bluuebunny/crossref_metadata_2025 huggingface dataset:
Erythropoietin guides multipotent hematopoietic progenitor cells toward an erythroid fate
Authors: Grover Amit , Mancini Elena , Moore Susan , Mead Adam J. , Atkinson Deborah , Rasmussen Kasper D. , O’Carroll Donal , Jacobsen Sten Eirik W. , Nerlov Claus
Published: February 2014

The erythroid stress cytokine erythropoietin (Epo) supports the development of committed erythroid progenitors, but its ability to act on upstream, multipotent cells remains to be established. We observe that high systemic levels of Epo reprogram the transcriptomes of multi- and bipotent hematopoietic stem/progenitor cells in vivo. This induces erythroid lineage bias at all lineage bifurcations known to exist between hematopoietic stem cells (HSCs) and committed erythroid progenitors, leading to increased erythroid and decreased myeloid HSC output. Epo, therefore, has a lineage instructive role in vivo, through suppression of non-erythroid fate options, demonstrating the ability of a cytokine to systematically bias successive lineage choices in favor of the generation of a specific cell type.
A Formal Framework for Representing Mechanisms?
Authors: Gebharter Alexander
Published: February 2014

In this article I tackle the question of how the hierarchical order of mechanisms can be represented within a causal graph framework. I illustrate an answer to this question proposed by Casini, Illari, Russo, and Williamson and provide an example that their formalism does not support two important features of nested mechanisms: (i) a mechanism’s submechanisms are typically causally interacting with other parts of said mechanism, and (ii) intervening in some of a mechanism’s parts should have some influence on the phenomena the mechanism brings about. Finally, I sketch an alternative approach taking (i) and (ii) into account.
Nonepistemic Values and the Multiple Goals of Science
Authors: Elliott Kevin C. , McKaughan Daniel J.
Published: February 2014

Recent efforts to argue that nonepistemic values have a legitimate role to play in assessing scientific models, theories, and hypotheses typically either reject the distinction between epistemic and nonepistemic values or incorporate nonepistemic values only as a secondary consideration for resolving epistemic uncertainty. Given that scientific representations can legitimately be evaluated not only based on their fit with the world but also with respect to their fit with the needs of their users, we show in two case studies that nonepistemic values can play a legitimate role as factors that override epistemic considerations in assessing scientific representations for practical purposes.
The cleverSuite approach for protein characterization: predictions of structural properties, solubility, chaperone requirements and RNA-binding abilities
Authors: Klus Petr , Bolognesi Benedetta , Agostini Federico , Marchese Domenica , Zanzoni Andreas , Tartaglia Gian Gaetano
Published: February 2014

Motivation: The recent shift towards high-throughput screening is posing new challenges for the interpretation of experimental results. Here we propose the cleverSuite approach for large-scale characterization of protein groups.

Description: The central part of the cleverSuite is the cleverMachine (CM), an algorithm that performs statistics on protein sequences by comparing their physico-chemical propensities. The second element is called cleverClassifier and builds on top of the models generated by the CM to allow classification of new datasets.

Results: We applied the cleverSuite to predict secondary structure properties, solubility, chaperone requirements and RNA-binding abilities. Using cross-validation and independent datasets, the cleverSuite reproduces experimental findings with great accuracy and provides models that can be used for future investigations.

Availability: The intuitive interface for dataset exploration, analysis and prediction is available at http://s.tartaglialab.com/clever_suite.

Contact:  gian.tartaglia@crg.es

Supplementary information:  Supplementary data are available at Bioinformatics online.
HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization
Authors: Paulsen Jonas , Sandve Geir Kjetil , Gundersen Sveinung , Lien Tonje G. , Trengereid Kai , Hovig Eivind
Published: February 2014

Summary: Recently developed methods that couple next-generation sequencing with chromosome conformation capture-based techniques, such as Hi-C and ChIA-PET, allow for characterization of genome-wide chromatin 3D structure. Understanding the organization of chromatin in three dimensions is a crucial next step in the unraveling of global gene regulation, and methods for analyzing such data are needed. We have developed HiBrowse, a user-friendly web-tool consisting of a range of hypothesis-based and descriptive statistics, using realistic assumptions in null-models.

Availability and implementation: HiBrowse is supported by all major browsers, and is freely available at http://hyperbrowser.uio.no/3d. Software is implemented in Python, and source code is available for download by following instructions on the main site.

Contact:  jonaspau@ifi.uio.no

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Zola's
fin-de-siècle
Reproductive Politics
Authors: Counter Andrew J.
Published: February 2014

This article offers a synoptic reading of Émile Zola's fictional and journalistic writings from the mid-1890s to his death in 1902, considering these in light of the novelist's engagement with the Third Republic's politics of pronatalism, and with questions of reproduction more broadly. It explores Zola's particular conception of the problem of depopulation (the declining French birth rate at the end of the nineteenth century) as an aesthetic question demanding an aesthetic solution, before examining how he attempted to provide such a solution in his later fiction. The final novels are shown to be incessantly preoccupied, and at several levels, with an idealized figure of the child. The article finally considers the intolerance that Zola displayed in his last few novels towards all individuals — homosexuals, ‘new women’, priests, Catholics, decadent novelists, childless heterosexuals — whom he imagined as failing to conform to his own reproductive ideal.
La Bruyère: Virtue and Disinterestedness
Authors: Moriarty Michael
Published: February 2014

This article studies the notion of virtue put forward in La Bruyère's
Les Caractères
. La Bruyère upholds the Aristotelian notion (rejected by hard-line Augustinians of his own century) of virtue as doing good deeds for their own sake: he examines the relationship between virtue and motive, denying that virtue is present where the behaviour is subordinated to the pursuit of self-interest. The pursuit of glory, on the other hand, may be laudable if the means to that end involve acting for the common good rather than for selfish advantage. Particular stress is laid on doing good to other people, especially when this entails self-sacrifice. Friendship, too, is evaluated in respect of its freedom from self-interestedness. Disinterestedness is not simply a moral value, but a potential source of happiness and fulfilment, in that it liberates the individual from humiliating social dependence; it is also a social ideal, capable of regenerating society, by encouraging people to focus on using their talents for the good of the community rather than for seeking advancement through favour.
Dispersal of the introduced red king crab (Paralithodes camtschaticus) in Norwegian waters: a tag-recapture study
Authors: Windsland Kristin , Hvingel Carsten , Nilssen Einar M. , Sundet Jan H.
Published: February 2014

The aim of this study was to explore the effect of sex, size, region, and density on dispersal rate of the introduced red king crab (Paralithodes camtschaticus) in Norwegian waters. We examined the effect of these factors using logistic regression analysis. Tag-recapture data corrected for fishing effort enabled us to estimate dispersal rates from four main regions along the Norwegian coast: Varangerfjorden, Tanafjorden, Laksefjorden, and Porsangerfjorden. The probability of dispersal was independent of sex and size, but both the logistic regression and the evaluation of corrected tag-recapture data revealed differences in dispersal between region and with increasing duration. The recapture data indicated a relationship between population density and dispersal within research regions but not between population density and dispersal between research regions. Our main conclusion is that there are large individual differences in dispersal ability and the range expansion of red king crab is a result of (i) the presence of long-distance dispersers and (ii) time-dependent slow migration by short distance dispersers. We also conclude that there appears less dispersal in Norwegian waters than in native waters, which might be caused by differences in geographical complexity.
Active opportunist species as potential diagnostic markers for comparative tracking of complex marine ecosystem responses to global trends
Authors: Bakun Andrew
Published: February 2014

As it becomes ever clearer that on longer time scales marine ecosystems function as non-linear “complex adaptive systems”, potential consequences of global change become obscured within a maze of multiple possibilities. This essay attempts to route one pathway to a potentially more robust conceptual synthesis, employing the globally important example of anchovies and sardines as a model. Expressly, the anchovy emerges as an efficient specialist of neritic origin. In contrast, the sardine's oceanic-based adaptations equip it to deal with intermittent episodes of poorly productive conditions and to take advantage of associated reduction in predation pressure on early life stages of their offspring. Based on the overall synthesis, the nimble, wide-ranging, actively opportunistic sardine appears notably well equipped to deal with climate-related disruptions and dislocations and even to profit from their adverse effects on predators and competitors. Global-scale multispecies population synchronies in the 1970s to the mid-1980s suggest that a variety of different species types might be flagged for investigation as perhaps embodying similar “active opportunist” attributes. If so, events and anecdotes might, as global changes proceed, be viewed within a developing universal framework that could support increasingly effective transfers of experience and predictive foresight across different species groups and regional ecosystems.
Absolute proper motion of IRAS 00259+5625 with VERA: Indication of superbubble expansion motion
Authors: Sakai Nobuyuki , Sato Mayumi , Motogi Kazuhito , Nagayama Takumi , Shibata Katsunori M. , Kanaguchi Masahiro , Honma Mareki
Published: February 2014

We present the first measurement of the absolute proper motions of IRAS 00259+5625 (CB3, LBN594) associated with the H i loop called the “NGC 281 superbubble” that extends from the Galactic plane over ∼ 300 pc toward decreasing galactic latitude. The proper motion components measured with VLBI Exploration of Radio Astrometry (VERA) are (μαcos δ, μδ) = (−2.48 ± 0.32, −2.85 ± 0.65) mas yr−1, converted into (μlcos b, μb) = (−2.72 ± 0.32, −2.62 ± 0.65) mas yr−1 in the Galactic coordinates. The measured proper motion perpendicular to the Galactic plane (μb) shows vertical motion away from the Galactic plane with a significance of about ∼ 4 σ. As for the source distance, the distance measured with VERA is marginal, $2.4^{+1.0}_{-0.6}$ kpc. Using the distance, an absolute vertical motion (vb) of −17.9 ± 12.2 km s−1 is determined with ∼ 1.5 σ significance. The tendency towards the large vertical motion is consistent with previous very long baseline interferometry (VLBI) results for NGC 281 associated with the same superbubble. Thus, our VLBI results indicate superbubble expansion motion whose origin is believed to be sequential supernova explosions.
The effect of the broad-line region with geometrical structures on gamma-ray absorption in blazars
Authors: Lei Maichang , Wang Jiancheng
Published: February 2014

The broad-line region (BLR) is an important component of blazars, especially for flat spectrum radio quasars. The soft photons arising from the BLR will substantially affect the transparency of the γ-ray photons produced in the relativistic jet. We study the effect of the geometrical structure of the BLR on the absorption of γ-rays. We find that the γ-ray optical depth strongly depends on the geometrical structure of the BLR. For a “flat” BLR geometry, γ-ray photons with specified energies could escape transparently even if their emission region is located inside the cavity of the BLR.
Photon surfing and magic speed revisited: Translucent effect
Authors: Fukue Jun
Published: February 2014

Under the radiative environment of the intense radiation field around active phenomena such as black hole accretion disks, gaseous particles receive a strong radiative flux, which accelerates them, while they suffer from radiation drag by aberrated photons, which decelerates them. As a result, the acceleration of gaseous particles—photon surfing—would terminate at some magical speed βm(=v/c); (4-√7)/3 ∼ 0.45 for acceleration above an infinite flat radiator (Icke 1989, A&A, 216, 294). In a realistic gaseous cloud, part of the radiation would be absorbed by the cloud, some would be reflected, and some transmitted. We examine these translucent effects for a geometrically thin gaseous cloud (stratus). When the optical depth of the stratus is sufficiently large, the terminal speed is the well known magical speed βm for a particle. When the optical depth is around or less than unity, on the other hand, the terminal magical speed becomes large, up to ∼ 0.7c. This is just the translucent effect; the aberrated photons from the top of the stratus transmit the stratus much more than the direct photons from the bottom of the stratus facing the source.
What’s Wrong With Factory Farming?
Authors: Anomaly Jonathan
Published: February 2014

Factory farming continues to grow around the world as a low-cost way of producing animal products for human consumption. However, many of the practices associated with intensive animal farming have been criticized by public health professionals and animal welfare advocates. The aim of this essay is to raise three independent moral concerns with factory farming, and to explain why the practices associated with factory farming flourish despite the cruelty inflicted on animals and the public health risks imposed on people. I conclude that the costs of factory farming as it is currently practiced far outweigh the benefits, and offer a few suggestions for how to improve the situation for animals and people.
Role of anoctamins in cancer and apoptosis
Authors: Wanitchakool Podchanart , Wolf Luisa , Koehl Gudrun E. , Sirianant Lalida , Schreiber Rainer , Kulkarni Sucheta , Duvvuri Umamaheswar , Kunzelmann Karl
Published: February 2014

Anoctamin 1 (TMEM16A, Ano1) is a recently identified Ca
2+
-activated chloride channel and a member of a large protein family comprising 10 paralogues. Before Ano1 was identified as a chloride channel protein, it was known as the cancer marker DOG1. DOG1/Ano1 is expressed in gastrointestinal stromal tumours (GIST) and particularly in head and neck squamous cell carcinoma, at very high levels never detected in other tissues. It is now emerging that Ano1 is part of the 11q13 locus, amplified in several types of tumour, where it is thought to augment cell proliferation, cell migration and metastasis. Notably, Ano1 is upregulated through histone deacetylase (HDAC), corresponding to the known role of HDAC in HNSCC. As Ano1 does not enhance proliferation in every cell type, its function is perhaps modulated by cell-specific factors, or by the abundance of other anoctamins. Thus Ano6, by regulating Ca
2+
-induced membrane phospholipid scrambling and annexin V binding, supports cellular apoptosis rather than proliferation. Current findings implicate other cellular functions of anoctamins, apart from their role as Ca
2+
-activated Cl
−
channels.
Ion channels and transporters in the development of drug resistance in cancer cells
Authors: Hoffmann Else K. , Lambert Ian H.
Published: February 2014

Multi-drug resistance (MDR) to chemotherapy is the major challenge in the treatment of cancer. MDR can develop by numerous mechanisms including decreased drug uptake, increased drug efflux and the failure to undergo drug-induced apoptosis. Evasion of drug-induced apoptosis through modulation of ion transporters is the main focus of this paper and we demonstrate how pro-apoptotic ion channels are downregulated, while anti-apoptotic ion transporters are upregulated in MDR. We also discuss whether upregulation of ion transport proteins that are important for proliferation contribute to MDR. Finally, we discuss the possibility that the development of MDR involves sequential and localized upregulation of ion channels involved in proliferation and migration and a concomitant global and persistent downregulation of ion channels involved in apoptosis.
Luteimicrobium xylanilyticum sp. nov., isolated from the gut of a long-horned beetle, Massicus raddei
Authors: Kim Hyangmi , Oh Hyun-Woo , Kim Ji-Ae , Park Doo-Sang , Park Hee-Moon , Bae Kyung Sook
Published: February 2014

A novel strain, designated W-15T, was isolated from the gut of a long-horned beetle, Massicus raddei, collected in South Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strains belonged to the suborder

Micrococcineae

. Strain W-15T was most closely related to

Luteimicrobium album

RI148-Li105T (97.9 % similarity). Strain W-15T was Gram-stain-positive, rod- and coccus-shaped and non-motile. Growth was observed at 15–37 °C, at pH 4.5–8.5 and in the presence of 0–5.0 % NaCl. The cell-wall peptidoglycan of the strain was A4α (l-Lys–d-Ser–d-Asp). The major menaquinone present in this strain was MK-8 (H2) and the major cellular fatty acids were anteiso-C15 : 0, iso-C16 : 0, iso-C15 : 0 and anteiso-C17 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylinositol, an unknown lipid, an unknown phospholipid and an unknown phosphoglycolipid. The G+C content of genomic DNA of the strain was 73.8 mol%. On the basis of evidence from our polyphasic taxonomic study, strain W-15T is classified as representing a novel species in the suborder

Micrococcineae

, for which the name Luteimicrobium xylanilyticum sp. nov. is proposed. The type strain of this species is strain W-15T ( = KCTC 19882T = JCM 18090T).
Nocardia sungurluensis sp. nov., isolated from soil
Authors: Camas Mustafa , Veyisoglu Aysel , Sahin Nevzat
Published: February 2014

A novel Gram-reaction-positive, rod-shaped, non-motile and mycolic acid-containing strain, CR3272T, isolated from soil, was studied using a polyphasic approach. The organism showed a combination of chemotaxonomic and morphological properties typical of the genus

Nocardia

. The cell wall contained meso-diaminopimelic acid (type IV) and whole-cell sugars were galactose, glucose, arabinose and xylose. The predominant menaquinone was MK-8(H4cyc). The major phospholipids were diphosphatidylglycerol and phosphatidylinositol mannosides. Major fatty acids were C16 : 0, C18 : 1
cis9, C18 : 0 10-methyl (TBSA) and C16 : 1
cis9. The novel strain formed distinct phyletic line in the

Nocardia

16S rRNA gene tree and was closely associated with

Nocardia goodfellowii

A2012T (98.6 % 16S rRNA gene sequence similarity),

Nocardia alba

YIM 30243T (98.5 %) and

Nocardia caishijiensis

F829T (97.9 %). However, DNA–DNA relatedness values and phenotypic data demonstrated that strain CR3272T was clearly distinguished from all closely related species of the genus

Nocardia

. It is concluded that the organism be classified as representing a novel species of the genus

Nocardia

, for which the name Nocardia sungurluensis is proposed. The type strain is CR3272T ( = DSM 45714T = KCTC 29094T).
Halomonas songnenensis sp. nov., a moderately halophilic bacterium isolated from saline and alkaline soils
Authors: Jiang Juquan , Pan Yuanyuan , Hu Shaoxin , Zhang Xiaoxia , Hu Baozhong , Huang Haipeng , Hong Shan , Meng Jing , Li Cheng , Wang Kaibiao
Published: February 2014

A moderately halophilic bacterium (strain NEAU-ST10-39T) was isolated from saline and alkaline soils in the oilfield of Daqing City, Heilongjiang Province, China. The strain was strictly aerobic, Gram-stain-negative, rod-shaped and motile by peritrichous flagella. Its colonies were yellow. It grew at NaCl concentrations of 0.2–15 % (w/v) (optimum 4 %, w/v), at temperatures of 4–40 °C (optimum 35 °C) and at pH 5–10 (optimum pH 7). It did not produce acids from sugars or alcohols. Its DNA G+C content was 57.4 mol%. Phylogenetic analyses based on 16S rRNA gene sequences and concatenated 16S rRNA, gyrB and rpoD gene sequences indicated that it belonged to the genus

Halomonas

in the class

Gammaproteobacteria

. The most phylogenetically related species were

Halomonas axialensis

,

Halomonas meridiana

and

Halomonas aquamarina

, whose types shared 98.3 % (16S rRNA), 82.7 % (gyrB) and 83.9–84.5 % (rpoD) sequence similarity with strain NEAU-ST10-39T. The results of DNA–DNA hybridization assays showed 20±2 %–50±1 % relatedness between strain NEAU-ST10-39T and the most closely related species including

Halomonas axialensis

DSM 15723T,

Halomonas meridiana

DSM 5425T,

Halomonas aquamarina

DSM 30161T,

Halomonas johnsoniae

DSM 21197T,

Halomonas stevensii

DSM 21198T,

Halomonas nanhaiensis

CCTCC AB 2012911T,

Halomonas hamiltonii

DSM 21196T and

Halomonas arcis

CGMCC 1.6494T. The major fatty acids were C18 : 1ω7c (47.2 %), C16 : 1ω7c and/or C16 : 1ω6c (18.9 %) and C16 : 0 (16.3 %), the only respiratory quinone detected was ubiquinone 9 and polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unknown phospholipids and three unknown lipids. The new isolate is proposed to represent a novel species with the name Halomonas songnenensis sp. nov., NEAU-ST10-39T ( = CGMCC 1.12152T = DSM 25870T) being the type strain.
Saccharopolyspora indica sp. nov., an actinomycete isolated from the rhizosphere of Callistemon citrinus (Curtis)
Authors: Vaddavalli Radha , Peddi Sneha , Kothagauni Srilekha Yadav , Begum Zareena , Gaddam Bhagyanarayana , Periketi Madhusudhanachary , Linga Venkateswar Rao
Published: February 2014

A novel actinomycete strain, designated VRC122T, was isolated from a Callistemon citrinus rhizosphere sample collected from New Delhi, India, and its taxonomic status was determined by using a polyphasic approach. Strain VRC122T was a Gram-stain-positive, aerobic, non-motile, non-acid–alcohol-fast strain. Phylogenetic analysis based on 16S rRNA gene sequences showed the strain was placed in a well-separated sub-branch within the genus

Saccharopolyspora

. The highest levels of 16S rRNA gene sequence similarity were found with

Saccharopolyspora hirsuta subsp. kobensis

JCM 9109T (98.71 %),

Saccharopolyspora antimicrobica

I05-00074T (98.69 %) and

Saccharopolyspora jiangxiensis

W12T (98.66 %); 16S rRNA gene sequence similarities with type strains of all other species of the genus

Saccharopolyspora

were below 98 %. Chemosystematic studies revealed that it contained meso-diaminopimelic acid. Arabinose and galactose were the predominant whole-cell sugars. Diagnostic polar lipids were diphosphatidylglycerol, phosphatidylinositol and phosphatidylcholine. MK-9(H6) was the predominant menaquinone. C14 : 0, C16 : 0, iso-C15 : 0, iso-C16 : 0, iso-C17 : 0, anteiso-C15 : 0, anteiso-C17 : 0, C17 : 0 cyclo and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) were the major cellular fatty acids. The G+C content of the genomic DNA was 69.5 mol%. The results of DNA–DNA hybridization (30 %, 22 % and 25 %, respectively) with type strains of the above-mentioned species, in combination with differences in physiological and biochemical data supported that strain VRC122T represents a novel species of the genus

Saccharopolyspora

, for which the name Saccharopolyspora indica sp. nov., is proposed. The type strain is VRC122T ( = KCTC 29208T = MTCC 11564T = MCC 2206T = ATCC BAA-2551T).
Canibacter oris gen. nov., sp. nov., isolated from an infected human wound
Authors: Aravena-Román M. , Inglis T. J. J. , Siering C. , Schumann P. , Yassin A. F.
Published: February 2014

A facultatively anaerobic, Gram-reaction-positive, catalase- and oxidase-negative, rod-shaped bacterium isolated from an infected human wound caused by a dog bite was characterized by phenotypic and molecular genetic methods. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain IMMIB Q2029717T was a member of the order

Micrococcales

of the class

Actinobacteria

, displaying 91.6 % to 96 % sequence similarity with members of the family

Microbacteriaceae

. Phylogentic trees generated by different algorithms indicated that the strain forms an independent phylogenetic line of descent that consistently clustered proximal to the base of the genus

Leucobacter

. Chemical studies revealed the presence of a cell-wall murein based on l-lysine (type B1α), major menaquinone (MK-10) and a DNA G+C content of 56.9 mol%. The distinct phylogenetic position, ribotyping and matrix-assisted laser desorption/ionization time-of-flight MS profiles and the significant phenotypic differences clearly separate strain IMMIB Q2029717T from its nearest phylogenetic neighbour and support its classification as a representative of a novel genus and species, with the suggested name Canibacter oris gen. nov., sp. nov. The type strain is IMMIB Q2029717T ( = DSM 27064T = CCUG 64069T).
Polaribacter atrinae sp. nov., isolated from the intestine of a comb pen shell, Atrina pectinata
Authors: Hyun Dong-Wook , Shin Na-Ri , Kim Min-Soo , Kim Pil Soo , Jung Mi-Ja , Kim Joon Yong , Whon Tae Woong , Bae Jin-Woo
Published: February 2014

A novel Gram-staining-negative, aerobic, non-motile, yellow-to-orange carotenoid-type-pigmented and rod-shaped bacterium, designated strain WP25T, was isolated from the intestine of a comb pen shell, Atrina pectinata, which was collected from the South Sea near Yeosu in Korea. The isolate grew optimally at 20 °C, at pH 7 and with 2 % (w/v) NaCl. 16S rRNA gene sequence analysis showed that strain WP25T belonged to the genus

Polaribacter

in the family

Flavobacteriaceae

and the highest sequence similarity was shared with the type strain of

Polaribacter sejongensis

(98.5 %). The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, C15 : 1ω6c and iso-C15 : 0 3-OH. The main respiratory quinone was menaquinone MK-6. The polar lipids of strain WP25T were phosphatidylethanolamine, two unidentified aminolipids, an unidentified phospholipid and four unidentified lipids. The genomic DNA G+C content was 31.2 mol%. DNA–DNA hybridization experiments indicated <12.6 % genomic relatedness with closely related strains. Based on phylogenetic, phenotypic and genotypic analyses, strain WP25T represents a novel species in the genus

Polaribacter

, for which the name

Polaribacter

atrinae sp. nov. is proposed, with the type strain WP25T ( = KACC 17473T = JCM 19202T).
Novel two-component regulatory systems play a role in biofilm formation of Lactobacillus reuteri rodent isolate 100-23
Authors: Su Marcia Shu-Wei , Gänzle Michael G.
Published: February 2014

This study characterized the two-component regulatory systems encoded by bfrKRT and cemAKR, and assessed their influence on biofilm formation by Lactobacillus reuteri 100-23. A method for deletion of multiple genes was employed to disrupt the genetic loci of two-component systems. The operons bfrKRT and cemAKR showed complementary organization. Genes bfrKRT encode a histidine kinase, a response regulator and an ATP-binding cassette-type transporter with a bacteriocin-processing peptidase domain, respectively. Genes cemAKR code for a signal peptide, a histidine kinase and a response regulator, respectively. Deletion of single or multiple genes in the operons bfrKRT and cemAKR did not affect cell morphology, growth or the sensitivity to various stressors. However, gene disruption affected biofilm formation; this effect was dependent on the carbon source. Deletion of bfrK or cemA increased sucrose-dependent biofilm formation in vitro. Glucose-dependent biofilm formation was particularly increased by deletion of cemK. The expression of cemK and cemR was altered by deletion of bfrK, indicating cross-talk between these two regulatory systems. These results may contribute to our understanding of the genetic factors related to the biofilm formation and competitiveness of L. reuteri in intestinal ecosystems.
Morphological and metabolic shifts of Yarrowia lipolytica induced by alteration of the dissolved oxygen concentration in the growth environment
Authors: Bellou Stamatia , Makri Anna , Triantaphyllidou Irene-Eva , Papanikolaou Seraphim , Aggelis George
Published: February 2014

Yarrowia lipolytica, an ascomycete with biotechnological potential, is able to form either yeast cells or hyphae and pseudohyphae in response to environmental conditions. This study shows that the morphology ofY. lipolytica, cultivated in batch cultures on hydrophilic (glucose and glycerol) and hydrophobic (olive oil) media, was not affected by the nature of the carbon source, nor by the nature or the concentration of the nitrogen source. By contrast, dissolved oxygen concentration (DOC) should be considered as the major factor affecting yeast morphology. Specifically, when growth occurred at low or zero DOC the mycelial and/or pseudomycelial forms predominated over the yeast form independently of the carbon and nitrogen sources used. Experimental data obtained from a continuous culture ofY. lipolyticaon glycerol, being used as carbon and energy source, demonstrated that the mycelium-to-yeast form transition occurs when DOC increases from 0.1 to 1.5 mg l−1. DOC also affected the yeast physiology, as the activity of enzymes implicated in lipid biosynthesis (i.e. ATP-citrate lyase, malic enzyme) was upregulated at high DOC whereas the activity of enzymes implicated in glycerol assimilation (such as glycerol dehydrogenase and kinase) remained fundamentally unaffected in the cell-free extract.
β-Phosphoglucomutase contributes to aciduricity in Streptococcus mutans
Authors: Buckley Andrew A. , Faustoferri Roberta C. , Quivey Robert G.
Published: February 2014

Streptococcus mutansencounters an array of sugar moieties within the oral cavity due to a varied human diet. One such sugar is β-d-glucose 1-phosphate (βDG1P), which must be converted to glucose 6-phosphate (G6P) before further metabolism to lactic acid. The conversion of βDG1P to G6P is mediated by β-phosphoglucomutase, which has not been previously observed in any oral streptococci, but has been extensively characterized and the gene designatedpgmBinLactococcus lactis. An orthologue was identified inS. mutans, SMU.1747c, and deletion of the gene resulted in the inability of the deletion strain to convert βDG1P to G6P, indicating that SMU.1747c is a β-phosphoglucomutase and should be designatedpgmB. In this study, we sought to characterize how deletion ofpgmBaffected known virulence factors ofS. mutans, specifically acid tolerance. The ΔpgmBstrain showed a decreased ability to survive acid challenge. Additionally, the strain lacking β-phosphoglucomutase had a diminished glycolytic profile compared with the parental strain. Deletion ofpgmBhad a negative impact on the virulence ofS. mutansin theGalleria mellonella(greater wax worm) animal model. Our results indicate thatpgmBplays a role at the juncture of carbohydrate metabolism and virulence.
Phosphorylation of human immunodeficiency virus type 1 capsid protein at serine 16, required for peptidyl-prolyl isomerase-dependent uncoating, is mediated by virion-incorporated extracellular signal-regulated kinase 2
Authors: Dochi Takeo , Nakano Takashi , Inoue Mutsumi , Takamune Nobutoki , Shoji Shozo , Sano Kouichi , Misumi Shogo
Published: February 2014

We reported previously that Pin1 facilitates human immunodeficiency virus type 1 (HIV-1) uncoating by interacting with the capsid core through the phosphorylated Ser16-Pro17 motif. However, the specific kinase responsible for Ser16 phosphorylation has remained unknown. Here, we showed that virion-associated extracellular signal-regulated kinase 2 (ERK2) phosphorylates Ser16. The characterization of immature virions produced by exposing chronically HIV-1LAV-1-infected CEM/LAV-1 cells to 10 µM saquinavir indicated that Ser16 is phosphorylated after the initiation of Pr55Gag processing. Furthermore, a mass spectrometry-based in vitro kinase assay demonstrated that ERK2 specifically phosphorylated the Ser16 residue in the Ser16-Pro17 motif-containing substrate. The treatment of CEM/LAV-1 cells with the ERK2 inhibitor sc-222229 decreased the Ser16 phosphorylation level inside virions, and virus partially defective in Ser16 phosphorylation showed impaired reverse transcription and attenuated replication owing to attenuated Pin1-dependent uncoating. Furthermore, the suppression of ERK2 expression by RNA interference in CEM/LAV-1 cells resulted in suppressed ERK2 packaging inside virions and decreased the Ser16 phosphorylation level inside virions. Interestingly, the ERK2-packaging-defective virus showed impaired reverse transcription and attenuated HIV-1 replication. Taken together, these findings provide insights into the as-yet-obscure processes in Pin1-dependent HIV-1 uncoating.
Automated ensemble assembly and validation of microbial genomes
Authors: Koren Sergey , Treangen Todd J. , Hill Christopher M. , Pop Mihai , Phillippy Adam M.
Published: February 2014

Background

The continued democratization of DNA sequencing has sparked a new wave of development of genome assembly and assembly validation methods. As individual research labs, rather than centralized centers, begin to sequence the majority of new genomes, it is important to establish best practices for genome assembly. However, recent evaluations such as GAGE and the Assemblathon have concluded that there is no single best approach to genome assembly. Instead, it is preferable to generate multiple assemblies and validate them to determine which is most useful for the desired analysis; this is a labor-intensive process that is often impossible or unfeasible.

Results

To encourage best practices supported by the community, we present iMetAMOS, an automatedensemble assembly pipeline; iMetAMOS encapsulates the process of running, validating, and selecting a single assembly from multiple assemblies. iMetAMOS packages several leading open-source tools into a single binary that automates parameter selection and execution of multiple assemblers, scores the resulting assemblies based on multiple validation metrics, and annotates the assemblies for genes and contaminants. We demonstrate the utility of the ensemble process on 225 previously unassembledMycobacterium tuberculosisgenomes as well as aRhodobacter sphaeroidesbenchmark dataset. On these real data, iMetAMOS reliably produces validated assemblies and identifies potential contamination without user intervention. In addition, intelligent parameter selection produces assemblies ofR. sphaeroidesthat exceed the quality of those from the GAGE-B evaluation, affecting the relative ranking of some assemblers.

Conclusions

Ensemble assembly with iMetAMOS provides users with multiple, validated assemblies for each genome. Although computationally limited to small or mid-sized genomes, this approach is the most effective and reproducible means for generating high-quality assemblies and enables users to select an assembly best tailored to their specific needs.
Epistasis within the MHC contributes to the genetic architecture of celiac disease
Authors: Goudey Benjamin , Abraham Gad , Kikianty Eder , Wang Qiao , Rawlinson Dave , Shi Fan , Haviv Izhak , Stern Linda , Kowalczyk Adam , Inouye Michael
Published: February 2014

Epistasis has long been thought to contribute to the genetic aetiology of complex diseases, yet few robust epistatic interactions in humans have been detected. We have conducted exhaustive genome-wide scans for pairwise epistasis in five independent celiac disease (CD) case-control studies, using a rapid model-free approach to examine over 500 billion SNP pairs in total. We found 20 significant epistatic signals within the HLA region which achieved stringent replication criteria across multiple studies and were independent of known CD risk HLA haplotypes. The strongest independent CD epistatic signal corresponded to genes in the HLA class III region, in particularPRRC2AandGPANK1/C6orf47,which are known to contain variants for non-Hodgkin’s lymphoma and early menopause, co-morbidities of celiac disease. Replicable evidence for epistatic variants outside the MHC was not observed. Both within and between European populations, we observed striking consistency of epistatic models and epistatic model distribution. Within the UK population, models of CD based on both epistatic and additive single-SNP effects increased explained CD variance by approximately 1% over those of single SNPs. Models of only epistatic pairs or additive single-SNPs showed similar levels of CD variance explained, indicating the existence of a substantial overlap of additive and epistatic components. Our findings have implications for the determination of genetic architecture and, by extension, the use of human genetics for validation of therapeutic targets.
Analysis of Complementarity Requirements for Plant MicroRNA Targeting Using a Nicotiana benthamiana Quantitative Transient Assay
Authors: Liu Qikun , Wang Feng , Axtell Michael J.
Published: February 2014

MicroRNAs (miRNAs) guide RNA-induced silencing complexes to target RNAs based on miRNA-target complementarity. Using a dual-luciferase based sensor system in Nicotiana benthamiana, we quantitatively assessed the relationship between miRNA-target complementarity and silencing efficacy measured at both the RNA and protein levels, using several conserved miRNAs and their known target sites from Arabidopsis thaliana. We found that naturally occurring sites have variable efficacies attributable to their complementarity patterns. We also observed that sites with a few mismatches to the miRNA 3′ regions, which are common in plants, are often equally effective and sometimes more effective than perfectly matched sites. By contrast, mismatches to the miRNA 5′ regions strongly reduce or eliminate repression efficacy but are nonetheless present in several natural sites, suggesting that in some cases, suboptimal miRNA efficacies are either tolerated or perhaps selected for. Central mismatches fully abolished repression efficacy in our system, but such sites then became effective miRNA target mimics. Complementarity patterns that are functional in animals (seed sites, 3′-supplementary sites, and centered sites) did not reliably confer repression, regardless of context (3′-untranslated region or open reading frame) or measurement type (RNA or protein levels). Overall, these data provide a robust and empirical foundation for understanding, predicting, and designing functional miRNA target sites in plants.
Crisis communication and terrorism: the Norway attacks on 22 July 2011
Authors: Falkheimer Jesper
Published: February 2014

Purpose

– The aim of this paper is two-fold: to describe and to consider the implications of the synthesis between terrorism, the media and strategic communication, using the Norway attacks as an example; and to describe and analyze the challenges and execution of crisis communication during and after the Norwegian attacks.

Design/methodology/approach

– The article is based on earlier research and secondary data (an extensive assessment made by the Norwegian police authority in 2012), as well as a minor media analysis focusing on representation of the perpetrator. An interview with two high-ranking communication officials working for the crisis management coordination secretariat in Norway has served as supplementary material.

Findings

– The crisis challenged the linear process of standard planning and information transmission. The terrorist attacks in Norway and how they were framed, especially before the perpetrator was identified, are linked to a global discourse on terrorists, and demonstrate the need for developing specific terrorism crisis communication theory. The news media coverage gave the perpetrator and his political messages publicity, but more as a lone disturbed individual, associated with school shootings more than with terrorism. There is a need for increased knowledge about terrorism as strategic communication or public relations. The variety among stakeholders and the increased possibilities for terrorists to control and plan their communications in have implications during all phases of a crisis. New strategies and tactics that oppose and defeat the terrorist's communication goals must be developed.

Originality/value

– The article views terrorism from a communication perspective and develops important questions about the relationship between terrorism, media, strategic communication and crisis communication.
Internal communication for employee enablement
Authors: Mazzei Alessandra
Published: February 2014

Purpose

– This paper aims to understand if, and how, internal communication strategies can promote strategic employee communicative actions such as to disseminate positive information that enhances the company's reputation. These communicative actions sustain the competitive advantage of a company.

Design/methodology/approach

– This paper is based on interviews with internal communication experts; internal communication managers in ten American and 22 Italian companies. Three focus groups in Italy comprised of internal communication managers, scholars and experts.

Findings

– Employee communicative actions have been categorized into: exploration, interpretation, sharing and acting. Internal communication strategies enable employees to be effective communicators.

Research limitations/implications

– A survey among employees was used to investigate the link between employee communicative actions and internal communication and relationship quality.

Practical implications

– Internal communication managers are expected first, to become enablers towards employees and line managers; and second, to facilitate sense-making processes and the quality relationship building.

Originality/value

– This article provides empirical evidence of the emerging issues of employee communicative actions and the enablement function of internal communication. It adds a broader and validated range of employee communicative actions to those that had previously been studied, and develops a preliminary inventory of enablement strategies that have been adopted by leading companies.
Organizational blogging: a case study of a corporate weblog from an employee perspective
Authors: Agerdal-Hjermind Annette
Published: February 2014

Purpose

– The aim of this paper is to address and discuss usage and implications of a weblog in a corporate communication context from an employees' perspective.

Design/methodology/approach

– The paper is a case study of a government agency's corporate blogging activity, traced through focus group interviews with the organizational bloggers and analyzed using situational analysis and thematic network analysis.

Findings

– The study problematizes the predominant focus on the promises of interactivity and dialogue as a repeated positive motivation for corporate bloggers by shedding a light on blogging as experienced from inside an organization. The study shows that employee bloggers use the blog platform in a varied way and do not agree internally on the appropriate corporate blog usage. Four main positions that encapsulate the variation in blog usage – the official, the debater, the engineer and the passionate blogger – are identified, and the implications (opportunities and barriers) of blogging for the blogging employees' behavior and motivation are unfolded and discussed.

Practical implications

– The findings are useful for managers to get insight into the challenges, barriers and opportunities, which employees experience when acting as bloggers on behalf of an organization, as well as when acting on other transparent Web 2.0 mediated communications platforms for corporate purposes. The findings also indicate and give recommendations to the internal resources required to support the employees when letting them out into the blogosphere.

Originality/value

– The paper provides a documented, nuanced and deep insight and understanding into blog usage in a corporate context from the perspective of the employee bloggers. This insight is as critical to our understanding of blogging and social media in a corporate context, as it is to our understanding of transparent and participatory organizational culture.
International mediation as a distinct form of conflict management
Authors: Vukovic Sinisa
Published: February 2014

Purpose

– This paper aims to provide a structured overview of the most important research conducted in the field of international mediation. Although there are still strong similarities between the processes of international and domestic mediation, lack of a clear structure on the international level suggests that international mediation activities could be separately academically scrutinized. This literature review is aimed at illustrating the unique nature of international mediation.

Design/methodology/approach

– Various factors that affect the overall process and the outcome of international mediation efforts were clustered in four distinct yet interrelated groups. The first section illustrates various mediators' characteristics that might induce the disputants to accept mediation and agree to specific terms that were mediated in the process. In the second section two distinct factors affecting the mediation outcome were explained: contextual and behavioral. Finally, in the third sections various types of mediators were discussed.

Findings

– The article shows the intricate complexities of international mediation, highlighting four distinct features that might have an effect on the mediation outcome: mediator's characteristics, contextual features, behavioral factors, and types of mediators.

Originality/value

– This article attempts to offer a comprehensive overview of the current state of the art in international mediation, and suggests potential areas of future research.
A current literature review of international mediation
Authors: Duursma Allard
Published: February 2014

Purpose

– A rapidly expanding body of literature on international mediation, as well as the central role international mediation plays in modern-day conflict resolution, make it necessary to review and analyze this vastly evolving field of study. This study seeks to review the most significant trends and debates in the literature on international mediation, with an emphasis on the literature of the past six years.

Design/methodology/approach

– Reflecting Wallet al.'s staged conceptualization of the mediation process; this review essay is divided in three sections that cover the antecedents of mediation, possible mediation approaches, and the outcomes these approaches yield – making it possible to review and analyze the diverse sets of theories within the field of mediation, as well the various methodological approaches employed to test these theories.

Findings

– Much research to date has focused on how international mediation in armed conflicts affects the likelihood of reaching a negotiated agreement, while other possible outcomes of mediation have been understudied. Accordingly, research needs to be done on the effects of mediation attempts that did not lead to a peace agreement, as well as the accumulative effect of peace agreements. Furthermore, the relation between negative peace and mediation has been studied extensively, but how mediation affects the degree of positive peace has received scant scholarly attention. Finally, the interlinkages between the different phases of the mediation process need to be examined more extensively.

Originality/value

– This review identifies the state of the art knowledge concerning the international mediation process, which allows peacemakers to make informed decisions in order to prevent and resolve armed conflict in the twenty-first century.