- Volume 63, Issue Pt_1, 2013
Volume 63, Issue Pt_1, 2013
- New Taxa
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- Bacteroidetes
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Algoriphagus machipongonensis sp. nov., co-isolated with a colonial choanoflagellate
A Gram-negative, non-motile, non-spore-forming bacterial strain, PR1T, was isolated from a mud core sample containing colonial choanoflagellates near Hog Island, Virginia, USA. Strain PR1T grew optimally at 30 °C and with 3 % (w/v) NaCl. Strain PR1T contained MK-7 as the major menaquinone as well as carotenoids but lacked pigments of the flexirubin-type. The predominant fatty acids were iso-C15 : 0 (29.4 %), iso-C17 : 1ω9c (18.5 %) and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c; 11.3 %). The major polar lipids detected in strain PR1T were phosphatidylethanolamine, an unknown phospholipid, an aminophospholipid, an aminolipid and two lipids of unknown character. The DNA G+C content was 38.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain PR1T fell within the cluster comprising the genus Algoriphagus and was most closely related to Algoriphagus halophilus JC 2051T (95.4 % sequence similarity) and Algoriphagus lutimaris S1-3T (95.3 % sequence similarity). The 16S rRNA gene sequence similarity between strain PR1T and the type strains of other species of the genus Algoriphagus were in the range 91–95 %. Differential phenotypic properties and phylogenetic and genetic distinctiveness of strain PR1T demonstrated that this strain was distinct from other members of the genus Algoriphagus , including its closest relative, A. halophilus . Based on phenotypic, chemotaxonomic, phylogenetic and genomic data, strain PR1T should be placed in the genus Algoriphagus as a representative of a novel species, for which the name Algoriphagus machipongonensis sp. nov. is proposed. The type strain is PR1T ( = ATCC BAA-2233T = DSM 24695T).
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Description of Riemerella columbipharyngis sp. nov., isolated from the pharynx of healthy domestic pigeons (Columba livia f. domestica), and emended descriptions of the genus Riemerella , Riemerella anatipestifer and Riemerella columbina
A group of 11 bacterial strains was isolated during microbiological investigations of pharyngeal swabs collected from domestic pigeons (Columba livia f. domestica). Phenotypic properties of the isolates closely resembled those of members of the genus Riemerella within the family Flavobacteriaceae . The genus presently contains two species, Riemerella anatipestifer and Riemerella columbina . The pigeon isolates differed from R. columbina by their lack of pigment production and negative CAMP co-haemolysis reaction. They grew more slowly at 37 °C under microaerobic conditions and showed reduced viability during storage under aerobic conditions at different temperatures, compared with both Riemerella species. Comparisons of protein profiles with matrix-assisted laser desorption/ionization–time of flight (MALDI-TOF) MS analysis allowed differentiation between the new pigeon isolates and both R. anatipestifer and R. columbina . Phylogenetic analysis based on 16S rRNA gene and rpoB gene (encoding RNA polymerase beta subunit) sequences supported the affiliation of the 11 strains to a novel species within the genus Riemerella , for which we propose the name Riemerella columbipharyngis sp. nov. The type strain is 8151T ( = DSM 24015T = LMG 26094T). Emended descriptions of the genus Riemerella and of its species Riemerella anatipestifer and Riemerella columbina are also presented.
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Pedobacter tournemirensis sp. nov., isolated from a fault water sample of a deep Toarcian argillite layer
More LessA Gram-negative bacterium, designated TF5-37.2-LB10T, was isolated from subsurface water of the Toarcian geological layer of Tournemire, France. Cells were non-motile straight rods that formed cream to light pink colonies on 10-fold diluted LB agar. Strain TF5-37.2-LB10T contained menaquinone 7 and its major fatty acids were iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C17 : 0 3-OH and iso-C17 : 1ω9c. The G+C content of the genomic DNA was 46 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed strain TF5-37.2-LB10T within the genus Pedobacter , family Sphingobacteriaceae . Pedobacter composti TR6-06T and Pedobacter oryzae DSM 19973T were the closest phylogenetic relatives (93.5 and 93.3 % 16S rRNA gene sequence similarity, respectively). On the basis of 16S rRNA gene sequence comparison and physiological and biochemical characteristics, strain TF5-37.2-LB10T represents a novel species of the genus Pedobacter , for which the name Pedobacter tournemirensis sp. nov. is proposed. The type strain is TF5-37.2-LB10T ( = DSM 23085T = CIP 110085T = MOLA 820T).
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Pontibacter lucknowensis sp. nov., isolated from a hexachlorocyclohexane dump site
More LessA Gram-negative, orange-pigmented, rod-shaped, motile and aerobic bacterial strain designated DM9T was isolated from hexachlorocyclohexane (HCH)-contaminated soil (Lucknow, India) and its taxonomic position was determined using a polyphasic approach. 16S rRNA gene sequence analysis showed that the isolate belonged to the phylum Bacteroidetes and confirmed its placement in the genus Pontibacter , with sequence similarity ranging from 93.92 to 96.21 % with other members of the genus Pontibacter . The major cellular fatty acids of the novel strain were iso-C17 : 0 3-OH (6.00 %), iso-C15 : 0 (21.54 %) and summed feature 4 (comprising C17 : 1 iso I/anteiso B; 32.3 %). The polar lipid profile of strain DM9T showed the presence of phosphatidylethanolamine, an unidentified aminophospholipid, two unknown aminolipids and four unknown polar lipids. Strain DM9T contained MK-7 as the predominant menaquinone and its DNA G+C content was 49.2 mol%. sym-Homospermidine was the major polyamine observed in the cell. The results obtained on the basis of phenotypic characteristics, phylogenetic analysis, biochemical and physiological tests clearly distinguished DM9T from closely related members of the genus Pontibacter . It is proposed that DM9T represents a novel species, Pontibacter lucknowensis sp. nov.; the type strain is DM9T ( = CCM 7955T = MTCC 11079T).
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Winogradskyella damuponensis sp. nov., isolated from seawater
More LessA novel bacterium, designated F081-2T, isolated from seawater from Damupo beach in Pohang, Korea, was investigated using a polyphasic taxonomic approach. Cells were yellow-pigmented, strictly aerobic, motile by gliding, Gram-negative-staining and rod-shaped. The temperature, pH and NaCl ranges for growth were 4–35 °C, pH 5.5–9.5 and 1.0–5.0 %, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain F081-2T belonged to a distinct lineage in the genus Winogradskyella of the family Flavobacteriaceae , sharing 93.7–98.1 % similarity with recognized members of the genus. Low levels of DNA–DNA relatedness values were found between strain F081-2T and Winogradskyella eximia KCTC 12219T (61.1 %), Winogradskyella thalassocola KCTC 12221T (47.0 %), Winogradskyella echinorum KCTC 22026T (39.3 %), Winogradskyella rapida CCUG 56098T (34.3 %) and Winogradskyella arenosi JCM 17633T (33.4 %). The major cellular fatty acids were iso-C15 : 0 (25.3 %), iso-C15 : 1 G (14.6 %), iso-C17 : 0 3-OH (9.3 %), anteiso-C15 : 0 (7.8 %) and iso-C15 : 0 3-OH (7.6 %). The polar lipid profile was composed of phosphatidylethanolamine, one unidentified aminolipid, one unidentified phospholipid, one unidentified aminophospholipid and six unidentified lipids. The major respiratory quinone was menaquinone-6 and the DNA G+C content of the strain was 32.3 mol%. On the basis of phenotypic, phylogenetic and genotypic data, strain F081-2T represents a novel species within the genus Winogradskyella , for which the name Winogradskyella damuponensis sp. nov. is proposed. The type strain is F081-2T ( = KCTC 23552T = JCM 17633T).
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Aestuariibaculum suncheonense gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from a tidal flat and emended descriptions of the genera Gaetbulibacter and Tamlana
More LessA Gram-staining-negative, yellow-pigmented, strictly aerobic bacterium, designated strain SC17T, was isolated from sediment of a tidal flat of Suncheon bay in South Korea. Cells were halotolerant, catalase- and oxidase-positive and non-motile rods. Growth of strain SC17T was observed at 5–40 °C (optimum, 25–30 °C), at pH 6.0–8.5 (optimum, pH 7.0) and in the presence of 1–8 % (w/v) NaCl (optimum, 1–2 %). The major cellular fatty acids were iso-C15 : 0, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c and/or iso-C15 : 0 2-OH), iso-C17 : 0 3-OH, iso-C15 : 1 G and anteiso-C15 : 0. The polar lipid content consisted of phosphatidylethanolamine and unidentified amino lipids and lipids. The G+C content of the genomic DNA was 46.4 mol% and the only respiratory quinone detected was menaquinone-6 (MK-6). Phylogenetic inference based on 16S rRNA gene sequences showed that strain SC17T formed a distinct phyletic lineage within the family Flavobacteriaceae and was most closely related to members of the genera Gaetbulibacter and Tamlana with 95.0–95.8 % sequence similarity. On the basis of phenotypic and molecular features, strain SC17T represents a novel genus of the family Flavobacteriaceae , for which the name Aestuariibaculum suncheonense gen. nov., sp. nov. is proposed. The type strain is SC17T ( = KACC 16186T = JCM 17789T). Emended descriptions of the genera Gaetbulibacter and Tamlana are also proposed.
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Pedobacter ruber sp. nov., a psychrophilic bacterium isolated from soil
More LessA Gram-staining-negative, red-pigmented, psychrophilic, non-motile and rod-shaped bacterial strain, designated W1T, was isolated from soil and subjected to a polyphasic taxonomic investigation. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain W1T grouped with members of the genus Pedobacter and formed a distinct cluster with the type strain of Pedobacter composti (97.8 % 16S rRNA gene sequence similarity). Levels of 16S rRNA gene sequence similarity between strain W1T and the type strains of all other recognized species of the genus Pedobacter available at the time of writing were <97.0 %. The predominant cellular fatty acids (≥10 %) of strain W1T were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c) and anteiso-C15 : 0. The only menaquinone was MK-7. The genomic DNA G+C content was 39.0 mol% (HPLC). Combined data from phenotypic, phylogenetic and DNA–DNA relatedness studies demonstrated that strain W1T is a representative of a novel species of the genus Pedobacter , for which we propose the name Pedobacter ruber sp. nov. The type strain is W1T ( = DSM 24536T = LMG 26240T).
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- Other Bacteria
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Haloferula chungangensis sp. nov., isolated from marine sediment
A Gram-stain-negative, non-spore-forming, non-motile, strictly aerobic, rod-shaped bacterial strain, designated CAU 1074T, was isolated from marine sediment and its taxonomic position was investigated using a polyphasic approach. Strain CAU 1074T grew optimally at 30 °C and pH 6.5. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CAU 1074T formed a distinct lineage within the genus Haloferula and was most closely related to Haloferula harenae KCTC 22198T (96.0 % similarity). Strain CAU 1074T contained MK-9 as the major isoprenoid quinone, and iso-C14 : 0, C16 : 1ω9c and C16 : 0 as the major fatty acids. The cell wall peptidoglycan contained meso-diaminopimelic acid. The major whole-cell sugars were glucose, xylose, mannose and ribose. The polar lipids were composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, aminoglycolipid and two unidentified phospholipids. The DNA G+C content of the strain was 64.0 mol%. On the basis of phenotypic and chemotaxonomic data, and phylogenetic inference, strain CAU 1074T should be classified as a member of a novel species in the genus Haloferula , for which the name Haloferula chungangensis sp. nov. is proposed; the type strain is CAU 1074T ( = KCTC 23578T = CCUG 61920T). An emended description of the genus Haloferula is also provided.
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Ornatilinea apprima gen. nov., sp. nov., a cellulolytic representative of the class Anaerolineae
More LessA novel obligately anaerobic, mesophilic, organotrophic bacterium, strain P3M-1T, was isolated from a microbial mat formed in a wooden bath filled with hot water emerging from a 2775 m-deep well in the Tomsk region of western Siberia, Russia. Cells of strain P3M-1T were rod-shaped, 0.3–0.7 µm in width and formed multicellullar filaments that reached up to 400 µm in length. Strain P3M-1T grew optimally at 42–45 °C, pH 7.5–8.0, and with 0.1% (w/v) NaCl. Under optimal conditions, the doubling time was 6 h. The isolate was able to ferment a variety of proteinaceous substrates and sugars, including microcrystalline cellulose. Acetate, ethanol and H2 were the main products of glucose fermentation. The genomic DNA G+C content was 55 mol%. 16S rRNA gene sequence-based phylogenetic analyses showed that strain P3M-1T was a member of the class Anaerolinea , with 92.8 % sequence similarity to Levilinea saccharolytica KIBI-1T. Based on phylogenetic analysis and physiological properties, strain P3M-1T represents a novel species in a new genus, for which the name Ornatilinea apprima gen. nov., sp. nov. is proposed; the type strain of O. apprima is P3M-1T ( = DSM 23815T = VKM B-2669T).
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- Eukaryotic Micro-organisms
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Lachancea lanzarotensis sp. nov., an ascomycetous yeast isolated from grapes and wine fermentation in Lanzarote, Canary Islands
More LessDuring the characterization of the microbiota biodiversity associated with grapes and wineries in different bioclimatic conditions of the Canary Islands (Spain), a novel yeast species was isolated from Lanzarote, the driest wine-producing region of the archipelago. Seven strains isolated from grapes, microvinifications and wineries are described. Sequence analysis of the D1/D2 domain of the LSU rDNA gene and 5.8S-ITS regions revealed that the isolates were phylogenetically a member of the genus Lachancea and are closely related to Lachancea meyersii NRRL Y-27269T and Lachancea nothofagi NRRL Y-48670T. On the basis of morphological, biochemical and physiological characterization and phylogenetic analysis, a novel ascosporogenous yeast species, Lachancea lanzarotensis sp. nov., is proposed. The type strain is L2C-15T ( = CBS 12615T = CECT 13066T) which was isolated from grape berries of Vitis vinifera L. cv. Listán Negro red grape variety in Tinajo, Lanzarote. The MycoBank no. is MB 801390.
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Zygosaccharomyces sapae sp. nov., isolated from Italian traditional balsamic vinegar
More LessFourteen yeast isolates were recovered from two traditional balsamic vinegar (TBV) samples collected in the provinces of Modena and Reggio Emilia, Italy. Microsatellite-primed-PCR (MSP-PCR) was used to de-replicate the isolate collection into two representative strains, ABT301T and ABT601. Phylogenetic analysis based on the D1/D2 domains of the 26S rRNA gene indicated that these strains represented a distinct species of the genus Zygosaccharomyces, closely related to Zygosaccharomyces rouxii and Zygosaccharomyces mellis. Physiological and morphological tests supported the recognition of a novel taxon of halotolerant, osmotolerant, non-psychrotolerant and maltose-fermentation-negative yeasts showing a chain or star-shaped pattern of budding cells, which remained attached to each other. Morphological observations offered evidence of ascospore formation. A novel species, Zygosaccharomyces sapae sp. nov., is proposed to accommodate these strains, with strain ABT301T ( = CBS 12607T = MUCL 54092T) as the type strain. Based on D1/D2 domain phylogenetic analysis, the novel strains shared the highest sequence similarity (100 %) with Zygosaccharomyces sp. strain NCYC 3042, previously isolated from sugar [James, S. A., Bond, C. J., Stratford, M. & Roberts, I. N. (2005). FEMS Yeast Res 5, 747–755]. However, based on phylogenetic (internal transcribed spacers, ITS), PCR fingerprinting and physiological analyses, marked differences were observed between the novel species and strain NCYC 3042, and these results are discussed in more detail.
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Yamadazyma terventina sp. nov., a yeast species of the Yamadazyma clade from Italian olive oils
During an investigation of olive oil microbiota, three yeast strains were found to be divergent from currently classified yeast species according to the sequences of the D1/D2 domain of the gene encoding the rRNA large subunit (LSU) and the internal transcribed spacer region including the gene for 5.8S rRNA. Phylogenetic analysis revealed that these strains, designated CBS 12509, CBS 12510T and CBS 12511, represent a novel anascosporogenous species described herein as Yamadazyma terventina sp. nov; the type strain is DAPES 1924T ( = CBS 12510T = NCAIM Y.02028T). This novel species was placed in the Yamadazyma clade, with Yamadazyma scolyti, Candida conglobata and Candida aaseri as closest relatives. Y. terventina differs from the above-mentioned species in the ability to strongly assimilate dl-lactate and weakly assimilate ethanol.
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Leptochlorella corticola gen. et sp. nov. and Kalinella apyrenoidosa sp. nov.: two novel Chlorella-like green microalgae (Trebouxiophyceae, Chlorophyta) from subaerial habitats
More LessThe diversity of green microalgae in subaerial habitats remains largely unexplored and a number of new genus- and species-level lineages have been discovered recently. The traditional green algal genus, Chlorella, which accommodated coccoid unicellular green algal species with globular to oval cells, reproducing entirely by autospores, has been found to be polyphyletic. In this study, we provide a detailed characterization of two strains of microalgae isolated from tree bark in the Mediterranean. These algae share the general Chlorella-like morphology and their 18S rRNA and rbcL gene sequences place them in the Trebouxiophyceae. Strain CAUP H8401 forms an independent trebouxiophycean lineage, together with three previously published 18S rRNA gene environmental sequences of undescribed microalgae, which were retrieved from profoundly different habitats. In contrast, strain CAUP H7902 is related to Kalinella bambusicola in the Watanabea clade of the Trebouxiophyceae on the basis of its 18S rRNA gene sequence. This relationship is also supported by the rbcL gene sequence, acquired from the type strain of K. bambusicola. The investigated strains are described as representatives of a novel species in a new genus, Leptochlorella corticola gen. et sp. nov., and a novel species, Kalinella apyrenoidosa sp. nov., according to the International Code of Nomenclature for Algae, Fungi and Plants.
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Starmerella jinningensis sp. nov., a yeast species isolated from flowers of Erianthus rufipilus
Five yeast strains (Ym24403, Ym24404, Ym24408, Ym24409 and Ym24410T) were isolated from different flowers of Erianthus rufipilus (Gramineae), a wild plant growing in the phosphorus-rich region in Yunnan Province, south-western China, and were found to be phenotypically and genetically divergent from currently recognized yeast species. Sequence analysis of the D1/D2 domain of the large subunit rRNA gene revealed that the five strains represented a novel species described as Starmerella jinningensis sp. nov. The type strain is Ym24410T ( = CBS 11864T = CCTCC AY 2011002T). Phylogenetic analysis based on the D1/D2 region of the large subunit rRNA gene suggested that S. jinningensis sp. nov. is placed within the Starmerella clade.
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Candida ecuadorensis sp. nov., an ascomycetous yeast species found in two separate regions of Ecuador
In the course of an on-going study aimed at cataloguing the natural yeast biodiversity found in Ecuador, two strains (CLQCA 13-025 and CLQCA 20-004T) were isolated from samples of cow manure and rotten wood collected in two separate provinces of the country (Orellana and Bolívar). These strains were found to represent a novel yeast species based on the sequences of their D1/D2 domain of the large-subunit (LSU) rRNA gene and their physiological characteristics. Phylogenetic analysis based on LSU D1/D2 sequences revealed this novel species to belong to the Metschnikowia clade and to be most closely related to Candida suratensis, a species recently discovered in a mangrove forest in Thailand. The species name of Candida ecuadorensis sp. nov. is proposed to accommodate these strains, with strain CLQCA 20-004T ( = CBS 12653T = NCYC 3782T) designated as the type strain.
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- Erratum
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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)