classe:100923
[Lr] Data última revisão:
100923
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:100501
[St] Status:MEDLINE
[do] DOI:10.1093/molbev/msq111


  7 / 9 MEDLINE  
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[PMID]:19411323
[Au] Autor:Ramos-Vera WH; Berg IA; Fuchs G
[Ad] Endereço:Mikrobiologie, Fakultät Biologie, Albert Ludwigs Universität-Freiburg, Freiburg, Germany
[Ti] Título:Autotrophic carbon dioxide assimilation in Thermoproteales revisited.
[So] Source:J Bacteriol;191(13):4286-97, 2009 Jul.
[Is] ISSN:1098-5530
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:For Crenarchaea, two new autotrophic carbon fixation cycles were recently described. Sulfolobales use the 3-hydroxypropionate/4-hydroxybutyrate cycle, with acetyl-coenzyme A (CoA)/propionyl-CoA carboxylase as the carboxylating enzyme. Ignicoccus hospitalis (Desulfurococcales) uses the dicarboxylate/4-hydroxybutyrate cycle, with pyruvate synthase and phosphoenolpyruvate carboxylase being responsible for CO(2) fixation. In the two cycles, acetyl-CoA and two inorganic carbons are transformed to succinyl-CoA by different routes, whereas the regeneration of acetyl-CoA from succinyl-CoA proceeds via the same route. Thermoproteales would be an exception to this unifying concept, since for Thermoproteus neutrophilus, the reductive citric acid cycle was proposed as a carbon fixation mechanism. Here, evidence is presented for the operation of the dicarboxylate/4-hydroxybutyrate cycle in this archaeon. All required enzyme activities were detected in large amounts. The key enzymes of the cycle were strongly upregulated under autotrophic growth conditions, indicating their involvement in autotrophic CO(2) fixation. The corresponding genes were identified in the genome. (14)C-labeled 4-hydroxybutyrate was incorporated into the central building blocks in accordance with the key position of this compound in the cycle. Moreover, the results of previous (13)C-labeling studies, which could be reconciled with a reductive citric acid cycle only when some assumptions were made, were perfectly in line with the new proposal. We conclude that the dicarboxylate/4-hydroxybutyrate cycle is operating in CO(2) fixation in the strict anaerobic Thermoproteales as well as in Desulfurococcales.
[Mh] Termos MeSH primário: Proteínas Arqueais/metabolismo
Processos Autotróficos/fisiologia
Dióxido de Carbono/metabolismo
Thermoproteales/metabolismo
[Mh] Termos MeSH secundário: Acetilcoenzima A/metabolismo
Acil Coenzima A/metabolismo
Hidroxibutiratos/metabolismo
Metilmalonil-CoA Descarboxilase/metabolismo
Modelos Biológicos
Fosfoenolpiruvato Carboxilase/metabolismo
Piruvato Sintase/metabolismo
Transdução de Sinais
Thermoproteales/enzimologia
Thermoproteales/crescimento & desenvolvimento
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Acyl Coenzyme A); 0 (Archaeal Proteins); 0 (Hydroxybutyrates); 142M471B3J (Carbon Dioxide); 604-98-8 (succinyl-coenzyme A); 72-89-9 (Acetyl Coenzyme A); EC 1.2.7.1 (Pyruvate Synthase); EC 4.1.1.31 (Phosphoenolpyruvate Carboxylase); EC 4.1.1.41 (Methylmalonyl-CoA Decarboxylase)
[Em] Mês de entrada:0906
[Cu] Atualização por classe:170220
[Lr] Data última revisão:
170220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:090505
[St] Status:MEDLINE
[do] DOI:10.1128/JB.00145-09


  8 / 9 MEDLINE  
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[PMID]:18832079
[Au] Autor:Sugahara J; Kikuta K; Fujishima K; Yachie N; Tomita M; Kanai A
[Ad] Endereço:Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.
[Ti] Título:Comprehensive analysis of archaeal tRNA genes reveals rapid increase of tRNA introns in the order thermoproteales.
[So] Source:Mol Biol Evol;25(12):2709-16, 2008 Dec.
[Is] ISSN:1537-1719
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The analysis of archaeal tRNA genes is becoming more important to evaluate the origin and evolution of tRNA molecule. Even with the recent accumulation of complete genomes of numerous archaeal species, several tRNA genes are still required for a full complement of the codon table. We conducted comprehensive screening of tRNA genes from 47 archaeal genomes by using a combination of different types of tRNA prediction programs and extracted a total of 2,143 reliable tRNA gene candidates including 437 intron-containing tRNA genes, which covered more than 99.9% of the codon tables in Archaea. Previously, the content of intron-containing tRNA genes in Archaea was estimated to be approximately 15% of the whole tRNA genes, and most of the introns were known to be located at canonical positions (nucleotide position between 37 and 38) of precursor tRNA (pre-tRNA). Surprisingly, we observed marked enrichment of tRNA introns in five species of the archaeal order Thermoproteales; about 70% of tRNA gene candidates were found to be intron-containing tRNA genes, half of which contained multiple introns, and the introns were located at various noncanonical positions. Sequence similarity analysis revealed that approximately half of the tRNA introns found at Thermoproteales-specific intron locations were highly conserved among several tRNA genes. Intriguingly, identical tRNA intron sequences were found within different types of tRNA genes that completely lacked exon sequence similarity, suggesting that the tRNA introns in Thermoproteales could have been gained via intron insertion events at a later stage of tRNA evolution. Moreover, although the CCA sequence at the 3' terminal of pre-tRNA is added by a CCA-adding enzyme after gene transcription in Archaea, most of the tRNA genes containing highly conserved introns already encode the CCA sequence at their 3' terminal. Based on these results, we propose possible models explaining the rapid increase of tRNA introns as a result of intron insertion events via retrotransposition of pre-tRNAs. The sequences and secondary structures of the tRNA genes and their bulge-helix-bulge motifs were registered in SPLITSdb (http://splits.iab.keio.ac.jp/splitsdb/), a novel and comprehensive database for archaeal tRNA genes.
[Mh] Termos MeSH primário: Archaea/genética
Íntrons
RNA Arqueal/genética
RNA de Transferência/genética
Thermoproteales/genética
[Mh] Termos MeSH secundário: Archaea/química
Sequência de Bases
Bases de Dados Genéticas
Endonucleases/metabolismo
Genes Arqueais
Dados de Sequência Molecular
Conformação de Ácido Nucleico
Processamento de RNA
RNA Arqueal/química
RNA de Transferência/química
Alinhamento de Sequência
Thermoproteales/classificação
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (RNA, Archaeal); 9014-25-9 (RNA, Transfer); EC 3.1.- (Endonucleases)
[Em] Mês de entrada:0812
[Cu] Atualização por classe:081117
[Lr] Data última revisão:
081117
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:081004
[St] Status:MEDLINE
[do] DOI:10.1093/molbev/msn216


  9 / 9 MEDLINE  
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[PMID]:15653928
[Au] Autor:Judicial Commission of the International Committee on Systematics of Prokaryotes
[Ti] Título:The nomenclatural types of the orders Acholeplasmatales, Halanaerobiales, Halobacteriales, Methanobacteriales, Methanococcales, Methanomicrobiales, Planctomycetales, Prochlorales, Sulfolobales, Thermococcales, Thermoproteales and Verrucomicrobiales are the genera Acholeplasma, Halanaerobium, Halobacterium, Methanobacterium, Methanococcus, Methanomicrobium, Planctomyces, Prochloron, Sulfolobus, Thermococcus, Thermoproteus and Verrucomicrobium, respectively. Opinion 79.
[So] Source:Int J Syst Evol Microbiol;55(Pt 1):517-8, 2005 Jan.
[Is] ISSN:1466-5026
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:The Judicial Commission of the International Committee on Systematics of Prokaryotes has corrected the nomenclatural types of 12 orders: Acholeplasmatales, Halanaerobiales, Halobacteriales, Methanobacteriales, Methanococcales, Methanomicrobiales, Planctomycetales, Prochlorales, Sulfolobales, Thermococcales, Thermoproteales and Verrucomicrobiales.
[Mh] Termos MeSH primário: Archaea/classificação
Halobacteriales/classificação
Terminologia como Assunto
[Mh] Termos MeSH secundário: Methanobacteriales/classificação
Methanococcales/classificação
Methanomicrobiales/classificação
Sulfolobales/classificação
Thermococcales/classificação
Thermoproteales/classificação
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:0503
[Cu] Atualização por classe:071115
[Lr] Data última revisão:
071115
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:050118
[St] Status:MEDLINE



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