bluuebunny/crossref_metadata_2025 huggingface dataset:
Hydrogen adsorption and desorption with 3D silicon nanotube-network and film-network structures: Monte Carlo simulations
Authors: Li Ming , Huang Xiaobo , Kang Zhan
Published: August 2015

Hydrogen is clean, sustainable, and renewable, thus is viewed as promising energy carrier. However, its industrial utilization is greatly hampered by the lack of effective hydrogen storage and release method. Carbon nanotubes (CNTs) were viewed as one of the potential hydrogen containers, but it has been proved that pure CNTs cannot attain the desired target capacity of hydrogen storage. In this paper, we present a numerical study on the material-driven and structure-driven hydrogen adsorption of 3D silicon networks and propose a deformation-driven hydrogen desorption approach based on molecular simulations. Two types of 3D nanostructures, silicon nanotube-network (Si-NN) and silicon film-network (Si-FN), are first investigated in terms of hydrogen adsorption and desorption capacity with grand canonical Monte Carlo simulations. It is revealed that the hydrogen storage capacity is determined by the lithium doping ratio and geometrical parameters, and the maximum hydrogen uptake can be achieved by a 3D nanostructure with optimal configuration and doping ratio obtained through design optimization technique. For hydrogen desorption, a mechanical-deformation-driven-hydrogen-release approach is proposed. Compared with temperature/pressure change-induced hydrogen desorption method, the proposed approach is so effective that nearly complete hydrogen desorption can be achieved by Si-FN nanostructures under sufficient compression but without structural failure observed. The approach is also reversible since the mechanical deformation in Si-FN nanostructures can be elastically recovered, which suggests a good reusability. This study may shed light on the mechanism of hydrogen adsorption and desorption and thus provide useful guidance toward engineering design of microstructural hydrogen (or other gas) adsorption materials.
Optical anisotropy of porous polymer film with inverse slanted nanocolumnar structure revealed via generalized spectroscopic ellipsometry
Authors: Liang Dan , Sekora Derek , Rice Charles , Schubert Eva , Schubert Mathias
Published: August 2015

We use generalized spectroscopic ellipsometry to characterize the biaxial optical properties of porous polymer and slanted nanocolumnar template thin films. The porous polymer with inverse columnar structure was prepared via infiltrating polymer into the voids of the slanted nanocolumnar film and selectively removing the column material (cobalt). The anisotropic Bruggeman effective medium approximation was employed to analyze the ellipsometry data of the porous polymer film and nanocolumnar template. The classification and structure of optical anisotropy are found to be identical for both samples. The interchangeable optical behaviors between two complementary structures are attributed to the equivalency in their anisotropic polarizabilities.
Cherenkov neutron detector for fusion reaction and runaway electron diagnostics
Authors: Cheon MunSeong , Kim Junghee
Published: August 2015

A Cherenkov-type neutron detector was newly developed and neutron measurement experiments were performed at Korea Superconducting Tokamak Advanced Research. It was shown that the Cherenkov neutron detector can monitor the time-resolved neutron flux from deuterium-fueled fusion plasmas. Owing to the high temporal resolution of the detector, fast behaviors of runaway electrons, such as the neutron spikes, could be observed clearly. It is expected that the Cherenkov neutron detector could be utilized to provide useful information on runaway electrons as well as fusion reaction rate in fusion plasmas.
Ion-molecule reaction dynamics: Velocity map imaging studies of N+ and O+ with CD3OD
Authors: Pei Linsen , Farrar James M.
Published: August 2015

We present a study of the charge transfer reactions of the atomic ions N+and O+ with methanol in the collision energy range from ∼2 to 4 eV. Charge transfer is driven primarily by energy resonance, although the widths of the product kinetic energy distributions suggest that significant interchange between relative translation and product vibration occurs. Charge transfer with CD3OD is more exoergic for N+, and the nascent parent ion products appear to be formed in excited B̃ and C̃ electronic states, and fragment to CD2OD+ by internal conversion and vibrational relaxation to the ground electronic state. The internal excitation imparted to the parent ion is sufficient to result in loss of one or two D atoms from the carbon atom. The less exoergic charge transfer reaction of O+ forms nascent parent ions in the excited Ã state, and internal conversion to the ground state only results in ejection of single D atom. Selected isotopomers of methanol were employed to identify reaction products, demonstrating that deuterium atom loss from nascent parent ions occurs by C–D bond cleavage. Comparison of the kinetic energy distributions for charge transfer to form CD3OD+ and CD2OD+ by D atom loss with the known dynamics for hydride abstraction from a carbon atom provides strong evidence that the D loss products are formed by dissociative charge transfer rather than hydride (deuteride) transfer. Isotopic labeling also demonstrates that chemical reaction in the N+ + CD3OD system to form NO+ + CD4 does not occur in the energy range of these experiments, contrary to earlier speculation in the literature.
Flexible parylene-film optical waveguide arrays
Authors: Yamagiwa S. , Ishida M. , Kawano T.
Published: August 2015

Modulation of neuronal activities by light [e.g., laser or light-emitting diode] using optogenetics is a powerful tool for studies on neuronal functions in a brain. Herein, flexible thin-film optical waveguide arrays based on a highly biocompatible material of parylene are reported. Parylene-C and -N thin layers with the different refractive indices form the clad and the core of the waveguide, respectively, and neural recording microelectrodes are integrated to record optical stimuli and electrical recordings simultaneously using the same alignment. Both theoretical and experimental investigations confirm that light intensities of more than 90% can propagate in a bent waveguide with a curvature radius of >5 mm. The proposed flexible thin-film waveguide arrays with microelectrodes can be used for numerous spherical bio-tissues, including brain and spinal cord samples.
Imaging free-falling particles for multipoint measurement of plasma fluctuations
Authors: Roberts T. M. , Mauel M. E. , Abler M. C. , Makansi B. K.
Published: August 2015

The measurement of plasma fluctuations by insertable probes is sometimes limited by the perturbation of the probe on the plasma, and some non-invasive diagnostics such as photodiode arrays can only measure integrated values. In this paper, we introduce a new approach to plasma fluctuation measurement using small, free-falling particles imaged with a fast camera to provide simultaneous multipoint measurement of visible light emissions surrounding each particle. We find that the fluctuations measured in this manner are in agreement with existing diagnostics, and the particle signals are correlated to those measured on inserted floating potential probes. Signals from multiple particles demonstrate an application of multipoint measurement of the plasma spatial structure and coherence.
Electronic structure evolution in doping of fullerene (C60) by ultra-thin layer molybdenum trioxide
Authors: Wang Chenggong , Liu Xiaoliang , Wang Congcong , Kauppi John , Gao Yongli
Published: August 2015

Ultra-thin layer molybdenum oxide doping of fullerene has been investigated using ultraviolet photoemission spectroscopy (UPS) and X-ray photoemission spectroscopy (XPS). The highest occupied molecular orbital (HOMO) can be observed directly with UPS. It is observed that the Fermi level position in fullerene is modified by ultra-thin-layer molybdenum oxide doping, and the HOMO onset is shifted to less than 1.3 eV below the Fermi level. The XPS results indicate that charge transfer was observed from the C60 to MoOx and Mo6+ oxides is the basis as hole dopants.
Effects of polymer chain confinement on thermal conductivity of ultrathin amorphous polystyrene films
Authors: Ma Hao , Tian Zhiting
Published: August 2015

The thermal properties of polymers are intricately related to the structural elements. Using equilibrium molecular dynamics simulations, we study the thermal conductivity of ultrathin amorphous polystyrene films versus density,  ρ, film thickness, dz, and the ratio of thickness to the radius of gyration, dz/Rg , known as the chain confinement indicator. We find that the thermal conductivity increases linearly as dz/Rg  increases, or in other words, that stronger confinement and less entanglement lead to lower thermal conductivity. This underlines the fundamental difference in heat conduction between amorphous polymers and crystalline polymers.
Investigation of defect-induced abnormal body current in fin field-effect-transistors
Authors: Liu Kuan-Ju , Chang Ting-Chang , Chen Ching-En , Yang Ren-Ya , Tsai Jyun-Yu , Lu Ying-Hsin , Liu Xi-Wen , Cheng Osbert , Huang Cheng-Tung
Published: August 2015

This letter investigates the mechanism of abnormal body current at the linear region in n-channel high-k/metal gate stack fin field effect transistors. Unlike body current, which is generated by impact ionization at high drain voltages, abnormal body current was found to increase with decreasing drain voltages. Notably, the unusual body leakage only occurs in three-dimensional structure devices. Based on measurements under different operation conditions, the abnormal body current can be attributed to fin surface defect-induced leakage current, and the mechanism is electron tunneling to the fin via the defects, resulting in holes left at the body terminal.
Controlling the conduction band offset for highly efficient ZnO nanorods based perovskite solar cell
Authors: Dong Juan , Shi Jiangjian , Li Dongmei , Luo Yanhong , Meng Qingbo
Published: August 2015

The mechanism of charge recombination at the interface of n-type electron transport layer (n-ETL) and perovskite absorber on the carrier properties in the perovskite solar cell is theoretically studied. By solving the one dimensional diffusion equation with different boundary conditions, it reveals that the interface charge recombination in the perovskite solar cell can be suppressed by adjusting the conduction band offset (ΔEC) at ZnO ETL/perovskite absorber interface, thus leading to improvements in cell performance. Furthermore, Mg doped ZnO nanorods ETL has been designed to control the energy band levels. By optimizing the doping amount of Mg, the conduction band minimum of the Mg doped ZnO ETL has been raised up by 0.29 eV and a positive ΔEC of about 0.1 eV is obtained. The photovoltage of the cell is thus significantly increased due to the relatively low charge recombination.
Epitaxial growth and characterization of thick multi-layer 4H-SiC for very high-voltage insulated gate bipolar transistors
Authors: Miyazawa Tetsuya , Nakayama Koji , Tanaka Atsushi , Asano Katsunori , Ji Shi-yang , Kojima Kazutoshi , Ishida Yuuki , Tsuchida Hidekazu
Published: August 2015

Techniques to fabricate thick multi-layer 4H-SiC epitaxial wafers were studied for very high-voltage p- and n-channel insulated gate bipolar transistors (IGBTs). Multi-layer epitaxial growth, including a thick p− drift layer (∼180 μm), was performed on a 4H-SiC n+ substrate to form a p-IGBT structure. For an n-IGBT structure, an inverted growth process was employed, in which a thick n− drift layer (∼180 μm) and a thick p++ injector layer (>55 μm) were epitaxially grown. The epitaxial growth conditions were modified to attain a low defect density, a low doping concentration, and a long carrier lifetime in the drift layers. Reduction of the forward voltage drop was attempted by using carrier lifetime enhancement processes, specifically, carbon ion implantation/annealing and thermal oxidation/annealing or hydrogen annealing. Simple PiN diodes were fabricated to demonstrate the effective conductivity modulation in the thick drift layers. The forward voltage drops of the PiN diodes with the p- and n-IGBT structures promise to obtain the extremely low-loss and very high-voltage IGBTs. The change in wafer shape during the processing of the very thick multi-layer 4H-SiC is also discussed.
Polymer/metal oxide hybrid dielectrics for low voltage field-effect transistors with solution-processed, high-mobility semiconductors
Authors: Held Martin , Schießl Stefan P. , Miehler Dominik , Gannott Florentina , Zaumseil Jana
Published: August 2015

Transistors for future flexible organic light-emitting diode (OLED) display backplanes should operate at low voltages and be able to sustain high currents over long times without degradation. Hence, high capacitance dielectrics with low surface trap densities are required that are compatible with solution-processable high-mobility semiconductors. Here, we combine poly(methyl methacrylate) (PMMA) and atomic layer deposition hafnium oxide (HfOx) into a bilayer hybrid dielectric for field-effect transistors with a donor-acceptor polymer (DPPT-TT) or single-walled carbon nanotubes (SWNTs) as the semiconductor and demonstrate substantially improved device performances for both. The ultra-thin PMMA layer ensures a low density of trap states at the semiconductor-dielectric interface while the metal oxide layer provides high capacitance, low gate leakage and superior barrier properties. Transistors with these thin (≤70 nm), high capacitance (100–300 nF/cm2) hybrid dielectrics enable low operating voltages (<5 V), balanced charge carrier mobilities and low threshold voltages. Moreover, the hybrid layers substantially improve the bias stress stability of the transistors compared to those with pure PMMA and HfOx dielectrics.
Three-dimensional spectrum mapping of bright emission centers: Investigating the brightness-limiting process in Eu-doped GaN red light emitting diodes
Authors: Ishii Masashi , Koizumi Atsushi , Fujiwara Yasufumi
Published: August 2015

A pulse-driven emission-spectroscopy mapping technique is used to investigate the bright emission centers in Eu-doped GaN (GaN:Eu) red light emitting diodes (LED). The LEDs are operated in pulse-driven mode, and the emission spectra are acquired for a range of pulse frequencies. This ensemble of emission spectral data yields a three-dimensional mapping that allows the origin of emission lines to be identified by visual inspection. The identification was achieved even for a weak 5D0 → 7F3 transition in conventional photoluminescence measurements. A peculiar split is observed in the 5D0 → 7F3 transition for the bright emission center referred to as OMVPE 8. Despite the unique transition at this emission center, the emission efficiencies for the 5D0 → 7F3 and 5D0 → 7F2 transitions were identical. This finding indicates that the excitation of the emission centers, rather than the radiative transitions, is the limiting process that determines the GaN:Eu red LED brightness.
Exact solutions of atmospheric (3+1)-dimensional nonlinear incompressible non-hydrostatic Boussinesq equations with viscosity
Authors: Liu Ping , Zeng Bao-Qing , Deng Bo-Bo , Yang Jian-Rong
Published: August 2015

The symmetry reduction equations, similarity solutions, sub-groups and exact solutions of the (3+1)-dimensional nonlinear incompressible non-hydrostatic Boussinesq equations with viscosity (INHBV equations), which describe the atmospheric gravity waves, are researched in this paper. Calculation on symmetry shows that the equations are invariant under the Galilean transformations, scaling transformations, rotational transformations and space-time translations. Three types of symmetry reduction equations and similar solutions for the (3+1)-dimensional INHBV equations are proposed. Traveling wave solutions of the INHBV equations are demonstrated by means of symmetry method. The evolutions on the wind velocities and temperature perturbation are demonstrated by figures.
Manipulating effective spin orbit coupling based on proximity effect in magnetic bilayers
Authors: Zhang Y. Q. , Sun N. Y. , Che W. R. , Li X. L. , Zhang J. W. , Shan R. , Zhu Z. G. , Su G.
Published: August 2015

A proximity effect of spin orbit coupling (SOC) is proposed in nonmagnetic metal/ferromagnet (NM/FM) bilayers by extending the Crépieux-Bruno (CB) theory. We demonstrate that over 1000% enhancement of the SOC strength can be realized based on this effect (Pt/FM bilayers) and it brings greatly enhanced anomalous Hall effect and anomalous Nernst effect. This work could help maximize the performance of magnetic transport property for the spintronics device using NM/FM as the key structure.
Optical constants and dynamic conductivities of single layer MoS2, MoSe2, and WSe2
Authors: Morozov Yurii V. , Kuno Masaru
Published: August 2015

The complex optical constants of single layer MoS2, MoSe2, and WSe2 transition metal dichalcogenides (TMDCs) have been measured using concerted frequency-dependent transmittance and reflectance measurements. Absolute absorptivities as well as complex refractive indices and dielectric permittivities have been extracted. Comparisons to associated bulk responses reveal differences due to increased electron-hole interactions in single layer TMDCs. In parallel, corresponding complex optical conductivities (σ) have been determined. For MoS2, extracted σ-values qualitatively agree with recent theoretical estimates. Significant differences exist, though, between experiment and theory regarding the imaginary part of σ. In all cases, the current approach distinguishes itself to other measurements of single layer TMDC optical constants in which it does not rely on Kramers-Kronig transformations of reflectance data.
The in-plane anisotropic magnetic damping of ultrathin epitaxial Co2FeAl film
Authors: Qiao Shuang , Yan Wei , Nie Shuaihua , Zhao Jianhua , Zhang Xinhui
Published: August 2015

The in-plane orientation-dependent effective damping of ultrathin Co2FeAl film epitaxially grown on GaAs(001) substrate by molecular beam epitaxy (MBE) has been investigated by employing the time-resolved magneto-optical Kerr effect (TR-MOKE) measurements. It is found that the interface-induced uniaxial anisotropy is favorable for precession response and the anisotropy of precession frequency is mainly determined by this uniaxial anisotropy, while the magnetic relaxation time and damping factor exhibit the fourfold anisotropy at high-field regime. The field-independent anisotropic damping factor obtained at high fields indicates that the effective damping shows an intrinsic fourfold anisotropy for the epitaxial Co2FeAl thin films.
The development of laser-plasma interaction program LAP3D on thousands of processors
Authors: Hu Xiaoyan , Hao Liang , Liu Zhanjun , Zheng Chunyang , Li Bin , Guo Hong
Published: August 2015

Modeling laser-plasma interaction (LPI) processes in real-size experiments scale is recognized as a challenging task. For explorering the influence of various instabilities in LPI processes, a three-dimensional laser and plasma code (LAP3D) has been developed, which includes filamentation, stimulated Brillouin backscattering (SBS), stimulated Raman backscattering (SRS), non-local heat transport and plasmas flow computation modules. In this program, a second-order upwind scheme is applied to solve the plasma equations which are represented by an Euler fluid model. Operator splitting method is used for solving the equations of the light wave propagation, where the Fast Fourier translation (FFT) is applied to compute the diffraction operator and the coordinate translations is used to solve the acoustic wave equation. The coupled terms of the different physics processes are computed by the second-order interpolations algorithm. In order to simulate the LPI processes in massively parallel computers well, several parallel techniques are used, such as the coupled parallel algorithm of FFT and fluid numerical computation, the load balance algorithm, and the data transfer algorithm. Now the phenomena of filamentation, SBS and SRS have been studied in low-density plasma successfully with LAP3D. Scalability of the program is demonstrated with a parallel efficiency above 50% on about ten thousand of processors.
Formation of ZnSe/Bi2Se3 QDs by surface cation exchange and high photothermal conversion
Authors: Jia Guozhi , Wang Peng , Wu Zengna , Li Qiang , Zhang Yanbang , Yao Jianghong , Chang Kai
Published: August 2015

Water-dispersed core/shell structure ZnSe/Bi2Se3 quantum dots were synthesized by ultrasonicwave-assisted cation exchange reaction. Only surface Zn ion can be replaced by Bi ion in ZnSe quantum dots, which lead to the ultrathin Bi2Se3 shell layer formed. It is significance to find to change the crystal of QDs due to the acting of ultrasonicwave. Cation exchange mechanism and excellent photothermal conversion properties are discussed in detail.
Assembly of New Merocyanine Chromophores with a 1,8-Naphthalimide Core by a New Method for the Synthesis of the Methine Function
Authors: Vasilev Aleksey A. , Baluschev Stanislav , Cheshmedzhieva Diana , Ilieva Sonia , Castaño Obis D. , Vaquero Juan J. , Angelova Silvia E. , Landfester Katharina
Published: August 2015

A new method for the synthesis of the monomethine group using nitro as a leaving group in an SN-Ar reaction is described. A series of novel merocyanine dyes has been synthesised and their photophysical properties have been elucidated. The longest wavelength absorption occurs in the range 519–619 nm and the molar absorptivities vary with the substituents and are in the range 1000–47700 L mol–1 cm–1. The dyes show high chemical and photostability. One example from the series has the ability to distinguish methanol from ethanol. The introduction of a quinoid fragment into the structure leads to a pronounced intramolecular charge transfer and hence a noticeable positive solvatochromism. The structures and electronic properties of the compounds have been studied by density functional theory (DFT) and time-dependent DFT.
An architecture for encoding sentence meaning in left mid-superior temporal cortex
Authors: Frankland Steven M. , Greene Joshua D.
Published: August 2015

Significance

The 18th-century Prussian philosopher Wilhelm von Humbolt famously noted that natural language makes “infinite use of finite means.” By this, he meant that language deploys a finite set of words to express an effectively infinite set of ideas. As the seat of both language and thought, the human brain must be capable of rapidly encoding the multitude of thoughts that a sentence could convey. How does this work? Here, we find evidence supporting a long-standing conjecture of cognitive science: that the human brain encodes the meanings of simple sentences much like a computer, with distinct neural populations representing answers to basic questions of meaning such as “Who did it?” and “To whom was it done?”
Oligoribonuclease is a central feature of cyclic diguanylate signaling in
Pseudomonas aeruginosa
Authors: Cohen Dorit , Mechold Undine , Nevenzal Hadas , Yarmiyhu Yafit , Randall Trevor E. , Bay Denice C. , Rich Jacquelyn D. , Parsek Matthew R. , Kaever Volkhard , Harrison Joe J. , Banin Ehud
Published: August 2015

Significance

Many bacteria possess enzymes that synthesize and degrade the intracellular second messenger cyclic diguanylate (c-di-GMP). Bacteria use this molecule to relay environmental signals into physiological responses that control motility, virulence, and biofilm formation. There are two pathways for enzymatic c-di-GMP degradation. One of these pathways involves the production of an intermediate molecule called 5ʹ-phosphoguanylyl-(3ʹ,5ʹ)-guanosine (pGpG). Although many enzymes responsible for c-di-GMP degradation have been characterized, microbiologists have long sought those responsible for pGpG degradation. Here we identify that oligoribonuclease (Orn) mediates pGpG degradation and show that Orn is important for c-di-GMP signaling in the human pathogen
Pseudomonas aeruginosa
. This discovery reveals that nanoribonucleases, which have been considered housekeeping proteins crucial for mRNA turnover, also have a key role in c-di-GMP signaling.
Neural coding underlying the cue preference for celestial orientation
Authors: el Jundi Basil , Warrant Eric J. , Byrne Marcus J. , Khaldy Lana , Baird Emily , Smolka Jochen , Dacke Marie
Published: August 2015

Significance

Many animals use the sun or moon and the polarization pattern for navigation. We combined behavioral experiments with physiological measurements of brain activity to reveal which celestial cue dominates the orientation compass of diurnal and nocturnal dung beetles. The preference found behaviorally precisely matches the preference encoded neurally and shows how the brain dynamically controls the cue preference for orientation at different levels: The sun or moon always dominates the orientation behavior and neural tuning of diurnal beetles, whereas in nocturnal beetles, celestial bodies dominate tuning only in bright light, with a switch to polarized light at night. This flexible neural tuning in the nocturnal species provides a simple mechanism that allows it to use the most reliable available orientation cue.
Telomerase RNA stem terminus element affects template boundary element function, telomere sequence, and shelterin binding
Authors: Webb Christopher J. , Zakian Virginia A.
Published: August 2015

Significance

We demonstrate that the fission yeast telomerase RNA has a stem terminus element (STE) that it is essential for telomerase action in vivo and in vitro. Using a partial loss-of-function STE allele, we show that the STE is required for wild-type telomeric sequence. This is the first example, to our knowledge, of a sequence that is not part of the telomerase RNA core region that affects the sequence of telomeric DNA. Because mutating the STE has the same phenotypes as mutating the template boundary element (TBE), the STE promotes TBE function. The association of two sequence-specific telomere binding proteins is impaired in the STE mutant. Thus, the STE is critical to assemble the normal sequence and chromatin structure of fission yeast telomeres.
Fungal biosynthesis of the bibenzoquinone oosporein to evade insect immunity
Authors: Feng Peng , Shang Yanfang , Cen Kai , Wang Chengshu
Published: August 2015

Significance

Oosporein, a red 1,4-bibenzoquinone derivative, was first identified from fungi in the 1960s and exhibits antibiotic, antiviral, antifungal, and insecticidal activities. We report, to our knowledge, for the first time the novel pathway for oosporein biosynthesis in
Beauveria bassiana
that includes the polyketide synthase oosporein synthase 1 (OpS1) to produce the precursor orsellinic acid for OpS4 hydroxylation and then OpS7 oxidation to benzenetetrol, and the dimerization of the intermediate to oosporein is catalyzed by the catalase OpS5. The gene cluster is regulated by the transcription factor OpS3. We also found that oosporein is required for fungal virulence by inhibiting insect immunity. These results advance the knowledge of quinone biosynthetic machineries and demonstrate that a small molecule contributes to fungus–host interactions.
Genome-wide RNAi screening identifies host restriction factors critical for in vivo AAV transduction
Authors: Mano Miguel , Ippodrino Rudy , Zentilin Lorena , Zacchigna Serena , Giacca Mauro
Published: August 2015

Significance

Viral vectors based on the adeno-associated virus (AAV) are at the forefront of human gene therapy; yet, the molecular biology of these vectors is largely unexplored. The aim of this work was to unravel, in a systematic manner, the effect of the individual knockdown of over 18,000 human genes on the efficiency of AAV-mediated transduction. The results obtained connect AAV biology to the processing of cellular DNA damage and pave the way to practical applications to improve therapeutic gene transfer.
Fate of a mutation in a fluctuating environment
Authors: Cvijović Ivana , Good Benjamin H. , Jerison Elizabeth R. , Desai Michael M.
Published: August 2015

Significance

Evolution in variable environments depends crucially on the fates of new mutations in the face of fluctuating selection pressures. In constant environments, the relationship between the selective effect of a mutation and the probability that it will eventually fix or go extinct is well understood. However, our understanding of fixation probabilities in fluctuating environmental conditions is limited. Here, we show that temporal fluctuations in environmental conditions can have dramatic effects on the fate of each new mutation, reducing the efficiency of natural selection and increasing the fixation probability of all mutations, including those that are strongly deleterious on average. This makes it difficult for a population to maintain specialist adaptations, even if their benefits outweigh their costs.
Native root-associated bacteria rescue a plant from a sudden-wilt disease that emerged during continuous cropping
Authors: Santhanam Rakesh , Luu Van Thi , Weinhold Arne , Goldberg Jay , Oh Youngjoo , Baldwin Ian T.
Published: August 2015

Significance

Plant roots associate with the diverse microbial community in soil and can establish mutualistic relationships with microbes. The genetic characterization of the plant microbiome (total microbiota of plants) has intensified, but we still lack experimental proof of the ecological function of the root microbiome. Without such an understanding, the use of microbial communities in sustainable agricultural practices will be poorly informed. Through continuous cropping of a seed-sterilized native plant, we inadvertently recapitulated a common agricultural dilemma: the accumulation of phytopathogens. Experimental inoculations of seeds with native bacterial consortium during germination significantly attenuated plant mortality, demonstrating that a plant’s opportunistic mutualistic associations with soil microbes have the potential to increase the resilience of crops.
IFN-γ ameliorates autoimmune encephalomyelitis by limiting myelin lipid peroxidation
Authors: Sosa Rebecca A. , Murphey Cathi , Robinson Rachel R. , Forsthuber Thomas G.
Published: August 2015

Significance

The mechanisms guiding tissue repair in autoimmune-mediated diseases of the CNS are not fully understood, but cytokines are believed to play an important role. The proinflammatory cytokine IFN-γ has been implicated in the pathogenesis of multiple sclerosis and its animal model, experimental autoimmune encephalomyelitis (EAE). Paradoxically, knockout studies in mice showed that EAE is exacerbated when the cytokine’s signaling is disrupted, but its mechanism of protection has not been resolved. Here, we show a critical role for IFN-γ in activating antigen-presenting cells toward a protective phenotype in the CNS by removing extracellular myelin debris and limiting the availability of substrate for oxidative stress-generated neurotoxic lipid peroxidation products.
Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus
Nitrospira
Authors: Koch Hanna , Lücker Sebastian , Albertsen Mads , Kitzinger Katharina , Herbold Craig , Spieck Eva , Nielsen Per Halkjaer , Wagner Michael , Daims Holger
Published: August 2015

Significance

Nitrification, the sequential aerobic oxidation of ammonia via nitrite to nitrate, is a key process of the biogeochemical nitrogen cycle and catalyzed by two aerobic microbial guilds (nitrifiers): ammonia oxidizers and nitrite-oxidizing bacteria (NOB). NOB are generally considered as metabolically restricted and dependent on ammonia oxidizers. Here, we report that, surprisingly, key NOB of many ecosystems (
Nitrospira
) convert urea, an important ammonia source in nature, to ammonia and CO
2
. Thus,
Nitrospira
supply urease-negative ammonia oxidizers with ammonia and receive nitrite produced by ammonia oxidation in return, leading to a reciprocal feeding interaction of nitrifiers. Moreover,
Nitrospira
couple formate oxidation with nitrate reduction to remain active in anoxia. Accordingly,
Nitrospira
are unexpectedly flexible and contribute to nitrogen cycling beyond nitrite oxidation.
Instability of thermoremanence and the problem of estimating the ancient geomagnetic field strength from non-single-domain recorders
Authors: Shaar Ron , Tauxe Lisa
Published: August 2015

Significance

The evolution of Earth’s magnetic field is one of the greatest riddles of Earth’s past. Despite decades of paleomagnetic research, some fundamental properties of the geomagnetic field, such as the nature of its intensity fluctuation (paleointensity), are still elusive. Paleointensity is recovered from ancient materials that were thermally magnetized in the presence of the ancient field. The paleointensity procedure is based on the assumption that the ancient magnetization is stable with time. Here we show that this assumption is violated for many of the widely used materials, such as, for example, crystalline volcanic rocks. Our results put in question the reliability of much of the available paleointensity information, posing new challenges to our understanding of the ancient Earth.
Structural basis of antizyme-mediated regulation of polyamine homeostasis
Authors: Wu Hsiang-Yi , Chen Shin-Fu , Hsieh Ju-Yi , Chou Fang , Wang Yu-Hsuan , Lin Wan-Ting , Lee Pei-Ying , Yu Yu-Jen , Lin Li-Ying , Lin Te-Sheng , Lin Chieh-Liang , Liu Guang-Yaw , Tzeng Shiou-Ru , Hung Hui-Chih , Chan Nei-Li
Published: August 2015

Significance

Polyamines are small organic compounds that carry multiple positive charges at physiological pH. With a high capacity to interact with the acidic surface patches of proteins and nucleic acids, polyamines may regulate a variety of cellular processes, and the fluctuations in the intracellular polyamine levels are rigorously controlled during cell growth and differentiation through the interplay between the enzyme ornithine decarboxylase (ODC) and two regulatory proteins: antizyme (Az) and antizyme inhibitor (AzIN). ODC initiates the polyamine biosynthetic pathway, whereas Az decreases polyamine concentrations by both inhibiting ODC activity and channeling ODC for proteolytic degradation. AzIN neutralizes Az function to restore polyamine levels. Here we provide the long-sought structural information and previously unidentified functional insights into this delicate regulatory circuit.
Conserved mechanism for coordinating replication fork helicase assembly with phosphorylation of the helicase
Authors: Bruck Irina , Kaplan Daniel L.
Published: August 2015

Significance

The replication fork helicase unwinds double-stranded DNA at a replication fork, and assembly and activation of this helicase are tightly controlled. This paper describes a biological mechanism to link two essential functions related to helicase assembly and activation. Sld3, a protein required for initiation of DNA replication, coordinates the assembly of the replication fork helicase with the chemical modification of a helicase protein subunit. This chemical modification is important for subsequent activation of the helicase.
Lack of mitochondrial topoisomerase I (
TOP1mt
) impairs liver regeneration
Authors: Khiati Salim , Baechler Simone A. , Factor Valentina M. , Zhang Hongliang , Huang Shar-yin N. , Dalla Rosa Ilaria , Sourbier Carole , Neckers Leonard , Thorgeirsson Snorri S. , Pommier Yves
Published: August 2015

Significance

The liver is rich in mitochondria and has an exceptional regenerative capacity after partial hepatectomy or transplantation, viral infections, or chemical injuries; however, relatively little is known about the genetic factors for mitochondrial DNA (mtDNA) replication during liver regeneration. Here, we show that liver regeneration is markedly reduced in mice lacking mitochondrial topoisomerase I (
TOP1mt
). This defect is linked with reduced production of mtDNA and defective mitochondrial functions during acute energy demand for liver regeneration. Additionally,
TOP1mt
KO primary hepatocytes from CCl
4
-treated mice showed reduced and damaged mitochondria, decreased O
2
consumption, and ATP production. Together with mtDNA depletion and regeneration experiments with ethidium bromide, these results demonstrate that Top1mt is required for mtDNA synthesis and appropriate liver regeneration.
Burkholderia
bacteria infectiously induce the proto-farming symbiosis of
Dictyostelium
amoebae and food bacteria
Authors: DiSalvo Susanne , Haselkorn Tamara S. , Bashir Usman , Jimenez Daniela , Brock Debra A. , Queller David C. , Strassmann Joan E.
Published: August 2015

Significance

Symbionts can provide hosts with many advantages including defensive capabilities and novel nutrients. However, symbionts may begin as pathogens that only subsequently become beneficial. In the
Dictyostelium discoideum
farming symbiosis some amoebas stably associate with bacterial partners. We demonstrate that amoeba-associated
Burkholderia
can initiate a farming symbiosis with naive amoeba hosts.
Burkholderia
decreases amoeba spore productivity in food-rich conditions but, because of the induction of bacterial food carriage, sometimes increases spore productivity in food-scarce conditions. Detrimental effects of
Burkholderia
colonization differ among
Burkholderia
genotypes and, in some cases, between new and old amoeba hosts, suggesting some coevolution within the association. These results suggest that
Burkholderia
exerts both pathogenic and mutualistic effects on its host in conditionally dependent ways.
Structure of an intermediate conformer of the spindle checkpoint protein Mad2
Authors: Hara Mayuko , Özkan Engin , Sun Hongbin , Yu Hongtao , Luo Xuelian
Published: August 2015

Significance

The spindle checkpoint is a cellular surveillance system that ensures the fidelity of chromosome segregation and guards against aneuploidy and its associated disease states. The critical checkpoint protein mitotic arrest deficient 2 (Mad2) is an unusual protein with multiple, topologically distinct conformers, including the inactive, open conformer (O-Mad2) and the active, closed conformer (C-Mad2). C-Mad2 can form an asymmetric dimer with O-Mad2 to convert it to another C-Mad2, through an intermediate conformer (I-Mad2). This study determines the structure of the intermediate conformer of the multistate Mad2 protein, revealing how one Mad2 conformer molds the other into itself in a prion-like conformational propagation process.
Evasion of affinity-based selection in germinal centers by Epstein–Barr virus LMP2A
Authors: Minamitani Takeharu , Yasui Teruhito , Ma Yijie , Zhou Hufeng , Okuzaki Daisuke , Tsai Chiau-Yuang , Sakakibara Shuhei , Gewurz Benjamin E. , Kieff Elliott , Kikutani Hitoshi
Published: August 2015

Significance

Epstein–Barr virus (EBV) is a human herpesvirus that establishes persistent infection of the B-cell compartment. EBV is associated with autoimmune diseases, including systemic lupus erythematosus (SLE). However, the molecular mechanisms by which EBV contributes to autoimmunity remain unclear. We used previously undescribed mouse models to study the role of EBV-encoded latent membrane protein 2A (LMP2A), which mimics B-cell receptor signaling. Interestingly, LMP2A not only enhanced B-cell survival but also upregulated the transcription factor zinc finger and bric-a-brac, tramtrack domain-containing protein 20 and promoted plasma cell differentiation. When expressed late in B-cell development, LMP2A also caused prominent features of SLE, including autoantibody production with kidney immune complex deposition. Our findings suggest that LMP2A has important roles in B-cell activation and differentiation and in the development of EBV-associated autoimmune diseases.
Synapse-specific IL-1 receptor subunit reconfiguration augments vulnerability to IL-1β in the aged hippocampus
Authors: Prieto G. Aleph , Snigdha Shikha , Baglietto-Vargas David , Smith Erica D. , Berchtold Nicole C. , Tong Liqi , Ajami Dariush , LaFerla Frank M. , Rebek Julius , Cotman Carl W.
Published: August 2015

Significance

There is a growing understanding that inflammation impairs synaptic plasticity and cognition and that the aged brain has an elevated sensitivity to cognitive impairment by the proinflammatory cytokine interleukin 1β (IL-1β). IL-1β activates different pathways via AcP (proinflammatory) or AcPb (prosurvival) IL-1 receptor subunits. This study demonstrates that the IL-1 receptor subunit system undergoes an age-dependent reconfiguration in hippocampal synapses. This previously undescribed reconfiguration, characterized by an increase in the AcP/AcPb ratio, is responsible for potentiating impairments of synaptic plasticity and memory by IL-1β. Our data reveal a previously unidentified mechanism that explains the age-related vulnerability of hippocampal function to impairment by inflammation and adds another dimension beyond glia to understanding how inflammation causes cognitive decline in aging.
Uterine activin receptor-like kinase 5 is crucial for blastocyst implantation and placental development
Authors: Peng Jia , Monsivais Diana , You Ran , Zhong Hua , Pangas Stephanie A. , Matzuk Martin M.
Published: August 2015

Significance

Although many studies have yielded tremendous insights into the roles of TGF-β superfamily signaling pathways in physiological and pathophysiological processes, the in vivo roles of TGF-β signaling pathways in many aspects of reproduction remain largely unknown. To address these functions in females, we conditionally deleted the TGF-β type 1 receptor (activin receptor-like kinase 5, ALK5) and demonstrated that absence of TGF-β signaling through ALK5 in the uterus leads to striking abnormalities at different stages of pregnancy, including delayed implantation, disorganization of the trophoblast cells, significantly fewer uterine natural killer cells, and defects in spiral artery remodeling. Our findings provide a mouse model to investigate TGF-β signaling in reproduction and pave the way toward a better understanding of the pathogenesis of pregnancy-related complications in women.
Role of PKA signaling in D2 receptor-expressing neurons in the core of the nucleus accumbens in aversive learning
Authors: Yamaguchi Takashi , Goto Akihiro , Nakahara Ichiro , Yawata Satoshi , Hikida Takatoshi , Matsuda Michiyuki , Funabiki Kazuo , Nakanishi Shigetada
Published: August 2015

Significance

The nucleus accumbens (NAc) is a key neural substrate that controls aversive learning through D1 receptor-expressing direct pathway neurons and D2 receptor-expressing indirect pathway neurons. We explored how aversive learning is controlled by intracellular PKA signaling in these two types of neurons in the NAc. We approached this issue not only by pathway-specific inhibition of PKA in either direct or indirect pathway neurons, but also by microendoscopic analysis of FRET responses of the PKA biosensor distinctly expressed in the two types of neurons. We obtained consistent findings from these two different approaches, and demonstrate that activation of PKA in the indirect pathway neurons plays a pivotal role in both the formation and the retention of aversive memory.
Recognition and sequestration of ω-fatty acids by a cavitand receptor
Authors: Mosca Simone , Ajami Dariush , Rebek Julius
Published: August 2015

Significance

We report on the design and synthesis of a deeper cavitand and its binding properties for biologically relevant long-chain unsaturated ω-fatty acids and structural analogues in aqueous media. Nature evolved fatty acid binding proteins (FABPs) for this purpose, embedding hydrophobic cavities into hydrophilic structures. Synthetic container molecules have lacked the capacity to accommodate guest molecules of the length and shape of the fatty acids. Abiotic structures capable of mimicking the complexation ability of FABPs can help identify the structural and dynamic features required for fatty acid recognition. Further development of cavitands as synthetic container compounds is expected to stimulate practical applications in sensing and sequestration of physiologically relevant fatty acids.
An integrated curriculum approach to increasing habitual physical activity in deprived South Asian children
Authors: Eyre E. L. J. , Cox V. M. , Birch S. L. , Duncan M. J.
Published: August 2015

Integrating physical activity (PA) within a school curriculum is a promising approach for increasing PA in children. To date, no research has examined its effectiveness in increasing the low levels of PA witnessed in deprived South Asian (SA) children. The study aims to ascertain whether an integrated school‐based curriculum and pedometer intervention could increase PA in children from deprived SA backgrounds. Following ethical approval and informed consent, 134 deprived SA children (63 boys, 71 girls, control (n = 40, mean age = 11.12 years, SD = 0.32 years) and intervention (n = 94, mean age = 9.48 years, SD = 0.62 years)) from a primary school in England, UK, completed a 6‐week integrated PA intervention based on virtually walking from their school (middle of the country) to the coast and back (March–July 2013). Habitual PA was determined at baseline and post 6 weeks intervention for both groups, and determined weekly during the intervention in the experimental group. The results indicated that average daily steps were significantly higher at post 6 weeks compared to baseline for the intervention group (intervention mean change = 8694 steps/day, SD = 7428 steps/day vs. control mean change = −1121 steps/day, SD = 5592 steps/day, 95% CI of difference, 6726–7428 steps/day, P = .001, d = 1.76). In addition, significant decreases in BF% and waist circumference were observed in the intervention group post 6 weeks (mean change for BF% = −4.5%, mean change for WC = −1.7 cm, P = .001). School‐based integrated curriculum and pedometer interventions provide a feasible and effective mechanism for increasing habitual PA in primary school children from deprived SA backgrounds.
Polarized E-cadherin endocytosis directs actomyosin remodeling during embryonic wound repair
Authors: Hunter Miranda V. , Lee Donghoon M. , Harris Tony J.C. , Fernandez-Gonzalez Rodrigo
Published: August 2015

Embryonic epithelia have a remarkable ability to rapidly repair wounds. A supracellular actomyosin cable around the wound coordinates cellular movements and promotes wound closure. Actomyosin cable formation is accompanied by junctional rearrangements at the wound margin. We used in vivo time-lapse quantitative microscopy to show that clathrin, dynamin, and the ADP-ribosylation factor 6, three components of the endocytic machinery, accumulate around wounds in Drosophila melanogaster embryos in a process that requires calcium signaling and actomyosin contractility. Blocking endocytosis with pharmacological or genetic approaches disrupted wound repair. The defect in wound closure was accompanied by impaired removal of E-cadherin from the wound edge and defective actomyosin cable assembly. E-cadherin overexpression also resulted in reduced actin accumulation around wounds and slower wound closure. Reducing E-cadherin levels in embryos in which endocytosis was blocked rescued actin localization to the wound margin. Our results demonstrate a central role for endocytosis in wound healing and indicate that polarized E-cadherin endocytosis is necessary for actomyosin remodeling during embryonic wound repair.