bluuebunny/crossref_metadata_2025 huggingface dataset:
DNA-binding specificities of plant transcription factors and their potential to define target genes
Authors: Franco-Zorrilla José M. , López-Vidriero Irene , Carrasco José L. , Godoy Marta , Vera Pablo , Solano Roberto
Published: January 2014

Significance

We described the high-throughput identification of DNA-binding specificities of 63 plant transcription factors (TFs) and their relevance as
cis-
regulatory elements in vivo. Almost half of the TFs recognized secondary motifs partially or completely differing from their corresponding primary ones. Analysis of coregulated genes, transcriptomic data, and chromatin hypersensitive regions revealed the biological relevance of more than 80% of the binding sites identified. Our combined analysis allows the prediction of the function of a particular TF as activator or repressor through a particular DNA sequence. The data support the correlation between
cis-
regulatory elements in vivo and the sequence determined in vitro. Moreover, it provides a framework to explore regulatory networks in plants and contributes to decipher the transcriptional regulatory code.
Astronomical reach of fundamental physics
Authors: Burrows Adam S. , Ostriker Jeremiah P.
Published: January 2014

Using basic physical arguments, we derive by dimensional and physical analysis the characteristic masses and sizes of important objects in the universe in terms of just a few fundamental constants. This exercise illustrates the unifying power of physics and the profound connections between the small and the large in the cosmos we inhabit. We focus on the minimum and maximum masses of normal stars, the corresponding quantities for neutron stars, the maximum mass of a rocky planet, the maximum mass of a white dwarf, and the mass of a typical galaxy. To zeroth order, we show that all these masses can be expressed in terms of either the Planck mass or the Chandrasekar mass, in combination with various dimensionless quantities. With these examples, we expose the deep interrelationships imposed by nature between disparate realms of the universe and the amazing consequences of the unifying character of physical law.
The ‘internationalization’ of social sciences as an ‘obstacle’ to understanding the ongoing Arab revolts
Authors: Kabbanji Jacques E.
Published: January 2014

This paper addresses two main topics. First, the ways in and extent to which scholars from, or originated from, the ‘Global South’ have avoided succumbing to the appeal of dominant ‘Western’ perspectives when practising their vocation as social scientists. Second, the price paid for lack of appropriate knowledge when social scientists adopt dominant paradigms in studying ‘undisciplined’ societies, i.e. the ones that do not ‘correspond’ to dominant ideal types. Approaches based on the Weberian paradigm will be specifically considered in this regard. Jacques Kabbanji concedes that there has indeed been a shift from the colonial era, which produced the Orientalism that Edward Said and others so effectively exposed as subjective and instrumental to Western hegemony. Yet, he argues, in the post-colonial era the way in which many Arab scholars have responded to the Orientalist critique, together with other critiques of mainstream social science by scholars from the Global South, has ended up endorsing a newly hegemonic social science that actually reinvents ‘Arab exceptionalism’. This poses a problem for would-be analysts of the Arab revolts that began in 2010.
Myosin Va mediates Rab8A-regulated GLUT4 vesicle exocytosis in insulin-stimulated muscle cells
Authors: Sun Yi , Chiu Tim T. , Foley Kevin P. , Bilan Philip J. , Klip Amira
Published: January 2014

Rab-GTPases are important molecular switches regulating intracellular vesicle traffic, and we recently showed that Rab8A and Rab13 are activated by insulin in muscle to mobilize GLUT4-containing vesicles to the muscle cell surface. Here we show that the unconventional motor protein myosin Va (MyoVa) is an effector of Rab8A in this process. In CHO-IR cell lysates, a glutathione S-transferase chimera of the cargo-binding COOH tail (CT) of MyoVa binds Rab8A and the related Rab10, but not Rab13. Binding to Rab8A is stimulated by insulin in a phosphatidylinositol 3-kinase–dependent manner, whereas Rab10 binding is insulin insensitive. MyoVa-CT preferentially binds GTP-locked Rab8A. Full-length green fluorescent protein (GFP)–MyoVa colocalizes with mCherry-Rab8A in perinuclear small puncta, whereas GFP–MyoVa-CT collapses the GTPase into enlarged perinuclear depots. Further, GFP–MyoVa-CT blocks insulin-stimulated translocation of exofacially myc-tagged GLUT4 to the surface of muscle cells. Mutation of amino acids in MyoVa-CT predicted to bind Rab8A abrogates both interaction with Rab8A (not Rab10) and inhibition of insulin-stimulated GLUT4myc translocation. Of importance, small interfering RNA–mediated MyoVa silencing reduces insulin-stimulated GLUT4myc translocation. Rab8A colocalizes with GLUT4 in perinuclear but not submembrane regions visualized by confocal total internal reflection fluorescence microscopy. Hence insulin signaling to the molecular switch Rab8A connects with the motor protein MyoVa to mobilize GLUT4 vesicles toward the muscle cell plasma membrane.
Alternate pleckstrin homology domain orientations regulate dynamin-catalyzed membrane fission
Authors: Mehrotra Niharika , Nichols Justin , Ramachandran Rajesh
Published: January 2014

The self-assembling GTPase dynamin catalyzes endocytic vesicle scission via membrane insertion of its pleckstrin homology (PH) domain. However, the molecular mechanisms underlying PH domain–dependent membrane fission remain obscure. Membrane-curvature–sensing and membrane-curvature–generating properties have been attributed, but it remains to be seen whether the PH domain is involved in either process independent of dynamin self-assembly. Here, using multiple fluorescence spectroscopic and microscopic techniques, we demonstrate that the isolated PH domain does not act to bend membranes but instead senses high membrane curvature through hydrophobic insertion into the membrane bilayer. Furthermore, we use a complementary set of short- and long-distance Förster resonance energy transfer approaches to distinguish PH-domain orientation from proximity at the membrane surface in full-length dynamin. We reveal, in addition to the GTP-sensitive “hydrophobic mode,” the presence of an alternate, GTP-insensitive “electrostatic mode” of PH domain–membrane interactions that retains dynamin on the membrane surface during the GTP hydrolysis cycle. Stabilization of this alternate orientation produces dramatic variations in the morphology of membrane-bound dynamin spirals, indicating that the PH domain regulates membrane fission through the control of dynamin polymer dynamics.
PUmPER: phylogenies updated perpetually
Authors: Izquierdo-Carrasco Fernando , Cazes John , Smith Stephen A. , Stamatakis Alexandros
Published: January 2014

Summary: New sequence data useful for phylogenetic and evolutionary analyses continues to be added to public databases. The construction of multiple sequence alignments and inference of huge phylogenies comprising large taxonomic groups are expensive tasks, both in terms of man hours and computational resources. Therefore, maintaining comprehensive phylogenies, based on representative and up-to-date molecular sequences, is challenging. PUmPER is a framework that can perpetually construct multi-gene alignments (with PHLAWD) and phylogenetic trees (with ExaML or RAxML-Light) for a given NCBI taxonomic group. When sufficient numbers of new gene sequences for the selected taxonomic group have accumulated in GenBank, PUmPER automatically extends the alignment and infers extended phylogenetic trees by using previously inferred smaller trees as starting topologies. Using our framework, large phylogenetic trees can be perpetually updated without human intervention. Importantly, resulting phylogenies are not statistically significantly worse than trees inferred from scratch.

Availability and implementation: PUmPER can run in stand-alone mode on a single server, or offload the computationally expensive phylogenetic searches to a parallel computing cluster. Source code, documentation, and tutorials are available at https://github.com/fizquierdo/perpetually-updated-trees.

Contact:  Fernando.Izquierdo@h-its.org

Supplementary information:  Supplementary Material is available at Bioinformatics online.
Opportunism and Honest Incompetence—Seeking Explanations for Noncompliance in Public Procurement
Authors: Kauppi Katri , van Raaij Erik M.
Published: January 2014

This article utilizes agency theory to explain maverick buying in governmental agencies, that is, noncompliance to centrally negotiated frame agreements. Traditional agency theory assumes the agent to be an opportunistic self-interest seeker. A complementary view of agency problems portrays man as an honest, yet not fully competent, actor; both agents and principals may be burdened by “honest incompetence.” We apply both perspectives on principal-agent relationships to study maverick buying in government procurement and link agency problems to three governance mechanisms: monitoring, training, and guidance. We find that guidance and training help to reduce governmental employees’ noncompliance, but output monitoring does not. Our findings further indicate that maverick buying is related to goal incongruence and two different types of information asymmetry: Agency problems may arise not only because the agent has information the principal is not aware of but also because the principal may have information the agent is not aware of. Future research in public management using agency theory to study instances of hidden action could benefit from applying a similar dual lens to behaviors previously examined as purely opportunistic.
Mapping of six somatic linker histone H1 variants in human breast cancer cells uncovers specific features of H1.2
Authors: Millán-Ariño Lluís , Islam Abul B. M. M. K. , Izquierdo-Bouldstridge Andrea , Mayor Regina , Terme Jean-Michel , Luque Neus , Sancho Mónica , López-Bigas Núria , Jordan Albert
Published: January 2014

Seven linker histone H1 variants are present in human somatic cells with distinct prevalence across cell types. Despite being key structural components of chromatin, it is not known whether the different variants have specific roles in the regulation of nuclear processes or are differentially distributed throughout the genome. Using variant-specific antibodies to H1 and hemagglutinin (HA)-tagged recombinant H1 variants expressed in breast cancer cells, we have investigated the distribution of six H1 variants in promoters and genome-wide. H1 is depleted at promoters depending on its transcriptional status and differs between variants. Notably, H1.2 is less abundant than other variants at the transcription start sites of inactive genes, and promoters enriched in H1.2 are different from those enriched in other variants and tend to be repressed. Additionally, H1.2 is enriched at chromosomal domains characterized by low guanine–cytosine (GC) content and is associated with lamina-associated domains. Meanwhile, other variants are associated with higher GC content, CpG islands and gene-rich domains. For instance, H1.0 and H1X are enriched at gene-rich chromosomes, whereas H1.2 is depleted. In short, histone H1 is not uniformly distributed along the genome and there are differences between variants, H1.2 being the one showing the most specific pattern and strongest correlation with low gene expression.
Multiplexing clonality: combining RGB marking and genetic barcoding
Authors: Cornils Kerstin , Thielecke Lars , Hüser Svenja , Forgber Michael , Thomaschewski Michael , Kleist Nadja , Hussein Kais , Riecken Kristoffer , Volz Tassilo , Gerdes Sebastian , Glauche Ingmar , Dahl Andreas , Dandri Maura , Roeder Ingo , Fehse Boris
Published: January 2014

RGB marking and DNA barcoding are two cutting-edge technologies in the field of clonal cell marking. To combine the virtues of both approaches, we equipped LeGO vectors encoding red, green or blue fluorescent proteins with complex DNA barcodes carrying color-specific signatures. For these vectors, we generated highly complex plasmid libraries that were used for the production of barcoded lentiviral vector particles. In proof-of-principle experiments, we used barcoded vectors for RGB marking of cell lines and primary murine hepatocytes. We applied single-cell polymerase chain reaction to decipher barcode signatures of individual RGB-marked cells expressing defined color hues. This enabled us to prove clonal identity of cells with one and the same RGB color. Also, we made use of barcoded vectors to investigate clonal development of leukemia induced by ectopic oncogene expression in murine hematopoietic cells. In conclusion, by combining RGB marking and DNA barcoding, we have established a novel technique for the unambiguous genetic marking of individual cells in the context of normal regeneration as well as malignant outgrowth. Moreover, the introduction of color-specific signatures in barcodes will facilitate studies on the impact of different variables (e.g. vector type, transgenes, culture conditions) in the context of competitive repopulation studies.
Structural basis of sodium–potassium exchange of a human telomeric DNA quadruplex without topological conversion
Authors: Wang Zi-Fu , Li Ming-Hao , Hsu Shang-Te Danny , Chang Ta-Chau
Published: January 2014

Understanding the mechanism of Na+/K+-dependent spectral conversion of human telomeric G-quadruplex (G4) sequences has been limited not only because of the structural polymorphism but also the lack of sufficient structural information at different stages along the conversion process for one given oligonucleotide. In this work, we have determined the topology of the Na+ form of Tel23 G4, which is the same hybrid form as the K+ form of Tel23 G4 despite the distinct spectral patterns in their respective nuclear magnetic resonance (NMR) and circular dichroism spectra. The spectral difference, particularly the well-resolved imino proton NMR signals, allows us to monitor the structural conversion from Na+ form to K+ form during Na+/K+ exchange. Time-resolved NMR experiments of hydrogen–deuterium exchange and hybridization clearly exclude involvement of the global unfolding for the fast Na+/K+ spectral conversion. In addition, the K+ titration monitored by NMR reveals that the Na+/K+ exchange in Tel23 G4 is a two-step process. The addition of K+ significantly stabilizes the unfolding kinetics of Tel23 G4. These results offer a possible explanation of rapid spectral conversion of Na+/K+ exchange and insight into the mechanism of Na+/K+ structural conversion in human telomeric G4s.
Vascular Access in Resuscitation
Authors: Anson Jonathan A.
Published: January 2014

Intraosseous vascular access is a time-tested procedure which has been incorporated into the 2010 American Heart Association Guidelines for Cardiopulmonary Resuscitation. Intravenous access is often difficult to achieve in shock patients, and central line placement can be time consuming. Intraosseous vascular access, however, can be achieved quickly with minimal disruption of chest compressions. Newer insertion devices are easy to use, making the intraosseous route an attractive alternative for venous access during a resuscitation event. It is critical that anesthesiologists, who are often at the forefront of patient resuscitation, understand how to properly use this potentially life-saving procedure.
Nanohydroxyapatite shape and its potential role in bone formation: an analytical study
Authors: Kalia Priya , Vizcay-Barrena Gema , Fan Jian Ping , Warley Alice , Di Silvio Lucy , Huang Jie
Published: January 2014

Bone cells (osteoblasts) produce a collagen-rich matrix called osteoid, which is mineralized extracellularly by nanosized calcium phosphate (CaP). Synthetically produced CaP nanoparticles (NPs) have great potential for clinical application. However few studies have compared the effect of CaP NPs with different properties, such as shape and aspect ratio, on the survival and behaviour of active bone-producing cells, such as primary human osteoblasts (HOBs). This study aimed to investigate the biocompatibility and ultrastructural effects of two differently shaped hydroxyapatite [Ca
10
(PO
4
)
6
(OH)
2
] nanoparticles (HA NPs), round- (aspect ratio 2.12, AR2) and rice-shaped (aspect ratio 3.79, AR4). The ultrastructural response and initial extracellular matrix (ECM) formation of HOBs to HA NPs were observed, as well as matrix vesicle release. A transmission electron microscopy (TEM)-based X-ray microanalytical technique was used to measure cytoplasmic ion levels, including calcium (Ca), phosphorus (P), sodium (Na) and potassium (K). K/Na ratios were used as a measure of cell viability. Following HA NP stimulation, all measured cytoplasmic ion levels increased. AR2 NPs had a greater osteogenic effect on osteoblasts compared with AR4 NPs, including alkaline phosphatase activity and matrix vesicle release. However, they produced only a moderate increase in intracellular Ca and P levels compared with AR4. This suggests that particular Ca and P concentrations may be required for, or indicative of, optimal osteoblast activity. Cell viability, as measured by Na and K microanalysis, was best maintained in AR2. Initial formation of osteoblast ECM was altered in the presence of either HA NP, and immuno-TEM identified fibronectin and matrilin-3 as two ECM proteins affected. Matrilin-3 is here described for the first time as being expressed by cultured osteoblasts. In summary, this novel and in-depth study has demonstrated that HA NP shape can influence a range of different parameters related to osteoblast viability and activity.
Bacillus luteus sp. nov., isolated from soil
Authors: Subhash Y. , Sasikala Ch. , Ramana Ch. V.
Published: January 2014

Two bacterial strains (JC167T and JC168) were isolated from a soil sample collected from Mandpam, Tamilnadu, India. Colonies of both strains were orange and cells Gram-stain-positive. Cells were small rods, and formed terminal endospores of ellipsoidal to oval shape. Both strains were positive for catalase, oxidase and hydrolysis of starch/gelatin, and negative for chitin hydrolysis, H2S production, indole production and nitrate reduction activity. Major fatty acids of both strains (>5 %) were anteiso-C15 : 0, iso-C16 : 0, iso-C15 : 0, anteiso-C17 : 0, iso-C14 : 0 and C16 : 0 with minor (<5 but >1 %) amounts of iso-C17 : 0, anteiso-C17 : 0 B/iso-C17 : 0 I and C16 : 1ω11c. Diphosphatydilglycerol, phosphatidylethanolamine and phosphatidylglycerol were the major polar lipids of both strains. Cell wall amino acids were l-alanine, d-alanine, d-glutamic acid and meso-diaminopimelic acid. β-Carotene and five unidentified carotenoids were present in both strains. Mean genomic DNA G+C content was 53.4±1 mol% and the two strains were closely related (mean DNA–DNA hybridization >90 %). 16S rRNA gene sequence comparisons of both strains indicated that they represent species of the genus

Bacillus

within the family

Bacillaceae

of the phylum

Firmicutes

. Both strains had a sequence similarity of 97.6 % with

Bacillus saliphilus

6AGT and <96.8 % with other members of the genus

Bacillus

. Sequence similarity between strain JC167T and 168 was 100 %. Strain JC167T showed 25.8±1 % reassociation (based on DNA–DNA hybridization) with

B. saliphilus

DSM 15402T ( = 6AGT). Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of strain JC167T as a representative of a novel species of the genus

Bacillus

, for which the name Bacillus luteus sp. nov. is proposed. The type strain is JC167T ( = KCTC 33100T = LMG 27257T).
Streptomyces graminisoli sp. nov. and Streptomyces rhizophilus sp. nov., isolated from bamboo (Sasa borealis) rhizosphere soil
Authors: Lee Hyo-Jin , Whang Kyung-Sook
Published: January 2014

Four strains of actinomycete, designated strains JR-19T, JR-12, JR-29 and JR-41T were isolated from bamboo (Sasa borealis) rhizosphere soil. Phylogenetic, morphological, chemotaxonomic and phenotypic analysis demonstrated that the four strains belong to the genus

Streptomyces

. Microscopic observation revealed that the four strains produced spirales spore chains with spiny surfaces. The cell-wall peptidoglycan of the four strains contained ll-diaminopimelic acid, glutamic acid, alanine and glycine. Whole-cell hydrolysates mainly contained glucose and ribose. The predominant menaquinones were MK-9 (H6) and MK-9 (H8). Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that these strains and the members of the genus

Streptomyces

exhibited moderately high 16S rRNA gene sequence similarities of 98.3–99.3 %, with the most closely related strains being

Streptomyces shenzhenensis

172115T and

Streptomyces gramineus

JR-43T. Based on the phenotypic and genotypic data, the four strains are considered to represent two novel species of the genus

Streptomyces

, for which the names Streptomyces graminisoli sp. nov. [to accommodate strains JR-19T (type strain;  = KACC 16472T = NBRC 108883T), JR-12 ( = KACC 16471) and JR-29 ( = KACC 16473)] and Streptomyces rhizophilus sp. nov. [for strain JR-41T ( = KACC 16580T = NBRC 108885T)] are proposed.
Noviherbaspirillum
suwonense sp. nov., isolated from an air sample
Authors: Kim Soo-Jin , Moon Ji-Young , Weon Hang-Yeon , Hong Seung-Beom , Seok Soon-Ja , Kwon Soon-Wo
Published: January 2014

A Gram-stain-negative bacterium, strain 5410S-62T, was isolated from an air sample collected in Suwon, Republic of Korea. It was aerobic, motile, mesophilic and formed rod-shaped cells. Colonies on R2A agar were convex, circular and pale orange with entire margins. Growth occurred at pH 5–9 (optimally at pH 7) and at 10–40 °C (optimally at 28 °C). It did not grow in the presence of 1 % NaCl. Comparative analyses of 16S rRNA gene sequences demonstrated that the novel strain was closely related to members of the genus

Noviherbaspirillum

. Strain 5410S-62T showed the highest sequence similarity (98.2 %) to

Glaciimonas singularis

A2-57T. It also showed high 16S rRNA gene sequence similarity (98.1–95.6 %) to members of the genus

Noviherbaspirillum

(98.1 % to

Noviherbaspirillum aurantiacum

SUEMI08T, 97.8 % to

Noviherbaspirillum soli

SUEMI10T and

Noviherbaspirillum canariense

SUEMI03T, 97.6 % to

Noviherbaspirillum psychrotolerans

PB1T and 95.6 % to

Noviherbaspirillum malthae

CC-AFH3T). The strain contained summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) as major fatty acids, Q-8 as the only ubiquinone and large amounts of phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. Strain 5410S-62T revealed less than 70 % DNA–DNA relatedness with the type strains of closely related species of the genera

Noviherbaspirillum

and

Herbaspirillum

and

Glaciimonas singularis

. Based on the physiological, biochemical and chemotaxonomic data obtained in this study, it is proposed that strain 5410S-62T represents a novel species, Noviherbaspirillum suwonense sp. nov., with 5410S-62T ( = KACC 16657T =  NBRC 108944T) as the type strain.
Rhizobium azibense sp. nov., a nitrogen fixing bacterium isolated from root-nodules of Phaseolus vulgaris
Authors: Mnasri Bacem , Liu Tian Yan , Saidi Sabrine , Chen Wen Feng , Chen Wen Xin , Zhang Xiao Xia , Mhamdi Ridha
Published: January 2014

Three microbial strains isolated from common beans, 23C2T (Tunisia), Gr42 (Spain) and IE4868 (Mexico), which have been identified previously as representing a genomic group closely related to

Rhizobium gallicum

, are further studied here. Their 16S rRNA genes showed 98.5–99 % similarity with

Rhizobium loessense

CCBAU 7190BT,

R. gallicum

R602spT,

Rhizobium mongolense

USDA 1844T and

Rhizobium yanglingense

CCBAU 71623T. Phylogenetic analysis based on recA, atpD, dnaK and thrC sequences showed that the novel strains were closely related and could be distinguished from the four type strains of the closely related species. Strains 23C2T, Gr42 and IE4868 could be also differentiated from their closest phylogenetic neighbours by their phenotypic and physiological properties and their fatty acid contents. All three strains harboured symbiotic genes specific to biovar gallicum. Levels of DNA–DNA relatedness between strain 23C2T and the type strains of

R. loessense

,

R. mongolense

,

R. gallicum

and

R. yanglingense

ranged from 58.1 to 61.5 %. The DNA G+C content of the genomic DNA of strain 23C2T was 59.52 %. On the basis of these data, strains 23C2T, Gr42 and IE4868 were considered to represent a novel species of the genus

Rhizobium

for which the name Rhizobium azibense is proposed. Strain 23C2T ( = CCBAU 101087T = HAMBI3541T) was designated as the type strain.
Salegentibacter chungangensis sp. nov., isolated from a sea sand and emended description of the genus Salegentibacter
Authors: Siamphan Chatuphon , Kim Wonyong
Published: January 2014

A Gram-stain-negative, non-motile, rod-shaped, strictly aerobic bacterial strain, designated CAU 1289T, was isolated from a marine sand and its taxonomic position was investigated using a polyphasic approach. It grew optimally at pH 6.5 and 30 °C and in the presence of 3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CAU 1289T belonged to the genus

Salegentibacter

, exhibiting sequence similarity values of 93.6–96.3 % to members of this genus, and was related most closely to

Salegentibacter mishustinae

KMM 6049T (96.3 % similarity). Strain CAU 1289T contained MK-6 as the predominant menaquinone. The major fatty acid was iso-C15 : 0. The cell-wall peptidoglycan of strain CAU 1289T contained meso-diaminopimelic acid. The polar lipids were composed of phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylcholine, an unidentified phospholipid, an unidentified aminolipid, an unidentified aminophospholipid, an unidentified glycolipid and ten unidentified lipids. The DNA G+C content was 38.7 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic inference, strain CAU 1289T is considered to represent a novel species of the genus

Salegentibacter

, for which the name Salegentibacter chungangensis sp. nov. is proposed. The type strain is CAU 1289T (KCTC 24000T = CCUG 64793T). An emended description of the genus

Salegentibacter

is also proposed.
Winogradskyella wandonensis sp. nov., isolated from a tidal flat
Authors: Park Sooyeon , Park Ji-Min , Won Sung-Min , Bae Kyung Sook , Yoon Jung-Hoon
Published: January 2014

A Gram-stain-negative, non-flagellated, non-gliding, aerobic, rod-shaped bacterium, designated WD-2-2T, was isolated from a tidal flat of Wando, an island of South Korea, and subjected to a polyphasic taxonomic analysis. Strain WD-2-2T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain WD-2-2T belonged to the genus

Winogradskyella

, clustering coherently with the type strain of

Winogradskyella litorisediminis

. Strain WD-2-2T exhibited 16S rRNA gene sequence similarity of 97.4 % to

W. litorisediminis

DPS-8T and 94.5–96.6 % to the type strains of the other species of the genus

Winogradskyella

. Strain WD-2-2T contained MK-6 as the predominant menaquinone and iso-C15 : 1 G, iso-C17 : 0 3-OH and iso-C15 : 0 as the major fatty acids. The major polar lipids detected in strain WD-2-2T were phosphatidylethanolamine, one unidentified lipid and one unidentified aminolipid. The DNA G+C content was 36.4 mol%, and DNA–DNA relatedness with

W. litorisediminis

DPS-8T was 13 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain WD-2-2T is separate from recognized species of the genus

Winogradskyella

. On the basis of the data presented, strain WD-2-2T is considered to represent a novel species of the genus

Winogradskyella

, for which the name Winogradskyella wandonensis sp. nov. is proposed. The type strain is WD-2-2T ( = KCTC 32579T = CECT 8445T).
Evaluation of the Clinical and Laboratory Standards Institute phenotypic confirmatory test to detect the presence of extended-spectrum β-lactamases from 4005 Escherichia coli, Klebsiella oxytoca, Klebsiella pneumoniae and Proteus mirabilis isolates
Authors: Morrissey Ian , Bouchillon Samuel K. , Hackel Meredith , Biedenbach Douglas J. , Hawser Stephen , Hoban Daryl , Badal Robert E.
Published: January 2014

A subset of Escherichia coli, Klebsiella oxytoca, Klebsiella pneumoniae and Proteus mirabilis isolates collected for the Study for Monitoring Antimicrobial Resistance Trends that were positive for the Clinical and Laboratory Standards Institute (CLSI) extended-spectrum β-lactamase (ESBL) phenotypic confirmatory test (n = 3245) or had an ertapenem MIC of ≥0.5 µg ml−1 (n = 293), or both (n = 467), were analysed for ESBL genes. Most ESBL phenotype E. coli or K. pneumoniae possessed an ESBL gene (95.8 and 88.4 %, respectively), and this was 93.1 % if carbapenem-non-susceptible K. pneumoniae were removed. This rate was lower for P. mirabilis (73.4 %) and K. oxytoca (62.5 %). Virtually all ESBL-positive isolates (99.5 %) were cefotaxime non-susceptible [CLSI or European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints)]. Fewer isolates (82 %) were ceftazidime non-susceptible (CLSI breakpoints). In addition, 21.1 % of E. coli, 25 % of K. oxytoca and 78.7 % of P. mirabilis isolates were ceftazidime susceptible but ESBL positive. This suggests that CLSI breakpoints for ceftazidime are too high to detect ESBLs. The lower EUCAST breakpoints detected ESBLs in E. coli and K. oxytoca better, but 59.6 % of ESBL-positive isolates of P. mirabilis were ceftazidime susceptible. For isolates with ertapenem MICs ≥0.5 µg ml−1, more accurate ESBL phenotype analysis was observed for E. coli and K. pneumoniae (sensitivity >95 % for both, specificity 94.4 and 54.1 %, respectively). If carbapenemase-positive K. pneumoniae were excluded, the specificity increased to 78 %. The positive predictive values for the ESBL phenotypic test with E. coli and K. pneumoniae were 97.6 and 81.8 %, respectively, and negative predictive values were 75.9 and 95.2 %, respectively. We therefore suggest that it would be prudent to confirm phenotypic ESBL-positive P. mirabilis, K. pneumoniae and K. oxytoca with molecular analysis.
3′ end formation of pre-mRNA and phosphorylation of Ser2 on the RNA polymerase II CTD are reciprocally coupled in human cells
Authors: Davidson Lee , Muniz Lisa , West Steven
Published: January 2014

3′ end formation of pre-mRNAs is coupled to their transcription via the C-terminal domain (CTD) of RNA polymerase II (Pol II). Nearly all protein-coding transcripts are matured by cleavage and polyadenylation (CPA), which is frequently misregulated in disease. Understanding how transcription is coordinated with CPA in human cells is therefore very important. We found that the CTD is heavily phosphorylated on Ser2 (Ser2p) at poly(A) (pA) signals coincident with recruitment of the CstF77 CPA factor. Depletion of the Ser2 kinase Cdk12 impairs Ser2p, CstF77 recruitment, and CPA, strongly suggesting that the processes are linked, as they are in budding yeast. Importantly, we additionally show that the high Ser2p signals at the 3′ end depend on pA signal function. Down-regulation of CPA results in the loss of a 3′ Ser2p peak, whereas a new peak is formed when CPA is induced de novo. Finally, high Ser2p signals are generated by Pol II pausing, which is a well-known feature of pA site recognition. Thus, a reciprocal relationship between early steps in pA site processing and Ser2p ensures efficient 3′ end formation.
μ-Cyanido-κ2C:N-dicyanido-κ2C-bis(N-ethylethylenediamine-κ2N,N′)copper(II)copper(I)
Authors: Corfield Peter W. R. , Michalski Joseph F.
Published: January 2014

In the title complex, [CuICuII(CN)3(C4H12N2)2], the CuIand CuIIions and a bridging cyanide group lie on a twofold rotation axis. The CuIIion is in a slightly-distorted square-pyramidal coordination environment, with the N atoms of the two symmetry-relatedN-ethylethylenediamine ligands occupying the basal positions and an N-bonded cyanide group in the apical position. The CuIion is in a trigonal-planar coordination environment, bonded to the C atom of the bridging cyanide group and to two terminal cyanide groups. In the crystal, N—H...N hydrogen bonds involving two of the symmetry-unique N—H groups of theN-ethylethylenediamine ligands and the N atoms of the terminal cyanide ligands link the molecules into strands along [010].
3-[2-(4-Fluorophenyl)-2-oxoethyl]-5,5-diphenylimidazolidine-2,4-dione
Authors: Mague Joel T. , Abdel-Aziz Alaa A.-M. , El-Azab Adel S.
Published: January 2014

The title compound, C23H17FN2O3, crystallizes with two independent molecules in the asymmetric unit. The molecules are connected by pairs of N—H...O hydrogen bonds and have slightly different conformations, as indicated by the dihedral angles between the central imidazolidine-2,4-dione ring and its three substituents. In one molecule, these are 60.56 (1) and 82.66 (9)° to the phenyl rings and 84.35 (16)° to the 2-(4-fluorophenyl)-2-oxoethyl side chain. In the other molecule, the corresponding angles are 66.35 (10), 84.94 (9) and 86.31 (16)°. In the crystal, weak C—H...O interactions leading to a three-dimensional supramolecular architecture.
2-Methoxy-4,6-diphenylnicotinonitrile
Authors: Mague Joel T. , Abdel-Aziz Alaa A.-M. , El-Azab Adel S. , Al-Swaidan Ibrahim A.
Published: January 2014

In the title compound, C19H14N2O, the phenyl rings form dihedral angles of 10.90 (10) and 42.14 (6)° with pyridine ring and an angle of 35.7 (2)° with each other. The orientation of the methoxy group is defined by the C—O—C—N torsion angle of 4.9 (2)°.
[2-(3,4-Dimethoxyphenyl)ethyl](3-{N-[2-(3,4-dimethoxyphenyl)ethyl]carbamoyl}propyl)azanium chloride dihydrate
Authors: Saidov Abdusalom Sh. , Turgunov Kambarali K.
Published: January 2014

The asymmetric unit of the title hydrated salt, C24H35N2O5+·Cl−·2H2O, contains one organic cation that has its protonation site at the amine function, one chloride anion and two lattice water molecules. In the crystal, one pair of lattice water molecules and two chloride anions form a four-membered centrosymmetric hydrogen-bond cycle. In addition, O—H...O, N—H...O and N—H...Cl hydrogen bonds involving the N—H groups, the water molecules and the C=O group are observed. As a result, a hydrogen-bonded layer parallel to (100) is formed. The thickness of such a layer corresponds to the length of theaaxis [21.977 (3) Å].
1,3,5-Tris(4-bromophenyl)benzene prenucleation clusters from metadynamics
Authors: Salvalaglio Matteo , Giberti Federico , Parrinello Michele
Published: January 2014

Recent experimental evidence has shown that the nucleation of 1,3,5-tris(4-bromophenyl)benzene (3BrY) follows a two-step mechanism. In this work, the formation of clusters of 3BrY from homogeneous water and methanol solutions is simulated using metadynamics. The local structure of 3BrY molecules in the clusters is then compared with the low-temperature crystal structure of 3BrY, as well as with an alternative 3BrY high-pressure crystal packing obtained through Parrinello–Rahaman molecular dynamics simulations. It is found that the interactions between the aromatic cores of 3BrY represent the main supramolecular motif observed in both the local structure of the prenucleation clusters and in the crystalline state. Within the clusters, these interactions lead to the presence of dimers and trimers locally arranged in crystal-like configurations.
Computational materials discovery: the case of the W–B system
Authors: Cheng Xi-Yue , Chen Xing-Qiu , Li Dian-Zhong , Li Yi-Yi
Published: January 2014

By means of variable-compositional evolutionary algorithms, in combination with first-principles calculations, the compositions, structures and mechanical properties of the W–B system have been theoretically investigated. As well as confirming the experimental observations (including their crystal structures) for the four known compounds W2B, WB, WB2and WB3, the new stable compound W8B7and two nearly stable compounds, W2B3and WB4, have also been predicted in the ground state. The elastic properties and estimated Vickers hardnesses of all these borides have been systematically derived. The results show that, among these borides,hP6-WB2exhibits the largest ultra-incompressibility along thecaxis, with the highestC33value (953 GPa, comparable with that of the most incompressible diamond).hP16-WB3exhibits the highest hardness of 36.9 GPa, in good agreement with the experimentally measured data from 28.1 to 43.3 GPa, close to the superhard threshold, andoC8-WB shows the highest bulk modulus of about 350 GPa. The new stable compound W8B7crystallizes in the monoclinicmP15 phase, with infinite zigzag B chains running parallel to the W-atom layers, resulting in a relatively high estimated hardness of 19.6 GPa. The anisotropic Young's modulusEand torsion shear modulusGthave been derived for bothoC8-WB andhP16-WB3. The current state of research and the historic inconsistency of the W–B system are briefly summarized, in particular clarifying the fact that the previous experimentally attributedhP20-WB4is in fact the defect-containinghP16-WB3.
A two-dimensional hydrogen-bonded water layer in the structure of a cobalt(III) cubane complex
Authors: Qi Ji , Zhai Xiang-Sheng , Zhu Hong-Lin , Lin Jian-Li
Published: January 2014

A tetranuclear CoIIIoxide complex with cubane topology, tetrakis(2,2′-bipyridine-κ2N,N′)di-μ2-carbonato-κ4O:O′-tetra-μ3-oxido-tetracobalt(III) pentadecahydrate, [Co4(CO3)2O4(C10H8N2)4]·15H2O, with an unbounded hydrogen-bonded water layer, has been synthesized by reaction of CoCO3and 2,2′-bipyridine. The solvent water molecules form a hydrogen-bonded net with tetrameric and pentameric water clusters as subunits. The Co4O4cubane-like cores are sandwiched between the water layers, which are further stacked into a three-dimensional metallo-supramolecular network.
Local spillovers and durable adoption: evidence from durable consumptions in rural China
Authors: Rong Zhao , Feng Yao
Published: January 2014

Purpose

– The effects of social learning and network externalities in the diffusion of a new product imply that there should be local spillovers from existing owners to new adopters in a closely related community. Using the data from a unique household survey in rural China, this paper aims to examine the importance of local spillovers in the diffusion of two major durable goods, washing machine and refrigerator.

Design/methodology/approach

– Based on a 1999 rural household survey of durable goods consumption conducted by the National Bureau of Statistics (NBS) of China, the authors examine the likelihood of rural households adopting a washing machine and a refrigerator during 1998-1999, respectively.

Findings

– The estimation results indicate that a household is more likely to buy its first durable good in villages where a large share of households already own one. Further evidence suggests that these patterns are unlikely to be explained by unobserved local characteristics. When examined in more detail, the extent of local spillovers appears to be positively related to the household education level.

Originality/value

– First, the study reveals the importance of local spillovers in the diffusion of these two durables. Specifically, 64 percent of washing machine adoptions during 1998-1999 are due to these spillovers. For refrigerator adoptions, the proportion is 55 percent. Second, to the authors' best knowledge, the authors are among the first to test and provide evidence on the interaction between education level and local spillovers based on the learning hypothesis.
An economy-wide analysis of impacts on Taiwan of reducing tariff escalation on agriculture-related products in WTO Doha Round negotiations
Authors: Lee Huey-Lin , Chang Ching-Cheng , Weng Yungho , Hsu Sheng-Ming , Hsu Shih-Hsun , Chen Yi-Chieh
Published: January 2014

Purpose

– The purpose of this paper is to assess the degree of tariff escalation in Taiwan's agriculture-related commodities and the economy-wide impact of tariff harmonization.

Design/methodology/approach

– A computable general equilibrium model of the Taiwan economy is applied to simulate for the economy-wide impact of three alternative proposals that reduce tariff rates as well as the degree of tariff escalation in agriculture-related products.

Findings

– The paper shows that reduction in tariff wedge helps increase social welfare of Taiwan at the expense of some agricultural sectors. Based on the pair-wise comparisons of the three tariff reduction proposals, the scenario where the upstream products have the least reduction would have agricultural sectors fare better than in the other scenarios where more negative impact on output and employment would occur to agricultural sectors.

Originality/value

– The paper assesses quantitatively the economy-wide impact of reducing tariff wedges between unprocessed and processed products, which is rarely seen in the literature using a detailed computable general equilibrium model.
Do China's food safety standards affect agricultural trade? The case of dairy products
Authors: Sun Dingqiang , Huang Jikun , Yang Jun
Published: January 2014

Purpose

– The purpose of this paper is to empirically examine how China's food safety standards affect agricultural trade in the case of dairy products.

Design/methodology/approach

– A gravity model is applied to quantitatively address the impacts of changing food safety standards in China in the case of its dairy imports. The paper considers the trade impacts of not only a specific hazard substance but also overall strictness of safety standards.

Findings

– The paper shows that changes in food safety standards of dairy products have no effect on China's dairy imports. The finding is not particularly surprising considering special characteristics of China's food safety standards. Given the fact that China's safety standards are relatively lower than that in its major exporters, the trade-impeding effect may not be substantial.

Research limitations/implications

– First, this study is unable to estimate the trade-enhancing and trade-impending effects separately. Second, the study does not account for a potential endogeneity issue associated with food safety standards.

Originality/value

– This paper contributes to the debate on how food safety standards affect trade by demonstrating that safety standards in developing countries like China can affect international trade differently from that in developed countries. Although results are specific to China's dairy imports, the explanations are applicable to food safety standards in other developing countries.
Relationship of OPAC users' satisfaction with their demographic characteristics, computer skills, user education, user assistance and user-friendly OPAC
Authors: Kumar Shiv
Published: January 2014

Purpose

– The main aim of this paper is to identify whether user demographic characteristics, computer skills, user education, user assistance and user-friendly OPAC (online public access catalog) have an impact on their satisfaction in the context of users in an Indian university setting.

Design/methodology/approach

– The survey method was utilized and a questionnaire was designed to collect data. The study is based on a sample of the 384 questionnaires from the three universities located in the Union Territory of Chandigarh and Punjab State. To analyze the data collected, SPSS package (version 14.0) was used, and also to produce requisite cross-tabulations. Chi-square testing was performed to determine the association of user satisfaction with the variables covered in the study.

Findings

– The findings highlighted that overall there was a low degree of satisfaction among the users. With the exception of academic majors, in general, there were no significant differences between satisfaction and user demographic characteristics. Overall satisfaction was significantly higher for those who were possessed with adequate knowledge on OPAC, and had received staff assistance, as well as necessary education on OPAC. The study showed that satisfaction with ease of usage of OPAC was higher. It was also found that users were well-equipped with computers and had attained skills while frequently searching the web, however, it was also revealed that mere possession of computer skills was not sufficient for efficient use of OPAC, resulting in the attainment of a high level of satisfaction.

Originality/value

– The paper brings out the fact of how user demographic characteristics, computer skills, user education, user assistance, and user-friendly OPAC, influence user satisfaction in a university educational set up. The findings will be beneficial for increasing user satisfaction levels in order to retain existing OPAC users because OPAC will continue to be a necessary tool for accessing quality academic information available in both print and electronic format.
Exploring the value and innovative pricing strategy of digital archives
Authors: Wang Ping , Hu In-Lin , Chang Chen-Chi
Published: January 2014

Purpose

– The research issues of digital preservation have apparently moved from how to set up the digital archives to on-going business models. The aim of this paper is to investigate the key factors for digital archives' success. This paper provides a business model for the sustainability of digital archives.

Design/methodology/approach

– Both pricing strategies and business models related to digital archives are very important. From the point of archive preservation, how to preserve digital archives permanently and make them accessible are the most important research issues. This paper, based on a review of the academic literature, adopts the innovative pricing approach to develop the business models and pricing strategy.

Findings

– The research defines the different needs at start-up versus the on-going operations for digital preservation. Considering digital archives as information goods, this study adopts the TRIZ method to establish a pricing strategy for digital preservation. It discusses the pricing strategy for digital preservation using an innovative method of creative problem-solving theory from the perspectives of the archives institutes, materials providers and consumers.

Originality/value

– This study recommends the pricing strategies for the digital preservation programs and the government's price policy based on the TRIZ analysis method.