bluuebunny/crossref_metadata_2025 huggingface dataset:
β
-
catenin is central to
DUX4
-driven network rewiring in facioscapulohumeral muscular dystrophy
Authors: Banerji Christopher R. S. , Knopp Paul , Moyle Louise A. , Severini Simone , Orrell Richard W. , Teschendorff Andrew E. , Zammit Peter S.
Published: November 2014

Facioscapulohumeral muscular dystrophy (FSHD) is an incurable disease, characterized by skeletal muscle weakness and wasting. Genetically, FSHD is characterized by contraction or hypomethylation of repeat D4Z4 units on chromosome 4, which causes aberrant expression of the transcription factor
DUX4
from the last repeat. Many genes have been implicated in FSHD pathophysiology, but an integrated molecular model is currently lacking. We developed a novel differential network methodology, Interactome Sparsification and Rewiring (
InSpiRe
), which detects network rewiring between phenotypes by integrating gene expression data with known protein interactions. Using
InSpiRe
, we performed a meta-analysis of multiple microarray datasets from FSHD muscle biopsies, then removed secondary rewiring using non-FSHD datasets, to construct a unified network of rewired interactions. Our analysis identified β-catenin as the main coordinator of FSHD-associated protein interaction signalling, with pathways including canonical Wnt, HIF1-α and TNF-α clearly perturbed. To detect transcriptional changes directly elicited by
DUX4
, gene expression profiling was performed using microarrays on murine myoblasts. This revealed that
DUX4
significantly modified expression of the genes in our FSHD network. Furthermore, we experimentally confirmed that Wnt/β-catenin signalling is affected by
DUX4
in murine myoblasts. Thus, we provide the first unified molecular map of FSHD signalling, capable of uncovering pathomechanisms and guiding therapeutic development.
Toughening mechanisms in bioinspired multilayered materials
Authors: Askarinejad Sina , Rahbar Nima
Published: November 2014

Outstanding mechanical properties of biological multilayered materials are strongly influenced by nanoscale features in their structure. In this study, mechanical behaviour and toughening mechanisms of abalone nacre-inspired multilayered materials are explored. In nacre's structure, the organic matrix, pillars and the roughness of the aragonite platelets play important roles in its overall mechanical performance. A micromechanical model for multilayered biological materials is proposed to simulate their mechanical deformation and toughening mechanisms. The fundamental hypothesis of the model is the inclusion of nanoscale pillars with near theoretical strength (
σ
th
~
E
/30). It is also assumed that pillars and asperities confine the organic matrix to the proximity of the platelets, and, hence, increase their stiffness, since it has been previously shown that the organic matrix behaves more stiffly in the proximity of mineral platelets. The modelling results are in excellent agreement with the available experimental data for abalone nacre. The results demonstrate that the aragonite platelets, pillars and organic matrix synergistically affect the stiffness of nacre, and the pillars significantly contribute to the mechanical performance of nacre. It is also shown that the roughness induced interactions between the organic matrix and aragonite platelet, represented in the model by asperity elements, play a key role in strength and toughness of abalone nacre. The highly nonlinear behaviour of the proposed multilayered material is the result of distributed deformation in the nacre-like structure due to the existence of nano-asperities and nanopillars with near theoretical strength. Finally, tensile toughness is studied as a function of the components in the microstructure of nacre.
Preventing Alzheimer's disease by means of natural selection
Authors: Demetrius Lloyd A. , Driver Jane A.
Published: November 2014

The amyloid cascade model for the origin of sporadic forms of Alzheimer's disease (AD) posits that the imbalance in the production and clearance of beta-amyloid is a necessary condition for the disease. A competing theory called the entropic selection hypothesis asserts that the primary cause of sporadic AD is age-induced mitochondrial dysregulation and the following cascade of events: (i) metabolic reprogramming—the upregulation of oxidative phosphorylation in compensation for insufficient energy production in neurons, (ii) natural selection—competition between intact and reprogrammed neurons for energy substrates and (iii) propagation—the spread of the disease due to the selective advantage of neurons with upregulated metabolism. Experimental studies to evaluate the predictions of the amyloid cascade model are being continually retuned to accommodate conflicts of the predictions with empirical data. Clinical trials of treatments for AD based on anti-amyloid therapy have been unsuccessful. We contend that these anomalies and failures stem from a fundamental deficit of the amyloid hypothesis: the model derives from a nuclear-genomic perspective of sporadic AD and discounts the bioenergetic processes that characterize the progression of most age-related disorders. In this article, we review the anomalies of the amyloid model and the theoretical and empirical support for the entropic selection theory. We also discuss the new therapeutic strategies based on natural selection which the model proposes.
A novel dysregulated pathway-identification analysis based on global influence of within-pathway effects and crosstalk between pathways
Authors: Han Junwei , Li Chunquan , Yang Haixiu , Xu Yanjun , Zhang Chunlong , Ma Jiquan , Shi Xinrui , Liu Wei , Shang Desi , Yao Qianlan , Zhang Yunpeng , Su Fei , Feng Li , Li Xia
Published: November 2014

Identifying dysregulated pathways from high-throughput experimental data in order to infer underlying biological insights is an important task. Current pathway-identification methods focus on single pathways in isolation; however, consideration of crosstalk between pathways could improve our understanding of alterations in biological states. We propose a novel method of pathway analysis based on global influence (PAGI) to identify dysregulated pathways, by considering both within-pathway effects and crosstalk between pathways. We constructed a global gene–gene network based on the relationships among genes extracted from a pathway database. We then evaluated the extent of differential expression for each gene, and mapped them to the global network. The random walk with restart algorithm was used to calculate the extent of genes affected by global influence. Finally, we used cumulative distribution functions to determine the significance values of the dysregulated pathways. We applied the PAGI method to five cancer microarray datasets, and compared our results with gene set enrichment analysis and five other methods. Based on these analyses, we demonstrated that PAGI can effectively identify dysregulated pathways associated with cancer, with strong reproducibility and robustness. We implemented PAGI using the freely available R-based and Web-based tools (http://bioinfo.hrbmu.edu.cn/PAGI).
A consistent muscle activation strategy underlies crawling and swimming inCaenorhabditis elegans
Authors: Butler Victoria J. , Branicky Robyn , Yemini Eviatar , Liewald Jana F. , Gottschalk Alexander , Kerr Rex A. , Chklovskii Dmitri B. , Schafer William R.
Published: November 2014

Although undulatory swimming is observed in many organisms, the neuromuscular basis for undulatory movement patterns is not well understood. To better understand the basis for the generation of these movement patterns, we studied muscle activity in the nematodeCaenorhabditis elegans. Caenorhabditis elegansexhibits a range of locomotion patterns: in low viscosity fluids the undulation has a wavelength longer than the body and propagates rapidly, while in high viscosity fluids or on agar media the undulatory waves are shorter and slower. Theoretical treatment of observed behaviour has suggested a large change in force–posture relationships at different viscosities, but analysis of bend propagation suggests that short-range proprioceptive feedback is used to control and generate body bends. How muscles could be activated in a way consistent with both these results is unclear. We therefore combined automated worm tracking with calcium imaging to determine muscle activation strategy in a variety of external substrates. Remarkably, we observed that across locomotion patterns spanning a threefold change in wavelength, peak muscle activation occurs approximately 45° (1/8th of a cycle) ahead of peak midline curvature. Although the location of peak force is predicted to vary widely, the activation pattern is consistent with required force in a model incorporating putative length- and velocity-dependence of muscle strength. Furthermore, a linear combination of local curvature and velocity can match the pattern of activation. This suggests that proprioception can enable the worm to swim effectively while working within the limitations of muscle biomechanics and neural control.
Robust and precise morphogen-mediated patterning: trade-offs, constraints and mechanisms
Authors: Lo Wing-Cheong , Zhou Shaohua , Wan Frederic Y.-M. , Lander Arthur D. , Nie Qing
Published: November 2014

The patterning of many developing tissues is organized by morphogens. Genetic and environmental perturbations of gene expression, protein synthesis and ligand binding are among the sources of unreliability that limit the accuracy and precision of morphogen-mediated patterning. While it has been found that the robustness of morphogen gradients to the perturbation of morphogen synthesis can be enhanced by particular mechanisms, how such mechanisms affect robustness to other perturbations, such as to receptor synthesis for the same morphogen, has been little explored. Here, we investigate the interplay between the robustness of patterning to the changes in receptor synthesis and morphogen synthesis and to the effects of cell-to-cell variability. Our analysis elucidates the trade-offs and constraints that arise as a result of achieving these three performance objectives simultaneously in the context of simple, steady-state morphogen gradients formed by diffusion and receptor-mediated uptake. Analysis of the interdependence between length scales of patterning and these performance objectives reveals several potential mechanisms for mitigating such trade-offs and constraints. One involves downregulation of receptor synthesis in the morphogen source, while another involves the presence of non-signalling cell-surface morphogen-binding molecules. Both of these mechanisms occur inDrosophilawing discs during their patterning. We computationally elucidate how these mechanisms improve the robustness and precision of morphogen-mediated patterning.
Collective action and the collaborative brain
Authors: Gavrilets Sergey
Published: November 2014

Humans are unique both in their cognitive abilities and in the extent of cooperation in large groups of unrelated individuals. How our species evolved high intelligence in spite of various costs of having a large brain is perplexing. Equally puzzling is how our ancestors managed to overcome the collective action problem and evolve strong innate preferences for cooperative behaviour. Here, I theoretically study the evolution of social-cognitive competencies as driven by selection emerging from the need to produce public goods in games against nature or in direct competition with other groups. I use collaborative ability in collective actions as a proxy for social-cognitive competencies. My results suggest that collaborative ability is more likely to evolve first by between-group conflicts and then later be utilized and improved in games against nature. If collaborative abilities remain low, the species is predicted to become genetically dimorphic with a small proportion of individuals contributing to public goods and the rest free-riding. Evolution of collaborative ability creates conditions for the subsequent evolution of collaborative communication and cultural learning.
Active regulation of longitudinal arch compression and recoil during walking and running
Authors: Kelly Luke A. , Lichtwark Glen , Cresswell Andrew G.
Published: November 2014

The longitudinal arch (LA) of the human foot compresses and recoils in response to being cyclically loaded. This has typically been considered a passive process, however, it has recently been shown that the plantar intrinsic foot muscles have the capacity to actively assist in controlling LA motion. Here we tested the hypothesis that intrinsic foot muscles, abductor hallucis (AH), flexor digitorum brevis (FDB) and quadratus plantae (QP), actively lengthen and shorten during the stance phase of gait in response to loading of the foot. Nine participants walked at 1.25 m s−1and ran at 2.78 and 3.89 m s−1on a force-instrumented treadmill while foot and ankle kinematics were recorded according to a multisegment foot model. Muscle–tendon unit (MTU) lengths, determined from the foot kinematics, and intramuscular electromyography (EMG) signals were recorded from AH, FDB and QP. Peak EMG amplitude was determined during the stance phase for each participant at each gait velocity. All muscles underwent a process of slow active lengthening during LA compression, followed by a rapid shortening as the arch recoiled during the propulsive phase. Changes in MTU length and peak EMG increased significantly with increasing gait velocity for all muscles. This is the firstin vivoevidence that the plantar intrinsic foot muscles function in parallel to the plantar aponeurosis, actively regulating the stiffness of the foot in response to the magnitude of forces encountered during locomotion. These muscles may therefore contribute to power absorption and generation at the foot, limit strain on the plantar aponeurosis and facilitate efficient foot ground force transmission.
Magnetically induced behaviour of ferritin corpuscles in avian ears: can cuticulosomes function as magnetosomes?
Authors: Jandacka Petr , Burda Hynek , Pistora Jaromir
Published: November 2014

Magnetoreception is an enigmatic, poorly understood sensory ability, described mainly on the basis of behavioural studies in animals of diverse taxa. Recently, corpuscles containing superparamagnetic iron-storage protein ferritin were found in the inner ear hair cells of birds, a predominantly single ferritin corpuscle per cell. It was suggested that these corpuscles might represent magnetosomes and function as magnetosensors. Here we determine ferritin low-field paramagnetic susceptibility to estimate its magnetically induced intracellular behaviour. Physical simulations show that ferritin corpuscles cannot be deformed or rotate in weak geomagnetic fields, and thus cannot provide magnetoreception via deformation of the cuticular plate. Furthermore, we reached an alternative hypothesis that ferritin corpuscle in avian ears may function as an intracellular electromagnetic oscillator. Such an oscillator would generate additional cellular electric potential related to normal cell conditions. Though the phenomenon seems to be weak, this effect deserves further analyses.
The ontogeny of visual–motor memory and its importance in handwriting and reading: a developing construct
Authors: Waterman Amanda H. , Havelka Jelena , Culmer Peter R. , Hill Liam J. B. , Mon-Williams Mark
Published: November 2014

Humans have evolved a remarkable ability to remember visual shapes and use these representations to generate motor activity (from Palaeolithic cave drawings through Jiahu symbols to cursive handwriting). The term visual–motor memory (VMM) describes this psychological ability, which must have conveyed an evolutionary advantage and remains critically important to humans (e.g. when learning to write). Surprisingly, little empirical investigation of this unique human ability exists—almost certainly because of the technological difficulties involved in measuring VMM. We deployed a novel technique for measuring this construct in 87 children (6–11 years old, 44 females). Children drew novel shapes presented briefly on a tablet laptop screen, drawing their responses from memory on the screen using a digitizer stylus. Sophisticated algorithms (using point-registration techniques) objectively quantified the accuracy of the children's reproductions. VMM improved with age and performance decreased with shape complexity, indicating that the measure captured meaningful developmental changes. The relationship between VMM and scores on nationally standardized writing assessments were explored with the results showing a clear relationship between these measures, even after controlling for age. Moreover, a relationship between VMM and the nationally standardized reading test was mediated via writing ability, suggesting VMM's wider importance within language development.
Calibration uncertainty in molecular dating analyses: there is no substitute for the prior evaluation of time priors
Authors: Warnock Rachel C. M. , Parham James F. , Joyce Walter G. , Lyson Tyler R. , Donoghue Philip C. J.
Published: November 2014

Calibration is the rate-determining step in every molecular clock analysis and, hence, considerable effort has been expended in the development of approaches to distinguish good from bad calibrations. These can be categorized intoa priorievaluation of the intrinsic fossil evidence, anda posteriorievaluation of congruence through cross-validation. We contrasted these competing approaches and explored the impact of different interpretations of the fossil evidence upon Bayesian divergence time estimation. The results demonstrate thata posterioriapproaches can lead to the selection of erroneous calibrations. Bayesian posterior estimates are also shown to be extremely sensitive to the probabilistic interpretation of temporal constraints. Furthermore, the effective time priors implemented within an analysis differ for individual calibrations when employed alone and in differing combination with others. This compromises the implicit assumption of all calibration consistency methods, that the impact of an individual calibration is the same when used alone or in unison with others. Thus, the most effective means of establishing the quality of fossil-based calibrations is througha priorievaluation of the intrinsic palaeontological, stratigraphic, geochronological and phylogenetic data. However, effort expended in establishing calibrations will not be rewarded unless they are implemented faithfully in divergence time analyses.
Could the human papillomavirus vaccines drive virulence evolution?
Authors: Murall Carmen Lía , Bauch Chris T. , Day Troy
Published: November 2014

The human papillomavirus (HPV) vaccines hold great promise for preventing several cancers caused by HPV infections. Yet little attention has been given to whether HPV could respond evolutionarily to the new selection pressures imposed on it by the novel immunity response created by the vaccine. Here, we present and theoretically validate a mechanism by which the vaccine alters the transmission–recovery trade-off that constrains HPV's virulence such that higher oncogene expression is favoured. With a high oncogene expression strategy, the virus is able to increase its viral load and infected cell population before clearance by the vaccine, thus improving its chances of transmission. This new rapid cell-proliferation strategy is able to circulate between hosts with medium to high turnover rates of sexual partners. We also discuss the importance of better quantifying the duration of challenge infections and the degree to which a vaccinated host can shed virus. The generality of the models presented here suggests a wider applicability of this mechanism, and thus highlights the need to investigate viral oncogenicity from an evolutionary perspective.
Global phylogenetic structure of the hyperdiverse ant genusPheidolereveals the repeated evolution of macroecological patterns
Authors: Economo Evan P. , Klimov Pavel , Sarnat Eli M. , Guénard Benoit , Weiser Michael D. , Lecroq Beatrice , Knowles L. Lacey
Published: November 2014

Adaptive radiations are of particular interest owing to what they reveal about the ecological and evolutionary regulation of biodiversity. This applies to localized island radiations such as Darwin's finches, and also to rapid radiations occurring on a global scale. Here we analyse the macroevolution and macroecology ofPheidole,a famously hyperdiverse and ecologically dominant ant genus. We generate and analyse four novel datasets: (i) a robust global phylogeny including 285Pheidolespecies, (ii) a global database on regionalPheidolerichness in 365 political areas summarizing over 97 000 individual records from more than 6500 studies, (iii) a global database ofPheidolerichness from 3796 local communities and (iv) a database ofPheidolebody sizes across species. Analysis of the potential climate drivers of richness revealed that the patterns are statistically very similar across different biogeographic regions, with both regional and local richness associated with the same coefficients of temperature and precipitation. This similarity occurs even though phylogenetic analysis shows thatPheidolereached dominance in communities through serial localized radiations into different biomes within different continents and islands.Pheidolebody size distributions have likewise converged across geographical regions. We propose these cases of convergence indicate that the global radiation ofPheidoleis structured by deterministic factors regulating diversification and diversity.
Interspecific competition in honeybee intracellular gut parasites is asymmetric and favours the spread of an emerging infectious disease
Authors: Natsopoulou Myrsini E. , McMahon Dino P. , Doublet Vincent , Bryden John , Paxton Robert J.
Published: November 2014

There is increasing appreciation that hosts in natural populations are subject to infection by multiple parasite species. Yet the epidemiological and ecological processes determining the outcome of mixed infections are poorly understood. Here, we use two intracellular gut parasites (Microsporidia), one exotic and one co-evolved in the western honeybee (
Apis mellifera
), in an experiment in which either one or both parasites were administered either simultaneously or sequentially. We provide clear evidence of within-host competition; order of infection was an important determinant of the competitive outcome between parasites, with the first parasite significantly inhibiting the growth of the second, regardless of species. However, the strength of this ‘priority effect’ was highly asymmetric, with the exotic
Nosema ceranae
exhibiting stronger inhibition of
Nosema apis
than vice versa. Our results reveal an unusual asymmetry in parasite competition that is dependent on order of infection. When incorporated into a mathematical model of disease prevalence, we find asymmetric competition to be an important predictor of the patterns of parasite prevalence found in nature. Our findings demonstrate the wider significance of complex multi-host–multi-parasite interactions as drivers of host–pathogen community structure.
On-board recordings reveal no jamming avoidance in wild bats
Authors: Cvikel Noam , Levin Eran , Hurme Edward , Borissov Ivailo , Boonman Arjan , Amichai Eran , Yovel Yossi
Published: November 2014

Animals often deal with situations in which vast sensory input is received simultaneously. They therefore must possess sophisticated mechanisms to select important input and ignore the rest. In bat echolocation, this problem is at its extreme. Echolocating bats emit sound signals and analyse the returning echoes to sense their environment. Bats from the same species use signals with similar frequencies. Nearby bats therefore face the difficulty of distinguishing their own echoes from the signals of other bats, a problem often referred to as jamming. Because bats commonly fly in large groups, jamming might simultaneously occur from numerous directions and at many frequencies. Jamming is a special case of the general phenomenon of sensory segregation. Another well-known example is the human problem of following conversation within a crowd. In both situations, a flood of auditory incoming signals must be parsed into important versus irrelevant information. Here, we present a novel method, fitting wild bats with a miniature microphone, which allows studying jamming from the bat's ‘point of view’. Previous studies suggested that bats deal with jamming by shifting their echolocation frequency. On-board recordings suggest otherwise. Bats shifted their frequencies, but they did so because they were responding to the conspecifics as though they were nearby objects rather than avoiding being jammed by them. We show how bats could use alternative measures to deal with jamming instead of shifting their frequency. Despite its intuitive appeal, a spectral jamming avoidance response might not be the prime mechanism to avoid sensory interference from conspecifics.
Population mixing promotes arms race host–parasite coevolution
Authors: Gómez Pedro , Ashby Ben , Buckling Angus
Published: November 2014

The consequences of host–parasite coevolution are highly contingent on the qualitative coevolutionary dynamics: whether selection fluctuates (fluctuating selection dynamic; FSD), or is directional towards increasing infectivity/resistance (arms race dynamic; ARD). Both genetics and ecology can play an important role in determining whether coevolution follows FSD or ARD, but the ecological conditions under which FSD shifts to ARD, and vice versa, are not well understood. The degree of population mixing is thought to increase host exposure to parasites, hence selecting for greater resistance and infectivity ranges, and we hypothesize this promotes ARD. We tested this by coevolving bacteria and viruses in soil microcosms and found that population mixing shifted bacteria–virus coevolution from FSD to ARD. A simple theoretical model produced qualitatively similar results, showing that mechanisms that increase host exposure to parasites tend to push dynamics towards ARD. The shift from FSD to ARD with increased population mixing may help to explain variation in coevolutionary dynamics between different host–parasite systems, and more specifically the observed discrepancies between laboratory and field bacteria–virus coevolutionary studies.
Mucilaginibacter aquaedulcis sp. nov., isolated from fresh water
Authors: Joung Yochan , Kang Heeyoung , Lee Beom-Il , Kim Haneul , Joh Kiseong , Kim Kyu-Joong
Published: November 2014

An aerobic, Gram-stain-negative, rod-shaped bacterium, designated strain PGW1-R01T, was isolated from fresh water from the Yeongju in the Republic of Korea. The strain grew optimally at 30 °C and at pH 6-8 on R2A agar. The major cellular fatty acids were summed feature 3 [comprising C16 : 1ω7c and/or C16 : 1ω6c (50.2 %) and iso-C15 : 0 (24.8 %)]. The major respiratory quinone was MK-7. The G+C contents were 39.4 mol% and the predominant respiratory quinone was MK-7. Based on 16S rRNA gene phylogeny, the strain belongs to the genus

Mucilaginibacter

. The strain PGW1-R01T was closely related to ‘
Mucilaginibacter

ginsenosidivorax’ (96.6 % sequence similarity),

Mucilaginibacter lappiensis

(96.4 %) and

Mucilaginibacter flavus

(96.4 %). On the basis of the evidence presented in this study, strain PGW1-R01T represents a novel species of the genus

Mucilaginibacter

, for which the name Mucilaginibacter
http://dx.doi.org/10.1601/nm.11437
aquaedulcis sp. nov., is proposed. The type strain is PGW1-R01T( = KCTC 23942T = CECT 8102T).
Phylogenomic analyses and molecular signatures for the class Halobacteria and its two major clades: a proposal for division of the class Halobacteria into an emended order Halobacteriales and two new orders, Haloferacales ord. nov. and Natrialbales ord. nov., containing the novel families Haloferacaceae fam. nov. and Natrialbaceae fam. nov.
Authors: Gupta Radhey S. , Naushad Sohail , Baker Sheridan
Published: November 2014

TheHalobacteriaconstitute one of the largest groups within theArchaea. The hierarchical relationship among members of this large class, which comprises a single order and a single family, has proven difficult to determine based upon 16S rRNA gene trees and morphological and physiological characteristics. This work reports detailed phylogenetic and comparative genomic studies on >100 halobacterial (haloarchaeal) genomes containing representatives from 30 genera to investigate their evolutionary relationships. In phylogenetic trees reconstructed on the basis of 32 conserved proteins, using both neighbour-joining and maximum-likelihood methods, two major clades (clades A and B) encompassing nearly two-thirds of the sequenced haloarchaeal species were strongly supported. Clades grouping the same species/genera were also supported by the 16S rRNA gene trees and trees for several individual highly conserved proteins (RpoC, EF-Tu, UvrD, GyrA, EF-2/EF-G). In parallel, our comparative analyses of protein sequences from haloarchaeal genomes have identified numerous discrete molecular markers in the form of conserved signature indels (CSI) in protein sequences and conserved signature proteins (CSPs) that are found uniquely in specific groups of haloarchaea. Thirteen CSIs in proteins involved in diverse functions and 68 CSPs that are uniquely present in all or most genome-sequenced haloarchaea provide novel molecular means for distinguishing members of the classHalobacteriafrom all other prokaryotes. The members of clade A are distinguished from all other haloarchaea by the unique shared presence of two CSIs in the ribose operon protein and small GTP-binding protein and eight CSPs that are found specifically in members of this clade. Likewise, four CSIs in different proteins and five other CSPs are present uniquely in members of clade B and distinguish them from all other haloarchaea. Based upon their specific clustering in phylogenetic trees for different gene/protein sequences and the unique shared presence of large numbers of molecular signatures, members of clades A and B are indicated to be distinct from all other haloarchaea because of their uniquely shared evolutionary histories. Based upon these results, it is proposed that clades A and B be recognized as two new orders,Natrialbalesord. nov. andHaloferacalesord. nov., within the classHalobacteria, containing the novel familiesNatrialbaceaefam. nov. andHaloferacaceaefam. nov. Other members of the classHalobacteriathat are not members of these two orders will remain part of the emended orderHalobacterialesin an emended familyHalobacteriaceae.
Dysgonomonas termitidis sp. nov., isolated from the gut of the subterranean termite Reticulitermes speratus
Authors: Pramono Ajeng K. , Sakamoto Mitsuo , Iino Takao , Hongoh Yuichi , Ohkuma Moriya
Published: November 2014

A facultatively anaerobic, Gram-stain-negative, non-motile and rod-shaped bacterium, strain N-10T, was isolated from the gut of the termite Reticulitermes speratus. Strain N-10T was closely related to

Dysgonomonas gadei

JCM 16698T according to 16S rRNA gene sequence similarity analysis (98 %) and DNA–DNA relatedness value (≤61.3 %). The optimum growth temperature of strain N-10T was 30 °C, which was distinct from that (37 °C) of known species of the genus

Dysgonomonas

. Growth of strain N-10T was inhibited on medium containing 5 or 20 % bile, unlike other species of the genus

Dysgonomonas

. In addition, acid production in the API 20A system and enzymic reactions in the Rapid ID 32A system of strain N-10T differed from those of other species of the genus

Dysgonomonas

. Based on these characteristics, strain N-10T represents a novel species of the genus

Dysgonomonas

, for which the name Dysgonomonas termitidis sp. nov. is proposed. The type strain is N-10T ( = JCM 30204T = CCUG 66188T).
Vitellibacter nionensis sp. nov., isolated from a shallow water hydrothermal vent
Authors: Rajasabapathy Raju , Mohandass Chellandi , Yoon Jung-Hoon , Dastager Syed Gulam , Liu Qing , Khieu Thi-Nhan , Son Chu Ky , Li Wen-Jun , Colaço Ana
Published: November 2014

A novel, Gram-stain-negative, non-motile, rod-shaped yellow bacterium, designated VBW088T was isolated from a shallow water hydrothermal vent in Espalamaca in the Azores. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain VBW088T clustered with three type strains of species of the genus

Vitellibacter

and exhibited a sequence similarity of 97.3 % with

Vitellibacter soesokkakensis

RSSK-12T. However, strain VBW088T and

V. soesokkakensis

RSSK-12T exhibited low DNA–DNA relatedness (12.7±3.5 %). Strain VBW088T was positive for catalase and oxidase. Growth occurred at 10–37 °C, with the optimum at 30 °C, and at pH 6.0–8.0 (optimum pH 6.0) and in up to 5 % (w/v) NaCl with optimum growth at 1–2 % (w/v) NaCl. The major fatty acids (>10 %) were iso-C15 : 0 (33.5 %) and iso-C17 : 0 3-OH (32.0 %). The polar lipids detected in strain VBW088T consisted of phosphatidylethanolamine, one unidentified aminolipid and three unidentified phospholipids. The DNA G+C content of strain VBW088T was 36.7 mol%. On the basis of phylogenetic inference, DNA–DNA relatedness, chemotaxonomic analysis and physiological data, the isolate represents a novel species of the genus

Vitellibacter

, for which the name Vitellibacter nionensis sp. nov. is proposed, with the type strain as VBW088T ( = KCTC 32420T = MCC 2354T).
Visualizing spatial population structure with estimated effective migration surfaces
Authors: Petkova Desislava , Novembre John , Stephens Matthew
Published: November 2014

Genetic data often exhibit patterns that are broadly consistent with “isolation by distance” – a phenomenon where genetic similarity tends to decay with geographic distance. In a heterogeneous habitat, decay may occur more quickly in some regions than others: for example, barriers to gene flow can accelerate the genetic differentiation between groups located close in space. We use the concept of “effective migration” to model the relationship between genetics and geography: in this paradigm, effective migration is low in regions where genetic similarity decays quickly. We present a method to quantify and visualize variation in effective migration across the habitat, which can be used to identify potential barriers to gene flow, from geographically indexed large-scale genetic data. Our approach uses a population genetic model to relate underlying migration rates to expected pairwise genetic dissimilarities, and estimates migration rates by matching these expectations to the observed dissimilarities. We illustrate the potential and limitations of our method using simulations and geo-referenced genetic data from elephant, human andArabidopsis thalianapopulations. The resulting visualizations highlight important features of the spatial population structure that are difficult to discern using existing methods for summarizing genetic variation such as principal components analysis.
Promotion of Testa Rupture during Garden Cress Germination Involves Seed Compartment-Specific Expression and Activity of Pectin Methylesterases
Authors: Scheler Claudia , Weitbrecht Karin , Pearce Simon P. , Hampstead Anthony , Büttner-Mainik Annette , Lee Kieran J.D. , Voegele Antje , Oracz Krystyna , Dekkers Bas J.W. , Wang Xiaofeng , Wood Andrew T.A. , Bentsink Leónie , King John R. , Knox J. Paul , Holdsworth Michael J. , Müller Kerstin , Leubner-Metzger Gerhard
Published: November 2014

Pectin methylesterase (PME) controls the methylesterification status of pectins and thereby determines the biophysical properties of plant cell walls, which are important for tissue growth and weakening processes. We demonstrate here that tissue-specific and spatiotemporal alterations in cell wall pectin methylesterification occur during the germination of garden cress (Lepidium sativum). These cell wall changes are associated with characteristic expression patterns of PME genes and resultant enzyme activities in the key seed compartments CAP (micropylar endosperm) and RAD (radicle plus lower hypocotyl). Transcriptome and quantitative real-time reverse transcription-polymerase chain reaction analysis as well as PME enzyme activity measurements of separated seed compartments, including CAP and RAD, revealed distinct phases during germination. These were associated with hormonal and compartment-specific regulation of PME group 1, PME group 2, and PME inhibitor transcript expression and total PME activity. The regulatory patterns indicated a role for PME activity in testa rupture (TR). Consistent with a role for cell wall pectin methylesterification in TR, treatment of seeds with PME resulted in enhanced testa permeability and promoted TR. Mathematical modeling of transcript expression changes in germinating garden cress and Arabidopsis (Arabidopsis thaliana) seeds suggested that group 2 PMEs make a major contribution to the overall PME activity rather than acting as PME inhibitors. It is concluded that regulated changes in the degree of pectin methylesterification through CAP- and RAD-specific PME and PME inhibitor expression play a crucial role during Brassicaceae seed germination.
Inelastic X-ray scattering with 0.75 meV resolution at 25.7 keV using a temperature-gradient analyzer
Authors: Ishikawa Daisuke , Ellis David S. , Uchiyama Hiroshi , Baron Alfred Q. R.
Published: November 2014

The use of temperature-gradient analyzers for non-resonant high-resolution inelastic X-ray scattering is investigated. The gradient compensates for geometrical broadening of the energy resolution by adjusting the lattice spacing of the analyzer crystal. Applying a ∼12 mK temperature gradient across a 9.5 cm analyzer, resolutions of 0.75 (2) meV FWHM at 25.7 keV for Si(13 13 13) and 1.25 (2) meV at 21.7 keV for Si(11 11 11) were measured, while retaining large (250 mm) clearance between the sample position and detector, and reasonable (9.3 mrad × 8.8 mrad) analyzer acceptance. The temperature control and stability are discussed.
Confocal soft X-ray scanning transmission microscopy: setup, alignment procedure and limitations
Authors: Späth Andreas , Raabe Jörg , Fink Rainer H.
Published: November 2014

Zone-plate-based scanning transmission soft X-ray microspectroscopy (STXM) is a well established technique for high-contrast imaging of sufficiently transparent specimens (e.g.ultrathin biological tissues, polymer materials, archaeometric specimens or magnetic thin films) with spatial resolutions in the regime of 20 nm and high spectroscopic or chemical sensitivity. However, due to the relatively large depth of focus of zone plates, the resolution of STXM along the optical axis so far stays unambiguously behind for thicker X-ray transparent specimens. This challenge can be addressed by the implementation of a second zone plate in the detection pathway of the beam, resulting in a confocal arrangement. Within this paper a first proof-of-principle study for a confocal STXM (cSTXM) and an elaborate alignment procedure in transmission and fluorescence geometry are presented. Based on first confocal soft X-ray micrographs of well known specimens, the advantage and limitation of cSTXM as well as further development potentials for future applications are discussed.
X-ray irradiation induces local rearrangement of silica particles in swollen rubber
Authors: Shinohara Yuya , Yamamoto Naoko , Kishimoto Hiroyuki , Amemiya Yoshiyuki
Published: November 2014

X-ray photon correlation spectroscopy (XPCS) of swollen rubber containing spherical silica nanoparticles is reported. It is shown that irradiation by intense X-rays leads to the breakdown of cross-links, thereby inducing the local rearrangement of silica nanoparticles. This rearrangement process depends on the cross-link density and is characterized by a compressed exponential relaxation with aging behaviour, which resembles a common feature of complex fluids observed with XPCS.
Power and transformational leadership in public organizations
Authors: Barth-Farkas Faye , Vera Antonio
Published: November 2014

Purpose

– The purpose of this paper is to examine the relationship between perceived power and transformational leadership in the public sector.

Design/methodology/approach

– The authors investigate this topic empirically in the context of German police forces using a between-groups design, manipulating power and statistically analyzing the results on the multifactor leadership questionnaire.

Findings

– Police officers with a high perception of power achieve significantly lower scores on transformational leadership compared to their low power counterparts.

Research limitations/implications

– The study contributes to advancing public leadership theory by showing that transformational leadership, which is considered as particularly useful in public organizations, is likely to be adversely affected by leaders’ power. Furthermore, it also extends on the literature on power by providing first empirical evidence that power has a significant impact not only on factors such as the pursuit of a goal, social behavior, or affect, but also on leadership.

Practical implications

– The results suggest either to control power accumulation in leadership positions of public organizations, for instance by implementing flat hierarchies, or to come to terms with more authoritative leadership styles in top management.

Originality/value

– To the best of knowledge, the authors provide the first study that investigates the impact of power on transformational leadership in the public sector using an experimental design and quantitative empirical data.
Is selfless leadership an impossible ideal for public leaders?
Authors: Brookes Stephen
Published: November 2014

Purpose

– The purpose of this paper is to introduce the notion of the “Selfless Leader” and to pose the question as to whether this is an impossible ideal. It locates the importance of values within the context of public leadership and puts forward a new perspective on principle-based leadership that incorporates selflessness as its foundation.

Design/methodology/approach

– It primarily involves a literature review in relation to the importance of virtues and values based on an historical review, and the wider language of leadership. It draws briefly upon primary research based on realistic evaluation (Pawson and Tilley, 1997) across a range of public service organisations in various differing contexts but is, primarily, a conceptual paper aimed at encouraging further debate and research.

Findings

– Given the fact that we are innately selfish, the requirement to lead in the public interest provides a real challenge for all leaders particularly as leaders are encouraged more towards achievement of competitive advantage, rather than collaborative advantage. The paper will suggest that values-based leadership is highly relevant to the challenges facing public leaders, and will present a principle-based framework for the practice and processes of public leadership.

Research limitations/implications

– The paper seeks to generate a debate in relation to principle-based leadership that incorporates selflessness as its foundation, primarily through a literature review but supported by selected findings from a range of research projects in the area of public leadership.

Practical implications

– The approach to realistic evaluation is helpful, not only as a research methodology, but also in relation to the development and assessment of leadership practice.

Social implications

– This is considered to represent a unique approach to the study of leading in the public interest by focusing on the concept of selflessness.

Originality/value

– This is considered to represent a unique approach to the study of leading in the public interest by focusing on the concept of selflessness.
New insights for corporate strategists from a renowned value investor
Authors: Calandro, Jr Joseph
Published: November 2014

Purpose

– This “masterclass” article explains how modern value investing analysis can guide corporate strategists and corporate development departments. It shows how executives can use some key insights from the recently published book by Martin J. Whitman and Fernando Diz, Modern Security Analysis (Hoboken, NJ: Wiley, 2013).

Design/methodology/approach

– This masterclass includes an interview with the lead author of the book, value investor Martin J. Whitman.

Findings

– The insights contained within Modern Security Analysis can and should be leveraged by corporate executives and strategists to create value for their firms.

Practical implications

– This article supports earlier work published in Strategy & Leadership that shows Graham and Dodd-based valuation and analysis is a viable avenue of academic research and a viable method with which to assess corporate strategic initiatives (such as mergers and acquisitions, share buy-backs, risk management, etc.).

Originality/value

– This analysis provides senior executives with a guide to the assessment tools used by the most successful value investors and an explanation of their relevance to corporate strategy.
Why Apple’s product magic continues to amaze – skills of the world’s #1 value chain integrator
Authors: Mitchell Will
Published: November 2014

Purpose

– Apple’s amazing run of blockbusters – iPhone, iPad, iPod, iTunes, multiple iterations of the Mac computer, and going all the way back to the Apple II – has created a fan base of consumers willing to pay premium prices and produced enormous corporate value. This case aims to look at the strategies, value chain integration skills and management practices that underlie Apple’s ability to bring its designs to commercial stardom and propel shareholder value.

Design/methodology/approach

– The case examines two related skills that the company has developed since the late 1990s that are critical complements to Apple’s design talents: its ability to combine “build, borrow and buy” strategies and its world-leading abilities as a value chain integrator.

Findings

– Apple has uniquely sophisticated “build, borrow and buy” (BBB) expertise throughout its management, going all the way up to its CEO Tim Cook. The company’s lengthy success record proves it knows when and how to develop products and components internally, when to ally with other firms and when and how to acquire and integrate other companies.

Research limitations/implications

– This case is based on publically available sources.

Practical implications

– Despite working with such a large and powerful set of vendors and partners, Apple harvests much of the value in the relationships.

Originality/value

– The case shows how corporate leaders and personnel throughout the company maintain a systematic view of customer value, the value chain that delivers that value and the competitive and social contexts that shape value demands, so that they can communicate and coordinate activities of multiple vendors throughout the ecosystem rather than simply manage a series of one-to-one relationships.
Seizing opportunities and dodging threats with a dual operating system
Authors: P. Kotter John
Published: November 2014

Purpose

– This internationally recognized innovation expert asserts that today's organizations need a powerful new operating system to address the challenges posed by mounting complexity and rapid change.

Design/methodology/approach

– As a consultant to companies seeking to re-invigorate the innovation process, the author can describe how they have implemented the dual operating system – a network and a hierarchy – that he advocates.

Findings

– When organizations are dangerously slow to adapt to competitive threats and to pursue promising innovations, the solution to, which has been adopted successfully by many organizations, is to add a second operating system that is organized as a network that can create agility and speed.

Practical implications

– The author explains how all successful organizations operate with a dual system more or less during the most dynamic growth period in their life cycle, so a dual operating system will be somewhat familiar to veteran leaders.

Originality/value

– The organization's top management plays a crucial role in starting and maintaining the network and managing its communications with the hierarchy. For senior practitioners, the author describes the five basic principles of a well-functioning dual operating system.