- Volume 67, Issue 9, 2017
Volume 67, Issue 9, 2017
- New taxa
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Cellvibrio zantedeschiae sp. nov., isolated from the roots of Zantedeschia aethiopica
More LessA bacterial strain, designated TPY-10T, was isolated from calla lily roots in Taiwan and characterized by using a polyphasic taxonomy approach. Cells of strain TPY-10T were Gram-stain-negative, strictly aerobic, motile and creamy white rods. Growth occurred at 15–35 °C (optimum, 25–30 °C), at pH 6–7 (optimum, pH 6) and with 0–1 % NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TPY-10T belonged to the genus Cellvibrio and was most closely related to Cellvibriomixtus ACM 2601T with sequence similarity of 97.8 %. Strain TPY-10T contained C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C18 : 1ω7c as the predominant fatty acids. The only isoprenoid quinone was Q-9. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content of the genomic DNA was 49.8 mol%. The DNA–DNA hybridization value for strain TPY-10T with Cellvibriomixtus ACM 2601T was less than 21 %. On the basis of the phylogenetic inference and phenotypic data, strain TPY-10T should be classified as a novel species, for which the name Cellvibrio zantedeschiae sp. nov. is proposed. The type strain is TPY-10T (=BCRC 80525T=LMG 27291T=KCTC 32239T).
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Salinirussus salinus gen. nov., sp. nov., isolated from a marine solar saltern
More LessA halophilic archaeal strain, YGH44T, was isolated from the Yinggehai marine solar saltern in Hainan Province of China. Cells were rod-shaped, stained Gram-negative and formed red-pigmented colonies on agar plates. Optimal growth was obtained with 3.4 M NaCl (range: 2.6–4.8 M), 0.5 M MgCl2 (range: 0.005–1.0 M), at 37 °C (range: 25–55 °C) and at pH 7.0 (range: pH 5.0–9.0). The cells lysed in distilled water, and the minimal NaCl concentration to prevent cell lysis was 1.7 M. Phylogenetic tree reconstructions based on 16S rRNA genes and rpoB′ genes revealed that strain YGH44T was distinct from the related genera, Halovenus , Halapricum , Halorientalis , Halorhabdus and Halosimplex of the order Halobacteriales . The major polar lipids of the strain were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and three unidentified glycolipids. The DNA G+C content of strain YGH44Twas 69.0 mol%. The phenotypic, chemotaxonomic and phylogenetic properties suggested that strain YGH44T (=CGMCC 1.12234T=JCM 18646T) represents a novel species of a new genus within the order Halobacteriales , for which the name Salinirussus salinus gen. nov., sp. nov. is proposed.
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Pacificibacter aestuarii sp. nov., isolated from a tidal flat
More LessA Gram-stain-negative, strictly aerobic bacterium, designated KJ21T, was isolated from a tidal flat in South Korea. Cells were non-motile rods showing oxidase- and catalase-positive activities. Growth of strain KJ21T was observed at 10–35 °C (optimum, 30 °C), at pH 6.0–8.5 (optimum, pH 7.0) and in the presence of 1–5 % (w/v) NaCl (optimum, 2 %). Strain KJ21T contained summed feature 8 (comprising C18 : 1ω7c/C18 : 1ω6c), C16 : 0, 10-methyl C19 : 0 and C10 : 0 3-OH as the major fatty acids and ubiquinone-10 as the major isoprenoid quinone. Phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, an unknown aminolipid and an unknown lipid were detected as the major polar lipids. The G+C content of the genomic DNA was 53.9 mol%. Phylogenic analysis based on 16S rRNA gene sequences showed that strain KJ21T formed a tight phylogenetic lineage with the members of the genus Pacificibacter with a 100 % bootstrap value. Strain KJ21T was most closely related to Pacificibacter maritimus KMM 9031T (98.7 %) and Pacificibacter marinus HDW-9T (98.4 %), and the DNA–DNA relatedness values between strain KJ21T and the type strains of P. maritimus and P. marinus were 46.9±4.2 % and 39.8±5.7, respectively. On the basis of phenotypic, chemotaxonomic and molecular properties, it is clear that strain KJ21T represents a novel species of the genus Pacificibacter , for which the name Pacificibacter aestuarii sp. nov. is proposed. The type strain is KJ21T (=KACC 19098T=JCM 31805T).
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Brenneria populi subsp. brevivirga subsp. nov. isolated from symptomatic bark of Populus × euramericana canker, and description of Brenneria populi subsp. populi subsp. nov.
More LessTwo Gram-stain-negative, facultatively anaerobic, motile bacterial strains isolated from symptomatic bark of Populus × euramericana canker in China were investigated using a polyphasic approach, including 16S rRNA gene sequencing, multilocus sequence analysis, and biochemical and physiological assays. 16S rRNA gene sequencing indicated that these strains belonged to the genus Brenneria , family Pectobacteriaceae , and had the highest sequence similarity with Brenneria populi CFCC 11963T (98 %). DNA–DNA hybridization experiments revealed DNA–DNA relatedness values of 72.1–78.2 % between the new isolates and strains of B. populi , revealing that these strains belonged to the same species. The 16S rRNA gene sequencing and multilocus sequence analysis suggested that the two novel strains and those of B. populi are phylogenetically closely related but form two clearly separated subgroups. Based on the data, the two novel isolates represent a subspecies of B. populi for which the name B. populi subsp. brevivirga subsp. nov. is proposed with D8-10-4-5T (=CFCC 11935T=KCTC 42841T) as the type strain, with the automatic creation of B. populi subsp. populi subsp. nov. (type strain D9-5T=CFCC 11963T=KCTC 42088T).
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Lactobacillus silagincola sp. nov. and Lactobacillus pentosiphilus sp. nov., isolated from silage
Three Gram-stain positive, non-motile, non-spore-forming, catalase-negative and rod-shaped bacterial strains (IWT5T, IWT25T and IWT140), isolated from silage, were investigated by using a polyphasic taxonomic approach. Strains IWT5T and IWT25T grew at 10–37 °C and 30–37 °C, and at pH 4.0–7.5 and 4.0–7.0, respectively. The G+C contents of genomic DNA of strains IWT5T and IWT25T were 43.2 and 44.4 mol%, respectively. Strains IWT5T and IWT25T contained C16 : 0, C18 : 1 ω9c and summed feature 7 (unknown 18.846/C19 : 1 ω6c/C19 : 0cyclo ω10c) as the major fatty acids. Strain IWT5T was most closely related to the type strains of Lactobacillus mixtipabuli (99.9 % 16S rRNA gene sequence similarity) and Lactobacillus silagei (99.5 %). For IWT25T, the 16S rRNA gene sequence similarities with the closely related neighbour type strains L. mixtipabuli and L. silagei were 99.5 and 99.5 %, respectively. The 16S rRNA gene sequence similarities among the three novel isolates were 99.5–99.9 %. The average nucleotide identities of strains IWT5T and IWT25T to other neighbours of the genus Lactobacillus were less than 82 % and the genomes of IWT25T and IWT140 shared 97.3 % average nucleotide identity, demonstrating that the three strains were allocated to two different novel species of the genus Lactobacillus . Together with multilocus sequence analysis, phenotypic and chemotaxonomic characteristics, strains IWT5T (=JCM 31144T=DSM 102973T) and IWT25T (=JCM 31145T=DSM 102974T) are proposed as the type strains of novel species of the genus Lactobacillus , with the names Lactobacillus silagincola sp. nov. and Lactobacillus pentosiphilus sp. nov., respectively.
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Pathogenic, phenotypic and molecular characterisation of Xanthomonas nasturtii sp. nov. and Xanthomonas floridensis sp. nov., new species of Xanthomonas associated with watercress production in Florida
More LessWe describe two new species of the genus Xanthomonas , represented by yellow mucoid bacterial strains isolated from diseased leaves of watercress (Nasturtium officinale) produced in Florida, USA. One strain was pathogenic on watercress, but not in other species including a range of brassicas; other strains were not pathogenic in any of the tested plants. Data from Biolog carbon source utilization tests and nucleotide sequence data from 16S and gyrB loci suggested that both pathogenic and non-pathogenic strains were related to, yet distinct from, previously described Xanthomonas species. Multilocus sequence analysis and whole genome-wide comparisons of the average nucleotide identity (ANI) of genomes of two strains from watercress showed that these are distinct and share less than 95 % ANI with all other known species; the non-pathogenic strain WHRI 8848 is close to Xanthomonas cassavae (ANI of 93.72 %) whilst the pathogenic strain WHRI 8853 is close to a large clade of species that includes Xanthomonas vesicatoria (ANI ≤90.25 %). Based on these results, we propose that both strains represent new Xanthomonas species named Xanthomonas floridensis sp. nov. (type strain WHRI 8848=ATCC TSD-60=ICMP 21312=LMG 29665=NCPPB 4601) and Xanthomonas nasturtii sp. nov. (type strain WHRI 8853=ATCC TSD-61=ICMP 21313=LMG 29666=NCPPB 4600), respectively. The presence of non-pathogenic Xanthomonas strains in watercress and their interaction with pathogenic strains needs to be further investigated. Although the importance of the new pathogenic species is yet to be determined, the bacterial disease that it causes constitutes a threat to watercress production and its distribution should be monitored.
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Altererythrobacter xixiisoli sp. nov., isolated from wetland soil
More LessA Gram-stain-negative, coccoid, yellow, non-motile, aerobic bacterium, designated strain S36T, was isolated from soil of the Xixi wetland in Zhejiang province, PR China. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain S36T could represent a novel species of genus Altererythrobacter showing highest similarity to Altererythrobacter atlanticus 26DY36T (96.31 % 16S rRNA gene sequence similarity). The temperature, pH and NaCl concentration ranges for growth were 10–37 °C (optimum 32 °C), pH 5.0–10.0 (optimum pH 7.0) and 0.5–3 % (optimum 1 %, w/v), respectively. The predominant respiratory quinone of strain S36T was Q-10. The major fatty acids were C16 : 0, C17 : 1ω6c, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The G+C content of the genomic DNA was 62.7 mol%. These data all support the affiliation of strain S36T to the genus Altererythrobacter . The polar lipids profile of strain S36T comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unidentified phospholipids and two unidentified glycolipids. The results of physiological and biochemical tests allowed differentiation of strain S36T from other members of the genus Altererythrobacter . Therefore, strain S36T represents a novel species of the genus Altererythrobacter , for which the name Altererythrobacter xixiisoli sp. nov. is proposed; the type strain is S36T (=CGMCC 1.12804T=NBRC 110413T).
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Defining the taxonomic status of Streptococcus suis serotype 33: the proposal for Streptococcus ruminantium sp. nov.
To clarify the taxonomic classification of Streptococcus suis serotype 33, we performed biochemical and molecular genetic analyses using isolates (GUT-183, GUT-184, GUT-185, GUT-186, GUT-187T, GUT-188, GUT-189, GUT-190, GUT-191, GUT-192 and GUT-193) from bovine endocarditis. A comparative sequence analysis showed 99.2–100 % sequence similarity among the reference strain of S. suis serotype 33 and our isolates for the 16S rRNA gene. These similarities were higher than those between the isolate GUT-187T and S. suis and other streptococci. Comparison of sodA genes also showed high degrees of similarities among the reference strain of S. suis serotype 33 and our isolates (99.7–100 %), which were higher than those between the GUT-187T and S. suis and other streptococci. DNA–DNA relatedness among three isolates (GUT-186, GUT-187T, the reference strain of S. suis serotype 33) was over 76.7 %. In contrast, the relatedness between GUT-187T and the other streptococcal species ( S. suis , Streptococcus parasuis , Streptococcus acidominimus and Streptococcus porci ) was 8.4–24.9 %. Phylogenetic analyses showed that the isolates did not affiliate closely to any known species of the genus Streptococcus . Moreover, GUT-187T could be distinguished from S. suis and other closely related species of genus Streptococcus using biochemical tests. On the basis of the phenotypic and molecular genetic data, we propose that the isolates of S. suis serotype 33 should be classified into the genus Streptococcus , Streptococcus ruminantium sp. nov. with the type strain GUT-187T (=DSM 104980T=JCM 31869T).
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Phytophthora pseudopolonica sp. nov., a new species recovered from stream water in subtropical forests of China
More LessA new species of the genus Phytophthora was isolated from stream water in the subtropical forests of China during a survey of forest Phytophthora from 2011 to 2013. This new species is formally described here and named Phytophthora pseudopolonica sp. nov. This new homothallic species is distinct from other known Phytophthora species in morphology and produces nonpapillate and noncaducous sporangia with internal proliferation. Spherical hyphal swellings and thin-walled chlamydospores are abundant when the species is kept in sterile water. The P. pseudopolonica sp. nov. forms smooth oogonia with paragynous and sometimes amphigynous antheridia. The optimum growth temperature of the species is 30 °C in V8-juice agar with β-sitosterol, yet it barely grows at 5 °C and 35 °C. Based on sequences of the internal transcribed spacer and the combined β-tubulin and elongation factor 1α gene sequence data, isolates of the new species cluster together into a single branch and are close to Phytophthora polonicabelonging to clade 9.
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Spirosoma lacussanchae sp. nov., a phosphate-solubilizing bacterium isolated from a freshwater reservoir
More LessA phosphate-solubilizing bacterium, designated CPCC 100624T, was isolated from a freshwater reservoir in south-west China. The 16S rRNA gene sequence comparison of strain CPCC 100624T with the available sequences in the GenBank database showed that the isolate was closely related to members of the genus Spirosoma . In the phylogenetic tree based on 16S rRNA gene sequences, strain CPCC 100624T formed a stable phylogenetic subclade with Spirosoma soli MIMBbqt12T within the genus Spirosoma , which indicated that strain CPCC 100624T could be identified as a member of the genus Spirosoma . The strain grew at 10–40 °C (optimum 30 °C), at pH 6.5–8.0 (optimum pH 7.0–7.5) and in the presence of 0–5 % (w/v) NaCl (optimum 0–1 %). MK-7 was detected as the main menaquinone, with a minor amount of MK-7(H6) in its menaquinone system. Cells contained summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 1ω5c and iso-C15 : 0 as the major fatty acids. The polar lipids of strain CPCC 100624T contained phosphatidylethanolamine, one unidentified aminolipid, two aminophospholipids and three unidentified lipids. The genomic DNA G+C content was 49.3 mol%. On the basis of the above taxonomic data and differences in physiological characteristics from the closely related type strains, strain CPCC 100624T represents a novel species of the genus Spirosoma , for which the name Spirosoma lacussanchae sp. nov. is proposed. The type strain is CPCC 100624T (=NBRC 111852T=DSM 101771T).
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- Research Article
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Molecules illuminate morphology: phylogenomics confirms convergent evolution among ‘oligotrichous’ ciliates
More Less‘Oligotrichous’ ciliates have been traditionally placed in a presumed monophyletic taxon called the Oligotrichia. However, gene sequences of the small subunit rRNA gene, and several other genes, suggest that the taxon is not monophyletic: although statistical support for this is not strong, the oligotrich Halteria grandinella is associated with the hypotrich ciliates and not with other oligotrich genera, such as Strombidium and Strombidinopsis. This has convinced some taxonomists to emphasize that morphological features strongly support the monophyly of the oligotrichs. To further test this hypothesis of monophyly, we have undertaken a phylogenomic analysis using the transcriptome of H. grandinella cells amplified by a single-cell technique. One hundred and twenty-six of 159 single-gene trees placed H. grandinella as sister to hypotrich species, and phylogenomic analyses based on a subset of 124 genes robustly rejected the monophyly of the Oligotrichia and placed the genus Halteria as sister to the hypotrich genera Stylonychia and Oxytricha. We use these phylogenomic analyses to assess the convergent nature of morphological features of oligotrichous ciliates. A particularly ‘strong’ morphological feature supporting monophyly of the oligotrichs is enantiotropic cell division, which our results suggest is nevertheless a convergent feature, arising through the need for dividing ciliates to undertake rotokinesis to complete cell division.
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- Taxonomic Note
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Proposal to modify Rule 10a and to delete Recommendation 10a(3) from the International Code of Nomenclature of Prokaryotes
More LessPrinciple 2 of the Prokaryotic Code, as modified by the ICSP in 1999, reads: ‘The nomenclature of prokaryotes is not independent of botanical and zoological nomenclature. When naming new taxa in the rank of genus or higher, due consideration is to be given to avoiding names which are regulated by the International Code of Zoological Nomenclature and the International Code of Nomenclature for algae, fungi and plants’. But in the current version of the Prokaryotic Code no Rule implements this version of Principle 2. I therefore propose adding the following sentence to Rule 10a: ‘As from January 2001, newly proposed generic names must not be later homonyms of names in use in botany or zoology’. Recommendation 10a(3) of the Code states: ‘Avoid introducing into bacteriology as generic names such names as are in use in botany or zoology, in particular well-known names’. This Recommendation contravenes the current version of Principle 2 and the proposed new version of Rule 10a. Therefore I propose to delete Recommendation 10a(3) from the Prokaryotic Code.
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- ICSP Matters
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Proposal to designate Methylothermus subterraneus Hirayama et al. 2011 as the type species of the genus Methylothermus. Request for an Opinion
More LessMethylothermus thermalis , the designated type species of the genus Methylothermus , is not available from culture collections and its nomenclatural type is a patent strain. According to Rule 20a of the International Code of Nomenclature of Prokaryotes, only species whose names are legitimate may serve as types of genera. Therefore, the name Methylothermus and the names of the species Methylothermus thermalis and Methylothermus subterraneus are not validly published and are illegitimate. We therefore submit a Request for an Opinion to the Judicial Commission of the ICSP to consider the later-named Methylothermus subterraneus as the new type species of the genus Methylothermus based on Rule 20e(2).
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Proposal to correct the generic name Flaviaesturariibacter Kang, Chun, Seo, Kim and Jahng 2015, 2212 to Flavaestuariibacter. Request for an Opinion
More LessThe generic name Flaviaesturariibacter Kang, Chun, Seo, Kim and Jahng 2015, 2212 is malformed: being derived from the Latin noun aestuarium, …aestuarii… instead of …aesturarii… is required. Moreover, according to Appendix 9 of the Prokaryotic Code, a connecting vowel must be dropped when the following word element starts with a vowel. I therefore propose to correct the name Flaviaesturariibacter to Flavaestuariibacter.
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Proposal to designate the order Actinomycetales Buchanan 1917, 162 (Approved Lists 1980) as the nomenclatural type of the class Actinobacteria. Request for an Opinion
More LessThe name of the class Actinobacteria is illegitimate according to Rules 15, 22 and 27(3) because it was proposed without the designation of a nomenclatural type. I therefore propose to designate the order Actinomycetales Buchanan 1917, 162 (Approved Lists 1980) as its nomenclatural type, based on Rule 22 of the International Code of Nomenclature of Prokaryotes.
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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)