- Volume 63, Issue Pt_9, 2013
Volume 63, Issue Pt_9, 2013
- New Taxa
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- Other Bacteria
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Maribacter aestuarii sp. nov., isolated from tidal flat sediment, and an emended description of the genus Maribacter
More LessA Gram-staining-negative, strictly aerobic bacterial strain, motile by gliding, designated GY20T, was isolated from a tidal flat at Gwangyang Bay, South Korea. Cells were moderately halophilic, catalase- and oxidase-positive rods. Growth of strain GY20T was observed at 10–30 °C (optimum, 25 °C), at pH 6.5–11.0 (optimum, pH 7.0–8.0) and in the presence of 1–5 % (w/v) NaCl (optimum, 2–3 %). MK-6 was detected as the sole isoprenoid quinone, and iso-C15 : 0, iso-C15 : 1 G, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), summed feature 9 (iso-C17 : 1ω9c and/or 10-methyl C16 : 0), iso-C17 : 0 3-OH and iso-C15 : 0 3-OH as major fatty acids. Strain GY20T contained phosphatidylethanolamine, one unidentified glycolipid and one unidentified lipid as major polar lipids. The G+C content of the genomic DNA was 39.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain GY20T formed a tight phyletic lineage with members of the genus Maribacter . Strain GY20T was most closely related to Maribacter dokdonensis DSW-8T, with sequence similarity of 96.2 %. On the basis of phenotypic, chemotaxonomic and molecular properties, strain GY20T was shown to represent a novel species within the genus Maribacter , for which the name Maribacter aestuarii sp. nov. is proposed. The type strain is GY20T ( = KACC 16440T = JCM 18631T). An emended description of the genus Maribacter is also proposed.
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Muricauda antarctica sp. nov., a marine member of the Flavobacteriaceae isolated from Antarctic seawater
More LessA Gram-stain-negative, rod-shaped bacterium with appendages, designated Ar-22T, was isolated from a seawater sample collected from the western part of Prydz Bay, near Cape Darnley, Antarctica. Strain Ar-22T grew optimally at 35 °C, at pH 7.5 and in the presence of 1–3 % (w/v) NaCl. The isolate was positive for casein, gelatin and Tween 20 decomposition and negative for H2S production and indole formation. Chemotaxonomic analysis showed that MK-6 was the major isoprenoid quinone and phosphatidylethanolamine was the major polar lipid. The major fatty acids were iso-C17 : 0 3-OH, iso-C15 : 1 G, iso-C15 : 0 and C16 : 1ω7c/iso-C15 : 0 2OH. The genomic DNA G+C content was 44.8 mol%. Comparative 16S rRNA gene sequence analysis revealed that strain Ar-22T is closely related to members of the genus Muricauda , sharing 94.2–97.3 % sequence similarity with the type strains of species of the genus Muricauda and being most closely related to the Muricauda aquimarina . Phylogenetic analysis based on the 16S rRNA gene sequence comparison confirmed that strain Ar-22T formed a deep lineage with Muricauda flavescens . Sequence similarity between strain Ar-22T and Muricauda ruestringensis DSM 13258T, the type species of the genus Muricauda , was 96.9 %. Strain Ar-22T exhibited mean DNA–DNA relatedness values of 40.1 %, 49.4 % and 25.7 % to M. aquimarina JCM 11811T, M. flavescens JCM 11812T and Muricauda lutimaris KCTC 22173T, respectively. On the basis of phenotypic and genotypic data, strain Ar-22T represents a novel species of the genus Muricauda , for which the name Muricauda antarctica sp. nov. (type strain Ar-22T = CGMCC 1.12174T = JCM 18450T) is proposed.
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Mongoliicoccus alkaliphilus sp. nov. and Litoribacter alkaliphilus sp. nov., isolated from salt pans
More LessFour bacterial strains (JC165T, JC166T, JC169 and JC170) were isolated from salt pan soils from a coastal region of Tamilnadu, India. They were obligately aerobic, pink- to red-pigmented, mesophilic, haloalkaliphiles having chemoorganoheterotrophic growth on various carbon sources and were catalase- and oxidase-positive. Phototrophic growth and bacteriochlorophyll a were absent in all four strains. Major carotenoids present were β-carotene and rhodoxanthin. The main fatty acid in all strains was iso-C15 : 0. The main polar lipids were phosphatidylethanolamine (PE) and phosphatidylcholine (PC) as well as a few unidentified lipids. Bacterial hopane derivatives and diplopterol (DPL) were detected in all four strains. Based on the 16S rRNA gene sequences, all four strains belong to the family Cyclobacteriaceae in the phylum Bacteroidetes . Strains JC165T and JC169 had a sequence similarity of 97.2 % with Mongoliicoccus roseus MIM28T, while strains JC166T and JC170 had a sequence similarity of 99.5 % with Litoribacter ruber YIM CH208T. Strains JC165T/JC169 and JC166T/JC170 had genomic DNA reassociation values (based on DNA–DNA hybridization) of 21±2 % and 23±1 % with M. roseus KCTC 19808T ( = MIM28T) and L. ruber KCTC 22899T ( = YIM CH208T), respectively, suggesting that they represented novel species. The reassociation values of >85 % between strains JC165T and JC169, and JC166T and JC170 suggested they were strains of the same species. The genomic information was supported by phenotypic observations leading to the proposal of two novel species, Mongoliicoccus alkaliphilus sp. nov. (type strain, JC165T = KCTC 32210T = LMG 27255T) and Litoribacter alkaliphilus sp. nov. (type strain, JC166T = KCTC 32217T = LMG 27256T).
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Flavobacterium aquaticum sp. nov., isolated from a water sample of a rice field
More LessStrain JC164T was isolated from a water sample from a rice field at Jamdih, Mau, Uttar Pradesh, India. Colonies of strain JC164T were brown–yellow and cells were Gram-stain-negative. Catalase, oxidase and amylase were present. iso-C15 : 0, iso-C16 : 0, iso-C15 : 1 G, iso-C15 : 0 3-OH and iso-C14 : 0 were the predominant fatty acids with minor amounts of iso-C16 : 0 3-OH, anteiso-C15 : 0, C16 : 0, iso-C16 : 1 H, iso-C14 : 0 3-OH and iso-C13 : 0. Strain JC164T contained phosphatidylethanolamine and a few unidentified lipids (L1, L3 and L6) as major polar lipids. Bacteriohopane derivative 1 (BHD1) and diplopterol (DPL) were the major hopanoids. β-Carotene was one among the several spirilloxanthin series carotenoids present in strain JC164T. Genomic DNA G+C content was 39.6 mol%. 16S rRNA gene sequence comparisons indicated that strain JC164T represents a member of the genus Flavobacterium (family Flavobacteriaceae , class Flavobacteriia ). The most closely related taxa to strain JC164T were Flavobacterium sasangense YC6274T (98.5 %), Flavobacterium cucumis R2A45-3T (98.1 %), Flavobacterium cheniae NJ-26T (97.2 %) and the novel strain possessed <95.1 % sequence similarity with other members of the genus Flavobacterium . However, strain JC164T showed 12.5±2, 13.6±1 and 17.4±2 % genomic DNA association (based on DNA–DNA hybridization) with Flavobacterium sasangense KCTC 22246T, Flavobacterium cucumis DSM 18830T and Flavobacterium cheniae CGMCC 1.6844T, respectively. The distinct genomic difference and morphological, physiological and chemotaxonomic differences from the previously described taxa support the classification of strain JC164T as a representative of a novel species of the genus Flavobacterium , for which the name Flavobacterium aquaticum sp. nov. is proposed. The type strain is JC164T ( = KCTC 32196T = CGMCC 1.12398 = LMG 27251T).
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Parabacteroides chinchillae sp. nov., isolated from chinchilla (Chincilla lanigera) faeces
Strains of Gram-stain-negative, anaerobic, rod-shaped bacteria were isolated from chinchilla (Chinchilla lanigera) faeces, and strain ST166T was investigated taxonomically. Phylogenetic analyses of 16S rRNA gene sequences revealed that strain ST166T belonged to the genus Parabacteroides . Strain ST166T formed a distinct line of descent, and the highest sequence similarity to ST166T was found with Parabacteroides merdae JCM 9497T (95.6 %) and Parabacteroides johnsonii JCM 13406T (95.0 %). Analysis of hsp60 gene sequences also supported these relationships. Based on the phenotypic and phylogenetic characteristics, the novel species Parabacteroides chinchillae sp. nov. is proposed. The type strain of P. chinchillae sp. nov. is ST166T ( = JCM 17104T = CCUG 62154T).
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Marinoscillum luteum sp. nov., isolated from marine sediment
A novel strain, designated SJP7T, was isolated from sediment of the Tofua Arc of the Tonga Trench. The 16S rRNA gene sequence of the isolate showed the highest similarity to that of Marinoscillum pacificum KCCM 42325T (95.9 %). Phylogenetic analysis revealed that the isolate formed a distinct phyletic line with Marinoscillum pacificum KCCM 42325T and Marinoscillum furvescens LMG 13023T within the family Cytophagaceae . Cells of strain SJP7T were Gram-stain-negative and appeared as long rods that were motile by gliding. Growth was observed at 15–40 °C (optimum, 30 °C), at pH 5.5–9.0 (optimum, pH 7.5–8.0) and in the presence of 0.5–7.0 % (w/v) NaCl (optimum, 2.5–3 %). The major respiratory quinone was MK-7. The dominant fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0 and C16 : 1ω5c. The DNA G+C content was 43.5 mol%. These properties support the affiliation of strain SJP7T with the genus Marinoscillum . Further phenotypic differentiation of strain SJP7T from other species of the genus Marinoscillum was indicated by the results of physiological and biochemical tests. On the basis of evidence from our polyphasic taxonomic study, strain SJP7T represents a novel species of the genus Marinoscillum , for which the name Marinoscillum luteum sp. nov. is proposed. The type strain of Marinoscillum luteum is SJP7T ( = KCTC 23939T = NCAIM B02491T).
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Tenacibaculum xiamenense sp. nov., an algicidal bacterium isolated from coastal seawater
A Gram-stain-negative, elongated rod-shaped, yellow-pigmented, aerobic bacterial strain, designated WJ-1T, was isolated from coastal seawater in Xiamen, Fujian province, China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain WJ-1T fell within the genus Tenacibaculum and was most closely associated with Tenacibaculum aestuarii SMK-4T (96.7 % 16S rRNA gene sequence similarity); lower similarities were shown to other members of the genus Tenacibaculum (<96.2 %). The strain formed a distinct lineage with Tenacibaculum litopenaei B-IT (96.0 %), Tenacibaculum geojense YCS-6T (94.5 %) and Tenacibaculum jejuense CNURIC 013T (95.4 %). Growth was observed at temperatures from 16 to 38 °C, at salinities from 2 to 4 % and at pH 6–9. The major fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), iso-C17 : 0 3-OH, iso-C15 : 0 and iso-C15 : 0 3-OH. The DNA G+C content of strain WJ-1T was 33.2 mol% and the major respiratory quinone was menaquinone-6 (MK-6). Differential phenotypic properties and phylogenetic distinctiveness in this study distinguished strain WJ-1T from all other members of the genus Tenacibaculum . According to the morphology, physiology, fatty acid composition and 16S rRNA gene sequence data, strain WJ-1T represents a novel species of the genus Tenacibaculum , for which the name Tenacibaculum xiamenense sp. nov. is proposed. The type strain is WJ-1T ( = CGMCC 1.12378T = LMG 27422T).
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Niabella hirudinis and Niabella drilacis sp. nov., isolated from the medicinal leech Hirudo verbana
More LessTwo Gram-negative, rod-shaped bacteria, strains E96T and E90T, were isolated from medicinal leeches (Hirudo verbana) and characterized by a polyphasic taxonomic approach. Phylogenetic analysis based on the nearly full-length 16S rRNA gene sequence showed that the two strains shared 98.1 % sequence similarity and were affiliated with the genus Niabella within the phylum Bacteroidetes , with 94.4–97.6 % sequence similarity to type strains of species of the genus Niabella and highest sequence similarity to the type strain of Niabella aurantiaca (97.3 and 97.6 %, respectively). Niabella -related 16S rRNA gene sequences were recently detected in the bladders of Hirudo verbana; however, no cultured representatives were so far available. Genomic fingerprint analysis using repetitive element primed (rep)- and randomly amplified polymorphic DNA (RAPD)-PCRs and DNA–DNA hybridization experiments clearly showed that the strains were different from each other (DNA–DNA relatedness values of 39.1 %, reciprocal 28.0 %) and from the type strains of N. aurantiaca (<19.7 %) and Niabella tibetensis (<41.1 %). Chemotaxonomic analyses confirmed the affiliation to the genus Niabella . Both strains contained MK-7 as the predominant menaquinone. The major fatty acids of both strains were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), which is characteristic for the genus Niabella . Based on genotypic, chemotaxonomic and physiological characterization, we propose two novel species of the genus Niabella , Niabella hirudinis sp. nov., with strain E96T ( = DSM 25812T = CCM 8411T = LMG 26956T) as the type strain, and Niabella drilacis sp. nov., with strain E90T ( = DSM 25811T = CCM 8410T = LMG 26954T) as the type strain.
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Algibacter agarivorans sp. nov. and Algibacter agarilyticus sp. nov., isolated from seawater, reclassification of Marinivirga aestuarii as Algibacter aestuarii comb. nov. and emended description of the genus Algibacter
More LessTwo yellow-pigmented, rod-shaped, non-motile, Gram-reaction-negative and aerobic bacterial strains, designated KYW560T and KYW563T, were isolated from seawater collected from Gwangyang Bay, Republic of Korea. The isolates required sea salts for growth. Flexirubin-type pigments were absent. The common major cellular fatty acids (>5 % of total) of the two strains were C16 : 0, C18 : 0, iso-C15 : 0, anteiso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). Strain KYW560T also contained iso-C15 : 0 3-OH and C20 : 1ω9c as major fatty acids. The main polar lipids were phosphatidylethanolamine, an unidentified aminolipid and two unidentified lipids. The predominant isoprenoid quinone was MK-6. The DNA G+C contents of strains KYW560T and KYW563T were 41.0±0.7 and 38.3±0.4 mol% (mean±sd of three determinations), respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolates belonged to the family Flavobacteriaceae , and were related to the genus Algibacter . Based on data from this taxonomic study using a polyphasic approach, it is proposed that the isolates represent novel species of the genus Algibacter , for which the names Algibacter agarivorans sp. nov. (type strain, KYW560T = KCTC 23855T = JCM 18285T) and Algibacter agarilyticus sp. nov. (type strain, KYW563T = KCTC 23857T = JCM 18275T) are proposed. Reclassification of Marinivirga aestuarii as Algibacter aestuarii comb. nov. and emended description of the genus Algibacter are also proposed.
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- Eukaryotic Micro-organisms
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Sympodiomycopsis yantaiensis sp. nov., a basidiomycetous yeast isolated from insect frass
More LessTwo strains (NYNU 121010T and NYNU 121032) of a novel basidiomycetous yeast species belonging to the genus Sympodiomycopsis were isolated from insect frass collected from trunks of a pagoda tree (Sophora japonica L.) in Yantai, Shandong province, east China. The sequence analyses of the D1/D2 domain of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region indicated that the closest relatives were Sympodiomycopsis kandeliae FIRDI 007T, Sympodiomycopsis paphiopedili CBS 7429T and Sympodiomycopsis sp. S6A. The D1/D2 sequences of the novel strains differed by 12 nt substitutions (2 %) from the type strain of S. kandeliae, and by 13 nt substitutions (2.2 %) from the type strain of S. paphiopedili and from Sympodiomycopsis sp. S6A. The novel strains differed from closely related species by more than 4.6 % substitutions in the ITS region. The novel strains can also be distinguished from S. kandeliae and S. paphiopedili on the basis of a number of morphological and physiological characteristics and represent a novel species in the genus Sympodiomycopsis, for which the name Sympodiomycopsis yantaiensis sp. nov. is proposed. The type strain is NYNU 121010T ( = CICC 32998T = CBS 12813T). The Mycobank deposit number is MB 804119.
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Redescriptions of three trachelocercid ciliates (Protista, Ciliophora, Karyorelictea), with notes on their phylogeny based on small subunit rRNA gene sequences
More LessThree trachelocercid ciliates, Kovalevaia sulcata (Kovaleva, 1966) Foissner, 1997, Trachelocerca sagitta (Müller, 1786) Ehrenberg, 1840 and Trachelocerca ditis (Wright, 1982) Foissner, 1996, isolated from two coastal habitats at Qingdao, China, were investigated using live observation and silver impregnation methods. Data on their infraciliature and morphology are supplied. The small subunit rRNA (SSU rRNA) genes of K. sulcata and Trachelocerca sagitta were sequenced for the first time. Phylogenetic analyses based on SSU rRNA gene sequence data indicate that both organisms, and the previously sequenced Trachelocerca ditis, are located within the trachelocercid assemblage and that K. sulcata is sister to an unidentified taxon forming a clade that is basal to the core trachelocercids.
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Morphology and small-subunit rRNA gene sequences of two novel marine ciliates, Metanophrys orientalis spec. nov. and Uronemella sinensis spec. nov. (Protista, Ciliophora, Scuticociliatia), with an improved diagnosis of the genus Uronemella
More LessThe morphology and infraciliature of two novel marine scuticociliates, Metanophrys orientalis spec. nov. and Uronemella sinensis spec. nov., collected from sandy beaches at Qingdao, China, were investigated using live observation and protargol-staining methods. Metanophrys orientalis spec. nov. is distinguished by the following characteristics: marine habitat and a slender to elongate oval body with pointed anterior end and rounded caudal end, in vivo about 25–50 µm long; buccal field about a quarter to a third of body length; nine or ten somatic kineties with dikinetids approximately in anterior half of body, monokinetids in posterior half; membranelles 1 and 2 almost equal in length and composed of two and three longitudinal rows of kinetids respectively; paroral membrane with zigzag structure extending anteriorly to middle portion of membranelle 2; contractile vacuole pore located at posterior end of somatic kinety 1. The genus Uronemella is redefined as follows: marine form with an elongate-elliptical or inverted pear-shaped body; apical plate conspicuous; buccal field about two-thirds of body length, cytostome subequatorially located; oral apparatus Uronema-like; somatic kineties comprising a mixture of dikinetids and monokinetids. Uronemella sinensis spec. nov. is recognized by having an elongate-elliptical body with truncated apical frontal plate, size in vivo about 25–35×15–20 µm, nine or ten somatic kineties, membranelle 1 consisting of two or three basal bodies, contractile vacuole pore at posterior end of somatic kinety 1. This study also compared the small-subunit rRNA gene sequences of these two species with other closely related species to show the sequence divergence, which ranged from 3.53 to 9.60 %. Phylogenetic analyses support the contention that the genus Uronemella is monophyletic, while Metanophrys is non-monophyletic.
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- Evolution, Phylogeny and Biodiversity
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Phylogeny and classification of Dickeya based on multilocus sequence analysis
More LessBacterial heart rot of pineapple reported in Hawaii in 2003 and reoccurring in 2006 was caused by an undetermined species of Dickeya . Classification of the bacterial strains isolated from infected pineapple to one of the recognized Dickeya species and their phylogenetic relationships with Dickeya were determined by a multilocus sequence analysis (MLSA), based on the partial gene sequences of dnaA, dnaJ, dnaX, gyrB and recN. Individual and concatenated gene phylogenies revealed that the strains form a clade with reference Dickeya sp. isolated from pineapple in Malaysia and are closely related to D. zeae ; however, previous DNA–DNA reassociation values suggest that these strains do not meet the genomic threshold for consideration in D. zeae , and require further taxonomic analysis. An analysis of the markers used in this MLSA determined that recN was the best overall marker for resolution of species within Dickeya . Differential intraspecies resolution was observed with the other markers, suggesting that marker selection is important for defining relationships within a clade. Phylogenies produced with gene sequences from the sequenced genomes of strains D. dadantii Ech586, D. dadantii Ech703 and D. zeae Ech1591 did not place the sequenced strains with members of other well-characterized members of their respective species. The average nucleotide identity (ANI) and tetranucleotide frequencies determined for the sequenced strains corroborated the results of the MLSA that D. dadantii Ech586 and D. dadantii Ech703 should be reclassified as Dickeya zeae Ech586 and Dickeya paradisiaca Ech703, respectively, whereas D. zeae Ech1591 should be reclassified as Dickeya chrysanthemi Ech1591.
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- ICSP
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- Request for Opinion
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Proposal to change the name Rhodoligotrophos Fukuda et al. 2012, 1947 to Rhodoligotrophus. Request for an Opinion
More LessIn the opinion of the authors, the genus name Rhodoligotrophos was formed in violation of Principle 3 and Rule 10a of the International Code of Nomenclature of Prokaryotes which requires that genus names are to be treated as Latin substantives. We therefore propose renaming the genus Rhodoligotrophos as Rhodoligotrophus. A Request for an Opinion is submitted to the Judicial Commission of the International Committee on Systematics of Prokaryotes regarding this proposed name change.
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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)