- Volume 63, Issue Pt_10, 2013
Volume 63, Issue Pt_10, 2013
- New Taxa
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- Bacteroidetes
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Taibaiella smilacinae gen. nov., sp. nov., an endophytic member of the family Chitinophagaceae isolated from the stem of Smilacina japonica, and emended description of Flavihumibacter petaseus
More LessA light-yellow-coloured bacterium, designated strain PTJT-5T, was isolated from the stem of Smilacina japonica A. Gray collected from Taibai Mountain in Shaanxi Province, north-west China, and was subjected to a taxonomic study by using a polyphasic approach. The novel isolate grew optimally at 25–28 °C and pH 6.0–7.0. Flexirubin-type pigments were produced. Cells were Gram-reaction-negative, strictly aerobic, rod-shaped and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PTJT-5T was a member of the phylum Bacteroidetes , exhibiting the highest sequence similarity to Lacibacter cauensis NJ-8T (87.7 %). The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 and iso-C17 : 0 3-OH. The only polyamine was homospermidine and the major polar lipid was phosphatidylethanolamine. The only respiratory quinone was MK-7 and the DNA G+C content was 40.3 mol%. Based on the phenotypic, phylogenetic and genotypic data, strain PTJT-5T is considered to represent a novel species of a new genus in the family Chitinophagaceae , for which the name Taibaiella smilacinae gen. nov., sp. nov. is proposed. The type strain of Taibaiella smilacinae is PTJT-5T ( = CCTCC AB 2013017T = KCTC 32316T). An emended description of Flavihumibacter petaseus is also proposed.
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Heliimonas saccharivorans gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from a mineral water aquifer, and emended description of Filimonas lacunae
More LessTwo isolates, with optimum growth temperature and pH of about 30 °C and 6.0–7.0, were recovered from a borehole head of a mineral water aquifer in Portugal. The closest relatives based on 16S rRNA gene sequence analysis were species of genera of the family Chitinophagaceae . Strains L2-4T and L2-109 formed translucent colonies and non-motile pleomorphic cells. Strains were strictly aerobic, and oxidase- and catalase-positive. The major fatty acids of strains L2-4T and L2-109 were 17 : 0 iso 3-OH, 15 : 0 iso and 15 : 1 iso G. The major polar lipids were phosphatidylethanolamine, one unidentified phospholipid, four unidentified aminophospholipids, four unidentified aminolipids and three unidentified polar lipids. Menaquinone 7 was the only respiratory quinone. The G+C content of the DNA of strains L2-4T and L2-109 was 42.0 and 41.4 mol%, respectively. Based on 16S rRNA gene sequence analysis, physiological and biochemical characteristics, strains L2-4T ( = CECT 8122T = LMG 26919T) and L2-109 ( = CECT 8121 = LMG 26920) are considered to represent a novel species of a new genus, for which the name Heliimonas saccharivorans gen. nov., sp. nov. is proposed. The type strain of Heliimonas saccharivorans is L2-4T. Due to additional results obtained in this study an emended description of Filimonas lacunae is provided.
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Fluviimonas pallidilutea gen. nov., sp. nov., a new member of the family Cytophagaceae isolated from a freshwater river
More LessA bacterial strain designated TQQ6T was isolated from a freshwater river in Taiwan and characterized using a polyphasic taxonomy approach. Cells of strain TQQ6T were strictly aerobic, Gram-staining-negative, poly-β-hydroxybutyrate-containing, non-motile, non-spore-forming, long rods surrounded by a thick capsule and forming pale orange colonies. Growth occurred at 20–40 °C (optimum, 25 °C), at pH 7.0–9.0 (optimum, pH 8.0) and with 0–0.5 % NaCl (optimum, 0 %). The predominant fatty acids were iso-C15 : 0, summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c), iso-C17 : 0 3-OH, C16 : 1ω5c and C16 : 0. The major isoprenoid quinone was MK-7 and the DNA G+C content was 42.2 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, two uncharacterized aminophospholipids and three uncharacterized phospholipids. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TQQ6T represents a distinct phyletic line that reflects a novel generic status within the family Cytophagaceae with relatively low sequence similarities (less than 90 %) to members of other genera with validly published names. On the basis of the genotypic and phenotypic data, strain TQQ6T represents a new genus and novel species of the family Cytophagaceae , for which the name Fluviimonas pallidilutea gen. nov., sp. nov. is proposed. The type strain is TQQ6T ( = BCRC 80447T = LMG 27056T = KCTC 32035T).
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- Eukaryotic Micro-organisms
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Trichonympha burlesquei n. sp. from Reticulitermes virginicus and evidence against a cosmopolitan distribution of Trichonympha agilis in many termite hosts
More LessHistorically, symbiotic protists in termite hindguts have been considered to be the same species if they are morphologically similar, even if they are found in different host species. For example, the first-described hindgut and hypermastigote parabasalian, Trichonympha agilis (Leidy, 1877) has since been documented in six species of Reticulitermes, in addition to the original discovery in Reticulitermes flavipes. Here we revisit one of these, Reticulitermes virginicus, using molecular phylogenetic analysis from single-cell isolates and show that the Trichonympha in R. virginicus is distinct from isolates in the type host and describe this novel species as Trichonympha burlesque i n. sp. We also show the molecular diversity of Trichonympha from the type host R. flavipes is greater than supposed, itself probably representing more than one species. All of this is consistent with recent data suggesting a major underestimate of termite symbiont diversity.
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Description of Ambrosiozyma oregonensis sp. nov., and reassignment of Candida species of the Ambrosiozyma clade to Ambrosiozyma kashinagacola f.a., comb. nov., Ambrosiozyma llanquihuensis f.a., comb. nov., Ambrosiozyma maleeae f.a., comb. nov., Ambrosiozyma pseudovanderkliftii f.a., comb. nov., and Ambrosiozyma vanderkliftii f.a., comb. nov.
More LessAmbrosiozyma oregonensis sp. nov. is described from two strains, one isolated from a mountain stream in Oregon, USA (NRRL Y-6106T = CBS 5560T), and a second (NRRL YB-4169) from an unknown substrate from Marion, Illinois, USA. The species forms four hat-shaped ascospores in each deliquescent ascus and appears to be homothallic. Abundant true hyphae are produced with some having apparent dolipore-like septa. Analyses of nuclear gene sequences for the D1/D2 domains of large-subunit rRNA, small-subunit rRNA, translation elongation factor-1α, and subunits B1 and B2 of RNA polymerase II show the proposed novel species to be distinct from other species of the Ambrosiozyma clade. Because of their placement in the Ambrosiozyma clade, Candida kashinagacola, Candida llanquihuensis, Candida maleeae, Candida pseudovanderkliftii and Candida vanderkliftii are reassigned to the genus Ambrosiozyma as new combinations, and the description of the genus Ambrosiozyma is emended to reflect the resulting changes in phenotypic characters.
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Rhodotorula portillonensis sp. nov., a basidiomycetous yeast isolated from Antarctic shallow-water marine sediment
More LessDuring the characterization of the mycobiota associated with shallow-water marine environments from Antarctic sea, a novel pink yeast species was isolated. Sequence analysis of the D1/D2 domain of the LSU rDNA gene and 5.8S-ITS regions revealed that the isolated yeast was closely related to Rhodotorula pallida CBS 320T and Rhodotorula benthica CBS 9124T. On the basis of morphological, biochemical and physiological characterization and phylogenetic analyses, a novel basidiomycetous yeast species, Rhodotorula portillonensis sp. nov., is proposed. The type strain is Pi2T ( = CBS 12733T = CECT 13081T) which was isolated from shallow-water marine sediment in Fildes Bay, King George Island, Antarctica.
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Kurtzmanomyces shapotouensis sp. nov., an anamorphic, basidiomycetous yeast isolated from desert soil crusts
More LessTwo yeast strains isolated from soil crusts in the Shapotou region of Tengger Desert (north-western China) were grouped in the genus Kurtzmanomyces based on morphological characteristics. rRNA gene sequence analyses (including the D1/D2 domain of the large subunit rRNA gene and internal transcribed spacer region) indicated that these two strains represented a novel species of the genus Kurtzmanomyces, for which the name Kurtzmanomyces shapotouensis sp. nov. is proposed (type strain: CPCC 300020T = DSM 26579T = CBS 12707T). The MycoBank number of the novel species is MB 804959.
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Starmerella neotropicalis f. a., sp. nov., a yeast species found in bees and pollen
A novel yeast species was found repeatedly and in high cell densities in underground-nesting stingless bees of the species Melipona quinquefasciata and their provisions in northern Minas Gerais (Brazil). One additional strain was isolated from bee-collected pollen in Cuba. Phylogenetic analyses based on rRNA gene sequences (D1/D2 large subunit gene and internal transcribed spacer) indicated that the novel species belongs to the Starmerella clade and is most closely related to Candida (iter. nom. Starmerella) apicola. Growth reactions on carbon and nitrogen sources were typical of those observed in related species of the Starmerella clade. PCR-fingerprinting with mini- and microsatellite specific primers allowed the distinction of the novel species from Candida apicola, Candida bombi and a yet undescribed species represented by strain CBS 4353. On the basis of phylogenetic relationships, the novel species is assigned to the genus Starmerella despite the failure to observe sexual reproduction after extensive mating tests. We propose the name Starmerella neotropicalis f. a., sp. nov. (Mycobank MB 804285) and designate UFMG PST 09T ( = MUCL 53320T = CBS 12811T) as the type strain.
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- Other Bacteria
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Seleniivibrio woodruffii gen. nov., sp. nov., a selenate- and arsenate-respiring bacterium in the Deferribacteraceae
A Gram-type-negative, obligately anaerobic, selenate-respiring bacterium, strain S4T, was isolated from activated sludge of a wastewater treatment plant in New Jersey after enrichment with 10 mM selenate as the sole electron acceptor. In addition to its selenate-respiring capability, strain S4T also respired arsenate with acetate as carbon source and electron donor. Fermentative growth was not observed. The optimum growth temperature was 37 °C and optimum pH was pH 7. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain S4T is a novel member of the family Deferribacteraceae , with the type strain of Denitrovibrio acetiphilus as its closest cultivated relative, with 91.5 % sequence similarity. The cellular fatty acid profile was composed predominantly of straight-chain fatty acids C14 : 0, C15 : 0, C16 : 0, C17 : 0 and C18 : 0, which distinguishes this organism from its closest relatives. The DNA G+C content was 47.7 mol%. Together, these findings support the conclusion that strain S4T represents a novel genus and species, for which the name Seleniivibrio woodruffii gen. nov., sp. nov. is proposed. The type strain of Seleniivibrio woodruffii is S4T ( = DSM 24984T = ATCC BAA-2290T).
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- Evolution, Phylogeny and Biodiversity
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Evaluation of the DNA-dependent RNA polymerase β-subunit gene (rpoB) for phytoplasma classification and phylogeny
More LessPhytoplasmas are classified into 16Sr groups and subgroups and ‘Candidatus Phytoplasma ’ species, largely or entirely based on analysis of 16S rRNA gene sequences. Yet, distinctions among closely related ‘Ca. Phytoplasma ’ species and strains based on 16S rRNA genes alone have limitations imposed by the high degree of rRNA nucleotide sequence conservation across diverse phytoplasma lineages and by the presence in a phytoplasma genome of two, sometimes sequence-heterogeneous, copies of the 16S rRNA gene. Since the DNA-dependent RNA polymerase (DpRp) β-subunit gene (rpoB) exists as a single copy in the phytoplasma genome, we explored the use of rpoB for phytoplasma classification and phylogenetic analysis. We sequenced a clover phyllody (CPh) phytoplasma genetic locus containing ribosomal protein genes, a complete rpoB gene and a partial rpoC gene encoding the β′-subunit of DpRp. Primers and reaction conditions were designed for PCR-mediated amplification of rpoB gene fragments from diverse phytoplasmas. The rpoB gene sequences from phytoplasmas classified in groups 16SrI, 16SrII, 16SrIII, 16SrX and 16SrXII were subjected to sequence similarity and phylogenetic analyses. The rpoB gene sequences were more variable than 16S rRNA gene sequences, more clearly distinguishing among phytoplasma lineages. Phylogenetic trees based on 16S rRNA and rpoB gene sequences had similar topologies, and branch lengths in the rpoB tree facilitated distinctions among closely related phytoplasmas. Virtual RFLP analysis of rpoB gene sequences also improved distinctions among closely related lineages. The results indicate that the rpoB gene provides a useful additional marker for phytoplasma classification that should facilitate studies of disease aetiology and epidemiology.
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- Taxonomic Note
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Taxonomic study of the genera Halogeometricum and Halosarcina : transfer of Halosarcina limi and Halosarcina pallida to the genus Halogeometricum as Halogeometricum limi comb. nov. and Halogeometricum pallidum comb. nov., respectively
More LessMembers of the haloarchaeal genera Halosarcina and Halogeometricum (family Halobacteriaceae ) are closely related to each other and show 96.6–98 % 16S rRNA gene sequence similarity. This is higher than the accepted threshold value (95 %) to separate two genera, and a taxonomic study using a polyphasic approach of all four members of the two genera was conducted to clarify their relationships. Polar lipid profiles indicated that Halogeometricum rufum RO1-4T, Halosarcina pallida BZ256T and Halosarcina limi RO1-6T are related more to each other than to Halogeometricum borinquense CGMCC 1.6168T. Phylogenetic analyses using the sequences of three different genes (16S rRNA gene, rpoB′ and EF-2) strongly supported the monophyly of these four species, showing that they formed a distinct clade, separate from the related genera Halopelagius , Halobellus , Haloquadratum , Haloferax and Halogranum . The results indicate that the four species should be assigned to the same genus, and it is proposed that Halosarcina pallida and Halosarcina limi be transferred to the genus Halogeometricum as Halogeometricum pallidum comb. nov. (type strain, BZ256T = KCTC 4017T = JCM 14848T) and Halogeometricum limi comb. nov. (type strain, RO1-6T = CGMCC 1.8711T = JCM 16054T).
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Genome sequence analyses show that Neisseria oralis is the same species as ‘ Neisseria mucosa var. heidelbergensis’
More LessPhylogenies generated from whole genome sequence (WGS) data provide definitive means of bacterial isolate characterization for typing and taxonomy. The species status of strains recently defined with conventional taxonomic approaches as representing Neisseria oralis was examined by the analysis of sequences derived from WGS data, specifically: (i) 53 Neisseria ribosomal protein subunit (rps) genes (ribosomal multi-locus sequence typing, rMLST); and (ii) 246 Neisseria core genes (core genome MLST, cgMLST). These data were compared with phylogenies derived from 16S and 23S rRNA gene sequences, demonstrating that the N. oralis strains were monophyletic with strains described previously as representing ‘ Neisseria mucosa var. heidelbergensis’ and that this group was of equivalent taxonomic status to other well-described species of the genus Neisseria . Phylogenetic analyses also indicated that Neisseria sicca and Neisseria macacae should be considered the same species as Neisseria mucosa and that Neisseria flavescens should be considered the same species as Neisseria subflava . Analyses using rMLST showed that some strains currently defined as belonging to the genus Neisseria were more closely related to species belonging to other genera within the family; however, whole genome analysis of a more comprehensive selection of strains from within the family Neisseriaceae would be necessary to confirm this. We suggest that strains previously identified as representing ‘ N. mucosa var. heidelbergensis’ and deposited in culture collections should be renamed N. oralis . Finally, one of the strains of N. oralis was able to ferment lactose, due to the presence of β-galactosidase and lactose permease genes, a characteristic previously thought to be unique to Neisseria lactamica , which therefore cannot be thought of as diagnostic for this species; however, the rMLST and cgMLST analyses confirm that N. oralis is most closely related to N. mucosa .
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Proposed reclassification of Pasteurella lymphangitidis Sneath & Stevens 1990 as Yersinia pseudotuberculosis
More LessThe 16S rRNA gene sequences of Pasteurella lymphangitidis , Yersinia pseudotuberculosis and Yersinia pestis were found to be identical and multilocus sequence analysis could not discriminate between the three species. The susceptibility to a Y. pseudotuberculosis phage and the presence of the Y. pseudotuberculosis -specific invasin gene in P. lymphangitidis indicate that the latter should be reclassified as Y. pseudotuberculosis .
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- Erratum
Volumes and issues
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Volume 74 (2024)
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Volume 73 (2023)
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Volume 72 (2022 - 2023)
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Volume 71 (2020 - 2021)
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Volume 70 (2020)
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Volume 69 (2019)
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Volume 68 (2018)
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Volume 67 (2017)
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Volume 66 (2016)
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Volume 65 (2015)
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Volume 64 (2014)
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Volume 63 (2013)
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Volume 62 (2012)
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Volume 61 (2011)
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Volume 60 (2010)
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Volume 59 (2009)
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Volume 58 (2008)
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Volume 57 (2007)
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Volume 56 (2006)
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Volume 55 (2005)
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Volume 54 (2004)
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Volume 53 (2003)
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Volume 52 (2002)
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Volume 51 (2001)
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Volume 50 (2000)
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Volume 49 (1999)
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Volume 48 (1998)
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Volume 47 (1997)
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Volume 46 (1996)
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Volume 45 (1995)
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Volume 44 (1994)
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Volume 43 (1993)
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Volume 42 (1992)
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Volume 41 (1991)
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Volume 40 (1990)
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Volume 39 (1989)
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Volume 38 (1988)
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Volume 37 (1987)
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Volume 36 (1986)
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Volume 35 (1985)
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Volume 34 (1984)
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Volume 33 (1983)
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Volume 32 (1982)
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Volume 31 (1981)
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Volume 30 (1980)
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Volume 29 (1979)
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Volume 28 (1978)
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Volume 27 (1977)
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Volume 26 (1976)
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Volume 25 (1975)
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Volume 24 (1974)
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Volume 23 (1973)
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Volume 22 (1972)
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Volume 21 (1971)
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Volume 20 (1970)
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Volume 19 (1969)
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Volume 18 (1968)
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Volume 17 (1967)
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Volume 16 (1966)
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Volume 15 (1965)
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Volume 14 (1964)
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Volume 13 (1963)
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Volume 12 (1962)
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Volume 11 (1961)
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Volume 10 (1960)
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Volume 9 (1959)
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Volume 8 (1958)
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Volume 7 (1957)
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Volume 6 (1956)
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Volume 5 (1955)
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Volume 4 (1954)
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Volume 3 (1953)
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Volume 2 (1952)
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Volume 1 (1951)