bluuebunny/crossref_metadata_2025 huggingface dataset:
Inorganic polyphosphate is a potent activator of the mitochondrial permeability transition pore in cardiac myocytes
Authors: Seidlmayer Lea K. , Gomez-Garcia Maria R. , Blatter Lothar A. , Pavlov Evgeny , Dedkova Elena N.
Published: April 2012

Mitochondrial dysfunction caused by excessive Ca2+ accumulation is a major contributor to cardiac cell and tissue damage during myocardial infarction and ischemia–reperfusion injury (IRI). At the molecular level, mitochondrial dysfunction is induced by Ca2+-dependent opening of the mitochondrial permeability transition pore (mPTP) in the inner mitochondrial membrane, which leads to the dissipation of mitochondrial membrane potential (ΔΨm), disruption of adenosine triphosphate production, and ultimately cell death. Although the role of Ca2+ for induction of mPTP opening is established, the exact molecular mechanism of this process is not understood. The aim of the present study was to test the hypothesis that the adverse effect of mitochondrial Ca2+ accumulation is mediated by its interaction with inorganic polyphosphate (polyP), a polymer of orthophosphates linked by phosphoanhydride bonds. We found that cardiac mitochondria contained significant amounts (280 ± 60 pmol/mg of protein) of short-chain polyP with an average length of 25 orthophosphates. To test the role of polyP for mPTP activity, we investigated kinetics of Ca2+ uptake and release, ΔΨm and Ca2+-induced mPTP opening in polyP-depleted mitochondria. polyP depletion was achieved by mitochondria-targeted expression of a polyP-hydrolyzing enzyme. Depletion of polyP in mitochondria of rabbit ventricular myocytes led to significant inhibition of mPTP opening without affecting mitochondrial Ca2+ concentration by itself. This effect was observed when mitochondrial Ca2+ uptake was stimulated by increasing cytosolic [Ca2+] in permeabilized myocytes mimicking mitochondrial Ca2+ overload observed during IRI. Our findings suggest that inorganic polyP is a previously unrecognized major activator of mPTP. We propose that the adverse effect of polyphosphate might be caused by its ability to form stable complexes with Ca2+ and directly contribute to inner mitochondrial membrane permeabilization.
Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data
Authors: Kearse Matthew , Moir Richard , Wilson Amy , Stones-Havas Steven , Cheung Matthew , Sturrock Shane , Buxton Simon , Cooper Alex , Markowitz Sidney , Duran Chris , Thierer Tobias , Ashton Bruce , Meintjes Peter , Drummond Alexei
Published: April 2012

Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data.

Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl.

Contact:  peter@biomatters.com
Speeding up tandem mass spectral identification using indexes
Authors: Liu Xiaowen , Mammana Alessandro , Bafna Vineet
Published: April 2012

Motivation: Tandem mass spectrometry (MS/MS) has been routinely used in proteomics studies. Post-translational modification (PTM) identification is a challenging problem in tandem mass spectral analysis.

Results: In this article, we define two scoring functions for identifying peptides/proteins with PTMs from MS/MS spectra: match scores and diagonal scores, as well as two spectral identification problems based on the two scores. We propose several index-based algorithms for the two problems. Both theoretical and experimental analyses show that the index-based algorithms significantly improve on speed when compared with existing algorithms.

Contact:  xil018@cs.ucsd.edu
DAVID-WS: a stateful web service to facilitate gene/protein list analysis
Authors: Jiao Xiaoli , Sherman Brad T. , Huang Da Wei , Stephens Robert , Baseler Michael W. , Lane H. Clifford , Lempicki Richard A.
Published: April 2012

Summary: The database for annotation, visualization and integrated discovery (DAVID), which can be freely accessed at http://david.abcc.ncifcrf.gov/, is a web-based online bioinformatics resource that aims to provide tools for the functional interpretation of large lists of genes/proteins. It has been used by researchers from more than 5000 institutes worldwide, with a daily submission rate of ∼1200 gene lists from ∼400 unique researchers, and has been cited by more than 6000 scientific publications. However, the current web interface does not support programmatic access to DAVID, and the uniform resource locator (URL)-based application programming interface (API) has a limit on URL size and is stateless in nature as it uses URL request and response messages to communicate with the server, without keeping any state-related details. DAVID-WS (web service) has been developed to automate user tasks by providing stateful web services to access DAVID programmatically without the need for human interactions.

Availability: The web service and sample clients (written in Java, Perl, Python and Matlab) are made freely available under the DAVID License at http://david.abcc.ncifcrf.gov/content.jsp?file=WS.html.

Contact:  xiaoli.jiao@nih.gov; rlempicki@nih.gov
The Assessment of Substance Misusers
Authors: Booker Matthew
Published: April 2012

Misuse of illicit substances is a common problem encountered in general practice, among both adults and young people. It varies from casual experimentation to problematic harmful dependence and requires specific considerations with regard to physical, psychological and social well-being. Many generalists find the holistic assessment of substance users a daunting prospect, particularly as the language and subculture of substance misuse can be somewhat enigmatic. GPs are actually well placed and skilled to deliver a comprehensive assessment of drug users, to deliver important harm reduction advice and to negotiate and jointly embark upon an effective treatment pathway.
The societal significance of catalysis and the growing practical importance of single-site heterogeneous catalysts
Authors: Thomas John Meurig
Published: April 2012

The concept of single-site heterogeneous catalysis, herein defined and extensively illustrated, offers a strategy for the design of new solid catalysts. By capitalizing on the opportunities presented by nanoporous materials to assemble a wide range of new, well-defined, catalytically active centres, it is possible to bring about numerous environmentally benign processes that can replace traditional methods of chemical production. The latter often employs aggressive, corrosive or hazardous reagents. By using both microporous (less than 20 Å diameter) and mesoporous solids (20–500 Å diameter), abundant scope exists for the construction and application of shape-selective, regio-selective and enantioselective catalysts.
State-resolved spectroscopy of high vibrational levels of water up to the dissociative continuum
Authors: Maksyutenko Pavlo , Grechko Maxim , Rizzo Thomas R. , Boyarkin Oleg V.
Published: April 2012

We summarize here our experimental studies of the high rovibrational energy levels of water. The use of double-resonance vibrational overtone excitation followed by energy-selective photofragmentation and laser-induced fluorescence detection of OH fragments allowed us to measure previously inaccessible rovibrational energies above the seventh OH-stretch overtone. Extension of the experimental approach to triple-resonance excitation provides access to rovibrational levels via transitions with significant transition dipole moments (mainly OH-stretch overtones) up to the dissociation threshold of the O–H bond. A collisionally assisted excitation scheme enables us to probe vibrations that are not readily accessible via pure laser excitation. Observation of the continuous absorption onset yields a precise value for the O–H bond dissociation threshold, 41 145.94 ± 0.15 cm
−1
. Finally, we detect long-lived resonances as sharp peaks in spectra above the dissociation threshold.
Bradyrhizobium daqingense sp. nov., isolated from soybean nodules
Authors: Wang Jing Yu , Wang Rui , Zhang Yan Ming , Liu Hong Can , Chen Wen Feng , Wang En Tao , Sui Xin Hua , Chen Wen Xin
Published: April 2012

Thirteen slow-growing rhizobial strains isolated from root nodules of soybean (Glycine maxL.) grown in Daqing city in China were classified in the genusBradyrhizobiumbased on 16S rRNA gene sequence analysis. Multilocus sequence analysis of IGS,atpD,glnIIandrecAgenes revealed that the isolates represented a novel clade in this genus. DNA–DNA relatedness lower than 42.5 % between the representative strain CCBAU 15774Tand the type strains of the closely related speciesBradyrhizobium liaoningenseUSDA 3622T,Bradyrhizobium yuanmingenseCCBAU 10071TandBradyrhizobium betaeLMG 21987T, further confirmed that this group represented a novel species. CCBAU 15774Tshared seven cellular fatty acids with the three above-mentioned species, but the fatty acids 15 : 0 iso and summed feature 5 (18 : 2ω6,9cand/or 18 : 0 anteiso) were unique for this strain. The respiratory quinone in CCBAU 15774Twas ubiquinone-10 and the cellular polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, cardiolipin and unknown aminolipid, polar lipid and phospholipid. In addition, some phenotypic features could be used to differentiate the novel group from the related species. On basis of these results, we propose the nameBradyrhizobium daqingensesp. nov., with CCBAU 15774T( = LMG 26137T = HAMBI 3184T = CGMCC 1.10947T) as the type strain. The DNA G+C content of the type strain is 61.2 mol% (Tm).
Desulfosporosinus burensis sp. nov., a spore-forming, mesophilic, sulfate-reducing bacterium isolated from a deep clay environment
Authors: Mayeux Bruno , Fardeau Marie-Laure , Bartoli-Joseph Manon , Casalot Laurie , Vinsot Agnès , Labat Marc
Published: April 2012

A novel anaerobic, Gram-positive, spore-forming, curved rod-shaped, mesophilic and sulfate-reducing bacterium was isolated from pore water collected in a borehole at −490 m in Bure (France). This strain, designated BSREI1T, grew at temperatures between 5 °C and 30 °C (optimum 25 °C) and at a pH between 6 and 8 (optimum 7). It did not require NaCl for growth, but tolerated it up to 1.5 % NaCl. Sulfate, thiosulfate and elemental sulfur were used as terminal electron acceptors. Strain BSREI1T used crotonate, formate, lactate, pyruvate, fructose, glycerol and yeast extract as electron donors in the presence of sulfate. The sole quinone was MK-7. The G+C content of the genomic DNA was 43.3 mol%. Strain BSREI1T had the type strains of

Desulfosporosinus lacus

(16S rRNA gene sequence similarity of 96.83 %),

Desulfosporosinus meridiei

(96.31 %) and

Desulfosporosinus hippei

(96.16 %) as its closest phylogenetic relatives. On the basis of phylogenetic and physiological properties, strain BSREI1T is proposed as a representative of a novel species of the genus

Desulfosporosinus

, Desulfosporosinus burensis sp. nov.; the type strain is BSREI1T ( = DSM 24089T = JCM 17380T).
Blautia faecis sp. nov., isolated from human faeces
Authors: Park Seong-Kyu , Kim Min-Soo , Bae Jin-Woo
Published: April 2012

A strictly anoxic, Gram-stain-positive, non-motile

Blautia

-like bacterium, designated strain M25T, was isolated from a human faecal sample. Strain M25T was negative for both catalase and oxidase activity, utilized carbohydrates as fermentable substrates, produced lactate and acetate as the major end products of glucose fermentation in PYG medium, and had a DNA G+C content of 41.6 mol%. Comparative 16S rRNA gene sequencing showed that strain M25T was closely related to

Ruminococcus obeum

ATCC 29174T (96.40 % 16S rRNA gene sequence similarity) and

Blautia glucerasea

HFTH-1T (96.17 %) within the family

Lachnospiraceae

. Straight-chain saturated and monounsaturated cellular fatty acids were also detected, the majority being C14 : 0, C16 : 0 and C16 : 0 dimethyl acetal acids. Based on the phenotypic, genotypic and phylogenetic characteristics presented in this study, strain M25T represents a novel species within the genus

Blautia

for which the name Blautia faecis sp. nov. is proposed. The type strain is M25T ( = KCTC 5980T = JCM 17205T).
Listeria weihenstephanensis sp. nov., isolated from the water plant Lemna trisulca taken from a freshwater pond
Authors: Lang Halter Evi , Neuhaus Klaus , Scherer Siegfried
Published: April 2012

The phylogenetic position and phenotypic characteristics of two non-spore-forming bacilli similar to members of the genus

Listeria

were studied. The Gram-reaction-positive, slightly motile, facultatively anaerobic strains were isolated from the water plant Lemna trisulca sampled from a freshwater pond in Bavaria, Germany. Although no identification was possible employing the API

Listeria

test (bioMérieux), 16S rRNA sequence analysis confirmed a close phylogenetic similarity to

Listeria rocourtiae

DSM 22097T (99.0 % sequence similarity) and a more distant relationship to other

Listeria

species (96.0 % to

Listeria monocytogenes

DSM 20600T and 95.0 % similarity to

Listeria grayi

DSM 20601T). DNA–DNA hybridization analysis between the isolates and

Listeria rocourtiae

DSM 22097T yielded a similarity of 22.5 %. Analysis of partial sequences of sigB, prs, recA and HSP60 were studied and compared with those of other members of the genus

Listeria

and

Brochothrix thermosphacta

DSM 20171T supporting the relationships indicated by 16S rRNA gene sequences. The studied isolates were non-haemolytic and were not associated with cases of human or animal disease. While the results demonstrate that the strains belong to the genus

Listeria

, phenotypic and genotypic differences from

Listeria rocourtiae

DSM 22097T suggest that the strains represent a novel species for which the name Listeria weihenstephanensis sp. nov. is proposed; the type strain is WS 4560T ( = DSM 24698T = LMG 26374T), with WS 4615 ( = DSM 24699 = LMG 26375) as a second strain of the species.
Wickerhamomyces xylosica sp. nov. and Candida phayaonensis sp. nov., two xylose-assimilating yeast species from soil
Authors: Limtong Savitree , Nitiyon Sukanya , Kaewwichian Rungluk , Jindamorakot Sasitorn , Am-In Somjit , Yongmanitchai Wichien
Published: April 2012

Two strains (NT29T and NT31T) of xylose-assimilating yeasts were obtained from soils collected in northern Thailand. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics, and sequence analysis of the D1/D2 domain of the large subunit rRNA gene and the internal transcribed spacer region, the two strains were found to represent two novel ascomycete yeast species. Strain NT29T was assigned to the genus Candida belonging to the Pichia clade as a representative of Candida phayaonensis sp. nov.; the type strain is NT29T ( = BCC 47634T = NBRC 108868T = CBS 12319T). Strain NT31T represented a novel Wickerhamomyces species, which was named Wickerhamomyces xylosica sp. nov.; the type strain is NT31T ( = BCC 47635T = NBRC 108869T = CBS 12320T).
Sphingobium baderi sp. nov., isolated from a hexachlorocyclohexane dump site
Authors: Kaur Jasvinder , Moskalikova Hana , Niharika Neha , Sedlackova Miroslava , Hampl Ales , Damborsky Jiri , Prokop Zbynek , Lal Rup
Published: April 2012

A Gram-stain-negative, rod-shaped and white-coloured bacterial strain, designated LL03T, was isolated from hexachlorocyclohexane-contaminated soil at Spolana Neratovice, Czech Republic, where lindane was formerly produced. Strain LL03T was found to be a degrader of α-, γ- and δ-isomers of hexachlorocyclohexane, although no significant degradation activity was observed for the β-isomer. A neighbour-joining tree based on 16S rRNA gene sequences showed that strain LL03T occupied a distinct phylogenetic position in the

Sphingobium

cluster, showing the highest similarity with

Sphingobium wenxiniae

JZ-1T (99.2 %). The DNA G+C content of strain LL03T was 67.0 mol%. DNA–DNA relatedness values of strain LL03T with its close phylogenetic neighbours were below the threshold level of 70 %, supporting its identification as a representative of a novel species of the genus

Sphingobium

. The predominant respiratory quinone was ubiquinone Q-10. The polar lipid profile of strain LL03T also corresponded to those reported for other

Sphingobium

species (phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylmonomethylethanolamine and sphingoglycolipid), supporting its identification as a member of the genus

Sphingobium

. Spermidine was identified as the major polyamine. The predominant fatty acids were 16 : 0, summed feature 3 (16 : 1ω7c and/or 16 : 1ω6c), summed feature 8 (18 : 1ω7c and/or 18 : 1ω6c) and 14 : 0 2-OH. The polar lipid pattern, the presence of spermidine and ubiquinone Q-10, the predominance of the cellular fatty acids C18 : 1ω7c, C16 : 0 and C14 : 0 2-OH and the G+C content of the genomic DNA supported the affiliation of the strain to the genus

Sphingobium

. The results obtained after DNA–DNA hybridization, biochemical and physiological tests clearly distinguished it from closely related species of the genus

Sphingobium

. Therefore, strain LL03T represents a novel species of the genus

Sphingobium

for which the name Sphingobium baderi LL03T sp. nov. is proposed; the type strain is LL03T ( = CCM 7981T = DSM 25433T).
Arenibacter hampyeongensis sp. nov., a marine bacterium isolated from a tidal flat
Authors: Jeong Sang Hyeon , Jin Hyun Mi , Kim Jeong Myeong , Jeon Che Ok
Published: April 2012

A Gram-staining-negative, dark orange, strictly aerobic bacterium, designated strain HP12T, was isolated from a tidal flat at Hampyeong in South Korea. Cells were moderately halotolerant, catalase- and oxidase-positive, non-motile rods. Growth was observed at 5–35 °C (optimum, 25 °C), at pH 6.0–8.5 (optimum, pH 7.0–7.5), and in the presence of 1–6 % (w/v) NaCl (optimum, 1–2 %). The major cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), iso-C17 : 0 3-OH, C15 : 0, iso-C15 : 1 G and iso-C15 : 0. The polar lipid pattern indicated the presence of phosphatidylethanolamine and two unidentified lipids. The G+C content of the genomic DNA was 37.1 mol% and the predominant respiratory quinone was menaquinone-6. Phylogenetic analysis based on 16S rRNA gene sequences showed that the novel strain formed a tight phyletic lineage with members of the genus

Arenibacter

and was most closely related to

Arenibacter palladensis

KMM 3961T,

Arenibacter troitsensis

KMM 3674T and

Arenibacter echinorum

KMM 6032T, with 16S rRNA gene sequence similarities of 98.1 %, 98.0 % and 97.8 %, respectively. However, the DNA–DNA relatedness values between strain HP12T and

A. palladensis

JCM 13509T,

A. troitsensis

KCTC 12362T and

A. echinorum

KCTC 22013T were only 20.2±0.3 %, 22.6±0.6 % and 9.1±2.6 %, respectively. On the basis of phenotypic and molecular features, strain HP12T represents a novel species of the genus

Arenibacter

, for which the name Arenibacter hampyeongensis sp. nov. is proposed. The type strain is HP12T ( = KACC 16193T = JCM 17788T).
Bacteroides reticulotermitis sp. nov., isolated from the gut of a subterranean termite (Reticulitermes speratus)
Authors: Sakamoto Mitsuo , Ohkuma Moriya
Published: April 2012

An obligately anaerobic, non-pigmented, non-spore-forming, Gram-staining-negative, rod-shaped bacterium, designated strain Rs-03T, was isolated from the gut of the subterranean termite Reticulitermes speratus. The taxonomic position of the novel strain was determined by following a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Rs-03T was a member of the genus

Bacteroides

and was most closely related to

Bacteroides thetaiotaomicron

JCM 5827T (95.0 % sequence similarity),

Bacteroides faecis

JCM 16478T (94.8 %) and

Bacteroides xylanisolvens

JCM 15633T (94.3 %). The results of hsp60 gene sequence analysis indicated that the novel strain was different from established members of the genus

Bacteroides

. Strain Rs-03T was saccharolytic and produced succinic and acetic acids, with small amounts of propionic acid, as metabolic end products. The major cellular fatty acids of strain Rs-03T were anteiso-C15 : 0, C18 : 1ω9c and iso-C17 : 0 3-OH. The major menaquinones were MK-10 and MK-9 and the genomic DNA G+C content was 44.9 mol%. Based on these data, strain Rs-03T represents a novel species in the genus

Bacteroides

, for which the name Bacteroides reticulotermitis sp. nov. is proposed. The type strain is Rs-03T ( = JCM 10512T = CCUG 62153T).
Rhizobium subbaraonis sp. nov., an endolithic bacterium isolated from beach sand
Authors: Ramana Ch. V. , Parag B. , Girija K. R. , Ram B. Raghu , Ramana V. Venkata , Sasikala Ch.
Published: April 2012

Two strains (JC85T and JC108) of Gram-stain-negative, motile bacteria were isolated from endolithic beach sand samples on an oligotrophic medium. Based on the 16S rRNA gene sequence analysis, both strains were identified as belonging to the genus

Rhizobium

. Strain JC108 had 16S rRNA gene sequence similarity of 100 % with

Rhizobium pusense

NRCPB10T and formed a cluster with this strain. Strain JC85T had 96.9 % 16S rRNA gene sequence similarity and was 18 % related (based on DNA–DNA hybridization) to

Rhizobium borbori

DN316T. With other strains of the genus

Rhizobium

, the 16S rRNA gene sequence similarity was less than 96.3 %. Strain JC85T could tolerate up to 3 % salinity, fix N2, was resistant to ampicillin (10 µg) and was positive for catalase and oxidase. The major fatty acid was C18 : 1ω7c (69 %) with minor amounts of C19 : 0
cyclo ω8c (8.9 %), C16 : 0 (6.9 %), C12 : 0 (5.7 %) and C19 : 1ω7c/C19 : 1ω6c (2.2 %). Polar lipids of strain JC85T include two unidentified aminophospholipids (APL1,2), two unidentified phospholipids (PL1,2), phosphatidylcholine and four unidentified lipids (L1–4). Q-10 is the major quinone of strain JC85T. Based on polyphasic taxonomic analysis, strain JC85T represents a novel species for which, the name Rhizobium subbaraonis JC85T is proposed. The type strain is JC85T ( = DSM 24765T = KCTC 23614T).
Huanghella arctica gen. nov., sp. nov., a bacterium of the family

Cytophagaceae

isolated from Arctic tundra soil
Authors: Jiang Fan , Xiao Mengchen , Chen Lu , Kan Wenjing , Peng Fang , Dai Jun , Chang Xulu , Li Wenxin , Fang Chengxiang
Published: April 2012

A novel, strictly aerobic, red-pigmented, Gram-reaction-negative bacterium, designated strain R9-9T, was isolated from tundra soil collected near Ny-Ålesund, Svalbard Archipelago, Norway (78° N). The novel strain was subjected to a taxonomic study using a polyphasic approach. It grew optimally at 20–22 °C and at pH 7.0. Flexirubin-type pigments were absent. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain R9-9T represents a distinct phyletic line that reflects a novel generic status within the family

Cytophagaceae

. The novel strain showed relatively low 16S rRNA gene sequence similarities (<88.0 %) to members of established genera. Strain R9-9T contained summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C17 : 0 3-OH, iso-C15 : 0 and C16 : 1ω5c as its major cellular fatty acids, phosphatidylethanolamine as its main polar lipid, and MK-7 as its major respiratory quinone. The genomic DNA G+C content was 56.1 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain R9-9T is considered to represent a novel species in a new genus in the family

Cytophagaceae

, for which the name Huanghella arctica gen. nov., sp. nov. is proposed. The type strain is R9-9T ( = CCTCC AB 2010418T = NRRL B-59750T).
Psychroserpens damuponensis sp. nov., isolated from seawater
Authors: Lee Dong-Heon , Cho Sun Ja , Kim Suk Min , Lee Sun Bok
Published: April 2012

A novel bacterium, designated strain F051-1T, isolated from a seawater sample collected from the coast at Damupo beach in Pohang, Korea, was investigated in a polyphasic taxonomic study. Cells were yellow-pigmented, strictly aerobic, Gram-staining-negative and rod-shaped. The temperature, pH and NaCl ranges for growth were 4–30 °C, pH 6.0–9.0 and 1.0–6.0 % (w/v), respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain F051-1T belongs to the genus

Psychroserpens

in the family

Flavobacteriaceae

. Its closest relatives were

Psychroserpens burtonensis

ACAM 188T (96.8 % 16S rRNA gene sequence similarity) and

Psychroserpens mesophilus

KOPRI 13649T (95.7 %). The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G and anteiso-C15 : 0. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, two unidentified aminolipids, one unidentified phospholipid and eight unidentified lipids. The major respiratory quinone was menaquinone-6 and the genomic DNA G+C content of the strain was 33.5 mol%. On the basis of phenotypic, phylogenetic and genotypic data, strain F051-1T represents a novel species within the genus

Psychroserpens

, for which the name Psychroserpens damuponensis sp. nov. is proposed. The type strain is F051-1T ( = KCTC 23539T  = JCM 17632T).
Effects of Pooling Samples on the Performance of Classification Algorithms: A Comparative Study
Authors: Kusonmano Kanthida , Netzer Michael , Baumgartner Christian , Dehmer Matthias , Liedl Klaus R. , Graber Armin
Published: April 2012

A pooling design can be used as a powerful strategy to compensate for limited amounts of samples or high biological variation. In this paper, we perform a comparative study to model and quantify the effects of virtual pooling on the performance of the widely applied classifiers, support vector machines (SVMs), random forest (RF),k-nearest neighbors (k-NN), penalized logistic regression (PLR), and prediction analysis for microarrays (PAMs). We evaluate a variety of experimental designs using mock omics datasets with varying levels of pool sizes and considering effects from feature selection. Our results show that feature selection significantly improves classifier performance for non-pooled and pooled data. All investigated classifiers yield lower misclassification rates with smaller pool sizes. RF mainly outperforms other investigated algorithms, while accuracy levels are comparable among all the remaining ones. Guidelines are derived to identify an optimal pooling scheme for obtaining adequate predictive power and, hence, to motivate a study design that meets best experimental objectives and budgetary conditions, including time constraints.
Mental Health among Former Child Soldiers and Never-Abducted Children in Northern Uganda
Authors: Moscardino Ughetta , Scrimin Sara , Cadei Francesca , Altoè Gianmarco
Published: April 2012

The present study aimed to evaluate posttraumatic stress symptoms, psychological distress, and emotional and behavioral problems in former Ugandan child soldiers in comparison with civilian children living in the same conflict setting. Participants included 133 former child soldiers and 101 never-abducted children in northern Uganda, who were interviewed about exposure to traumatic war-related experiences, posttraumatic stress symptoms, psychological distress, and emotional and behavioral problems. Results indicated that former child soldiers had experienced significantly more war-related traumatic events than nonabducted children, with 39.3% of girls having been forced to engage in sexual contact. Total scores on measures of PTSD symptoms, psychological distress, and emotional and behavioral problems were significantly higher among child soldiers compared to their never-abducted peers. Girls reported significantly more emotional and behavioral difficulties than boys. In never-abducted children, more mental health problems were associated with experiencing physical harm, witnessing the killings of other people, and being forced to engage in sexual contact.
Physicochemical Evaluation of the Upper Litani River Watershed, Lebanon
Authors: Saadeh Mark , Semerjian Lucy , Amacha Nabil
Published: April 2012

This study aims to determine the extent of groundwater damage in the Upper Litani River Basin (ULRB) after years of water mismanagement and overfertilization in what is considered to be Lebanon’s largest fertile area. Physical and chemical samples were collected between 2005 and 2010 and analyzed using “The Standard Methods for the Examination of Water and Wastewater” (APHA, AWWA) in order to determine the extent of this pollution. The parameters included pH, ammonia, nitrate, nitrite, sulfate, phosphate, dissolved oxygen, and total dissolved solids.
Genetic Evidence for the Reduction of Brassinosteroid Levels by a BAHD Acyltransferase-Like Protein in Arabidopsis
Authors: Roh Hyungmin , Jeong Cheol Woong , Fujioka Shozo , Kim Youn Kyung , Lee Sookjin , Ahn Ji Hoon , Do Choi Yang , Lee Jong Seob
Published: April 2012

Brassinosteroids (BRs) are a group of steroidal hormones involved in plant development. Although the BR biosynthesis pathways are well characterized, the BR inactivation process, which contributes to BR homeostasis, is less understood. Here, we show that a member of the BAHD (for benzylalcohol O-acetyltransferase, anthocyanin O-hydroxycinnamoyltransferase, anthranilate N-hydroxycinnamoyl/benzoyltransferase, and deacetylvindoline 4-O-acetyltransferase) acyltransferase family may play a role in BR homeostasis in Arabidopsis (Arabidopsis thaliana). We isolated two gain-of-function mutants, brassinosteroid inactivator1-1Dominant (bia1-1D) and bia1-2D, in which a novel BAHD acyltransferase-like protein was transcriptionally activated. Both mutants exhibited dwarfism, reduced male fertility, and deetiolation in darkness, which are typical phenotypes of plants defective in BR biosynthesis. Exogenous BR treatment rescued the phenotypes of the bia1-1D mutant. Endogenous levels of BRs were reduced in the bia1-1D mutant, demonstrating that BIA1 regulates endogenous BR levels. When grown in darkness, the bia1 loss-of-function mutant showed a longer hypocotyl phenotype and was more responsive to exogenous BR treatment than the wild-type plant. BIA1 expression was predominantly observed in the root, where low levels of BRs were detected. These results indicate that the BAHD acyltransferase family member encoded by BIA1 plays a role in controlling BR levels, particularly in the root and hypocotyl in darkness. Taken together, our study provides new insights into a mechanism that maintains BR homeostasis in Arabidopsis, likely via acyl conjugation of BRs.
The impact of knowledge governance on knowledge sharing
Authors: Cao Yong , Xiang Yang
Published: April 2012

Purpose

Knowledge governance is an organizational mechanism that formally and informally defines how the firm manages the activities related knowledge, thus it has a significant influence on knowledge sharing. The purpose of this study is to analyze the impact of knowledge governance, including formal and informal knowledge governance, on knowledge sharing. Further, the authors examine the mediating role of guanxi effect between knowledge governance and knowledge sharing.

Design/methodology/approach

Based upon their research, the authors chose to use the logic deduction approach for hypotheses and analytical frameworks. Questionnaires and interviews were used to collect data from 339 employees in 39 Chinese strategic emerging firms. Finally, regression analysis and structure equation models by SPSS AMOS were used for data analysis and hypotheses testing.

Findings

This study points to the impact that knowledge governance bears upon knowledge sharing based on the mediation of guanxi effect in China. The results first show that knowledge governance, including formal and informal knowledge governance, plays a key role in knowledge sharing; second, that guanxi effect partly mediates between informal knowledge governance and knowledge sharing; thirdly, guanxi effect plays a whole mediating role between formal knowledge governance and knowledge sharing.

Research limitations/implications

This study presents a framework for Chinese strategic emerging industries to better comprehend the impact of knowledge governance upon knowledge sharing and thus enhance their firm's guanxi networks to maximize economic and social benefit. The managerial implications are that firms should strengthen knowledge governance to promote employee knowledge sharing and infuse a more harmonious atmosphere to strengthen the positive effects of guanxi among employees. Ultimately, Chinese firms must consider and encourage the benefits of the guanxi effect. This study only investigated 339 employees in 39 organizations located in central China. It is limited by employees' cognition. In further research, the authors will identify more samples and develop a large‐scale questionnaire to explore these impacts in more detail and thus enhance their current research.

Originality/value

It is the first attempt in China to systematically investigate the impact of knowledge governance on knowledge sharing based on the mediation of guanxi effect. The results provide a theoretical and methodological contribution to the study of knowledge governance and can thus improve managerial practice in an era of knowledge‐based economies.
CEO experience as micro‐level origin of dynamic capabilities
Authors: Rodenbach Marc , Brettel Malte
Published: April 2012

Purpose

The aim of this paper is to corroborate with empirical validations the theoretical considerations about the influence of chief executive officers (CEOs) and their experience as micro‐level origin of dynamic capabilities in organisations.

Design/methodology/approach

The paper empirically analyses the impact of CEO experience (CEO firm experience, CEO age, CEO international experience, CEO functional experience) as a micro‐level origin of dynamic marketing and research and development (R&D) capabilities.

Findings

The results show that CEO experience influences dynamic capabilities and corroborate the theoretical considerations about the influence of micro‐level origins, i.e. CEO firm experience and CEO age influence the development of dynamic capabilities, dependent on environmental conditions.

Research limitations/implications

The findings encourage more research on the important role of micro‐level origins of dynamic capabilities. With a view to the theoretical background, it would be useful to know whether CEO experience at the individual level and its impact on dynamic capabilities can be transferred to the organisational level.

Practical implications

CEO experience can significantly improve or downgrade dynamic marketing and R&D capabilities, e.g. organisations in turbulent environments have an advantage when their CEO is young, whereas organisations in less turbulent environments benefit from an older CEO.

Originality/value

The paper helps build a better understanding of the role of CEOs and their experience as a micro‐level origin of dynamic capabilities in organisations. It extends the suggestion that micro‐level origins are important in the development of dynamic capabilities.
Measuring HRM and organisational performance: concepts, issues, and framework
Authors: Singh Satwinder , Darwish Tamer K. , Costa Ana Cristina , Anderson Neil
Published: April 2012

Purpose

The purpose of this paper is to contribute to the understanding of the HRM and organisational performance (OP) nexus by drawing attention to the complex interplay of internal and external factors affecting OP, and to further provide an integrated framework for the testing of this nexus.

Design/methodology/approach

Relevant literature is reviewed and assessed critically. A theoretical framework is provided with the objective to measure the HRM‐OP nexus.

Findings

Whilst the majority of the extant literature on HRM has focused mainly on internal factors, the authors suggest that the domain of the internal factors considered thus far needs to be widened and external factors need to be acknowledged explicitly. They provide a schematic model portraying the intricate nature of internal and external factors. They subsequently provide an integrated framework of factors in order to measure HRM practices' effects on OP.

Research limitations/implications

The suggested framework is theoretical pending empirical testing. The framework can serve as a template for future research.

Practical implications

The framework can be put into a universally testable template for use by researchers.

Originality/value

The paper, for the first time, schematically brings together and discusses the elements affecting the HRM‐OP nexus, and further provides a framework in the form of a set of exhaustive factors – which will facilitate this nexus being put to empirical test.
Influencing foreign subsidiary decisions through headquarter performance measurement systems
Authors: Mahlendorf Matthias D. , Rehring Jochen , Schäffer Utz , Wyszomirski Elmar
Published: April 2012

Purpose

This paper aims to investigate the ability of performance measurement systems (PMS) that were implemented by headquarters at foreign subsidiaries to influence decisions made by the subsidiary. This is important because PMS are important control mechanisms in the relationship between headquarters and subsidiaries within multinational firms.

Design/methodology/approach

Acknowledging that controlling foreign subsidiaries is particularly challenging when they are geographically distant to headquarters, the authors collect survey‐based data from Chinese subsidiaries of multinational firms. They develop several hypotheses which are tested on a sample of 148 subsidiaries using multiple regression analysis.

Findings

The results suggest that the influence of headquarter‐designed PMS on subsidiary decisions is higher when the compensation of subsidiary management is linked to PMS, when additional formal control is enforced, when PMS are affected by external events, when PMS are comprehensive, and when subsidiaries are embedded into the local business environment. Also, the authors find a negative interaction effect between comprehensive PMS and the extent to which PMS are affected by external events on the decision‐influence of PMS.

Research limitations/implications

Limitations arise from the study setting in China. As management accounting research originates from and has mostly focused on Western countries, it remains somewhat unclear whether the constructs and instruments used in this study are fully transferable to China, despite the statistical and conceptual remedies that were applied.

Originality/value

The study offers new insights into the role of PMS in multinational companies. It extends earlier research by offering empirical evidence from one of the most important emerging economies. As such, the results are relevant for almost every global firm using PMS to control foreign subsidiaries.
“Every man for himself”
Authors: Richards James , Chillas Shiona , Marks Abigail
Published: April 2012

Purpose

This paper aims to examine the practice of teamwork in an under‐researched, yet growing industrial setting.

Design/methodology/approach

Longitudinal ethnographic‐styled methods of data collection were used and data was examined using the Team Dimensions Model.

Findings

The findings suggest the Team Dimensions Model, with the addition of a customer service perspective, is of use for identifying managerial objectives and organisational outcomes of teamwork. However, this does not suggest that teamworking is easy to implement in the hospitality setting.

Research limitations/implications

The findings were obtained using unobtrusive participatory and observational methods and based on a single company.

Practical implications

The paper allows management practitioners to reflect on realities of implementing teamworking under a corporate customer service initiative.

Originality/value

The paper takes an existing theory on teamworking and develops the theory in an under‐researched and growing industrial sector.
“Virtual teams are literally and metaphorically invisible”
Authors: Au Yee , Marks Abigail
Published: April 2012

Purpose

This paper aims to examine the impact of perceived cultural differences in forging identity in virtual teams. Whilst there has been a great deal of research on team identification, little has been written about the influences of the virtual context on this process.

Design/methodology/approach

The study reported in this paper was conducted in four companies and seven virtual teams operating across the UK, the USA, Brazil, Singapore, Malaysia and Myanmar.

Findings

The results show that perceived differences in national cultures and the way people work within the cultures has a significant impact on identification in virtual teams. This can lead to unhealthy racial and national stereotypes, which cause conflict between team members. The findings of this study highlight the importance of encouraging team members to value and understand differences and that it is necessary to promote a common goal to foster identification in international virtual teams.

Originality/value

The research provides a critical analysis of virtual working across international boundaries, focusing on employees rather than the technology.
The practice of teamwork in health industry call centres
Authors: Valsecchi Raffaella , Wise Sarah , Mueller Frank , Smith Chris
Published: April 2012

Purpose

This paper aims to explore the introduction of teamwork in two health call centres, NHS Direct and NHS24, and intervenes in the emergent debate over teamwork in call centres. Although within the call centre work environment there is no obvious functional rationale for teamwork, teams can be “accounted for” with reference to other purposes, including performance management, normative control, governmentality and institutional isomorphism/management fads. This research provides additional explanations for the use of teamwork in such an adverse work environment.

Design/methodology/approach

The paper is based on qualitative data (interviews and non‐participant observations) from NHS Direct and NHS24, the English and Scottish tele‐nursing organisations in the UK.

Findings

In the two tele‐nursing case studies analysed, teamwork was introduced as an expression of managers' aspirations to emulate private sector practices and to reinforce new public management ideals. However, informal teamwork, which cut across organisationally prescribed forms, provided both emotional support and spontaneous knowledge sharing among nurses.

Originality/value

This is an innovative study because teamwork has not been thoroughly explored in a health call centre environment.
Developing ideas and concepts in teamwork research: where do we go from here?
Authors: Marks Abigail , Richards James
Published: April 2012

Purpose

This editorial seeks to explore changes in both teamwork and developments in teamwork research over the last decade.

Design/methodology/approach

The editorial review importantly focuses on the key debates that emerge from the papers covered in this special issue.

Findings

A review of the papers in this special issue, as well as historical analysis of teamwork research, indicate that while traditionally, analysis of teamwork was embedded in a manufacturing archetype, much of the contemporary research on teamwork is centred on service sector work where issues of cultural diversity, customer service, and lack of normative integration or task interdependence are increasingly apparent. This editorial suggests that we need to take account of the expansion of the service sector when attempting to conceptualise teamwork and the challenges that collective forms of working in such an environment bring.

Originality/value

This editorial and the special issue more generally provide an important contribution to the development of understanding of how changes in the workplace have had an impact on organisational and academic interest in teamwork.
Job and work attitudes, engagement and employee performance
Authors: Robertson Ivan T. , Jansen Birch Alex , Cooper Cary L.
Published: April 2012

Purpose

This article aims to test the hypothesis that employee productivity levels will be better predicted by a combination of positive job and work attitudes (employee engagement) and psychological well‐being than by positive job and work attitudes alone.

Design/methodology/approach

Survey data using psychometrically sound measures of the key constructs were collected for a sample of over 9,000 people across 12 organisations.

Findings

Multiple regression analyses reveal that psychological well‐being has incremental value over and above that of positive job and work attitudes in predicting self‐reported levels of performance.

Research limitations/implications

The study design involves cross sectional self‐report data and as such firm conclusions about causality cannot be drawn.

Practical implications

The results suggest that if employers focus only on job and work attitudes and ignore employee psychological well‐being, they will limit the benefits that can be obtained through initiatives such as programmes designed to improve employee engagement.

Originality/value

The study provides evidence that two previously separate constructs are both important in predicting measures of employee productivity.