- Volume 67, Issue 10, 2017
Volume 67, Issue 10, 2017
- New taxa
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- Proteobacteria
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Massilia glaciei sp. nov., isolated from the Muztagh Glacier
A Gram-stain-negative, rod-shaped, bacterial strain, B448-2T, was isolated from an ice core from the Muztagh Glacier, on the Tibetan Plateau. B448-2T grew optimally at pH 7.0 and 20 °C in the presence of 0–1.0 % (w/v) NaCl. The results of 16S rRNA gene sequence similarity analysis indicated that B448-2T was closely related to Massilia eurypsychrophila CGMCC 1.12828T, Rugamonas rubra CCM3730T and Duganella zoogloeoides JCM20729T at levels of 97.8, 97.7 and 97.3 %, respectively. The predominant fatty acids of B448-2T were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The predominant isoprenoid quinone was Q-8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The genomic DNA G+C content of the strain was 66.1 mol%. In DNA–DNA hybridization tests, B448-2T shared 37.6 % DNA–DNA relatedness with Massilia eurypsychrophila CGMCC 1.12828T. On the basis of the results for phenotypic and chemotaxonomic characteristics, B448-2T was considered to represent a novel species of the genus Massilia , for which the name Massilia glaciei sp. nov. is proposed. The type strain is B448-2T (=JCM 30271T=CGMCC 1.12920T).
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Acinetobacter guangdongensis Feng et al. 2014 is a junior heterotypic synonym of Acinetobacter indicus Malhotra et al. 2012
More LessA draft whole-genome sequence was obtained for Acinetobacter guangdongensis strain KCTC 42012T and compared against those of the type strains of all Acinetobacter species with validly published names. High similarity was found to Acinetobacter indicus CCM 7832T (average nucleotide identity based on blast and digital DNA–DNA hybridization values of 96.3 and 70.4 %, respectively). In addition, the metabolic, physiological and chemotaxonomic features of KCTC 42012T were shown to be congruent with those of A. indicus . We conclude that Acinetobacter guangdongensis Feng et al. 2014 is a later heterotypic synonym of Acinetobacter indicus Malhotra et al. 2012.
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Microbulbifer aggregans sp. nov., isolated from estuarine sediment from a mangrove forest
More LessA novel, rod-shaped, Gram-stain-negative, halophilic and non-motile bacterium, designated CCB-MM1T, was isolated from a sample of estuarine sediment collected from Matang Mangrove Forest, Malaysia. The cells possessed a rod–coccus cell cycle in association with growth phase and formed aggregates. Strain CCB-MM1T was both catalase and oxidase positive, and able to degrade starch. Optimum growth occurred at 30 °C and pH 7.0 in the presence of 2–3 % (w/v) NaCl. The 16S rRNA gene sequence of strain CCB-MM1T showed 98.12, 97.46 and 97.33 % sequence similarity with Microbulbifer rhizosphaerae Cs16bT, Microbulbifer maritimus TF-17T and Microbulbifer gwangyangensis GY2T respectively. Strain CCB-MM1T and M. rhizosphaerae Cs16bT formed a cluster in the phylogenetic tree. The major cellular fatty acids were iso-C17 : 1 ω9c and iso-C15 : 0, and the total polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, phosphoaminolipid, two unidentified lipids, an unidentified glycolipid and an unidentified aminolipid. The major respiratory quinone was ubiquinone Q-8 and the genomic DNA G+C content of the strain was 58.9 mol%. On the basis of the phylogenetic, phenotypic and genotypic data presented here, strain CCB-MM1T represents a novel species of the genus Microbulbifer , for which the name Microbulbifer aggregans sp. nov. is proposed. The type strain is CCB-MM1T (=LMG 29920T=JCM 31875T).
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Loktanella acticola sp. nov., isolated from seawater
More LessA Gram-stain-negative, aerobic, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated OISW-6T, was isolated from seawater near Oido, a South Korean island, and subjected to a polyphasic taxonomic study. Strain OISW-6T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2.0–3.0 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences showed that strain OISW-6T fell within the clade comprising the type strains of Loktanella species. Strain OISW-6T exhibited 16S rRNA gene sequence similarity values of 97.0–98.9 % to Loktanella maricola , Loktanella tamlensis , Loktanella rosea , Loktanella maritima , Loktanella sediminilitoris and Loktanella litorea , and of 94.0–96.3 % to the type strains of the other Loktanella species. Strain OISW-6T contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c as the major fatty acid. The major polar lipids detected in strain OISW-6T were phosphatidylcholine, phosphatidylglycerol and one unidentified aminolipid. The DNA G+C content of strain OISW-6T was 57.3 mol% and its DNA–DNA relatedness values with the type strains of the six phylogenetically closely related Loktanella species were 8–25 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain OISW-6T is separated from recognized species of the genus Loktanella . On the basis of the data presented, strain OISW-6T is considered to represent a novel species of the genus Loktanella , for which the name Loktanella acticola sp. nov. is proposed. The type strain is OISW-6T (=KCTC 52837T=NBRC 112781T).
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Hydrogenophaga soli sp. nov., isolated from rice field soil
More LessA novel Gram-stain-negative bacterial strain, designated strain S10T, was isolated from soil collected in a rice field in Goyang, South Korea. Cells of strain S10T were strictly aerobic, motile and rod-shaped. Colonies were round, convex, smooth and white. The strain grew optimally at 37 °C, pH 7.0 and 0 % (w/v) NaCl. Phylogenetic analysis of the 16S rRNA gene sequence of strain S10T revealed that the bacterium belongs to the family Comamonadaceae and is related to members of the genus Hydrogenophaga , with Hydrogenophaga caeni EMB71T being its closest relative (97.9 % sequence similarity). The DNA G+C content of strain S10T was 68.2 mol%. Strain S10T contained phosphatidylethanolamine and diphosphatidylglycerol as the major polar lipids. The major fatty acids were C16 : 0 and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH). The predominant respiratory quinone was ubiquinone Q-8. DNA–DNA hybridization values of strain S10T with Hydrogenophaga caeni KCTC 12613T, Hydrogenophaga atypica DSM 15342T and Hydrogenophaga defluvii DSM 15341T were 16.1±4.8, 49.0±3.2 and 21.9±8.8 %, respectively. Based on phylogenetic distinctiveness, DNA–DNA hybridization and specific physiological and biochemical characteristics, strain S10T (=KCTC 52520T=JCM 31711T) is classified as a novel species of the genus Hydrogenophaga , for which the name Hydrogenophaga soli sp. nov. is proposed.
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Reclassification of Thiomicrospira hydrogeniphila (Watsuji et al. 2016) to Thiomicrorhabdus hydrogenophila comb. nov., with emended description of Thiomicrorhabdus (Boden et al., 2017)
More LessThe genus Thiomicrorhabdus (Tmr) in the Piskirickettsiaceae in the Thiotrichales of the Gammaproteobacteria contains four species of sulfur-oxidising obligate chemolithoautotroph with validly published names, all previously classified as Thiomicrospira (Tms) species. Here we demonstrate that Thiomicrospira hydrogeniphila , a recently published hydrogen-utilising chemolithoautotroph closely related to Thiomicrorhabdus frisia (type species of Thiomicrorhabdus ) should be classified as a member of the genus Thiomicrorhabdus and not Thiomicrospira , as Thiomicrorhabdus hydrogeniphila comb. nov., on the basis of comparative physiology and morphology as well as 16S rRNA (rrs) gene identity of Tms. hydrogeniphila MAS2T being closer to that of Tmr. frisia JB-A2T (99.1 %) than to Tms. pelophila DSM 1534T (90.5 %) or Hydrogenovibrio marinus MH-110T (94.1 %), and on the basis of the topology of 16S rRNA gene maximum likelihood trees, which clearly place Tms. hydrogeniphila within the genus Thiomicrorhabdus . It was also noted that thiosulfate-grown Thiomicrorhabdus spp. can be distinguished from Thiomicrospira spp. or Hydrogenovibrio spp. on the basis of the 3 dominant fatty acids (C16 : 1, C18 : 1 and C16 : 0), and from other Thiomicrorhabdus spp. on the basis of the fourth dominant fatty acid, which varies between the species of this genus – which could provide a useful diagnostic method. We provide an emended description of Thiomicrorhabdus (Boden R, Scott KM, Williams J, Russel S, Antonen K et al. Int J Syst Evol Microbiol 2017;67:1140–1151) to take into account the properties of Thiomicrorhabdus hydrogeniphila comb. nov.
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Erythrobacter arachoides sp. nov., isolated from ice core
A Gram-stain-negative, rod-shaped bacterial strain, designed RC4-10-4T, belonging to the genus Erythrobacter , was isolated from the East Rongbuk Glacier on the Tibetan Plateau. Strain RC4-10-4T grew optimally at pH 7.0, at 25 °C and in the presence of 2 % (w/v) NaCl. Summed feature 3 (C16 : 1 ω6c and/or iso-C15 : 0 2-OH), summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C16 : 0 were the major fatty acids. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, sphingoglycolipid and phosphatidylcholine. Carotenoid was detected in the cells. The DNA G+C content of the novel strain was 66.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain RC4-10-4T formed a distinct phylogenetic lineage within the cluster comprising Erythrobacter strains. Similarities between the 16S rRNA gene sequences of strain RC4-10-4T and the closely related strains Erythrobacter luteus KCTC 42179T, Erythrobacter gangjinensis KCTC 22330T, Erythrobacter odishensis KCTC 23981T and Erythrobacter atlanticuls KCTC 42697T were 98.0, 97.6, 97.5 and 97.2 %. The DNA–DNA hybridization values were 37.6, 15.4, 29.8 and 35.8 %, respectively. Based on the phenotypic and phylogenetic characteristics, strain RC4-10-4T represents a novel species of the genus Erythrobacter , for which the name Erythrobacter arachoides sp. nov. is proposed, with the type strain RC4-10-4T (=CGMCC 1.15507T=JCM 31277T).
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Dyella agri sp. nov., isolated from reclaimed grassland soil
More LessA novel strain, DKC-1T, was isolated from reclaimed grassland soil and was characterized taxonomically by a polyphasic approach. Strain DKC-1T was a Gram-staining-negative, light-yellow-coloured and rod shaped bacterium, motile with polar flagellum. It was able to grow at 20–37 °C, at pH 4.5–9.0 and with 0–3 % (w/v) NaCl concentration. Based on the 16S rRNA gene sequence analysis, strain DKC-1T formed a clade within the members of the genus Dyella and showed highest sequence similarities to Dyella japonica XD53T (98.36 %), Rhodanobacter aciditrophus sjH1T (97.92 %), Rhodanobacter koreensis THG-DD7T (97.74 %), Dyella kyungheensis THG-B117T (97.65 %) and Rhodanobacter terrae GP18-1T (97.40 %). The only respiratory quinone was ubiquinone-8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidyl-N-methylethanolamine. The predominant fatty acids of strain DKC-1T were iso-C16 : 0, iso-C15 : 0, summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl), iso-C17 : 0, iso-C11 : 0 3-OH and iso-C11 : 0. The genomic DNA G+C content of this novel strain was 63.1 mol%. The DNA–DNA relatedness between strain DKC-1T and its reference strains ( D. japonica XD53T, R. aciditrophus sjH1T, R. koreensis THG-DD7T, D. kyungheensis THG-B117T and R. terrae GP18-1T) was 52.3, 44.7, 38.7, 49.0 and 32.7 %, respectively, which falls below the threshold value of 70 % for the strain to be considered as novel. The morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished this strain from its closest phylogenetic neighbours. Thus, strain DKC-1T represents a novel species of the genus Dyella , for which the name Dyella agri sp. nov. is proposed. The type strain is DKC-1T (=KEMB 9005-571T=KACC 19176T=JCM 31925T).
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Marivibrio halodurans gen. nov., sp. nov., a marine bacterium in the family Rhodospirillaceae isolated from underground rock salt
More LessGram-negative, spiral or curved rod-shaped cells of a bacterial strain, designated ZC80T, were isolated from a rock salt sample collected at Yunnan salt mine, China. Analysis of the strain's 16S rRNA gene sequence revealed a clear affiliation of this novel strain within the family Rhodospirillaceae . Strain ZC80T formed a robust cluster with Pelagibius litoralis CL-UU02T at a 16S rRNA gene sequence similarity level of 88.1 %. Strain ZC80T shared no more than 91.0 % 16S rRNA gene sequence similarity with the type strains of other species in the family Rhodospirillaceae . Strain ZC80T was able to grow in the presence of 2–15 % (w/v) NaCl, and grew at 10–50 °C and pH 6.0–10.0. The major fatty acids were C19 : 0 cyclo ω8c (41.3 %). The major isoprenoid quinone was ubiquinone 10 (Q-10). The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and an unidentified aminolipid. The DNA G+C content of strain ZC80T was 60.8 mol%. On the basis of phylogenetic analyses and chemotaxonomic and physiological data, strain ZC80T is considered to represent a novel species of a new genus in the family Rhodospirillaceae , for which the name Marivibrio halodurans gen. nov., sp. nov. is proposed. The type strain of Marivibrio halodurans is ZC80T (=CGMCC 1.15697T=NBRC 112461T).
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Elstera cyanobacteriorum sp. nov., a novel bacterium isolated from cyanobacterial aggregates in a eutrophic lake
More LessA bacterial strain, TH019T, was isolated from cyanobacterial aggregates in a eutrophic lake, Taihu Lake, China. Cells were observed to be slightly curved rod-shaped and stained Gram-negative. Optimal growth was obtained at pH 7.0 (range, 5.0–9.0) and 28 °C (range, 20-37 °C) in R2A broth. The cells were found to be positive for oxidase and catalase activities, nitrate reduction and denitrification. The major respiratory quinone was ubiquinone Q-10. The major fatty acids were identified as C18 : 1 ω6c/C18 : 1 ω7c and C18 : 1 2OH. The 16S rRNA gene sequence of strain TH019T was phylogenetically related to Elstera litoralis Dia-1T (97.9 % similarity). The genomic G+C content of strain TH019T was 62.4 mol% based on total genome calculations. Average nucleotide identity and digital DNA–DNA hybridization values for complete genomes were 78.8 and 19.8 %, respectively, between strain TH019T and Elstera litoralis Dia-1T. The phenotypic, chemotaxonomic and phylogenetic properties, and genome analysis suggested that strain TH019T represented a novel species within the genus Elstera , for which the name Elstera cyanobacteriorum sp. nov. is proposed. The type strain is TH019T (=CGMCC 1.15802T=LMG 29721T).
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On names of genera of prokaryotes that are later homonyms of generic names with standing in the zoological or the botanical nomenclature. Proposal of Neomegalonema gen. nov. and Neomegalonema perideroedes comb. nov. as replacements for the prokaryotic generic name Meganema and the species name Meganema perideroedes
More LessI here present a survey of generic names with standing in the prokaryotic nomenclature that have homonyms with standing under the International Code of Zoological Nomenclature and/or the International Code of Nomenclature for algae, fungi, and plants. I especially discuss such names added after Principle 2 of the Bacteriological Code/Prokaryotic Code was changed in 1999 to make the prokaryote nomenclature not independent of botanical and zoological nomenclature. Cases include the genera Micromonas , Quadrococcus, Yania , Sinococcus, and Meganema . The generic name Meganema was not previously recognized as a homonym of two genera with standing in the zoological nomenclature. Therefore, I here propose renaming Meganema and Meganema perideroedes as Neomegalonema gen. nov. and Neomegalonema perideroedes comb. nov., respectively.
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- Eukaryotic Micro-organisms
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Spathaspora boniae sp. nov., a D-xylose-fermenting species in the Candida albicans/Lodderomyces clade
Two yeast isolates producing asci-containing elongate ascospores with curved ends typical of the genus Spathaspora were isolated from rotting wood samples collected in an Atlantic rainforest ecosystem in Brazil. Phylogenetic analysis of the LSU rRNA gene D1/D2 domain sequences demonstrated that the strains represent a new species and placed it next to Candida blackwellae, in a clade that also contains Candida albicans and Candida dubliniensis. Other sequences of the ribosomal gene cluster supported same placementin the same clade, and a phylogenomic analysis placed this new species in an early emerging position relative to the larger C. albicans/Lodderomyces clade. One interpretation is that the genus Spathaspora is, in fact, paraphyletic. In conformity with this view, we propose the novel species Spathaspora boniae sp. nov. to accommodate the isolates. The type strain of Spathaspora boniae sp. nov. is UFMG-CM-Y306T (=CBS 13262T). The MycoBank number is MB 821297. A detailed analysis of xylose metabolism was conducted for the new species.
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Prototheca blaschkeae subsp. brasiliensis subsp. nov., isolated from cow milk
A strain of an achlorophyllic alga, named PR24T, was isolated from cow milk samples from the state of Minas Gerais, Brazil. Based on 18S rDNA, 28S rRNA, D1/D2 region of the LSU rDNA and SSU rRNA gene sequence similarities, this strain was found to be a member of the genus Prototheca and closely related to Prototheca blaschkeae SAG2064T. However, the novel strain could easily be distinguished from recognized Prototheca species by internal transcribed spacer, species-specific PCR, single-strand conformation polymorphism-PCR analysis and phenotypic characteristics. The inability to grow in Sabouraud broth at pH 4.0 and the different cellular fatty acid composition clearly distinguished PR24T from the reference strain of P. blaschkeae. The combination of genotypic and phenotypic data indicates that strain PR24T represents a subspecies of P. blaschkeae, for which the name Prototheca blaschkeae subsp. brasiliensis subsp. nov. is proposed. The respective type strain is PR24T (=DSM 103592T=IHEM 26958T).
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Three novel species of d-xylose-assimilating yeasts, Barnettozyma xylosiphila sp. nov., Barnettozyma xylosica sp. nov. and Wickerhamomyces xylosivorus f.a., sp. nov.
More LessThis study describes three novel xylose-assimilating yeasts, which were isolated from decayed wood collected from Bung Hatta Botanical Garden in West Sumatra and Cibodas Botanic Garden in West Java, or from litter from Eka Karya Bali Botanic Garden in Bali, Indonesia. Phylogenetic analysis was performed based on the sequences of the D1/D2 domains of the large ribosomal subunit (LSU), the small ribosomal subunit (SSU), the internal transcribed spacer (ITS) and elongation factor-1α (EF-1α), and the three strains were found to represent three novel species belonging to genera Barnettozyma or Wickerhamomyces. The morphological, biochemical and physiological characteristics indicated that the strains were distinct from other closely related species. Strains 13Y206T and 14Y196T belonging to the Barnettozyma clade are described as the type strains of Barnettozyma xylosiphila sp. nov. (type strain 13Y206T=NBRC 110202T=InaCC Y726T; MycoBank MB808598) and Barnettozyma xylosica sp. nov. (type strain 14Y196T=NBRC 111558T=InaCC Y1030T; MycoBank MB819485). Strain 14Y125T belonging to the Wickerhamomyces clade is described as the type strain of Wickerhamomyces xylosivorus f.a., sp. nov. (type strain 14Y125T=NBRC 111553T=InaCC Y1026T; MycoBank MB819484).
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Meyerozyma amylolytica sp. nov. from temperate deciduous trees and the transfer of five Candida species to the genus Meyerozyma
More LessIn the course of two independent studies three yeasts have been isolated from temperate deciduous trees in Hungary and Germany. Analyses of nucleotide sequences of D1/D2 domains of the 26S rRNA gene (LSU) suggested that these strains belong to the Meyerozyma clade in Debaryomycetaceae (Saccharomycetales). The phylogenetic analysis of a concatenated alignment of the ITS region and LSU gene sequences confirmed the placement of the three strains in the Meyerozyma clade close to Candida elateridarum. If mixed in proper combinations, the strains formed one to two hat shaped ascospores in deliquescent asci. In addition to the ascospore formation, the three studied strains differed from Candida elateridarum and other members of the Meyerozyma clade in terms of ribosomal gene sequence and some physiological properties. To accommodate the above-noted strains, we describe the new species as Meyerozyma amylolytica sp. nov. (holotype: DSM 27310T; ex-type cultures: NCAIM Y.02140T=MUCL 56454T, allotype: NCAIM Y.01955A; ex-allotype culture: DSM 27468), MB 821663. Additionally, we propose the transfer of five non-ascosporic members of the Meyerozyma clade to the genus Meyerozyma as the following new taxonomic combinations Meyerozyma athensensis f.a., comb. nov. (MB 821664), Meyerozyma carpophila f.a., comb. nov. (MB 821665), Meyerozyma elateridarum f.a., comb. nov. (MB 821666), Meyerozyma neustonensis f.a., comb. nov. (MB 821667), and Meyerozyma smithsonii f.a., comb. nov. (MB 821668).
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- ICSP Matters
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Correction of the name Amycolatopsis albidoflavus to Amycolatopsis albidiflava corrig. Request for an Opinion
More LessThe name Amycolatopsis albidoflavus Lee and Hah 2001 is malformed because the genus name Amycolatopsis has the feminine gender. It is here proposed to correct the name to Amycolatopsis albidiflava corrig.
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- Errata
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Erratum: Proposal for the reclassification of obligately purine-fermenting bacteria Clostridium acidurici (Barker 1938) and Clostridium purinilyticum (Dürre et al. 1981) as Gottschalkia acidurici gen. nov. comb. nov. and Gottschalkia purinilytica comb. nov. and of Eubacterium angustum (Beuscher and Andreesen 1985) as Andreesenia angusta gen. nov. comb. nov. in the family Gottschalkiaceae fam. nov.
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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 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)