bluuebunny/crossref_metadata_2025 huggingface dataset:
Electronic properties of substitutional impurities in InGaN monolayer quantum wells
Authors: Alfieri G. , Tsutsumi T. , Micheletto R.
Published: May 2015

InGaN alloys and, in particular, InGaN monolayer quantum wells (MLQWs) are attracting an increasing amount of interest for opto-electronic applications. Impurities, incorporated during growth, can introduce electronic states that can degrade the performance of such devices. For this reason, we present a density functional and group theoretical study of the electronic properties of C, H, or O impurities in an InGaN MLQW. Analysis of the formation energy and symmetry reveals that these impurities are mostly donors and can be held accountable for the reported degradation of InGaN-based devices.
A computational study of droplet evaporation with fuel vapor jet ejection induced by localized heat sources
Authors: Sim Jaeheon , Im Hong G. , Chung Suk Ho
Published: May 2015

Droplet evaporation by a localized heat source under microgravity conditions was numerically investigated in an attempt to understand the mechanism of the fuel vapor jet ejection, which was observed experimentally during the flame spread through a droplet array. An Eulerian-Lagrangian method was implemented with a temperature-dependent surface tension model and a local phase change model in order to effectively capture the interfacial dynamics between liquid droplet and surrounding air. It was found that the surface tension gradient caused by the temperature variation within the droplet creates a thermo-capillary effect, known as the Marangoni effect, creating an internal flow circulation and outer shear flow which drives the fuel vapor into a tail jet. A parametric study demonstrated that the Marangoni effect is indeed significant at realistic droplet combustion conditions, resulting in a higher evaporation constant. A modified Marangoni number was derived in order to represent the surface force characteristics. The results at different pressure conditions indicated that the nonmonotonic response of the evaporation rate to pressure may also be attributed to the Marangoni effect.
Sensitivity of the threshold voltage of organic thin-film transistors to light and water
Authors: Feng Cong , Marinov Ognian , Deen M. Jamal , Selvaganapathy Ponnambalam Ravi , Wu Yiliang
Published: May 2015

Analyses of extensive experiments with organic thin-film transistors (OTFTs) indicate that the threshold voltage VT of an OTFT has a temporal differential sensitivity. In particular, VT changes initially by changing the light illumination intensity or making/removing a contact of water with the organic semiconductor. Keeping the conditions stationary, then the initial shift of VT diminishes, since the time dependence of VT gradually recovers the OTFT to the state before applying the change in the environmental conditions. While still causing a differential and time-variant shift of VT, the deionized water does not have a dramatic impact on OTFTs that use the polymer DKPP-βT (diketopyrrolopyrrole β-unsubstituted quaterthiophene) as the active semiconductor material. Observations for the impact of water are made from experiments with an OTFT that has a microfluidic channel on the top the electrical channel, with the water in the microfluidic channel in direct contact with the electrical channel of the OTFT. This arrangement of electrical and microfluidic channels is a novel structure of the microfluidic OTFT, suitable for sensing applications of liquid analytes by means of organic electronics.
Isotropic-nematic phase transition of polydisperse clay rods
Authors: Woolston Phillip , van Duijneveldt Jeroen S.
Published: May 2015

Rod-like colloidal particles are known to display an isotropic-nematic phase transition on increase of concentration, as predicted already by Onsager. Both natural clay particles and synthetic rods tend to be polydisperse, however, and the question arises how to allow for this in comparing experimental observations with theory. Experimental data for a wide range of samples (both from the literature and the new results) have been collated, with aspect ratios ranging from 14 to 35. As a characteristic, the concentration is taken where half of the sample volume is nematic. Experimental data agree well with predictions for monodisperse finite aspect ratio rods. However, compared to these predictions, the width of the transition (taken as the ratio of isotropic and nematic limiting concentrations) is noticeably broadened. Still, in most cases, the transition can be characterised by a linear increase of the nematic phase volume with sample concentration. The transition width is in broad agreement with theoretical predictions for infinitely thin rods.
Spatial evolution of a quasi-two-dimensional Kármán vortex street subjected to a strong uniform magnetic field
Authors: Hamid Ahmad H. A. , Hussam Wisam K. , Pothérat Alban , Sheard Gregory J.
Published: May 2015

A vortex decay model for predicting spatial evolution of peak vorticity in a wake behind a cylinder is presented. For wake vortices in the stable region behind the formation region, results have shown that the presented model has a good capability of predicting spatial evolution of peak vorticity within an advecting vortex across 0.1 ≤ β ≤ 0.4, 500 ≤ H ≤ 5000, and 1500 ≤ ReL ≤ 8250. The model is also generalized to predict the decay behaviour of wake vortices in a class of quasi-two-dimensional magnetohydrodynamic duct flows. Comparison with published data demonstrates remarkable consistency.
A non-perturbative approach to spatial instability of weakly non-parallel shear flows
Authors: Huang Zhangfeng , Wu Xuesong
Published: May 2015

Boundary-layer instability is influenced by non-parallel-flow effects, that is, the streamwise variation of the mean flow not only modifies directly the growth rate but also distorts the shape (i.e., the transverse distribution) of the disturbance, thereby affecting the growth rate indirectly. In this paper, we present a simple but effective local approach to spatial instability of three-dimensional boundary layers, which takes into account both direct and indirect effects of non-parallelism. Unlike existing WKB/multi-scale type of methods, the present approach is non-perturbative in which non-parallelism does not need to be a higher-order correction to the leading-order prediction by the parallel-flow approximation. The non-parallel-flow effects are accounted for by expanding the local mean flow and the shape function as Taylor series, and this leads to a sequence of extended eigenvalue problems, depending on the order of truncation of the Taylor series. These eigenvalue problems can be solved effectively by standard numerical methods. In the case of the Blasius boundary layer, the predictions are verified and confirmed by direct numerical simulation results as well as by the non-parallel theory of Gaster. The non-parallel-flow effects on the eigenvalues, eigenfunctions, and neutral curves for planar and oblique Tollmien-Schlichting (T-S) waves are discussed. The distortion of the eigenfunction is found to have a significant effect, which may be stabilizing or destabilizing depending on the ranges of the Reynolds number and frequency.
Theoretic base of Edge Local Mode triggering by vertical displacements
Authors: Wang Z. T. , He Z. X. , Wang Z. H. , Wu N. , Tang C. J.
Published: May 2015

Vertical instability is studied with R-dependent displacement. For Solovev's configuration, the stability boundary of the vertical instability is calculated. The pressure gradient is a destabilizing factor which is contrary to Rebhan's result. Equilibrium parallel current density, j//, at plasma boundary is a drive of the vertical instability similar to Peeling-ballooning modes; however, the vertical instability cannot be stabilized by the magnetic shear which tends towards infinity near the separatrix. The induced current observed in the Edge Local Mode (ELM) triggering experiment by vertical modulation is derived. The theory provides some theoretic explanation for the mitigation of type-I ELMS on ASDEX Upgrade. The principle could be also used for ITER.
A non-commuting stabilizer formalism
Authors: Ni Xiaotong , Buerschaper Oliver , Van den Nest Maarten
Published: May 2015

We propose a non-commutative extension of the Pauli stabilizer formalism. The aim is to describe a class of many-body quantum states which is richer than the standard Pauli stabilizer states. In our framework, stabilizer operators are tensor products of single-qubit operators drawn from the group 〈αI, X, S〉, where α = eiπ/4 and S = diag(1, i). We provide techniques to efficiently compute various properties related to bipartite entanglement, expectation values of local observables, preparation by means of quantum circuits, parent Hamiltonians, etc. We also highlight significant differences compared to the Pauli stabilizer formalism. In particular, we give examples of states in our formalism which cannot arise in the Pauli stabilizer formalism, such as topological models that support non-Abelian anyons.
Decoupling of epitaxial graphene via gold intercalation probed by dispersive Raman spectroscopy
Authors: Pillai P. B. , DeSouza M. , Narula R. , Reich S. , Wong L. Y. , Batten T. , Pokorny J.
Published: May 2015

Signatures of a superlattice structure composed of a quasi periodic arrangement of atomic gold clusters below an epitaxied graphene (EG) layer are examined using dispersive Raman spectroscopy. The gold-graphene system exhibits a laser excitation energy dependant red shift of the 2D mode as compared to pristine epitaxial graphene. The phonon dispersions in both the systems are mapped using the experimentally observed Raman signatures and a third-nearest neighbour tight binding electronic band structure model. Our results reveal that the observed excitation dependent Raman red shift in gold EG primarily arise from the modifications of the phonon dispersion in gold-graphene and shows that the extent of decoupling of graphene from the underlying SiC substrate can be monitored from the dispersive nature of the Raman 2D modes. The intercalated gold atoms restore the phonon band structure of epitaxial graphene towards free standing graphene.
Static dielectric properties of dense ionic fluids
Authors: Zarubin Grigory , Bier Markus
Published: May 2015

The static dielectric properties of dense ionic fluids, e.g., room temperature ionic liquids (RTILs) and inorganic fused salts, are investigated on different length scales by means of grandcanonical Monte Carlo simulations. A generally applicable scheme is developed which allows one to approximately decompose the electric susceptibility of dense ionic fluids into the orientation and the distortion polarization contribution. It is shown that at long range, the well-known plasma-like perfect screening behavior occurs, which corresponds to a diverging distortion susceptibility, whereas at short range, orientation polarization dominates, which coincides with that of a dipolar fluid of attached cation-anion pairs. This observation suggests that the recently debated interpretation of RTILs as dilute electrolyte solutions might not be simply a yes-no-question but it might depend on the considered length scale.
Multi-mode technique for the determination of the biaxial Y2SiO5 permittivity tensor from 300 to 6 K
Authors: Carvalho N. C. , Le Floch J-M. , Krupka J. , Tobar M. E.
Published: May 2015

The Y2SiO5 (YSO) crystal is a dielectric material with biaxial anisotropy with known values of refractive index at optical frequencies. It is a well-known rare-earth (RE) host material for optical research and more recently has shown promising performance for quantum-engineered devices. In this paper, we report the first microwave characterization of the real permittivity tensor of a bulk YSO sample, as well as an investigation of the temperature dependence of the tensor components from 296 K down to 6 K. Estimated uncertainties were below 0.26%, limited by the precision of machining the cylindrical dielectric. Also, the electrical Q-factors of a few electromagnetic modes were recorded as a way to provide some information about the crystal losses over the temperature range. To solve the tensor components necessary for a biaxial crystal, we developed the multi-mode technique, which uses simultaneous measurement of low order whispering gallery modes. Knowledge of the permittivity tensor offers important data, essential for the design of technologies involving YSO, such as microwave coupling to electron and hyperfine transitions in RE doped samples at low temperatures.
Dual-band quasi-zero refraction and negative refraction in coin-shaped metamaterial
Authors: Zhang Min , Hou Zhi-Ling , Liu Ya-Min , Li Zhong-Jun , Liu Xingda , Fang Hui-Min
Published: May 2015

This paper demonstrates a metamaterial capable of realizing a dual-band quasi-zero refractive index and a negative refractive index, which consists of a coin-shaped slice and two parallel planar wires. The zero refractive index is achieved over a very wide frequency range. The bandwidth of the first band of the quasi-zero index can reach up to 3 GHz, and the width of the second band exhibiting low loss is 0.4 GHz. Between these two bands, the negative refractive index band is 9.0–13.9 GHz. The corresponding formulas of electric plasma frequency and magnetic plasma frequency are established, and the theoretical results agree well with the simulated results. The proposed metamaterial may have potential applications in multiband or broadband devices.
Nonlinear dynamics of three-magnon process driven by ferromagnetic resonance in yttrium iron garnet
Authors: Cunha R. O. , Holanda J. , Vilela-Leão L. H. , Azevedo A. , Rodríguez-Suárez R. L. , Rezende S. M.
Published: May 2015

We report an investigation of the dynamics of the three-magnon splitting process associated with the ferromagnetic resonance (FMR) in films of the insulating ferrimagnet yttrium iron garnet (YIG). The experiments are performed with a 6 μm thick YIG film close to a microstrip line fed by a microwave generator operating in the 2–6 GHz range. The magnetization precession is driven by the microwave rf magnetic field perpendicular to the static magnetic field, and its dynamics is observed by monitoring the amplitude of the FMR absorption peak. The time evolution of the amplitude reveals that if the frequency is lowered below a critical value of 3.3 GHz, the FMR mode pumps two magnons with opposite wave vectors that react back on the FMR, resulting in a nonlinear dynamics of the magnetization. The results are explained by a model with coupled nonlinear equations describing the time evolution of the magnon modes.
Superpermittivity of nanoconfined water
Authors: Renou Richard , Szymczyk Anthony , Maurin Guillaume , Malfreyt Patrice , Ghoufi Aziz
Published: May 2015

Nowadays, it is well established that the physical properties of confined liquids strongly differ from those in bulk phase. While dynamical and structural properties were strongly explored, dielectric properties are poorly studied despite their importance in the understanding and the modelling of molecular mechanism in a number of nano-applications such as nanofluidics, nanofiltration, and nanomedicine. Among them, the dielectric permittivity is probably one of the most important. The lack of knowledge about it strongly limits our ability to model fluid-material interactions and more generally our understanding of the behaviour of confined fluids. Recently, the dielectric permittivity of confined water in silica, Metal Organic Frameworks, and graphene materials was found to be slightly higher than the permittivity of water in bulk phase. In this work, the permittivity of water and dichloromethane confined in carbon nanotubes was predicted by means of molecular dynamics simulations. The static dielectric constant was found to be 700, i.e., 10-fold higher than the bulk value. This superpermittivity has, for origin, the excluded volume and the presence of an unconfined direction leading to a pre-orientation of water molecules close to the pore wall and an increase in dipolar fluctuations.
A high-temperature calorimetric flow sensor employing ion conduction in zirconia
Authors: Persson A. , Lekholm V. , Thornell G. , Klintberg L.
Published: May 2015

This paper presents the use of the temperature-dependent ion conductivity of 8 mol % yttria-stabilized zirconia (YSZ8) in a miniature high-temperature calorimetric flow sensor. The sensor consists of 4 layers of high-temperature co-fired ceramic (HTCC) YSZ8 tape with a 400 μm wide, 100 μm deep, and 12 500 μm long internal flow channel. Across the center of the channel, four platinum conductors, each 80 μm wide with a spacing of 160 μm, were printed. The two center conductors were used as heaters, and the outer, up- and downstream conductors were used to probe the resistance through the zirconia substrate around the heaters. The thermal profile surrounding the two heaters could be made symmetrical by powering them independently, and hence, the temperature sensing elements could be balanced at zero flow. With nitrogen flowing through the channel, forced convection shifted the thermal profile downstream, and the resistance of the temperature sensing elements diverged. The sensor was characterized at nitrogen flows from 0 to 40 sccm, and resistances at zero-flow from 10 to 50 MΩ. A peak sensitivity of 3.1 MΩ/sccm was obtained. Moreover, the sensor response was found to be linear over the whole flow range, with R2 of around 0.999, and easy to tune with the individual temperature control of the heaters. The ability of the sensor to operate in high temperatures makes it promising for use in different harsh environments, e.g., for close integration with microthrusters.
Computational imaging using a mode-mixing cavity at microwave frequencies
Authors: Fromenteze Thomas , Yurduseven Okan , Imani Mohammadreza F. , Gollub Jonah , Decroze Cyril , Carsenat David , Smith David R.
Published: May 2015

We present a 3D computational imaging system based on a mode-mixing cavity at microwave frequencies. The core component of this system is an electrically large rectangular cavity with one corner re-shaped to catalyze mode mixing, often called a Sinai Billiard. The front side of the cavity is perforated with a grid of periodic apertures that sample the cavity modes and project them into the imaging scene. The radiated fields are scattered by the scene and are measured by low gain probe antennas. The complex radiation patterns generated by the cavity thus encode the scene information onto a set of frequency modes. Assuming the first Born approximation for scattering dynamics, the received signal is processed using computational methods to reconstruct a 3D image of the scene with resolution determined by the diffraction limit. The proposed mode-mixing cavity is simple to fabricate, exhibits low losses, and can generate highly diverse measurement modes. The imaging system demonstrated in this letter can find application in security screening and medical diagnostic imaging.
Note: Simple leak sealing technique for ultra-high vacuum cryostat by using freezable liquid
Authors: Kim Min-Seong , Kim Ji-Ho , Lyo In-Whan
Published: May 2015

Here we introduce a simple, low-cost, contamination-free, and highly reliable technique for sealing an ultra-high vacuum (UHV) cryostat by using cryogenically freezable liquid. We demonstrate it by sealing an UHV cryostat with dry leaks in the high vacuum range; ethanol was utilized to fill and block the leakage pathways through the subsequent in situ solidification by LN2. The seal is reversible and can be maintained as long as the cryostat is kept at cryogenic temperature.
Electric field and temperature dependence of dielectric permittivity in strontium titanate investigated by a photoemission study on Pt/SrTiO3:Nb junctions
Authors: Hirose Sakyo , Okushi Hideyo , Ueda Shigenori , Yoshikawa Hideki , Adachi Yutaka , Ando Akira , Ohsawa Takeo , Haneda Hajime , Ohashi Naoki
Published: May 2015

Schottky junctions made from platinum and niobium-doped strontium titanate (SrTiO3:Nb) were investigated by hard X-ray photoemission (HXPES) and through a band bending behavior simulation using a phenomenological model, which assumes a decrease in dielectric constant due to an electric field. Thus, we confirmed that the observed HXPES spectra at relatively high temperatures, e.g., >250 K, were well simulated using this phenomenological model. In contrast, it was inferred that the model was not appropriate for junction behavior at lower temperatures, e.g., <150 K. Therefore, a reconstruction of the phenomenological model is necessary to adequately explain the dielectric properties of SrTiO3.
X-ray beam compression by tapered waveguides
Authors: Chen H.-Y. , Hoffmann S. , Salditt T.
Published: May 2015

We have fabricated linear tapered waveguide channels filled with air and imbedded in silicon for the hard x-ray regime, using a processing scheme involving e-beam lithography, reactive ion etching, and wafer bonding. Beam compression in such channels is demonstrated by coupling a pre-focused undulator beam into the channels, and recording the exit flux and far-field diffraction patterns. We achieved a compressed beam with a spot size of 16.48 nm (horizontal) × 14.6 nm (vertical) near the waveguide exit plane, as determined from the reconstructed near-field distribution, at an exit flux which is eight times higher than that of an equivalent straight channel. Simulations indicate that this gain could reach three to four orders of magnitude for longer channels with tapering in two directions.
Excitonic luminescence of SiGe/Si quantum wells δ-doped with boron
Authors: Bagaev V. S. , Krivobok V. S. , Nikolaev S. N. , Novikov A. V. , Onishchenko E. E. , Pruchkina A. A.
Published: May 2015

Low-temperature photoluminescence of undoped and moderately δ-doped Si1−xGex/Si (x < 0.1) quantum wells has been studied. The influence of boron δ-layer on the excitonic luminescence and the luminescence caused by a dense electron plasma was demonstrated. The conditions under which the luminescence spectra of quantum wells are dominated by impurity-bound excitons (BE) have been established. Some unusual properties of these BE are explained in terms of type II band-offset in Si1−xGex/Si (x < 0.1) quantum wells, which favors a spatial separation of electrons and holes. It is shown that the temperature dependence of an excitonic emission in the quantum wells allows to calculate the BE-related density of states and, thus, can be used for contactless estimation of the impurity concentration in quantum wells.
Condition of larvae of western rock lobster (Panulirus cygnus) in cyclonic and anticyclonic eddies of the Leeuwin Current off Western Australia
Authors: Wang Miao , O'Rorke Richard , Waite Anya M. , Beckley Lynnath E. , Thompson Peter , Jeffs Andrew G.
Published: May 2015

Changes in the offshore oceanographic processes are suspected to be the cause of a recent dramatic decline in the settlement of post-larvae of the Western Australian spiny lobster (Panulirus cygnus), which has greatly reduced the productivity from the world’s second-largest spiny lobster fishery. The present study assessed whether there are differences in the nutritional condition of the larvae of P. cygnus sampled from two pairs of cyclonic eddies (CEs) and anticyclonic eddies (AEs). Morphometric and biochemical analyses were undertaken on the mid–late-stage larvae (VI, VII, VIII) sampled offshore from two pairs of adjacent counter-rotating mesoscale eddies in the Leeuwin Current off Western Australia. The results showed that larvae captured from CEs had greater average total dry mass (P<0.001) than those from AEs. Stage VIII larvae from CEs contained more protein (P<0.008) (38.5% ±5.4s.e.) and lipid (P<0.005) (67.2% ±12.1) than did those from AEs. The possible causes for these differences are uncertain but may be related to differences in water temperatures in CEs v. AEs influencing the ability of phyllosomas to accumulate nutritional reserves.
A natural experiment of social network formation and dynamics
Authors: Phan Tuan Q. , Airoldi Edoardo M.
Published: May 2015

Significance

This paper presents an empirical analysis of the short- and long-term causal effects of a hurricane on social structure. Establishing causal relationships in social network formation and dynamics has historically been difficult because of the complexity of engineering social relations in a controlled environment, and the lack of time-resolved data about individuals' behavior. In addition, large-scale interventions of network structure are not feasible in practice. Here, we design an observational study that enables the estimation of causal effects by leveraging the locally well-defined impact of a hurricane. This aspect allows us to conceptualize the analysis of individuals’ behavior as a natural experiment, where the intervention is randomized by nature to locales, leaving only issues of balance to consider.
A tortoise–hare pattern seen in adapting structured and unstructured populations suggests a rugged fitness landscape in bacteria
Authors: Nahum Joshua R. , Godfrey-Smith Peter , Harding Brittany N. , Marcus Joseph H. , Carlson-Stevermer Jared , Kerr Benjamin
Published: May 2015

Significance

The “adaptive landscape” characterizes the relationship between genotype and fitness. As the landscape becomes more rugged, evolution can become more constrained. During the modern evolutionary synthesis, different views about the process of adaptation reflected different assumptions about landscape topography, which motivated the empirical assessment of adaptive landscapes in biological systems. Here, we describe how evolutionary patterns within experimental populations can yield information about landscape topography. Specifically, metapopulations ofEscherichia coliare evolved under different patterns of migration. We find bacteria reach higher fitness and accumulate more mutations under restricted migration than unrestricted migration, which is consistent with a rugged topography. In this way, experimental manipulation of population structure can provide insight into fundamental evolutionary constraints.
Body size affects the evolution of eyespots in caterpillars
Authors: Hossie Thomas John , Skelhorn John , Breinholt Jesse W. , Kawahara Akito Y. , Sherratt Thomas N.
Published: May 2015

Significance

Eyespots are a widespread form of antipredator defense that have long captured the imagination of evolutionary biologists, geneticists, psychologists, and artists. These markings are particularly common within Lepidoptera, and eyespots on caterpillars have been shown to deter avian predators; however, why eyespots have evolved in particular caterpillar species, and why they are not even more widespread, remain unclear. Here we answer this question using a powerful three-pronged approach. Our phylogenetically controlled analysis of hawkmoths demonstrates that eyespots are typically restricted to large caterpillars, and our field and laboratory experiments provide an explanation for this. Eyespots are costly to small caterpillars because they enhance detectability without providing a protective advantage, but they are beneficial to large caterpillars because they deter predators.
Effect of warming temperatures on US wheat yields
Authors: Tack Jesse , Barkley Andrew , Nalley Lawton Lanier
Published: May 2015

Significance

This study provides insights for wheat breeding efforts, public policy, and agricultural decision making related to climate change. Our findings provide opportunities for the international wheat breeding community to intensify research efforts to increase resistance to heat stress during focused developmental stages. These efforts could result in net positive warming effects since reduced exposure to freeze was found to be a yield-enhancing benefit of warming. Our results indicate that advancements in heat resistance could come at the expense of higher average yields, and that there is currently limited scope for producer adaptation through alternative variety selection. Our results also suggest that irrigation could help mitigate the effects of warming, which has implications for policies focused on the conservation of increasingly scarce water resources.
Atmospheric composition 1 million years ago from blue ice in the Allan Hills, Antarctica
Authors: Higgins John A. , Kurbatov Andrei V. , Spaulding Nicole E. , Brook Ed , Introne Douglas S. , Chimiak Laura M. , Yan Yuzhen , Mayewski Paul A. , Bender Michael L.
Published: May 2015

Significance

Bubbles of ancient air trapped in ice cores permit the direct reconstruction of atmospheric composition and allow us to link greenhouse gases and global climate over the last 800 ky. Here, we present new ice core records of atmospheric composition roughly 1 Ma from a shallow ice core drilled in the Allan Hills blue ice area, Antarctica. These records confirm that interglacial CO
2
concentrations decreased by 800 ka. They also show that the link between CO
2
and Antarctic temperature extended into the warmer world of the mid-Pleistocene.
The two-domain tree of life is linked to a new root for the Archaea
Authors: Raymann Kasie , Brochier-Armanet Céline , Gribaldo Simonetta
Published: May 2015

Significance

An archaeal origin for eukaryotes is an exciting recent finding. Nevertheless, it has been based largely on the reconstruction of universal trees. The use of an alternative strategy based on markers shared between Archaea and eukaryotes and Archaea and Bacteria bypasses potential problems linked to the analysis of the three domains simultaneously. Comparison of the phylogenies obtained by these two complementary sets of markers supports a sister relationship between eukaryotes and the Thaumarchaeota/“Aigarchaeota” (candidate phylum)/Crenarchaeota/Korarchaeota lineage but also robustly indicates a root of the tree of Archaea that challenges the traditional topology of this domain. This sensibly changes our perspective of the ancient evolution of the Archaea, early life, and Earth.
Major evolutionary transitions in individuality
Authors: West Stuart A. , Fisher Roberta M. , Gardner Andy , Kiers E. Toby
Published: May 2015

The evolution of life on earth has been driven by a small number of major evolutionary transitions. These transitions have been characterized by individuals that could previously replicate independently, cooperating to form a new, more complex life form. For example, archaea and eubacteria formed eukaryotic cells, and cells formed multicellular organisms. However, not all cooperative groups are en route to major transitions. How can we explain why major evolutionary transitions have or haven’t taken place on different branches of the tree of life? We break down major transitions into two steps: the formation of a cooperative group and the transformation of that group into an integrated entity. We show how these steps require cooperation, division of labor, communication, mutual dependence, and negligible within-group conflict. We find that certain ecological conditions and the ways in which groups form have played recurrent roles in driving multiple transitions. In contrast, we find that other factors have played relatively minor roles at many key points, such as within-group kin discrimination and mechanisms to actively repress competition. More generally, by identifying the small number of factors that have driven major transitions, we provide a simpler and more unified description of how life on earth has evolved.
Human caspase-4 mediates noncanonical inflammasome activation against gram-negative bacterial pathogens
Authors: Casson Cierra N. , Yu Janet , Reyes Valeria M. , Taschuk Frances O. , Yadav Anjana , Copenhaver Alan M. , Nguyen Hieu T. , Collman Ronald G. , Shin Sunny
Published: May 2015

Significance

The innate immune system provides a first line of defense against invading pathogens. The inflammasome is an innate immune complex that activates inflammatory caspases upon infection, causing cell death and IL-1 cytokine release, which initiate defense against gram-negative bacterial pathogens but also mediate septic shock. Many inflammasome studies have been performed using cells from mice, but mice and humans differ in their complement of inflammatory caspases. Instead of caspase-11, humans encode the putative orthologs caspase-4 and caspase-5. Here, we show that caspase-4 plays a conserved role in inflammasome activation in response to virulent gram-negative pathogens in primary human macrophages. Our findings provide important insight into how inflammasomes are regulated in human cells.
Insights into ParB spreading from the complex structure of Spo0J and
parS
Authors: Chen Bo-Wei , Lin Ming-Hsing , Chu Chen-Hsi , Hsu Chia-En , Sun Yuh-Ju
Published: May 2015

Significance

In the ParABS (partition system of ParA, ParB, and
parS
) bacterial chromosome partitioning system, ParB (partition protein B) spreads along the chromosomal DNA and a high-order complex is required for this function. Although ParB spreading has been studied, the detailed mechanism is still unclear. Herein, we report the crystal structure of the C-terminal domain truncated protein (Ct-
Hp
Spo0J)-
parS
complex and reveal the structural basis for ParB spreading and chromosomal DNA condensation. Our structural and biochemical data show that ParB forms a high-order nucleoprotein: the ParB-
parS
complex. From these results, we propose how ParB possibly associates with other proteins through its protruded N-terminal domains, how ParB spreads along the chromosomal DNA by
parS
binding, and how ParB bridges DNA to compact and condense the chromosome during chromosome partitioning.
Sigma-1 receptor regulates Tau phosphorylation and axon extension by shaping p35 turnover via myristic acid
Authors: Tsai Shang-Yi A. , Pokrass Michael J. , Klauer Neal R. , Nohara Hiroshi , Su Tsung-Ping
Published: May 2015

Significance

Neurodegeneration is tightly linked to tauopathy as a result of the overactivated cyclin-dependent kinase (cdk) 5 in the form of cdk5/p25. P35, another activator of cdk5, which is short-lived and myristoylated, is cleaved by calpain to the degradation-resistant activator p25. One way to tune down the aberrant, overreactive cdk/p25 is to reduce available p35. The sigma-1 receptor (Sig-1R) is an endoplasmic reticulum (ER) chaperone of unknown relation to tauopathy. Here we found that Sig-1Rs bind myristic acid and promote the degradation of p35. Further, the aberrant tau hyperphosphorylation and stunting of axon elongation in Sig-1R–KO neurons are mitigated by exogenously added myristic acid. Our results establish the role of ER Sig-1Rs in tauopathy and implicate the importance of myristic acid as a substance to fight against neurodegeneration.
Generalized receptor law governs phototaxis in the phytoplankton
Euglena gracilis
Authors: Giometto Andrea , Altermatt Florian , Maritan Amos , Stocker Roman , Rinaldo Andrea
Published: May 2015

Significance

Many phytoplankton species sense light and move toward or away from it. Such directed movement, called phototaxis, has major ecological implications because it contributes to the largest biomass migration on Earth, diel vertical migration of organisms responsible for roughly one-half of the global photosynthesis. We experimentally studied phototaxis for the flagellate alga
Euglena gracilis
by tracking algal populations over time in accurately controlled light fields. Observations coupled with formal model comparison lead us to propose a generalized receptor law governing phototaxis of phytoplankton. Such a model accurately reproduces experimental patterns resulting from accumulation and dispersion dynamics. Direct applications concern phytoplankton migrations and vertical distribution, bioreactor optimization, and the experimental study of biological invasions in heterogeneous environments.
Infection of phytoplankton by aerosolized marine viruses
Authors: Sharoni Shlomit , Trainic Miri , Schatz Daniella , Lehahn Yoav , Flores Michel J. , Bidle Kay D. , Ben-Dor Shifra , Rudich Yinon , Koren Ilan , Vardi Assaf
Published: May 2015

Significance

Marine viruses constitute a major ecological and evolutionary driving force in marine ecosystems and are responsible for cycling of major nutrients; however, their dispersal mechanisms remain underexplored. By using one of the most established host–pathogen planktonic model systems we provide strong evidence that specific viruses of marine coccolithophores can be transmitted and stay infective as marine aerosols. Being transported by the wind, phytoplankton viruses can be conveyed long distances and transmit the infection to remote locations to which coccolithophore blooms can be extended. We show that this effective transmission mechanism that has been studied in human, animal, and plant diseases could play an important role in host–virus dynamics during phytoplankton blooms in the ocean.
Let-7 family of microRNA is required for maturation and adult-like metabolism in stem cell-derived cardiomyocytes
Authors: Kuppusamy Kavitha T. , Jones Daniel C. , Sperber Henrik , Madan Anup , Fischer Karin A. , Rodriguez Marita L. , Pabon Lil , Zhu Wei-Zhong , Tulloch Nathaniel L. , Yang Xiulan , Sniadecki Nathan J. , Laflamme Michael A. , Ruzzo Walter L. , Murry Charles E. , Ruohola-Baker Hannele
Published: May 2015

Significance

The adult human heart is incapable of significant regeneration after injury. Human embryonic stem cells (hESCs) have the capacity to generate an unlimited number of cardiomyocytes (CMs). However, hESC-derived CMs (hESC-CMs) are at a fetal state with respect to their functional and physiological characteristics, diminishing their utility for modeling adult-related heart disease and therapeutic screening. Thus, the potential for hESC-CMs may improve immensely in cardiac-related therapeutic applications if factors that drive their maturation are uncovered. In this study, we show that members of let-7 miRNA family control CM metabolism, cell size, and force contractility, making them one of the best factors identified to date in promoting maturity of stem cell derivatives.
Rate, spectrum, and evolutionary dynamics of spontaneous epimutations
Authors: van der Graaf Adriaan , Wardenaar René , Neumann Drexel A. , Taudt Aaron , Shaw Ruth G. , Jansen Ritsert C. , Schmitz Robert J. , Colomé-Tatché Maria , Johannes Frank
Published: May 2015

Significance

Changes in the methylation status of cytosine nucleotides are a source of heritable epigenetic and phenotypic diversity in plants. Here we derive robust estimates of the rate at which cytosine methylation is spontaneously gained (forward epimutation) or lost (backward epimutation) in the genome of the model plant
Arabidopsis thaliana
. We show that the forward–backward dynamics of selectively neutral epimutations have a major impact on methylome evolution and shape genome-wide patterns of methylation diversity among natural populations in this species. The epimutation rates presented here can serve as reference values in future empirical and theoretical population epigenetic studies in plants.
The recent invasion of natural
Drosophila simulans
populations by the P-element
Authors: Kofler Robert , Hill Tom , Nolte Viola , Betancourt Andrea J. , Schlötterer Christian
Published: May 2015

Significance

Transposable elements (TEs) persist via two evolutionary strategies—in the short term, they selfishly propagate within genomes, and over the long term, they spread horizontally between species. Famously, the P-element invaded
Drosophila melanogaster
populations some time before 1950 and spread rapidly worldwide. Here, we show that it has also invaded a close relative,
Drosophila simulans
, from which it was absent until recently. The genomic tools at our disposal offer the unique opportunity to study the dynamics of a TE invasion at multiple levels and to compare the spread of the P-element in
D. simulans
with the well-investigated invasion of
D. melanogaster
.
Inositol phosphate pathway controls transcription of telomeric expression sites in trypanosomes
Authors: Cestari Igor , Stuart Ken
Published: May 2015

Significance

African trypanosomes cause human and animal diseases and evade the host immune systems by periodically switching which variant surface glycoprotein (VSG) they express. The mechanisms that result in expression of one of the numerous VSG genes at a time and the switching of expression between different VSG genes are poorly understood. We show that specific steps in the inositol phosphate (IP) pathway control both monoallelic VSG gene transcription and the switching of VSG gene expression. The data indicate that the cellular amounts, locations, and molecular interactions of specific IP pathway enzymes and their metabolites control both processes. The results offer new drug targets and insights into the epigenetic control of gene expression by this biologically ubiquitous pathway.
Minimal genomes of mycoplasma-related endobacteria are plastic and contain host-derived genes for sustained life within Glomeromycota
Authors: Naito Mizue , Morton Joseph B. , Pawlowska Teresa E.
Published: May 2015

Significance

Arbuscular mycorrhizal fungi (AMF) are soil fungi associated with the majority of land plants worldwide. They supply plants with mineral nutrients in exchange for photosynthates. Most AMF harbor endobacteria from the Mollicutes class. Exploring metagenomes of endobacterial populations in three AMF species, we discovered that these endobacteria have minimal genomes and are metabolically dependent on their fungal host. Despite vertical transmission, endobacterial genomes are uniquely plastic. In addition, the endobacteria contain multiple genes horizontally transferred from fungi. Many of these genes encode products thought to interact with fungal host proteins. Overall, the endobacterial genomes reveal a tightly knit network of interactions with the fungal host and highlight the importance of associations between bacteria and fungi.
Light signaling controls nuclear architecture reorganization during seedling establishment
Authors: Bourbousse Clara , Mestiri Imen , Zabulon Gerald , Bourge Mickaël , Formiggini Fabio , Koini Maria A. , Brown Spencer C. , Fransz Paul , Bowler Chris , Barneche Fredy
Published: May 2015

Significance

Nuclear organization and genome expression are subject to massive reprogramming during most developmental transitions. The mechanisms triggering them in response to environmental stimuli are only poorly understood. Here we describe that dynamic changes in higher-order nuclear organization occurring in cotyledons (embryonic leaves) upon germination are impacted by light availability in the plant
Arabidopsis thaliana
. Upon light perception, master regulators of the light signaling pathway trigger rapid and massive nuclear expansion, condensation of large chromatin domains, and increased transcriptional activity of genes. These findings establish a foundation for deciphering the relationships between topological genome organization and transcriptional regulation associated with the establishment of photosynthesis.
Deep-sea hydrothermal vent bacteria related to human pathogenic
Vibrio
species
Authors: Hasan Nur A. , Grim Christopher J. , Lipp Erin K. , Rivera Irma N. G. , Chun Jongsik , Haley Bradd J. , Taviani Elisa , Choi Seon Young , Hoq Mozammel , Munk A. Christine , Brettin Thomas S. , Bruce David , Challacombe Jean F. , Detter J. Chris , Han Cliff S. , Eisen Jonathan A. , Huq Anwar , Colwell Rita R.
Published: May 2015

Significance

During
Alvin
and
Nautile
dives in 1999, samples were collected from water surrounding sulfide chimneys of a hydrothermal vent along the East Pacific Rise and four mesophilic bacteria were isolated, including a novel
Vibrio
species,
Vibrio antiquarius
. Genomic, functional, and phylogenetic analyses indicate an intriguing blend of genomic features related to adaptation and animal symbiotic association, and also revealed the presence of virulence genes commonly found in
Vibrio
species pathogenic for humans. The presence of these virulence genes in an ecologically distinct
Vibrio
species was surprising. It is concluded that pathogenicity genes serve a far more fundamental ecological role than solely causation of human disease.
Hydrological change in Southern Europe responding to increasing North Atlantic overturning during Greenland Stadial 1
Authors: Bartolomé Miguel , Moreno Ana , Sancho Carlos , Stoll Heather M. , Cacho Isabel , Spötl Christoph , Belmonte Ánchel , Edwards R. Lawrence , Cheng Hai , Hellstrom John C.
Published: May 2015

Significance

This study presents robust evidence of two hydrological phases within the Greenland Stadial 1 (GS-1) cold event (12.8−11.7 ka B.P.) in Southern Europe. We present a well-dated high-resolution speleothem record (Seso Cave, Central Pyrenees) where temperature and hydrological signals are independently reconstructed. Detailed interpretation of stable isotopes and trace elements allow characterizing a first dry period followed, after 12,500 y before 2000 A.D., by more humid conditions. Our findings point to the resumption of the Atlantic overturning circulation as the main mechanism behind the hydrological response in Europe during this mid–GS-1 transition. The second phase, cold in Greenland but humid in Western Europe, represents a new paradigm in the well-established model of dry, cold stadials during the last glacial period.
Prolonged daily light exposure increases body fat mass through attenuation of brown adipose tissue activity
Authors: Kooijman Sander , van den Berg Rosa , Ramkisoensing Ashna , Boon Mariëtte R. , Kuipers Eline N. , Loef Marieke , Zonneveld Tom C. M. , Lucassen Eliane A. , Sips Hetty C. M. , Chatzispyrou Iliana A. , Houtkooper Riekelt H. , Meijer Johanna H. , Coomans Claudia P. , Biermasz Nienke R. , Rensen Patrick C. N.
Published: May 2015

Significance

Increased light exposure has been associated with obesity in both humans and mice. In this article, we elucidate a mechanistic basis of this association by performing studies in mice. We report that prolonging daily light exposure increases adiposity by decreasing energy expenditure rather than increasing food intake or locomotor activity. This was caused by a light-exposure period-dependent attenuation of the noradrenergic activation of brown adipose tissue that has recently been shown to contribute substantially to energy expenditure by converting fatty acids and glucose into heat. Therefore, we conclude that impaired brown adipose tissue activity may mediate the relationship between increased light exposure and adiposity.
Optimized tools for multicolor stochastic labeling reveal diverse stereotyped cell arrangements in the fly visual system
Authors: Nern Aljoscha , Pfeiffer Barret D. , Rubin Gerald M.
Published: May 2015

Significance

Nervous systems contain vast numbers of neurons with diverse shapes and complex spatial relationships. We describe new genetic tools for the efficient visualization by light microscopy of individual neurons and their relative positions in
Drosophila
. The application of these methods to the visual system revealed an unexpected diversity of cell-type–specific arrangements of neuronal processes within a single brain region. This wide range of stereotyped cell arrangements provides distinct circuit elements for processing visual information and implies the existence of a surprisingly large number of genetic programs that produce these arrangements during development.
Regulation of AMPA receptor phosphorylation by the neuropeptide PACAP38
Authors: Toda Alyssa M. A. , Huganir Richard L.
Published: May 2015

Significance

AMPA receptors (AMPARs) conduct the majority of excitatory synaptic transmission in the brain. Through changes in AMPAR synaptic localization or conductance the strength of a synapse can be altered. It is hypothesized that such changes underlie complex behaviors such as learning and memory. AMPAR phosphorylation is one signaling event used to alter receptor targeting and conductance. We demonstrate the neuropeptide PACAP38 stimulates AMPAR GluA1 subunit phosphorylation at S845 and dephosphorylation at T840. Investigation of PACAP38-dependent changes in AMPAR phosphorylation will help us to better understand the factors involved in regulating AMPAR function.