bluuebunny/crossref_metadata_2025 huggingface dataset:
Transfer of Bacillus ehimensis and Bacillus chitinolyticus to the genus Paenibacillus with emended descriptions of Paenibacillus ehimensis comb. nov. and Paenibacillus chitinolyticus comb. nov.
Authors: Lee Jung-Sook , Pyun Yu-Ryang , Bae Kyung Sook
Published: May 2004

The taxonomic status of Bacillus ehimensis and Bacillus chitinolyticus was examined, based on their 16S rDNA sequences, DNA–DNA hybridization and other taxonomic characteristics. A phylogenetic analysis using 16S rDNA sequences revealed that the two species belong to the genus Paenibacillus. In particular, B. ehimensis KCTC 3748T and B. chitinolyticus KCTC 3791T were found to be phylogenetically closely related to Paenibacillus koreensis YC300T (98·3 % sequence similarity) and Paenibacillus chinjuensis WN9T (95·2 % sequence similarity), respectively. DNA–DNA hybridization values between B. ehimensis KCTC 3748T and P. koreensis YC300T were less than 26 %. An experiment using Paenibacillus-specific PCR primers, PAEN515F and 1377R, revealed that B. ehimensis and B. chitinolyticus had the same amplified 16S rDNA fragment as members of the genus Paenibacillus. Accordingly, it is proposed that B. ehimensis and B. chitinolyticus be transferred to the genus Paenibacillus as Paenibacillus ehimensis comb. nov. and Paenibacillus chitinolyticus comb. nov., respectively.
Delineation of the genus Actinobacillus by comparison of partial infB sequences
Authors: Nørskov-Lauritsen Niels , Christensen Henrik , Okkels Henrik , Kilian Mogens , Bruun Brita
Published: May 2004

A 426 bp fragment ofinfB, a housekeeping gene that encodes translation initiation factor 2, was sequenced from 59 clinical isolates and type strains ofActinobacillusspecies and sequences were compared. Partial sequences of 16S rRNA genes were also obtained. By comparinginfBsequences,Actinobacillus pleuropneumoniae,Actinobacillus equuli,Actinobacillus suis,Actinobacillus ureae,Actinobacillus arthritidis,Actinobacillus hominisand two unnamed genomospecies showed more than 85 % similarity to the type strain of the type species of the genus,Actinobacillus lignieresii. The taxonomic position ofActinobacillus capsulatuswas unresolved; this species is more remotely related toA. lignieresii. The two speciesA. lignieresiiandA. pleuropneumoniaecould not be clearly separated byinfBsequence analysis. The phylogeny of the genusActinobacillusbased oninfBanalysis was essentially congruent with relationships inferred from 16S rRNA sequence comparisons and DNA hybridization studies. Discrepancies were encountered with single strains or taxa at the periphery of the genus. Greater intraspecies variation was observed withinfBsequences than with 16S rRNA gene sequences, with notable exceptions. The apparent subdivision of some species by 16S rRNA analysis was most likely caused by RNA operon heterogeneity.
Vibrio gallicus sp. nov., isolated from the gut of the French abalone Haliotis tuberculata
Authors: Sawabe Tomoo , Hayashi Karin , Moriwaki Jun , Thompson Fabiano L. , Swings Jean , Potin Philippe , Christen Richard , Ezura Yoshio
Published: May 2004

Five alginolytic, facultatively anaerobic, non-motile bacteria were isolated from the gut of the abaloneHaliotis tuberculata. Phylogenetic analyses based on 16S rDNA data indicated that these strains are related toVibrio wodanis,Vibrio salmonicida,Vibrio logeiandVibrio fischeri(but with <97 % 16S rRNA gene sequence similarity). DNA–DNA hybridization and fluorescence amplified fragment length polymorphism fingerprinting demonstrated that the five strains constituted a single species that was different from all currently known vibrios. The nameVibrio gallicussp. nov. (type strain, CIP 107863T=LMG 21878T=HT2-1T; DNA G+C content, 43·6–44·3 mol%) is proposed for this novel taxon. Several phenotypic features were disclosed that discriminatedV. gallicusfrom otherVibriospecies:V. gallicuscan be differentiated fromVibrio halioticolion the basis of four traits (β-galactosidase test and assimilation of three carbon compounds) and fromVibrio superstesby 16 traits.
Paenibacillus lactis sp. nov., isolated from raw and heat-treated milk
Authors: Scheldeman Patsy , Goossens Karen , Rodriguez-Diaz Marina , Pil Annelies , Goris Johan , Herman Lieve , De Vos Paul , Logan Niall A. , Heyndrickx Marc
Published: May 2004

Endospore-forming bacteria were recovered from individual packages from different processing lines in a dairy plant during a tenacious periodical contamination of their UHT-milk production. Two colony types were seen, one of which was identified asBacillus sporothermodurans. Analysis of the 16S rRNA gene of the second colony type placed these isolates within the genusPaenibacillus, withPaenibacillus lautusas the closest known relative. Moreover, over 99 % similarity was observed to the 16S rDNA sequence of MB 2035, a strain isolated previously from raw milk during a survey at dairy farms for very heat-resistant spore-forming bacteria. Nine other potentially closely related strains among the dairy farm isolates were found using rep-PCR typing. The taxonomic positions of these 19 isolates were further investigated using 16S rRNA gene sequencing and DNA–DNA hybridizations of representative strains. All 19 isolates shared a high degree of phenotypic similarity and were easily distinguished from closely related members of the genus. Anteiso-C15 : 0, C16 : 0and iso-C15 : 0were among the major fatty acids and the genomic DNA G+C content was 51·6–51·7 mol%. Therefore, based on their phenotypic, phylogenetic and genomic distinctiveness, these 19 strains, isolated from both raw and heat-treated milk, are placed in the genusPaenibacillusasPaenibacillus lactissp. nov. The type strain is MB 1871T(=LMG 21940T=DSM 15596T).
Pseudonocardia benzenivorans sp. nov.
Authors: Kämpfer Peter , Kroppenstedt Reiner M.
Published: May 2004

A Gram-positive, rod-shaped, non-spore-forming bacterium (B5T) was isolated from an enrichment culture that contained 1,2,3,5-tetrachlorobenzene as the sole source of carbon. On the basis of 16S rRNA gene sequence similarity studies, strain B5Twas shown to belong to the familyPseudonocardiaceaeand was related most closely toPseudonocardia sulfidoxydans(98·8 %) andPseudonocardia hydrocarbonoxydans(98·3 %). 16S rRNA gene sequence similarity to otherPseudonocardiaspecies was <97 %. Chemotaxonomic data [major menaquinone, MK-8(H4); major polar lipids, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol; major fatty acids, C16 : 0, iso-C16 : 0and iso-C15 : 0] supported the affiliation of strain B5Tto the genusPseudonocardia. The results of DNA–DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain B5TfromP. sulfidoxydansandP. hydrocarbonoxydans. Strain B5Ttherefore represents a novel species of the genusPseudonocardia, for which the namePseudonocardia benzenivoranssp. nov. is proposed, with the type strain B5T(=DSM 44703T=CIP 107928T).
Sphingomonas yabuuchiae sp. nov. and Brevundimonas nasdae sp. nov., isolated from the Russian space laboratory Mir
Authors: Li Ying , Kawamura Yoshiaki , Fujiwara Nagatoshi , Naka Takashi , Liu Hongsheng , Huang Xinxiang , Kobayashi Kazuo , Ezaki Takayuki
Published: May 2004

On the basis of phenotypic and genotypic characteristics and 16S rRNA gene sequence analysis, novel species belonging to the generaSphingomonasandBrevundimonaswere identified from samples taken from the Russian space laboratory Mir. Strain A1-18Twas isolated from the air. 16S rDNA sequence analysis showed that strain A1-18Tformed a coherent cluster withSphingomonas sanguinis,Sphingomonas parapaucimobilis,Sphingomonas paucimobilisandSphingomonas roseiflavawith sequence similarity of 97·5–98·6 %. Similar to otherSphingomonasspecies, the G+C content was 66·1 mol%, but DNA–DNA hybridization rates at optimal temperatures among these related species were only 24·7–51·7 %. Strain A1-18Tcan be differentiated biochemically from related species. Strain W1-2BTwas isolated from condensation water. It forms a distinct lineage within the genusBrevundimonas, forming a coherent cluster withBrevundimonas vesicularis,Brevundimonas aurantiacaandBrevundimonas intermedia. 16S rDNA sequence similarities were 98·6–99·5 % and the G+C content was 66·5 mol%, similar to otherBrevundimonasspecies, but DNA–DNA relatedness was only 50·2–54·8 %. Strain W1-2BTalso showed some differential biochemical properties from its related species. A series of polyphasic taxonomic studies led to the proposal of two novel species,Sphingomonas yabuuchiaesp. nov. (type strain A1-18T=GTC 868T=JCM 11416T=DSM 14562T) andBrevundimonas nasdaesp. nov. (type strain W1-2BT=GTC 1043T=JCM 11415T=DSM 14572T).
Gulosibacter molinativorax gen. nov., sp. nov., a molinate-degrading bacterium, and classification of ‘Brevibacterium helvolum’ DSM 20419 as Pseudoclavibacter helvolus gen. nov., sp. nov.
Authors: Manaia Célia M. , Nogales Balbina , Weiss Norbert , Nunes Olga C.
Published: May 2004

A Gram-positive, molinate-degrading bacterium, strain ON4T(=DSM 13485T=LMG 21909T), was isolated from a mixed bacterial culture able to mineralize the herbicide molinate. The strain was strictly aerobic, oxidase- and catalase-positive and non-acid-fast, with a growth temperature of 10–41 °C. It contained the major menaquinone MK-9 and a cell-wall peptidoglycan based ond-ornithine. 16S rDNA sequence analysis revealed that the strain formed a distinct line of descent in the familyMicrobacteriaceae, showing the highest 16S rDNA similarity (∼95 %) to members of the genusCurtobacteriumand ‘Brevibacterium helvolum’ DSM 20419 (=ATCC 13715). The latter was reported to have the cell-wall peptidoglycan type B2γand the major menaquinone MK-9, which are typical ofClavibacter, but it is clearly separated from this genus at the phylogenetic level. Based on low values of 16S rDNA sequence similarity to previously described genera and their distinctive phenotypic characteristics, it is proposed that strains ON4Tand ‘B. helvolum’ DSM 20419 be classified as two novel genera and species, with the respective namesGulosibacter molinativoraxgen. nov., sp. nov. andPseudoclavibater helvolusgen. nov., sp. nov.
Proposal to accommodate Burkholderia cepacia genomovar VI as Burkholderia dolosa sp. nov.
Authors: Vermis Karen , Coenye Tom , LiPuma John J. , Mahenthiralingam Eshwar , Nelis Hans J. , Vandamme Peter
Published: May 2004

Phenotypic and genotypic studies revealed new tools for differentiating Burkholderia cepacia genomovar VI from Burkholderia multivorans and other B. cepacia-complex species. Hence, the name Burkholderia dolosa sp. nov. is proposed, with LMG 18943T (=CCUG 47727T) as the type strain. B. dolosa can be differentiated from other B. cepacia-complex bacteria by its inability to assimilate tryptamine, azelaic acid and salicin and by its failure to grow on the B. cepacia-selective medium PCAT. Both 16S rDNA and recA RFLP analysis revealed unique B. dolosa restriction patterns. In addition, new 16S rDNA- and recA-based PCR assays allowed its specific identification.
Syntrophomonas curvata sp. nov., an anaerobe that degrades fatty acids in co-culture with methanogens
Authors: Zhang Chunyang , Liu Xiaoli , Dong Xiuzhu
Published: May 2004

A strict anaerobe (strain GB8-1T) that degraded straight-chain fatty acids with C4–C18 in syntrophic association with methanogens was isolated from an up-flow anaerobic sludge blanket reactor treating beer wastewater. Strain GB8-1T degraded 1 mol butyrate into about 2 mol acetate and 1 mol (presumably) H2 in co-culture with a methanogen. Neither branched-chain fatty acids nor benzoate could be degraded. Strain GB8-1T could grow on crotonate in pure culture and converted 1 mol crotonate to 0·5 mol butyrate and 1 mol acetate. Generation time was about 11 h when grown on crotonate at 37 °C. Fumarate, sulfate, thiosulfate, sulfur and nitrate could not serve as electron acceptors for strain GB8-1T to degrade butyrate. Cells of strain GB8-1T were curved rods with Gram-negative cell walls; no spores were observed. The DNA G+C content was 46·6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain GB8-1T was related most closely to the fatty acid-oxidizing, syntrophic bacterium Syntrophomonas sapovorans DSM 3441T; however, the relationship was not very close (95·4 % sequence similarity). Some phenotypic features also differentiated strain GB8-1T from Syntrophomonas sapovorans DSM 3441T. Therefore, a novel species, Syntrophomonas curvata sp. nov., is proposed. The type strain is GB8-1T (=CGMCC 1.5010T=DSM 15682T).
Anaerobranca californiensis sp. nov., an anaerobic, alkalithermophilic, fermentative bacterium isolated from a hot spring on Mono Lake
Authors: Gorlenko Vladimir , Tsapin Alexandre , Namsaraev Zorigto , Teal Tracy , Tourova Tatyana , Engler Diane , Mielke Randy , Nealson Kenneth
Published: May 2004

A novel, obligately anaerobic, alkalithermophilic, chemo-organotrophic bacterium was isolated from the sediment of an alkaline hot spring located on Paoha Island in Mono Lake, California, USA. This rod-shaped bacterium was motile via peritrichous flagella. Isolated strains grew optimally in 5–25 g NaCl l−1, at pH 9·0–9·5 and at a temperature of 58°C and were fermentative and mainly proteolytic, utilizing peptone, Casamino acids and yeast extract. Optimal growth was seen in the presence of elemental sulfur, polysulfide or thiosulfate with concomitant reduction to hydrogen sulfide. Sulfite was also formed in an equal ratio to sulfide during reduction of thiosulfate. The novel isolate could also reduce Fe(III) and Se(IV) in the presence of organic matter. On the basis of physiological properties, 16S rRNA gene sequence and DNA–DNA hybridization data, strain PAOHA-1T (=DSM 14826T=UNIQEM 227T) belongs to the genus Anaerobranca and represents a novel species, Anaerobranca californiensis sp. nov.
Reclassification of Lactobacillus cellobiosus Rogosa et al. 1953 as a later synonym of Lactobacillus fermentum Beijerinck 1901
Authors: Dellaglio Franco , Torriani Sandra , Felis Giovanna E.
Published: May 2004

The name Lactobacillus cellobiosus is validly published, but the species is often neglected in taxonomic studies, due to its high similarity to Lactobacillus fermentum. In the present paper, literature data concerning the two species were reviewed. Phylogenetic placement of L. cellobiosus was obtained based on 16S rDNA sequences, and genetic similarity was further investigated by comparing partial recA gene sequences for the type strains of L. cellobiosus and L. fermentum. Based on the high identity values for 16S rDNA (99 %) and recA gene (98 %) sequences, the results of DNA–DNA hybridization assays and phenotypic traits available from the literature, it is proposed that L. cellobiosus be reclassified and, as a rule of priority, renamed as L. fermentum, the first described species.
Corynebacterium caspium sp. nov., from a Caspian seal (Phoca caspica)
Authors: Collins Matthew D. , Hoyles Lesley , Foster Geoffrey , Falsen Enevold
Published: May 2004

A previously unknown Gram-positive, non-spore-forming, non-lipophilic, catalase-positive, irregular rod-shaped bacterium (M/106/00/5T) was isolated, in mixed culture, from the penis of a Caspian seal (Phoca caspica). The strain was a facultative anaerobe that was able to grow at 22 and 42 °C. Comparative 16S rRNA gene sequencing showed that the organism formed a hitherto unknown subline within the genus Corynebacterium. Sequence divergence values of more than 5 % from other described Corynebacterium species, together with phenotypic differences, showed that the unidentified bacterium represents a previously unrecognized member of this genus. On the basis of phenotypic and phylogenetic considerations, it is proposed that the unknown bacterium isolated from a Caspian seal (strain M/106/00/5T=CCUG 44566T=CIP 107965T) be classified as the type strain of a novel species of the genus Corynebacterium, Corynebacterium caspium sp. nov.
Anoxybacillus contaminans sp. nov. and Bacillus gelatini sp. nov., isolated from contaminated gelatin batches
Authors: De Clerck Elke , Rodríguez-Díaz Marina , Vanhoutte Tom , Heyrman Jeroen , Logan Niall A. , De Vos Paul
Published: May 2004

Aerobic, endospore-forming bacteria that are attributed to the genus Bacillus or related genera constitute a hazard to the quality of gelatin. During repetitive extragenic palindromic DNA (rep)-PCR screening of gelatin isolates, a group of five isolates (group 1) and a group of 66 isolates (group 2) that did not match any pattern in our database were found. On the basis of 16S rDNA sequence analysis, representative strains of the different rep-PCR fingerprint types of group 1 were shown to be related most closely to Anoxybacillus species, but with sequence similarity of <97 %. Likewise, representative strains of group 2 were shown to be related most closely to Bacillus species, with 16S rDNA sequence similarity of <97 %. DNA–DNA reassociation values of isolates that displayed the most divergent rep-PCR profiles revealed that strains within each group belonged to a single species, according to recommendations for species delineation. A mean fatty acid profile could be calculated for each group. Isolates within a single group had similar patterns of results in API and other phenotypic tests; no correlation of patterns of results with rep-PCR groups was seen. Physiological characterization of group 1 isolates allows their distinction from other Anoxybacillus species. Despite the weak reaction of group 2 isolates in API tests, physiological characterization allows distinction between Bacillus species that react weakly in API tests. Two novel species are therefore proposed, with the names Anoxybacillus contaminans sp. nov. (type strain, LMG 21881T=DSM 15866T) and Bacillus gelatini sp. nov. (type strain, LMG 21880T=DSM 15865T).
Clostridium hastiforme is a later synonym of Tissierella praeacuta
Authors: Bae Jin-Woo , Park Ja Ryeong , Chang Young-Hyo , Rhee Sung-Keun , Kim Byung-Chun , Park Yong-Ha
Published: May 2004

The previously proposed species Clostridium hastiforme and Tissierella praeacuta appear to be similar from their published descriptions. Accordingly, the aim of the current study was to perform phenotypic and genetic analyses of the type strains of both species, in order to clarify their taxonomic positions. The type strains of C. hastiforme (DSM 5675T) and T. praeacuta (NCTC 11158T) exhibited identical biochemical profiles and their 16S rRNA gene sequences displayed 99·9 % similarity. DNA–DNA hybridization was also estimated to be 96·5 %. Thus, it was concluded that C. hastiforme and T. praeacuta are synonyms, where T. praeacuta has priority. An emended description of the genus Tissierella is also given.
Viral Virulence Protein Suppresses RNA Silencing–Mediated Defense but Upregulates the Role of MicroRNA in Host Gene Expression[W]
Authors: Chen Jun , Li Wan Xiang , Xie Daoxin , Peng Jin Rong , Ding Shou Wei
Published: May 2004

Small interfering RNAs (siRNAs) and microRNAs (miRNAs) are processed by the ribonuclease Dicer from distinct precursors, double-stranded RNA (dsRNA) and hairpin RNAs, respectively, although either may guide RNA silencing via a similar complex. The siRNA pathway is antiviral, whereas an emerging role for miRNAs is in the control of development. Here, we describe a virulence factor encoded by turnip yellow mosaic virus, p69, which suppresses the siRNA pathway but promotes the miRNA pathway in Arabidopsis thaliana. p69 suppression of the siRNA pathway is upstream of dsRNA and is as effective as genetic mutations in A. thaliana genes involved in dsRNA production. Possibly as a consequence of p69 suppression, p69-expressing plants contained elevated levels of a Dicer mRNA and of miRNAs as well as a correspondingly enhanced miRNA-guided cleavage of two host mRNAs. Because p69-expressing plants exhibited disease-like symptoms in the absence of viral infection, our findings suggest a novel mechanism for viral virulence by promoting the miRNA-guided inhibition of host gene expression.
maternally expressed gene1Is a Novel Maize Endosperm Transfer Cell–Specific Gene with a Maternal Parent-of-Origin Pattern of Expression[W]
Authors: Gutieérrez-Marcos Jose F. , Costa Liliana M. , Biderre-Petit Corinne , Khbaya Bouchaib , O'Sullivan Donal M. , Wormald Mark , Perez Pascual , Dickinson Hugh G.
Published: May 2004

Growth of the maize (Zea mays) endosperm is tightly regulated by maternal zygotic and sporophytic genes, some of which are subject to a parent-of-origin effect. We report here a novel gene, maternally expressed gene1 (meg1), which shows a maternal parent-of-origin expression pattern during early stages of endosperm development but biallelic expression at later stages. Interestingly, a stable reporter fusion containing the meg1 promoter exhibits a similar pattern of expression. meg1 is exclusively expressed in the basal transfer region of the endosperm. Further, we show that the putatively processed MEG1 protein is glycosylated and subsequently localized to the labyrinthine ingrowths of the transfer cell walls. Hence, the discovery of a parent-of-origin gene expressed solely in the basal transfer region opens the door to epigenetic mechanisms operating in the endosperm to regulate certain aspects of nutrient trafficking from the maternal tissue into the developing seed.
The transparent testa4 Mutation Prevents Flavonoid Synthesis and Alters Auxin Transport and the Response of Arabidopsis Roots to Gravity and Light[W]
Authors: Buer Charles S. , Muday Gloria K.
Published: May 2004

We examined whether flavonoids act as endogenous auxin transport regulators during gravity vector and light intensity changes in Arabidopsis thaliana roots. Flavonoid deficient transparent testa4 [tt4(2YY6)] seedlings had elevated root basipetal auxin transport compared with the wild type, consistent with the absence of a negative auxin transport regulator. The tt4(2YY6) roots had delayed gravitropism that was chemically complemented with a flavonoid intermediate. Flavonoid accumulation was found in wild-type columella cells, the site of gravity perception, and in epidermal and cortical cells, the site of differential growth, but flavonoid accumulation was absent in tt4(2YY6) roots. Flavonoid accumulation was higher in gravity-stimulated root tips as compared with vertical controls, with maximum differences coinciding with the timing of gravitropic bending, and was located in epidermal cells. Exogenous indole-3-acetic acid (IAA) also elevated flavonoid accumulation, suggesting that flavonoid changes in response to gravity might be partly as a result of changing IAA distribution. Acropetal IAA transport was also elevated in roots of tt4(2YY6). Flavonoid synthesis was repressed in the dark, as were differences in root acropetal transport in tt4(2YY6). These results are consistent with light- and gravity-induced flavonoid stimulation that alters auxin transport in roots and dependent physiological processes, including gravitropic bending and root development.
Limitations of asymmetric parallel-beam geometry
Authors: Raftery N. A. , Vogel R.
Published: May 2004

Bragg diffraction peak profiles and intensities in asymmetric (Ω–2θ) diffraction using a mirror-based parallel-beam geometry were compared with symmetric parallel-beam (θ–2θ) and conventional Bragg–Brentano (θ–2θ) diffraction for a powdered quartz sample and the NIST standard reference material (SRM) 660a (LaB6, lanthanum hexaboride). A comparison of the intensities and line widths (full width at half-maximum, FWHM) of these techniques demonstrated that low incident angles (Ω < 5°) are preferable for the parallel-beam setup. For higher Ω values, if 2θ < 2Ω, mass absorption reduces the intensities significantly compared with the Bragg–Brentano setup. The diffraction peak shapes for the mirror geometry are more asymmetric and have larger FWHM values than corresponding peaks recorded with a Bragg–Brentano geometry. An asymmetric mirror-based parallel-beam geometry offers some advantages in respect of intensity when compared with symmetric geometries, and hence may be well suited to quantitative studies, such as those involving Rietveld analysis. A trial Rietveld refinement of a 50% quartz–50% corundum mixture was performed and produced adequate results.
In situX-ray diffraction analysis of iron ore sinter phases
Authors: Scarlett Nicola V. Y. , Madsen Ian C. , Pownceby Mark I. , Christensen Axel N.
Published: May 2004

Owing to the depletion of world lump iron ore stocks, pre-treated agglomerates of fine ores are making up a growing proportion of blast-furnace feedstock (∼80%). These agglomerations, or `sinters', are generally composed of iron oxides, ferrites (most of which are silicoferrites of calcium and aluminium, SFCAs), glasses and dicalcium silicates (C2S). SFCA is the most important bonding phase in iron ore sinter, and its composition, structural type and texture greatly affect its physical properties. Despite its prevalence and importance, the mechanism of SFCA formation is not fully understood.In situpowder X-ray diffraction investigations have been conducted into the formation of SFCA, allowing the study of the mechanism of its formation and the observation of intermediate phases with respect to time and temperature. Studies have been carried out to investigate the effects of changing the substitution levels of aluminium for iron. The use of the Rietveld method for phase quantification gives an indication of the order and comparative rates of phase formation throughout the experiments.
A flux- and background-optimized version of the NanoSTAR small-angle X-ray scattering camera for solution scattering
Authors: Pedersen Jan Skov
Published: May 2004

A commercially available small-angle X-ray scattering camera, NanoSTAR from Bruker AXS, has been modified to optimize its use for weakly scattering solution samples. The original NanoSTAR is a pinhole camera with two Göbel mirrors for monochromating and making the beam parallel, and with a two-dimensional position-sensitive gas detector (HiSTAR) for data collection. The instrument has one integrated vacuum. It was constructed for position-resolved studies and thus has a small beam size at the sample position. In the present work, the instrumental configuration has been optimized by numerical calculations based on phase-space analysis and Monte Carlo simulations in order to obtain a higher flux. This has led to a setup in which the beam at the sample is larger and the collimation part of the instrument is longer, so that divergence of the beam is similar to that of the original camera. An extra pinhole is included after the Göbel mirrors to make the beam size well defined after the mirrors. The camera thus has genuine three-pinhole collimation. The use of electron-microscope pinholes minimizes parasitic scattering. At the University of Aarhus, the modified camera is installed on a powerful rotating-anode X-ray source (MacScience 6 kW Cu with a 0.3 × 0.3 mm effective source size). Measurements have been performed on a wide variety of weakly scattering samples, such as surfactant micelles, homopolymer solutions, block copolymer micelles, proteinsetc. The data are routinely converted to absolute scale using the scattering from water as a primary standard. The standard configuration covers the range of scattering vectors from 0.01 to 0.35 Å−1with a flux of 1.7 × 107photons s−1for CuKα radiation at a generator power of 4.05 kW. The camera is easily converted to a high-resolution version covering 0.0037 to 0.22 Å−1with a loss of flux of about a factor of 10, as well as to a position-resolved version.
Line broadening analysis using integral breadth methods: a critical review
Authors: Scardi P. , Leoni M. , Delhez R.
Published: May 2004

Integral breadth methods for line profile analysis are reviewed, including modifications of the Williamson–Hall method recently proposed for the specific case of dislocation strain broadening. Two cases of study, supported by the results of a TEM investigation, are considered in detail: nanocrystalline ceria crystallized from amorphous precursors and highly deformed nickel powder produced by extensive ball milling. A further application concerns a series of Fe–Mo powder specimens that were ball milled for increasing time. Traditional and modified Williamson–Hall methods confirm their merits for a rapid overview of the line broadening effects and possible understanding of the main causes. However, quantitative results are generally not reliable. Limits in the applicability of integral breadth methods and reliability of the results are discussed in detail.
Effect of trimethylgallium flow on the structural and optical properties of InGaN/GaN multiple quantum wells
Authors: Zhang J. C. , Wang J. F. , Wang Y. T. , Wu M. , Liu J. P. , Zhu J. J. , Yang H.
Published: May 2004

InGaN/GaN multiple quantum wells (MQWs) are grown by metal-organic chemical vapour deposition on (0001) sapphire substrates. Triple-axis X-ray diffraction (TXRD) and photoluminescence (PL) spectra are used to assess the influence of trimethylgallium (TMGa) flow on structural defects, such as dislocations and interface roughness, and the optical properties of the MQWs. In this paper, a method, involving an ω scan of every satellite peak of TXRD, is presented to measure the mean dislocation density of InGaN/GaN MQWs. The experimental results show that under certain conditions which keep the trimethlyindium flow constant, dislocation density and interface roughness decrease with the increase of TMGa flow, which will improve the PL properties. It can be concluded that dislocations, especially edge dislocations, act as non-radiative recombination centres in InGaN/GaN MQWs. Also noticed is that changing the TMGa flow has more influence on edge dislocations than screw dislocations.
Use of plastic capillaries for macromolecular crystallization
Authors: Potter Rachel R. , Hong Young S. , Ciszak Ewa M.
Published: May 2004

Techniques of crystallization of biomolecules in plastic fluorocarbon-formulated capillaries (Nalgene 870 PFA tubing) are presented. These crystallization methods employ batch, free-interface liquid–liquid diffusion alone, or a combination with vapor diffusion. The growth of crystals of test proteins such as thaumatin and glucose isomerase, as well as of proteins studied in the laboratory, such as dihydrolipoamide dehydrogenase, has been demonstrated. Once the solutions were loaded in capillaries, they were stored in the tubes in frozen state at cryogenic temperatures until required for crystallization experiments.
Robust indexing for automatic data collection
Authors: Sauter Nicholas K. , Grosse-Kunstleve Ralf W. , Adams Paul D.
Published: May 2004

Improved methods for indexing diffraction patterns from macromolecular crystals are presented. The novel procedures include a more robust way to verify the position of the incident X-ray beam on the detector, an algorithm to verify that the deduced lattice basis is consistent with the observations, and an alternative approach to identify the metric symmetry of the lattice. These methods help to correct failures commonly experienced during indexing, and increase the overall success rate of the process. Rapid indexing, without the need for visual inspection, will play an important role as beamlines at synchrotron sources prepare for high-throughput automation.
Abinitiostructure determination ofm-toluidine by powder X-ray diffraction
Authors: Rukiah Mwaffak , Lefebvre Jacques , Descamps Marc , Hemon Stephanie , Dzyabchenko Alexander
Published: May 2004

The powder X-ray diffraction pattern of the crystalline phase ofm-toluidine has been recorded with a sensitive curved detector (CPS120) at 150 K. The structure has been solved by real-space methods (simulated annealing) followed by Rietveld refinements with phenyl rings as rigid bodies and with soft constraints on bond lengths for peripheral atoms. The cell is monoclinic with space groupP21/candZ= 8. Equivalent molecules form chains alongc. The crystalline cohesion is achieved by N—H...N hydrogen bonds between neighbouring chains of non-equivalent molecules and by van der Waals interactions of neighbouring chains of equivalent molecules. The hydrogen-bonding network has been confirmed by lattice-energy minimization. Anisotropic strain effects of the cell have been calculated. The directions of the minimal strains correspond to the directions of the hydrogen bonds. An explanation of the difficulty to crystallize the metastable phase is given.
UMWEG: a program for the calculation and graphical representation of multiple-diffraction patterns. I. Polarization
Authors: Rossmanith Elisabeth
Published: May 2004

The expressions concerning the polarization in the three-beam case used in the programUMWEG[Rossmanith (2003).J. Appl. Cryst.36, 1467–1474] are given. As an application, the effect of polarization on the intensities of multiple-diffraction patterns, as well as on the asymmetries of three-beam interference profiles, is discussed. Examples for the inversion of the asymmetry of three-wave intensity profiles for π-polarized incident radiation [Juretschke (1986).Phys. Status Solidi B,135, 455–466] are presented.
Correction method for the asymmetry of the tangential beam in Couette (or Searle) geometry used in rheo-small-angle neutron scattering
Authors: Nettesheim Florian , Olsson Ulf , Lindner Peter , Richtering Walter
Published: May 2004

A method of correcting the asymmetry in the scattering of the tangential beam configuration in a rheo-small-angle neutron scattering experiment is proposed. The asymmetry of the scattering in the tangential beam configuration can be attributed to the difference in pathlength for neutrons that are scattered toward compared with those which are scattered away from the axis of rotation of the shear cell. The pathlength problem is solved and a final expression for the two-dimensional scattering intensity is given. The results from these calculations are compared with experimental data, which offer a different option to correct this asymmetry, namely by just measuring the scattering of H2O/D2O mixtures with absolute scattering cross sections identical to those of the respective samples. However, the situation for anisotropic media is more complex and the correction procedure described here is less effective.
A crystallization plate for controlling evaporation in hanging drops
Authors: Nneji Gweneth A. , Chayen Naomi E.
Published: May 2004

The modification and use of a crystallization plate for controlling the evaporation in hanging-drop trials is described. In this plate, known as the Nextal Crystallization Tool, each well is sealed by a screw cap that incorporates the cover-slip. Graduation marks were introduced on the outer circumference of the wells to enable accurate and reproducible adjustment of the tightness of the seal on the well. This design allows variable amounts of evaporation without exposing the drop. Crystallization experiments of α-crustacyanin from lobster shell, for which controlled evaporation was applied to regulate the number and size of the crystals, are presented.
Cold pressing of copper single crystals for a large-area doubly focusing monochromator
Authors: Mildner D. F. R. , Brand P. C. , Clem D. L.
Published: May 2004

The design for a large-area doubly focusing neutron monochromator consists of a large number of small square copper single crystals mounted onto thin aluminium blades that both buckle and rotate independently. This avoids the need for large individual alignment mechanisms for each crystal that introduce unacceptably high levels of background. However, it does require that the crystals be oriented such that the diffracting crystallographic planes are parallel to the crystal face. Cold pressing broadens the natural narrow mosaic of the virgin crystal discs to increase the diffracted intensity. This introduces anisotropy into the crystal that determines its orientation in the final monochromator. The alignment procedure used for each crystal before cutting out the square tile in the correct orientation is described. A few crystals are characterized in detail by neutron diffraction at various stages of the operation, revealing the variation in the mosaic width and the angular position of the reciprocal-lattice vector as a function of the azimuthal angle by rotating the crystal about the normal to its face. The twofold symmetry of the mosaic width of the pressed crystal is modulated by the 2π periodicity introduced by the precession of the reciprocal-lattice vector around the crystal face normal. Satisfactorily aligned crystals have a variation in the angular position for diffraction within the allowed tolerance.
Grain-scale characterization of transformation textures
Authors: Godet S. , Glez J. C. , He Y. , Jonas J. J. , Jacques P. J.
Published: May 2004

Orientation relationships during the austenite-to-ferrite (γ-to-α) phase transformation were investigated using electron back-scattered diffraction (EBSD) on a bainitic steel containing retained austenite. The steel was hot rolled within the austenite phase field, but below the `no-recrystallization' temperature, to two different strains. The observed orientation relationships between the bainite and retained austenite are expressed in Rodrigues–Frank space. The exact Kurdjumov–Sachs relation was never found. The local spread of orientation in the parent austenite (owing to deformation) is seen to be inherited by the bainite. This is attributed to the displacive mode of transformation to bainite. The influence of austenite prior deformation on the occurrence of variant selection was also studied. It is shown that a critical strain is necessary in order to observe a significant amount of variant selection.
First-, second- and third-order correlation function in time-resolved X-ray diffraction experiments
Authors: Techert Simone
Published: May 2004

In the past decade, sustained progress has been made in the field of time-resolved X-ray diffraction and photocrystallography. Laser systems have been developed rapidly, and the combination of pulsed laser sources with pulsed X-ray sources, particularly by using synchrotron X-ray radiation and X-rays generated by plasma sources, has made the application of pump-probe schemes routine. So far, however, most studies have been focused on two questions: (i) the refinement of structural changes during the course of a reaction, and (ii) possible relations between transient structural changes and the intermediates found by optical spectroscopy. In this work, a kinetic description for different time laws in time-resolved X-ray diffraction experiments is derived in the framework of time-dependent correlation functions. The derived time laws were applied to time-resolved studies on a [2+2] photodimerization and a reversible reaction undergoing structural reorganization.
A new method to detect an X-ray diffracted beam at an angle of 90°
Authors: Hönnicke Marcelo Goncalves , Kakuno Edson Massayuki , Cusatis Cesar , Mazzaro Irineu
Published: May 2004

A standard procedure cannot be used to detect a back-diffracted X-ray beam (h-beam) at a diffraction angle of 90° (back-diffraction) because the detector will intercept the incident beam. A new method is proposed in which a silicon single crystal simultaneously back-diffracts and detects the variation of the photon counting rate when the crystal is in and out of the X-ray back-diffraction condition. The detected intensity shows the inverted diffraction profile; that is, a dip in the photon counting rate due to the photons that are being back-diffracted. The experimental results presented here show such a dip, referred to here as the anti-h peak or the inverted rocking curve (IRC), for different situations.
Supply chain risk management
Authors: Finch Peter
Published: May 2004

This article presents a secondary analysis of the literature, supplemented by case studies to determine if large companies increase their exposure to risk by having small‐ and medium‐size enterprises (SMEs) as partners in business critical positions in the supply chain, and to make recommendations concerning best practice. A framework defining the information systems (IS) environment is used to structure the review. The review found that large companies’ exposure to risk appeared to be increased by inter‐organisational networking. Having SMEs as partners in the supply chain further increased the risk exposure. SMEs increased their own exposure to risk by becoming partners in a supply chain. These findings indicate the importance of undertaking risk assessments and considering the need for business continuity planning when a company is exposed to inter‐organisational networking.
The effect of within‐genet and between‐genet competition on sexual reproduction and vegetative spread in Potentilla anserina ssp. egedii
Authors: RAUTIAINEN PIRJO , KOIVULA KARI , HYVÄRINEN MARKO
Published: May 2004

Patterns of biomass allocation to sexual and vegetative reproduction were examined in a perennial stoloniferous clonal plant, Potentilla anserina (L.) Rydb. ssp. egedii (Wormsk.) Hiitonen, in relation to intraspecific competition between monoclonal and multiclonal ramets.

We predicted that a lack of competition would generate allocation to rapid, short‐distance spread (vegetative propagation), while the presence of competition would increase allocation to long‐distance dispersal (sexual reproduction), and that the allocation shift would be more pronounced where the competing ramets were related.

P. anserina ramets were grown in a glasshouse in small pots, either alone (no competition) or with a size‐matched ramet that originated from the same clone (within‐genet competition) or a different one (between‐genet competition).

Competition suppressed both growth and reproduction, but there was no treatment response in relative investment at the level of a whole genet, although both mother ramets and their daughters showed clear effects when analysed separately.

When experiencing competition, the mother ramet allocated relatively more to flowers, whereas allocation to vegetative growth was more intense when competition was absent. Allocation patterns were independent of the relatedness of competitors.

The results imply that P. anserina can modify the allocation of resources to different life‐history traits according to competitive stress. Such flexibility is likely to reflect a shift in the optimal allocation strategy during the life cycle of a plant with a guerilla growth form with rapid exploitation of free space in a new patch by vegetative spread favoured. When spread becomes limited by competition, long‐distance dispersal in space (seeds) or time (persistence) becomes beneficial.
Climatic and landscape controls of the boreal forest fire regime: Holocene records from Alaska
Authors: LYNCH JASON A. , HOLLIS JEREMY L. , HU FENG SHENG
Published: May 2004

The response of ecosystems to past and future climatic change is difficult to understand due to the uncertainties in the direction and magnitude of changes and the relative importance of interactions between climate and local factors. In boreal ecosystems such interactions may dictate the response to climatic change, but the interaction of climate, vegetation composition and the fire regime remains poorly understood.

Sediment cores from lakes in south‐central Alaska were analysed for lithology, macrofossils, pollen and charcoal to investigate the relationships between moisture availability, species composition and mean fire return intervals (MFI).

Macrofossil and lithological evidence suggests that variations in effective moisture occurred over the past 7000 years and that the regional climate has been wetter during the past c. 3800 years than before.

Boreal forests existed in the region throughout the past 7000 years. Picea glauca and Picea mariana were the prevalent forest species around Chokasna Lake, whereas P. glauca and hardwood species (e.g. Betula) co‐dominated the landscape around Moose Lake. Picea mariana replaced P. glauca as the dominant Picea species around Chokasna Lake at c. 2000 bp.

MFI was > 500 years before 3800 bp, except from 5800 to 5000 bp at Moose Lake and 5400 to 4550 bp at Chokasna Lake, when values were c. 200 years. MFI decreased to c. 200 years during the late‐Holocene at both sites and to c. 150 years after 2000 bp at Chokasna Lake.

At both sites, fires occurred more frequently under wetter climatic conditions. Our results therefore support other recent studies demonstrating that warmer/drier climatic conditions do not necessarily induce greater fire importance. A combination of increased ignition by lightning strikes and seasonal‐moisture variability probably resulted in more frequent fires under wetter conditions.
The millennial dynamics of a boreal forest stand from buried trees
Authors: ARSENEAULT DOMINIQUE , SIROIS LUC
Published: May 2004

We reconstructed the dynamics of a black spruce (Picea mariana) and jack pine (Pinus banksiana) forest stand in northern Québec using a continuous, 5200‐year‐long sequence of stem remains buried in adjacent peatland. Simulations of recruitment of such remains provided guidelines for inferring past ecosystem structure and composition at the stand scale.

Compared with the late Holocene (4650–0 cal. yearBP(CYBP)), the mid Holocene (5200–4650 CYBP) period was characterized by faster tree growth, larger stems and higher stem density, indicating higher forest productivity in association with a milder climate.

The presence of stem remains of both species from 17 out of 20 contiguous 250‐year time intervals suggests that the spruce‐pine stand exhibited high compositional stability, with both species regenerating after fire from canopy‐stored seed banks.

Relative species abundance closely followed the duration of past fire intervals deduced from the number of tree rings in buried conifers. Time periods of long (4650–3950, 3400–1850 and 250–0 CYBP) and short fire intervals (4950–4650, 3950–3400 and 1850–250 CYBP) were associated, respectively, with decreasing and increasing pine abundance, probably reflecting faster juvenile growth, lower shade tolerance, earlier sexual maturity and shorter longevity in jack pine compared with black spruce.

We conclude that both climate change and climate‐induced fire disturbance have been driving long‐term ecosystem dynamics. Our field evidence supports the idea that interactions between disturbances and the life‐history traits of species modulate the impact of climate change at the scale of forest stands. At the same time, disturbances may result in long‐term stability of disturbance‐adapted ecosystems.
‘Talking Stones’: An Interview Technique for Disaffected Students
Authors: Wearmouth Janice
Published: May 2004

This paper describes and discusses the use of an interview technique derived from Personal Construct Theory, ‘Talking Stones’, that is designed to support self advocacy, particularly for groups of disaffected students whose views may be difficult to ascertain. This technique assumes that for the individual learner everything is perceived and mediated by what is socially and personally salient. The paper illustrates how this tool lends itself to practice in schools. It can help to lay bare problematic relationships, usually between teenagers and staff, and open up dialogue.