bluuebunny/crossref_metadata_2025 huggingface dataset:
The be going to periphrasis in if-clauses
Authors: Lansari Laure
Published: October 2009

This paper examines the use of the future periphrases be going to and aller + infinitive in conditional clauses introduced by if and si. Both monolingual and translated data is investigated. It shows that there is no equivalence between the two periphrases in such a constrained syntactic environment. The sequence if + be going to, which is not truly conditional as claimed throughout the analysis, is frequent in contemporary English, whereas aller + infinitive is hardly compatible with conditionals. Be going to in if-clauses is thus mainly translated by devoir, which emphasizes the inevitability component of the English periphrasis, or by vouloir when the intentional meaning of be going to is foregrounded. It is nevertheless argued that aller + infinitive can occur in conditionals, but only in very specific situations: when the si-clause is clearly attributable to a source of disourse distinct from the speaker.
Governing education through data: Scotland, England and the European education policy space
Authors: Grek Sotiria , Ozga Jenny
Published: October 2009

This paper draws on interview data from national policy makers in England, Scotland and the European Commission to illustrate differences in the referencing of ‘Europe’ in education policy‐making in England and Scotland in order to highlight the emergent complexity of post‐devolution policy‐making in education through a focus on relations and interactions with Europe, as expressed in the negotiation and development of performance data systems. We suggest that policy‐makers in England reference global influences, rather than Europe, while policy‐makers in Scotland reference Europe in order to project a new positioning of Scotland in closer alignment with Europe. Europeanisation in education thus produces differing policy responses from closely aligned, indeed, in the case of England and Scotland, contiguous policy spaces. Thus the paper seeks to contribute to the literature on ‘travelling’ education policy and its ‘local’ mediation and to connect the development of devolution and the changing policy space of education in Europe.
Understanding public attitudes in Britain towards faith schools
Authors: Clements Ben
Published: October 2009

This paper provides a detailed analysis of different aspects of public attitudes towards faith schools in Britain. It examines two questions relating to government policy on this issue and two questions that ask about the perceived outcomes of this type of school. After discussing existing public opinion on this issue it uses data from the British Social Attitudes Survey 2007 to analyse the bivariate relationships between attitudes towards faith schools and religious characteristics. It then assesses the relative impact of religious characteristics on public attitudes when estimating logistic regression models that simultaneously examine for the effects of other explanatory variables. These include demographic characteristics, socio‐economic status, party‐political affiliation and ideological beliefs. The main findings are that religious characteristics, especially attendance at religious services and perceived religiosity, have a strong impact in all four model estimations, while previous or current attendance at a private school by a household member and ideological beliefs also play a role.
Switch recombination and somatic hypermutation are controlled by the heavy chain 3′ enhancer region
Authors: Dunnick Wesley A. , Collins John T. , Shi Jian , Westfield Gerwin , Fontaine Clinton , Hakimpour Paul , Papavasiliou F. Nina
Published: November 2009

Both class switch recombination (CSR) and somatic hypermutation (SHM) require transcription and the trans-acting factor activation-induced cytidine deaminase (AID), and must be up-regulated during antigen-dependent differentiation of B lymphocytes. To test the role of the heavy chain 3′ enhancers in both CSR and SHM, we used a BAC transgene of the entire heavy chain constant region locus. Using Cre-loxP recombination to delete a 28-kb region that contains the four known 3′ heavy chain enhancers, we isolated lines of BAC transgenic mice with an intact heavy chain locus and paired lines in the same chromosomal insertion site lacking the 3′ enhancers. Intact heavy chain transgenes undergo CSR to all heavy chain genes and mutate their transgenic VDJ exon. In paired transgenes lacking the 3′ enhancer region, CSR to most heavy chain genes is reduced to ∼1% of the levels for intact heavy chain loci; SHM is also reduced. Finally, we find that in B cells with a transgene lacking the 3′ enhancers, interchromosomal recombination between the transgenic VDJ exon and the endogenous heavy chain C genes is more easily detected than CSR within the transgene.
Histone H2AX stabilizes broken DNA strands to suppress chromosome breaks and translocations during V(D)J recombination
Authors: Yin Bu , Savic Velibor , Juntilla Marisa M. , Bredemeyer Andrea L. , Yang-Iott Katherine S. , Helmink Beth A. , Koretzky Gary A. , Sleckman Barry P. , Bassing Craig H.
Published: November 2009

The H2AX core histone variant is phosphorylated in chromatin around DNA double strand breaks (DSBs) and functions through unknown mechanisms to suppress antigen receptor locus translocations during V(D)J recombination. Formation of chromosomal coding joins and suppression of translocations involves the ataxia telangiectasia mutated and DNA-dependent protein kinase catalytic subunit serine/threonine kinases, each of which phosphorylates H2AX along cleaved antigen receptor loci. Using Abelson transformed pre–B cell lines, we find that H2AX is not required for coding join formation within chromosomal V(D)J recombination substrates. Yet we show that H2AX is phosphorylated along cleaved Igκ DNA strands and prevents their separation in G1 phase cells and their progression into chromosome breaks and translocations after cellular proliferation. We also show that H2AX prevents chromosome breaks emanating from unrepaired RAG endonuclease-generated TCR-α/δ locus coding ends in primary thymocytes. Our data indicate that histone H2AX suppresses translocations during V(D)J recombination by creating chromatin modifications that stabilize disrupted antigen receptor locus DNA strands to prevent their irreversible dissociation. We propose that such H2AX-dependent mechanisms could function at additional chromosomal locations to facilitate the joining of DNA ends generated by other types of DSBs.
MicroRazerS: rapid alignment of small RNA reads
Authors: Emde Anne-Katrin , Grunert Marcel , Weese David , Reinert Knut , Sperling Silke R.
Published: October 2009

Motivation: Deep sequencing has become the method of choice for determining the small RNA content of a cell. Mapping the sequenced reads onto their reference genome serves as the basis for all further analyses, namely for identification and quantification. A method frequently used is Mega BLAST followed by several filtering steps, even though it is slow and inefficient for this task. Also, none of the currently available short read aligners has established itself for the particular task of small RNA mapping.

Results: We present MicroRazerS, a tool optimized for mapping small RNAs onto a reference genome. It is an order of magnitude faster than Mega BLAST and comparable in speed with other short read mapping tools. In addition, it is more sensitive and easy to handle and adjust.

Availability: MicroRazerS is part of the SeqAn C++ library and can be downloaded from http://www.seqan.de/projects/MicroRazerS.html.

Contact:  emde@inf.fu-berlin.de; grunert@molgen.mpg.de
Experimental Adjustment on Drug Interactions through Intestinal CYP3A Activity in Rat: Impacts of Kampo Medicines Repeat Administered
Authors: Kinoshita Natsumi , Yamaguchi Yuriko , Hou Xiao-Long , Takahashi Kyoko , Takahashi Koichi
Published: November 2009

To provide the information that is necessary for making the proper use of kampo medicines, we have proposed the adequate methodology focused on the following issues: (i) kampo medicines emphasize the effects produced by the combination of herbal drugs rather than the individual effect of any single herb and (ii) Intestinal CYP3A has become a key factor for the bioavailability of orally administrated drugs. In the present study, we investigated both thein vivoandin vitroeffects of Saireito and Hochuekkito (kampo formulas) on CYP3A activities. From our study, oral pre‐treatment with Saireito or Hochuekkito did not affect the pharmacokinetics of nifedipine after intravenous administration to rats. When nifedipine was administered to rat intrajejunum, a significant decrease of AUC was showed by pre‐treatment with both kampo formulas. Saireito pre‐treatment led to 80% decrease inCmax of nifedipine. Saireito caused significant increases in both protein expression and metabolic activity of CYP3A in intestinal microsome, whereas it had no effect on CYP3A in hepatic microsome. Our result also showed that this affect of Saireito can be gone by wash‐out with 1 week. These findings demonstrated that Saireito may induce CYP3A activity of intestine but not of liver in rats. When resources for research are limited, well‐designed scientific studies except clinical trials also have many advantages.
Gemella asaccharolytica sp. nov., isolated from human clinical specimens
Authors: Ulger-Toprak Nurver , Summanen Paula H. , Liu Chengxu , Rowlinson Marie-Claire , Finegold Sydney M.
Published: November 2009

Three strains of an unidentified Gram-stain-variable, fastidious, catalase-negative, capnophilic, non-spore-forming, coccus-shaped bacterium from human wound specimens were characterized by phenotypic and molecular taxonomic methods. Initially, these strains were anaerobic; with repeated culture, they became aerotolerant. Comparative 16S rRNA gene sequencing studies demonstrated that the unknown strains were genealogically homogeneous and constituted a novel subline within the genus Gemella. The unknown bacterium was readily distinguished from other Gemella species by biochemical tests. On the basis of both phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium from clinical specimens be classified as Gemella asaccharolytica sp. nov. The type strain is WAL 1945JT (=ATCC BAA-1630T =CCUG 57045T).
Chelativorans multitrophicus gen. nov., sp. nov. and Chelativorans oligotrophicus sp. nov., aerobic EDTA-degrading bacteria
Authors: Doronina Nina V. , Kaparullina Elena N. , Trotsenko Yuri A. , Nörtemann Bernd , Bucheli-Witschel Margarete , Weilenmann Hans-Ueli , Egli Thomas
Published: November 2009

Two previously isolated strains (DSM 9103Tand LPM-4T) able to grow with EDTA (facultatively and obligately, respectively) as the source of carbon, nitrogen and energy were investigated in order to clarify their taxonomic positions. The strains were strictly aerobic, Gram-negative, asporogenous and non-motile rods that required biotin for growth. Reproduction occurred by binary fission. The strains were mesophilic and neutrophilic. Their major fatty acids were summed feature 7 (consisting of C18 : 1ω7c, C18 : 1ω9tand/or C18 : 1ω12t) and C19 : 0cycloω8c. The polyamine pattern revealed homospermidine as a major polyamine. Predominant polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylmonomethylethanolamine and diphosphatidylglycerol.Mesorhizobium-specific ornithine lipid was absent. The predominant isoprenoid quinone was Q-10. The DNA G+C values were 60.8 and 63.1 mol% (Tm) for strains LPM-4Tand DSM 9103T, respectively. The level of 16S rRNA gene sequence similarity between these EDTA-utilizers was 99.3 % while the DNA–DNA hybridization value was only 37 %. Both strains were phylogenetically related to members of the generaAminobacterandMesorhizobium(95–97 % sequence similarity). However, DNA–DNA hybridization values between the novel EDTA-degrading strains andAminobacter aminovoransDSM 7048TandMesorhizobium lotiDSM 2626Twere low (10–11 %). Based on their genomic and phenotypic properties, the new alphaproteobacterial strains are assigned to a novel genus,Chelativoransgen. nov., with the namesChelativorans multitrophicussp. nov. (type strain DSM 9103T=VKM B-2394T) andChelativorans oligotrophicussp. nov. (type strain LPM-4T=VKM B-2395T=DSM 19276T).
Desulfovibrio africanus subsp. uniflagellum subsp. nov., a sulfate-reducing bacterium from a uranium-contaminated subsurface aquifer
Authors: Castañeda-Carrión I. Nydia , Sheik Cody S. , Krumholz Lee R.
Published: November 2009

The bacterial strain SR-1Twas isolated from subsurface sediments of a uranium-contaminated site in Shiprock, New Mexico, USA. Cells are vibrioid and motile by means of a single polar flagellum. Strain SR-1Tgrows on sulfate, oxidizing formate, lactate and H2, but not malate, and ferments pyruvate. The DNA sequences of the 16S rRNA gene and the 16S–23S internal transcribed spacer of strain SR-1Tshowed 99.9 and 99.4 % similarity, respectively, to those of the type strainDesulfovibrio africanusDSM 2603T. The DNA sequence of the ITS region is 300 bases in length and contains two tRNA genes (tRNAIle, tRNAAla). The partial DNA sequence of thedsrABgene showed 94.6 % amino acid sequence similarity to that ofD. africanus. The DNA G+C content of strain SR-1Twas 62.4 mol% and it showed 72 % DNA–DNA similarity toD.africanus. DNA typing methods that target gene clusters and whole genomes revealed characteristic genomic fingerprints for strain SR-1T. A small plasmid was detected by gel electrophoresis. On the basis of distinct phenotypic and genotypic characteristics, strain SR-1Trepresents a novel subspecies ofD.africanus, for which the nameDesulfovibrio africanussubsp.uniflagellumsubsp. nov. is proposed. The type strain is SR-1T(=JCM 15510T=LS KCTC 5649T).
Brevibacterium pityocampae sp. nov., isolated from caterpillars of Thaumetopoea pityocampa (Lepidoptera, Thaumetopoeidae)
Authors: Katı Hatice , İnce İkbal Agah , Demir İsmail , Demirbağ Zihni
Published: November 2009

This work deals with the taxonomic study of a bacterium, strain Tp12T, isolated from caterpillars of the pine processionary moth (Thaumetopoea pityocampaDenis & Schiffermüller, 1775; Lepidoptera, Thaumetopoeidae). The isolate was assigned to the genusBrevibacteriumon the basis of a polyphasic taxonomic study, including morphological and biochemical characteristics, 16S rRNA gene sequence analysis, fatty acid analysis and DNA G+C content. The highest 16S rRNA gene sequence similarity to this isolate was approximately 96 %, with the type strains ofBrevibacterium albumandBrevibacterium samyangense. Cellular fatty acids of the isolate are of the branched type, with the major components being anteiso-C15 : 0and anteiso-C17 : 0. The DNA G+C content was 69.8 mol%. Although the strain was related toB. albumandB. samyangenseaccording to 16S rRNA gene sequence analysis, it differed from any known species ofBrevibacterium. Based on this evidence, the novel speciesBrevibacterium pityocampaesp. nov. is proposed, with strain Tp12T(=DSM 21720T=NCCB 100255T) as the type strain.
Hyunsoonleella jejuensis gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from seawater
Authors: Yoon Byoung-Jun , Lee Dong-Heon , Kang Bong-Jo , Kahng Hyung-Yeel , Oh You-Sung , Sohn Jung-Hoon , Choi Eui-Sung , Oh Duck-Chul
Published: November 2009

A novel marine, Gram-staining-negative, yellow-pigmented, rod-shaped bacterial strain, designated CNU004T, was isolated from a seawater sample collected on the coastline of Jeju Island, South Korea. The strain was strictly aerobic, non-flagellated, non-gliding and oxidase- and catalase-positive. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CNU004Tbelongs to a distinct lineage in the familyFlavobacteriaceae. Strain CNU004Texhibited levels of 16S rRNA gene sequence similarity of 93.8–93.9 % to its nearest phylogenetic neighbours, members of the generaGaetbulibacter,YeosuanaandAlgibacter. The new isolate required sea salts or artificial seawater for growth. The optimum ranges of temperature and pH for growth were 30–35 °C and pH 7.0–8.0. The DNA G+C content of strain CNU004Twas 37.7 mol%. The major fatty acids were iso-C15 : 0, iso-C15 : 1G, iso-C17 : 03-OH and iso-C15 : 03-OH. Menaquinone-6 was the major respiratory quinone. Zeaxanthin was the major carotenoid pigment produced, and flexirubin-type pigments were not produced. Strain CNU004Twas able to degrade starch and agar. Based on its phenotypic and genotypic characteristics and on the phylogenetic evidence presented, strain CNU004Tis considered to represent a novel species of a new genus in the familyFlavobacteriaceae, for which the nameHyunsoonleella jejuensisgen. nov., sp. nov. is proposed. The type strain ofHyunsoonleella jejuensissp. nov. is CNU004T(=KCTC 22242T=DSM 21035T).
Friedmanniella luteola sp. nov., Friedmanniella lucida sp. nov., Friedmanniella okinawensis sp. nov. and Friedmaniella sagamiharensis sp. nov., isolated from spiders
Authors: Iwai Kimika , Aisaka Kazuo , Suzuki Makoto
Published: November 2009

Four Gram-positive, non-motile, aerobic actinobacteria were isolated from spiders and their webs. Their genetic, phenotypic and chemical properties were studied. The 16S rRNA gene sequence data suggested that the four novel isolates belonged to the genus Friedmanniella. Two strains (FA1T and FA2T) formed a cluster together with Friedmanniella capsulata and Friedmanniella lacustris and the other two strains (FB1T and FB2T) formed a cluster together with Friedmanniella antarctica and Friedmanniella spumicola. The cell-wall peptidoglycan contained ll-A2pm and mycolic acids were absent. Isoprenoid quinones were mainly composed of MK-9(H4), MK-9(H2) and MK-9 and the predominant fatty acids were 12-methyltetradecanoic acid (ai-C15 : 0) and 13-methyltetradecanoic acid (i-C15 : 0). The major polar lipids were phosphatidylinositol and phosphatidylglycerol. In addition, strain FA1T, FB1T, and FB2T contained diphosphatidylglycerol and phosphatidylcholine. The DNA G+C contents were: 72 mol%, 73 mol%, 74 mol% and 75 mol% for strains FA1T, FA2T, FB1T, and FB2T, respectively. DNA–DNA hybridization studies demonstrated that the novel strains showed low relatedness values to F. capsulata, F. lacustris, F. antarctica and F. spumicola. These data support the proposal that strains FA1T, FA2T, FB1T and FB2T represent novel species of the genus Friedmanniella. Therefore, the names Friedmanniella luteola (type strain FA1T=DSM 21741T=NBRC 104963T), Friedmanniella lucida (type strain FA2T=DSM 21742T=NBRC 104964T), Friedmanniella okinawensis (type strain FB1T=DSM 21744T=NBRC 104966T) and Friedmanniella sagamiharensis (type strain FB2T=DSM 21743T=NBRC 104965T) are proposed for these new strains.
Sphingobium scionense sp. nov., an aromatic hydrocarbon-degrading bacterium isolated from contaminated sawmill soil
Authors: Liang Quanfeng , Lloyd-Jones Gareth
Published: November 2009

This study characterized strain WP01T, a Gram-staining-negative, rod-shaped, aerobic bacterium isolated from a polycyclic aromatic hydrocarbon-contaminated soil in New Zealand. Strain WP01Tshared many characteristics of the genusSphingobium: the predominant respiratory quinone (89 %) was ubiquinone with ten isoprene units (Q-10); the major fatty acids were C18 : 1ω7c, C16 : 1ω7c, C16 : 0and C14 : 02-OH; spermidine was the major polyamine; the DNA G+C content was 63.8 mol%; and theSphingobium-specific 16S rRNA signatures were conserved. A point of difference from other species of the genusSphingobiumwas that strain WP01Treduced nitrate to nitrite. The polar lipid pattern consisted of the predominant compounds diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipids. 16S rRNA gene sequence analysis showed that, amongst the recognized species of the genusSphingobium, strain WP01Twas most similar toSphingobium yanoikuyaeGIFU 9882TandSphingobium amienseYTT(>97 % 16S rRNA gene sequence similarities). The low DNA–DNA relatedness values between strain WP01TandS. yanoikuyaeGIFU 9882T(46.6 %) andS. amienseDSM 16289T(25.6 %) indicated no relatedness at the species level. On the basis of these characteristics, it is concluded that strain WP01Tshould be considered as representing a novel species within the genusSphingobium, for which the nameSphingobium scionensesp. nov. is proposed. The type strain is WP01T(=DSM 19371T=ICMP 13533T).
Kribbella ginsengisoli sp. nov., isolated from soil of a ginseng field
Authors: Cui Ying-Shun , Lee Jung-Sook , Lee Sung-Taik , Im Wan-Taek
Published: November 2009

A Gram-positive, non-spore-forming, aerobic bacterium, designated Gsoil 001T, was isolated from the soil of a ginseng field in Pocheon province, South Korea. On the basis of 16S rRNA gene sequence analysis, strain Gsoil 001T was shown to belong to the genus Kribbella. The closest phylogenetic relatives were Kribbella koreensis LM 161T (99.0 % 16S rRNA gene sequence similarity), Kribbella flavida KACC 20248T (98.8 %) and Kribbella alba (98.8%). Lower similarity (98.4–96.9 %) was found with the other recognized species of the genus Kribbella. The major quinone was MK-9(H4), the major fatty acids were anteiso-C15 : 0 and iso-C16 : 0 and the major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol and phosphatidylinositol. The cell-wall peptidoglycan contained ll-2,6-diaminopimelic acid. These chemotaxonomic data and the high genomic DNA G+C content (66.3 mol%) supported the affiliation of strain Gsoil 001T to the genus Kribbella. The results of physiological and biochemical tests differentiated strain Gsoil 001T genotypically and phenotypically from the Kribbella species with validly published names. Therefore, this isolate represents a novel species, for which the name Kribbella ginsengisoli sp. nov. is proposed, with the type strain Gsoil 001T (=KCTC 19134T =DSM 17941T).
Arenibacter nanhaiticus sp. nov., isolated from marine sediment of the South China Sea
Authors: Sun Fengqin , Wang Baojiang , Du Yaping , Liu Xiupian , Lai Qiliang , Li Guangyu , Luo Jie , Shao Zongze
Published: November 2009

An aerobic, Gram-stain-negative, rod-shaped bacterial isolate, strain NH36AT, was isolated from a sandy sediment sample from the South China Sea. Colonies of the isolate were dark orange on M2 agar. Optimal growth was observed at pH 7.0–8.5, 30 °C and in the presence of 0.5–4.0 % (w/v) NaCl. The major fatty acids were C15 : 0, iso-C15 : 0, anteiso-C15 : 0, iso-C15 : 1, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH and summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1
ω7c). The DNA G+C content was 38.9 mol%. 16S rRNA gene sequence analysis revealed that strain NH36AT was most closely related to members of the genus Arenibacter, exhibiting 94.3–96.2 % sequence similarity to the type strains of Arenibacter species. On the basis of phenotypic, chemotaxonomic and phylogenetic data, this organism should be classified as a representative of a novel species in the genus Arenibacter. The name Arenibacter nanhaiticus sp. nov. is proposed and the type strain is NH36AT (=LMG 24842T=CCTCC AB 208315T=MCCC 1A04137T).
Taxonomic study of Marinomonas strains isolated from the seagrass Posidonia oceanica, with descriptions of Marinomonas
balearica sp. nov. and Marinomonas
pollencensis sp. nov.
Authors: Espinosa Elena , Marco-Noales Ester , Gómez Daniel , Lucas-Elío Patricia , Ordax Mónica , Garcías-Bonet Neus , Duarte Carlos M. , Sanchez-Amat Antonio
Published: November 2009

Novel aerobic, Gram-negative bacteria with DNA G+C contents below 50 mol% were isolated from the culturable microbiota associated with the Mediterranean seagrass Posidonia oceanica. 16S rRNA gene sequence analyses revealed that they belong to the genus Marinomonas. Strain IVIA-Po-186 is a strain of the species Marinomonas mediterranea, showing 99.77 % 16S rRNA gene sequence similarity with the type strain, MMB-1T, and sharing all phenotypic characteristics studied. This is the first description of this species forming part of the microbiota of a marine plant. A second strain, designated IVIA-Po-101T, was closely related to M. mediterranea based on phylogenetic studies. However, it differed in characteristics such as melanin synthesis and tyrosinase, laccase and antimicrobial activities. In addition, strain IVIA-Po-101T was auxotrophic and unable to use acetate. IVIA-Po-101T shared 97.86 % 16S rRNA gene sequence similarity with M. mediterranea MMB-1T, but the level of DNA–DNA relatedness between the two strains was only 10.3 %. On the basis of these data, strain IVIA-Po-101T is considered to represent a novel species of the genus Marinomonas, for which the name Marinomonas balearica sp. nov. is proposed. The type strain is IVIA-Po-101T (=CECT 7378T =NCIMB 14432T). A third novel strain, IVIA-Po-185T, was phylogenetically distant from all recognized Marinomonas species. It shared the highest 16S rRNA gene sequence similarity (97.4 %) with the type strain of Marinomonas pontica, but the level of DNA–DNA relatedness between the two strains was only 14.5 %. A differential chemotaxonomic marker of this strain in the genus Marinomonas is the presence of the fatty acid C17 : 0 cyclo. Strain IVIA-Po-185T is thus considered to represent a second novel species of the genus, for which the name Marinomonas
pollencensis sp. nov. is proposed. The type strain is IVIA-Po-185T (=CECT 7375T =NCIMB 14435T). An emended description of the genus Marinomonas is given based on the description of these two novel species, as well as other Marinomonas species described after the original description of the genus.
Chryseobacterium solincola sp. nov., isolated from soil
Authors: Benmalek Yam , Cayol Jean-Luc , Bouanane Nabila A. , Hacene Hocine , Fauque Guy , Fardeau Marie-Laure
Published: November 2009

A Gram-staining-negative, yellow-pigmented, strictly aerobic bacterium, designated strain 1YB-R12T, was isolated from a soil sample in western Algeria. The novel isolate was heterotrophic, chemoorganotrophic, halotolerant and psychrotolerant. The temperature and pH optima for growth were 28–30 °C and pH 7.3–8. The bacterium tolerated up to 6 % (w/v) NaCl. Cells were non-motile, non-gliding and non-spore-forming, and were characterized by a variable morphological cycle. Flexirubin-type pigments were not detected. 16S rRNA gene sequence analysis showed that strain 1YB-R12Toccupied a distinct lineage within the genusChryseobacteriumand shared highest sequence similarity withChryseobacterium haifenseLMG 24029T(96.5 %). The DNA G+C content of strain 1YB-R12Twas 40.9 mol%. The predominant cellular fatty acids were anteiso-C15 : 0(41.4 %) and iso-C15 : 0(14.4 %). On the basis of phenotypic properties and phylogenetic distinctiveness, strain 1YB-R12Tis considered to represent a novel species of the genusChryseobacterium, for which the nameChryseobacterium solincolasp. nov. is proposed. The type strain is 1YB-R12T(=DSM 22468T=CCUG 55604T).
Sphingopyxis ummariensis sp. nov., isolated from a hexachlorocyclohexane dump site
Authors: Sharma Pooja , Verma Mansi , Bala Kiran , Nigam Aeshna , Lal Rup
Published: November 2009

A Gram-negative, motile, rod-shaped, yellow-pigmented bacterium, strain UI2T, was isolated from a hexachlorocyclohexane (HCH) dump site located in Ummari, in northern India. 16S rRNA gene sequence analysis revealed that strain UI2Tbelongs to the genusSphingopyxisand showed highest 16S rRNA gene sequence similarity withSphingopyxis terraeIFO 15098T(98.6 %). DNA–DNA relatedness values between strain UI2TandSphingopyxis terraeIFO 15098Tand other related strains were found to be less than 46 %. The major cellular fatty acids of strain UI2Twere C18 : 1ω7c(28.3 %), C16 : 0(14.4 %), 11-methyl C18 : 1ω7c(10.9 %), C17 : 1ω6c(9.6 %) and summed feature 3 (consisting of C16 : 1ω7cand/or C15 : 0iso 2-OH; 14.7 %). The DNA G+C content of strain UI2Twas 68 mol%. On the basis of DNA–DNA hybridization, phenotypic characteristics and phylogenetic analysis, strain UI2Tis found to represent a novel species of the genusSphingopyxis, for which the nameSphingopyxis ummariensissp. nov. is proposed. The type strain is UI2T(=CCM 7428T=MTCC 8591T).
Bacillus horneckiae sp. nov., isolated from a spacecraft-assembly clean room
Authors: Vaishampayan Parag , Probst Alexander , Krishnamurthi Srinivasan , Ghosh Sudeshna , Osman Shariff , McDowall Alasdair , Ruckmani Arunachalam , Mayilraj Shanmugam , Venkateswaran Kasthuri
Published: November 2009

Five Gram-stain-positive, motile, aerobic strains were isolated from a clean room of the Kennedy Space Center where the Phoenix spacecraft was assembled. All strains are rod-shaped, spore-forming bacteria, whose spores were resistant to UV radiation up to 1000 J m−2. The spores were subterminally positioned and produced an external layer. A polyphasic taxonomic study including traditional biochemical tests, fatty acid analysis, cell-wall typing, lipid analyses, 16S rRNA gene sequencing and DNA–DNA hybridization studies was performed to characterize these novel strains. 16S rRNA gene sequencing and lipid analyses convincingly grouped these novel strains within the genus Bacillus as a cluster separate from already described species. The similarity of 16S rRNA gene sequences among the novel strains was >99 %, but the similarity was only about 97 % with their nearest neighbours Bacillus pocheonensis, Bacillus firmus and Bacillus bataviensis. DNA–DNA hybridization dissociation values were <24 % to the closest related type strains. The novel strains had a G+C content 35.6±0.5 mol% and could liquefy gelatin but did not utilize or produce acids from any of the carbon substrates tested. The major fatty acids were iso-C15 : 0 and anteiso-C15 : 0 and the cell-wall diamino acid was meso-diaminopimelic acid. Based on phylogenetic and phenotypic results, it is concluded that these strains represent a novel species of the genus Bacillus, for which the name Bacillus horneckiae sp. nov. is proposed. The type strain is 1P01SCT (=NRRL B-59162T =MTCC 9535T).
Sphingomonas histidinilytica sp. nov., isolated from a hexachlorocyclohexane dump site
Authors: Nigam Aeshna , Jit Simran , Lal Rup
Published: November 2009

A Gram-negative, non-spore-forming, cream-coloured bacterial strain, UM2T, was isolated from an open hexachlorocyclohexane (HCH) dump site at Ummari village in Lucknow, India. Data generated from a polyphasic approach including phenotypic, genotypic and chemotaxonomic analyses confirmed that strain UM2Tbelonged to the genusSphingomonas. The highest similarity found to the 16S rRNA gene sequence of strain UM2Twas 99.4 %, withSphingomonas wittichiiDSM 6014T, whereas the DNA–DNA relatedness value between these strains was 31 %, indicating that they represent separate species. The DNA G+C content of UM2Twas 66.9 mol%. The respiratory pigment ubiquinone Q-10 was present. The predominant fatty acids were summed feature 8 (C18 : 1ω6cand/or C18 : 1ω7c; 32.9 %), C19 : 0cycloω8c(15.5 %) and C16 : 0(12.1 %). The major polar lipids were phosphatidylcholine, phosphatidylglycerol and phosphatidyldimethylethanolamine.sym-Homospermidine was the major polyamine observed. On the basis of the data reported, it was concluded that UM2Trepresents a novel species of the genusSphingomonas, for which the nameSphingomonas histidinilyticasp. nov. is proposed. The type strain is UM2T(=MTCC 9473T=CCM 7545T).
Shinella fusca sp. nov., isolated from domestic waste compost
Authors: Vaz-Moreira Ivone , Faria Cátia , Lopes Ana R. , Svensson Liselott A. , Moore Edward R. B. , Nunes Olga C. , Manaia Célia M.
Published: November 2009

A bacterium, designated strain DC-196T, isolated from kitchen refuse compost was analysed by using a polyphasic approach. Strain DC-196T was characterized as a Gram-negative short rod that was catalase- and oxidase-positive, and able to grow at 10–40 °C, pH 6–9 and in NaCl concentrations as high as 3 %. Chemotaxonomically, C18 : 1 was observed to be the predominant cellular fatty acid and ubiquinone 10 (Q10) was the predominant respiratory quinone. The G+C content of the genomic DNA was determined to be 66 mol%. On the basis of the genotypic, phenotypic and chemotaxonomic characteristics, strain DC-196T was assigned to the genus Shinella, although with distinctive features. At the time of writing, 16S rRNA gene sequence similarities of 97.6–96.8 % and the low DNA–DNA hybridization values of 38.2–32.2 % with the type strains of the three recognized Shinella species confirmed that strain DC-196T represents a novel species of the genus, for which the name Shinella fusca sp. nov. is proposed (type strain DC-196T=CCUG 55808T=LMG 24714T).
Paenibacillus pocheonensis sp. nov., a facultative anaerobe isolated from soil of a ginseng field
Authors: Baek Sang-Hoon , Yi Tae-Hoo , Lee Sung-Taik , Im Wan-Taek
Published: November 2009

A Gram-positive, aerobic or facultatively anaerobic, rod-shaped, spore-forming bacterium, strain Gsoil 1138T, was isolated from soil of a ginseng field in Pocheon Province, South Korea, and was characterized in order to determine its taxonomic position. On the basis of 16S rRNA gene sequence analysis, strain Gsoil 1138T was shown to belong to the family Paenibacillaceae and was most closely related to the type strains of Paenibacillus chondroitinus (98.2 % similarity) and Paenibacillus alginolyticus (96.5 %). Levels of 16S rRNA gene sequence similarity between strain Gsoil 1138T and the type strains of other recognized species of the genus Paenibacillus were below 96.5 %. The G+C content of the genomic DNA of strain Gsoil 1138T was 52.1±0.2 mol% (mean±sd of three determinations). Phenotypic and chemotaxonomic data (MK-7 as the major menaquinone and anteiso-C15 : 0 and iso-C16 : 0 as the predominant fatty acids) supported the affiliation of strain Gsoil 1138T to the genus Paenibacillus. The results of DNA–DNA hybridization experiments and physiological and biochemical tests allowed strain Gsoil 1138T to be distinguished genotypically and phenotypically from recognized species of the genus Paenibacillus. Strain Gsoil 1138T is therefore considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus pocheonensis sp. nov. is proposed. The type strain is Gsoil 1138T (=KCTC 13941T=LMG 23404T).
Parapusillimonas granuli gen. nov., sp. nov., isolated from granules from a wastewater-treatment bioreactor
Authors: Kim Yeon-Ju , Kim Myung Kyum , Im Wan-Taek , Srinivasan Sathiyaraj , Yang Deok-Chun
Published: November 2009

A novel betaproteobacterium, designated strain Ch07T, was isolated from granules from the wastewater-treatment bioreactor of an alcohol fermentation factory in South Korea. In order to determine its taxonomic position, the novel strain was characterized using a polyphasic approach. The new strain was Gram-negative, facultatively anaerobic, non-spore-forming, motile and short rod-shaped. 16S rRNA gene sequence analysis revealed that strain Ch07T belonged to the class Betaproteobacteria, being related to Pusillimonas noertemannii BN9T (gene sequence similarity 97.30 %), Achromobacter xylosoxidans subsp. xylosoxidans DSM 10346T (97.09 %), Bordetella pertussis DSM 5571T (97.01 %), Pigmentiphaga kullae DSM 13608T (96.68 %) and Castellaniella defragrans DSM 1214T (96.47 %). The results of DNA–DNA hybridization tests showed that reassociation values were less than 62 % with respect to these closely related type strains. Chemotaxonomic data showed that strain Ch07T possessed ubiquinone Q-8. The G+C content of the genomic DNA was 67.9±0.1 mol%. The major polyamine of strain Ch07T was putrescine. The major polar lipids of strain Ch07T were phosphatidylethanolamine, followed by diphosphatidylglycerol and phosphatidylglycerol. When strain Ch07T was incubated on tryptic soy agar, the major cellular fatty acids were C16 : 0, C17 : 0 cyclo, summed feature 3 (C16 : 1
ω7c/iso C15 : 0 2-OH) and summed feature 5 (C18 : 1
ω7c/ω9t/ω12t). The results of DNA–DNA hybridizations, in combination with the chemotaxonomic and physiological data, demonstrated that strain Ch07T represents a novel species of a new genus, for which the name Parapusillimonas granuli gen. nov., sp. nov. is proposed. The type strain of the type species is Ch07T (=KCTC 12668T=LMG 24012T).
Virgibacillus byunsanensis sp. nov., isolated from a marine solar saltern
Authors: Yoon Jung-Hoon , Kang So-Jung , Jung Yong-Taek , Lee Keun Chul , Oh Hyun Woo , Oh Tae-Kwang
Published: November 2009

A Gram-variable, motile, endospore-forming and rod-shaped bacterial strain, ISL-24T, was isolated from a marine solar saltern of the Yellow Sea, Korea, and its taxonomic position was investigated by a polyphasic study. Strain ISL-24T grew optimally at pH 7.0–8.0, at 30–37 °C and in the presence of 8 % (w/v) NaCl. It contained MK-7 as the predominant menaquinone and anteiso-C15 : 0 as the predominant fatty acid. The DNA G+C content was 37.6 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain ISL-24T fell within the genus Virgibacillus, clustering with Virgibacillus
carmonensis LMG 20964T and Virgibacillus
necropolis LMG 19488T, with a bootstrap resampling value of 92.3 %, and exhibiting 97.3 and 97.4 % 16S rRNA gene sequence similarity, respectively, to these strains. Strain ISL-24T exhibited 94.8–96.8 % 16S rRNA gene sequence similarity to the type strains of the other Virgibacillus species. Mean DNA–DNA relatedness values between strain ISL-24T and V. carmonensis DSM 14868T and V. necropolis DSM 14866T were 11 and 19 %, respectively. Differential phenotypic properties of strain ISL-24T, together with the phylogenetic and genetic distinctiveness, revealed that this strain is different from recognized Virgibacillus species. On the basis of phenotypic, phylogenetic and genetic data, strain ISL-24T represents a novel species of the genus Virgibacillus, for which the name Virgibacillus byunsanensis sp. nov. is proposed. The type strain is ISL-24T (=KCTC 13259T =CCUG 56754T).
Thermovenabulum gondwanense sp. nov., a thermophilic anaerobic Fe(III)-reducing bacterium isolated from microbial mats thriving in a Great Artesian Basin bore runoff channel
Authors: Ogg Christopher D. , Greene Anthony C. , Patel Bharat K. C.
Published: November 2009

A strictly anaerobic, thermophilic bacterium, designated strain R270T, was isolated from microbial mats thriving in the thermal waters (66 °C) of a Great Artesian Basin bore (registered no. 17263) runoff channel. Cells of strain R270Twere straight to slightly curved rods (3.50–6.00×0.75–1.00 μm) that stained Gram-positive, but possessed a Gram-negative cell-wall ultrastructure. Strain R270Tgrew optimally in tryptone-yeast extract-Casamino acids medium at 65 °C (growth temperature range between 50 and 70 °C) and at pH 7.0 (growth pH range between 6.0 and 9.0). In the presence of 0.02 and 0.10 % yeast extract, pyruvate and Casamino acids were the only substrates fermented from a wide spectrum of substrates tested. Fe(III), Mn(IV), thiosulfate and elemental sulfur were used as electron acceptors in the presence 0.2 % yeast extract, but not sulfate, sulfite, nitrate, nitrite or fumarate. Growth of strain R270Tincreased in the presence of Fe(III), which was reduced in the presence of peptone, tryptone, Casamino acids, amyl media, starch, pyruvate, H2and CO2, but not in the presence of acetate, lactate, propionate, formate, benzoate, glycerol or ethanol. Growth and Fe(III) reduction were inhibited by chloramphenicol, streptomycin, tetracycline, penicillin, ampicillin and 2 % NaCl (w/v). The DNA G+C content of strain R270Twas 41±1 mol% (Tm) and phylogenetic analysis of the 16S rRNA gene indicated that this isolate was closely related toThermovenabulum ferriorganovorumDSM 14006T(similarity value of 96.1 %) within the family ‘Thermoanaerobacteraceae’, class ‘Clostridia’, phylum ‘Firmicutes’. On the basis of the phylogenetic distance separating the two, together with differences in a number of key phenotypic characteristics, strain R270Trepresents a novel species of the genusThermovenabulum, for which the nameThermovenabulum gondwanensesp. nov. is proposed; the type strain is R270T(=KCTC 5616T=DSM 21133T).
Actinoplanes toevensis sp. nov. and Actinoplanes tereljensis sp. nov., isolated from Mongolian soil
Authors: Ara Ismet , Yamamura Hideki , Tsetseg Baljinova , Daram Damdinsuren , Ando Katsuhiko
Published: November 2009

Two novel actinomycetes, designated MN07-A0368T and MN07-A0371T, were isolated from soil of Terelj, Töv Province, Mongolia, and subjected to phenotypic and genotypic characterization. They produced well-developed, non-fragmenting, extensively branched substrate hyphae from which oval to irregular sporangia were produced. Chemotaxonomic characteristics, i.e. cell wall diaminopimelic acid, whole-cell sugars, fatty acid components and major menaquinones, suggested that the two organisms belonged to the genus Actinoplanes. A comparative analysis of 16S rRNA gene sequences indicated that strains MN07-A0368T and MN07-A0371T formed a distinct clade within the genus and were closely related to the type strains of: Actinoplanes ferrugineus (97.7 % sequence similarity); Actinoplanes brasiliensis (97.7–97.8 %); Actinoplanes deccanensis (97.6–97.9 %); Actinoplanes durhamensis (96.9–97.0 %); and Actinoplanes globisporus (96.5–96.8 %). Strains MN07-A0368T and MN07-A0371T could be differentiated from each other and from strains of closely related species of the genus Actinoplanes by DNA–DNA hybridization, physiological and biochemical characteristics, fatty acid composition, and whole-cell sugar components. The broad range of phenotypic and genetic characters supported the suggestion that these strains represent two novel species of the genus Actinoplanes, for which the names Actinoplanes toevensis sp. nov. (type strain MN07-A0368T=NBRC 105298T=VTCC D9-11T) and Actinoplanes tereljensis sp. nov. (type strain MN07-A0371T=NBRC 105297T=VTCC D9-10T) are proposed.
Halonotius pteroides gen. nov., sp. nov., an extremely halophilic archaeon recovered from a saltern crystallizer
Authors: Burns David G. , Janssen Peter H. , Itoh Takashi , Kamekura Masahiro , Echigo Akinobu , Dyall-Smith Mike L.
Published: November 2009

Strains 1.15.5T, 2.27.5, 5.24.4 and 6.14.5 were isolated from a solar saltern. They have flattened, rod-shaped cells and are aerobic, extremely halophilic members of the domain Archaea and family Halobacteriaceae. Cells stained Gram-negative and grew optimally in media around neutral pH and containing 20–24 % (w/v) (strains 1.15.5T and 2.27.5) or 22–24 % (w/v) (5.24.4 and 6.14.5) salts. Mg2+ was not required. The DNA G+C contents of these isolates were all close to 58 mol%, and DNA–DNA cross-hybridization showed a mean relatedness of 77 %. Their 16S rRNA gene sequences differed by no more than 1.6 % from each other. Phylogenetic tree reconstructions with other recognized members of the Halobacteriaceae indicated that they formed a distinct clade, with the closest relative being Halorubrum saccharovorum (86.6–87.6 % 16S rRNA gene sequence similarity to the type strain). The only major polar lipid of all four isolates was the sulfated diglycosyl diether lipid S-DGD-1. By phase-contrast microscopy, the long, flattened cells of these strains often displayed a ‘wing-like’ shape. The phenotypic and phylogenetic data support the placement of these isolates into a novel species in a new genus within the Halobacteriaceae, for which we propose the name Halonotius pteroides gen. nov., sp. nov. The type strain of Halonotius pteroides is 1.15.5T (=JCM 14355T =CECT 7525T =DSM 18729T), with the additional reference strains 2.27.5 (=JCM 14356 =DSM 18671), 5.24.4 (=JCM 14357 =DSM 18673) and 6.14.5 (=JCM 14358 =DSM 18692).
Salinisphaera dokdonensis sp. nov., isolated from surface seawater
Authors: Bae Gi Duk , Hwang Chung Yeon , Kim Hye Min , Cho Byung Cheol
Published: November 2009

A Gram-negative, strictly aerobic bacterium, designated CL-ES53T, was isolated from surface water of the East Sea in Korea. Cells of strain CL-ES53T were short rods and motile by means of monopolar flagella. Strain CL-ES53T grew with 4–21 % NaCl (optimum 10 %) and at 5–40 °C (optimum 25 °C) and pH 5.2–8.8 (optimum pH 6.3–7.2). The major isoprenoid quinone was Q-8. The major fatty acids were C18 : 1
ω7c (42.0 %), C18 : 1
ω9c (14.8 %) and C14 : 0 (9.4 %). The genomic DNA G+C content was 64.9 mol%. Analysis of the 16S rRNA gene sequence of strain CL-ES53T revealed that it was a member of the genus Salinisphaera and most closely related to Salinisphaera shabanensis
E1L3A
T (96.9 % sequence similarity) and Salinisphaera hydrothermalis EPR70T (93.8 %). Phylogenetic analyses based on the 16S rRNA gene sequence showed that strain CL-ES53T formed a robust cluster with S. shabanensis
E1L3A
T. Although the 16S rRNA gene sequence similarity between strain CL-ES53T and S. shabanensis
E1L3A
T was rather high (96.9 %), DNA–DNA relatedness between these strains was 12 %, suggesting that they represent genomically distinct species. Strain CL-ES53T was differentiated from S. shabanensis
E1L3A
T and S. hydrothermalis EPR70T on the basis of optimum temperature for growth and certain phenotypic characteristics. The phylogenetic analysis and physiological and chemotaxonomic data show that strain CL-ES53T should be classified in the genus Salinisphaera within a novel species, for which the name Salinisphaera dokdonensis sp. nov. is proposed. The type strain is CL-ES53T (=KCCM 90064T =DSM 19549T).
Polynucleobacter cosmopolitanus sp. nov., free-living planktonic bacteria inhabiting freshwater lakes and rivers
Authors: Hahn Martin W. , Lang Elke , Brandt Ulrike , Lünsdorf Heinrich , Wu Qinglong L. , Stackebrandt Erko
Published: November 2009

Five heterotrophic, aerobic, catalase- and oxidase-positive, non-motile strains were characterized from freshwater habitats located in Austria, France, Uganda, P. R. China and New Zealand. The strains shared 16S rRNA gene similarities of ≥99.3 %. The novel strains grew on NSY medium over a temperature range of 10–35 °C (two strains also grew at 5 °C and one strain grew at 38 °C) and a NaCl tolerance range of 0.0–0.3 % (four strains grew up to 0.5 % NaCl). The predominant fatty acids were C16 : 0, C18 : 1
ω7c, C12 : 0 3-OH, and summed feature 3 (including C16 : 1
ω7c). The DNA G+C content of strain MWH-MoIso2T was 44.9 mol%. Phylogenetic analysis of 16S rRNA gene sequences demonstrated that the five new strains formed a monophyletic cluster closely related to Polynucleobacter necessarius (96–97 % sequence similarity). This cluster also harboured other isolates as well as environmental sequences which have been obtained from several habitats. Investigations with taxon-specific FISH probes demonstrated that the novel bacteria dwell as free-living, planktonic cells in freshwater systems. Based on the revealed phylogeny and pronounced chemotaxonomic differences to P. necessarius (presence of >7 % C12 : 0 3-OH and absence of C12 : 0 and C12 : 0 2-OH), the new strains are suggested to represent a novel species, for which the name Polynucleobacter cosmopolitanus sp. nov. is proposed. The type strain is MWH-MoIso2T (=DSM 21490T=CIP 109840T=LMG 25212T). The novel species belongs to the minority of described species of free-living bacteria for which both in situ data from their natural environments and culture-based knowledge are available.