bluuebunny/crossref_metadata_2025 huggingface dataset:
Nucleation and growth kinetics of nanocrystals formed upon pulsed-laser ablation in liquid
Authors: Wang C. X. , Liu P. , Cui H. , Yang G. W.
Published: November 2005

To have a clear physical insight into the nanocrystal formation upon pulsed-laser ablation in liquid, we proposed a theoretical kinetic approach to elucidate the nucleation and growth of nanocrystals with respect to the capillary effect of the nanometer-sized curvature of crystalline nuclei. Taking the nanodiamond synthesis by pulsed-laser ablating a graphite target in water as an example, we predicted the nucleation time, growth velocity, and the grown size of nanodiamonds on the basis of the proposed kinetic model, and found that these theoretical results are in well agreement with our experiment cases. We expected that the kinetic approach is generally applicable to understanding the basic physics of nanocrystal formation in pulsed-laser ablation in liquid.
Nonlinear all-optical GaN∕AlGaN multi-quantum-well devices for 100Gb∕s applications at λ=1.55μm
Authors: Sun Greg , Khurgin Jacob B. , Soref Richard A.
Published: November 2005

Using quantum-mechanical analysis, a strain-balanced stack of coupled GaN∕AlGaN quantum wells has been engineered for bandwidth-optimized all-optical switching at low switching powers. Intersubband transitions between three conduction subbands provide the basis for the large, fast, nonlinear optical response. Optimized performance for a given symbol rate is obtained by engineering the response time and nonlinear phase shift.
Evidence for Au(I)…Au(I) Interactions in a Sterically Congested Environment: Two-Coordinate Gold(I) Halide Phosphine Complexes
Authors: Bott Raymond C. , Healy Peter C. , Smith Graham
Published: November 2005

Two-coordinate tris(2-methylphenyl)phosphine and tris(4-methylphenyl)phosphinegold(I) halide complexes, [AuP(otol)3X], [AuP(ptol)3X], where X = Cl, Br, and I, have been crystallized from dimethylformamide and characterized by single-crystal X-ray structure determinations. The P(otol)3 structures comprise an isomorphous series distinct from the previously published chloride, crystallizing with two independent molecules in the asymmetric unit in the space group Pbca, with a ≈ 20.0, b ≈ 28.0, c ≈ 14.0 Å. The molecules associate to form dimers through a back-to-back sextuple phenyl embrace (6PE). The P(ptol)3 complexes are isomorphous with the previously published chloride, crystallizing with two independent molecules in the unit cell in the space group P21/c, with a ≈ 10.0, b ≈ 22.0, c ≈ 19.5 Å, β ≈ 99°. The molecules associate through edge-to-face interactions along the direction of the a-axis. Preparation of the chloride by anodic dissolution of gold in an acetonitrile solution of the ligand and aqueous HCl yields a new polymorph, crystallizing in the space group Aba2, with a 19.738(2), b 11.813(3), c 17.645(1) Å. Despite the bulkiness of the phosphine ligand, this form of [AuP(ptol)3Cl] exhibits a short intermolecular Au…Au contact distance of 3.375(1) Å, indicative of a significant aurophilic interaction. The ranges for the Au—P, Au—Cl, Au—Br, Au—I bond lengths and P—Au—X bond angles in the series are: 2.201(3)–2.265(4), 2.255(3)–2.290(4), 2.388(2)–2.411(2), 2.542(1)–2.556(2) Å, and 173.2(2)–179.6(1)° respectively.
Formulation of Cocaine-Imprinted Polymers Utilizing Molecular Modelling and NMR Analysis
Authors: Holdsworth Clovia I. , Bowyer Michael C. , Lennard Chris , McCluskey Adam
Published: November 2005

Molecular imprinted polymers (MIPs) have distinctive features that make them attractive as an inexpensive, reusable, and robust field-based detection system for illicit substances. Optimizing MIP performance is traditionally attained by the synthesis and evaluation of a plethora of individual formulations. A non-covalently imprinted polymer for cocaine has been prepared using a commercially available molecular modelling package (Spartan 02) to predict energetically favourable monomer–template interactions between the target (T) and two different functional monomers (FM)—methacrylic acid (MAA) and 4-vinylpyridine (4VP). NMR studies undertaken to assess target–monomer behaviour in solution were in good agreement with the computational data. MIPs involving three target-to-functional monomer ratios (1 : 2, 1 : 6, and 1 : 14) were prepared and evaluated. Target rebinding was found to be most favourable in the 1 : 2 formulation with a target-selective binding of 0.48 ppm and an imprinting factor (I) of 2.8 obtained for 10 mg of test polymer.
Kinetic and Mechanistic Study on the Reactions of [Pd(dien)H2O]2+ and [Pt(dien)H2O]2+ with L-Cysteine and S-Methyl-L-cysteine
Authors: Petrović Biljana V. , Bugarčić Živadin D.
Published: November 2005

The reactions of [Pd(dien)H2O]2+ and [Pt(dien)H2O]2+ (dien = diethylenetriamine or 1,5-diamino-3-azapentane) with l-cysteine and S-methyl-l-cysteine were studied in an aqueous 0.10 M NaClO4 solution using stopped-flow and conventional UV-vis spectrophotometry. The second-order rate constants for the reactions of [Pd(dien)H2O]2+ at pH 1.0 are k1298 = (9.11 ± 0.11) × 102 M−1 s−1 for l-cysteine, and k1298 = (33.79 ± 0.63) × 102 M−1 s−1 for S-methyl-l-cysteine. The second-order rate constants for the reactions of [Pt(dien)H2O]2+ at pH 1.0 with l-cysteine is k1298 = (1.28 ± 0.08) × 10−2 M−1 s−1 and for S-methyl-l-cysteine is k1298 = (3.87 ± 0.02) × 10−2 M−1 s−1. Activation parameters were determined for all reactions, and the negative values of entropy of activation support an associative complex formation mechanism. Substitution reactions were also studied at pH 0.5, 1.0, and 1.5. The rate constants increase with increase in pH. These results are discussed in terms of protolitic equilibrium.
Agricultural soils irrigated with acidic mine water: acidity, heavy metals, and crop contamination
Authors: Lin C. , Lu W. , Wu Y.
Published: November 2005

Agricultural soils irrigated with acidic mine water from the Guangdong Dabaoshan Mine, China, were investigated. The pH of the soils could be as low as 3.9. However, most of the mineral acids introduced into the soils by irrigation were transformed to insoluble forms through acid buffering processes and thus temporarily stored in the soils. Different heavy metals exhibited different fraction distribution patterns, with Zn and Cu being mainly associated with organic matter and Pb being primarily bound to oxides (statistically significant at P = 0.05). Although the mean of exchangeable Cd was greatest among the Cd fractions, there was no statistically significant difference between the exchangeable Cd and the oxide-bound Cd (the 2nd greatest fraction) or between the exchangeable Cd and the carbonate-bound Cd (the 3rd greatest fraction). It was also found that there were generally good relationships between the concentrations of various Zn, Cu, Pb, and Cd fractions and pH, suggesting that a major proportion of each heavy metal in the soils was mainly derived from the acidic irrigation water. The results also show that the crops grown in these soils were highly contaminated by heavy metals, particularly Cd. The concentration of Cd in the edible portions of most crops was far in excess of the limits set in China National Standards for Vegetables and Fruits and this can be attributable to the extremely high transfer rate of Cd from the soils to the crops under the cropping system adopted in the study area.
Colour variation in standard soil-colour charts
Authors: Sánchez-Marañón M. , Huertas R. , Melgosa M.
Published: November 2005

This paper presents colourimetric analyses of 6 standard soil-colour charts (1372 chips) from different manufacturers, editions, and degrees of use. The CIELAB hab, L*, and C*ab were found to have significant (analysis of variance, P < 0.05) variations among tested charts, and the Munsell hue, value, and chroma measured in most chips varied from their notation by as much as 1 unit. This discrepancy can be attributed to printing differences and/or colour fading. The Munsell loci of constant hue and chroma plotted in CIELAB colour space showed that colour fading is not uniform, so that visual steps between neighbouring chips change, and constant hue and chroma lines become deformed. The colour difference between chips identically designated in two charts ranged from 0.94 CIEDE2000 units (above perception threshold) for charts from the same manufacturer and degree of use, to 3.72 CIEDE2000 units for old charts from 2 different manufacturers. Chips from old charts became yellowish, darker, and less saturated. These colour changes are consistent with the responses of 10 observers who, on assessing 10 soil-colour samples, reported Munsell notations to have redder hue, lighter value and greater chroma. Periodic colourimetric checking of soil-colour charts would be advisable in order to avoid mistakes in soil-colour description.
The effectiveness of coal fly-ash to decrease phosphorus loss from grassland soils
Authors: McDowell R. W.
Published: November 2005

Phosphorus (P) loss from soils can impair surface water quality. A study was conducted to test the efficacy of fly-ash to decrease phosphorus loss in 11 grassland soils. A preliminary toxicity and leaching experiment indicated that heavy metal concentrations (As, Cd, Pb, Se) in leachate and pasture from a soil treated with ash up to 50 mg/kg were not different from the control (unamended soil). Heavy metal concentrations in the ash were generally below limits for maximum concentrations in soil. Following incubation of fly ash at a rate of 20 mg/kg for 3 months with 11 grassland soils packed into boxes, overland flow was generated by simulated rainfall on each boxed soil. Analysis of overland flow indicated that in 2 semi-arid soils, P loss decreased due to decreased particulate P (PP) loss and low organic C concentration (<20 g/kg) that facilitated soil dispersion and slaking and increased soil strength. However, in 4 other soils (including 3 volcanic-ash soils with organic C >70 g/kg), P loss increased due to increased soil pH from 6 to 7 where P is most soluble. In all soils, despite an increase in P in recalcitrant soil P fractions, increased soil pH stimulated soil C and P mineralisation (decreased organic C by, on average, 4.1 g/kg), decreased soil organic P, and increased inorganic P in labile fractions. It is concluded that the application of fly-ash from this source should not be used as an amendment to decrease P loss in pastures where soil pH is commonly <6.0, but could provide useful both as a supplement to lime and in mitigating P loss in cropping soils.
Mapping boron deficiency risk in soils of south-west Western Australia using a weight of evidence model
Authors: Wong M. T. F. , Bell R. W. , Frost K.
Published: November 2005

The aim of this work was to develop a risk map for boron (B) deficiency in the grain cropping regions of Western Australia (WA), whilst avoiding the high costs associated with direct B measurements for an area as vast as the south-west of WA. The study firstly determined relationships between 0.01 m CaCl2-extractable soil B levels and readily available data on soil properties and parent materials for Reference Soils of south-west Australia and secondly assembled direct evidence of B deficiency risk from surveys of farmers’ crops and soils and from glasshouse experiments. Across 73 Reference Soils, there was a positive relationship between 0.01 m CaCl2-extractable soil B levels and clay (r
2 = 0.50) and pH (r
2 = 0.43) in the surface horizon. Soils containing <0.5 mg B/kg generally had <5% clay and pH CaCl2 <5.5. Plant and soil analysis surveys in farmers’ fields revealed 10–20% of fields had B levels below tentative critical levels. In a glasshouse experiment, B response in oilseed rape was obtained in 4 sandy acid soils, all developed on sandstone parent materials. From this prior evidence of B deficiency, spatial data layers for surface soil pH, subsurface pH, surface clay level, and geology in south-western Australia were weighted and combined using the Dempster-Shafer weight of evidence model to map B-deficiency risk. The weightings of evidence layers were revised to increase the correspondence between predicted areas of high risk and field areas with measured low B or B deficiency from a validation dataset. The model helps overcome the high cost associated with direct B measurements for risk mapping. A similar approach may have value for mapping risk of other deficiencies of relevance to agriculture.
A rice-based edible vaccine expressing multiple T cell epitopes induces oral tolerance for inhibition of Th2-mediated IgE responses
Authors: Takagi Hidenori , Hiroi Takachika , Yang Lijun , Tada Yoshifumi , Yuki Yoshikazu , Takamura Kaoru , Ishimitsu Ryotaro , Kawauchi Hideyuki , Kiyono Hiroshi , Takaiwa Fumio
Published: November 2005

Peptide immunotherapy using multiple predominant allergen-specific T cell epitopes is a safe and promising strategy for the control of type I allergy. In this study, we developed transgenic rice plants expressing mouse dominant T cell epitope peptides of Cry j I and Cry j II allergens of Japanese cedar pollen as a fusion protein with the soybean seed storage protein glycinin. Under the control of the rice seed storage protein glutelin
GluB-1
promoter, the fusion protein was specifically expressed and accumulated in seeds at a level of 0.5% of the total seed protein. Oral feeding to mice of transgenic rice seeds expressing the T cell epitope peptides of Cry j I and Cry j II before systemic challenge with total protein of cedar pollen inhibited the development of allergen-specific serum IgE and IgG antibody and CD4
+
T cell proliferative responses. The levels of allergen-specific CD4
+
T cell-derived allergy-associated T helper 2 cytokine production of IL-4, IL-5, and IL-13 and histamine release in serum were significantly decreased. Moreover, the development of pollen-induced clinical symptoms was inhibited in our experimental sneezing mouse model. These results indicate the potential of transgenic rice seeds in production and mucosal delivery of allergen-specific T cell epitope peptides for the induction of oral tolerance to pollen allergens.
Residue-rotamer-reduction algorithm for the protein side-chain conformation problem
Authors: Xie Wei , Sahinidis Nikolaos V.
Published: November 2005

Motivation: The protein side-chain conformation problem is a central problem in proteomics with wide applications in protein structure prediction and design. Computational complexity results show that the problem is hard to solve. Yet, instances from realistic applications are large and demand fast and reliable algorithms.

Results: We propose a new global optimization algorithm, which for the first time integrates residue reduction and rotamer reduction techniques previously developed for the protein side-chain conformation problem. We show that the proposed approach simplifies dramatically the topology of the underlining residue graph. Computations show that our algorithm solves problems using only 1–10% of the time required by the mixed-integer linear programming approach available in the literature. In addition, on a set of hard side-chain conformation problems, our algorithm runs 2–78 times faster than SCWRL 3.0, which is widely used for solving these problems.

Availability: The implementation is available as an online server at

Contact:  nikos@uiuc.edu
Nathanael Vincent and Confucius's ‘great learning’ in restoration England
Authors: Jenkinson Matt
Published: November 2005

This paper outlines the sinological activities of Nathanael Vincent (d. 1722), an obscure and elusive fellow of the Royal Society (1683–7; readmitted 1694) who was also fellow of Clare Hall in Cambridge and chaplain in ordinary to Charles II. An amateur scientist operating in the shadow of the great fellows of the early Royal Society, Vincent's involvement ranged from investigating the work of Denis Papin to presenting a manuscript of Isaac Newton'sPhilosophiæ Naturalis Principia Mathematica. However, his greatest contribution to the intellectual history of the Restoration is located in his 1685 translation of Confucius's ‘Great Learning’, which seems to be the first time that a Confucian book began to be printed in the English language. Hitherto unnoticed, hidden away in an appendix to a court sermon, it nonetheless represented part of the interest in Chinese culture in the circles of the early Royal Society. This paper places Vincent in the context of the activities of the early Royal Society and offers an overview of this interest in sinology. It then considers how Vincent gained access to Confucian texts, how he was able to ‘translate’ from them, and what ramifications the philosophy had for an Anglican divine in Restoration England.
Magnetic field transport and kinematic dynamo effect: a Lagrangian interpretation
Authors: Celani A , Mazzino A , Vincenzi D
Published: November 2005

The growth of magnetic fluctuations in the inertial range of turbulence is investigated in terms of fluid particle dynamics. The existence of dynamo effect is related to the time behaviour of the correlations between tangent vectors evolving along Lagrangian trajectories. In the presence of dynamo effect, the correlations between tangent vectors grow exponentially in time; in the absence of dynamo effect they decay as power laws. The above behaviours are intimately related to statistical conservation laws for the Lagrangian dynamics.
TheN-vortex problem on a rotating sphere. I Multi-frequency configurations
Authors: Newton Paul K , Shokraneh Houman
Published: November 2005

The problem ofN-point vortices moving on a rotating unit sphere is considered. Through a sequence of linear coordinate transformations, which takes into account the orientation of the centre of vorticity vector with respect to the axis of rotation, we show how to reduce the problem to that on a non-rotating sphere, where the centre of vorticity vector is aligned with thez-axis. As a consequence, we prove that integrability on the rotating sphere is the same as on the non-rotating sphere, namely, the three-vortex problem on the rotating sphere is integrable for all vortex strengths, while the four-vortex problem is integrable in the special case where the centre of vorticity is zero. Rigid multi-frequency configurations that retain their shape while rotating about two independent axes with two independent frequencies are obtained, and necessary conditions for one- and two-frequency motions are derived. Examples including dipoles which exhibit global ‘wobbling’ and ‘tumbling’ dynamics, rings, and Platonic solid configurations are shown to undergo either periodic or quasi-periodic evolution on the rotating sphere depending on the ratio of the solid-body rotational frequencyΩto the rotational frequencyωassociated with the rigid structure.
Fathers have lower salivary testosterone levels than unmarried men and married non-fathers in Beijing, China
Authors: Gray Peter B , Jeffrey Yang Chi-Fu , Pope Harrison G
Published: November 2005

A growing body of evidence, almost entirely from North America, has found that male testosterone levels are positively associated with mating effort (male–male competition and mate-seeking behaviour), while lower testosterone levels have been associated with affiliative pair bonding and paternal care. To expand the cross-cultural scope of this research, here we investigate variation in salivary testosterone levels among Chinese men in relation to marital and parenting variables. One hundred and twenty-six men drawn from a Beijing university setting between the ages of 21 and 38 completed a questionnaire and provided both morning and late afternoon saliva samples from which testosterone levels were measured. The 66 unmarried men had slightly higher levels of testosterone than the 30 married non-fathers, but this difference was not statistically significant. However, the 30 fathers exhibited significantly lower testosterone levels than both unmarried men and married non-fathers. Among married non-fathers, marital relationship quality was not significantly related to testosterone levels. Among married fathers, men with children aged less than 4 years of age did not have lower testosterone levels than men with older children. These data are the first outside of North America to show lower testosterone levels among fathers, and lend support to the theoretical view that male testosterone levels differ according to mating and parenting effort.
A mechanistic link between chick diet and decline in seabirds?
Authors: Kitaysky Alexander S , Kitaiskaia Evgenia V , Piatt John F , Wingfield John C
Published: November 2005

A climatic regime shift during the mid-1970s in the North Pacific resulted in decreased availability of lipid-rich fish to seabirds and was followed by a dramatic decline in number of kittiwakes breeding on the Pribilof Islands. Although production of chicks in the mid-1970s was adequate to sustain kittiwake populations in the early 1980s, the disappearance of birds from breeding colonies apparently exceeded recruitment. No mechanism has been proposed to explain why recruitment would differ among fledglings fed lipid-rich or lipid-poor fish during development. Here we show that diets low in lipids induce nutritional stress and impair cognitive abilities in young red-legged kittiwakes,Rissa brevirostris. Specifically, growth retardation, increased secretion of stress hormones and inferior ability to associate food distribution with visual cues were observed in individuals fed lipid-poor diets. We conclude that lipid-poor diets during development affect the quality of young seabirds, which is likely to result in their increased mortality and low recruitment.
Description of Gluconacetobacter swingsii sp. nov. and Gluconacetobacter rhaeticus sp. nov., isolated from Italian apple fruit
Authors: Dellaglio Franco , Cleenwerck Ilse , Felis Giovanna E. , Engelbeen Katrien , Janssens Danielle , Marzotto Marta
Published: November 2005

Two Gram-negative, rod-shaped, non-spore-forming bacteria (DST GL01Tand DST GL02T) were isolated from apple fruit juice in the region of the Italian Alps. On the basis of 16S rRNA gene sequence similarities, strains DST GL01Tand DST GL02Twere shown to belong to theα-subclass of theProteobacteria, and, in particular, to the genusGluconacetobacter, in theGluconacetobacter xylinusbranch (98·5–100 %). Chemotaxonomic data (major ubiquinone, Q10; predominant fatty acid, C18 : 1ω7c, accounting for approximately 50 % of the fatty acid content) support the affiliation of both strains to the genusGluconacetobacter. The results of DNA–DNA hybridizations, together with physiological and biochemical data, allowed genotypic and phenotypic differentiation between strains DST GL01Tand DST GL02Tand from the 11 validly publishedGluconacetobacterspecies. They therefore represent two new species, for which the namesGluconacetobacter swingsiisp. nov. andGluconacetobacter rhaeticussp. nov. are proposed, with the type strains DST GL01T(=LMG 22125T=DSM 16373T) and DST GL02T(=LMG 22126T=DSM 16663T), respectively.
Methylosarcina lacus sp. nov., a methanotroph from Lake Washington, Seattle, USA, and emended description of the genus Methylosarcina
Authors: Kalyuzhnaya Marina G. , Stolyar Sergey M. , Auman Ann J. , Lara Jimmie C. , Lidstrom Mary E. , Chistoserdova Ludmila
Published: November 2005

An obligately methanotrophic bacterial strain, LW14T, isolated from the sediment of Lake Washington, Seattle, USA, is described taxonomically. The isolate is an aerobic, Gram-negative, non-motile bacterium capable of growth on methane, and possesses type I intracytoplasmic membranes (i.e. it is a type I methanotroph). The strain possesses particulate methane monooxygenase (MMO) and has no soluble MMO. Formaldehyde is assimilated via the ribulose monophosphate cycle. The isolate grows within a pH range of 4–8, with the optimum between pH 5·5 and 6·5. The cellular fatty acid profile is dominated by C16 : 
ω18c, C16 : 1
ω7c and C16 : 1
ω5t fatty acids. The DNA G+C content is 53·3±0·4 mol%. On the basis of sequence analysis of the 16S rRNA gene, isolate LW14T is related most closely to representatives of the genus Methylosarcina. However, DNA–DNA hybridization analysis reveals only a distant relationship between isolate LW14T and the previously described Methylosarcina species. On the basis of its phenotypic and genotypic characteristics, LW14T represents a novel species of the genus Methylosarcina, for which the name Methylosarcina lacus sp. nov. is proposed, with LW14T (=ATCC BAA-1047T=JCM 13284T) as the type strain.
Luteibacter rhizovicinus gen. nov., sp. nov., a yellow-pigmented gammaproteobacterium isolated from the rhizosphere of barley (Hordeum vulgare L.)
Authors: Johansen Jens E. , Binnerup Svend J. , Kroer Niels , Mølbak Lars
Published: November 2005

Three strains of Gram-negative, aerobic, yellow-pigmented, chemo-organotrophic bacteria, motile by a polar flagellum, were isolated from the rhizosphere of spring barley (Hordeum vulgareL.) at a research field near Copenhagen, Denmark. The three strains, LJ79, LJ96Tand LJ99, formed visible colonies on one-tenth-strength tryptic soy broth supplemented with agar (1/10 TSBA) after incubation for 6 days at 15 °C. The strains hydrolysed starch, casein (skimmed milk), gelatin and various pentoses and hexoses and grew on MacConkey agar and full-strength TSBA. Growth on 1/10 TSBA occurred at 4–30 °C, pH 6–9 and 0–3 % (w/v) NaCl. The strains had identical 16S rRNA gene sequences and ERIC (enterobacterial repetitive intergenic consensus sequence) fingerprint profiles, but could be differentiated by their RAPD (random amplified polymorphic DNA) fingerprint patterns. Strain LJ96Thad a DNA G+C content of 64·3 mol% and the major fatty acids were 15 : 0 iso (23·4 %), 17 : 1 isoω9c(25·5 %) and 17 : 0 iso (18·1 %). Phylogenetic analysis of the 16S rRNA gene sequences of the three strains showed 96 % sequence similarity toRhodanobacter lindaniclasticus LMG 18385T, 95 % toFrateuria aurantiaDSM 6220Tand 96 % toFulvimonas soliLMG 19981T. Using LJ96TDNA as probe, DNA–DNA hybridizations documented the relationship of the three strains to a single species (87·4–98·7 % relatedness) and showed less than 30 % relatedness toFrateuria aurantiaDSM 6220TandFulvimonas soliDSM 14263T.Rhodanobacter lindaniclasticus LMG 18385Tis not extant and the strain not available from any public strain collections, thus DNA–DNA hybridization could not include this strain. On the basis of genotypic and phenotypic characteristics, the three yellow-pigmented strains could also be differentiated fromFrateuria aurantia,Fulvimonas soliandRhodanobacter lindaniclasticus. The nameLuteibacter rhizovicinusgen. nov., sp. nov. is proposed, with the type strain LJ96T(=DSM 16549T=ATCC BAA-1015T).
Spiroplasma leucomae sp. nov., isolated in Poland from white satin moth (Leucoma salicis L.) larvae
Authors: Oduori Marietta A. , Lipa Jerzy J. , Gasparich Gail E.
Published: November 2005

Spiroplasma sp. strain SMAT, isolated in Poland from white satin moth larvae, Leucoma salicis L. (Lepidoptera: Lymantriidae), was serologically distinct from other Spiroplasma species, groups or subgroups. Dark-field microscopy of the cells revealed the classical helical shape and subsequent transmission electron microscopy revealed cells surrounded by only a single cell membrane (lacking a cell wall). Growth of strain SMAT occurred in M1D medium at 30 °C. Strain SMAT catabolized both glucose and arginine, but did not hydrolyse urea. The G+C content of the DNA was 24±1 mol% as determined by melting temperature analysis. Serological analysis revealed a very weak cross-reactivity (positive reaction only up to a 1 : 80 dilution) with two Spiroplasma strains, 277F (Spiroplasma sp. group I-4) and LB-12 (Spiroplasma sp. group I-5). Strain SMAT (=ATCC BAA-521T=NBRC 100392T) is designated the type strain of a novel species, Spiroplasma leucomae sp. nov. (class Mollicutes: order Entomoplasmatales: family Spiroplasmataceae).
Halolactibacillus halophilus gen. nov., sp. nov. and Halolactibacillus miurensis sp. nov., halophilic and alkaliphilic marine lactic acid bacteria constituting a phylogenetic lineage in Bacillus rRNA group 1
Authors: Ishikawa Morio , Nakajima Kazuyuki , Itamiya Yuko , Furukawa Sayumi , Yamamoto Yasushi , Yamasato Kazuhide
Published: November 2005

Eleven novel strains of marine-inhabiting lactic acid bacteria that were isolated from living and decaying marine organisms collected from a temperate area of Japan are described. The isolates were motile with peritrichous flagella and non-sporulating. They lacked catalase, quinones and cytochromes. Fermentation products from glucose were lactate, formate, acetate and ethanol. Lactate yield as percentage conversion from glucose was affected by the pH of the fermentation medium: ∼55 % at the optimal growth pH of 8·0, greater than ∼70 % at pH 7·0 and less than ∼30 % at pH 9·0. The molar ratio of the other three products was the same at each cultivation pH, approximately 2 : 1 : 1. Carbohydrates and related compounds were aerobically metabolized to acetate and pyruvate as well as lactate. The isolates were slightly halophilic, highly halotolerant and alkaliphilic. The optimum NaCl concentration for growth was 2·0–3·0 % (w/v), with a range of 0–25·5 %. The optimum pH for growth was 8·0–9·5, with a range of 6·0–10·0. The G+C content of the DNA was 38·5–40·7 mol%. The isolates constituted two genomic species (DNA–DNA relatedness of less than 41 %) each characterized by sugar fermentation profiles. The cell-wall peptidoglycan of both phenotypes containedmeso-diaminopimelic acid. The major cellular fatty acids were C16 : 0and a-C13 : 0. Comparative sequence analysis of the 16S rRNA genes revealed that these isolates represent novel species constituting a phylogenetic unit outside the radiation of typical lactic acid bacteria and an independent line of descent within the group composed of the halophilic/halotolerant/alkaliphilic and/or alkalitolerant species inBacillusrRNA group 1, with 94·8–95·1 % similarity to the genusParaliobacillus, 93·7–94·1 % to the genusGracilibacillusand 93·8–94·2 % toVirgibacillus marismortui. On the basis of possession of physiological and biochemical characteristics common to typical lactic acid bacteria withinBacillusrRNA group 1, chemotaxonomic characteristics and phylogenetic independence, a new genus and two species,Halolactibacillus halophilusgen. nov., sp. nov. andHalolatibacillus miurensissp. nov., are proposed. The type strains areHalolactibacillus halophilusM2-2T(=DSM 17073T=IAM 15242T=NBRC 100868T=NRIC 0628T) (G+C content 40·2 mol%) andHalolactibacillus miurensisM23-1T(=DSM 17074T=IAM 15247T=NBRC 100873T=NRIC 0633T) (G+C content 38·5 mol%).
Reclassification of Alcaligenes latus strains IAM 12599T and IAM 12664 and Pseudomonas saccharophila as Azohydromonas lata gen. nov., comb. nov., Azohydromonas australica sp. nov. and Pelomonas saccharophila gen. nov., comb. nov., respectively
Authors: Xie Cheng-Hui , Yokota Akira
Published: November 2005

The aim of this study was to clarify the taxonomic position of the nitrogen-fixing and hydrogen-oxidizing bacteria Alcaligenes latus strains IAM 12599T, IAM 12664 and IAM 12665 and Pseudomonas saccharophila IAM 14368T. It was found that the type strain of Alcaligenes latus, IAM 12599T, showed 99·9 and 96·1 % 16S rRNA gene sequence similarity to strains IAM 12665 and IAM 12664, respectively. A comparison using DNA–DNA hybridization suggested that strains IAM 12599T and IAM 12665 belong to a single species (89·7 %) and that strain IAM 12664 (35·1 %) forms a separate species. The phenotypic characteristics also support the conclusion that these bacteria should be identified as two species of a new genus: Azohydromonas lata gen. nov., comb. nov. (type strain IAM 12599T=DSM 1122T=LMG 3321T=ATCC 29712T; reference strain IAM 12665=DSM 1123=LMG 3325=ATCC 29714) and Azohydromonas australica sp. nov. (type strain IAM 12664T=DSM 1124T=LMG 3324T=ATCC 29713T). Pseudomonas saccharophila IAM 14368T was found to be closely related to the phototrophic bacterium Roseateles depolymerans, with 96·8 % 16S rRNA gene sequence similarity, but the two bacteria are quite different with respect to their metabolism and some significant phenotypic characteristics, suggesting that they cannot be included in a single genus. Further studies on their nifH gene sequences, G+C content of the DNA and cellular fatty acid composition confirm that Pseudomonas saccharophila should be reclassified: the name Pelomonas saccharophila gen. nov., comb. nov. is proposed, with the type strain IAM 14368T (=LMG 2256T=ATCC 15946T).
Pseudoalteromonas byunsanensis sp. nov., isolated from tidal flat sediment in Korea
Authors: Park Yoon-Dong , Baik Keun Sik , Yi Hana , Bae Kyung Sook , Chun Jongsik
Published: November 2005

A Gram-negative, motile, strictly aerobic, violet-pigment-producing bacterium, designated strain FR1199T, was isolated from tidal flat sediment of Byunsan, South Korea. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain FR1199Trepresents a distinct line of descent within the genusPseudoalteromonas. The phenotypic features of strain FR1199Twere similar to those ofPseudoalteromonas phenolicaandPseudoalteromonas luteoviolacea, but several physiological and chemotaxonomical properties readily distinguished strain FR1199Tfrom these species. Major fatty acids were straight-chain saturated (C16 : 0) and monounsaturated C18 : 1ω7cfatty acids. The DNA G+C content was 39 mol%. On the basis of polyphasic evidence, it is concluded that the isolate represents a novel species within the genusPseudoalteromonas, for which the namePseudoalteromonas byunsanensissp. nov. is proposed. The type strain is FR1199T(=JCM 12483T=KCTC 12274T).
Paenibacillus mendelii sp. nov., from surface-sterilized seeds of Pisum sativum L.
Authors: Šmerda Jakub , Sedláček Ivo , Páčová Zdena , Durnová Eva , Smíšková Alexandra , Havel Ladislav
Published: November 2005

A Gram-variable, facultatively anaerobic, endospore-forming bacterium was isolated from surface-sterilized seeds of the garden pea and characterized with phenotypic and molecular methods. A PCR with thePaenibacillus-specific primer PAEN515F and the 16S rRNA gene sequence indicated that strain C/2Tbelongs to the genusPaenibacillusand is closely related toPaenibacillus phyllosphaerae(94·0 % sequence similarity). Strain C/2Tgenerated a unique phenotypic profile, in particular for the production of acid from substrates. The DNA G+C content (50·8 mol%) and the major fatty acid (anteiso-C15 : 0) are consistent with the genusPaenibacillus. DNA–DNA hybridization distinguished strain C/2Tfrom other phylogenetically relatedPaenibacillusspecies and, therefore, strain C/2T(=CCM 4839T=LMG 23002T) is here described as the type strain of a novel species, for which the namePaenibacillus mendeliisp. nov. is proposed.
Photobacterium aplysiae sp. nov., a lipolytic marine bacterium isolated from eggs of the sea hare Aplysia kurodai
Authors: Seo Hae Jeom , Bae Seung Seob , Yang Sung Hyun , Lee Jung-Hyun , Kim Sang-Jin
Published: November 2005

A bacterium, named GMD509T, showing lipolytic activity was isolated from the eggs of the sea hare Aplysia kurodai collected at Mogiyeo (depth, 12 m), an uninhabited small island in the South Sea of Korea. The strain is Gram-negative, motile, facultatively anaerobic, mesophilic and weakly halophilic. Optimal growth of strain GMD509T occurs in the presence of 3·0 % (w/v) NaCl and at pH 8 and 25 °C. The whole-cell fatty acid profile of the isolate includes C16 : 1, C16 : 0 and C18 : 1 as major fatty acids and its DNA G+C content is 45 mol%. Phylogenetic analyses of 16S rRNA gene sequences place this bacterium in the γ-Proteobacteria, within the genus Photobacterium. The 16S rRNA gene sequence of strain GMD509T is most similar to those of Photobacterium frigidiphilum (97·8 %), Photobacterium profundum (97·5 %) and Photobacterium indicum (97·4 %). DNA–DNA relatedness levels between the isolate and its closest known phylogenetic relatives, P. frigidiphilum and P. indicum, are 25·3 and 13·7 %, respectively. Strain GMD509T therefore represents a novel species, for which the name Photobacterium aplysiae sp. nov. is proposed, with the type strain GMD509T (=KCTC 12383T=JCM 12948T).
Terrabacter terrae sp. nov., a novel actinomycete isolated from soil in Spain
Authors: Montero-Barrientos Marta , Rivas Raúl , Velázquez Encarna , Monte Enrique , Roig Manuel G.
Published: November 2005

A Gram-positive, aerobic, long-rod-shaped, non-spore-forming bacterium (strain PPLBT) was isolated from soil mixed with Iberian pig hair. This actinomycete showed keratinase activity in vitro when chicken feathers were added to the culture medium. Strain PPLBT was oxidase-negative and catalase-positive and produced lipase and esterase lipase. This actinomycete grew at 40 °C on nutrient agar and in the same medium containing 5 % (w/v) NaCl. Growth was observed with many different carbohydrates as the sole carbon source. On the basis of 16S rRNA gene sequence similarity, strain PPLBT was shown to belong to the genus Terrabacter of the family Intrasporangiaceae. Strain PPLBT showed 98·8 % 16S rRNA gene sequence similarity to Terrabacter tumescens. Chemotaxonomic data, such as the main ubiquinone (MK-8), the main polar lipids (phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylinositol) and the main fatty acids (i-C15 : 0, ai-C15 : 0, i-C16 : 0 and ai-C17 : 0) supported the affiliation of strain PPLBT to the genus Terrabacter. The G+C content of the DNA was 71 mol%. The results of DNA–DNA hybridization (36·6 % relatedness between Terrabacter tumescens and strain PPLBT) and physiological and biochemical tests suggested that strain PPLBT belongs to a novel species of the genus Terrabacter, for which the name Terrabacter terrae sp. nov. is proposed. The type strain is PPLBT (=CECT 3379T=LMG 22921T).
Methylobacterium isbiliense sp. nov., isolated from the drinking water system of Sevilla, Spain
Authors: Gallego Virginia , García Maria Teresa , Ventosa Antonio
Published: November 2005

Three pink-pigmented facultatively methylotrophic bacteria were isolated from drinking water. These strains (designated AR24T, AR25 and GR32) have been characterized on the basis of phenotypic traits, 16S rRNA gene sequence analysis and DNA–DNA hybridization. According to the results of these analyses, the three strains belong to the genusMethylobacterium. Analysis of 16S rRNA gene sequences revealed that the three isolates constituted a single phylogenetic group. The level of 16S rRNA gene sequence similarities with respect to the type strains of the genusMethylobacteriumwere less than 96·5 %, except for the type strain ofMethylobacterium nodulans(98·1 %). The G+C content of their DNA ranged from 69·0 to 69·7 mol%. DNA–DNA hybridization values confirmed that they constitute a novel species for which we propose the nameMethylobacterium isbiliensesp. nov. The type strain is AR24T(=CECT 7068T=CCM 7304T).
‘Candidatus Phytoplasma graminis' and ‘Candidatus Phytoplasma caricae’, two novel phytoplasmas associated with diseases of sugarcane, weeds and papaya in Cuba
Authors: Arocha Yaima , López Mercedes , Piñol Berta , Fernández Miriam , Picornell Buenaventura , Almeida Roberto , Palenzuela Iris , Wilson Michael R. , Jones Phil
Published: November 2005

During 2003, surveys of sugarcane yellow leaf disease and papaya bunchy top-like disease were carried out on plantations in Havana province, Cuba, to determine the roles of weeds and Auchenorrhyncha insects in the epidemiology of these diseases. More than 250 plant and insect samples were collected and indexed by using a nested PCR for phytoplasma 16S rDNA with the generic primer pairs P1/P7 and R16F2n/R16R2. The PCR products were further characterized by restriction fragment length polymorphism using HaeIII, AluI, Sau3AI, Tru9I, HhaI, HpaII and TaqI endonucleases, giving patterns that distinguished them from those of the other reference phytoplasmas analysed. Phylogenetic analysis of 16S rRNA gene sequences identified the phytoplasmas present in sugarcane (Saccharum officinarum L.), Cynodon dactylon L., Conyza canadensis L. Cronq., Sorghum halepense L. Pers., Macroptilium lathyroides L. Urb., Saccharosydne saccharivora (Westwood) and Cedusa spp., and those in papaya (Carica papaya L.) and Empoasca papayae, as two novel provisional phytoplasma species. We propose that these phytoplasmas should be given Candidatus status, as ‘Candidatus Phytoplasma graminis' and ‘Candidatus Phytoplasma caricae’, respectively.
Oryzihumus leptocrescens gen. nov., sp. nov.
Authors: Kageyama Akiko , Takahashi Yoko , Seki Tamae , Tomoda Hiroshi , Ōmura Satoshi
Published: November 2005

Three novel strains were isolated from a soil sample collected in Japan using GPM agar plates supplemented with superoxide dismutase and/or catalase. The strains were Gram-positive, catalase-positive, irregular rod-shaped bacteria withmeso-diaminopimelic acid as a peptidoglycan diagnostic diamino acid, and the acyl type of the peptidoglycan was acetyl. The major menaquinone was MK-8(H4). Mycolic acids were not detected. The G+C content of the DNA was 72–73 mol%. On the basis of morphological and chemotaxonomic properties and a phylogenetic analysis using 16S rRNA gene sequences, these strains were classified as a novel genus and species,Oryzihumus leptocrescensgen. nov., sp. nov., in the familyIntrasporangiaceaeof the orderActinomycetales. The type strain is KV-628T(=NRRL B-24347T=JCM 12835T=NBRC 100762T).
Shewanella pneumatophori sp. nov., an eicosapentaenoic acid-producing marine bacterium isolated from the intestines of Pacific mackerel (Pneumatophorus japonicus)
Authors: Hirota Kikue , Nodasaka Yoshinobu , Orikasa Yoshitake , Okuyama Hidetoshi , Yumoto Isao
Published: November 2005

An eicosapentaenoic acid-producing bacterium, previously described asShewanellasp. strain SCRC-2738, was classified by phenotypic characterization, chemotaxonomic analysis, 16S rRNA gene sequence analysis and DNA–DNA hybridization. The isolate was Gram-negative, rod-shaped and motile by using polar flagella. The strain grew at 4–32 °C; the optimum growth temperature was 27 °C. NaCl was required for growth. The major isoprenoid quinones were ubiquinone-7 and ubiquinone-8 and its DNA G+C content was 42·8 mol%. The whole-cell fatty acids mainly (above 5 %) consisted of iso-C13 : 0, iso-C15 : 0, C16 : 0, C16 : 1ω7c, C18 : 1ω7cand C20 : 5ω3 (eicosapentaenoic acid). Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain SCRC-2738Twas related closely (sequence similarities above 99 %) toShewanella marinintestina(99·3 %),Shewanella sairae(99·3 %) andShewanella schlegeliana(99·2 %). DNA–DNA hybridization and phenotypic characteristics confirmed that strain SCRC-2738Tmerited classification as a novel species of the genusShewanella, for which the nameShewanella pneumatophorisp. nov. is proposed. The type strain is SCRC-2738T(=JCM 13187T=NCIMB 14060T).
Nonlabens tegetincola gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from a microbial mat in a subtropical estuary
Authors: Lau Stanley C. K. , Tsoi Mandy M. Y. , Li Xiancui , Plakhotnikova Ioulia , Dobretsov Sergey , Wong Po-Keung , Pawlik Joseph R. , Qian Pei-Yuan
Published: November 2005

An orange-pigmented, Gram-negative, non-motile, rod-shaped, strictly aerobic bacterium (UST030701-324T) was isolated from a microbial mat in an estuary in the Bahamas. The DNA G+C content was 33·6 mol%. Predominant fatty acids were i15 : 0, i16 : 0, i17 : 0 3-OH, and summed feature 3, comprising i15 : 0 2-OH and/or 16 : 1ω7c. MK-6 was the only respiratory quinone. Flexirubin-type pigments were not produced. Phylogenetic analysis based on 16S rRNA gene sequences placed UST030701-324Tin a distinct lineage in the familyFlavobacteriaceaewith less than 90·7 % sequence similarity to the members of the nearest genus,Psychroflexus. UST030701-324Tcan be distinguished from other members ofFlavobacteriaceaeby a number of chemotaxonomic and phenotypic characteristics. It is thus proposed that UST030701-324Trepresents a novel taxon designatedNonlabens tegetincolagen. nov., sp. nov. The type strain is UST030701-324T(=NRRL B-41136T=JCM 12886T).
Dokdonia donghaensis gen. nov., sp. nov., isolated from sea water
Authors: Yoon Jung-Hoon , Kang So-Jung , Lee Choong-Hwan , Oh Tae-Kwang
Published: November 2005

Two Gram-negative, non-motile, non-spore-forming, slightly halophilic bacterial strains, DSW-1T and DSW-21, were isolated from sea water and subjected to a polyphasic taxonomic study. They grew optimally at 30 °C and in the presence of 2 % (w/v) NaCl. Strains DSW-1T and DSW-21 were characterized chemotaxonomically as containing MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 as the major fatty acids. Their DNA G+C content was 38 mol%. Strains DSW-1T and DSW-21 exhibited four nucleotide differences in their 16S rRNA gene sequences and possessed a mean DNA–DNA relatedness level of 78 %. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strains DSW-1T and DSW-21 formed a distinct lineage within the family Flavobacteriaceae. The 16S rRNA gene sequences of strains DSW-1T and DSW-21 had similarity levels of less than 92·2 % to the sequences of other members of the family Flavobacteriaceae. There were some differences in phenotypic properties between the two strains and Cellulophaga species, the nearest phylogenetic neighbours. On the basis of phenotypic, phylogenetic and genetic data, strains DSW-1T (=KCTC 12391T=DSM 17200T) and DSW-21 were classified in a novel genus and species, Dokdonia donghaensis gen. nov., sp. nov.
Pontibacter actiniarum gen. nov., sp. nov., a novel member of the phylum ‘Bacteroidetes’, and proposal of Reichenbachiella gen. nov. as a replacement for the illegitimate prokaryotic generic name Reichenbachia Nedashkovskaya et al. 2003
Authors: Nedashkovskaya Olga I. , Kim Seung Bum , Suzuki Makoto , Shevchenko Lyudmila S. , Lee Myung Sook , Lee Kang Hyun , Park Myung Soo , Frolova Galina M. , Oh Hyun Woo , Bae Kyung Sook , Park Ho-Yong , Mikhailov Valery V.
Published: November 2005

The taxonomic position of a marine, gliding, pink-pigmented, aerobic, heterotrophic and Gram-negative bacterium was established using a polyphasic approach. 16S rRNA gene sequence analysis indicated that the strain was a member of the phylum ‘Bacteroidetes’ in which it occupied a separate lineage. The predominant cellular fatty acids were C15 : 0 iso, C17 : 0 iso 3-OH, summed feature 3 and summed feature 4. The DNA G+C content was 48·7 mol%. Phylogenetic evidence and the results of phenotypic, genotypic and chemotaxonomic analyses strongly support the assignment of the newly isolated bacterium as a member of a novel genus and species, for which the name Pontibacter actiniarum gen. nov., sp. nov. is proposed. The type strain is KMM 6156T (=KCTC 12367T=LMG 23027T). It is also proposed that the illegitimate names Reichenbachia and Reichenbachia agariperforans are replaced with Reichenbachiella and Reichenbachiella agariperforans, respectively.