bluuebunny/crossref_metadata_2025 huggingface dataset:
Bacillus hwajinpoensis sp. nov. and an unnamed Bacillus genomospecies, novel members of Bacillus rRNA group 6 isolated from sea water of the East Sea and the Yellow Sea in Korea
Authors: Yoon Jung-Hoon , Kim In-Gi , Kang Kook Hee , Oh Tae-Kwang , Park Yong-Ha
Published: May 2004

Two Gram-positive or -variable, endospore-forming, slightly halophilic strains (SW-72Tand SW-93) were isolated from sea water of the East Sea and the Yellow Sea in Korea, respectively, and subjected to polyphasic taxonomic study. Both strains had cell-wall peptidoglycan that was based onmeso-diaminopimelic acid and MK-7 as the predominant menaquinone. The two strains contained large amounts of saturated and branched fatty acids, with anteiso-C15 : 0as the major fatty acid. The DNA G+C contents of strains SW-72Tand SW-93 were 40·9 and 41·0 mol%, respectively. Phylogenetic analysis based on 16S rDNA sequences showed that strains SW-72Tand SW-93 fall within the radiation of the cluster that comprises members of the genusBacillus, particularlyBacillusrRNA group 6. There were five nucleotide differences between the 16S rDNA sequences of strains SW-72Tand SW-93. The mean level of DNA–DNA relatedness between strains SW-72Tand SW-93 was 21·5 %. Strains SW-72Tand SW-93 showed 93·1–95·2 % 16S rDNA sequence similarity to the type strains ofBacillusspecies that are assigned to rRNA group 6. Strains SW-72Tand SW-93 could not be differentiated clearly by using their phenotypic properties. On the basis of phenotypic properties, phylogeny and genomic data, it is proposed that strain SW-72T(=KCCM 41641T=JCM 11807T) should be placed in the genusBacillusas the type strain of a novel species,Bacillus hwajinpoensissp. nov., and that strain SW-93 (=KCCM 41640=JCM 11806) should be placed in the genusBacillusas an unnamedBacillusgenomospecies.
Psychroflexus tropicus sp. nov., an obligately halophilic Cytophaga–Flavobacterium–Bacteroides group bacterium from an Hawaiian hypersaline lake
Authors: Donachie Stuart P. , Bowman John P. , Alam Maqsudul
Published: May 2004

A Gram-negative bacterium designated LA1T was isolated from water collected in hypersaline Lake Laysan on Laysan Island in the Northwestern Hawaiian Islands. Cells occurred singly as fine rods to short filaments. Growth in 50 % strength marine broth occurred optimally when the medium contained 7·5–10 % (w/v) NaCl. The major fatty acids in LA1T grown at 15 and 30 °C were 12-methyl tetradecanoic acid and 13-methyl tetradecanoic acid, respectively. The nucleotide sequence of the 16S rRNA gene showed that LA1T belonged in the Cytophaga–Flavobacterium–Bacteroides (CFB) group in the domain Bacteria. The closest described neighbour in terms of 16S rRNA gene sequence identity was Psychroflexus torquis ACAM 623T (94·4 % over 1423 bases), an obligate psychrophile from Antarctic sea-ice. The G+C content of 35·0 mol% was consistent with this affiliation. Phenotypic and genotypic analyses, including DNA hybridization, indicated that LA1T could be assigned to the genus Psychroflexus but, based on significant differences, including growth at 43 °C, it constitutes a novel species, Psychroflexus tropicus sp. nov., for which LA1T (=ATCC BAA-734T=DSM 15496T) is the type strain.
Mycobacterium saskatchewanense sp. nov., a novel slowly growing scotochromogenic species from human clinical isolates related to Mycobacterium interjectum and Accuprobe-positive for Mycobacterium avium complex
Authors: Turenne C. Y. , Thibert L. , Williams K. , Burdz T. V. , Cook V. J. , Wolfe J. N. , Cockcroft D. W. , Kabani A.
Published: May 2004

A pigmented, slowly growingMycobacterium aviumcomplex AccuProbe-positive organism was isolated from the sputum and pleural fluid of a 72-year-old female with bronchiectasis. The unusual morphology of the organism prompted further identification by 16S rRNA gene sequencing, revealing a perfect identity with previously uncharacterized strainMycobacteriumsp. MCRO 8 (GenBank accession no. X93034), with the closest established species by 16S rDNA analysis beingMycobacterium interjectum. HPLC of the organism corresponded to previously obtained patterns identified asM. interjectum-like and, upon sequence evaluation of a selection of strains with a similar profile, more were subsequently identified as MCRO 8. A total of 16 strains isolated from human respiratory samples were evaluated in the characterization of this novel species, for which the nameMycobacterium saskatchewanensesp. nov. is proposed. The type strain is strain 00-250T(=ATCC BAA-544T=DSM 44616T=CIP 108114T).
Halomonas boliviensis sp. nov., an alkalitolerant, moderate halophile isolated from soil around a Bolivian hypersaline lake
Authors: Quillaguamán Jorge , Hatti-Kaul Rajni , Mattiasson Bo , Alvarez Maria Teresa , Delgado Osvaldo
Published: May 2004

Halomonas boliviensis sp. nov. is proposed for two moderately halophilic, psychrophilic, alkalitolerant bacteria, LC1T (=DSM 15516T=ATCC BAA-759T) and LC2 (=DSM 15517=ATCC BAA-760), both of which were isolated from a soil sample around the lake Laguna Colorada, located at 4300 m above sea level in the south-west region of Bolivia. The bacteria are aerobic, motile, Gram-negative rods that produce colonies with a cream pigment. Moreover, they are heterotrophs that are able to utilize various carbohydrates as carbon sources. The organisms reduce nitrate and show tryptophan deaminase activity. The genomic DNA G+C contents were 51·4 mol% for isolate LC1T and 52·6 mol% for isolate LC2. Based on 16S rDNA sequence analysis, isolates LC1T and LC2 were identified as members of the genus Halomonas and clustered closely with Halomonas variabilis DSM 3051T and Halomonas meridiana DSM 5425T. However, DNA–DNA relatedness between the new isolates and the closest related Halomonas species was low.
Herbaspirillum chlorophenolicum sp. nov., a 4-chlorophenol-degrading bacterium
Authors: Im Wan-Taek , Bae Hee-Sung , Yokota Akira , Lee Sung Taik
Published: May 2004

A 4-chlorophenol-degrading bacterial strain, formerly designated as a strain of Comamonas testosteroni, was reclassified as a member of the genus Herbaspirillum based on its phenotypic and chemotaxonomic characteristics, as well as phylogenetic analysis using 16S rDNA sequences. Phylogenetic inference based on 16S rDNA sequences showed that strain CPW301T clusters in a phylogenetic branch that contains Herbaspirillum species. 16S rDNA sequence similarity of strain CPW301T to species of the genus Herbaspirillum with validly published names is in the range 98·7–98·9 %. Despite the considerably high 16S rDNA sequence similarity, strain CPW301T could be distinguished clearly from type strains of Herbaspirillum species with validly published names by DNA–DNA relatedness values, which were <15·7 %. The genomic DNA G+C content of strain CPW301T is 61·3 mol%. The predominant ubiquinone is Q-8 and the major cellular fatty acids are C16 : 0 and cyclo-C17 : 0. The strain does not fix nitrogen and is not plant-associated. It is an aerobic rod with one unipolar flagellum. On the basis of these characteristics, a novel Herbaspirillum species, Herbaspirillum chlorophenolicum sp. nov., is proposed. The type strain of the novel species is strain CPW301T (=KCTC 12096T=IAM 15024T).
Rothia aeria sp. nov., Rhodococcus baikonurensis sp. nov. and Arthrobacter russicus sp. nov., isolated from air in 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

Four Gram-positive bacteria, strains A1-17BT, A1-22T, A1-3Tand A1-8, isolated from the air in the Russian space laboratory Mir, were subjected to a polyphasic taxonomic study. Phylogenetic analysis of the bacteria based on their 16S rDNA sequence showed that they belong to the generaRothia(A1-17BT),Rhodococcus(A1-22T) andArthrobacter(A1-3Tand A1-8). Morphological, physiological, chemotaxonomic and genomic characteristics supported the assignments of these strains to these genera, but they could not be classified as any existing species within each respective genus. 16S rDNA similarity values between strain A1-17BTand its neighbours,Rothia dentocariosagenomovar II,Rothia dentocariosa,Rothia mucilaginosaandRothia nasimurium, were respectively 99·8, 98·0, 96·4 and 95·4 %. Polyphasic taxonomic evidence indicated that strain A1-17BTshould be categorized together with the unofficially namedRothia dentocariosagenomovar II, but clearly differentiated them from the established species of the genusRothia. Strain A1-22Tformed a coherent cluster withRhodococcus erythropolis,Rhodococcus globerulus,Rhodococcus marinonascensandRhodococcus percolatusin 16S rDNA sequence analysis, but DNA–DNA relatedness values were only 45·5, 35·3, 18·9 and 21·9 %. Strains A1-3Tand A1-8 shared 99·9 % 16S rDNA sequence similarity, and strain A1-3Tshowed the highest level of 16S rDNA similarity, 96·6 %, toArthrobacter polychromogenes. Contrasting biochemical characteristics were also identified. Finally, as a result of the polyphasic taxonomic study, three of the strains are proposed as type strains of novel species:Rothia aeriasp. nov. (A1-17BT=GTC 867T=JCM 11412T=DSM 14556T),Rhodococcus baikonurensissp. nov. (A1-22T=GTC 1041T=JCM 11411T=DSM 44587T) andArthrobacter russicussp. nov. (A1-3T=GTC 863T=JCM 11414T=DSM 14555T).
Systematics of the anamorphic basidiomycetous yeast genus Trichosporon Behrend with the description of five novel species: Trichosporon vadense, T. smithiae, T. dehoogii, T. scarabaeorum and T. gamsii
Authors: Middelhoven Wouter J. , Scorzetti Gloria , Fell Jack W.
Published: May 2004

Phylogenetic trees of the anamorphic basidiomycetous yeast genus Trichosporon Behrend, based on molecular sequence analysis of the internal transcribed spacer region and the D1/D2 region of the large subunit of ribosomal (26S) DNA, are presented. This study includes three novel species from soils, Trichosporon vadense sp. nov. (type strain, CBS 8901T), Trichosporon smithiae sp. nov. (type strain, CBS 8370T) and Trichosporon gamsii sp. nov. (type strain, CBS 8245T), one novel species from an insect, Trichosporon scarabaeorum sp. nov. (type strain, CBS 5601T) and one species of unknown origin, Trichosporon dehoogii sp. nov. (type strain, CBS 8686T). The phylogenetic positions and physiological characteristics that distinguish the new taxa from related species, based partly on growth tests that are not traditionally used in yeast taxonomy (uric acid, ethylamine, l-4-hydroxyproline, tyramine and l-phenylalanine as sources of carbon and nitrogen, and polygalacturonate, quinate, 4-ethylphenol, phloroglucinol, 2,3-dihydroxybenzoate and orcinol as sole carbon sources), are discussed. Assimilation of l-rhamnose and erythritol and maximum growth temperature were also used to delineate species.
Prevotella shahii sp. nov. and Prevotella salivae sp. nov., isolated from the human oral cavity
Authors: Sakamoto Mitsuo , Suzuki Masahito , Huang Yi , Umeda Makoto , Ishikawa Isao , Benno Yoshimi
Published: May 2004

Two bacterial strains, EHS11Tand EPSA11T, which were isolated from the human oral cavity, were characterized in terms of phenotypic and biochemical characteristics, cellular fatty acid profiles and phylogenetic position based on 16S rRNA gene sequence analysis. 16S rRNA gene sequence analysis showed that each of the isolates belonged to a novel species of the genusPrevotella. Strain EHS11Twas related toPrevotella loescheii(about 95 % similarity), whereas strain EPSA11Twas related toPrevotella oris(about 94 % similarity). Both strains were obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-negative rods. The cellular fatty acid composition of strain EPSA11Twas very similar to that ofP. orisJCM 8540T. On the other hand, the cellular fatty acid composition of strain EHS11Twas significantly different from those of otherPrevotellaspecies. The predominant fatty acids in strain EHS11Tare C18 : 1ω9c, C16 : 0and C16 : 03-OH, whereas otherPrevotellaspecies, except forP. loescheiiJCM 8530T, possess anteiso-C15 : 0, iso-C17 : 03-OH and C18 : 1ω9c. The predominant fatty acids inP. loescheiiJCM 8530Tare anteiso-C15 : 0, C16 : 0and C18 : 1ω9c. DNA–DNA hybridization experiments revealed a genomic distinction of strains EHS11Tand EPSA11TfromP. loescheiiJCM 8530TandP. orisJCM 8540T. On the basis of these data, two novelPrevotellaspecies are proposed:Prevotella shahiisp. nov. andPrevotella salivaesp. nov. The type strains ofP. shahiiandP. salivaeare EHS11T(=JCM 12083T=DSM 15611T) and EPSA11T(=JCM 12084T=DSM 15606T), respectively.
Streptomyces hebeiensis sp. nov.
Authors: Xu Ping , Li Wen-Jun , Wu Wen-long , Wang Dong , Xu Li-Hua , Jiang Cheng-Lin
Published: May 2004

A novel actinomycete strain, YIM 001T, was isolated from a soil sample collected from Hebei province, People's Republic of China. The strain was characterized by white to grey aerial mycelium. Long spore chains, borne on the aerial mycelium, were straight toRectiflexibiles; the spore chains were composed of non-motile and coccoid spores with a warty surface. The cell wall of strain YIM 001Tcontainedll-diaminopimelic acid (A2pm) and traces ofmeso-A2pm. Whole-cell hydrolysates contained mainly glucose and small amounts of xylose, galactose and arabinose. The menaquinones were MK-9(H4) (4·6 %), MK-9(H6) (60 %), MK-9(H8) (30·7 %) and MK-9(H10) (4·7 %). Phosphatidylethanolamine was the diagnostic phospholipid. The DNA G+C content of strain YIM 001Twas 71·4 mol%. Phylogenetic analysis indicated that strain YIM 001Tbelongs to the genusStreptomyces. Based on its phenotypic and genotypic characteristics, strain YIM 001T(=CCTCC AA 203005T=CIP 107974T=DSM 41837T) is proposed as the type strain of a novel species,Streptomyces hebeiensissp. nov.
Arthrobacter nitroguajacolicus sp. nov., a novel 4-nitroguaiacol-degrading actinobacterium
Authors: Kotoučková Ludmila , Schumann Peter , Durnová Eva , Spröer Cathrin , Sedláček Ivo , Neča Jiří , Zdráhal Zbyněk , Němec Miroslav
Published: May 2004

Three bacterial isolates from soil, capable of degradation or transformation of nitroaromatic compounds and displaying a rod–coccus growth cycle, were studied by a polyphasic approach. On the basis of 16S rRNA sequence analysis and of chemotaxonomic characteristics, such as type A3α peptidoglycan with an interpeptide bridge Ala–Thr–Ala, the major menaquinone MK-9(H2) and fatty acid composition, the isolates were assigned to the genus Arthrobacter. DNA–DNA hybridization, riboprinting and phenotypic studies revealed that the three strains constitute a single species, distinct from phylogenetically neighbouring Arthrobacter aurescens and Arthrobacter ilicis. A novel species, Arthrobacter nitroguajacolicus sp. nov., with the type strain G2-1T (=CCM 4924T=DSM 15232T) is proposed.
Nesterenkonia halotolerans sp. nov. and Nesterenkonia xinjiangensis sp. nov., actinobacteria from saline soils in the west of China
Authors: Li Wen-Jun , Chen Hua-Hong , Zhang Yu-Qin , Schumann Peter , Stackebrandt Erko , Xu Li-Hua , Jiang Cheng-Lin
Published: May 2004

The taxonomic position of two Gram-positive strains, YIM 70084Tand YIM 70097T, isolated from hypersaline soils was determined by a polyphasic approach. Cells of strain YIM 70084Tare motile cocci, whereas those of strain YIM 70097Tare non-motile rods. The G+C contents of their DNA are 64·4 and 66·7 mol%. Both strains had chemotaxonomic markers typical of the genusNesterenkoniaand formed a coherent cluster withNesterenkoniaspecies in a phylogenetic inference based on 16S rDNA sequence analysis, exhibiting less than 97 % similarity to each other and to the other two type strains of the genus. Phylogenetic distinction and differences in the peptidoglycan type, composition of cell-wall sugars, phospholipid patterns, the major menaquinones and other phenotypic characteristics indicate that the strains under study represent two novel species,Nesterenkonia halotoleranssp. nov. (type strain YIM 70084T=CCTCC AA 001022T=DSM 15474T) andNesterenkonia xinjiangensissp. nov. (type strain YIM 70097T=CCTCC AA 001025T=DSM 15475T).
Methanobacterium aarhusense sp. nov., a novel methanogen isolated from a marine sediment (Aarhus Bay, Denmark)
Authors: Shlimon Adris Georgis , Friedrich Michael W. , Niemann Helge , Ramsing Niels Birger , Finster Kai
Published: May 2004

Strain H2-LRT, a 5–18 μm long and 0·7 μm wide filamentous, mesophilic, moderately halophilic, non-motile hydrogenotrophic methanogen, was isolated from marine sediment of Aarhus Bay, Denmark, 1·7 m below the sediment surface. On the basis of 16S rRNA gene comparison with sequences of known methanogens, strain H2-LRT could be affiliated to the genus Methanobacterium. The strain forms a distinct line of descent within this genus, with Methanobacterium oryzae (95·9 % sequence identity) and Methanobacterium bryantii (95·7 % sequence identity) as its closest relatives. The 16S rRNA-based affiliation was supported by comparison of the mcrA gene, which encodes the α-subunit of methyl-coenzyme M reductase. Strain H2-LRT grew only on H2/CO2. The DNA G+C content is 34·9 mol%. Optimum growth temperature was 45 °C. The strain grew equally well at pH 7·5 and 8. No growth or methane production was observed below pH 5 or above pH 9. Strain H2-LRT grew well within an NaCl concentration range of 100 and 900 mM. No growth or methane production was observed at 1 M NaCl. At 50 mM NaCl, growth and methane production were reduced. Based on 16S rRNA gene sequence analysis, the isolate is proposed to represent a novel taxon within the genus Methanobacterium, namely Methanobacterium aarhusense sp. nov. The type strain is H2-LRT (=DSM 15219T=ATCC BAA-828T).
SPIRAL1Encodes a Plant-Specific Microtubule-Localized Protein Required for Directional Control of Rapidly Expanding Arabidopsis Cells[W]
Authors: Nakajima Keiji , Furutani Ikuyo , Tachimoto Hideki , Matsubara Hiroshige , Hashimoto Takashi
Published: May 2004

Highly organized interphase cortical microtubule (MT) arrays are essential for anisotropic growth of plant cells, yet little is known about the molecular mechanisms that establish and maintain the order of these arrays. The Arabidopsis thaliana spiral1 (spr1) mutant shows right-handed helical growth in roots and etiolated hypocotyls. Characterization of the mutant phenotypes suggested that SPR1 may control anisotropic cell expansion through MT-dependent processes. SPR1 was identified by map-based cloning and found to encode a small protein with unknown function. Proteins homologous to SPR1 occur specifically and ubiquitously in plants. Genetic complementation with green fluorescent protein fusion proteins indicated that the SPR1 protein colocalizes with cortical MTs and that both MT localization and cell expansion control are conferred by the conserved N- and C-terminal regions. Strong SPR1 expression was found in tissues undergoing rapid cell elongation. Plants overexpressing SPR1 showed enhanced resistance to an MT drug and increased hypocotyl elongation. These observations suggest that SPR1 is a plant-specific MT-localized protein required for the maintenance of growth anisotropy in rapidly elongating cells.
Extracellular Invertase Is an Essential Component of Cytokinin-Mediated Delay of Senescence[W]
Authors: Balibrea Lara Maria Encarnacioén , Gonzalez Garcia Maria-Cruz , Fatima Tahira , Ehneß Rainer , Lee Taek Kyun , Proels Reinhard , Tanner Widmar , Roitsch Thomas
Published: May 2004

Leaf senescence is the final stage of leaf development in which the nutrients invested in the leaf are remobilized to other parts of the plant. Whereas senescence is accompanied by a decline in leaf cytokinin content, exogenous application of cytokinins or an increase of the endogenous concentration delays senescence and causes nutrient mobilization. The finding that extracellular invertase and hexose transporters, as the functionally linked enzymes of an apolasmic phloem unloading pathway, are coinduced by cytokinins suggested that delay of senescence is mediated via an effect on source-sink relations. This hypothesis was further substantiated in this study by the finding that delay of senescence in transgenic tobacco (Nicotiana tabacum) plants with autoregulated cytokinin production correlates with an elevated extracellular invertase activity. The finding that the expression of an extracellular invertase under control of the senescence-induced SAG12 promoter results in a delay of senescence demonstrates that effect of cytokinins may be substituted by these metabolic enzymes. The observation that an increase in extracellular invertase is sufficient to delay leaf senescence was further verified by a complementing functional approach. Localized induction of an extracellular invertase under control of a chemically inducible promoter resulted in ectopic delay of senescence, resembling the naturally occurring green islands in autumn leaves. To establish a causal relationship between cytokinins and extracellular invertase for the delay of senescence, transgenic plants were generated that allowed inhibition of extracellular invertase in the presence of cytokinins. For this purpose, an invertase inhibitor was expressed under control of a cytokinin-inducible promoter. It has been shown that senescence is not any more delayed by cytokinin when the expression of the invertase inhibitor is elevated. This finding demonstrates that extracellular invertase is required for the delay of senescence by cytokinins and that it is a key element of the underlying molecular mechanism.
Differential Activation of the Rice Sucrose Nonfermenting1–Related Protein Kinase2 Family by Hyperosmotic Stress and Abscisic Acid[W]
Authors: Kobayashi Yuhko , Yamamoto Shuhei , Minami Hideyuki , Kagaya Yasuaki , Hattori Tsukaho
Published: May 2004

To date, a large number of sequences of protein kinases that belong to the sucrose nonfermenting1–related protein kinase2 (SnRK2) family are found in databases. However, only limited numbers of the family members have been characterized and implicated in abscisic acid (ABA) and hyperosmotic stress signaling. We identified 10 SnRK2 protein kinases encoded by the rice (Oryza sativa) genome. Each of the 10 members was expressed in cultured cell protoplasts, and its regulation was analyzed. Here, we demonstrate that all family members are activated by hyperosmotic stress and that three of them are also activated by ABA. Surprisingly, there were no members that were activated only by ABA. The activation was found to be regulated via phosphorylation. In addition to the functional distinction with respect to ABA regulation, dependence of activation on the hyperosmotic strength was different among the members. We show that the relatively diverged C-terminal domain is mainly responsible for this functional distinction, although the kinase domain also contributes to these differences. The results indicated that the SnRK2 protein kinase family has evolved specifically for hyperosmotic stress signaling and that individual members have acquired distinct regulatory properties, including ABA responsiveness by modifying the C-terminal domain.
Comparative Analysis of the Receptor-Like Kinase Family in Arabidopsis and Rice[W]
Authors: Shiu Shin-Han , Karlowski Wojciech M. , Pan Runsun , Tzeng Yun-Huei , Mayer Klaus F. X. , Li Wen-Hsiung
Published: May 2004

Receptor-like kinases (RLKs) belong to the large RLK/Pelle gene family, and it is known that the Arabidopsis thaliana genome contains >600 such members, which play important roles in plant growth, development, and defense responses. Surprisingly, we found that rice (Oryza sativa) has nearly twice as many RLK/Pelle members as Arabidopsis does, and it is not simply a consequence of a larger predicted gene number in rice. From the inferred phylogeny of all Arabidopsis and rice RLK/Pelle members, we estimated that the common ancestor of Arabidopsis and rice had >440 RLK/Pelles and that large-scale expansions of certain RLK/Pelle members and fusions of novel domains have occurred in both the Arabidopsis and rice lineages since their divergence. In addition, the extracellular domains have higher nonsynonymous substitution rates than the intracellular domains, consistent with the role of extracellular domains in sensing diverse signals. The lineage-specific expansions in Arabidopsis can be attributed to both tandem and large-scale duplications, whereas tandem duplication seems to be the major mechanism for recent expansions in rice. Interestingly, although the RLKs that are involved in development seem to have rarely been duplicated after the Arabidopsis–rice split, those that are involved in defense/disease resistance apparently have undergone many duplication events. These findings led us to hypothesize that most of the recent expansions of the RLK/Pelle family have involved defense/resistance-related genes.
An automated temperature-monitoring system for dry-shippers
Authors: Ridoutt Fernando , Mueller-Dieckmann Christoph , Tucker Paul A. , Weiss Manfred S.
Published: May 2004

A commercially available temperature-logging device (Tinytag Plus, Gemini Data Loggers) was fitted to a Taylor-Wharton CP100 dry-shipper, which is a widely used container for the storage and transport of macromolecular crystals. The temperature was monitored over periods of up to one week, which included the transport of the container from Hamburg (Germany) to Trieste (Italy) and back. Further control experiments were carried out in order to assess the effect of certain disturbing events on the temperature curve.
First results of digital topography applied to macromolecular crystals
Authors: Lovelace Jeffrey J. , Soares Alexei S. , Bellamy Henry D. , Sweet Robert M. , Snell Edward H. , Borgstahl Gloria E. O.
Published: May 2004

An inexpensive digital CCD camera was used to record X-ray topographs directly from large imperfect crystals of cubic insulin. The topographs recorded were not as detailed as those which can be measured with film or emulsion plates, but do show great promise. Six reflections were recorded using a set of finely spaced stills encompassing the rocking curve of each reflection. A complete topographic reflection profile could be digitally imaged in minutes. Interesting and complex internal structure was observed by this technique. The CCD chip used in the camera has anti-blooming circuitry and produced good data quality, even when pixels became overloaded.
Absorption corrections for diamond-anvil pressure cells implemented in the software packageAbsorb6.0
Authors: Angel R. J.
Published: May 2004

High-pressure single-crystal structure refinement requires intensity data that have been corrected for the various absorption effects in the pressure cell. In this contribution, the methods for calculating the absorption corrections for a transmission-geometry diamond-anvil pressure cell are reviewed. The ideas presented in this paper have been implemented in a software package for Microsoft Windows,Absorb6.0, available at http://www.crystal.vt.edu/.
Faster acquisition of structure-factor amplitudes in surface X-ray diffraction experiments
Authors: Torrelles X. , Rius J.
Published: May 2004

The traditional way of measuring intensities in surface X-ray diffraction experiments is by performing rocking scans. Owing to experimental time limitations, this rather slow procedure leads to incomplete data sets for large surface unit cells. This lack of information not only may affect adversely the accuracy of the refined atomic positions, but also hinders the application of three-dimensional direct methods of structure solution. Here the viability of the alternative data collection strategy proposed by Specht & Walker [J. Appl. Cryst.(1993),26, 166–171] is investigated by using as test material a 50 Å thick NBCO thin film grown on an SrTiO3(001) substrate. This procedure, which is based on stationaryLscans,i.e.the sample is kept fixed during theLscan, shortens the measuring time by an order of magnitude. In this study, special attention has been paid to the validation of the predicted theoretical Lorentz factor, which is specific for this experimental setup.
Use of a CCD diffractometer in crystal structure determinations at high pressure
Authors: Dawson Alice , Allan David R. , Parsons Simon , Ruf Michael
Published: May 2004

Although CCD instruments are now widely used in single-crystal diffraction, they have not been employed so extensively in crystallographic studies at high pressure. This paper describes some practical experience in the application of one CCD instrument, the Bruker–Nonius SMART APEX (a fixed-χ instrument). Centring a sample in a pressure cell is complicated by the restrictions on viewing the sample imposed by the body of the cell. The data collection strategy is defined by the requirements that (i) the incident beam must illuminate the sample and (ii) no more than 80% of the detector should be shaded by the body of the pressure cell. High-pressure diffraction images are contaminated by powder lines from the gasket and backing-disk materials, which form part of the pressure cell, and very intense spots from the diamond anvils. Procedures for the selection of spots for indexing are described. Integration routines attempt to harvest intensity data from regions of the detector that are shaded by the body of the pressure cell, and a procedure for generating dynamic masks is described. Shading also reduces the volume of reciprocal space that can be sampled, although this can be increased by performing data collections at more than one pressure-cell setting. Corrections for absorption are carried out in a two-stage procedure comprising an analytical correction for absorption by the cell, followed by a second multi-scan correction. Data sets collected at high pressure often contain some significant outliers; these can be identified during merging using a robust resistant weighting scheme, as described by Blessing [J. Appl. Cryst.(1997),30, 421–426].
A modified microdialysis button for use in protein crystallization
Authors: Lee Stephen S. J. , Cudney Robert
Published: May 2004

A modified microdialysis button for use in protein crystallization has been designed and manufactured. This new apparatus, called the Microdialysis Rod, allows easier handling and storage, and provides versatility to the users.
Divergence-slit intensity corrections for Bragg–Brentano diffractometers with circular sample surfaces and known beam intensity distribution
Authors: Krüger H. , Fischer R. X.
Published: May 2004

Bragg–Brentano powder diffractometers equipped with fixed-divergence slits show a loss of intensity at small 2θ angles as a result of the overflow of the beam exceeding the sample surface. To correct this effect, geometrically derived algorithms are presented to calculate correction factors for circular sample surfaces. It is shown that the algorithms for rectangular samples can be applied to circular samples with sufficient accuracy if the value for the length of the sample is replaced by a value intermediate between the diameter of the circular sample and the length of the corresponding rectangular sample. Inhomogeneous beam intensity distribution also has serious effects on the correction factors, especially for wide divergence-slit apertures.
ABS: a program to determine absolute configuration and evaluate anomalous scatterer substructure
Authors: Hao Quan
Published: May 2004

In single- or multi-wavelength anomalous dispersion (SAD/MAD) phasing, one of the essential steps is to find the absolute configuration (hand) of the anomalous scatterers. A computer program,ABS, based on an algorithm proposed by Woolfson & Yao [Acta Cryst. (1994), D50, 7–10] has been written to determine the absolute configuration by using anomalous scattering data. It also calculates a real-space figure of merit (FOM) that can be used to assess the quality of the solution for anomalous scatterer sites. TheABSprogram has been successfully applied in severalab initiophasing cases, including some previously unknown protein structures. The program is included in theCCP4suite.
Small‐seeded species produce more seeds per square metre of canopy per year, but not per individual per lifetime
Authors: MOLES ANGELA T. , FALSTER DANIEL S. , LEISHMAN MICHELLE R. , WESTOBY MARK
Published: May 2004

The trade‐off between seed mass and the number of seeds a plant can make for a given amount of energy underpins our understanding of seed ecology. However, there is little information on the magnitude of the fecundity advantage of small‐seeded species over an entire plant lifetime.

We compiled data from the literature to quantify the relationships between: (i) seed mass and plant size (because the photosynthetic area of a plant determines how much energy is available for allocation to seed production); (ii) seed mass and plant reproductive lifetime (the number of years a plant has to produce seeds); and (iii) seed mass and the number of seeds produced per individual per year, and per lifetime.

Seed mass was positively related to all measures of plant size (canopy area, plant height, stem diameter, plant mass and canopy volume). There were also positive correlations between seed mass and time to first reproduction, plant life span, and reproductive life span. Thus, although small‐seeded species produce more seeds per unit canopy area per year than large‐seeded species, large‐seeded species tend to have larger canopies and more reproductive years.

These patterns accord well with independently gathered data on annual and lifetime seed production. The negative relationship between seed mass and the number of seeds produced per year was much shallower on a per individual basis than on a per unit canopy basis. Seed mass was not significantly related to the total number of seeds produced by an individual plant throughout its lifetime.

Our previous understanding of seed mass as a spectrum from production of many small seeds, each with low establishment probability, to a few large seeds each with higher establishment probability, was missing some important elements. To understand the forces shaping the evolution of seed mass, we will need to consider plant size and longevity, as well as seedling survival rates and the number of seeds that can be produced for a given amount of energy.
Ground cover recovery patterns and life‐history traits: implications for restoration obstacles and opportunities in a species‐rich savanna
Authors: KIRKMAN L. K. , COFFEY K. L. , MITCHELL R. J. , MOSER E. B.
Published: May 2004

We identified species with low re‐colonization potential, which could be used as indicators of recovery of species‐rich pine savannas, by comparing the ground‐cover flora of a 64‐year‐old slash pine plantation (recovery site) with that of a nearby natural longleaf pine savanna (reference site). We also determined life‐history traits that were useful predictors of recolonization potential.

The high floristic overlap in species between reference and recovery sites and similar species richness at scales ≥ 10 m2 suggests that substantial vegetation recovery occurred over the 65‐year period. However, for areas < 10 m2 the lower species packing in the recovery sites indicates that coexistence of a high number of species at small scales is dependent on local dispersal and establishment, and may take much longer to achieve.

The absence, or near absence, of some species from the recovery site, even after 65 years, suggests that some species may be particularly vulnerable to disturbance and may re‐establish infrequently, if ever. Several dispersal distance‐restricted species were identified that require active reintroduction. While no particular guild of species was a strong indicator of recovery in this study, we identified a group of species that assess the absence of or the degree of recovery from, prior soil disturbance.

Local dispersal appears to be an important factor structuring species richness patterns in pine savannas. Limitations of dispersal distance in some species, particularly those with gravity and ant‐dispersal mechanisms, represent an obstacle to passive restoration that can only be overcome either by introduction of propagules in the restoration process or by allowing for longer periods of recruitment.

This study demonstrates a method for identifying a suite of species that may be unsuccessful at recolonization. The method would be applicable to numerous degraded ecosystems, particularly similar species‐rich savannas, grasslands and forests.
Seedling survival and seed size: a synthesis of the literature
Authors: MOLES ANGELA T. , WESTOBY MARK
Published: May 2004

Large‐seeded species have long been known to have higher survivorship during establishment than small‐seeded species. Here, we assessed the size of this advantage by compiling published data on survival through seedling emergence, seedling establishment and sapling establishment.

We found no relationship between seed mass and survival through the transition from viable seed in or on the soil to newly emerged seedlings (P = 0.47, n = 33 species).

Synthesis of data from experimental studies on the advantages of large‐seeded species establishing under particular hazards (such as shade, drought or herbivory) confirmed that seedlings of large‐seeded species perform better than those of small‐seeded species in most situations. However, the magnitude of this advantage was not sufficient to counterbalance the greater number of seeds produced by small‐seeded species m−2 of canopy outline year−1.

Synthesis of data from field studies of populations under natural conditions also showed that large‐seeded species have higher survival through early seedling establishment than small‐seeded species (P = 0.006, n = 112 species). However, the magnitude of this advantage would only be sufficient to counterbalance the greater number of seeds produced by small‐seeded species m−2 of canopy outline year−1 if mortality continued at the same rate for some time.

The time required for a species with 10‐fold larger seeds to recoup the advantage gained by a smaller‐seeded species during seed production ranged from 8.8 weeks for the smallest seeded species in the data set, up to an implausible 4.2 years for the largest‐seeded species. Thus, while large‐seeded species do have a survival advantage over small‐seeded species during seedling establishment, the available evidence suggests that advantages must also accrue during other stages in the life cycle. One possibility is that the greater seed production of small‐seeded species (m−2 of canopy outline year−1) is partly offset by larger canopies and longer reproductive life spans in large‐seeded species.
The relative dominance hypothesis explains interaction dynamics in mixed speciesAlnus rubra/Pseudotsuga menziesiistands
Authors: ANTHONY W. D’AMATO , KLAUS J. PUETTMANN
Published: May 2004

We used repeated measurements of tree growth and population‐level and neighbourhood conditions from three mixedAlnus rubra/Pseudotsuga menziesiiforests in the Pacific Northwest, USA to investigate why previous results regarding the importance of neighbourhood competition as a determinant of plant growth were inconsistent.

We propose that relative dominance of a particular species determines the importance of neighbourhood interactions, and tested whether growth performance of both species at various stand ages agrees with this relative dominance hypothesis.

Neighbourhood and relative dominance interaction indices were modified to accommodate two‐species mixtures and were incorporated into a growth model predicting relative diameter growth rates. The corrected Akaike Information Criterion (AICc) was used to identify the optimum interaction measures and model forms for each species and measurement period.

Interaction indices reflecting the size of a tree relative to the population were the best predictors of growth of the dominant (i.e. taller) species and neighbourhood interaction indices of the subordinate species.

Performance of interaction measures as predictors of relative growth rates in our study varied in agreement with the relative dominance hypothesis for both species and on all sites. Results from other studies suggest that the hypothesis may explain growth performances on a species and individual plant level and for a variety of life forms.

These findings suggest that the spatial scale of plant interactions is influenced by the size structure of plant populations. The relative dominance hypothesis offers a framework to provide insight into the mechanism of competition, based on the relative performance of competition indices.
Seed–seedling allometry in tropical rain forest trees: seed mass‐related patterns of resource allocation and the ‘reserve effect’
Authors: GREEN PETER T. , JUNIPER PETER A.
Published: May 2004

The seedlings of larger seeded species generally perform better than those of smaller seeded species under a variety of hazards. The reserve effect proposes that larger seeded species retain a greater proportion of their initial seed resources and their seedlings are therefore better provisioned to cope with post‐deployment resource deficits.

This hypothesis was tested with a suite of 32 Australian rain forest species with storage cotyledons, and seed reserve mass ranging from 36 mg to 25 g. Seedlings germinated in dim light were harvested as their first set of leaves became fully expanded, dissected into shoot, root and left‐over cotyledons, dried and weighed.

In cross‐species, allometric analyses, the mean mass of the shoot‐plus‐root scaled less than proportionately (slope c. 0.8), and mean cotyledon mass more than proportionately (slope c. 1.1) with either initial seed mass or seedling mass. These slopes were significantly different from each other. Both conditions for a reserve effect were therefore fulfilled. Cotyledons ranged from 45% of total seedling mass in the smallest species, to 92% in the largest.

Solid evidence for a reserve effect was detected within two of four families tested (Lauraceae and Myrtaceae), but only in 7 of the 22 species for which there were sufficient data.

Even if the reserve effect has present day utility for enhanced seedling performance in larger seeded species, it may have evolved in response to selection for a greater relative retention of initial seed mass during seedling deployment in larger seeded species, combined with selection for greater deployment of seed reserves to the initial shoot and root of smaller seeded species.
Pupils' Perceptions of the Efficacy of Target Setting and How it can be Made More Effective
Authors: Dagley Valerie
Published: May 2004

This article explores some of the substantive issues that arose from a qualitative research study into individual pupil target setting in a secondary school. A multiple case study approach was employed in order to reveal the experiences and perceptions of some ‘middle ability’ Key Stage 3 pupils. The benefits of the process of setting highly individualized targets are discussed from the pupils' perspective. Therelationship between target setting and Academic Tutoring is examined and the potential for pastoral staff to use target setting as part of a learning discourse is highlighted.
The Provision for Personal, Social, Health Education (PSHE) and Citizenship in School‐based Elements of Primary Initial Teacher Education
Authors: Mead Nick
Published: May 2004

This small‐scale research study looks at the PSHE/Citizenship framework and the opportunities for student teachers to understand and experience within school the relationship between values, personal and social development and learning. A questionnaire was given to two sets of student teachers on their final school‐based placements. The research suggests that there needs to be greater recognition of the centrality of multi‐cultural awareness and understanding within the political literacy section of the PSHE/Citizenship framework. This is the counterpart to a previous study of the opportunities for values education within the university‐based elements of Primary Initial Teacher Education (Mead, 2003).
Time to Change the Truancy Laws? Compulsory Education: Its Origin and Modern Dilemma
Authors: Zhang Ming
Published: May 2004

This paper critically debates the current development of parental prosecution for students'; unauthorized absence from school. The author examines the history of compulsory education in Europe and the USA and questions its pertinence today. The results of a survey of prosecution and truancy during the period 1999–2002, conducted in forty‐three LEAs in England and Wales, are presented. The findings question the effectiveness of such new legislation and practice.
The Three R's of Pastoral Care: Relationships, Respect and Responsibility
Authors: Grove Michael
Published: May 2004

The author argues that over the last twenty years we have witnessed an evolution in pastoral care that is unparalleled in any other field of education. There has been controversy over the definition and these different views are discussed. The paucity of research and literature in the field and particularly in relation to the pastoral needs of teachers andstaff is emphasized.

In this paper it is suggested that the needs of school staff in respect of pastoral care are relatively neglected in the literature. Using the three R's of pastoral care – relationships, respect and responsibility – this paper focuses attention on teachers and their needs in the workplace. It is argued that attention to relationships, respect and responsibility enablesa proactive collaborative approach in which all members of the school community play a crucial role in the pastoral care of students.
GOOD FOR YOU
Authors: LEBAR MARK
Published: May 2004

Abstract:  Theories of human well‐being struggle with a tension between opposing intuitions: on the one hand, that our welfare is subjectively determined by us as individuals, and on the other that there are objective constraints on what can count as our good. I argue that accounts driven primarily by subjectivist intuitions fail to come to grips with the signific‐ance of objectivist intuitions, by failing to explain where our objectivist intuitions come from and why they are important, and defend an alternative account of human welfare – what I call Aristotelian Constructivism.
Effects of an experimental drought on soil emissions of carbon dioxide, methane, nitrous oxide, and nitric oxide in a moist tropical forest
Authors: Davidson Eric A. , Ishida Françoise Yoko , Nepstad Daniel C.
Published: May 2004

Changes in precipitation in the Amazon Basin resulting from regional deforestation, global warming, and El Niño events may affect emissions of carbon dioxide (CO2), methane (CH4), nitrous oxide (N2O), and nitric oxide (NO) from soils. Changes in soil emissions of radiatively important gases could have feedback implications for regional and global climates. Here we report results of a large‐scale (1 ha) throughfall exclusion experiment conducted in a mature evergreen forest near Santarém, Brazil. The exclusion manipulation lowered annual N2O emissions by >40% and increased rates of consumption of atmospheric CH4 by a factor of >4. No treatment effect has yet been detected for NO and CO2 fluxes. The responses of these microbial processes after three rainy seasons of the exclusion treatment are characteristic of a direct effect of soil aeration on denitrification, methanogenesis, and methanotrophy. An anticipated second phase response, in which drought‐induced plant mortality is followed by increased mineralization of C and N substrates from dead fine roots and by increased foraging of termites on dead coarse roots, has not yet been detected. Analyses of depth profiles of N2O and CO2 concentrations with a diffusivity model revealed that the top 25 cm soil is the site of most of the wet season production of N2O, whereas significant CO2 production occurs down to 100 cm in both seasons, and small production of CO2 occurs to at least 1100 cm depth. The diffusivity‐based estimates of CO2 production as a function of depth were strongly correlated with fine root biomass, indicating that trends in belowground C allocation may be inferred from monitoring and modeling profiles of H2O and CO2.