bluuebunny/crossref_metadata_2025 huggingface dataset:
Tablet—next generation sequence assembly visualization
Authors: Milne Iain , Bayer Micha , Cardle Linda , Shaw Paul , Stephen Gordon , Wright Frank , Marshall David
Published: December 2009

Summary: Tablet is a lightweight, high-performance graphical viewer for next-generation sequence assemblies and alignments. Supporting a range of input assembly formats, Tablet provides high-quality visualizations showing data in packed or stacked views, allowing instant access and navigation to any region of interest, and whole contig overviews and data summaries. Tablet is both multi-core aware and memory efficient, allowing it to handle assemblies containing millions of reads, even on a 32-bit desktop machine.

Availability: Tablet is freely available for Microsoft Windows, Apple Mac OS X, Linux and Solaris. Fully bundled installers can be downloaded from http://bioinf.scri.ac.uk/tablet in 32- and 64-bit versions.

Contact:  tablet@scri.ac.uk
DataPflex: a MATLAB-based tool for the manipulation and visualization of multidimensional datasets
Authors: Hendriks Bart S. , Espelin Christopher W.
Published: December 2009

Motivation: DataPflex is a MATLAB-based application that facilitates the manipulation and visualization of multidimensional datasets. The strength of DataPflex lies in the intuitive graphical user interface for the efficient incorporation, manipulation and visualization of high-dimensional data that can be generated by multiplexed protein measurement platforms including, but not limited to Luminex or Meso-Scale Discovery. Such data can generally be represented in the form of multidimensional datasets [for example (time × stimulation × inhibitor × inhibitor concentration × cell type × measurement)]. For cases where measurements are made in a combinational fashion across multiple dimensions, there is a need for a tool to efficiently manipulate and reorganize such data for visualization. DataPflex accepts data consisting of up to five arbitrary dimensions in addition to a measurement dimension. Data are imported from a simple .xls format and can be exported to MATLAB or .xls. Data dimensions can be reordered, subdivided, merged, normalized and visualized in the form of collections of line graphs, bar graphs, surface plots, heatmaps, IC50’s and other custom plots. Open source implementation in MATLAB enables easy extension for custom plotting routines and integration with more sophisticated analysis tools.

Availability: DataPflex is distributed under the GPL license (http://www.gnu.org/licenses/) together with documentation, source code and sample data files at: http://code.google.com/p/datapflex.

Contact:  DataPflexinfo@gmail.com; bhendriks@merrimackpharma.com

Supplementary information:  Supplementary data available at Bioinformatics online.
Protein complex prediction based on simultaneous protein interaction network
Authors: Jung Suk Hoon , Hyun Bora , Jang Woo-Hyuk , Hur Hee-Young , Han Dong-Soo
Published: December 2009

Motivation: The increase in the amount of available protein–protein interaction (PPI) data enables us to develop computational methods for protein complex predictions. A protein complex is a group of proteins that interact with each other at the same time and place. The protein complex generally corresponds to a cluster in PPI network (PPIN). However, clusters correspond not only to protein complexes but also to sets of proteins that interact dynamically with each other. As a result, conventional graph-theoretic clustering methods that disregard interaction dynamics show high false positive rates in protein complex predictions.

Results: In this article, a method of refining PPIN is proposed that uses the structural interface data of protein pairs for protein complex predictions. A simultaneous protein interaction network (SPIN) is introduced to specify mutually exclusive interactions (MEIs) as indicated from the overlapping interfaces and to exclude competition from MEIs that arise during the detection of protein complexes. After constructing SPINs, naive clustering algorithms are applied to the SPINs for protein complex predictions. The evaluation results show that the proposed method outperforms the simple PPIN-based method in terms of removing false positive proteins in the formation of complexes. This shows that excluding competition between MEIs can be effective for improving prediction accuracy in general computational approaches involving protein interactions.

Availability:  http://code.google.com/p/simultaneous-pin/

Contact:  dshan@kaist.ac.kr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Biomarker detection in the integration of multiple multi-class genomic studies
Authors: Lu Shuya , Li Jia , Song Chi , Shen Kui , Tseng George C.
Published: December 2009

Motivation: Systematic information integration of multiple-related microarray studies has become an important issue as the technology becomes mature and prevalent in the past decade. The aggregated information provides more robust and accurate biomarker detection. So far, published meta-analysis methods for this purpose mostly consider two-class comparison. Methods for combining multi-class studies and considering expression pattern concordance are rarely explored.

Results: In this article, we develop three integration methods for biomarker detection in multiple multi-class microarray studies: ANOVA-maxP, min-MCC and OW-min-MCC. We first consider a natural extension of combining P-values from the traditional ANOVA model. Since P-values from ANOVA do not guarantee to reflect the concordant expression pattern information across studies, we propose a multi-class correlation (MCC) measure to specifically seek for biomarkers of concordant inter-class patterns across a pair of studies. For both ANOVA and MCC approaches, we use extreme order statistics to identify biomarkers differentially expressed (DE) in all studies (i.e. ANOVA-maxP and min-MCC). The min-MCC method is further extended to identify biomarkers DE in partial studies by incorporating a recently developed optimally weighted (OW) technique (OW-min-MCC). All methods are evaluated by simulation studies and by three meta-analysis applications to multi-tissue mouse metabolism datasets, multi-condition mouse trauma datasets and multi-malignant-condition human prostate cancer datasets. The results show complementary strength of the three methods for different biological purposes.

Availability:  http://www.biostat.pitt.edu/bioinfo/

Contact:  ctseng@pitt.edu

Supplementary information:  Supplementary data is available at Bioinformatics online.
Aqueous Extract from Hibiscus sabdariffa Linnaeus Ameliorate Diabetic Nephropathy via Regulating Oxidative Status and Akt/Bad/14‐3‐3γ in an Experimental Animal Model
Authors: Wang Shou-Chieh , Lee Shiow-Fen , Wang Chau-Jong , Lee Chao-Hsin , Lee Wen-Chin , Lee Huei-Jane
Published: December 2009

Several studies point out that oxidative stress maybe a major culprit in diabetic nephropathy. Aqueous extract of Hibiscus sabdariffa L. (HSE) has been demonstrated as having beneficial effects on anti‐oxidation and lipid‐lowering in experimental studies. This study aimed at investigating the effects of Hibiscus sabdariffa L. on diabetic nephropathy in streptozotocin induced type 1 diabetic rats. Our results show that HSE is capable of reducing lipid peroxidation, increasing catalase and glutathione activities significantly in diabetic kidney, and decreasing the plasma levels of triglyceride, low‐density lipoprotein (LDL) and increasing high‐density lipoprotein (HDL) value. In histological examination, HSE improves hyperglycemia‐caused osmotic diuresis in renal proximal convoluted tubules (defined as hydropic change) in diabetic rats. The study also reveals that up‐regulation of Akt/Bad/14‐3‐3γ and NF‐κB‐mediated transcription might be involved. In conclusion, our results show that HSE possesses the potential effects to ameliorate diabetic nephropathy via improving oxidative status and regulating Akt/Bad/14‐3‐3γ signaling.
Polysaccharide‐Containing Macromolecules in a Kampo (Traditional Japanese Herbal) Medicine, Hochuekkito: Dual Active Ingredients for Modulation of Immune Functions on Intestinal Peyer’s Patches and Epithelial cells
Authors: Kiyohara Hiroaki , Nonaka Kazuki , Sekiya Michiko , Matsumoto Tsukasa , Nagai Takayuki , Tabuchi Yoshiaki , Yamada Haruki
Published: December 2009

A traditional Japanese herbal (Kampo) medicine, Hochuekkito (Bu‐Zhong‐Yi‐Qi‐Tang in Chinese, TJ‐41) is a well‐known Kampo formula, and has been found to enhance antigen‐specific antibody response in not only local mucosal immune system in upper respiratory tract, but also systemic immune system through upper respiratory mucosal immune system. Although this immunopharmacological effect has been proposed to express by modulation of intestinal immune system including Peyer’s patches and intestinal epithelial cells, active ingredients are not known. TJ‐41 directly affected the production of bone marrow cell‐proliferative growth factors from murine Peyer’s patch immunocompetent cells in vitro. Among low molecular, intermediate size and macromolecular weight fractions prepared from TJ‐41, only fraction containing macromolecular weight ingredients showed Peyer’s patch‐mediated bone marrow cell‐proliferation enhancing activity. Anion‐exchange chromatography and gel filtration gave 17 subfractions comprising polysaccharides and lignins from the macromolecular weight fraction of TJ‐41, and some of the subfractions showed significant enhancing activities having different degrees. Some of the subfractions also expressed stimulating activity on G‐CSF‐production from colonic epithelial cells, and statistically significant positive correlation was observed among enhancing activities of the subfractions against Peyer’s patch immunocompetent cells and epithelial cells. Among the fractions from TJ‐41 oral administration of macromolecular weight ingredient fraction to mice succeeded to enhance antigen‐specific antibody response in systemic immune system through upper respiratory mucosal immune system, but all the separated fractions failed to enhance the in vivo antibody response in upper respiratory tract.
Relating marine ecosystem indicators to fishing and environmental drivers: an elucidation of contrasting responses
Authors: Link Jason S. , Yemane Dawit , Shannon Lynne J. , Coll Marta , Shin Yunne-Jai , Hill Louize , Borges Maria de Fatima
Published: December 2009

Link, J. S., Yemane, D., Shannon, L. J., Coll, M., Shin, Y-J., Hill, L., and Borges, M. F. 2010. Relating marine ecosystem indicators to fishing and environmental drivers: an elucidation of contrasting responses. – ICES Journal of Marine Science, 67: 787–795. The usefulness of indicators in detecting ecosystem change depends on three main criteria: the availability of data to estimate the indicator (measurability), the ability to detect change in an ecosystem (sensitivity), and the ability to link the said change in an indicator as a response to a known intervention or pressure (specificity). Here, we specifically examine the third aspect of indicator change, with an emphasis on multiple methods to explore the “relativity” of major ecosystem drivers. We use a suite of multivariate methods to explore the relationships between a pre-established set of fisheries-orientated ecosystem status indicators and the key drivers for those ecosystems (particularly emphasizing proxy indicators for fishing and the environment). The results show the relative importance among fishing and environmental factors, which differed notably across the major types of ecosystems. Yet, they also demonstrated common patterns in which most ecosystems, and indicators of ecosystem dynamics are largely driven by fisheries (landings) or human (human development index) factors, and secondarily by environmental drivers (e.g. AMO, PDO, SST). How one might utilize this empirical evidence in future efforts for ecosystem approaches to fisheries is discussed, highlighting the need to manage fisheries in the context of environmental and other human (e.g. economic) drivers.
Halarchaeum acidiphilum gen. nov., sp. nov., a moderately acidophilic haloarchaeon isolated from commercial solar salt
Authors: Minegishi Hiroaki , Echigo Akinobu , Nagaoka Shuhei , Kamekura Masahiro , Usami Ron
Published: December 2009

A novel halophilic archaeon, strain MH1-52-1T, was isolated from solar salt imported from Australia. Cells were pleomorphic, non-motile and Gram-negative. Strain MH1-52-1T required at least 3.0 M NaCl and 1 mM Mg2+ for growth. Strain MH1-52-1T was able to grow at pH 4.0–6.0 (optimum, pH 4.4–4.5) and 15–45 °C (optimum, 37 °C). The diether phospholipids phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester, derived from both C20C20 and C20C25 archaeol, were present. Four unidentified glycolipids were also detected. The 16S rRNA gene sequence showed the highest similarity to that of Halobacterium noricense A1T (91.7 %); there were lower levels of similarity to other members of the family Halobacteriaceae. The G+C content of its DNA was 61.4 mol%. Based on our phenotypic, genotypic and phylogenetic analyses, it is proposed that the isolate should be classified as a representative of a new genus and species, for which the name Halarchaeum acidiphilum gen. nov., sp. nov. is proposed. The type strain of Halarchaeum acidiphilum is MH1-52-1T (=JCM 16109T =DSM 22442T =CECT 7534T).
Bacillus methylotrophicus sp. nov., a methanol-utilizing, plant-growth-promoting bacterium isolated from rice rhizosphere soil
Authors: Madhaiyan Munusamy , Poonguzhali Selvaraj , Kwon Soon-Wo , Sa Tong-Min
Published: December 2009

A Gram-positive bacterium, designated strain CBMB205T, was isolated from the rhizosphere soil of traditionally cultivated, field-grown rice. Cells were strictly aerobic, motile, rod-shaped and formed endospores. The best growth was achieved at 30 °C and pH 7.0 in ammonium mineral salts (AMS) medium containing 600 mM methanol. A comparative 16S rRNA gene sequence-based phylogenetic analysis placed strain CBMB205T in a clade with the species Bacillus amyloliquefaciens, Bacillus vallismortis, Bacillus subtilis, Bacillus atrophaeus, Bacillus mojavensis and Bacillus licheniformis and revealed pairwise similarities ranging from 98.2 to 99.2 %. DNA–DNA hybridization experiments revealed a low level (<36 %) of DNA–DNA relatedness between strain CBMB205T and its closest relatives. The major components of the fatty acid profile were C15 : 0 anteiso, C15 : 0 iso, C16 : 0 iso and C17 : 0 anteiso. The diagnostic diamino acid of the cell wall was meso-diaminopimelic acid. The G+C content of the genomic DNA was 45.0 mol%. The lipids present in strain CBMB205T were diphosphatidylglycerol, phosphatidylglycerol, a minor amount of phosphatidylcholine and two unknown phospholipids. The predominant respiratory quinone was MK-7. Studies of DNA–DNA relatedness, morphological, physiological and chemotaxonomic analyses and phylogenetic data based on 16S rRNA gene sequencing enabled strain CBMB205T to be described as representing a novel species of the genus Bacillus, for which the name Bacillus methylotrophicus sp. nov. is proposed. The type strain is CBMB205T (=KACC 13105T=NCCB 100236T).
Natronoarchaeum mannanilyticum gen. nov., sp. nov., an aerobic, extremely halophilic archaeon isolated from commercial salt
Authors: Shimane Yasuhiro , Hatada Yuji , Minegishi Hiroaki , Mizuki Toru , Echigo Akinobu , Miyazaki Masayuki , Ohta Yukari , Usami Ron , Grant William D. , Horikoshi Koki
Published: December 2009

Strain YSM-123Twas isolated from commercial salt made from Japanese seawater in Niigata prefecture. Optimal NaCl and Mg2+concentrations for growth were 4.0–4.5 M and 5 mM, respectively. The isolate was a mesophilic and slightly alkaliphilic haloarchaeon, whose optimal growth temperature and pH were 37 °C and pH 8.0–9.0. Phylogenetic analysis based on 16S rRNA gene sequence analysis suggested that strain YSM-123Tis a member of the phylogenetic group defined by the familyHalobacteriaceae, but there were low similarities to type strains of other genera of this family (≤90 %); for example,Halococcus(similarity <89 %),Halostagnicola(<89 %),Natronolimnobius(<89 %),Halobiforma(<90 %),Haloterrigena(<90 %),Halovivax(<90 %),Natrialba(<90 %),Natronobacterium(<90 %) andNatronococcus(<90 %). The G+C content of the DNA was 63 mol%. Polar lipid analysis revealed the presence of phosphatidylglycerol, phosphatidylglycerophosphate methyl ester, disulfated diglycosyl diether and an unknown glycolipid. On the basis of the data presented, we propose that strain YSM-123Tshould be placed in a new genus and species,Natronoarchaeum mannanilyticumgen. nov., sp. nov. The type strain ofNatronoarchaeum mannanilyticumis strain YSM-123T(=JCM 16328T=CECT 7565T).
Vibrio atypicus sp. nov., isolated from the digestive tract of the Chinese prawn (Penaeus chinensis O'sbeck)
Authors: Wang Yan , Zhang Xiao-Hua , Yu Min , Wang Hong , Austin Brian
Published: December 2009

A culture (designated strain HHS02T) was isolated from Chinese prawn (Penaeus chinensis, O'sbeck) and determined to be a member of the genusVibrio. Strain HHS02Tcomprised slightly curved, rod-shaped, non-endospore-forming, Gram-negative, catalase-negative, oxidase-positive, O/129-sensitive and facultatively anaerobic cells that were motile by means of a single polar flagellum. Growth of strain HHS02Toccurred in 0.5–7 % (w/v) NaCl [optimally in 1–3 % (w/v) NaCl] and between pH 7.0 and 10.0 (optimally at pH 8.0–9.0). The strain showed growth between 16 and 30 °C (optimum 20 °C). Analysis using the 16S rRNA,gapA,gyrB,mreB,pyrH,recAandtopAgene sequences of the novel isolate revealed that the organism belonged to the genusVibrio, with ∼98, 98, 90, 88, 92, 89 and 83 % sequence similarity, respectively, with representatives of the genusVibrio. DNA–DNA hybridization experiments indicated that the novel strain was distinct from recognized species of the genusVibrio. The major fatty acid components were summed feature 3 (C16 : 1ω7cand/or iso-C15 : 02-OH, 38.7 %), C16 : 0(22.9 %) and C18 : 1ω7c(12.5 %). The G+C content of the genomic DNA was 44.4 mol%. On the basis of the polyphasic taxonomic evidence presented in this study, it is concluded that strain HHS02Tshould be classified as a novel species of the genusVibrio, for which the nameVibrio atypicussp. nov. is proposed. The type strain is HHS02T(=CGMCC 1.8461T=LMG 24781T).
Candida cabralensis sp. nov., a yeast species isolated from traditional Spanish blue-veined Cabrales cheese
Authors: Flórez Ana Belén , Belloch Carmela , Álvarez-Martín Pablo , Querol Amparo , Mayo Baltasar
Published: December 2009

Three yeast strains, 1AD8T, 3AD15 and 3AD23, belonging to a previously unknown yeast species were isolated from two independent batches of the Spanish blue-veined Cabrales cheese, a traditional cheese manufactured without the addition of starter and mould cultures. Physiological characterization revealed that the unknown yeast is not fermentative and does not assimilate lactose; rather it assimilates dl-lactic acid and ethanol, major end products of lactic acid bacteria metabolism in cheese. The novel yeast is anamorphic. Phylogenetic tree reconstruction based on nucleotide sequence comparison of the D1/D2 region of the 26S rRNA gene showed that Pichia terricola and Pichia fermentans are the closest relatives of the unknown species. The name Candida cabralensis sp. nov. is proposed, and the isolate 1AD8T (=CECT 13027T =CBS 11679T) is the type strain of this novel taxon.
The reference strain Aeromonas hydrophicla CIP 57.50 should be reclassified as Aeromonas salmonicida CIP 57.50
Authors: Miñana-Galbis David , Farfàn Maribel , Lorén J. Gaspar , Fusté M. Carmen
Published: December 2009

The use of reference strains is a critical element for the quality control of different assays, from the development of molecular methods to the evaluation of antimicrobial activities. Most of the strains used in these assays are not type strains and some of them are cited erroneously because of subsequent reclassifications and descriptions of novel species. In this study, we propose that the reference strain Aeromonas hydrophila CIP 57.50 be reclassified as Aeromonas salmonicida CIP 57.50 based on phenotypic characterization and sequence analyses of the cpn60, dnaJ, gyrB and rpoD genes.
Alkalibaculum bacchi gen. nov., sp. nov., a CO-oxidizing, ethanol-producing acetogen isolated from livestock-impacted soil
Authors: Allen Toby D. , Caldwell Matthew E. , Lawson Paul A. , Huhnke Raymond L. , Tanner Ralph S.
Published: December 2009

Phenotypic and phylogenetic studies were performed on three strains of an acetogenic bacterium isolated from livestock-impacted soil. The bacterium stained Gram-negative and was a non-spore-forming rod that was motile by peritrichous flagella. The novel strains had an optimum pH for growth of 8.0–8.5 and utilized H2 : CO2, CO : CO2, glucose, fructose, mannose, turanose, ribose, trimethylamine, pyruvate, methanol, ethanol,n-propanol andn-butanol as growth substrates. Acetate was produced from glucose. Acetate, CO2and ethanol were produced from CO : CO2. 16S rRNA gene sequence analysis indicated that the novel strains formed a new subline in the familyEubacteriaceae(rRNA cluster XV) of the low G+C-containing Gram-positive bacteria of the classClostridia. The DNA G+C base composition was 34 mol%. Cell wall analysis revealed the existence of a novel B-type peptidoglycan similar to the B2α-type (B4) configuration with a variation containing aspartic acid. Based on phylogenetic and phenotypic evidence, it is proposed that the new isolates represent a novel genus and species, for which the nameAlkalibaculum bacchigen. nov., sp. nov. is proposed. The type strain of the type species is CP11T(=ATCC BAA-1772T=DSM 22112T).
Re-examination of strains formerly assigned to Hyphopichia burtonii, the phylogeny of the genus Hyphopichia, and the description of Hyphopichia pseudoburtonii sp. nov.
Authors: Groenewald Marizeth , Smith Maudy Th.
Published: December 2009

On the basis of the nucleotide divergence in the internal transcribed spacer (ITS) domain of the rRNA gene and the D1/D2 domain of the 26S rRNA gene, species of the genus Hyphopichia can be divided into different phylogenetic groups. In this study, three distinct phylogenetic clusters as well as a novel species, Hyphopichia pseudoburtonii sp. nov. with type strain CBS 2455T (=JCM 16346T), are introduced. Mating studies indicate that strains belonging to Hyphopichia pseudoburtonii are heterothallic.
Marisediminicola antarctica gen. nov., sp. nov., an actinobacterium isolated from the Antarctic
Authors: Li Hui-Rong , Yu Yong , Luo Wei , Zeng Yin-Xin
Published: December 2009

Strain ZS314T was isolated from a sandy intertidal sediment sample collected from the coastal area off the Chinese Antarctic Zhongshan Station, east Antarctica (6 ° 22′ 13″ S 7 ° 21′ 41″ E). The cells were Gram-positive, motile, short rods. The temperature range for growth was 0–26 °C and the pH for growth ranged from 5 to 10, with optimum growth occurring within the temperature range 18–23 °C and pH range 6.0–8.0. Growth occurred in the presence of 0–6 % (w/v) NaCl, with optimum growth occurring in the presence of 2–4 % (w/v) NaCl. Strain ZS314T had MK-10 as the major menaquinone and anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0 as major fatty acids. The cell-wall peptidoglycan type was B2β with ornithine as the diagnostic diamino acid. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The genomic DNA G+C content was approximately 67 mol%. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strain ZS314T represents a new lineage in the family Microbacteriaceae. On the basis of the phylogenetic analyses and phenotypic characteristics, a new genus, namely Marisediminicola gen. nov., is proposed, harbouring the novel species Marisediminicola antarctica sp. nov. with the type strain ZS314T (=DSM 22350T =CCTCC AB 209077T).
Lactobacillus florum sp. nov., a fructophilic species isolated from flowers
Authors: Endo Akihito , Futagawa-Endo Yuka , Sakamoto Mitsuo , Kitahara Maki , Dicks Leon M. T.
Published: December 2009

Three strains of fructophilic lactic acid bacteria were isolated from flowers in South Africa. The isolates formed a subcluster in the Lactobacillus buchneri phylogenetic group, closely related to Lactobacillus fructivorans, Lactobacillus homohiochii, Lactobacillus lindneri and Lactobacillus sanfranciscensis according to phylogenetic analysis based on the 16S rRNA gene sequences. Levels of DNA–DNA relatedness indicated that the three strains belonged to the same taxon and formed a genetically distinct group, well separated from their phylogenetic relatives. The three strains produced acids from only two of the 49 carbohydrates tested, i.e. d-glucose and d-fructose. d-Fructose was more rapidly fermented than d-glucose. Good growth was recorded on d-fructose or d-glucose in the presence of external electron acceptors. However, delayed growth was recorded on d-glucose without electron acceptors. The novel strains produced lactic acid, ethanol and acetic acid from d-glucose at a ratio of 1 : 0.8 : 0.2. These characteristics were distinct from other species of the genus Lactobacillus. Based on the data provided, the three isolates represent a fructophilic and novel species of the genus Lactobacillus, for which the name Lactobacillus florum sp. nov. is proposed. The type strain is F9-1T (=JCM 16035T=DSM 22689T=NRIC 0771T).
Pseudonocardia tropica sp. nov., an endophytic actinomycete isolated from the stem of Maytenus austroyunnanensis
Authors: Qin Sheng , Zhu Wen-Yong , Jiang Ji-Hong , Klenk Hans-Peter , Li Jie , Zhao Guo-Zhen , Xu Li-Hua , Li Wen-Jun
Published: December 2009

A novel strain, designated YIM 61452T, was isolated from the stem ofMaytenus austroyunnanensiscollected from the tropical rainforest of Xishuangbanna, Yunnan Province, south-west China. The strain was characterized taxonomically by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 61452Tbelonged to the genusPseudonocardiaand was most closely related toPseudonocardia alniIMSNU 20049T(99.5 %),Pseudonocardia antarcticaDVS 5a1T(99.5 %) andPseudonocardia carboxydivoransY8T(99.4 %). The chemotaxonomic properties of strain YIM 61452T, for example MK-8(H4) as the predominant quinone system and iso-C16 : 0and iso-C16 : 1H as the major fatty acids, were also consistent with its classification within the genusPseudonocardia. Strain YIM 61452Tcould be differentiated from closely related species of the genusPseudonocardiaby phenotypic and genotypic analysis. DNA–DNA hybridization experiments between strain YIM 61452Tand closely related reference strains further confirmed that strain YIM 61452Trepresented a novel taxon of the genusPseudonocardia. Therefore, strain YIM 61452Trepresents a novel species, for which the namePseudonocardia tropicasp. nov. is proposed. The type strain is YIM 61452T(=DSM 45199T=CCTCC AA 208018T).
Tracing Cationic Nutrients from Xylem into Stem Tissue of French Bean by Stable Isotope Tracers and Cryo-Secondary Ion Mass Spectrometry
Authors: Metzner Ralf , Schneider Heike Ursula , Breuer Uwe , Thorpe Michael Robert , Schurr Ulrich , Schroeder Walter Heinz
Published: December 2009

Fluxes of mineral nutrients in the xylem are strongly influenced by interactions with the surrounding stem tissues and are probably regulated by them. Toward a mechanistic understanding of these interactions, we applied stable isotope tracers of magnesium, potassium, and calcium continuously to the transpiration stream of cut bean (Phaseolus vulgaris) shoots to study their radial exchange at the cell and tissue level with stem tissues between pith and phloem. For isotope localization, we combined sample preparation with secondary ion mass spectrometry in a completely cryogenic workflow. After 20 min of application, tracers were readily detectable to various degrees in all tissues. The xylem parenchyma near the vessels exchanged freely with the vessels, its nutrient elements reaching a steady state of strong exchange with elements in the vessels within 20 min, mainly via apoplastic pathways. A slow exchange between vessels and cambium and phloem suggested that they are separated from the xylem, parenchyma, and pith, possibly by an apoplastic barrier to diffusion for nutrients (as for carbohydrates). There was little difference in these distributions when tracers were applied directly to intact xylem via a microcapillary, suggesting that xylem tension had little effect on radial exchange of these nutrients and that their movement was mainly diffusive.
Real-Time Imaging of Cellulose Reorientation during Cell Wall Expansion in Arabidopsis Roots
Authors: Anderson Charles T. , Carroll Andrew , Akhmetova Laila , Somerville Chris
Published: December 2009

Cellulose forms the major load-bearing network of the plant cell wall, which simultaneously protects the cell and directs its growth. Although the process of cellulose synthesis has been observed, little is known about the behavior of cellulose in the wall after synthesis. Using Pontamine Fast Scarlet 4B, a dye that fluoresces preferentially in the presence of cellulose and has excitation and emission wavelengths suitable for confocal microscopy, we imaged the architecture and dynamics of cellulose in the cell walls of expanding root cells. We found that cellulose exists in Arabidopsis (Arabidopsis thaliana) cell walls in large fibrillar bundles that vary in orientation. During anisotropic wall expansion in wild-type plants, we observed that these cellulose bundles rotate in a transverse to longitudinal direction. We also found that cellulose organization is significantly altered in mutants lacking either a cellulose synthase subunit or two xyloglucan xylosyltransferase isoforms. Our results support a model in which cellulose is deposited transversely to accommodate longitudinal cell expansion and reoriented during expansion to generate a cell wall that is fortified against strain from any direction.
Thylakoid Protein Phosphorylation in Higher Plant Chloroplasts Optimizes Electron Transfer under Fluctuating Light
Authors: Tikkanen Mikko , Grieco Michele , Kangasjaݶrvi Saijaliisa , Aro Eva-Mari
Published: December 2009

Several proteins of photosystem II (PSII) and its light-harvesting antenna (LHCII) are reversibly phosphorylated according to light quantity and quality. Nevertheless, the interdependence of protein phosphorylation, nonphotochemical quenching, and efficiency of electron transfer in the thylakoid membrane has remained elusive. These questions were addressed by investigating in parallel the wild type and the stn7, stn8, and stn7 stn8 kinase mutants of Arabidopsis (Arabidopsis thaliana), using the stn7 npq4, npq4, npq1, and pgr5 mutants as controls. Phosphorylation of PSII-LHCII proteins is strongly and dynamically regulated according to white light intensity. Yet, the changes in phosphorylation do not notably modify the relative excitation energy distribution between PSII and PSI, as typically occurs when phosphorylation is induced by “state 2” light that selectively excites PSII and induces the phosphorylation of both the PSII core and LHCII proteins. On the contrary, under low-light conditions, when excitation energy transfer from LHCII to reaction centers is efficient, the STN7-dependent LHCII protein phosphorylation guarantees a balanced distribution of excitation energy to both photosystems. The importance of this regulation diminishes at high light upon induction of thermal dissipation of excitation energy. Lack of the STN7 kinase, and thus the capacity for equal distribution of excitation energy to PSII and PSI, causes relative overexcitation of PSII under low light but not under high light, leading to disturbed maintenance of fluent electron flow under fluctuating light intensities. The physiological relevance of the STN7-dependent regulation is evidenced by severely stunted phenotypes of the stn7 and stn7 stn8 mutants under strongly fluctuating light conditions.
Reactive Oxygen Species Are Involved in Plant Defense against a Gall Midge
Authors: Liu Xuming , Williams Christie E. , Nemacheck Jill A. , Wang Haiyan , Subramanyam Subhashree , Zheng Cheng , Chen Ming-Shun
Published: December 2009

Reactive oxygen species (ROS) play a major role in plant defense against pathogens, but evidence for their role in defense against insects is still preliminary and inconsistent. In this study, we examined the potential role of ROS in defense of wheat (Triticum aestivum) and rice (Oryza sativa) against Hessian fly (Mayetiola destructor) larvae. Rapid and prolonged accumulation of hydrogen peroxide (H2O2) was detected in wheat plants at the attack site during incompatible interactions. Increased accumulation of both H2O2 and superoxide was detected in rice plants during nonhost interactions with the larvae. No increase in accumulation of either H2O2 or superoxide was observed in wheat plants during compatible interactions. A global analysis revealed changes in the abundances of 250 wheat transcripts and 320 rice transcripts encoding proteins potentially involved in ROS homeostasis. A large number of transcripts encoded class III peroxidases that increased in abundance during both incompatible and nonhost interactions, whereas the levels of these transcripts decreased in susceptible wheat during compatible interactions. The higher levels of class III peroxidase transcripts were associated with elevated enzymatic activity of peroxidases at the attack site in plants during incompatible and nonhost interactions. Overall, our data indicate that class III peroxidases may play a role in ROS generation in resistant wheat and nonhost rice plants during response to Hessian fly attacks.
A Root-Expressed Magnesium Transporter of theMRS2/MGTGene Family inArabidopsis thalianaAllows for Growth in Low-Mg2+ Environments
Authors: Gebert Michael , Meschenmoser Karoline , Svidová Soňa , Weghuber Julian , Schweyen Rudolf , Eifler Karolin , Lenz Henning , Weyand Katrin , Knoop Volker
Published: December 2009

The MRS2/MGT gene family in Arabidopsis thaliana belongs to the superfamily of CorA-MRS2-ALR-type membrane proteins. Proteins of this type are characterized by a GMN tripeptide motif (Gly-Met-Asn) at the end of the first of two C-terminal transmembrane domains and have been characterized as magnesium transporters. Using the recently established mag-fura-2 system allowing direct measurement of Mg2+ uptake into mitochondria of Saccharomyces cerevisiae, we find that all members of the Arabidopsis family complement the corresponding yeast mrs2 mutant. Highly different patterns of tissue-specific expression were observed for the MRS2/MGT family members in planta. Six of them are expressed in root tissues, indicating a possible involvement in plant magnesium supply and distribution after uptake from the soil substrate. Homozygous T-DNA insertion knockout lines were obtained for four members of the MRS2/MGT gene family. A strong, magnesium-dependent phenotype of growth retardation was found for mrs2-7 when Mg2+ concentrations were lowered to 50 μM in hydroponic cultures. Ectopic overexpression of MRS2-7 from the cauliflower mosaic virus 35S promoter results in complementation and increased biomass accumulation. Green fluorescent protein reporter gene fusions indicate a location of MRS2-7 in the endomembrane system. Hence, contrary to what is frequently found in analyses of plant gene families, a single gene family member knockout results in a strong, environmentally dependent phenotype.
UK industrial relations state agencies
Authors: Gennard John
Published: December 2009

Purpose

The purpose of this Editorial is to outline the main functions of the UK industrial relations state agencies – the Certification Officer, the Central Arbitration Committee and The Advisory Conciliation and Arbitration Service.

Design/methodology/approach

The Editorial outlines the main functions of the UK industrial relations state agencies, explaining their history and roles.

Findings

The Editorial reveals detailed information about the main functions of the UK industrial relations state agencies.

Originality/value

The Editorial offers insights into the work of UK industrial relations state agencies.
The roles and functions of shop stewards in workplace partnership
Authors: Rittau Yasmin , Dundon Tony
Published: December 2009

Purpose

The purpose of this paper is to examine the roles and influence of shop stewards under workplace partnership regimes in five case study firms in the Republic of Ireland. It aims to assess the dynamics and potential longevity of partnership relationships.

Design/methodology/approach

A framework is utilised which analyses the scope, breadth and depth of union influence in terms of the structure of partnership processes and the capacity of agency to affect relations among shop stewards, union members and plant management.

Findings

The findings show that while union representatives view partnership in a positive light, there remain problems as to the longevity of partnership owing to management control and a disconnection between national (government) and local (workplace) support mechanisms for partnership. The paper concludes that social partnership is a process that remains anchored in a relationship of both antagonism and accommodation between capital and labour.

Originality/value

Much of the extant literature tends to focus on the outcomes of partnership in terms of the gains or losses to either management and/or unions. In this paper, the focus is on the way the “processes” of social partnership shape the behaviour and roles of workplace union representatives. A number of theoretical and policy implications are discussed.
Employees' attitudes towards diversity in a non‐western context
Authors: Alserhan Bakr Ahmad , Forstenlechner Ingo , Al‐Nakeeb Ahmad
Published: December 2009

Purpose

The purpose of this paper is to examine attitudes towards diversity in an emerging Gulf economy whose workforce is dominated by expatriates and is under significant pressure to accommodate host country citizens. It seeks to examine employees' attitudes towards workforce diversity in the banking sector in the United Arab Emirates (UAE).

Design/methodology/approach

A total of 100 employees from 11 banks are chosen randomly from banks operating in the UAE. Those employees are asked to answer a questionnaire containing various questions that cover the applauded benefits of diversity as identified in the related literature.

Findings

All banks have a diverse workforce, with nationals representing a minority in all of them. However, banks differ on the various indicators of diversity with some being more religiously diverse while others more diverse in terms of nationalities or languages. Overall, Islamic banks are the least diverse on all dimensions of diversity.

Research limitations/implications

Several obstacles are faced during the course of this study including limitations on access to employees, sampling limitations preventing more in‐depth analysis of certain aspects, lack of regional studies on diversity and the timing of the survey itself which coincide with the summer exodus of expatriates.

Originality/value

This paper provides useful information on attitudes toward diversity in an emerging Gulf economy, dominated by expatriates.
The changing nature of the traditional expatriate psychological contract
Authors: Pate Judy , Scullion Hugh
Published: December 2009

Purpose

The purpose of this paper is to examine whether traditional conventions of the expatriate psychological contract have altered from both employer and employee perspectives. In essence to what extent have multi‐national corporations adjusted organisational practices to reflect changing circumstances and to what extent have expatriates altered their mindset towards employers' obligations and requirements.

Design/methodology/approach

The paper draws on findings of three organisational case studies and is based on in‐depth interviews with HR managers, line managers and expatriates.

Findings

The findings reveale that the overall tone of the psychological contract from the employers' perspective is transactional. From an employee perspective, preliminary evidence suggests that the dynamics of the employment relationship is changing and that employees have responded to contract changes by seeking to ensure their employability and reduce their dependence on a single organisation.

Practical implications

The paper focuses on four areas for managers: first, pro‐actively influencing expatriates' expectations thereby minimising misunderstandings; second, organisations should be very aware of “the remuneration market rate” for a particular location; third, policies of support and contact would aid feelings of integration. Finally, more attention should be paid new approaches to strategic talent management.

Originality/value

This paper contributes theoretically and empirically to the literature on expatriates' psychological contracts, an area where there is a dearth of empirical research. The paper also increases the understanding of the variety of expatriate perceptions in different contexts, thereby deepening the understanding of the importance of context in this area.
How much would US union membership increase under a policy of non‐exclusive representation?
Authors: Harcourt Mark , Lam Helen
Published: December 2009

Purpose

In light of the low‐union density and a huge representation gap in the US representation system. The purpose of this paper is to examine the effectiveness of the system under majority rule and to provide some empirical evidence on how much union membership would increase in the USA if a policy of non‐exclusive representation, as adopted in New Zealand, are to be implemented.

Design/methodology/approach

The sample for the study consists of 227 New Zealand organizations, employing over 180,000 workers. Logistic regression is used for the analysis with the dichotomous dependent variable indicating whether there is majority union support.

Findings

If the USA allowed and supported minority unionism, union membership could increase by 30 percent or more. Workers in smaller, private‐sector organizations outside healthcare, education, and manufacturing are most disadvantaged by the majority‐rule system.

Practical implications

Given that many workers' needs for representation have not been addressed by the current US majority rule system, consideration of minority representation to enhance representation effectiveness and understanding its implications are of critical importance, especially for a democratic society.

Originality/value

The paper offers empirical data on the implications of a change of the US representation system and proposes three options for incorporating minority representation.
The use and sharing of information from Wikipedia by high‐tech professionals for work purposes
Authors: Chen Hsin‐liang
Published: December 2009

Purpose

The aim of this paper is to focus on discovering whether high‐tech professionals as a user community search for information from Wikipedia to fulfill their job duties and, if they do, how they share information with co‐workers and clients.

Design/methodology/approach

An online questionnaire was used, administered by a commercial provider. The questionnaire consisted of 15 Likert‐scaled questions to assess participants' agreement with each question along with an optional open‐ended explanation. A total of 68 participants successfully answered the questionnaire. Participants' Likert rating scores were analyzed by two‐way ANOVA, one‐way ANOVA and correlational analyses using SPSS.

Findings

The analyses examined relationships among participants' characteristics, their use of information resources for research and teaching, information‐sharing behaviors, and use/non‐use of Wikipedia. Findings indicated that the participants treated Wikipedia as a ready reference for general information. Their concern is that Wikipedia only has a limited number of entries available at this point. They suggested that Wikipedia needed to improve the contribution and editorial process and to make it more rigorous.

Originality/value

Personal information infrastructure affects how the high‐tech professionals surveyed use‐and‐share information from Wikipedia for work. In the current situation, the participants consider Wikipedia to be a developing information resource and show less interest in contributing to it. The project is an exploratory study and more considerations are needed for this research area.
Think culture: Europeana.eu from concept to construction
Authors: Purday Jon
Published: December 2009

Purpose

The purpose of this paper is to describe the construction of the prototype of Europeana.eu, the cross‐domain cultural heritage portal funded by the European Commission, to look at the political vision behind the project, and examine the user scenarios that informed the build, to detail Europeana's metadata schema and object model, and to give an overview of the new projects that will bring the prototype to full operational service.

Design/methodology/approach

As the project to build the prototype ends, this is a narrative of Europeana's genesis, development, launch, and an overview of the scope of future plans.

Findings

A cross‐domain, cross‐border cultural heritage site has been successfully created. A total of 4.5 million items across the range of image, video, text and sound formats have been integrated and user interest has proved higher than anticipated.

Research limitations/implications

Key issues have been found to be metadata standards and quality. Usability/searchability of Europeana.eu is only as good as the metadata provided by content owners.

Practical implications

Greater standardisation of metadata across the cultural heritage domain will increase in importance so providers can deliver content to portals and aggregators. Metadata enhancement, both by content providers and by using automated processes, will likewise become a priority.

Originality/value

This is the on‐the‐record account of the building of Europe's digital library, archive and museum.
Conversion of bibliographic records to MARC 21 format
Authors: Rudić Gordana , Surla Dušan
Published: December 2009

Purpose

The aim of this research is the conversion of the bibliographic records between the following different formats for bibliographic material processing – the YUMARC (which is a variant of the UNIMARC format in which the Serbian BISIS system operates), UNIMARC and MARC 21 format.

Design/methodology/approach

The CASE tools that support the information system developing methodology based on the XML technologies are used.

Findings

The result is the specification and implementation of information requirements for the conversion of the bibliographic records created in the BISIS system into the UNIMARC or MARC 21 format.

Research limitations/implications

The specification of the rules for bibliographic record conversion is not formalized, so the implementation of these rules cannot be done automatically. If the rules could be formalized, then a generator of the programming code could be developed for the implementation of the rules for the bibliographic record conversion.

Practical implications

The research result is applied for the conversion of the YUMARC bibliographic records in the Library of the Department for Mathematics and Informatics of Novi Sad University. The conversion of the records is made at first into the UNIMARC format and subsequently from the UNIMARC format into the records of the MARC 21 format. The task of conversion of the bibliographic records formed in the BISIS software system in the UNIMARC or the MARC 21 format is solved in that way.

Originality/value

The originality of the work is contained in the application of the XML technologies for the conversion of the bibliographic records between the different bibliographic formats (YUMARC, UNIMARC and MARC 21). For each of the formats an XML schema is formed and record conversion between the different formats is done by the XSLT transformations.