bluuebunny/crossref_metadata_2025 huggingface dataset:
ICL light in a z~0.5 cluster: the MUSE perspective
Authors: Pompei E. , Adami C. ,   the XXL team
Published: March 2017

Intracluster light is contributed by both stars and gas and it is an important tracer of the interaction history of galaxies within a cluster. We present here the results obtained from MUSE observations of an intermediate redshift (z~ 0.5) cluster taken from the XXL survey and we conclude that the most plausible process responsible for the observed amount of ICL is ram pressure stripping.
A new concept of transonic galactic outflows and its application to the Sombrero galaxy
Authors: Igarashi Asuka , Mori Masao , Nitta Shin-ya
Published: March 2017

We study fundamental properties of transonic galactic outflows in the gravitational potential of a cold dark matter halo (DMH) with a central super-massive black hole (SMBH) assuming a polytropic, steady and spherically symmetric state. We have classified the transonic solutions with respect to their topology in the phase space. As a result, we have found two types of transonic solutions characterized by a magnitude relationship between the gravity of DMH and that of SMBH. These two types of solutions have different loci of the transonic points; one transonic point is formed at a central region (< 0.01kpc) and another is at a distant region (> 100kpc). Also, mass fluxes and outflow velocities are different between the two solutions. These two transonic solutions may play different roles on the star formation history of galaxies and the metal contamination of intergalactic space. Furthermore, we have applied our model to the Sombrero galaxy. In this galaxy, the wide-spread hot gas is detected as an apparent trace of galactic outflows while the star-formation rate is disproportionately low, and the observed gas density distribution is quite similar to the hydrostatic state (Li et al. 2011). To solve this discrepancy, we propose a slowly accelerating outflow in which the transonic point forms in a distant region (~ 120 kpc) and the subsonic region spreads across the stellar distribution. In the subsonic region, the gas density distribution is similar to that of the hydrostatic state. Our model predicts the possibility of the slowly accelerating outflow in the Sombrero galaxy. Igarashi et al. 2014 used the isothermal model and well reproduced the observed gas density distribution, but the estimated mass flux (1.8M⊙/yr) is lager than the mass of the gas supplied by stars (0.3-0.4M⊙/yr). Then, we expect that the polytropic model may reproduce the observational mass of the supplied gas (Igarashi et al. 2015). Such slowly accelerating outflows should be distinguished from the conventional supersonic outflows frequently argued in star-forming galaxies.
A Citizen-Science-enabled Comprehensive Search for XUV-disk Galaxies
Authors: Thilker David A.
Published: March 2017

Initial efforts to identify extended UV disk (XUV-disk) galaxies were confined to nearby targets using image products from early in the GALEX mission. We developed a beta Zooniverse-based citizen science project to address this issue, specifically (1) allowing a dramatically larger galaxy sample by crowd-sourcing blink comparison UV-optical image inspection to volunteers, and (2) incorporating all archived GALEX data for each target considered. We aim to widely deploy this project to the public within the upcoming year.
Delving into the gas-phase of the CALIFA galaxies to trace O and N gradients
Authors: Pérez-Montero Enrique , García-Benito Rubén , Vílchez José M. ,   the CALIFA collaboration
Published: March 2017

We study the radial distribution of oxygen and nitrogen abundances in H ii regions in 350 galaxies observed in the CALIFA survey using the semi-empirical N-sensitive code Hii-Chi-mistry. A separate analysis of N/O when using [N ii] is justified as the dispersion in the O/H-N/O diagram is very large. In fact different O/H and N/O slope distributions and flattening in the outskirts are obtained.On the other hand there is a tight correlation between O/H and N/O when the values of the fittings at the effective radius are considered as representative of each galaxy.
The Structure of Halo Gas around M33
Authors: Keenan Olivia C. , Davies Jonathan I. , Taylor Rhys , Minchin Robert F.
Published: March 2017

Understanding the distribution of gas in and around galaxies is vital for our interpretation of galaxy formation and evolution. As part of the Arecibo Galaxy Environment Survey (AGES) we have observed the neutral hydrogen (HI) gas in and around the nearby Local Group galaxy M33 to a greater depth than previous observations. As part of this project we investigated the absence of optically detected dwarf galaxies in its neighbourhood, which is contrary to predictions of galaxy formation models. We observed 22 discrete clouds, 11 of which were previously undetected and none of which have optically detected counterparts. We find one particularly interesting hydrogen cloud, which has many similar characteristics to hydrogen distributed in the disk of a galaxy. This cloud, if it is at the distance of M33, has a HI mass of around 107 M⊙ and a diameter of 18 kpc, making it larger in size than M33 itself.
What can the outskirts of galaxies tell us about dark matter?
Authors: Power Chris
Published: March 2017

Deep observations of galaxy outskirts reveal faint extended stellar components (ESCs) of streams, shells, and halos, which are ghostly remnants of the tidal disruption of satellite galaxies. We use cosmological galaxy formation simulations in Cold Dark Matter (CDM) and Warm Dark Matter (WDM) models to explore how the dark matter model influences the spatial, kinematic, and orbital properties of ESCs. These reveal that the spherically averaged stellar mass density at large galacto-centric radius can be depressed by up to a factor of ~10 in WDM models relative to the CDM model, reflecting the anticipated suppressed abundance of satellite galaxies in WDM models. However, these differences are much smaller in WDM models that are compatible with observational limits, and are comparable in size to the system-to-system variation we find within the CDM model. This suggests that it will be challenging to place limits on dark matter using only the unresolved ESC.
Disentangling the intragroup HI in Compact Groups of galaxies by means of X3D visualization
Authors: Verdes-Montenegro Lourdes , Vogt Frederic , Aubery Claire , Duret Laetitie , Garrido Julián , Sánchez Susana , Yun Min S. , Borthakur Sanchayeeta , Hess Kelley , Cluver Michelle , del Olmo Ascensión , Perea Jaime
Published: March 2017

As an extreme kind of environment, Hickson Compact groups (HCGs) have shown to be very complex systems. HI-VLA observations revealed an intrincated network of HI tails and bridges, tracing pre-processing through extreme tidal interactions. We found HCGs to show a large HI deficiency supporting an evolutionary sequence where gas-rich groups transform via tidal interactions and ISM (interstellar medium) stripping into gas-poor systems. We detected as well a diffuse HI component in the groups, increasing with evolutionary phase, although with uncertain distribution. The complex net of detected HI as observed with the VLA seems hence so puzzling as the missing one. In this talk we revisit the existing VLA information on the HI distribution and kinematics of HCGs by means of X3D visualization. X3D constitutes a powerful tool to extract the most from HI data cubes and a mean of simplifying and easing the access to data visualization and publication via three-dimensional (3-D) diagrams.
Dense Cloud Cores revealed by ALMA CO observations in the low metallicity dwarf galaxy WLM
Authors: Rubio M. , Elmegreen B. , Hunter D. , Cortes J. , Brinks E. , Cigan P.
Published: March 2017

Understanding stellar birth requires observations of the clouds in which they form. These clouds are dense and self-gravitating, and in all existing observations, they are molecular with H2 the dominant species and CO the best available. When the abundances of carbon and oxygen are low compared to hydrogen, and the opacity from dust is also low, as in primeval galaxies and local dwarf irregular galaxies CO forms slowly and is easily destroyed, so it cannot accumulate inside dense clouds. Then we lose our ability to trace the gas in regions of star formation and we lose critical information on the temperatures, densities, and velocities of the material that collapses. I will report on high resolution observations with ALMA of CO clouds in the local group dwarf irregular galaxy WLM, which has a metallicity that is 13% of the solar value and 50% lower than the previous CO detection threshold and the properties derived of very small dense CO clouds mapped..
Populist radical right parties and mass polarization in the Netherlands
Authors: Castanho Silva Bruno
Published: March 2017

Radical parties have been found to succeed under conditions of mass polarization. It is argued that their message resonates better with voters at the extremes of an ideological spectrum. This paper investigates if the reverse also holds, meaning that radical parties may contribute to the polarization of the public. I test this claim in the Netherlands, a country that has experienced the rise of populist radical right parties since 2002, using a synthetic control model built with a pool of comparable countries and Eurobarometer survey data. Results show that, after the rise of Pim Fortuyn and Geert Wilders, the level of polarization among the Dutch public increased more than it otherwise would have. These findings contribute to understanding the connection between elite- and mass-level polarization, and the consequences of populist radical right parties’ emergence in Western Europe.
Mechanosignaling activation of TGFβ maintains intervertebral disc homeostasis
Authors: Bian Qin , Ma Lei , Jain Amit , Crane Janet L , Kebaish Khaled , Wan Mei , Zhang Zhengdong , Edward Guo X , Sponseller Paul D , Séguin Cheryle A , Riley Lee H , Wang Yongjun , Cao Xu
Published: March 2017

Intervertebral disc (IVD) degeneration is the leading cause of disability with no disease-modifying treatment. IVD degeneration is associated with instable mechanical loading in the spine, but little is known about how mechanical stress regulates nucleus notochordal (NC) cells to maintain IVD homeostasis. Here we report that mechanical stress can result in excessive integrin αvβ6-mediated activation of transforming growth factor beta (TGFβ), decreased NC cell vacuoles, and increased matrix proteoglycan production, and results in degenerative disc disease (DDD). Knockout of TGFβ type II receptor (TβRII) or integrin αvin the NC cells inhibited functional activity of postnatal NC cells and also resulted in DDD under mechanical loading. Administration of RGD peptide, TGFβ, and αvβ6-neutralizing antibodies attenuated IVD degeneration. Thus, integrin-mediated activation of TGFβ plays a critical role in mechanical signaling transduction to regulate IVD cell function and homeostasis. Manipulation of this signaling pathway may be a potential therapeutic target to modify DDD.
Spontaneous mutations of a model heterotrophic marine bacterium
Authors: Sun Ying , Powell Kate E , Sung Way , Lynch Michael , Moran Mary Ann , Luo Haiwei
Published: March 2017

Heterotrophic marine bacterioplankton populations display substantive genomic diversity that is commonly explained to be the result of selective forces imposed by resource limitation or interactions with phage and predators. Here we use a mutation-accumulation experiment followed by whole-genome sequencing of mutation lines to determine an unbiased rate and molecular spectrum of spontaneous mutations for a model heterotrophic marine bacterium in the globally important Roseobacter clade, Ruegeria pomeroyi DSS-3. We find evidence for mutational bias towards deletions over insertions, and this process alone could account for a sizable portion of genome size diversity among roseobacters and also implies that lateral gene transfer and/or selection must also play a role in maintaining roseobacters with large genome sizes. We also find evidence for a mutational bias in favor of changes from A/T to G/C nucleobases, which explains widespread occurrences of G/C-enriched Roseobacter genomes. Using the calculated mutation rate of 1.39 × 10−10 per base per generation, we implement a ‘mutation-rate clock’ approach to date the evolution of roseobacters by assuming a constant mutation rate along their evolutionary history. This approach gives an estimated date of Roseobacter genome expansion in good agreement with an earlier fossil-based estimate of ~250 million years ago and is consistent with a hypothesis of a correlated evolutionary history between roseobacters and marine eukaryotic phytoplankton groups.
White matter maturation is associated with the emergence of Theory of Mind in early childhood
Authors: Grosse Wiesmann Charlotte , Schreiber Jan , Singer Tania , Steinbeis Nikolaus , Friederici Angela D.
Published: March 2017

The ability to attribute mental states to other individuals is crucial for human cognition. A milestone of this ability is reached around the age of 4, when children start understanding that others can have false beliefs about the world. The neural basis supporting this critical step is currently unknown. Here, we relate this behavioural change to the maturation of white matter structure in 3- and 4-year-old children. Tract-based spatial statistics and probabilistic tractography show that the developmental breakthrough in false belief understanding is associated with age-related changes in local white matter structure in temporoparietal regions, the precuneus and medial prefrontal cortex, and with increased dorsal white matter connectivity between temporoparietal and inferior frontal regions. These effects are independent of co-developing cognitive abilities. Our findings show that the emergence of mental state representation is related to the maturation of core belief processing regions and their connection to the prefrontal cortex.
Genomic innovations linked to infection strategies across emerging pathogenic chytrid fungi
Authors: Farrer Rhys A. , Martel An , Verbrugghe Elin , Abouelleil Amr , Ducatelle Richard , Longcore Joyce E. , James Timothy Y. , Pasmans Frank , Fisher Matthew C. , Cuomo Christina A.
Published: March 2017

To understand the evolutionary pathways that lead to emerging infections of vertebrates, here we explore the genomic innovations that allow free-living chytrid fungi to adapt to and colonize amphibian hosts. Sequencing and comparing the genomes of two pathogenic species of Batrachochytrium to those of close saprophytic relatives reveals that pathogenicity is associated with remarkable expansions of protease and cell wall gene families, while divergent infection strategies are linked to radiations of lineage-specific gene families. By comparing the host–pathogen response to infection for both pathogens, we illuminate the traits that underpin a strikingly different immune response within a shared host species. Our results show that, despite commonalities that promote infection, specific gene-family radiations contribute to distinct infection strategies. The breadth and evolutionary novelty of candidate virulence factors that we discover underscores the urgent need to halt the advance of pathogenic chytrids and prevent incipient loss of biodiversity.
Hierarchical on-surface synthesis and electronic structure of carbonyl-functionalized one- and two-dimensional covalent nanoarchitectures
Authors: Steiner Christian , Gebhardt Julian , Ammon Maximilian , Yang Zechao , Heidenreich Alexander , Hammer Natalie , Görling Andreas , Kivala Milan , Maier Sabine
Published: March 2017

The fabrication of nanostructures in a bottom-up approach from specific molecular precursors offers the opportunity to create tailored materials for applications in nanoelectronics. However, the formation of defect-free two-dimensional (2D) covalent networks remains a challenge, which makes it difficult to unveil their electronic structure. Here we report on the hierarchical on-surface synthesis of nearly defect-free 2D covalent architectures with carbonyl-functionalized pores on Au(111), which is investigated by low-temperature scanning tunnelling microscopy in combination with density functional theory calculations. The carbonyl-bridged triphenylamine precursors form six-membered macrocycles and one-dimensional (1D) chains as intermediates in an Ullmann-type coupling reaction that are subsequently interlinked to 2D networks. The electronic band gap is narrowed when going from the monomer to 1D and 2D surface-confined π-conjugated organic polymers comprising the same building block. The significant drop of the electronic gap from the monomer to the polymer confirms an efficient conjugation along the triphenylamine units within the nanostructures.
Periodic potentials in hybrid van der Waals heterostructures formed by supramolecular lattices on graphene
Authors: Gobbi Marco , Bonacchi Sara , Lian Jian X. , Liu Yi , Wang Xiao-Ye , Stoeckel Marc-Antoine , Squillaci Marco A. , D’Avino Gabriele , Narita Akimitsu , Müllen Klaus , Feng Xinliang , Olivier Yoann , Beljonne David , Samorì Paolo , Orgiu Emanuele
Published: March 2017

The rise of 2D materials made it possible to form heterostructures held together by weak interplanar van der Waals interactions. Within such van der Waals heterostructures, the occurrence of 2D periodic potentials significantly modifies the electronic structure of single sheets within the stack, therefore modulating the material properties. However, these periodic potentials are determined by the mechanical alignment of adjacent 2D materials, which is cumbersome and time-consuming. Here we show that programmable 1D periodic potentials extending over areas exceeding 104 nm2 and stable at ambient conditions arise when graphene is covered by a self-assembled supramolecular lattice. The amplitude and sign of the potential can be modified without altering its periodicity by employing photoreactive molecules or their reaction products. In this regard, the supramolecular lattice/graphene bilayer represents the hybrid analogue of fully inorganic van der Waals heterostructures, highlighting the rich prospects that molecular design offers to create ad hoc materials.
Probing cytoskeletal modulation of passive and active intracellular dynamics using nanobody-functionalized quantum dots
Authors: Katrukha Eugene A. , Mikhaylova Marina , van Brakel Hugo X. , van Bergen en Henegouwen Paul M. , Akhmanova Anna , Hoogenraad Casper C. , Kapitein Lukas C.
Published: March 2017

The cytoplasm is a highly complex and heterogeneous medium that is structured by the cytoskeleton. How local transport depends on the heterogeneous organization and dynamics of F-actin and microtubules is poorly understood. Here we use a novel delivery and functionalization strategy to utilize quantum dots (QDs) as probes for active and passive intracellular transport. Rapid imaging of non-functionalized QDs reveals two populations with a 100-fold difference in diffusion constant, with the faster fraction increasing upon actin depolymerization. When nanobody-functionalized QDs are targeted to different kinesin motor proteins, their trajectories do not display strong actin-induced transverse displacements, as suggested previously. Only kinesin-1 displays subtle directional fluctuations, because the subset of microtubules used by this motor undergoes prominent undulations. Using actin-targeting agents reveals that F-actin suppresses most microtubule shape remodelling, rather than promoting it. These results demonstrate how the spatial heterogeneity of the cytoskeleton imposes large variations in non-equilibrium intracellular dynamics.
Real-time reliable determination of binding kinetics of DNA hybridization using a multi-channel graphene biosensor
Authors: Xu Shicai , Zhan Jian , Man Baoyuan , Jiang Shouzhen , Yue Weiwei , Gao Shoubao , Guo Chengang , Liu Hanping , Li Zhenhua , Wang Jihua , Zhou Yaoqi
Published: March 2017

Reliable determination of binding kinetics and affinity of DNA hybridization and single-base mismatches plays an essential role in systems biology, personalized and precision medicine. The standard tools are optical-based sensors that are difficult to operate in low cost and to miniaturize for high-throughput measurement. Biosensors based on nanowire field-effect transistors have been developed, but reliable and cost-effective fabrication remains a challenge. Here, we demonstrate that a graphene single-crystal domain patterned into multiple channels can measure time- and concentration-dependent DNA hybridization kinetics and affinity reliably and sensitively, with a detection limit of 10 pM for DNA. It can distinguish single-base mutations quantitatively in real time. An analytical model is developed to estimate probe density, efficiency of hybridization and the maximum sensor response. The results suggest a promising future for cost-effective, high-throughput screening of drug candidates, genetic variations and disease biomarkers by using an integrated, miniaturized, all-electrical multiplexed, graphene-based DNA array.
Retraction Note: Experimental orthotopic transplantation of a tissue-engineered oesophagus in rats
Authors: Sjöqvist Sebastian , Jungebluth Philipp , Lim Mei Ling , Haag Johannes C. , Gustafsson Ylva , Lemon Greg , Baiguera Silvia , Burguillos Miguel Angel , Del Gaudio Costantino , Rodríguez Antonio Beltrán , Sotnichenko Alexander , Kublickiene Karolina , Ullman Henrik , Kielstein Heike , Damberg Peter , Bianco Alessandra , Heuchel Rainer , Zhao Ying , Ribatti Domenico , Ibarra Cristián , Joseph Bertrand , Taylor Doris A. , Macchiarini Paolo
Published: March 2017

Nature Communications 5: Article number: 3562 (2014); Published 15 April 2014; Updated 21 March 2017 This Article is retracted by the authors. Nature Communications previously issued an Editorial Expression of Concern (http://www.nature.com/articles/ncomms13310) related to this Article, following the publication of a report commissioned by The Karolinska Institute and prepared by the Expert Group for Misconduct in Research at the Swedish Central Ethical Review Board.
A high-throughput framework for determining adsorption energies on solid surfaces
Authors: Montoya Joseph H. , Persson Kristin A.
Published: March 2017

In this work, we present a high-throughput workflow for calculation of adsorption energies on solid surfaces using density functional theory. Using open-source computational tools from the Materials Project infrastructure, we automate the procedure of constructing symmetrically distinct adsorbate configurations for arbitrary slabs. These algorithms are further used to construct and run workflows in a standard, automated way such that user intervention in the simulation procedure is minimal. To validate our approach, we compare results from our workflow to previous experimental and theoretical benchmarks from the CE27 database of chemisorption energies on solid surfaces. These benchmarks also illustrate how the task of performing and managing over 200 individual density functional theory calculations may be reduced to a single submission procedure and subsequent analysis. By enabling more efficient high-throughput computations of adsorption energies, these tools will accelerate theory-guided discovery of advanced materials for applications in catalysis and surface science.
A short discourse on vascular tissue engineering
Authors: Chang William G. , Niklason Laura E.
Published: March 2017

Vascular tissue engineering has significant potential to make a major impact on a wide array of clinical problems. Continued progress in understanding basic vascular biology will be invaluable in making further advancements. Past and current achievements in tissue engineering of microvasculature to perfuse organ specific constructs, small vessels for dialysis grafts, and modified synthetic and pediatric large caliber-vessel grafts will be discussed. An emphasis will be placed on clinical trial results with small and large-caliber vessel grafts. Challenges to achieving engineered constructs that satisfy the physiologic, immunologic, and manufacturing demands of engineered vasculature will be explored.
When scientific paradigms lead to tunnel vision: lessons from the study of fear
Authors: Paré Denis , Quirk Gregory J.
Published: March 2017

For the past 30 years, research on the amygdala has largely focused on the genesis of defensive behaviors as its main function. This focus originated from early lesion studies and was supported by extensive anatomical, physiological, and pharmacological data. Here we argue that while much data is consistent with the fear model of amygdala function, it has never been directly tested, in part due to overreliance on the fear conditioning task. In support of the fear model, amygdala neurons appear to signal threats and/or stimuli predictive of threats. However, recent studies in a natural threat setting show that amygdala activity does not correlate with threats, but simply with the movement of the rat, independent of valence. This was true for both natural threats as well as conditioned stimuli; indeed there was no evidence of threat signaling in amygdala neurons. Similar findings are emerging for prefrontal neurons that modulate the amygdala. These recent developments lead us to propose a new conceptualization of amygdala function whereby the amygdala inhibits behavioral engagement. Moreover, we propose that the goal of understanding the amygdala will be best served by shifting away from fear conditioning toward naturalistic approach and avoidance paradigms that involve decision-making and a larger repertoire of spontaneous and learned behaviors, all the while keeping an open mind.
A novel technique to determine the cell type specific response within an in vitro co-culture model via multi-colour flow cytometry
Authors: Clift Martin J. D. , Fytianos Kleanthis , Vanhecke Dimitri , Hočevar Sandra , Petri-Fink Alke , Rothen-Rutishauser Barbara
Published: March 2017

Determination of the cell type specific response is essential towards understanding the cellular mechanisms associated with disease states as well as assessing cell-based targeting of effective therapeutic agents. Recently, there have been increased calls for advanced in vitro multi-cellular models that provide reliable and valuable tools correlative to in vivo. In this pursuit the ability to assess the cell type specific response is imperative. Herein, we report a novel approach towards resolving each specific cell type of a multi-cellular model representing the human lung epithelial tissue barrier via multi-colour flow cytometry (FACS). We proved via ≤ five-colour FACS that the manipulation of this in vitro model allowed each cell type to be resolved with no impact upon cell viability. Subsequently, four-colour FACS verified the ability to determine the biochemical effect (e.g. oxidative stress) of each specific cell type. This technique will be vital in gaining information upon cellular mechanics when using next-level, multi-cellular in vitro strategies.
A Strategy to Delay the Development of Cisplatin Resistance by Maintaining a Certain Amount of Cisplatin-Sensitive Cells
Authors: Duan Guihua , Tang Qianyuan , Yan Hongli , Xie Lijuan , Wang Yun , Zheng Xi Emily , Zhuge Yuzheng , Shen Shanshan , Zhang Bin , Zhang Xiaoqi , Wang Jun , Wang Wei , Zou Xiaoping
Published: March 2017

Cisplatin (ddp), which is commonly employed in the treatment of many advanced cancers, often results in initial therapeutic success; however, rapid progression of ddp-resistant cells remains the main reason for treatment failure. Facd with such a problem, we investigated the fitness differences between ddp-sensitive and ddp-resistant cell lines. We found that the growth of ddp-resistant cells was significantly slower than that of sensitive cells due to elevated ROS levels, which suggested that the ddp resistance mechanisms may have negative impacts on the growth of resistant cells. Furthermore, we observed that, when mixed with ddp-sensitive cells, ddp-resistant cells failed to compete, and the growth of ddp-resistant cells could therefore be suppressed by treatment in vivo. We propose a mathematical model parameterized based on in vivo experiments to describe the allometric growth of tumors consisting of two competing subclones. According to our model, a quantitative strategy with a variant drug-dosing interval is proposed to control tumor growth. Taking advantage of intratumoral competition, our strategy with appropriate dosing intervals could remarkably delay the development of ddp resistance and prolong overall survival. Maintaining a certain number of ddp-sensitive cells rather than eradicating the tumor with continuous treatment is feasible for future tumor treatment.
Transcriptome and functional analysis reveals hybrid vigor for oil biosynthesis in oil palm
Authors: Jin Jingjing , Sun Yanwei , Qu Jing , syah Rahmad , Lim Chin-Huat , Alfiko Yuzer , Rahman Nur Estya Bte , Suwanto Antonius , Yue Genhua , Wong Limsoon , Chua Nam-Hai , Ye Jian
Published: March 2017

Oil palm is the most productive oil crop in the world and composes 36% of the world production. However, the molecular mechanisms of hybrids vigor (or heterosis) between Dura, Pisifera and their hybrid progeny Tenera has not yet been well understood. Here we compared the temporal and spatial compositions of lipids and transcriptomes for two oil yielding organs mesocarp and endosperm from Dura, Pisifera and Tenera. Multiple lipid biosynthesis pathways are highly enriched in all non-additive expression pattern in endosperm, while cytokinine biosynthesis and cell cycle pathways are highly enriched both in endosperm and mesocarp. Compared with parental palms, the high oil content in Tenera was associated with much higher transcript levels of EgWRI1, homolog of Arabidopsis thaliana WRINKLED1. Among 338 identified genes in lipid synthesis, 207 (61%) has been identified to contain the WRI1 specific binding AW motif. We further functionally identified EgWRI1-1, one of three EgWRI1 orthologs, by genetic complementation of the Arabidopsis wri1 mutant. Ectopic expression of EgWRI1-1 in plant produced dramatically increased seed mass and oil content, with oil profile changed. Our findings provide an explanation for EgWRI1 as an important gene contributing hybrid vigor in lipid biosynthesis in oil palm.
Non-classical monocytes are biased progenitors of wound healing macrophages during soft tissue injury
Authors: Olingy Claire E. , San Emeterio Cheryl L. , Ogle Molly E. , Krieger Jack R. , Bruce Anthony C. , Pfau David D. , Jordan Brett T. , Peirce Shayn M. , Botchwey Edward A.
Published: March 2017

Successful tissue repair requires the activities of myeloid cells such as monocytes and macrophages that guide the progression of inflammation and healing outcome. Immunoregenerative materials leverage the function of endogenous immune cells to orchestrate complex mechanisms of repair; however, a deeper understanding of innate immune cell function in inflamed tissues and their subsequent interactions with implanted materials is necessary to guide the design of these materials. Blood monocytes exist in two primary subpopulations, characterized as classical inflammatory or non-classical. While classical monocytes extravasate into inflamed tissue and give rise to macrophages or dendritic cells, the recruitment kinetics and functional role of non-classical monocytes remains unclear. Here, we demonstrate that circulating non-classical monocytes are directly recruited to polymer films within skin injuries, where they home to a perivascular niche and generate alternatively activated, wound healing macrophages. Selective labeling of blood monocyte subsets indicates that non-classical monocytes are biased progenitors of alternatively activated macrophages. On-site delivery of the immunomodulatory small molecule FTY720 recruits S1PR3-expressing non-classical monocytes that support vascular remodeling after injury. These results elucidate a previously unknown role for blood-derived non-classical monocytes as contributors to alternatively activated macrophages, highlighting them as key regulators of inflammatory response and regenerative outcome.
Novel molecular approach to define pest species status and tritrophic interactions from historical Bemisia specimens
Authors: Tay W. T. , Elfekih S. , Polaszek A. , Court L. N. , Evans G. A. , Gordon K. H. J. , De Barro P. J.
Published: March 2017

Museum specimens represent valuable genomic resources for understanding host-endosymbiont/parasitoid evolutionary relationships, resolving species complexes and nomenclatural problems. However, museum collections suffer DNA degradation, making them challenging for molecular-based studies. Here, the mitogenomes of a single 1912 Sri LankanBemisia emiliaecotype puparium, and of a 1942 JapaneseBemisiapuparium are characterised using a Next-Generation Sequencing approach. Whiteflies are small sap-sucking insects includingB.tabacipest species complex.Bemisia emiliae’s draft mitogenome showed a high degree of homology with publishedB.tabacimitogenomes, and exhibited 98–100% partial mitochondrial DNA Cytochrome Oxidase I (mtCOI) gene identity with theB.tabacispecies known as Asia II-7. The partial mtCOI gene of the Japanese specimen shared 99% sequence identity with theBemisia‘JpL’ genetic group. Metagenomic analysis identified bacterial sequences in bothBemisiaspecimens, while hymenopteran sequences were also identified in the JapaneseBemisiapuparium, including complete mtCOI and rRNA genes, and various partial mtDNA genes. At 88–90% mtCOI sequence identity to Aphelinidae wasps, we concluded that the 1942Bemisianymph was parasitized by anEretmocerusparasitoid wasp. Our approach enables the characterisation of genomes and associated metagenomic communities of museum specimens using 1.5 ng gDNA, and to infer historical tritrophic relationships inBemisiawhiteflies.
Feasible attack on detector-device-independent quantum key distribution
Authors: Wei Kejin , Liu Hongwei , Ma Haiqiang , Yang Xiuqing , Zhang Yong , Sun Yongmei , Xiao Jinghua , Ji Yuefeng
Published: March 2017

Recently, to bridge the gap between security of Measurement-device-independent quantum key distribution (MDI-QKD) and a high key rate, a novel protocol, the so-called detector-device-independent QKD (DDI-QKD), has been independently proposed by several groups and has attracted great interest. A higher key rate is obtained, since a single photon bell state measurement (BSM) setup is applied to DDI-QKD. Subsequently, Qi has proposed two attacks for this protocol. However, the first attack, in which Bob’s BSM setup is assumed to be completely a “black box”, is easily prevented by using some additional monitoring devices or by specifically characterizing the BSM. The second attack, which combines the blinding attack and the detector wavelength-dependent efficiency, is not explicitly discussed, and its feasibility is not experimentally confirmed. Here, we show that the second attack is not technically viable because of an intrinsically wavelength-dependent property of a realistic beam splitter, which is an essential component in DDI-QKD. Moreover, we propose a feasible attack that combines a well-known attack—detector blinding attack with intrinsic imperfections of single-photon detectors. The experimental measurement and proof-of-principle test results confirm that our attack can allow Eve to get a copy of quantum keys without being detected and that it is feasible with current technology.
Fabrication of nanotweezers and their remote actuation by magnetic fields
Authors: Iss Cécile , Ortiz Guillermo , Truong Alain , Hou Yanxia , Livache Thierry , Calemczuk Roberto , Sabon Philippe , Gautier Eric , Auffret Stéphane , Buda-Prejbeanu Liliana D. , Strelkov Nikita , Joisten Hélène , Dieny Bernard
Published: March 2017

A new kind of nanodevice that acts like tweezers through remote actuation by an external magnetic field is designed. Such device is meant to mechanically grab micrometric objects. The nanotweezers are built by using a top-down approach and are made of two parallelepipedic microelements, at least one of them being magnetic, bound by a flexible nanohinge. The presence of an external magnetic field induces a torque on the magnetic elements that competes with the elastic torque provided by the nanohinge. A model is established in order to evaluate the values of the balanced torques as a function of the tweezers opening angles. The results of the calculations are confronted to the expected values and validate the overall working principle of the magnetic nanotweezers.
X-ray ptychographic and fluorescence microscopy of frozen-hydrated cells using continuous scanning
Authors: Deng Junjing , Vine David J. , Chen Si , Jin Qiaoling , Nashed Youssef S. G. , Peterka Tom , Vogt Stefan , Jacobsen Chris
Published: March 2017

X-ray microscopy can be used to image whole, unsectioned cells in their native hydrated state. It complements the higher resolution of electron microscopy for submicrometer thick specimens, and the molecule-specific imaging capabilites of fluorescence light microscopy. We describe here the first use of fast, continuous x-ray scanning of frozen hydrated cells for simultaneous sub-20 nm resolution ptychographic transmission imaging with high contrast, and sub-100 nm resolution deconvolved x-ray fluorescence imaging of diffusible and bound ions at native concentrations, without the need to add specific labels. By working with cells that have been rapidly frozen without the use of chemical fixatives, and imaging them under cryogenic conditions, we are able to obtain images with well preserved structural and chemical composition, and sufficient stability against radiation damage to allow for multiple images to be obtained with no observable change.
Effects of ecological restoration projects on changes in land cover: A case study on the Loess Plateau in China
Authors: Zhao Jun , Yang Yanzheng , Zhao Qingxia , Zhao Zhong
Published: March 2017

Changes in land cover have become key components of global environmental change and represent the impact of human activity. To better understand the fundamental processes of land transition characteristics before and after the implementation of ecological programmes, we determined the dominant systematic changes in land cover in Yongshou, a hilly-gully region on the Loess Plateau. This was achieved by performing an in-depth analysis of a cross-tabulation matrix and a modified spatial dynamic degree model. Our results indicated that (1) forest land and cultivated land were the most important land cover types in Yongshou and their persistence would greatly affect the landscape pattern of the entire region; (2) the most significant changing signals in the study area during the periods 1992–2000 and 2000–2013 were from immature forest land to forest land, cultivated land to orchards and orchards to construction land; and (3) the region that experienced the most changes during 1992–2000 was the densely populated county seat of Yongshou; however, from 2000–2013, the region of most changes was Changning, a town located in the northcentral region of Yongshou. These findings reveal the main characteristics of the land cover changes in this region and provide insight into the processes underlying these changes.
Reconstruction of noise-driven nonlinear networks from node outputs by using high-order correlations
Authors: Chen Yang , Zhang Zhaoyang , Chen Tianyu , Wang Shihong , Hu Gang
Published: March 2017

Many practical systems can be described by dynamic networks, for which modern technique can measure their outputs, and accumulate extremely rich data. Nevertheless, the network structures producing these data are often deeply hidden in the data. The problem of inferring network structures by analyzing the available data, turns to be of great significance. On one hand, networks are often driven by various unknown facts, such as noises. On the other hand, network structures of practical systems are commonly nonlinear, and different nonlinearities can provide rich dynamic features and meaningful functions of realistic networks. Although many works have considered each fact in studying network reconstructions, much less papers have been found to systematically treat both difficulties together. Here we propose to use high-order correlation computations (HOCC) to treat nonlinear dynamics; use two-time correlations to decorrelate effects of network dynamics and noise driving; and use suitable basis and correlator vectors to unifiedly infer all dynamic nonlinearities, topological interaction links and noise statistical structures. All the above theoretical frameworks are constructed in a closed form and numerical simulations fully verify the validity of theoretical predictions.
De novo sequencing and comparative analysis of leaf transcriptomes of diverse condensed tannin-containing lines of underutilized Psophocarpus tetragonolobus (L.) DC
Authors: Singh Vinayak , Goel Ridhi , Pande Veena , Asif Mehar Hasan , Mohanty Chandra Sekhar
Published: March 2017

Condensed tannin (CT) or proanthocyanidin (PA) is a unique group of phenolic metabolite with high molecular weight with specific structure. It is reported that, the presence of high-CT in the legumes adversely affect the nutrients in the plant and impairs the digestibility upon consumption by animals. Winged bean (Psophocarpus tetragonolobus (L.) DC.) is one of the promising underutilized legume with high protein and oil-content. One of the reasons for its underutilization is due to the presence of CT. Transcriptome sequencing of leaves of two diverse CT-containing lines of P. tetragonolobus was carried out on Illumina Nextseq 500 sequencer to identify the underlying genes and contigs responsible for CT-biosynthesis. RNA-Seq data generated 102586 and 88433 contigs for high (HCTW) and low CT (LCTW) lines of P. tetragonolobus, respectively. Based on the similarity searches against gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) database revealed 5210 contigs involved in 229 different pathways. A total of 1235 contigs were detected to differentially express between HCTW and LCTW lines. This study along with its findings will be helpful in providing information for functional and comparative genomic analysis of condensed tannin biosynthesis in this plant in specific and legumes in general.
Functional confirmation of PLAG1 as the candidate causative gene underlying major pleiotropic effects on body weight and milk characteristics
Authors: Fink Tania , Tiplady Kathryn , Lopdell Thomas , Johnson Thomas , Snell Russell G. , Spelman Richard J. , Davis Stephen R. , Littlejohn Mathew D.
Published: March 2017

A major pleiotropic quantitative trait locus (QTL) located at ~25 Mbp on bovine chromosome 14 affects a myriad of growth and developmental traits in Bos taurus and indicus breeds. These QTL have been attributed to two functional variants in the bidirectional promoter of PLAG1 and CHCHD7. Although PLAG1 is a good candidate for mediating these effects, its role remains uncertain given that these variants are also associated with expression of five additional genes at the broader locus. In the current study, we conducted expression QTL (eQTL) mapping of this region using a large, high depth mammary RNAseq dataset representing 375 lactating cows. Here we show that of the seven previously implicated genes, only PLAG1 and LYN are differentially expressed by QTL genotype, and only PLAG1 bears the same association signature of the growth and body weight QTLs. For the first time, we also report significant association of PLAG1 genotype with milk production traits, including milk fat, volume, and protein yield. Collectively, these data strongly suggest PLAG1 as the causative gene underlying this diverse range of traits, and demonstrate new effects for the locus on lactation phenotypes.
Ca2+-permeable AMPA receptors in mouse olfactory bulb astrocytes
Authors: Droste Damian , Seifert Gerald , Seddar Laura , Jädtke Oliver , Steinhäuser Christian , Lohr Christian
Published: March 2017

Ca2+ signaling in astrocytes is considered to be mainly mediated by metabotropic receptors linked to intracellular Ca2+ release. However, recent studies demonstrate a significant contribution of Ca2+ influx to spontaneous and evoked Ca2+ signaling in astrocytes, suggesting that Ca2+ influx might account for astrocytic Ca2+ signaling to a greater extent than previously thought. Here, we investigated AMPA-evoked Ca2+ influx into olfactory bulb astrocytes in mouse brain slices using Fluo-4 and GCaMP6s, respectively. Bath application of AMPA evoked Ca2+ transients in periglomerular astrocytes that persisted after neuronal transmitter release was inhibited by tetrodotoxin and bafilomycin A1. Withdrawal of external Ca2+ suppressed AMPA-evoked Ca2+ transients, whereas depletion of Ca2+ stores had no effect. Both Ca2+ transients and inward currents induced by AMPA receptor activation were partly reduced by Naspm, a blocker of Ca2+-permeable AMPA receptors lacking the GluA2 subunit. Antibody staining revealed a strong expression of GluA1 and GluA4 and a weak expression of GluA2 in periglomerular astrocytes. Our results indicate that Naspm-sensitive, Ca2+-permeable AMPA receptors contribute to Ca2+ signaling in periglomerular astrocytes in the olfactory bulb.
Modulation of Central Carbon Metabolism by Acetylation of Isocitrate Lyase in Mycobacterium tuberculosis
Authors: Bi Jing , Wang Yihong , Yu Heguo , Qian Xiaoyan , Wang Honghai , Liu Jun , Zhang Xuelian
Published: March 2017

Several enzymes involved in central carbon metabolism such as isocitrate lyase and phosphoenolpyruvate carboxykinase are key determinants of pathogenesis of Mycobacterium tuberculosis (M. tb). In this study, we found that lysine acetylation plays an important role in the modulation of central carbon metabolism in M. tb. Mutant of M. tb defective in sirtuin deacetylase exhibited improved growth in fatty acid-containing media. Global analysis of lysine acetylome of M. tb identified three acetylated lysine residues (K322, K331, and K392) of isocitrate lyase (ICL1). Using a genetically encoding system, we demonstrated that acetylation of K392 increased the enzyme activity of ICL1, whereas acetylation of K322 decreased its activity. Antibodies that specifically recognized acetyllysine at 392 and 322 of ICL1 were used to monitor the levels of ICL1 acetylation in M. tb cultures. The physiological significance of ICL1 acetylation was demonstrated by the observation that M. tb altered the levels of acetylated K392 in response to changes of carbon sources, and that acetylation of K392 affected the abundance of ICL1 protein. Our study has uncovered another regulatory mechanism of ICL1.
Silicon and Carbon Nanocomposite Spheres with Enhanced Electrochemical Performance for Full Cell Lithium Ion Batteries
Authors: Wang Wei , Favors Zachary , Li Changling , Liu Chueh , Ye Rachel , Fu Chengyin , Bozhilov Krassimir , Guo Juchen , Ozkan Mihrimah , Ozkan Cengiz S.
Published: March 2017

Herein, facile synthesis of monodisperse silicon and carbon nanocomposite spheres (MSNSs) is achieved via a simple and scalable surface-protected magnesiothermic reduction with subsequent chemical vapor deposition (CVD) process. Li-ion batteries (LIBs) were fabricated to test the utility of MSNSs as an anode material. LIB anodes based on MSNSs demonstrate a high reversible capacity of 3207 mAh g−1, superior rate performance, and excellent cycling stability. Furthermore, the performance of full cell LIBs was evaluated by using MSNS anode and a LiCoO2 cathode with practical electrode loadings. The MSNS/LiCoO2 full cell demonstrates high gravimetric energy density in the order of 850 Wh L−1 with excellent cycling stability. This work shows a proof of concept of the use of monodisperse Si and C nanocomposite spheres toward practical lithium-ion battery applications.