bluuebunny/crossref_metadata_2025 huggingface dataset:
Green fluorescent organic light-emitting device with external quantum efficiency of nearly 10%
Authors: Okumoto Kenji , Kanno Hiroshi , Hamaa Yuji , Takahashi Hisakazu , Shibata Kenichi
Published: August 2006

Green fluorescent organic light-emitting device (OLED) exhibiting a high external quantum efficiency of nearly 10% has been developed. The OLED consists of simple three organic layers, using NPB, 0.8% C545T doped TPBA, and DBzA as a hole-transporting layer, an emitting layer, and an electron-transporting layer, respectively, [fluorocarbon coated indium tin oxide/NPB (60 nm)/08% C545T doped TPBA (40 nm)/DBzA (20 nm)/LiF (1 nm/Al], where NPB is 4,4′-bis (N-phenyl-1-naphthylamino)biphenyl, C545T is 10-(2-benzothiazolyl)-1,1,7,7-tetramethyl-2,3,6,7-tetrahydro-1H,5H,11H-benzo[l]pyrano[6 7 8-ij]quinolizin-11-one, TPBA is 9,9′,10,10′-tetraphenyl-2,2′-bianthracene, and DBzA is 9,10-bis[4-(6-methylbenzothiazol-2-yl)phenyl]anthracene. The high external quantum efficiency is maintained in the wide range of current density of 2–100 mA∕cm2. The current efficiency and power efficiency of the OLED are also very high, 29.8 cd/A and 26.2 lm/W, respectively, at a current density of 20 mA/cm2. The OLED is promising for practical use with high color purity with Commission Internationale de L’Eclairage coordinates of (0.24, 0.62) and long half-lifetime of 71h at a current density of 80mA∕cm2 (initial luminance of 23900cd∕m2).
Ferromagnetism and colossal magnetic moment in Gd-focused ion-beam-implanted GaN
Authors: Dhar S. , Kammermeier T. , Ney A. , Pérez L. , Ploog K. H. , Melnikov A. , Wieck A. D.
Published: August 2006

The structural and the magnetic properties of Gd-focused ion-beam-implanted GaN layers are studied. Gd3+ ions were uniformly implanted in molecular beam epitaxy grown GaN layers at room temperature with an energy of 300keV at doses ranging from 2.4×1011to1.0×1015cm−2 which corresponds to an average Gd concentration range of 2.4×1016–1.0×1020cm−3. The implanted samples were not subjected to any annealing treatment. No secondary phase related to Gd was detected by x-ray diffraction in these layers. Magnetic characterization with superconducting quantum interference device reveals a colossal magnetic moment of Gd and ferromagnetism with an order temperature above room temperature similar to that found in epitaxially grown Gd-doped GaN layers. The effective magnetic moment per Gd atom in these samples is, however, found to be an order of magnitude larger than that found in epitaxially grown layers for a given Gd concentration which indicates that the defects play an important role in giving rise to this effect.
Effects of strain gradient on charge offsets and pyroelectric properties of ferroelectric thin films
Authors: Zheng Yue , Wang Biao , Woo C. H.
Published: August 2006

The Landau-Ginzburg-Devonshire theory is used to study the effects of the strain gradient due to the epitaxial stresses in ferroelectric thin films sandwiched between two different substrates. The polarization in the film is found to be nonuniform, resulting in charge offsets and an asymmetric hysteresis response with characteristics similar to those in compositionally graded ferroelectric materials. The authors’ results suggest that the charge offset and pyroelectric effects can also be produced with effect of the strain gradient in film. In addition, such effects are found to be sensitive to an applied load.
Raman spectroscopy of sputtered AlN films: E2(high) biaxial strain dependence
Authors: Trodahl H. J. , Martin F. , Muralt P. , Setter N.
Published: August 2006

Sputtered [0001] AlN films with directly measured biaxial strain have been investigated by Raman spectroscopy to determine the strain dependence of the zone-center mode frequencies. The E2(high) feature near 655cm−1 is found to vary linearly with stress, and we determine the strain derivative of the line as −2.9±0.3cm−1∕GPa, confirming the lowest previously reported derivative and a factor of 2 smaller than the largest. The result is 13% larger than has been predicted by ab initio calculations. The other zone-center lines accessible under normally incident geometry from a c-axis film are shown to be unsuitable as strain gauges.
Vapour Pressure Study of Deuterium Exchange Reactions in Water-Ethanol Systems: Equilibrium Constant Determination
Authors: Phutela RC , Kooner ZS , Fenby DV
Published: August 2006

A method is proposed for the determination of the equilibrium constants of liquid-phase deuterium
exchange reactions from vapour pressure measurements. It is applied to water-ethanol systems
to give the equilibrium constant of the reaction
2C2H5OH(l) + D2(l) → 2C2H5OD(l) + H2O(l)
The value obtained, 1.05+0.02 at 298 K, is significantly greater than the 'random' value and is
more precise and reasonable than a recent calorimetric estimate. Vapour pressures at 298.14 K
are reported for the systems H2O+C2H5OH, H2O+C2H5OD, D2O + C2H5OH and D2O + C2H5OD.
Molar excess Gibbs functions are obtained from these vapour pressure measurements.
Immutable and Variable Transition State Structures. A Reply
Authors: McLennan DJ , Martin PL
Published: August 2006

The factual basis of, and
the theoretical reasoning behind, a recent suggestion by Poh
that transition state structures may or may not vary according to the severity
of substituent change are critically examined in terms of currently held views.
Both aspects of Poh's paper are found to be
defective. Some results on the rates of solvolysis of diarylmethyl
p-nitrobenzoates
in ethanol/water solvent mixtures are considered. A superficial examination of
the Hammett p and Winstein-Grunwald
m parameters indicates that Poh's suggestion of immutable transition states is
exemplified by this work, but a more detailed treatment shows that p and m are not necessarily functions of transition state charge
separations alone.
Nucleophilic Substitution Reactions of Tetrabutylammonium aci-Nitronates with p-Substituted Nitrobenzenes
Authors: Norris RK , Randles D
Published: August 2006

The reactions of tetrabutylammonium aci-nitronates with p-dinitrobenzene
in dimethyl sulfoxide, benzene or acetone proceed far more rapidly than the
reactions of the corresponding lithium salts and give, in unhindered cases,
good yields of C-arylates, e.g. p-(1-methyl-1-nitroethyl)nitrobenzene (in 73-89% yields) and p-nitro(l,3,3-trimethyl-1-nitrobuty1)benene (in 70% yield). With more sterically hindered nitronates, O-arylation
increases, giving phenols and ketoxime O-p-nitrophenyl
ethers, presumably derived from the novel, intermediate p-nitrophenyl aci-nitronate esters. aci-Nitronate ions with more than
two β-methyl groups gave no C-arylation.
Similar results were obtained with p-fluoronitrobenzene and p-nitrobenzonitrile, A mechanism for the conversion of the
intermediate aci-nitronate
esters into the ketoxime ethers is proposed.
Steric Effects on the Iodide-Induced Elimination of 2- and 3-Methanesulfonyloxy Groups from 5α-Cholestane Derivatives
Authors: Angyal SJ , Nicholls RG , Pinhey JT
Published: August 2006

Contrary to earlier reports
on closely related compounds, the reaction of all four diastereomers
of 5α-cholestane-2,3-diol bismethanesulfonate
with sodium iodide gives 5α-cholest-2-ene. The rate of the reaction
decreases in the order 2α,3α > 2α 3β � 28,3α ≈
2β,3β. The reactions of the 5α-cholestan-2- and -3-yl methanesulfonates with sodium iodide were also
investigated. The relative reaction rates are explained by considering the
steric effects of the substituents.
Novel Sesquiterpene Lactones from Callitris columellaris Heartwood
Authors: Brecknell DJ , Carman RM
Published: August 2006

Five new sesquiterpene
lactones, callitrin (1) (an elemanolide), callitrisin (2) and
dihydrocallitrisin (6) (eudesmanolides), and columellarin (4) and
dihydrocolumellarin (5) (guaianolides) have been isolated from Callitris
columellaris heartwood along with the germacranolide (3) which is a new natural
product previously only known synthetically. These compounds are the first
sesquiterpene lactones isolated from the Cupressaceae. Lactones (1), (2) and
(6) all share a novel cis-fused
lactone ring in which the C7-C11 bond is axial to a cyclohexane ring.
C-Glycosylflavonoids. III. The Synthesis of 5,7,4'-Tri-O-methylvitexin (8-C-β-D-Glucopyranosyl-5,7,4'-trimethoxyflavone)
Authors: Eade RA , Pham H
Published: August 2006

The reaction between
1,3,5-trimethoxybenzene and tetraacetyl-α-D-glucosyl
bromide in the presence of zinc oxide gave β-D-glucopyranosyl-2,4,6-trimethoxybenzene
tetraacetate (12). The tetraacetate (12) was converted by acetic anhydride and
anhydrous aluminium chloride into 3-β-D-
glucopyranosyl-2-hydroxy-4,6-dimethoxyacetophenone tetraacetate (15).
Condensation of the acetophenone tetraacetate (15)
with 4-methoxybenzaldehyde in the presence of sodium hydroxide gave 3'-β-D-glucopyranosyl-2'-hydroxy-4,4',6'-trimethoxychacone
(6). Reaction of the chalcone (6) with selenium
dioxide gave 8-C-β-D-glucopyranosyl-5,7,4'-trimethoxyflavone (5,7,4'-tri-O- methylvitexin)(10).
The chemical shifts of the olefinic protons of chalcones are discussed.
Alkaloids of Darlingia ferruginea
Authors: Bick IRC , Gillard JW , Leow H
Published: August 2006

Darlingia ferruginea J. F. Bailey
contains the new tropane alkaloids ferrugine (2) and 3α-benzoyloxy-2α-hydroxybenzyltropane
(4) as well as darlingine (1) and ferruginine (3),
which also occur in D. darlingiana.
Three New Aliphatic Acids from Lichens of Genus Parmelia (Subgenus Xanthoparmelia)
Authors: Chester DO , Elix JA
Published: August 2006

The aliphatic acids, constipatic acid
[2-(14'-hydroxypentadecyl)-4-methyl-5-oxo-2,5-dihydrofuran- 3-carboxylic acid],
protoconstipatic acid
[2-(14'-hydroxypentadecyl)-4-methylene-5-oxotetrahydro- furan-3-carboxylic
acid] and dehydroconstipatic acid [4-methy1-5-oxo-2-(14'-oxopentadecy1)-2,5-
dihydrofuran-3-carboxylic acid], have been identified as constituents of
various Xanthoparmelia lichens from
Australia.
Epigenetic properties of white–opaque switching in
Candida albicans
are based on a self-sustaining transcriptional feedback loop
Authors: Zordan Rebecca E. , Galgoczy David J. , Johnson Alexander D.
Published: August 2006

White–opaque switching in the human fungal pathogen
Candida albicans
is an alternation between two distinct types of cells, white and opaque. White and opaque cells differ in their appearance under the microscope, the genes they express, their mating behaviors, and the host tissues for which they are best suited. Each state is heritable for many generations, and switching between states occurs stochastically, at low frequency. In this article, we identify a master regulator of white–opaque switching (Wor1), and we show that this protein is a transcriptional regulator that is needed to both establish and maintain the opaque state. We show that in opaque cells, Wor1 forms a positive feedback loop: It binds its own DNA regulatory region and activates its own transcription leading to the accumulation of high levels of Wor1. We further show that this feedback loop is self-sustaining: Once activated, it persists for many generations. We propose that this Wor1 feedback loop accounts, at least in part, for the heritability of the opaque state. In contrast, white cells (and their descendents) lack appreciable levels of Wor1, and the feedback loop remains inactive. Thus, this simple model can account for both the heritability of the white and opaque states and the stochastic nature of the switching between them.
WASP-interacting Protein Is Important for Actin Filament Elongation and Prompt Pseudopod Formation in Response to a Dynamic Chemoattractant Gradient
Authors: Myers Scott A. , Leeper Laura R. , Chung Chang Y.
Published: August 2006

The role of WASP-interacting protein (WIP) in the process of F-actin assembly during chemotaxis of Dictyostelium was examined. Mutations of the WH1 domain of WASP led to a reduction in binding to WIPa, a newly identified homolog of mammalian WIP, a reduction of F-actin polymerization at the leading edge, and a reduction in chemotactic efficiency. WIPa localizes to sites of new pseudopod protrusion and colocalizes with WASP at the leading edge. WIPa increases F-actin elongation in vivo and in vitro in a WASP-dependent manner. WIPa translocates to the cortical membrane upon uniform cAMP stimulation in a time course that parallels F-actin polymerization. WIPa-overexpressing cells exhibit multiple microspike formation and defects in chemotactic efficiency due to frequent changes of direction. Reduced expression of WIPa by expressing a hairpin WIPa (hp WIPa) construct resulted in more polarized cells that exhibit a delayed response to a new chemoattractant source due to delayed extension of pseudopod toward the new gradient. These results suggest that WIPa is required for new pseudopod protrusion and prompt reorientation of cells toward a new gradient by initiating localized bursts of actin polymerization and/or elongation.
MASQOT-GUI: spot quality assessment for the two-channel microarray platform
Authors: Bylesjö Max , Sjödin Andreas , Eriksson Daniel , Antti Henrik , Moritz Thomas , Jansson Stefan , Trygg Johan
Published: August 2006

Summary: MASQOT-GUI provides an open-source, platform-independent software pipeline for two-channel microarray spot quality control. This includes gridding, segmentation, quantification, quality assessment and data visualization. It hosts a set of independent applications, with interactions between the tools as well as import and export support for external software. The implementation of automated multivariate quality control assessment, which is a unique feature of MASQOT-GUI, is based on the previously documented and evaluated MASQOT methodology. Further abilities of the application are outlined and illustrated.

Availability: MASQOT-GUI is Java-based and licensed under the GNU LGPL. Source code and installation files are available for download at

Contact: max.bylesjo@chem.umu.se

Supplementary information: Supplementary data are available at Bioinformatics online
Rhodococcus imtechensis sp. nov., a nitrophenol-degrading actinomycete
Authors: Ghosh Anuradha , Paul Debarati , Prakash Dhan , Mayilraj Shanmugam , Jain Rakesh K.
Published: August 2006

A Gram-positive actinobacterium, strain RKJ300T, capable of utilizingp-nitrophenol and 2,4-dinitrophenol, was isolated from a pesticide-contaminated site in India. The morphological and chemotaxonomic properties of the isolate were typical of members of the genusRhodococcus. The DNA G+C content was 72 mol%. Strain RKJ300Texhibited the highest level of sequence similarity withRhodococcus wratislaviensisNCIMB 13082T(99.3 %), followed byRhodococcus opacusDSM 43205T(98.8 %),Rhodococcus percolatusMBS1T(98.6 %) andRhodococcus koreensisDNP505T(98.1 %). The low levels of DNA–DNA relatedness (49–58 %) with the above micro-organisms, and the differences in the biochemical and physiological properties, suggest that strain RKJ300Tshould be classified within a novel species of the genusRhodococcus, for which the nameRhodococcus imtechensissp. nov. is proposed. The type strain is RKJ300T(=MTCC 7085T=JCM 13270T).
Thiorhodococcus mannitoliphagus sp. nov., a purple sulfur bacterium from the White Sea
Authors: Rabold Sandra , Gorlenko Vladimir M. , Imhoff Johannes F.
Published: August 2006

A novel purple sulfur bacterium, strain WST, was isolated from a microbial mat from an estuary of the White Sea. Individual cells are coccoid shaped, motile by flagella and do not contain gas vesicles. The mean cell diameter is 1.85 μm (range 1.5–2.0 μm). Cell suspensions exhibit a purple–violet colour. They contain bacteriochlorophyll a and carotenoids of the rhodopinal series as photosynthetic pigments. The novel bacterium is an anoxygenic photoautotroph, using sulfide, thiosulfate, sulfite and elemental sulfur as electron donors for photosynthesis and is capable of photoassimilating several organic carbon sources in the presence of carbonate and a reduced sulfur source (sulfide and/or thiosulfate). Sulfur globules, formed during oxidation of sulfide, are stored transiently inside the cells. Optimal salinity and pH for growth are at 0.5–2.0 % NaCl and pH 7.0–7.5. The DNA base composition of strain WST is 61.8 mol% G+C. 16S rRNA gene sequence analysis showed that the new isolate belongs to the genus Thiorhodococcus, with Thiorhodococcus minor CE2203T as the nearest relative (sequence similarity of 97.3 %). Several distinct differences from described species necessitate the description of a novel species. Thiorhodococcus mannitoliphagus sp. nov. is the proposed name, with strain WST (=ATCC BAA-1228T=VKM B-2393T) as the type strain.
Lentibacillus halophilus sp. nov., from fish sauce in Thailand
Authors: Tanasupawat Somboon , Pakdeeto Amnat , Namwong Sirilak , Thawai Chitti , Kudo Takuji , Itoh Takashi
Published: August 2006

Fifteen strains of extremely halophilic bacteria were isolated from fish sauce (nam-pla) collected in Thailand at various stages of the fish-fermentation process. The isolates were strictly aerobic, spore-forming, Gram-positive rods. They grew optimally in the presence of 20–26 % NaCl. The cell-wall peptidoglycan containedmeso-diaminopimelic acid. The predominant menaquinone was MK-7. The major cellular fatty acids were anteiso-C15 : 0and anteiso-C17 : 0. Polar lipid analysis revealed the presence of phosphatidylglycerol, diphosphatidylglycerol and two unidentified glycolipids. The DNA G+C content was 42.1–43.1 mol%. On the basis of the 16S rRNA gene sequence, a representative strain, PS11-2T, was found to be closely related toLentibacillus juripiscariusJCM 12147T(97.3 % similarity). The 15 strains were included in the same species on the basis that the levels of DNA–DNA relatedness with strain PS11-2Twere greater than 70 %. They could be distinguished fromL. juripiscariusand otherLentibacillusspecies on the basis of several phenotypic characteristics and low levels of DNA–DNA relatedness (⩽19.4 %). Therefore, the strains represent a novel species of the genusLentibacillus, for which the nameLentibacillus halophilussp. nov. is proposed. The type strain is PS11-2T(=JCM 12149T=TISTR 1549T=PCU 240T).
A new genus of the family Micromonosporaceae, Polymorphospora gen. nov., with description of Polymorphospora rubra sp. nov.
Authors: Tamura Tomohiko , Hatano Kazunori , Suzuki Ken-ichiro
Published: August 2006

Two actinomycete strains were isolated from soil surrounding mangrove roots. The isolates formed short spore chains with spores showing diverse shapes. The isolates contained glutamic acid, glycine, alanine and meso-diaminopimelic acid in the cell wall, 3-O-methylmannose, mannose, galactose and glucose as the whole-cell sugars and MK-10(H6), MK-10(H4), MK-9(H6) and MK-9(H4) as the predominant isoprenoid quinones. The isolates formed a distinct taxon in the phylogenetic tree of the Micromonosporaceae based on analysis of 16S rRNA gene sequences and showed chemical and phenotypic properties that were different from members of all of the other genera of this family. Based on these observations, it is proposed that the novel isolates belong to a new genus, Polymorphospora gen. nov. The type species of the genus is proposed as Polymorphospora rubra sp. nov., with strain TT 97-42T (=NBRC 101157T=DSM 44947T) as the type strain.
Actinocatenispora thailandica gen. nov., sp. nov., a new member of the family Micromonosporaceae
Authors: Thawai Chitti , Tanasupawat Somboon , Itoh Takashi , Kudo Takuji
Published: August 2006

Two actinomycete strains, TT2-10T and TT2-3, which produced long spore chains (more than 10 spores per chain), were isolated from peat swamp forest soil in Pattaloong Province, Thailand. Their taxonomic positions were determined using a polyphasic approach. The chemotaxonomic characteristics of these strains coincided with those of the family Micromonosporaceae, i.e. cell-wall chemotype II, muramic acid of the N-glycolyl type, whole-cell sugar pattern D and type II phospholipids. Analysis of the 16S rRNA gene sequences also indicated that these strains constitute a distinct lineage within the family Micromonosporaceae, sharing 91.3–93.8 % sequence similarity with members of this family. On the basis of their phenotypic and genotypic characteristics and their phylogenetic position, these strains represent a novel genus and species, for which the name Actinocatenispora thailandica gen. nov., sp. nov. is proposed. The type strain of Actinocatenispora thailandica is strain TT2-10T (=JCM 12343T=PCU 235T=DSM 44816T).
Novel nitrogen-fixing Acetobacter nitrogenifigens sp. nov., isolated from Kombucha tea
Authors: Dutta Debasree , Gachhui Ratan
Published: August 2006

The four nitrogen-fixing bacteria so far described in the familyAcetobacteraceaebelong to the generaGluconacetobacterandAcetobacter. Nitrogen-fixing bacterial strain RG1Twas isolated from Kombucha tea and, based on the phylogenetic analysis of 16S rRNA gene sequence which is supported by a high bootstrap value, was found to belong to the genusAcetobacter. Strain RG1Tdiffered fromAcetobacter aceti, the nearest member with a 16S rRNA gene sequence similarity of 98.2 %, and type strains of otherAcetobacterspecies with regard to several characteristics of growth features in culture media, growth in nitrogen-free medium, production ofγ-pyrone from glucose and dihydroxyacetone from glycerol. Strain RG1Tutilized maltose, glycerol, sorbitol, fructose, galactose, arabinose and ethanol, but not methanol as a carbon source. These results, along with electrophoretic mobility patterns of nine metabolic enzymes, suggest that strain RG1Trepresents a novel nitrogen-fixing species. The ubiquinone present was Q-9 and DNA G+C content was 64.1 mol%. Strain RG1Texhibited a low value of 2–24 % DNA–DNA relatedness to the type strains of related acetobacters, which placed it as a separate taxon. On the basis of this data, the nameAcetobacter nitrogenifigenssp. nov. is proposed, with the type strain RG1T(=MTCC 6912T=LMG 23498T).
Rhodanobacter spathiphylli sp. nov., a gammaproteobacterium isolated from the roots of Spathiphyllum plants grown in a compost-amended potting mix
Authors: De Clercq Deborah , Van Trappen Stefanie , Cleenwerck Ilse , Ceustermans An , Swings Jean , Coosemans Jozef , Ryckeboer Jaak
Published: August 2006

Three Gram-negative, yellow-pigmented strains were isolated from the rhizospheres ofSpathiphyllumplants grown in a compost-amended potting mix. The strains showed biological control activity towards the root-rot plant pathogenCylindrocladium spathiphylli, and were characterized to determine their taxonomic position. Cells of the strains were non-motile rods, and the strains were oxidase- and catalase-positive and unable to ferment most sugars tested. The three strains showed differences in growth temperature range, optimal growth temperature and some biochemical reactions. The majority of the fatty acids were branched, and large amounts of 15 : 0 iso and 17 : 1 isoω9cwere present. The 16S rRNA gene sequence (1497 bp) of strain B39Tshowed the highest level of similarity (98.5 %) to that ofRhodanobacter fulvusIAM 15025T, followed byRhodanobacter lindaniclasticusLMG 18385T(96.0 %; strain no longer extant),Dyella koreensisCCUG 50883T(96.4 %),Dyella japonicaDSM 16301T(96.3 %),Frateuria aurantiaLMG 1558T(96.2 %) andFulvimonas soliLMG 19981T(95.9 %). Less than 90 % 16S rRNA gene sequence similarity was observed for other members of theGammaproteobacteria. The mean DNA–DNA reassociation value for the three strains was 100 % and was 25 % when the strains were compared with DNA fromR. fulvusLMG 23003T. The strains had a mean DNA G+C content of 67.6 mol%. On the basis of their phylogenetic, genomic and phenotypic properties, the three strains represent a novel species within the genusRhodanobacter, for which the nameRhodanobacter spathiphyllisp. nov. is proposed. The type strain is strain B39T(=LMG 23181T=DSM 17631T).
Classification of Centers for Disease Control Group Eugonic Fermenter (EF)-4a and EF-4b as Neisseria animaloris sp. nov. and Neisseria zoodegmatis sp. nov., respectively
Authors: Vandamme Peter , Holmes Barry , Bercovier Hervé , Coenye Tom
Published: August 2006

A polyphasic taxonomic study was performed on isolates classified as Centers for Disease Control Group Eugonic Fermenter (EF)-4a and EF-4b. Comparative 16S rRNA gene sequence analysis confirmed that group EF-4a and EF-4b belong to the genus Neisseria with Neisseria canis and Neisseria dentiae as the nearest phylogenetic neighbours. DNA–DNA hybridizations and biochemical analyses demonstrated that isolates of group EF-4a and EF-4b represent two novel species within this sublineage of the genus Neisseria. Based on the results of the present study, isolates of group EF-4a and EF-4b are classified as Neisseria animaloris sp. nov. (type strain LMG 23011T=NCTC 12228T) and Neisseria zoodegmatis sp. nov. (type strain LMG 23012T=NCTC 12230T), respectively.
Amycolatopsis taiwanensis sp. nov., from soil
Authors: Tseng Min , Yang Shu-Feng , Li Wen-Jun , Jiang Cheng-Lin
Published: August 2006

An actinomycete strain (0345M-7T) was isolated from a soil sample from Yilan county, Taiwan. The isolate displayed substrate mycelia, upon which were borne short spore chains. The spore chains were composed of non-motile, smooth-surfaced, oval spores. Strain 0345M-7Thadmeso-diaminopimelic acid in its peptidoglycan. Whole-cell sugars were galactose, glucose, arabinose and ribose. The only phospholipid found was phosphatidylethanolamine. The predominant menaquinone was MK-9(H4). Mycolic acids were not detected. Major cellular fatty acids were iso-C16 : 0(38.1 %) and C17 : 1(25.4 %). The DNA G+C content of strain 0345M-7Twas 68.9 mol%. On the basis of phenotypic and genotypic data, it is proposed that strain 0345M-7T(=BCRC 16802T=KCTC 19116T) should be classified as the type strain of a novel species of the genusAmycolatopsis,Amycolatopsis taiwanensissp. nov.
Balneola vulgaris gen. nov., sp. nov., a member of the phylum Bacteroidetes from the north-western Mediterranean Sea
Authors: Urios Laurent , Agogué Hélène , Lesongeur Françoise , Stackebrandt Erko , Lebaron Philippe
Published: August 2006

A novel aerobic, Gram-negative bacterium, named 13IX/A01/164T, was isolated from surface waters in the coastal north-western Mediterranean Sea. Cells were motile, straight rods, 2.5 μm long and 0.2 μm wide, and formed orange colonies on marine agar medium. The G+C content of the genomic DNA of strain 13IX/A01/164T was 42 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed the strain in the phylum Bacteroidetes within the family Crenotrichaceae. On the basis of 16S rRNA gene sequence comparison and physiological and biochemical characteristics, this isolate represents a novel species of a new genus, for which the name Balneola vulgaris gen. nov., sp. nov. is proposed. The type strain of Balneola vulgaris is 13IX/A01/164T (=DSM 17893T=CIP 109092T=OOB 256T).
Sulfurivirga caldicuralii gen. nov., sp. nov., a novel microaerobic, thermophilic, thiosulfate-oxidizing chemolithoautotroph, isolated from a shallow marine hydrothermal system occurring in a coral reef, Japan
Authors: Takai Ken , Miyazaki Masayuki , Nunoura Takuro , Hirayama Hisako , Oida Hanako , Furushima Yasuo , Yamamoto Hiroyuki , Horikoshi Koki
Published: August 2006

Novel thermophilic bacteria, designated strains VW1 and MM1T, were isolated from hydrothermal fluid and microbial mat samples, respectively, collected from a shallow marine hydrothermal system (water depth 22 m) occurring in coral reefs off Taketomi Island, Okinawa, Japan. Cells of the two novel strains were motile rods with a single polar flagellum in the exponential growth phase. In a medium that included elemental sulfur, cells of the two strains became non-motile with oval to spherical cell shapes. For both strains, growth occurred at between 30 and 60 °C (optimum temperature of 50–55 °C; 60–80 min doubling time) and between pH 5.5 and 7.1 (optimum pH 6.0). The isolates were microaerobic chemolithoautotrophs capable of using thiosulfate or tetrathionate as the sole energy source, O2as the sole electron acceptor and CO2as the sole carbon source. Organic substrates, such as yeast extract and tryptone, inhibited growth of both strains. The G+C contents of genomic DNA were 51.3 and 49.5 mol% for strains VW1 and MM1T, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two strains were closely related to each other (99.9 % sequence similarity) and were distantly related to other previously described genera within theGammaproteobacteria. The novel isolates could also be differentiated from other gammaproteobacterial genera on the basis of their physiological properties. It is suggested that the novel isolates represent the type species of a new genus, for which the nameSulfurivirga caldicuraliigen. nov., sp. nov. (type strain MM1T=JCM 13439T=DSM 17737T) is proposed.
Candida floccosa sp. nov., a novel methanol-assimilating yeast species
Authors: Péter Gábor , Dlauchy Dénes , Tornai-Lehoczki Judit
Published: August 2006

Two methanol-assimilating yeast strains were isolated from a flux of a sessile oak (Quercus petrea) in Hungary and one genetically and phenotypically very similar strain from a flux of a red oak (Quercus rubra) in Canada. The strains exhibited ascomycetous affinity but ascospore formation was not observed. On the basis of the sequence of their D1/D2 domain of the large subunit rDNA, as well as of their physiological characteristics, they represent a novel yeast species of the genus Candida. Therefore Candida floccosa sp. nov. is proposed, with NCAIM Y.01581T (=CBS 10307T=NRRL Y-27951T) as the type strain.
Gillisia myxillae sp. nov., a novel member of the family Flavobacteriaceae, isolated from the marine sponge Myxilla incrustans
Authors: Lee On On , Lau Stanley C. K. , Tsoi Mandy M. Y. , Li Xiancui , Plakhotnikova Ioulia , Dobretsov Sergey , Wu Madeline C. S. , Wong Po-Keung , Qian Pei-Yuan
Published: August 2006

A yellow-pigmented, Gram-negative, rod-shaped, strictly aerobic bacterium (strain UST050418-085T) was isolated from the surface of a marine sponge, Myxilla incrustans, at Friday Harbor, WA, USA. The DNA G+C content of this strain was 34.6 mol%. The predominant fatty acids were i15 : 0, a15 : 0, i15 : 1, i16 : 0, i17 : 0 3-OH, 17 : 0 2-OH and summed feature 3, comprising i15 : 0 2-OH and/or 16 : 1ω7c (altogether representing 69.0 % of the total fatty acids). MK-6 was the only respiratory quinone detected. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the closest relatives of UST050418-085T were members of the genus Gillisia, with sequence similarities of 93.2–96.6 %. Strain UST050418-085T differed from its closest relatives by 11 to 18 phenotypic traits. Molecular evidence and phenotypic characteristics suggest that strain UST050418-085T represents a novel species within the genus Gillisia. The name Gillisia myxillae sp. nov. is proposed, with UST050418-085T (=JCM 13546T=NRRL B-41416T) as the type strain.
Reclassification of Pseudomonas beijerinckii Hof 1935 as Chromohalobacter beijerinckii comb. nov., and emended description of the species
Authors: Peçonek Janina , Gruber Claudia , Gallego Virginia , Ventosa Antonio , Busse Hans-Jürgen , Kämpfer Peter , Radax Christian , Stan-Lotter Helga
Published: August 2006

Pseudomonas beijerinckii(type strain DSM 7218T=ATCC 19372T=NCIMB 9041T) was isolated from salted beans and was first described by Hof in 1935. 16S rRNA gene sequence comparisons demonstrated its close relatedness (>97–99 %) to species of the genusChromohalobacter. A recent isolate from salted herrings originating from the Baltic Sea, strain 3b, also clustered phylogenetically within this genus. Phenotypic features, substrate utilization, fatty acid profile, quinone and polar lipid composition and whole-cell protein patterns supported the similarity of strain 3b toP. beijerinckiiDSM 7218Tand confirmed its relatedness to members of the genusChromohalobacter. The G+C content of the DNA from strain 3b andP. beijerinckiiDSM 7218Twas 60.4 and 60.7 mol%, respectively. DNA–DNA hybridization data showed that the two strains represent the same species, but are separated fromChromohalobacter canadensis, the closest species from a phylogenetic point of view. Therefore, the reclassification ofPseudomonas beijerinckiiasChromohalobacter beijerinckiicomb. nov. (type strain DSM 7218T=ATCC 19372T=NCIMB 9041T) is proposed. The species description has been emended considering the new data on both the type strain and strain 3b.
Open reading frame 132 of Heliocoverpa armigera nucleopolyhedrovirus encodes a functional per os infectivity factor (PIF-2)
Authors: Fang Minggang , Nie Yingchao , Wang Qian , Deng Fei , Wang Ranran , Wang Hanzhong , Wang Hualin , Vlak Just M. , Chen Xinwen , Hu Zhihong
Published: August 2006

Open reading frame 132 (Ha132) of Helicoverpa armigera nucleopolyhedrovirus (HearNPV) is a homologue of per os infectivity factor 2 (pif-2) of Spodoptera exigua multiple nucleopolyhedrovirus. Sequence analysis indicated that Ha132 encoded a protein of 383 aa with a predicted molecular mass of 44.5 kDa. Alignment of HA132 and its baculovirus homologues revealed that HA132 was highly conserved among baculoviruses, with 14 absolutely conserved cysteine residues. RT-PCR indicated that Ha132 was first transcribed at 24 h post-infection. Western blot analysis showed that a 43 kDa band was detectable in HearNPV-infected HzAM1 cells from 36 h post-infection. Western blots also indicated that HA132 was a component of the occlusion-derived virus, but not of budded virus. Deletion of Ha132 from HearNPV abolished per os infectivity, but had no effect on the infectivity of the budded virus phenotype.
The UL4 gene of pseudorabies virus encodes a minor infected-cell protein that is dispensable for virus replication
Authors: Fuchs Walter , Granzow Harald , Klopfleisch Robert , Klupp Barbara G. , Mettenleiter Thomas C.
Published: August 2006

Although homologues of the open reading frame (ORF) UL4 of herpes simplex virus 1 (Human herpesvirus 1) have been found in the genomes of all hitherto-analysed alphaherpesviruses, little is known about their function. In a project to analyse systematically, in an isogenic and standardized assay system, the gene products of the alphaherpesvirus pseudorabies virus (PrV; Suid herpesvirus 1), the PrV UL4 gene product was identified using a monospecific rabbit antiserum prepared against a bacterial fusion protein. Western blot and immunofluorescence analyses revealed that the 146 codon UL4 ORF of PrV was translated into a nuclear 15 kDa protein which was detectable from 6 h after infection of rabbit kidney cells, but was not found in purified virus particles. For functional analysis, a UL4-negative virus recombinant (PrV-ΔUL4F) was generated by mutagenesis of an infectious full-length clone of the PrV genome in E. coli. PrV-ΔUL4F was replication-competent in rabbit kidney cells, and plaque formation was not affected by the mutation. However, maximum virus titres of PrV-ΔUL4F were decreased about fivefold compared with wild-type PrV, and electron microscopy of infected cells demonstrated an impairment of release of mature virions. This growth defect of PrV-ΔUL4F could be corrected completely by propagation in UL4-expressing cells. Correlating with the inconspicuous in vitro phenotype, neurovirulence of PrV-ΔUL4F was also not affected significantly. Thus, UL4 encodes a non-structural protein of PrV that enhances virion formation but is not essential for PrV replication in vitro or in vivo.
Random mutagenesis of wheat streak mosaic virus HC-Pro: non-infectious interfering mutations in a gene dispensable for systemic infection of plants
Authors: Stenger Drake C. , Young Brock A. , French Roy
Published: August 2006

Mutations within the HC-Pro coding region of Wheat streak mosaic virus (WSMV) were introduced by misincorporation during PCR and evaluated for phenotype within the context of an infectious clone. Nine synonymous substitutions and 15 of 25 non-synonymous substitutions had no phenotypic effect. Four non-synonymous substitutions, including one that reverted consistently to wild type, resulted in attenuated systemic infection. Six non-synonymous substitutions and one nonsense substitution abolished systemic infectivity. Mutants bearing the GUS reporter gene were evaluated for the ability to establish primary infection foci. All attenuated mutants and two systemic infection-deficient mutants produced localized regions of GUS expression on inoculated leaves 3 days post-inoculation. In vitro assays revealed that mutants able to establish infection foci retained HC-Pro proteinase activity. Among mutants unable to establish infection foci, HC-Pro proteinase activity was retained, reduced or absent. As a complete HC-Pro deletion mutant can infect plants systemically, certain substitutions in this dispensable gene probably prevented infection of WSMV via interference.
Potato virus X RNA-mediated assembly of single-tailed ternary ‘coat protein–RNA–movement protein’ complexes
Authors: Karpova O. V. , Zayakina O. V. , Arkhipenko M. V. , Sheval E. V. , Kiselyova O. I. , Poljakov V. Yu. , Yaminsky I. V. , Rodionova N. P. , Atabekov J. G.
Published: August 2006

Different models have been proposed for the nature of the potexvirus transport form that moves from cell to cell over the infected plant: (i) genomic RNA moves as native virions; or (ii) in vitro-assembled non-virion ribonucleoprotein (RNP) complexes consisting of viral RNA, coat protein (CP) and movement protein (MP), termed TGBp1, serve as the transport form in vivo. As the structure of these RNPs has not been elucidated, the products assembled in vitro from potato virus X (PVX) RNA, CP and TGBp1 were characterized. The complexes appeared as single-tailed particles (STPs) with a helical, head-like structure composed of CP subunits located at the 5′-proximal region of PVX RNA; the TGBp1 was bound to the terminal CP molecules of the head. Remarkably, no particular non-virion RNP complexes were observed. These data suggest that the CP–RNA interactions resulting in head formation prevailed over TGBp1–RNA binding upon STP assembly from RNA, CP and TGBp1. STPs could be assembled from the 5′ end of PVX RNA and CP in the absence of TGBp1. The translational ability of STPs was characterized in a cell-free translation system. STPs lacking TGBp1 were entirely non-translatable; however, they were rendered translatable by binding of TGBp1 to the end of the head. It is suggested that the RNA-mediated assembly of STPs proceeds via two steps. Firstly, non-translatable CP–RNA STPs are produced, due to encapsidation of the 5′-terminal region. Secondly, the TGBp1 molecules bind to the end of a polar head, resulting in conversion of the STPs into a translatable form.
Complete nucleotide sequence, genomic organization and phylogenetic analysis of Citrus leprosis virus cytoplasmic type
Authors: Locali-Fabris E. C. , Freitas-Astúa J. , Souza A. A. , Takita M. A. , Astúa-Monge G. , Antonioli-Luizon R. , Rodrigues V. , Targon M. L. P. N. , Machado M. A.
Published: August 2006

The complete nucleotide sequence of the genomic RNA 1 (8745 nt) and RNA 2 (4986 nt) of Citrus leprosis virus cytoplasmic type (CiLV-C) was determined using cloned cDNA. RNA 1 contains two open reading frames (ORFs), which correspond to 286 and 29 kDa proteins. The 286 kDa protein is a polyprotein putatively involved in virus replication, which contains four conserved domains: methyltransferase, protease, helicase and polymerase. RNA 2 contains four ORFs corresponding to 15, 61, 32 and 24 kDa proteins, respectively. The 32 kDa protein is apparently involved in cell-to-cell movement of the virus, but none of the other putative proteins exhibit any conserved domain. The 5′ regions of the two genomic RNAs contain a ‘cap’ structure and poly(A) tails were identified in the 3′-terminals. Sequence analyses and searches for structural and non-structural protein similarities revealed conserved domains with members of the genera Furovirus, Bromovirus, Tobravirus and Tobamovirus, although phylogenetic analyses strongly suggest that CiLV-C is a member of a distinct, novel virus genus and family, and definitely demonstrate that it does not belong to the family Rhabdoviridae, as previously proposed. Based on these results it was proposed that Citrus leprosis virus be considered as the type member of a new genus of viruses, Cilevirus.
An ~140-kb deletion associated with feline spinal muscular atrophy implies an essentialLIX1function for motor neuron survival
Authors: Fyfe John C. , Menotti-Raymond Marilyn , David Victor A. , Brichta Lars , Schäffer Alejandro A. , Agarwala Richa , Murphy William J. , Wedemeyer William J. , Gregory Brittany L. , Buzzell Bethany G. , Drummond Meghan C. , Wirth Brunhilde , O'Brien Stephen J.
Published: August 2006

The leading genetic cause of infant mortality is spinal muscular atrophy (SMA), a clinically and genetically heterogeneous group of disorders. Previously we described a domestic cat model of autosomal recessive, juvenile-onset SMA similar to human SMA type III. Here we report results of a whole-genome scan for linkage in the feline SMA pedigree using recently developed species-specific and comparative mapping resources. We identified a novel SMA gene candidate,LIX1, in an ~140-kb deletion on feline chromosome A1q in a region of conserved synteny to human chromosome 5q15. ThoughLIX1function is unknown, the predicted secondary structure is compatible with a role in RNA metabolism.LIX1expression is largely restricted to the central nervous system, primarily in spinal motor neurons, thus offering explanation of the tissue restriction of pathology in feline SMA. An exon sequence screen of 25 human SMA cases, not otherwise explicable by mutations at theSMN1locus, failed to identify comparableLIX1mutations. Nonetheless, aLIX1-associated etiology in feline SMA implicates a previously undetected mechanism of motor neuron maintenance and mandates consideration ofLIX1as a candidate gene in human SMA whenSMN1mutations are not found.
Naltrexone versus acamprosate in the treatment of alcohol dependence: a multi‐centre, randomized, double‐blind, placebo‐controlled trial
Authors: Morley Kirsten C. , Teesson Maree , Reid Sophie C. , Sannibale Claudia , Thomson Clare , Phung Nghi , Weltman Martin , Bell James R. , Richardson Kylie , Haber Paul S.
Published: August 2006

Aim  To compare the efficacy of acamprosate and naltrexone in the treatment of alcohol dependence. 

Design  A double‐blind, placebo‐controlled trial. 

Setting  Three treatment centres in Australia. 

Participants  A total of 169 alcohol dependent subjects were given naltrexone (50 mg/day), acamprosate (1998 mg/day) or placebo for 12 weeks.

Intervention  All subjects were offered manualized compliance therapy, a brief intervention that targets problems that may affect treatment compliance such as ambivalence and misperceptions about medication.

Measurements  Time to the first drink, time to first relapse, drinks per drinking day and cumulative abstinence.

Findings  In intention‐to‐treat analyses, there were no differences between groups on outcome measures of drinking, craving or biochemical markers. Similarly, analyses of the 94 subjects that completed the study in full and demonstrated 80% compliance, revealed no significant treatment effects. Differential treatment effects were identified after stratification according to scores on the Alcohol Dependence Scale (ADS) and Depression Anxiety and Stress Scale (DASS). A significant beneficial treatment effect on time to first relapse was revealed for subjects with ‘no depression’ allocated to naltrexone (n = 56; P < 0.01). In addition, a significant beneficial treatment effect was revealed in subjects with ‘low dependence’ allocated to naltrexone (n = 34; P < 0.05).

Conclusions  The results of this study support the efficacy of naltrexone in the relapse prevention of alcoholism amongst those with low levels of clinical depression and alcohol dependence severity. No effect of acamprosate was found in our sample.
Identification of additional cytogenetic and molecular genetic abnormalities in acute myeloid leukaemia with t(8;21)/AML1‐ETO
Authors: Kuchenbauer F. , Schnittger S. , Look T. , Gilliland G. , Tenen D. , Haferlach T. , Hiddemann W. , Buske C. , Schoch C.
Published: August 2006

AML1‐ETO collaborates with further genetic abnormalities to induce acute myeloid leukaemia (AML). We analysed 99 patients with an AML1‐ETO rearrangement for additional aberrations. Frequent genetic abnormalities were, loss of a sex chromosome (56/99, 56·5%) and del(9)(q22) (24/99, 24·2%). The most frequent molecular aberrations were mutations of KITD816 (3/23, 13%) and NRAS (8/89, 8·9%). Further molecular abnormalities were FLT3 mutations (3/87, 3·4%), AML1 (1/26, 3·8%) and PU1 (1/14, 7·1%). MLL‐PTD, KRAS and CEBPA mutations were not found. These clinical findings support the model that AML1‐ETO collaborates with other genetic alterations, such as mutations of receptor tyrosine kinases, to induce AML.
Monoclonal gammopathy of undetermined significance
Authors: Kyle Robert A. , Vincent Rajkumar S.
Published: August 2006

Significant advances have been made in our understanding of the natural history, pathogenesis, mechanisms of progression and prognosis of monoclonal gammopathy of undetermined significance (MGUS). Although the overall incidence of MGUS progression is 1 per year, it is now possible to more accurately predict the risk of progression based on a new risk‐stratification model. However, it is still hard to design chemopreventive trials given that the absolute risk of progression per year is low, even in the high‐risk group. Therefore, further improvements in estimating the risk of progression are needed. Roughly 50% of MGUS may originate from primary translocation events at the heavy‐chain immunoglobulin locus at chromosome 14q32. In most of the remaining MGUS patients, the initiating event is associated with genomic instability that results in hyperdiploidy of certain odd numbered chromosomes. Cytogenetically distinct subtypes of MGUS may carry significant differences in the risk of progression to malignancy. New markers, such as measures of bone marrow angiogenesis and circulating plasma cells may be additional prognostic factors. A better understanding of the mechanisms underlying the transition of normal plasma cells to the MGUS phenotype, and the transition of MGUS to myeloma or related malignancy, will help identify new risk factors for progression and new targets for chemopreventive interventions.