bluuebunny/crossref_metadata_2025 huggingface dataset:
Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes
Authors: Szczelkun Mark D. , Tikhomirova Maria S. , Sinkunas Tomas , Gasiunas Giedrius , Karvelis Tautvydas , Pschera Patrizia , Siksnys Virginijus , Seidel Ralf
Published: May 2014

Significance

Clustered, regularly interspaced, short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems provide adaptive immunity for bacteria and archaea. They use a protein complex that targets invading nucleic acids using a bound RNA that hybridizes to complementary sequence stretches. On DNA targets, the resulting structure is an R-loop. By twisting single DNA molecules, we can directly observe R-loop formation and dissociation in two distinct types of CRISPR-Cas system. This allows us to investigate the role of different elements of the target sequence. Whereas upstream elements control the actual R-loop formation, downstream elements ensure R-loop stability, suggesting a directional R-loop formation. This provides insight into the recognition process by these enzymes, which is the crucial step to understand targeting in the rapidly emerging genetic engineering applications of CRISPR-Cas systems.
Mechanical constraints imposed by 3D cellular geometry and arrangement modulate growth patterns in the
Arabidopsis
embryo
Authors: Bassel George W. , Stamm Petra , Mosca Gabriella , Barbier de Reuille Pierre , Gibbs Daniel J. , Winter Robin , Janka Ales , Holdsworth Michael J. , Smith Richard S.
Published: May 2014

Significance

During plant growth and development, the gene expression that promotes growth does not always spatially correlate with observed growth. This suggests that additional factors guide morphogenesis. Here we propose that mechanical cues play an instructive role and test our hypothesis by using a full 3D cellular-level finite-element simulation model of the mature
Arabidopsis
embryo. We demonstrate that the size, shape, and arrangement of plant cells all influence their ability to grow in response to growth-promoting gene expression. These principles were sufficient to explain the displacement of growth from the center of growth-promoting gene expression. These findings represent a previously undescribed mechanism governing 3D growth patterns in multicellular plant organs.
Prosurvival Bcl-2 family members affect autophagy only indirectly, by inhibiting Bax and Bak
Authors: Lindqvist Lisa M. , Heinlein Melanie , Huang David C. S. , Vaux David L.
Published: May 2014

Significance

It is widely accepted that prosurvival B-cell lymphoma 2 (Bcl-2) family members not only inhibit apoptosis but also negatively regulate autophagy by binding to Beclin 1. Herein, we challenge this view and provide genetic and biochemical evidence that the effects of prosurvival Bcl-2 family members on autophagy are instead an indirect consequence of their inhibition of apoptosis mediators Bcl-2–associated X (Bax) and Bcl-2 homologous antagonist/killer (Bak). We show that in the absence of Bax and Bak, antagonizing or altering the levels of prosurvival Bcl-2 family members has no detectable impact on autophagy. Because several inhibitors of both autophagy and Bcl-2 are in clinical trials for the treatment of cancer, it is important to understand the cross-talk between these pathways.
Solid-state structures of peapod bearings composed of finite single-wall carbon nanotube and fullerene molecules
Authors: Sato Sota , Yamasaki Takashi , Isobe Hiroyuki
Published: May 2014

Significance

Carbonaceous entities possessing tubular and spherical shapes spontaneously form a host–guest complex. This supramolecular complex, so-called a peapod, is unique among host–guest pairs in that it is assembled solely by van der Waals interactions at the concave–convex interface of sp
2
-carbon networks. Recently, a molecular version of this supramolecular system revealed the presence of the extremely tight association concomitantly with the dynamic motions of the guest in apolar media. In this paper, an atomic-level structure of the molecular peapod is revealed by a crystallographic method to show the presence of an inflection-free surface inside the tubular molecule. Enjoying rotational freedom at this smooth surface, the guest fullerene molecule rolls dynamically even in the solid state.
Characterization and development of photoactivatable fluorescent proteins for single-molecule–based superresolution imaging
Authors: Wang Siyuan , Moffitt Jeffrey R. , Dempsey Graham T. , Xie X. Sunney , Zhuang Xiaowei
Published: May 2014

Significance

Photoactivatable fluorescent proteins (PAFPs) are important probes for superresolution fluorescence microscopy, which allows the spatial organization of proteins in living cells to be probed with sub–diffraction-limit resolution. Here, we compare four properties of PAFPs that are critical for superresolution imaging and report two new PAFPs that exhibit excellent performance in all four properties.
Commonness and rarity in the marine biosphere
Authors: Connolly Sean R. , MacNeil M. Aaron , Caley M. Julian , Knowlton Nancy , Cripps Ed , Hisano Mizue , Thibaut Loïc M. , Bhattacharya Bhaskar D. , Benedetti-Cecchi Lisandro , Brainard Russell E. , Brandt Angelika , Bulleri Fabio , Ellingsen Kari E. , Kaiser Stefanie , Kröncke Ingrid , Linse Katrin , Maggi Elena , O’Hara Timothy D. , Plaisance Laetitia , Poore Gary C. B. , Sarkar Santosh K. , Satpathy Kamala K. , Schückel Ulrike , Williams Alan , Wilson Robin S.
Published: May 2014

Significance

Tests of biodiversity theory have been controversial partly because alternative formulations of the same theory seemingly yield different conclusions. This has been a particular challenge for neutral theory, which has dominated tests of biodiversity theory over the last decade. Neutral theory attributes differences in species abundances to chance variation in individuals’ fates, rather than differences in species traits. By identifying common features of different neutral models, we conduct a uniquely robust test of neutral theory across a global dataset of marine assemblages. Consistently, abundances vary more among species than neutral theory predicts, challenging the hypothesis that community dynamics are approximately neutral, and implicating species differences as a key driver of community structure in nature.
Chaos–order transition in foraging behavior of ants
Authors: Li Lixiang , Peng Haipeng , Kurths Jürgen , Yang Yixian , Schellnhuber Hans Joachim
Published: May 2014

Significance

We have studied the foraging behavior of group animals that live in fixed colonies (especially ants) as an important problem in ecology. Building on former findings on deterministic chaotic activities of single ants, we uncovered that the transition from chaotic to periodic regimes results from an optimization scheme of the self-organization of such an animal colony. We found that an effective foraging of ants mainly depends on their nest as well as their physical abilities and knowledge due to experience. As an important outcome, the foraging behavior of ants is not represented by random, but rather by deterministic walks, in a random environment: Ants use their intelligence and experience to navigate.
Quantum critical behavior in heavy electron materials
Authors: Yang Yi-feng , Pines David
Published: May 2014

Significance

Quantum critical behavior occurs when a material is near a zero temperature phase transition between two ordered forms of matter. Kondo lattice materials, in which itinerant heavy (∼200 bare mass) electrons emerge through the collective hybridization of localized f electrons with background conduction electrons, provide a rich source of experimental information about how, for example, pressure and magnetic fields influence local moment antiferromagnetic order and its boundary with competing fully itinerant heavy electron behavior in the pressure–magnetic field plane. A phenomenological two-fluid model of coupled local moments and itinerant heavy electrons enables us to calculate both and obtain a quantitative account of related quantum critical behavior in two of the best-studied heavy electron materials, CeCoIn
5
and YbRh
2
Si
2
.
Regulatory T cells modulate granulomatous inflammation in an HLA-DP2 transgenic murine model of beryllium-induced disease
Authors: Mack Douglas G. , Falta Michael T. , McKee Amy S. , Martin Allison K. , Simonian Philip L. , Crawford Frances , Gordon Terry , Mercer Robert R. , Hoover Mark D. , Marrack Philippa , Kappler John W. , Tuder Rubin M. , Fontenot Andrew P.
Published: May 2014

Significance

Genetic linkage to major histocompatibility complex class II proteins has been observed in many immunological disorders; yet, little is known about the underlying mechanisms of these associations. For chronic beryllium disease (CBD), the linkage to
HLA-DPB1
alleles encoding a glutamic acid at position 69 of the β-chain is well established. We tested whether the presence of HLA-DP2 is sufficient for the development of a disease-specific model of CBD. HLA-DP2 transgenic mice developed a beryllium-specific adaptive immune response composed of CD4
+
T cells that secrete Th1-type cytokines and are HLA-DP2-restricted, thus replicating the major features of the human disease. In addition, regulatory T cells modulate granuloma formation in the lungs of beryllium oxide-exposed HLA-DP2 transgenic mice.
Synthesis of terephthalic acid via Diels-Alder reactions with ethylene and oxidized variants of 5-hydroxymethylfurfural
Authors: Pacheco Joshua J. , Davis Mark E.
Published: May 2014

Significance

Current, plant-based polyethylene terephthalate (PET) is produced from biomass-derived ethylene glycol [the terephthalic acid (PTA) used is not from biomass]. To have a 100% biomass-derived PET, PTA must be produced from biomass. Here, pathways for the production of renewable PTA, using Diels-Alder reactions between ethylene and oxidized derivatives of 5-hydroxymethylfurfural, a biomass-derived chemical, are reported. These pathways are enabled by new catalytic chemistry that may provide routes for the production of 100% biomass-derived PET.
The dialogic construction of certainty in legal contexts
Authors: Mininni Giuseppe , Scardigno Rosa , Grattagliano Ignazio
Published: May 2014

The contexts of legal communication are characterized by the maximum strain between the spread of doubtfulness and the aspiration to certainty. The distance between the versions of events proposed by prosecution and defense is clear evidence of the sense-making dynamic that marks the human condition as “insecuritas”. The analysis of legal contexts allows us to capture the complex process of the discursive construction of (un)certainty, that interweaves references on both the epistemic and value axes typical of a specific sense-enunciative community. In the discursive sphere of the “court” institution, all the enunciative positionings enacted by those who incriminate, defend, testify, guarantee and judge, disclose the several ways to relate to (un)certainty of their textual worlds. As a consequence, the meaning of “evidentials” is overdetermined by specific rhetorical structures that set up a wide range of personal styles in the management of (un)certainty . The analysis of texts produced in a judicial debate aims to display the dialogical principle pertaining to a specific modulation of evidentiality expressed by deontic forms, performing a “dehumanizing” rhetoric. They can be interpreted as a trace of the opportunity to emphasize the ethical roots of each claim for certainty.
Paradigms of Public Policies for Licit and Illicit Drugs in Brazil
Authors: Gigliotti Analice , Ribeiro Marcelo , Tapia Aguilera Amarílis , Rezende Elton , Ogata Perrenoud Luciane
Published: May 2014

Brazil is a country of continental dimensions that, over the last 3 decades, has been making increased efforts to develop effective public policies for controlling the use of both licit and illicit psychoactive substances. In the case of licit drugs, Brazil was a pioneer in following the guidance of the World Health Organization for tobacco control and has witnessed surprising results relating to reduction of smoking prevalence and correlated morbidity and mortality. Today, Brazil has a national structure for organizing, applying, and monitoring laws relating to tobacco. However, in the field of illicit drugs, with crack consumption as a paradigm, the situation is the opposite: its use has been increasing year by year and is being consumed at increasingly young ages and by all social classes. Thus, it is becoming an enormous challenge for public policies relating to prevention and treatment. In this context, the aim of this article is to present a review of the epidemiological data relating to tobacco and crack use in Brazil, with an analysis on the impact of public policies for controlling consumption over recent years. Despite the efforts made over the last 3 decades, Brazil still has a long way to go in order to construct a consistent and effective national drugs policy.
Collagen peptide and vitamin C additively attenuate age-related skin atrophy in Sod1-deficient mice
Authors: Shibuya Shuichi , Ozawa Yusuke , Toda Toshihiko , Watanabe Kenji , Tometsuka Chisa , Ogura Takayuki , Koyama Yoh-ichi , Shimizu Takahiko
Published: May 2014

Age-related skin thinning is correlated with a decrease in the content of collagen in the skin. Accumulating evidence suggests that collagen peptide (CP) and vitamin C (VC) transcriptionally upregulate type I collagen in vivo. However, the additive effects of CP and VC on age-related skin changes remain unclear. We herein demonstrate that CP and a VC derivative additively corrected age-related skin thinning via reduced oxidative damage in superoxide dismutase 1 (Sod1)-deficient mice. Co-treatment with these compounds significantly normalized the altered gene expression of Col1a1, Has2, and Ci1, a proton-coupled oligopeptide transporter, in Sod1−/− skin. The in vitro analyses further revealed that collagen oligopeptide, a digestive product of ingested CP, significantly promoted the bioactivity of the VC derivative with respect to the migration and proliferation of Sod1−/− fibroblasts. These findings suggest that combined treatment with CP and VC is effective in cases of age-related skin pathology.
Isolation of diploid baker’s yeast capable of strongly activating immune cells and analyses of the cell wall structure
Authors: Takada Yuki , Mizobuchi Ayano , Kato Takayuki , Kasahara Emiko , Ito Chinatsu , Watanabe Hajime , Kanzaki Ken , Kitagawa Seiichi , Tachibana Taro , Azuma Masayuki
Published: May 2014

Diploid baker’s yeast capable of strongly activating a mouse macrophage was constructed based on haploid mutant AQ-37 obtained previously. The obtained strain BQ-55 activated also human immune cells. To clarify a factor for the activation, the cell wall structure, especially the β-glucan structure, was analyzed, suggesting that the length of branching, β-1,6-glucan, may be one of the factors.
Characterization and genetic analyses of a carbazole-degrading gram-positive marine isolate, Janibacter sp. strain OC11
Authors: Oba Shintaro , Suzuki Toshihiro , Maeda Rintaro , Omori Toshio , Fuse Hiroyuki
Published: May 2014

Strain OC11 was isolated from seawater sampled at the coast of Chiba, Japan, in artificial seawater medium with carbazole (CAR) as the sole carbon source. Its 16S ribosomal RNA gene sequence suggested that strain OC11 belongs to the genus Janibacter. The CAR-degradation genes (car genes) of strain OC11 were PCR amplified, using degenerate primers designed based on the car gene sequences of other CAR-degrading bacteria. Complete nucleotide sequences encoding six complete open reading frames were determined, and the first known ferredoxin reductase gene (carAd) was found from a CAR-degrading bacterium isolated from the marine environment. An experiment using a mutant strain suggested that the car genes of strain OC11 are functional in CAR degradation. Southern hybridization indicated that strain OC11 had one car gene cluster in vivo. RT-PCR revealed that transcription of carOC11 constitutes an operon.
A simple proof of the Zeilberger–Bressoud 𝑞-Dyson theorem
Authors: Károlyi Gyula , Nagy Zoltán
Published: May 2014

As an application of the Combinatorial Nullstellensatz, we give a short polynomial proof of the

q
q

-analogue of Dyson’s conjecture formulated by Andrews and first proved by Zeilberger and Bressoud.
On doubly periodic phases
Authors: Stefan Marius
Published: May 2014

Every meromorphic function on

C

\mathbb {C}

with doubly periodic phase is equal to an elliptic function multiplied by a meromorphic function determined by the periods.
On generalized hypergeometric equations and mirror maps
Authors: Roques Julien
Published: May 2014

This paper deals with generalized hypergeometric differential equations of order

n
≥
3

n \geq 3

having maximal unipotent monodromy at

0
0

. We show that among these equations those leading to mirror maps with integral Taylor coefficients at

0
0

(up to simple rescaling) have special parameters, namely

R
R

-partitioned parameters. This result yields the classification of all generalized hypergeometric differential equations of order

n
≥
3

n \geq 3

having maximal unipotent monodromy at

0
0

such that the associated mirror map has the above integrality property.
Superconvergence analysis of the linear finite element method and a gradient recovery postprocessing on anisotropic meshes
Authors: Cao Weiming
Published: May 2014

For the linear finite element method based on general unstructured anisotropic meshes in two dimensions, we establish the superconvergence in energy norm of the finite element solution to the interpolation of the exact solution for elliptic problems. We also prove the superconvergence of the postprocessing process based on the globalL2L^2-projection of the gradient of the finite element solution. Our basic assumptions are: (i) the mesh is quasi-uniform under a Riemannian metric and (ii) each adjacent element pair forms an approximate (anisotropic) parallelogram. The analysis follows the same methodology developed by Bank and Xu in 2003 for the case of quasi-uniform meshes, and the results can be considered as an extension of their conclusion to the adaptive anisotropic meshes. Numerical examples involving both internal and boundary layers are presented in support of the theoretical analysis.
keeSeek: searching distant non-existing words in genomes for PCR-based applications
Authors: Falda Marco , Fontana Paolo , Barzon Luisa , Toppo Stefano , Lavezzo Enrico
Published: May 2014

Summary: The search for short words that are absent in the genome of one or more organisms (neverwords, also known as nullomers) is attracting growing interest because of the impact they may have in recent molecular biology applications. keeSeek is able to find absent sequences with primer-like features, which can be used as unique labels for exogenously inserted DNA fragments to recover their exact position into the genome using PCR techniques. The main differences with respect to previously developed tools for neverwords generation are (i) calculation of the distance from the reference genome, in terms of number of mismatches, and selection of the most distant sequences that will have a low probability to anneal unspecifically; (ii) application of a series of filters to discard candidates not suitable to be used as PCR primers. KeeSeek has been implemented in C++ and CUDA (Compute Unified Device Architecture) to work in a General-Purpose Computing on Graphics Processing Units (GPGPU) environment.

Availability and implementation: Freely available under the Q Public License at http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=keeseek

Contact:  stefano.toppo@unipd.it

Supplementary information:  Supplementary data are available at Bioinformatics online.
Age-specific cost of first reproduction in female southern elephant seals
Authors: Desprez Marine , Harcourt Robert , Hindell Mark A. , Cubaynes Sarah , Gimenez Olivier , McMahon Clive R.
Published: May 2014

When to commence breeding is a crucial life-history decision that may be the most important determinant of an individual's lifetime reproductive output and can have major consequences on population dynamics. The age at which individuals first reproduce is an important factor influencing the intensity of potential costs (e.g. reduced survival) involved in the first breeding event. However, quantifying age-related variation in the cost of first reproduction in wild animals remains challenging because of the difficulty in reliably recording the first breeding event. Here, using a multi-event capture–recapture model that accounts for both imperfect detection and uncertainty in the breeding status on an 18-year dataset involving 6637 individuals, we estimated age and state-specific survival of female elephant seals (
Mirounga leonina
) in the declining Macquarie Island population. We detected a clear cost of first reproduction on survival. This cost was higher for both younger first-time breeders and older first-time breeders compared with females recruiting at age four, the overall mean age at first reproduction. Neither earlier primiparity nor delaying primiparity appear to confer any evolutionary advantage, rather the optimal strategy seems to be to start breeding at a single age, 4 years.
John Hadji Argyris. 19 August 1913 — 2 April 2004
Authors: Spalding D. Brian
Published: May 2014

John Argyris was born in Greece; he was educated there and in Germany, made his scientific reputation in England, and spent the last part of his career in Germany, where he died at the age of 90 years.
Three-dimensional traction forces of Schwann cells on compliant substrates
Authors: López-Fagundo Cristina , Bar-Kochba Eyal , Livi Liane L. , Hoffman-Kim Diane , Franck Christian
Published: May 2014

The mechanical interaction between Schwann cells (SCs) and their microenvironment is crucial for the development, maintenance and repair of the peripheral nervous system. In this paper, we present a detailed investigation on the mechanosensitivity of SCs across a physiologically relevant substrate stiffness range. Contrary to many other cell types, we find that the SC spreading area and cytoskeletal actin architecture were relatively insensitive to substrate stiffness with pronounced stress fibre formation across all moduli tested (0.24–4.80 kPa). Consistent with the presence of stress fibres, we found that SCs generated large surface tractions on stiff substrates and large, finite material deformations on soft substrates. When quantifying the three-dimensional characteristics of the SC traction profiles, we observed a significant contribution from the out-of-plane traction component, locally giving rise to rotational moments similar to those observed in mesenchymal embryonic fibroblasts. Taken together, these measurements provide the first set of quantitative biophysical metrics of how SCs interact with their physical microenvironment, which are anticipated to aid in the development of tissue engineering scaffolds designed to promote functional integration of SCs into post-injury
in vivo
environments.
Nymphalid eyespot serial homologues originate as a few individualized modules
Authors: Oliver Jeffrey C. , Beaulieu Jeremy M. , Gall Lawrence F. , Piel William H. , Monteiro Antónia
Published: May 2014

Serial homologues are repeated traits that share similar development but occur in different parts of the body. Variation in number of repeats accounts for substantial diversity in animal form and considerable work has focused on identifying the factors accounting for this variation. Little is known, however, about how serial homologues originally become repeated, or about the relative timing of repeat individuation relative to repeat origin. Here, we show that the serially repeated eyespots on nymphalid butterfly wings most likely arose as a small cluster of units on the ventral hindwing that were later co-opted to the dorsal and anterior wing surfaces. Based on comparative analyses of over 400 species, we found support for a model of eyespot origin followed by redeployment, rather than by the conventional model, where eyespots arose as a complete row of undifferentiated units that later gained individuation. In addition, eyespots most likely evolved from simpler pattern elements, single-coloured spots, which were already individuated among different wing sectors. Finally, the late appearance of eyespots on the dorsal, hidden wing surface further suggests that these novel complex traits originally evolved for one function (thwarting predator attacks) and acquired a second function (sexual signalling) when moved to a different body location. This broad comparative analysis illustrates how serial homologues may initially evolve as a few units serving a particular function and subsequently become repeated in novel body locations with new functions.
Experimental evolution of bet hedging under manipulated environmental uncertainty in
Neurospora crassa
Authors: Graham Jeffrey K. , Smith Myron L. , Simons Andrew M.
Published: May 2014

All organisms are faced with environmental uncertainty. Bet-hedging theory expects unpredictable selection to result in the evolution of traits that maximize the geometric-mean fitness even though such traits appear to be detrimental over the shorter term. Despite the centrality of fitness measures to evolutionary analysis, no direct test of the geometric-mean fitness principle exists. Here, we directly distinguish between predictions of competing fitness maximization principles by testing Cohen's 1966 classic bet-hedging model using the fungus
Neurospora crassa
. The simple prediction is that propagule dormancy will evolve in proportion to the frequency of ‘bad’ years, whereas the prediction of the alternative arithmetic-mean principle is the evolution of zero dormancy as long as the expectation of a bad year is less than 0.5. Ascospore dormancy fraction in
N. crassa
was allowed to evolve under five experimental selection regimes that differed in the frequency of unpredictable ‘bad years’. Results were consistent with bet-hedging theory: final dormancy fraction in 12 genetic lineages across 88 independently evolving samples was proportional to the frequency of bad years, and evolved both upwards and downwards as predicted from a range of starting dormancy fractions. These findings suggest that selection results in adaptation to variable rather than to expected environments.
Bifidobacterium aesculapii sp. nov., from the faeces of the baby common marmoset (Callithrix jacchus)
Authors: Modesto M. , Michelini S. , Stefanini I. , Ferrara A. , Tacconi S. , Biavati B. , Mattarelli P.
Published: May 2014

Six Gram-positive-staining, microaerophilic, non-spore-forming, fructose-6-phosphate phosphoketolase-positive bacterial strains with a peculiar morphology were isolated from faecal samples of baby common marmosets (Callithrix jacchus). Cells of these strains showed a morphology not reported previously for a bifidobacterial species, which resembled a coiled snake, always coiled or ring shaped or forming a ‘Y’ shape. Strains MRM 3/1T and MRM 4/2 were chosen as representative strains and characterized further. The bacteria utilized a wide range of carbohydrates and produced urease. Glucose was fermented to acetate and lactate. Strain MRM 3/1T showed a peptidoglycan type unique among members of the genus

Bifidobacterium

. The DNA base composition was 64.7 mol% G+C. Almost-complete 16S rRNA, hsp60, clpC and rpoB gene sequences were obtained and phylogenetic relationships were determined. Comparative analysis of 16S rRNA gene sequences showed that strains MRM 3/1T and MRM 4/2 had the highest similarities to

Bifidobacterium scardovii

DSM 13734T (94.6 %) and

Bifidobacterium stellenboschense

DSM 23968T (94.5 %). Analysis of hsp60 showed that both strains were closely related to

B. stellenboschense

DSM 23968T (97.5 % similarity); however, despite this high degree of similarity, our isolates could be distinguished from

B. stellenboschense

DSM 23968T by low levels of DNA–DNA relatedness (30.4 % with MRM 3/1T). Strains MRM 3/1T and MRM 4/2 were located in an actinobacterial cluster and were more closely related to the genus

Bifidobacterium

than to other genera in the family

Bifidobacteriaceae

. On the basis of these results, strains MRM 3/1T and MRM 4/2 represent a novel species within the genus

Bifidobacterium

, for which the name Bifidobacterium aesculapii sp. nov. is proposed; the type strain is MRM 3/1T ( = DSM 26737T = JCM 18761T).
Roseibium
aquae sp. nov., isolated from a saline lake
Authors: Zhong Zhi-Ping , Liu Ying , Liu Hong-Can , Wang Fang , Zhou Yu-Guang , Liu Zhi-Pei
Published: May 2014

A Gram-staining-negative bacterium, strain DSG-S4-2T, was isolated from Dasugan Lake, a saline lake (salinity 3.1 %, w/v) in Qaidam basin, Qinghai, China and its taxonomic position was determined by using a polyphasic approach. Cells of strain DSG-S4-2T were non-spore-forming rods, 0.5–0.8 µm wide and 1.2–3.8 µm long and motile by means of a single polar flagellum. Strain DSG-S4-2T was strictly heterotrophic and aerobic, catalase-positive and oxidase-negative. PufLM and coxL genes were present, bacteriochlorophyll a (BChl a) and a carotenoid pigment were produced. Growth was observed in the presence of 0–8.0 % (w/v) NaCl (optimum, 1.0–2.0 %), at 20–40 °C (optimum, 35 °C) and pH 6.5–10.5 (optimum, pH 7.5–8.0). Strain DSG-S4-2T contained Q-10 as the sole respiratory quinone. The polar lipids contained two aminolipids, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, sulphoquinovosyldiacylglyceride, phosphatidylcholine and some unknown phospholipids, like the other members of the genus

Roseibium

. The predominant fatty acid (>70 %) was summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The DNA G+C content was 61.4 mol% (determined from melting temperature). Phylogenetic trees (neighbour-joining, maximum-likelihood and maximum-parsimony) based on 16S rRNA gene sequences showed that strain DSG-S4-2T was associated with the members of the genus

Roseibium

, with highest 16S rRNA gene sequence similarity to

Roseibium denhamense

OCh 254T (96.3 %) and

Roseibium hamelinense

OCh 368T (96.3 %). Based on the data presented above, it is concluded that strain DSG-S4-2T represents a novel species of the genus

Roseibium

, for which the name Roseibium aquae sp. nov. is proposed. The type strain is DSG-S4-2T ( = CGMCC 1.12426T = JCM 19310T).
Novel Natural Product Discovery from Marine Sponges and their Obligate Symbiotic Organisms
Authors: Monaco Regina R. , Quinlan Rena F.
Published: May 2014

Discovery of novel natural products is an accepted method for the elucidation of pharmacologically active molecules and drug leads. Best known sources for such discovery have been terrestrial plants and microbes, accounting for about 85% of the approved natural products in pharmaceutical use (1), and about 60% of approved pharmaceuticals and new drug applications annually (2). Discovery in the marine environment has lagged due to the difficulty of exploration in this ecological niche. Exploration began in earnest in the 1950’s, after technological advances such as scuba diving allowed collection of marine organisms, primarily at a depth to about 15m.

Natural products from filter feeding marine invertebrates and in particular, sponges, have proven to be a rich source of structurally unique pharmacologically active compounds, with over 16,000 molecules isolated thus far (3, 1) and a continuing pace of discovery at hundreds of novel bioactive molecules per year. All classes of pharmaceuticals have been represented in this discovery process, including antiprotazoals, pesticides, TGF-beta inhibitors, cationic channel blockers, anticancer, cytotoxic, antiviral, anti-inflammatory and antibacterial compounds. Important biosynthetic pathways found in sponges which give rise to these compounds include the terpenoid (4), fatty acid, polyketoid, quinone reductase, alkaloid, isoprenoid (5), and non-ribosomal protein synthase pathways.
Reconstructing Austronesian population history in Island Southeast Asia
Authors: Lipson Mark , Loh Po-Ru , Patterson Nick , Moorjani Priya , Ko Ying-Chin , Stoneking Mark , Berger Bonnie , Reich David
Published: May 2014

Austronesian languages are spread across half the globe, from Easter Island to Madagascar. Evidence from linguistics and archaeology indicates that the “Austronesian expansion,” which began 4–5 thousand years ago, likely had roots in Taiwan, but the ancestry of present-day Austronesian-speaking populations remains controversial. Here, focusing primarily on Island Southeast Asia, we analyze genome-wide data from 56 populations using new methods for tracing ancestral gene flow. We show that all sampled Austronesian groups harbor ancestry that is more closely related to aboriginal Taiwanese than to any present-day mainland population. Surprisingly, western Island Southeast Asian populations have also inherited ancestry from a source nested within the variation of present-day populations speaking Austro-Asiatic languages, which have historically been nearly exclusive to the mainland. Thus, either there was once a substantial Austro-Asiatic presence in Island Southeast Asia, or Austronesian speakers migrated to and through the mainland, admixing there before continuing to western Indonesia.
Efficient algorithms for calculating small-angle scattering from large model structures
Authors: Olds Daniel P. , Duxbury Phillip M.
Published: May 2014

This paper compares Monte Carlo approaches and fast Fourier transform (FFT) methods to efficiently calculate small-angle scattering (SAS) profiles from large morphological models. These methods enable calculation of SAS from complex nanoscale morphologies commonly encountered in modern polymeric and nanoparticle-based systems which have no exact analytical representation and are instead represented digitally using many millions of subunits, so that algorithms with linear or near-linear scaling are essential. The Monte Carlo method, referred to as the Monte Carlo distribution function method (MC-DFM), is presented and its accuracy validated using a number of simple morphologies, while the FFT calculations are based on the fastest implementations available. The efficiency, usefulness and inherent limits of DFM and FFT approaches are explored using a series of complex morphological models, including Gaussian chain ensembles and two-phase three-dimensional interpenetrating nanostructures.
The effect of Sn for Ti substitution on the average and local crystal structure of BaTi1−xSnxO3(0 ≤x≤ 0.20)
Authors: Veselinović Ljiljana , Mitrić Miodrag , Mančić Lidija , Vukomanović Marija , Hadžić Branka , Marković Smilja , Uskoković Dragan
Published: May 2014

The effect of Sn for Ti substitution on the crystal structure of a perovskite, barium titanate stannate (BTS), BaTi1−xSnxO3forx= 0, 0.025, 0.05, 0.07, 0.10, 0.12, 0.15 and 0.20, was investigated. The powders were prepared by the conventional solid-state reaction technique. The structural investigations of the BTS powders were done at room temperature by X-ray powder diffraction (XRD), transmission electron microscopy (TEM), high-resolution TEM (HRTEM), selected-area electron diffraction (SAED) and Raman spectroscopy analyses. Rietveld refinement of XRD data indicates that gradual replacement of titanium by tin in BaTiO3provokes a phase transition from tetragonal for 0 ≤x≤ 0.07 to cubic forx= 0.12, 0.15 and 0.20. The coexistence of tetragonal (P4mm) and cubic (Pm\overline 3m) crystal phases was established in powder with nominal composition BaTi0.9Sn0.1O3. The crystal phases determined by Rietveld refinement were confirmed by HRTEM and SAED analyses. The crystal structures of the BTS powders at short-range scale were studied by Raman spectroscopy, which shows tetragonal (P4mm) and a small fraction of orthorhombic (Pmm2) crystal phases for all the examined BTS powders, implying a lower local ordering when compared to the average symmetry.
A suite of software for processing MicroED data of extremely small protein crystals
Authors: Iadanza Matthew G. , Gonen Tamir
Published: May 2014

Electron diffraction of extremely small three-dimensional crystals (MicroED) allows for structure determination from crystals orders of magnitude smaller than those used for X-ray crystallography. MicroED patterns, which are collected in a transmission electron microscope, were initially not amenable to indexing and intensity extraction by standard software, which necessitated the development of a suite of programs for data processing. The MicroED suite was developed to accomplish the tasks of unit-cell determination, indexing, background subtraction, intensity measurement and merging, resulting in data that can be carried forward to molecular replacement and structure determination. Thisad hocsolution has been modified for more general use to provide a means for processing MicroED data until the technique can be fully implemented into existing crystallographic software packages. The suite is written in Python and the source code is available under a GNU General Public License.
Superparamagnetic regular nanopillar-like structures studied by grazing-incidence X-ray scattering: effect of vertical correlation
Authors: Paul Amitesh , Paul Neelima , Müller-Buschbaum Peter , Bauer Andreas , Böni Peter
Published: May 2014

Grazing-incidence small-angle X-ray scattering is reported from nanoclusters in superparamagnetic (SPM) polycrystalline Co separated by Au. The self-organization of the Co nanoclusters is in the form of nanopillar-like structures with high perpendicular magnetic anisotropy. A distinct signature of regular near-neighbour ordering is observed, which is commonly observed in patterned nanostructures. The estimated cluster sizes corroborate with those estimated from their magnetic field response. Most significantly, the SPM limit for these clusters can be raised to above room temperature (∼325 K) with an increase in the vertical correlation of the nanopillars. The slow response time of these uniform nanomagnetic grains (with respect to a 10 kHz AC field) suggests their possible usage as potential magnetic storage devices in the form of three-dimensional nanopillars.
Magnetic field dependent small-angle neutron scattering on a Co nanorod array: evidence for intraparticle spin misalignment
Authors: Günther A. , Bick J.-P. , Szary P. , Honecker D. , Dewhurst C. D. , Keiderling U. , Feoktystov A. V. , Tschöpe A. , Birringer R. , Michels A.
Published: May 2014

The structural and magnetic properties of a cobalt nanorod array have been studied by means of magnetic field dependent small-angle neutron scattering (SANS). Measurement of the unpolarized SANS cross section dΣ/dΩ of the saturated sample in the two scattering geometries where the applied magnetic fieldHis either perpendicular or parallel to the wavevectorkiof the incoming neutron beam allows one to separate nuclear from magnetic SANS, without employing the usual sector-averaging procedure. The analysis of the SANS data in the saturated state provides structural parameters (rod radius and centre-to-centre distance) that are in good agreement with results from electron microscopy. Between saturation and the coercive field, a strong field dependence of dΣ/dΩ is observed (in both geometries), which cannot be explained using the conventional expression of the magnetic SANS cross section of magnetic nanoparticles in a homogeneous nonmagnetic matrix. The origin of the strong field dependence of dΣ/dΩ is believed to be related to intradomain spin misalignment, due to magnetocrystalline and magnetoelastic anisotropies and magnetostatic stray fields.
Sampling statistics of diffraction from nanoparticle powder aggregates
Authors: Öztürk Hande , Yan Hanfei , Hill John P. , Noyan Ismail C.
Published: May 2014

In this study, the sampling statistics of X-ray diffraction data obtained from polycrystalline nanopowders are studied through analytical formulations and numerical modelling. It is shown that the very large acceptance angles of crystalline nanoparticles can cause issues in computing the number of diffracting grains scattering into a given Bragg reflection. These results intimate that formulations previously tested and verified for polycrystalline aggregates with grains larger than 500 nm should be revalidated for particles with coherent scattering lengths below 10 nm.
Quantifying the quality of the experiments used to grow protein crystals: theiQCsuite
Authors: Mele Katarina , Li Rongxin , Fazio Vincent J. , Newman Janet
Published: May 2014

Millions of crystallization trials are set up each year, with no clear metrics for determining if the experiments were correctly dispensed. This article reports the development of a software tool (iQC–image Quality Control) that recognizes factors associated with suboptimal experimental control during the setting up of protein crystallization trials. In its simplest form,iQCreturns a report that gives an overall rating to the quality of an experimental setup. TheiQCsoftware is able to identify many common problems observed in setting up crystallization trials – droplets that have associated splatter; droplets with air bubbles; the positional accuracy of droplet placement; elongated or otherwise `non-circular' drops – as well as detecting small and large droplets. An obvious use of this application is to track the status of the instrumentation used to set up crystallization trials in a multi-user laboratory.
The conditions and potential of RMB as an international reserve currency
Authors: Wu Jun , Pan Yingli , Zhu Qi
Published: May 2014

Purpose

– The purpose of this paper is to identify the determinants for currency internationalization and forecast the potential of RMB as an international reserve currency.

Design/methodology/approach

– This paper performs linear or non-linear regressions of the shares of eight major international reserve currencies as the reserve assets in global central banks on the macro economic and financial variables of their corresponding countries to identify the determinants for their international positions, and conducts an “counter-factual simulation” for the potential of RMB as an international reserve currency.

Findings

– This paper finds that the economic size and the “network externalities” are the most important determinants for the international status of a reserve currency; that exchange rate volatility has negative impacts; the conditions for the RMB internationalization are basically available. The simulation for the potential of RMB as an international reserve currency reveals that the international role of RMB could surpass that of the Japanese Yen and the British Pound, and get close to Euro in the coming 15 years. Based on the empirical evidence, this paper suggests a promoting strategy for RMB internationalization.

Research limitations/implications

– This paper has not taken the influence of economic systemic and political factors on the process of RMB internationalization into account.

Practical implications

– RMB internationalization promotion should follow the strategy of “stably create RMB international demand in the initial period and dramatically release the RMB overseas supply in the latter period” in the coming 15 years.

Originality/value

– The conclusions and policy implications are from the results of the empirical analysis on the 45-year historical experience on the eight main international currencies.
An embedding finite element method for viscous incompressible flows with complex immersed boundaries on Cartesian grids
Authors: Lo D.C. , Hsieh Chih-Min , Young D.L.
Published: May 2014

Purpose

– The main advantage of the proposed method is that the computations can be performed on a Cartesian grid with complex immersed boundaries (IBs). The purpose of this paper is to device a numerical scheme based on an embedding finite element method for the solution of two-dimensional (2D) Navier-Stokes equations.

Design/methodology/approach

– Geometries featuring the stationary solid obstacles in the flow are embedded in the Cartesian grid with special discretizations near the embedded boundary to ensure the accuracy of the solution in the cut cells. To comprehend the complexities of the viscous flows with IBs, the paper adopts a compact interpolation scheme near the IBs that allows to satisfy the second-order accuracy and the conservation property of the solver. The interpolation scheme is designed by virtue of the shape function in the finite element scheme.

Findings

– Three numerical examples are selected to demonstrate the accuracy and flexibility of the proposed methodology. Simulation of flow past a circular cylinder for a range of Re=20-200 shows excellent agreements with other results using different numerical schemes. Flows around a pair of tandem cylinders and several bodies are particularly investigated. The paper simulates the time-based variation of the flow phenomena for uniform flow past a pair of cylinders with various streamwise gaps between two cylinders. The results in terms of drag coefficient and Strouhal number show excellent agreements with the results available in the literature.

Originality/value

– Details of the flow characteristics, such as velocity distribution, pressure and vorticity fields are presented. It is concluded the combined embedding boundary method and FE discretizations are robust and accurate for solving 2D fluid flows with complex IBs.
Finite difference approach in porous media transport modeling for magnetohydrodynamic unsteady flow over a vertical plate
Authors: Ahmed Sahin , Batin Abdul , J. Chamkha Ali
Published: May 2014

Purpose

– The purpose of this paper is to examine the effects of Darcian drag force and radiation-conduction on unsteady two-dimensional magnetohydrodynamic flow of viscous, electrically conducting and Newtonian fluid over a vertical plate adjacent to a Darcian regime in presence of thermal radiation and transversal magnetic field. A well-tested, numerically stable Crank-Nicolson finite-difference procedure is employed for the conservation equations. Excellent agreement is obtained for numerical solutions with previously published work.

Design/methodology/approach

– In this investigation, an efficient, accurate, extensively validated and unconditionally stable finite-difference scheme based on the Crank-Nicolson model is developed to solve the governing coupled, non-linear partial differential equations. The accuracy and effectiveness of the method are demonstrated.

Findings

– Different numerical results are obtained and presented graphically to explain the effect of various physical parameters on the velocity and temperature profiles, local, as well as average, skin friction and Nusselt number. It is found that, with a rise in Darcian drag force, flow velocity and temperature are reduced, but increased for all times. Both average and local skin frictions are reduced considerably with an increase in Darcian drag force, but reversed behavior is observed for the local Nusselt number. Increasing the thermal radiation effects accelerated the flow velocity as well as the fluid temperature and wall local skin friction in a saturated porous medium, but effectively reduced the local Nusselt number and average Nusselt number at the wall. Comparison with previously published works in the limits shows excellent agreement.

Research limitations/implications

– The analysis is valid for unsteady, two-dimensional laminar flow of an optically thick no-gray gas, electrically conducting, and Newtonian fluid past an isothermal vertical surface adjacent to the Darcian regime with variable surface temperature. An extension to three-dimensional flow case is left for future work.

Practical implications

– Practical interest of such study includes applications in electromagnetic lubrication, boundary cooling, bio-physical systems and in many branches of engineering and science. It is well known that the effect of thermal radiation is important in space technology and high temperature processes. Thermal radiation also plays an important role in controlling heat transfer process in polymer processing industry.