bluuebunny/crossref_metadata_2025 huggingface dataset:
Proposal to elevate the genetic variant MAC-A, included in the Mycobacterium avium complex, to species rank as Mycobacterium chimaera sp. nov.
Authors: Tortoli Enrico , Rindi Laura , Garcia Maria J. , Chiaradonna Patrizia , Dei Rosanna , Garzelli Carlo , Kroppenstedt Reiner M. , Lari Nicoletta , Mattei Romano , Mariottini Alessandro , Mazzarelli Gianna , Murcia Martha I. , Nanetti Anna , Piccoli Paola , Scarparo Claudio
Published: August 2004

The possibility that the strains included within the Mycobacterium avium complex (MAC), but not belonging either to M. avium or to Mycobacterium intracellulare, may be members of undescribed taxa, has already been questioned by several taxonomists. A very homogeneous cluster of 12 strains characterized by identical nucleotide sequences both in the 16S rDNA and in the 16S–23S internal transcribed spacer was investigated. Similar strains, previously reported in the literature, had been assigned either to the species M. intracellulare on the basis of the 16S rDNA similarity or to the group of MAC intermediates. However, several phenotypical and epidemiological characteristics seem to distinguish these strains from all other MAC organisms. The unique mycolic acid pattern obtained by HPLC is striking as it is characterized by two clusters of peaks, instead of the three presented by all other MAC organisms. All of the strains have been isolated from humans and all but one came from the respiratory tract of elderly people. The clinical significance of these strains, ascertained for seven patients, seems to suggest an unusually high virulence. The characteristics of all the strains reported in the literature, genotypically identical to the ones described here, seem to confirm our data, without reports of isolations from animals or the environment or, among humans, from AIDS patients. Therefore, an elevation of the MAC variant was proposed and characterized here, with the name Mycobacterium chimaera sp. nov.; this increases the number of species included in the M. avium complex. The type strain is FI-01069T (=CIP 107892T=DSM 44623T).
Marinibacillus campisalis sp. nov., a moderate halophile isolated from a marine solar saltern in Korea, with emended description of the genus Marinibacillus
Authors: Yoon Jung-Hoon , Kim In-Gi , Schumann Peter , Oh Tae-Kwang , Park Yong-Ha
Published: August 2004

A Gram-positive, motile, round to ellipsoidal, endospore-forming, rod-shaped bacterial strain, SF-57T, was isolated from a marine solar saltern in Korea. This organism grew between 4 and 39 °C, with optimum growth at 30 °C. Strain SF-57T grew in the presence of 0·5–15·0 % NaCl, with optimum growth at 2–3 % NaCl. The peptidoglycan type of strain SF-57T was A1α linked directly through l-Lys. In strain SF-57T, menaquinone-7 (MK-7) was the predominant isoprenoid quinone and anteiso-C15 : 0 was the major fatty acid. The DNA G+C content was 41·8 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SF-57T formed a coherent cluster with Marinibacillus marinus, with a bootstrap resampling value of 100 %. The level of 16S rRNA gene sequence similarity between strain SF-57T and M. marinus DSM 1297T was 98·9 %. The mean DNA–DNA relatedness level between strain SF-57T and the type strain of M. marinus was 20·6 %. Based on phenotypic properties, phylogenetic analyses and genomic data, strain SF-57T merits placement in the genus Marinibacillus as a representative of a novel species, for which the name Marinibacillus campisalis sp. nov. is proposed. The type strain is SF-57T (=KCCM 41644T=JCM 11810T).
Swaminathania salitolerans gen. nov., sp. nov., a salt-tolerant, nitrogen-fixing and phosphate-solubilizing bacterium from wild rice (Porteresia coarctata Tateoka)
Authors: Loganathan P. , Nair Sudha
Published: August 2004

A novel species,Swaminathania salitoleransgen. nov., sp. nov., was isolated from the rhizosphere, roots and stems of salt-tolerant, mangrove-associated wild rice (Porteresia coarctataTateoka) using nitrogen-free, semi-solid LGI medium at pH 5·5. Strains were Gram-negative, rod-shaped and motile with peritrichous flagella. The strains grew well in the presence of 0·35 % acetic acid, 3 % NaCl and 1 % KNO3, and produced acid froml-arabinose,d-glucose, glycerol, ethanol,d-mannose,d-galactose and sorbitol. They oxidized ethanol and grew well on mannitol and glutamate agar. The fatty acids 18 : 1ω7c/ω9t/ω12tand 19 : 0cycloω8cconstituted 30·41 and 11·80 % total fatty acids, respectively, whereas 13 : 1 AT 12–13 was found at 0·53 %. DNA G+C content was 57·6–59·9 mol% and the major quinone was Q-10. Phylogenetic analysis based on 16S rRNA gene sequences showed that these strains were related to the generaAcidomonas,Asaia,Acetobacter,Gluconacetobacter,GluconobacterandKozakiain theAcetobacteraceae. Isolates were able to fix nitrogen and solubilized phosphate in the presence of NaCl. Based on overall analysis of the tests and comparison with the characteristics of members of theAcetobacteraceae, a novel genus and species is proposed for these isolates,Swaminathania salitoleransgen. nov., sp. nov. The type strain is PA51T(=LMG 21291T=MTCC 3852T).
‘Candidatus Phytoplasma cynodontis’, the phytoplasma associated with Bermuda grass white leaf disease
Authors: Marcone Carmine , Schneider Bernd , Seemüller Erich
Published: August 2004

Bermuda grass white leaf (BGWL) is a destructive, phytoplasmal disease of Bermuda grass (Cynodon dactylon). The causal pathogen, the BGWL agent, differs from other phytoplasmas that cluster in the same major branch of the phytoplasma phylogenetic clade in <2·5 % of 16S rDNA nucleotide positions, the threshold for assigning species rank to phytoplasmas under the provisional status ‘Candidatus’. Thus, the objective of this work was to examine homogeneity of BGWL isolates and to determine whether there are, in addition to 16S rDNA, other markers that support delineation of the BGWL agent at the putative species level. Phylogenetic analyses revealed that the 16S rDNA sequences of BGWL strains were identical or nearly identical. Clear differences that support separation of the BGWL agent from related phytoplasmas were observed within the 16S–23S rDNA spacer sequence, by serological comparisons, in vector transmission and in host-range specificity. From these results, it can be concluded that the BGWL phytoplasma is a discrete taxon at the putative species level, for which the name ‘Candidatus Phytoplasma cynodontis' is proposed. Strain BGWL-C1 was selected as the reference strain. Phytoplasmas that are associated with brachiaria white leaf, carpet grass white leaf and diseases of date palms showed 16S rDNA and/or 16S–23S rDNA spacer sequences that were identical or nearly identical to those of the BGWL phytoplasmas. However, the data available do not seem to be sufficient for a proper taxonomic assignment of these phytoplasmas.
‘Candidatus Phytoplasma asteris’, a novel phytoplasma taxon associated with aster yellows and related diseases
Authors: Lee I.-M. , Gundersen-Rindal D. E. , Davis R. E. , Bottner K. D. , Marcone C. , Seemüller E.
Published: August 2004

Aster yellows (AY) group (16SrI) phytoplasmas are associated with over 100 economically important diseases worldwide and represent the most diverse and widespread phytoplasma group. Strains that belong to the AY group form a phylogenetically discrete subclade within the phytoplasma clade and are related most closely to the stolbur phytoplasma subclade, based on analysis of 16S rRNA gene sequences. AY subclade strains are related more closely to their culturable relatives, Acholeplasma spp., than any other phytoplasmas known. Within the AY subclade, six distinct phylogenetic lineages were revealed. Congruent phylogenies obtained by analyses of tuf gene and ribosomal protein (rp) operon gene sequences further resolved the diversity among AY group phytoplasmas. Distinct phylogenetic lineages were identified by RFLP analysis of 16S rRNA, tuf or rp gene sequences. Ten subgroups were differentiated, based on analysis of rp gene sequences. It is proposed that AY group phytoplasmas represent at least one novel taxon. Strain OAY, which is a member of subgroups 16SrI-B, rpI-B and tufI-B and is associated with evening primrose (Oenothera hookeri) virescence in Michigan, USA, was selected as the reference strain for the novel taxon ‘Candidatus Phytoplasma asteris’. A comprehensive database of diverse AY phytoplasma strains and their geographical distribution is presented.
Maribacter gen. nov., a new member of the family Flavobacteriaceae, isolated from marine habitats, containing the species Maribacter sedimenticola sp. nov., Maribacter aquivivus sp. nov., Maribacter orientalis sp. nov. and Maribacter ulvicola sp. nov.
Authors: Nedashkovskaya Olga I. , Kim Seung Bum , Han Suk Kyun , Lysenko Anatoly M. , Rohde Manfred , Rhee Moon-Soo , Frolova Galina M. , Falsen Enevold , Mikhailov Valery V. , Bae Kyung Sook
Published: August 2004

Six novel gliding, heterotrophic, Gram-negative, yellow-pigmented, aerobic, oxidase- and catalase-positive bacteria were isolated from the green algaUlva fenestrata, sea water and a bottom sediment sample collected in the Gulf of Peter the Great, Sea of Japan. 16S rRNA gene sequence analysis revealed that the strains studied were members of the familyFlavobacteriaceae. On the basis of their phenotypic, chemotaxonomic, genotypic and phylogenetic characteristics, the novel bacteria have been assigned to the new genusMaribactergen. nov., asMaribacter sedimenticolasp. nov.,Maribacter orientalissp. nov.,Maribacter aquivivussp. nov. andMaribacter ulvicolasp. nov., with the type strains KMM 3903T(=KCTC 12966T=CCUG 47098T), KMM 3947T(=KCTC 12967T=CCUG 48008T), KMM 3949T(=KCTC 12968T=CCUG 48009T) and KMM 3951T(=KCTC 12969T=DSM 15366T), respectively.
Alteromonas stellipolaris sp. nov., a novel, budding, prosthecate bacterium from Antarctic seas, and emended description of the genus Alteromonas
Authors: Van Trappen Stefanie , Tan Tjhing-Lok , Yang Jifang , Mergaert Joris , Swings Jean
Published: August 2004

Seven novel, cold-adapted, strictly aerobic, facultatively oligotrophic strains, isolated from Antarctic sea water, were investigated by using a polyphasic taxonomic approach. The isolates were Gram-negative, chemoheterotrophic, motile, rod-shaped cells that were psychrotolerant and moderately halophilic. Buds were produced on mother and daughter cells and on prosthecae. Prostheca formation was peritrichous and prosthecae could be branched. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains belong to the γ-Proteobacteria and are related to the genus Alteromonas, with 98·3 % sequence similarity to Alteromonas macleodii and 98·0 % to Alteromonas marina, their nearest phylogenetic neighbours. Whole-cell fatty acid profiles of the isolates were very similar and included C16 : 0, C16 : 1
ω7c, C17 : 1
ω8c and C18 : 1
ω8c as the major fatty acid components. These results support the affiliation of these isolates to the genus Alteromonas. DNA–DNA hybridization results and differences in phenotypic characteristics show that the strains represent a novel species with a DNA G+C content of 43–45 mol%. The name Alteromonas stellipolaris sp. nov. is proposed for this novel species; the type strain is ANT 69aT (=LMG 21861T=DSM 15691T). An emended description of the genus Alteromonas is given.
Methanotorris formicicus sp. nov., a novel extremely thermophilic, methane-producing archaeon isolated from a black smoker chimney in the Central Indian Ridge
Authors: Takai Ken , Nealson Ken H. , Horikoshi Koki
Published: August 2004

A novel extremely thermophilic, methane-producing archaeon was isolated from a black smoker chimney at the Kairei field in the Central Indian Ridge. Cells of this isolate were irregular cocci with several flagella; motility was not observed. Growth was observed between 55 and 83 °C (optimum of 75 °C; 30 min doubling time) and between pH 6·0 and 8·5 (optimum of pH 6·7). The isolate was a strictly anaerobic, methanogenic autotroph capable of using hydrogen and carbon dioxide as sole energy and carbon sources. Formate was utilized as an alternative energy source. The G+C content of the genomic DNA was 33·3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate was most closely related toMethanotorris igneusstrain Kol 5T. The isolate, however, could be genetically differentiated from this species by DNA–DNA hybridization analysis and on the basis of its physiological properties. The nameMethanotorris formicicussp. nov. is proposed for this isolate; the type strain is Mc-S-70T(=JCM 11930T=ATCC BAA-687T).
Reclassification of Amycolatopsis mediterranei DSM 46095 as Amycolatopsis rifamycinica sp. nov.
Authors: Bala Shashi , Khanna Richie , Dadhwal M. , Prabagaran S. R. , Shivaji S. , Cullum John , Lal Rup
Published: August 2004

Previous experiments have suggested that the rifamycin-producing strain DSM 46095 might not belong to Amycolatopsis mediterranei. Analysis of its 16S rRNA gene sequence and construction of a phylogenetic tree showed most similarity to Amycolatopsis kentuckyensis NRRL B-24129T, Amycolatopsis lexingtonensis NRRL B-24129T and Amycolatopsis pretoriensis NRRL B-24133T, but the strain was probably not a member of any of these species. Results from DNA–DNA hybridization experiments and comparison of DNA profiling patterns using pulsed-field gel electrophoresis also supported the assignment of strain DSM 46095 to a novel species. Analyses of phospholipids, fatty acid methyl esters and physiological characteristics also showed that the differences between different isolates of A. mediterranei and A. mediterranei DSM 46095 were as large as those between Amycolatopsis species. Strain DSM 46095 represents a novel species of the genus Amycolatopsis for which the name Amycolatopsis rifamycinica sp. nov. is proposed, with the type strain NT 19T (=DSM 46095T=ATCC 27643T).
Tsukamurella pseudospumae sp. nov., a novel actinomycete isolated from activated sludge foam
Authors: Nam Sun-Woo , Kim Wonyong , Chun Jongsik , Goodfellow Michael
Published: August 2004

The taxonomic position of two Tsukamurella strains isolated from activated sludge foam was clarified. The organisms, isolates JC85 and N1176T, were found to have chemical and morphological properties typical of members of the genus Tsukamurella. DNA–DNA relatedness studies showed that the strains formed a distinct genomic species that was most closely related to Tsukamurella spumae. The two isolates also share a range of phenotypic properties that distinguishes them from representatives of all species of Tsukamurella with validly published names. It is evident from the data that the two organisms should be classified as a novel Tsukamurella species, Tsukamurella pseudospumae sp. nov. The type strain is N1176T (=DSM 44118T=NCIMB 13963T).
Algibacter lectus gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from green algae
Authors: Nedashkovskaya Olga I. , Kim Seung Bum , Han Suk Kyun , Rhee Moon-Soo , Lysenko Anatoly M. , Rohde Manfred , Zhukova Natalia V. , Frolova Galina M. , Mikhailov Valery V. , Bae Kyung Sook
Published: August 2004

Three strains of the marine, gliding, pigmented, facultatively anaerobic, heterotrophic, Gram-negative bacteria were isolated from the green algaeAcrosiphonia sonderi(Kütz) Kornm andUlva fenestrataRuprecht inhabiting the Sea of Japan. 16S rDNA sequence analysis indicated that the strains were members of the familyFlavobacteriaceae, in which they occupied separate lineages. The predominant cellular fatty acids were i15 : 0, a15 : 0, i15 : 1, 15 : 0, 15 : 1ω6c, i15 : 0 3-OH and i17 : 0 3-OH. The DNA base compositions were 31–33 mol% G+C. Based on the phenotypic, genotypic, chemotaxonomic and phylogenetic analyses, the novel bacteria should be placed in a novel taxon asAlgibacter lectusgen. nov., sp. nov. with type strain KMM 3902T(=KCTC 12103T=DSM 15365T).
Burkholderia unamae sp. nov., an N2-fixing rhizospheric and endophytic species
Authors: Caballero-Mellado Jesús , Martínez-Aguilar Lourdes , Paredes-Valdez Guadalupe , Santos Paulina Estrada-de los
Published: August 2004

It was shown recently that the genus Burkholderia is rich in N2-fixing bacteria that are associated with plants. A group of these diazotrophic isolates with identical or very similar 16S rDNA restriction patterns [designated amplified rDNA restriction analysis (ARDRA) genotypes 13, 14 and 15] was selected and a polyphasic taxonomic study was performed, which included new isolates that were recovered from rhizospheres, rhizoplanes or internal tissues of maize, sugarcane and coffee plants. Morphological, physiological and biochemical features, as well as multi-locus enzyme electrophoresis profiles and whole-cell protein patterns, of 20 strains were analysed. In addition, analysis of cellular fatty acid profiles, 16S rDNA sequence analysis and DNA–DNA reassociation experiments were performed with representative strains. The taxonomic data indicated that the strains analysed belong to a novel diazotrophic Burkholderia species, for which the name Burkholderia unamae sp. nov. is proposed. Strain MTl-641T (=ATCC BAA-744T=CIP 107921T), isolated from the rhizosphere of maize, was designated as the type strain. B. unamae was found as an endophyte of plants grown in regions with climates ranging from semi-hot subhumid to hot humid, but not from plants grown in regions with semi-hot or hot dry climates. Moreover, B. unamae was isolated from rhizospheres and plants growing in soils with pH values in the range 4·5–7·1, but not from soils with pH values higher than 7·5.
Paenibacillus massiliensis sp. nov., Paenibacillus sanguinis sp. nov. and Paenibacillus timonensis sp. nov., isolated from blood cultures
Authors: Roux Véronique , Raoult Didier
Published: August 2004

Gram-positive, spore-forming rods were isolated from blood cultures of three different patients. Based on phylogenetic analyses, these strains were placed within thePaenibacilluscluster and specific phenotypic characteristics for each strain were described. Levels of 16S rRNA gene sequence similarity between existingPaenibacillusspecies and the three novel strains 2301065T, 2301032Tand 2301083Twere 87·6–94·4, 88·5–95·4 and 87·5–96·0 %, respectively, and anteiso-branched C15 : 0was the major fatty acid. On the basis of phenotypic data and phylogenetic inference, it is proposed that these strains should be designatedPaenibacillus massiliensissp. nov.,Paenibacillus sanguinissp. nov. andPaenibacillus timonensissp. nov. The type strains are respectively strain 2301065T(=CIP 107939T=CCUG 48215T), strain 2301083T(=CIP 107938T=CCUG 48214T) and strain 2301032T(=CIP 108005T=CCUG 48216T).
Paenibacillus cineris sp. nov. and Paenibacillus cookii sp. nov., from Antarctic volcanic soils and a gelatin-processing plant
Authors: Logan Niall A. , De Clerck Elke , Lebbe Liesbeth , Verhelst An , Goris Johan , Forsyth Gillian , Rodríguez-Díaz Marina , Heyndrickx Marc , De Vos Paul
Published: August 2004

Seven strains of aerobic, endospore-forming bacteria were found in soil taken from an active fumarole on Lucifer Hill, Candlemas Island, South Sandwich archipelago, Antarctica, and four strains were from soil of an inactive fumarole at the foot of the hill. Amplified rDNA restriction analysis, 16S rDNA sequence comparisons, SDS-PAGE and routine phenotypic tests support the proposal of two novel species of Paenibacillus, Paenibacillus cineris sp. nov. and Paenibacillus cookii sp. nov., the type strains of which are LMG 18439T (=CIP 108109T) and LMG 18419T (=CIP 108110T), respectively. A further strain, isolated from a gelatin-production process, showed more than 99 % 16S rDNA sequence similarity to the proposed P. cookii type strain and, although the gelatin isolate was atypical when compared with the fumarole isolates by repeated element primed-PCR, SDS-PAGE and phenotypic analyses, it was shown by DNA–DNA reassociation studies to belong to the same species. Strains of P. cookii produce spreading growth with motile microcolonies. Both species produce swollen sporangia that are typical for the genus, they both show 97·6 % 16S rDNA sequence similarity to Paenibacillus azoreducens, they have 51·5–51·6 mol% G+C in their DNA and their major fatty acid is anteiso-C15 : 0; however, fatty acids C16 : 0 and anteiso-C17 : 0 represent, respectively, 18 and 10 % of the total in P. cineris, but 11 and 20 % in P. cookii.
Bradyrhizobium betae sp. nov., isolated from roots of Beta vulgaris affected by tumour-like deformations
Authors: Rivas Raúl , Willems Anne , Palomo José Luis , García-Benavides Pablo , Mateos Pedro F. , Martínez-Molina Eustoquio , Gillis Monique , Velázquez Encarna
Published: August 2004

Some varieties of sugar beet,Beta vulgaris, cultivated in northern Spain have large deformations that resemble the tumours produced byAgrobacteriumspecies. In an attempt to isolate the agent responsible for these deformations, several endophytic slow-growing bacterial strains were isolated, the macroscopic morphology of which resembled that ofBradyrhizobiumspecies. These strains were not able to produce tumours inNicotiana tabacumplants and, based on phylogenetic analysis of their 16S rRNA, they are closely related to the genusBradyrhizobium. Phenotypic and molecular characteristics of these strains revealed that they represent a species different from allBradyrhizobiumspecies previously described. Sequence analysis of the 16S–23S rDNA intergenic spacer region indicated that these novel strains form a homogeneous group, related toBradyrhizobium japonicum,Bradyrhizobium liaoningenseandBradyrhizobium yuanmingense. DNA–DNA hybridization confirmed that these strains represent a novel species of the genusBradyrhizobium, for which the nameBradyrhizobium betaesp. nov. is proposed. The type strain is PL7HG1T(=LMG 21987T=CECT 5829T).
Microbulbifer maritimus sp. nov., isolated from an intertidal sediment from the Yellow Sea, Korea
Authors: Yoon Jung-Hoon , Kim In-Gi , Oh Tae-Kwang , Park Yong-Ha
Published: August 2004

A Gram-negative, rod-shaped, non-spore-forming, slightly halophilic bacterium (strain TF-17T) was isolated from an intertidal sediment from the Yellow Sea, Korea. Pigment of strain TF-17T was similar to that of Microbulbifer
elongatus, but different from those of Microbulbifer
hydrolyticus and Microbulbifer
salipaludis. Strain TF-17T was distinguishable from M. elongatus by some phenotypic properties, including motility, optimal growth temperature and others. Phylogenetic analysis based on 16S rDNA sequences showed that strain TF-17T clustered with the type strains of the three Microbulbifer species with validly published names. Strain TF-17T exhibited 16S rDNA sequence similarity levels of 95·1–95·7 % to the type strains of the three Microbulbifer species. The predominant respiratory lipoquinone found in strain TF-17T was ubiquinone-8. The major fatty acid was iso-C15 : 0 and significant amounts of iso-C11 : 0 3-OH and iso-C17 : 1
ω9c were also present. The DNA G+C content of strain TF-17T was 59·9 mol%. Levels of DNA–DNA relatedness between strain TF-17T and the type strains of the three Microbulbifer species were in the range 10·0–13·0 %. On the basis of phenotypic and phylogenetic data and genotypic distinctiveness, strain TF-17T (=KCCM 41774T=JCM 12187T) is proposed as the type strain of a novel species of the genus Microbulbifer, Microbulbifer maritimus sp. nov.
Recommended standards for the description of new species of anoxygenic phototrophic bacteria
Authors: Imhoff Johannes F. , Caumette Pierre
Published: August 2004

Recommended standards for the description of new species of the anoxygenic phototrophic bacteria are proposed in accordance with Recommendation 30b of the International Code of Nomenclature of Bacteria. These standards include information on the natural habitat, ecology and phenotypic properties including morphology, physiology and pigments and on genetic information and nucleic acid data. The recommended standards were supported by the Subcommittee on the taxonomy of phototrophic bacteria of the International Committee on Systematics of Prokaryotes. They are considered as guidelines for authors to prepare descriptions of new species.
Taxonomy of Australian clinical isolates of the genus Photorhabdus and proposal of Photorhabdus asymbiotica subsp. asymbiotica subsp. nov. and P. asymbiotica subsp. australis subsp. nov.
Authors: Akhurst R. J. , Boemare N. E. , Janssen P. H. , Peel M. M. , Alfredson D. A. , Beard C. E.
Published: August 2004

The relationship of Photorhabdus isolates that were cultured from human clinical specimens in Australia to Photorhabdus asymbiotica isolates from human clinical specimens in the USA and to species of the genus Photorhabdus that are associated symbiotically with entomopathogenic nematodes was evaluated. A polyphasic approach that involved DNA–DNA hybridization, phylogenetic analyses of 16S rRNA and gyrB gene sequences and phenotypic characterization was adopted. These investigations showed that gyrB gene sequence data correlated well with DNA–DNA hybridization and phenotypic data, but that 16S rRNA gene sequence data were not suitable for defining species within the genus Photorhabdus. Australian clinical isolates proved to be related most closely to clinical isolates from the USA, but the two groups were distinct. A novel subspecies, Photorhabdus asymbiotica subsp. australis subsp. nov. (type strain, 9802892T=CIP 108025T=ACM 5210T), is proposed, with the concomitant creation of Photorhabdus asymbiotica subsp. asymbiotica subsp. nov. Analysis of gyrB sequences, coupled with previously published data on DNA–DNA hybridization and PCR-RFLP analysis of the 16S rRNA gene, indicated that there are more than the three subspecies of Photorhabdus luminescens that have been described and confirmed the validity of the previously proposed subdivision of Photorhabdus temperata. Although a non-luminescent, symbiotic isolate clustered consistently with P. asymbiotica in gyrB phylogenetic analyses, DNA–DNA hybridization indicated that this isolate does not belong to the species P. asymbiotica and that there is a clear distinction between symbiotic and clinical species of Photorhabdus.
Loktanella salsilacus gen. nov., sp. nov., Loktanella fryxellensis sp. nov. and Loktanella vestfoldensis sp. nov., new members of the Rhodobacter group, isolated from microbial mats in Antarctic lakes
Authors: Van Trappen Stefanie , Mergaert Joris , Swings Jean
Published: August 2004

A taxonomic study was performed on 26 strains isolated from microbial mats in Antarctic lakes of the Vestfold Hills and the McMurdo Dry Valleys. Phylogenetic analysis based on 16S rRNA gene sequences placed these strains within the Rhodobacter group of the α-subclass of the Proteobacteria. Sequence similarity values for the strains with their nearest phylogenetic neighbours (Jannaschia, Octadecabacter and Ketogulonicigenium) ranged between 94·0 and 95·8 %. DNA–DNA hybridizations and comparison of repetitive extragenic palindromic DNA–PCR (rep-PCR) fingerprinting patterns revealed that these strains are members of three distinct species. The isolates are Gram-negative, chemoheterotrophic, non-motile rods and their DNA G+C contents range from 59·4 to 66·4 mol%. Whole-cell fatty acid profiles are similar and the primary fatty acid in all the strains is 18 : 1 ω7c (74·1–87·7 % of total). Genotypic results together with phenotypic characteristics allowed the differentiation of these species from related recognized species of the α-Proteobacteria and the strains are assigned to a new genus, Loktanella gen. nov., with three novel species: Loktanella salsilacus sp. nov. (type species), consisting of ten strains with LMG 21507T (=CIP 108322T) as type strain; Loktanella fryxellensis sp. nov., consisting of 12 strains with LMG 22007T (=CIP 108323T) as type strain; and Loktanella vestfoldensis sp. nov., consisting of four strains with LMG 22003T (=CIP 108321T) as type strain.
Oceanicola granulosus gen. nov., sp. nov. and Oceanicola batsensis sp. nov., poly-β-hydroxybutyrate-producing marine bacteria in the order ‘Rhodobacterales’
Authors: Cho Jang-Cheon , Giovannoni Stephen J.
Published: August 2004

Three Gram-negative, chemoheterotrophic, non-motile, rod-shaped bacterial strains that accumulate poly-β-hydroxybutyrate granules were isolated from the Bermuda Atlantic Time-series Study site by high-throughput culturing methods and characterized by polyphasic approaches. DNA–DNA hybridization, DNA G+C content and phylogenetic analyses based on 16S rRNA gene sequences divided the three isolates into two distinct genospecies that were clearly differentiated by fatty acid profiles, carbon source utilization patterns, antibiotic susceptibility and biochemical characteristics. The strains utilized a wide range of substrates, including pentoses, hexoses, oligosaccharides, sugar alcohols, organic acids and amino acids. DNA G+C contents were 71·5, 70·9 and 67·3 mol% for strains HTCC2516T, HTCC2523 and HTCC2597T, respectively. The most dominant fatty acid was 18 : 1ω7c in strains HTCC2516T and HTCC2523, and cyclo 19 : 0 in strain HTCC2597T. The type strains HTCC2516T and HTCC2597T were clearly differentiated by the presence or absence of 12 : 0, 12 : 1ω11c, 14 : 0, 15 : 0 and methyl 18 : 1. Phylogenetic analyses indicated that the strains formed a distinct monophyletic lineage within the Roseobacter clade in the order ‘Rhodobacterales’ of the Alphaproteobacteria, and which did not associate with any of the described genera. Genotypic and phenotypic differences of the isolates from the previously described genera support the description of Oceanicola granulosus gen. nov., sp. nov. with the type strain HTCC2516T (=ATCC BAA-861T=DSM 15982T=KCTC 12143T) and of Oceanicola batsensis sp. nov. with the type strain HTCC2597T (=ATCC BAA-863T=DSM 15984T=KCTC 12145T).
Curvibasidium cygneicollum gen. nov., sp. nov. and Curvibasidium pallidicorallinum sp. nov., novel taxa in the Microbotryomycetidae (Urediniomycetes), and their relationship with Rhodotorula fujisanensis and Rhodotorula nothofagi
Authors: Sampaio José Paulo , Golubev Wladyslav I. , Fell Jack W. , Gadanho Mário , Golubev Nikita W.
Published: August 2004

Strains of Rhodotorula fujisanensis (Basidiomycota, Urediniomycetes, Microbotryomycetidae), including the type strain, are sexually compatible and produce clamped mycelium with teliospores. However, as teliospore germination had not been documented, the complete sexual cycle was not known. During the course of this work, the basidial stage of R. fujisanensis was characterized. In addition, mating studies employing isolates that were identified preliminarily as Rhodotorula nothofagi, a species that is related closely to R. fujisanensis, yielded mycelium with teliospores, which formed basidia and basidiospores. The new data were evaluated by using several criteria, including the available molecular phylogenetic framework for the Microbotryomycetidae. Curvibasidium gen. nov. is described here, to accommodate two teleomorphs: Curvibasidium cygneicollum sp. nov. (CBS 4551T), which is described as the sexual stage of R. fujisanensis, and Curvibasidium pallidicorallinum sp. nov. (CBS 9091T), which is related closely to R. nothofagi, but does not represent its sexual stage.
Phylogeny of the family Pasteurellaceae based on rpoB sequences
Authors: Korczak Bożena , Christensen Henrik , Emler Stefan , Frey Joachim , Kuhnert Peter
Published: August 2004

Sequences of the gene encoding theβ-subunit of the RNA polymerase (rpoB) were used to delineate the phylogeny of the familyPasteurellaceae. A total of 72 strains, including the type strains of the major described species as well as selected field isolates, were included in the study. Selection of universalrpoB-derived primers for the family allowed straightforward amplification and sequencing of a 560 bp fragment of therpoBgene. In parallel, 16S rDNA was sequenced from all strains. The phylogenetic tree obtained with therpoBsequences reflected the major branches of the tree obtained with the 16S rDNA, especially at the genus level. Only a few discrepancies between the trees were observed. In certain cases therpoBphylogeny was in better agreement with DNA–DNA hybridization studies than the phylogeny derived from 16S rDNA. TherpoBgene is strongly conserved within the various species of the family ofPasteurellaceae. Hence,rpoBgene sequence analysis in conjunction with 16S rDNA sequencing is a valuable tool for phylogenetic studies of thePasteurellaceaeand may also prove useful for reorganizing the current taxonomy of this bacterial family.
Preference of DNA Methyltransferases for CpG Islands in Mouse Embryonic Stem Cells
Authors: Hattori Naka , Abe Tetsuya , Hattori Naoko , Suzuki Masako , Matsuyama Tomoki , Yoshida Shigeo , Li En , Shiota Kunio
Published: August 2004

Many CpG islands have tissue-dependent and differentially methylated regions (T-DMRs) in normal cells and tissues. To elucidate how DNA methyltransferases (Dnmts) participate in methylation of the genomic components, we investigated the genome-wide DNA methylation pattern of the T-DMRs with Dnmt1-, Dnmt3a-, and/or Dnmt3b-deficient ES cells by restriction landmark genomic scanning (RLGS). Approximately 1300 spots were detected in wild-type ES cells. In Dnmt1-/- ES cells, additional 236 spots emerged, indicating that the corresponding loci are methylated by Dnmt1 in wild-type ES cells. Intriguingly, in Dnmt3a-/-Dnmt3b-/- ES cells, the same 236 spots also emerged, and no additional spots appeared differentially. Therefore, Dnmt1 and Dnmt3a/3b share targets in CpG islands. Cloning and virtual image RLGS revealed that 81% of the RLGS spots were associated with genes, and 62% of the loci were in CpG islands. By contrast to the previous reports that demethylation at repeated sequences was severe in Dnmt1-/- cells compared with Dnmt3a-/-Dnmt3b-/- cells, a complete loss of methylation was observed at RLGS loci in Dnmt3a-/-Dnmt3b-/- cells, whereas methylation levels only decreased to 16% to 48% in the Dnmt1-/- cells. We concluded that there are CpG islands with T-DMR as targets shared by Dnmt1 and Dnmt3a/3b and that each Dnmt has target preferences depending on the genomic components.
Structure of nanometre‐sized Xe particles embedded in Al crystals
Authors: SONG M. , MITSUISHI K. , FURUYA K. , ALLEN C. W. , BIRTCHER R. C. , DONNELLY S. E.
Published: August 2004

The structure and lattice parameters of Xe particles about 1 nm to about 6 nm in size embedded in Al were investigated with off‐Bragg condition high‐resolution transmission electron microscopy. An Xe particle about 1 nm in size had different structural properties from those 2–6 nm in sizes. Some 1‐nm Xe particles had an face‐centred cubic (f.c.c.) structure with the same orientation as the Al matrix, whereas others of the same size had a non‐f.c.c. structure. The lattice parameters of a 1‐nm f.c.c. Xe particle were about 20% smaller than the average value obtained from electron diffraction, i.e. the particle was compressed by about 80%. The lattice parameters of Xe crystals about 2 nm to about 6 nm in size were almost the same as those obtained from diffraction results. One of the reasons for the extra compression seen with a 1‐nm Xe particle is the increase in pressure inside an Xe particle with decreasing particle size.
Near‐field imaging of organic nanofibres
Authors: VOLKOV V. S. , BOZHEVOLNYI S. I. , BORDO V. G. , RUBAHN H.‐G.
Published: August 2004

The optical near‐field of orientated nanofibres of para‐hexaphenyl was investigated by a combination of localized far‐field ultraviolet excitation and scanning near‐field fluorescence detection. Morphological inhomogeneities of the nanofibres together with selective incoupling into the near‐field probe resulted in a detection sensitivity was dependent on individual nanoaggregates. Strongest near‐field intensity and radiation into the far‐field were observed at the crossing points of nanofibres. The near‐field observation of a distance‐dependent damping of the waveguiding along the nanofibres allowed us to determine the imaginary part of the dielectric function of the nanofibres, in quantitative agreement with far‐field optical data.
Atomic force microscopy study of DNA deposited on poly l‐ornithine‐coated mica
Authors: PODESTÀ A. , IMPERADORI L. , COLNAGHI W. , FINZI L. , MILANI P. , DUNLAP D.
Published: August 2004

Analyses of individual biomolecules, like DNA, or DNA–protein complexes, via atomic force microscopy, require ‘gentle’ methods to immobilize DNA on surfaces, which allow the ensemble of molecules to adopt conformations dictated primarily by their physical characteristics, and which possibly permit the use of a wide selection of buffers. We show that poly‐l‐ornithine‐coated mica is a good substrate for fast, reliable deposition of DNA for wet or dry imaging. The surface firmly secures DNA, which retains the B‐form helical rise (0.34 nm bp−1). The conformations of DNA that result are reminiscent of three‐dimensional random coils projected on to a plane. The contrast is good, especially in solution, and buffers with physiological concentrations of salt with or without divalent cations may be used. This is important for comparison of scanning probe microscopy results with those obtained by different techniques.
Combining Ar ion milling with FIB lift‐out techniques to prepare high quality site‐specific TEM samples
Authors: HUANG Z.
Published: August 2004

Focused ion beam (FIB) techniques can prepare site‐specific transmission electron microscopy (TEM) cross‐section samples very quickly but they suffer from beam damage by the high energy Ga+ ion beam. An amorphous layer about 20–30 nm thick on each side of the TEM lamella and the supporting carbon film makes FIB‐prepared samples inferior to the traditional Ar+ thinned samples for some investigations such as high resolution transmission electron microscopy (HRTEM) and electron energy loss spectroscopy (EELS). We have developed techniques to combine broad argon ion milling with focused ion beam lift‐out methods to prepare high‐quality site‐specific TEM cross‐section samples. Site‐specific TEM cross‐sections were prepared by FIB and lifted out using a Narishige micromanipulator onto a half copper‐grid coated with carbon film. Pt deposition by FIB was used to bond the lamellae to the Cu grid, then the coating carbon film was removed and the sample on the bare Cu grid was polished by the usual broad beam Ar+ milling. By doing so, the thickness of the surface amorphous layers is reduced substantially and the sample quality for TEM observation is as good as the traditional Ar+ milled samples.
Minimizing photobleaching during confocal microscopy of fluorescent probes bound to chromatin: role of anoxia and photon flux
Authors: BERNAS T. , ZARȨBSKI M. , COOK R. R. , DOBRUCKI J. W.
Published: August 2004

Exposure to light can destroy the ability of a molecule to fluoresce. Such photobleaching limits the use of fluorescence and confocal microscopy in biological studies. Loss of fluorescence decreases the signal‐to‐noise ratio and so image resolution; it also prevents the acquisition of meaningful data late during repeated scanning (e.g. when collecting three‐dimensional images). The aim of this work was to investigate the role of oxygen in the photobleaching of fluorophores bound to DNA in fixed cells, and to explore whether anoxia could minimize such bleaching. Anoxia significantly reduced bleaching rates and changed the order of reaction of both propidium iodide (an intercalator) and chromomycin A3 (a minor‐groove binder) bound to DNA; it afforded the greatest protection at low photon fluxes. However, it had no effect on the bleaching of the green fluorescent protein (GFP) covalently attached to a histone and so bound to DNA, probably because the protein shielded the chromophore from oxygen. Bleaching of all three fluorophores depended on photon flux. Practical ways of minimizing bleaching were examined, and examples of three‐dimensional images of DNA marked by propidium and GFP (collected under standard and optimized conditions) are presented.
Direct atomic force microscopy observations of monovalent ion induced binding of DNA to mica
Authors: ELLIS J. S. , ABDELHADY H. G. , ALLEN S. , DAVIES M. C. , ROBERTS C. J. , TENDLER S. J. B. , WILLIAMS P. M.
Published: August 2004

Multivalent ions in solution are known to mediate attraction between two like‐charged molecules. Such attraction has proved useful in atomic force microscopy (AFM) where DNA may be immobilized to a mica surface facilitating direct imaging in liquid. Theories of DNA immobilization suggest that either ‘salt bridging’ or fluctuation in the positions of counter ions about both the mica surface and DNA backbone secure DNA to the mica substrate. Whilst both theoretical and experimental evidence suggest that immobilization is possible in the presence of divalent ions, very few studies identify that such immobilization is possible with monovalent ions. Here we present direct AFM evidence of DNA immobilized to mica in the presence of only monovalent ions. Our data depict E. coli plasmid pBR322 adsorbed onto the negatively charged mica both after short (10 min) and long (24 h) incubation periods. These data suggest the need to re‐explore current theories of like‐charge attraction to include the possibility of monovalent interactions. We suggest that this DNA immobilization strategy may offer the potential to image natural processes with limited immobilization forces and hence enable maximum conformational freedom of the immobilized biomolecule.
Microwave exposure increases bone demineralization rate independent of temperature
Authors: TINLING S. P. , GIBERSON R. T. , KULLAR R. S.
Published: August 2004

There is a long‐standing controversy regarding an effect of microwaves, independent of increasing temperature, on the rate of bone demineralization. In this study, we exposed standardized samples of gerbil femur to constant microwave exposure while maintaining the demineralizing solution (ethylenediamine tetraacetic acid, EDTA) at 20 °C. Random samples were selected at 3 h intervals, embedded in plastic and sectioned for histological evaluation to determine the extent of demineralization. The time to complete demineralization was significantly faster with microwave exposure (33 h) compared to non‐exposure on a tissue rotator (45 h) in a limited amount (5 mL/24 h) of EDTA. The presence of bone marrow was a significant barrier to the rate of demineralization and resulted in an asymmetrical pattern of mineral extraction. Samples without bone marrow were completely demineralized after 21 h of exposure to microwaves and EDTA. Additional comparisons were made between samples exposed to an effectively infinite supply of demineralizing agent (bone marrow intact). There was a significant increase in rate with unlimited demineralizing agent with (24 h) or without (30 h) microwaves when compared to tissue demineralized on the rotator. Our results establish a positive effect of microwaves on the rate of bone demineralization which is independent of temperature.
Children of the Troubles: The Impact of Political Violence in Northern Ireland
Authors: Muldoon Orla T.
Published: August 2004

This article explores the effects of political violence on children and young people in Northern Ireland. The article begins with a brief historical account of the Northern Irish conflict and the recently negotiated Belfast Good Friday Agreement of 1998. This account illustrates, as is the case with many conflicts, its basis is religious, national, economic, and political, despite its frequent construction as a battle between Protestant and Roman Catholic. The article goes on to review young peoples' experience of conflict in Northern Ireland and the impact of conflict experiences on three related areas of young people's lives. These include the effects of the conflict on everyday aspects of life, social identity, and mental health.
Young Men as Victims and Perpetrators of Violence in Northern Ireland: A Qualitative Analysis
Authors: Reilly Jacqueline , Muldoon Orla T. , Byrne Clare
Published: August 2004

This article explores issues of masculinity and violence in the lives of young men in disadvantaged areas in Northern Ireland. Qualitative data were collected in four focus groups, one group of young men from the Catholic community, one group of young men from the Protestant community, one group of community representatives, and one group of Young Offenders (N= 28). Themes were extracted from the data using a grounded approach. Results indicate that social disadvantage is fundamental to experiences of violence and that young men understand the costs and benefits of a masculine identity that incorporates a capacity for violence. Discussion suggests that initiatives to reduce violent behavior should be compatible with socially and culturally acceptable constructions of masculinity.
Children and Socio‐Cultural Divisions in Northern Ireland
Authors: Trew Karen
Published: August 2004

This article focuses on young children and those in middle childhood. It explores the strengths and weaknesses of competing explanations and methodologies employed in research on the developing child's awareness and understanding of intergroup relations in Northern Ireland. The review highlights the ethical and methodological constraints involved in research into a sensitive topic and the strengths of a social psychological analysis that takes account of both the cognitive development of the child and their cultural setting.
Peace and Progress? Political and Social Change Among Young Loyalists in Northern Ireland
Authors: McAuley James W.
Published: August 2004

Politics in Northern Ireland remain dominated by the search for an enduring settlement resting on an agreed set of political values and arrangements, between Ulster Unionists and loyalists on the one side, and Irish nationalists and republicans, on the other. Sectarian divisions continue to emphasize the persistence of conflictual social relationships between these gropings. Central to any possibility of a resolution to conflict is the awareness of how conflictual or reconciliatory values are transmitted from one generation to another, and how young people reconstruct their understandings of society. This article examines processes of political socialization and political identity formation around children and young people in Northern Ireland. It focuses in particular on those growing up within the Ulster loyalist tradition.

“North Belfast is witnessing the creation of the next wave of paramilitary gunmen. Today they are aged eight, their stones bouncing harmlessly off the army and police Land Rovers… . But give them a decade and, unless things change remarkably in the meantime many of these children will know how to fire a rifle or revolver, will have learnt to manufacture and use blast‐bombs, and know exactly how much sugar is needed in a petrol bomb.”

          — McKittrick, 2001, p. 14

“Young people in Northern Ireland are heir to a historical legacy of sectarian social division. On the ethnic frontier these manifest themselves in the territorialization of economic, residential and cultural life.”

          — Bell, 1990, p. 96
Teachers' and Ppils' Educational Experiences and School‐Based Responses to the Conflict in Northern Ireland
Authors: Kilpatrick Rosemary , Leitch Ruth
Published: August 2004

This article describes a study which examined (a) the impact of the political conflict on teachers' and ppils' experiences of education in Northern Ireland and (b) the impact of curricular‐based interventions designed to support the ppils and reduce prejudice. The focus of the second part of the article is on the prejudice reduction initiatives identified. A total of 44 staff and 78 ppils spread across 8 schools participated and both teachers' and ppils' perspectives were identified, the latter being an extremely important dimension which has rarely been addressed in previous studies of this area. The findings, which highlight the complexity of the impact of the political conflict, are considered to have both practical and theoretical implications for prejudice reduction programs.

“Young people are asked to ‘voice’ their views not only because it is seen as beneficial to them personally, but because people believe they can learn from what they are saying.”

          —Hadfield and Hawe, 2001, p. 94