- Volume 54, Issue 4, 2004
Volume 54, Issue 4, 2004
- New Taxa
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- Gram-Positive Bacteria
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Streptomyces drozdowiczii sp. nov., a novel cellulolytic streptomycete from soil in Brazil
An actinomycete strain, isolated from a Mata Atlântica soil sample, showing cellulolytic activity was subjected to polyphasic taxonomic characterization to determine its identity. Strain M7aT presented morphological and chemotaxonomic characteristics consistent with its assignment to the genus Streptomyces. Phylogenetic analysis of its 16S rDNA sequence revealed that the strain differed from described streptomycetes available in the public databases; the most closely related species was Streptomyces laceyi, with 98·4 % nucleotide similarity. It also differed from other cellulolytic strains in its phenotypic characteristics. It is therefore proposed that strain M7aT, a cellulolytic strain with biotechnological potential, represents a novel species, named Streptomyces drozdowiczii sp. nov. The type strain is M7aT (=CBMAI 0498T=CIP 107837T=NRRL B-24297T).
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Kribbella solani sp. nov. and Kribbella jejuensis sp. nov., isolated from potato tuber and soil in Jeju, Korea
Two actinomycete strains, DSA1T and HD9T, were isolated from a potato tuber and soil from a potato-cultivating field in Jeju, Korea, respectively. A comprehensive 16S rDNA analysis revealed that the isolates belong to the genus Kribbella and share 97·7–98·6 % sequence similarity to Kribbella species. The strains also contained typical chemotaxonomic markers of the genus Kribbella: ll-diaminopimelic acid, alanine, glycine and glutamic acid in the cell wall peptidoglycan; mannose, glucose, galactose and ribose as whole cell sugars; diphosphatidylglycerol, phosphatidylcholine and phosphatidylinositol as characteristic phospholipids; and the major menaquinone MK-9 (H4). DNA–DNA hybridization experiments showed that the isolates represented two distinct genomic species. A number of phenotypic properties can be used to differentiate the two isolates from Kribbella species. On the basis of polyphasic evidence, two novel species are proposed: Kribbella solani sp. nov. for strain DSA1T (=KACC 20196T=JCM 12205T) and Kribbella jejuensis sp. nov. for strain HD9T (=KACC 20266T=JCM 12204T).
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Clover proliferation phytoplasma: ‘Candidatus Phytoplasma trifolii’
More LessClover proliferation phytoplasma (CPR) is designated as the reference strain for the CP phylogenetic group or subclade, on the basis of molecular analyses of genomic DNA, the 16S rRNA gene and the 16S–23S spacer region. Other strains related to CPR include alfalfa witches'-broom (AWB), brinjal little leaf (BLL), beet leafhopper-transmitted virescence (BLTV), Illinois elm yellows (ILEY), potato witches'-broom (PWB), potato yellows (PY), tomato big bud in California (TBBc) and phytoplasmas from Fragaria multicipita (FM). Phylogenetic analysis of the 16S rRNA gene sequences of BLL, CPR, FM and ILEY, together with sequences from 16 other phytoplasmas that belong to the ash yellows (AshY), jujube witches'-broom (JWB) and elm yellows (EY) groups that were available in GenBank, produced a tree on which these phytoplasmas clearly clustered as a discrete group. Three subgroups have been classified on the basis of sequence homology and the collective RFLP patterns of amplified 16S rRNA genes. AWB, BLTV, PWB and TBBc are assigned to taxonomic subgroup CP-A, FM belongs to subgroup CP-B and BLL and ILEY are assigned to subgroup CP-C. Genetic heterogeneity between different isolates of AWB, CPR and PWB has been observed from heteroduplex mobility assay analysis of amplified 16S rRNA genes and the 16S–23S spacer region. Two unique signature sequences that can be utilized to distinguish the CP group from others were present. On the basis of unique properties of the DNA from clover proliferation phytoplasma, the name ‘Candidatus Phytoplasma trifolii’ is proposed for the CP group.
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Bacillus farraginis sp. nov., Bacillus fortis sp. nov. and Bacillus fordii sp. nov., isolated at dairy farms
Forty-eight bacterial strains were isolated at dairy farms from raw milk, the milking apparatus, green fodder or feed concentrate after a heat treatment of 30 min at 100 °C. In this way, spore-forming bacteria with a very high intrinsic heat resistance were selected for. The aerobic spore-forming isolates were subjected to a polyphasic taxonomical study, including repetitive element sequence-based PCR typing, whole-cell protein profiling, 16S rDNA sequence analysis, DNA–DNA hybridizations, DNA base composition, fatty acid analysis, and morphological and biochemical characteristics. A comparison of the REP- and (GTG)5-PCR and whole-cell protein SDS-PAGE profiles resulted in three clusters of similar strains. Analysis of the 16S rDNA sequences and DNA–DNA relatedness data showed that these clusters represented three novel species. The highest 16S rDNA similarity to a recognized species found for the three groups was around 94 % with Bacillus lentus and Bacillus sporothermodurans. Further phenotypic characterization supported the proposal of three novel species in the genus Bacillus, Bacillus farraginis, Bacillus fortis and Bacillus fordii. The respective type strains are R-6540T (=LMG 22081T=DSM 16013T), R-6514T (=LMG 22079T=DSM 16012T) and R-7190T (=LMG 22080T=DSM 16014T); their G+C DNA base contents are 43·7, 44·3 and 41·9 mol%, respectively. Although in variable amounts, a predominance of the branched fatty acids iso-C15 : 0 and anteiso-C15 : 0 was observed in all three novel species.
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Lactobacillus saerimneri sp. nov., isolated from pig faeces
More LessIn studying the composition of the Lactobacillus flora of faeces from pigs fed different diets, isolates with notable differences in their 16S rRNA gene sequence compared to recognized species were found. Phenotypic characteristics together with 16S rRNA gene sequences revealed that the isolates represented a novel species belonging to the Lactobacillus mali subgroup of lactobacilli. The name Lactobacillus saerimneri sp. nov. is proposed (type strain GDA154T=LMG 22087T=DSM 16049T=CCUG 48462T).
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Bacillus indicus sp. nov., an arsenic-resistant bacterium isolated from an aquifer in West Bengal, India
More LessStrain Sd/3T (=MTCC 4374T=DSM 15820T), an arsenic-resistant bacterium, was isolated from a sand sample obtained from an arsenic-contaminated aquifer in Chakdah district in West Bengal, India (23° 3′ N 88° 35′ E). The bacterium was Gram-positive, rod-shaped, non-motile, endospore-forming and yellowish-orange pigmented. It possessed all the characteristics that conform to the genus Bacillus, such as it had A4 β murein type (l-orn-d-Asp) peptidoglycan variant, MK-7 as the major menaquinone and iso-C15 : 0 and anteiso-C15 : 0 as the major fatty acids. Based on its chemotaxonomic and phylogenetic characteristics, strain Sd/3T was identified as a species of the genus Bacillus. It exhibited maximum similarity (95 %) at the 16S rRNA gene level with Bacillus cohnii; however, DNA–DNA similarity with B. cohnii was 60·7 %. Strain Sd/3T also exhibited a number of phenotypic differences from B. cohnii (DSM 6307T). These data suggest that Sd/3T represents a novel species of the genus Bacillus. The name Bacillus indicus sp. nov. is proposed.
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Saccharothrix algeriensis sp. nov., isolated from Saharan soil
The taxonomic position of a soil isolate, strain SA 233T, recovered from Saharan soil from Algeria was established using a polyphasic approach. This isolate has been previously reported to produce three novel dithiolopyrrolone antibiotics, and preliminary chemotaxonomic and morphological characteristics suggested that it was representative of a member of the genus Saccharothrix. Phylogenetic analysis of the strain from 16S rDNA sequences, along with a detailed analysis of morphological, chemotaxonomic and physiological characteristics, indicates that it belongs to the genus Saccharothrix and represents a novel species that is readily distinguished from all recognized Saccharothrix species. The name Saccharothrix algeriensis sp. nov. is proposed for the isolate, with type strain SA 233T (=NRRL B-24137T=DSM 44581T).
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Reclassification of Promicromonospora pachnodae Cazemier et al. 2004 as Xylanimicrobium pachnodae gen. nov., comb. nov.
More LessThe recently described facultatively anaerobic Promicromonospora pachnodae is phylogenetically only moderately related to authentic members of Promicromonospora. P. pachnodae is closely related to Xylanibacterium ulmi and slightly less closely related to Xylanimonas cellulosilytica and Isoptericola variabilis (basonym Cellulosimicrobium variabile). Members of the different genera of Promicromonosporaceae have similar chemotaxonomic properties; they share the same peptidoglycan type (A4α) and have similar profiles of polar lipids, menaquinones, fatty acids and whole cell sugars. However, they differ from each other in the detailed amino acid composition of peptidoglycan, a taxonomically significant character that has previously been used in the delineation of actinobacterial genera. Recognized Promicromonospora species and Xylanibacterium ulmi exhibit the l-lys–l-ala–d-Glu type, Xylanimonas cellulosilytica and I. variabilis show the l-lys–d-Asp type, whereas P. pachnodae has the l-lys–l-ser–d-Glu type. This property, together with the distinct phylogenetic position of Promicromonospora pachnodae, suggests a novel genus for the xylanolytic organism Xylanimicrobium pachnodae (Cazemier et al. 2004) gen. nov., comb. nov.
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- Unicellular Eukaryotes
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Curvibasidium cygneicollum gen. nov., sp. nov. and Curvibasidium pallidicorallinum sp. nov., novel taxa in the Microbotryomycetidae (Urediniomycetes), and their relationship with Rhodotorula fujisanensis and Rhodotorula nothofagi
More LessStrains of Rhodotorula fujisanensis (Basidiomycota, Urediniomycetes, Microbotryomycetidae), including the type strain, are sexually compatible and produce clamped mycelium with teliospores. However, as teliospore germination had not been documented, the complete sexual cycle was not known. During the course of this work, the basidial stage of R. fujisanensis was characterized. In addition, mating studies employing isolates that were identified preliminarily as Rhodotorula nothofagi, a species that is related closely to R. fujisanensis, yielded mycelium with teliospores, which formed basidia and basidiospores. The new data were evaluated by using several criteria, including the available molecular phylogenetic framework for the Microbotryomycetidae. Curvibasidium gen. nov. is described here, to accommodate two teleomorphs: Curvibasidium cygneicollum sp. nov. (CBS 4551T), which is described as the sexual stage of R. fujisanensis, and Curvibasidium pallidicorallinum sp. nov. (CBS 9091T), which is related closely to R. nothofagi, but does not represent its sexual stage.
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Candida asparagi sp. nov., Candida diospyri sp. nov. and Candida qinlingensis sp. nov., novel anamorphic, ascomycetous yeast species
More LessAmong ascomycetous yeasts that were isolated from several nature reserve areas in China, three anamorphic strains isolated from soil (QL 5-5T) and fruit (QL 21-2T and SN 15-1T) were revealed, by conventional characterization and molecular phylogenetic analysis based on internal transcribed spacer and large subunit (26S) rRNA gene D1/D2 region sequencing, to represent three novel species in the genus Candida. Candida qinlingensis sp. nov. (type strain, QL 5-5T=AS 2.2524T=CBS 9768T) was related closely to a teleomorphic species, Williopsis pratensis. The close relatives of Candida diospyri sp. nov. (type strain, QL 21-2T=AS 2.2525T=CBS 9769T) are Candida friedrichii and Candida membranifaciens. Candida asparagi sp. nov. (type strain, SN 15-1T=AS 2.2526T=CBS 9770T) forms a clade with Candida fructus.
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- Evolution, Phylogeny And Biodiversity
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Comparative analysis of ribonuclease P RNA of the planctomycetes
More LessThe planctomycetes, order Planctomycetales, are a distinct phylum of domain Bacteria. Genes encoding the RNA portion of ribonuclease P (RNase P) of some planctomycete members were sequenced and compared with existing database planctomycete sequences. rnpB gene sequences encoding RNase P RNA were generated by a conserved primer PCR strategy for Planctomyces brasiliensis, Planctomyces limnophilus, Pirellula marina, Pirellula staleyi strain ATCC 35122, Isosphaera pallida, one other Isosphaera strain, Gemmata obscuriglobus and three other strains of the Gemmata group. These sequences were aligned against reference bacterial sequences and secondary structures of corresponding RNase P RNAs deduced by a comparative approach. P12 helices were found to be highly variable in length, as were helices P16.1 and P19, when present. RNase P RNA secondary structures of Gemmata isolates were found to have unusual features relative to other planctomycetes, including a long P9 helix and an insert in the P13 helix not found in any other member of domain Bacteria. These unique features are consistent with other unusual properties of this genus, distinguishing it from other bacteria. Phylogenetic analyses indicate that relationships between planctomycetes derived from RNase P RNA are consistent with 16S rRNA-based analyses.
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Phylogeny of the family Pasteurellaceae based on rpoB sequences
More LessSequences of the gene encoding the β-subunit of the RNA polymerase (rpoB) were used to delineate the phylogeny of the family Pasteurellaceae. A total of 72 strains, including the type strains of the major described species as well as selected field isolates, were included in the study. Selection of universal rpoB-derived primers for the family allowed straightforward amplification and sequencing of a 560 bp fragment of the rpoB gene. In parallel, 16S rDNA was sequenced from all strains. The phylogenetic tree obtained with the rpoB sequences reflected the major branches of the tree obtained with the 16S rDNA, especially at the genus level. Only a few discrepancies between the trees were observed. In certain cases the rpoB phylogeny was in better agreement with DNA–DNA hybridization studies than the phylogeny derived from 16S rDNA. The rpoB gene is strongly conserved within the various species of the family of Pasteurellaceae. Hence, rpoB gene sequence analysis in conjunction with 16S rDNA sequencing is a valuable tool for phylogenetic studies of the Pasteurellaceae and may also prove useful for reorganizing the current taxonomy of this bacterial family.
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- International Committee On Systematics Of Prokaryotes
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Recommended standards for the description of new species of anoxygenic phototrophic bacteria
More LessRecommended standards for the description of new species of the anoxygenic phototrophic bacteria are proposed in accordance with Recommendation 30b of the International Code of Nomenclature of Bacteria. These standards include information on the natural habitat, ecology and phenotypic properties including morphology, physiology and pigments and on genetic information and nucleic acid data. The recommended standards were supported by the Subcommittee on the taxonomy of phototrophic bacteria of the International Committee on Systematics of Prokaryotes. They are considered as guidelines for authors to prepare descriptions of new species.
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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)