bluuebunny/crossref_metadata_2025 huggingface dataset:
Electron modes of plasma generated at tunnel ionization of atoms by a circularly polarized radiation
Authors: Vagin K. Yu. , Uryupin S. A.
Published: October 2017

The collective modes of photoionized plasmas are studied using the model description of electron velocity distribution formed at tunnel ionization of atoms by circularly polarized radiation. The dispersion laws of transverse and approximately longitudinal high-frequency waves propagating at an arbitrary angle to the anisotropy axis of photoelectron distribution are obtained. The dispersion law of potential surface waves is derived. It is shown that the frequency of these waves may be greater than plasma frequency. The aperiodic instability of photoionized plasmas is described.
Foundations and latest advances in replica exchange transition interface sampling
Authors: Cabriolu Raffaela , Skjelbred Refsnes Kristin M. , Bolhuis Peter G. , van Erp Titus S.
Published: October 2017

Nearly 20 years ago, transition path sampling (TPS) emerged as an alternative method to free energy based approaches for the study of rare events such as nucleation, protein folding, chemical reactions, and phase transitions. TPS effectively performs Monte Carlo simulations with relatively short molecular dynamics trajectories, with the advantage of not having to alter the actual potential energy surface nor the underlying physical dynamics. Although the TPS approach also introduced a methodology to compute reaction rates, this approach was for a long time considered theoretically attractive, providing the exact same results as extensively long molecular dynamics simulations, but still expensive for most relevant applications. With the increase of computer power and improvements in the algorithmic methodology, quantitative path sampling is finding applications in more and more areas of research. In particular, the transition interface sampling (TIS) and the replica exchange TIS (RETIS) algorithms have, in turn, improved the efficiency of quantitative path sampling significantly, while maintaining the exact nature of the approach. Also, open-source software packages are making these methods, for which implementation is not straightforward, now available for a wider group of users. In addition, a blooming development takes place regarding both applications and algorithmic refinements. Therefore, it is timely to explore the wide panorama of the new developments in this field. This is the aim of this article, which focuses on the most efficient exact path sampling approach, RETIS, as well as its recent applications, extensions, and variations.
Experimental and theoretical studies of the reactions of ground-state sulfur atoms with hydrogen and deuterium
Authors: Thompson Kristopher M. , Gao Yide , Marshall Paul , Wang Han , Zhou Linsen , Li Yongle , Guo Hua
Published: October 2017

The gas-phase kinetics of S(3P) atoms with H2 and D2 have been studied via the laser flash photolysis—resonance fluorescence technique. S atoms were generated by pulsed photolysis of CS2 at 193 nm and monitored by time-resolved fluorescence at 181 nm. The rate coefficients for H2 (k1) and D2 (k2), respectively, are summarized as k1(600-1110 K) = 3.0 × 10−9 exp−1.317×105−2.703×107K/T8.314 T/K cm3 molecule−1 s−1 and k2(770-1110 K) = 2.2 × 10−14 (T/298 K)3.55 exp(−5420 K/T) cm3 molecule−1 s−1. Error limits are discussed in the text. The rate coefficients for formation of SH(SD) + H(D) on a newly developed triplet potential energy surface were characterized via ring polymer molecular dynamics and canonical variational transition-state theory. There is excellent agreement above about 1000 K between theory and experiment. At lower temperatures, the experimental rate coefficient is substantially larger than the results computed for the adiabatic reaction, suggesting a significant role for intersystem crossing to the singlet potential energy surface at lower temperatures.
Asymptotic growth laws for intrusion tongues in lock-exchange flows
Authors: Goncharov V. P. , Pavlov V. I.
Published: October 2017

The heuristic Fermi-Neumann box model is used to study the non-Boussinesq lock exchange flows in an infinite horizontal channel. This allowed us to find the asymptotic growth laws for intrusion tongues at a late stage of their development. It is shown that these laws are essentially different. The classical scenario of the linear growth x1∝t is supported only by the lower (heavy) intrusion tongue. The same is not true for the upper (light) intrusion tongue that obeys the law x2∝t/lnt.
Measuring viscosity with nonlinear self-excited microcantilevers
Authors: Mouro J. , Tiribilli B. , Paoletti P.
Published: October 2017

A viscosity sensor based on the nonlinear behaviour of a microcantilever embedded in a self-excitation loop with an adjustable phase-shifter is proposed. The self-sustained oscillation frequencies of the cantilever are experimentally and theoretically investigated as functions of the fluid viscosity and of the imposed phase shift of the signal along the self-excitation loop. The sensor performance is validated experimentally using different water-glycerol solutions. In contrast to existing rheological sensors, the proposed platform can be tuned to work in two different modes: a high-sensitivity device whose oscillation frequency changes smoothly with the rheological properties of the fluid or a critical viscosity threshold detector, where, for small changes in fluid viscosity, there is a step change in oscillation frequency.
Reduced dimensionality in drift-diffusion models of back-contact solar cells and scanning photocurrent microscopy
Authors: Lamboll Robin D. , Greenham Neil C.
Published: October 2017

Solar cells are three-dimensional objects frequently modeled as being one-dimensional for convenience. However, for more complex designs of solar cells or if the cells are only illuminated at one point, one-dimensional modeling is insufficient. Here, some conditions for reducing the complexity of multidimensional drift-diffusion simulations are investigated in realistic situations for a back-contact perovskite solar cell. The analysis investigates under what situations we may neglect vertical carrier density variation and approximate extraction currents to be linearly dependent on the vertically averaged carrier concentration. Analytic expressions for the linear relationship in both the low and high extraction velocity regimes are demonstrated, and the conditions where these approximations break down are investigated. It is shown that recombination is usually accurately modeled using only vertically averaged carrier concentrations when the distance between electrodes is many times the height and when less than half the charges that are generated recombine, although edge effects around the onset of electrodes are noted. These findings are then applied to a problem that often emerges in scanning photocurrent microscopy, a point-excited film with a laterally offset electrode. It is demonstrated that we expect the current recorded in this case to decay exponentially with the distance between excitation and electrode, with a decay constant that can be related to device parameters. The characteristic equilibration time for the system to reach this current, which can be extracted from the phase delay in a lock-in amplifier measurement, is demonstrated to increase linearly with distance. It is shown that information about the diffusion and recombination rates can be extracted from a wide variety of planar systems.
Asymmetric absorber with multiband and broadband for low-frequency sound
Authors: Long Houyou , Cheng Ying , Liu Xiaojun
Published: October 2017

We present the mechanism for the asymmetric absorption of acoustic waves in a two-port transparent waveguide system by shunting detuned Helmholtz resonators (HRs) pairs in cascade. Theoretical analysis, numerical simulations, and experimental measurements verify that sound energy is almost totally absorbed (96.1%) at ∼373 Hz when sound waves are incident from one side while it is largely reflected back from the opposite side by judiciously designed HRs to provide manipulated surface impedance matching/mismatching to that of air at the opposite sides of the waveguide. Thus, asymmetric acoustic absorber is achieved at a low frequency. We have further demonstrated the flexibility of this methodology to get non-reciprocal absorption and reflectance in multiband and broadband. Our design advances the concept of asymmetric acoustic manipulation in passive two-port systems and may enable sound-absorbing devices for more versatile applications.
Nuclear magnetic resonance probe head design for precision strain control
Authors: Kissikov T. , Sarkar R. , Bush B. T. , Lawson M. , Canfield P. C. , Curro N. J.
Published: October 2017

We present the design and construction of an NMR probe to investigate single crystals under strain at cryogenic temperatures. The probe head incorporates a piezoelectric-based apparatus from Razorbill Instruments that enables both compressive and tensile strain tuning up to strain values on the order of 0.3% with a precision of 0.001%.   75As NMR in BaFe2As2 reveals large changes to the electric field gradient and indicates that the strain is homogeneous to within 16% over the volume of the NMR coil.
The anisotropic size effect of the electrical resistivity of metal thin films: Tungsten
Authors: Zheng Pengyuan , Gall Daniel
Published: October 2017

The resistivity of nanoscale metallic conductors is orientation dependent, even if the bulk resistivity is isotropic and electron scattering cross-sections are independent of momentum, surface orientation, and transport direction. This is demonstrated using a combination of electron transport measurements on epitaxial tungsten layers in combination with transport simulations based on the ab initio predicted electronic structure, showing that the primary reason for the anisotropic size effect is the non-spherical Fermi surface. Electron surface scattering causes the resistivity of epitaxial W(110) and W(001) layers measured at 295 and 77 K to increase as the layer thickness decreases from 320 to 4.5 nm. However, the resistivity is larger for W(001) than W(110) which, if describing the data with the classical Fuchs-Sondheimer model, yields an effective electron mean free path λ* for bulk electron-phonon scattering that is nearly a factor of two smaller for the 110 vs the 001-oriented layers, with λ(011)*= 18.8 ± 0.3 nm vs λ(001)* = 33 ± 0.4 nm at 295 K. Boltzmann transport simulations are done by integration over real and reciprocal space of the thin film and the Brillouin zone, respectively, describing electron-phonon scattering by momentum-independent constant relaxation-time or mean-free-path approximations, and electron-surface scattering as a boundary condition which is independent of electron momentum and surface orientation. The simulations quantify the resistivity increase at the reduced film thickness and predict a smaller resistivity for W(110) than W(001) layers with a simulated ratio λ(011)*/λ(001)* = 0.59 ± 0.01, in excellent agreement with 0.57 ± 0.01 from the experiment. This agreement suggests that the resistivity anisotropy in thin films of metals with isotropic bulk electron transport is fully explained by the non-spherical Fermi surface and velocity distribution, while electron scattering at phonons and surfaces can be kept isotropic and independent of the surface orientation. The simulations correctly predict the anisotropy of the resistivity size effect, but underestimate its absolute magnitude. Quantitative analyses suggest that this may be due to (i) a two-fold increase in the electron-phonon scattering cross-section as the layer thickness is reduced to 5 nm or (ii) a variable wave-vector dependent relaxation time for electron-phonon scattering.
Bonding reactivity descriptor from conceptual density functional theory and its applications to elucidate bonding formation
Authors: Zhou Pan-Pan , Liu Shubin , Ayers Paul W. , Zhang Rui-Qin
Published: October 2017

Condensed-to-atom Fukui functions which reflect the atomic reactivity like the tendency susceptible to either nucleophilic or electrophilic attack demonstrate the bonding trend of an atom in a molecule. Accordingly, Fukui functions based concepts, that is, bonding reactivity descriptors which reveal the bonding properties of molecules in the reaction were put forward and then applied to pericyclic and cluster reactions to confirm their effectiveness and reliability. In terms of the results from the bonding descriptors, a covalent bond can readily be predicted between two atoms with large Fukui functions (i.e., one governs nucleophilic attack while the other one governs electrophilic attack, or both of them govern radical attacks) for pericyclic reactions. For SinOm clusters’ reactions, the clusters with a low O atom ratio readily form a bond between two Si atoms with big values of their Fukui functions in which they respectively govern nucleophilic and electrophilic attacks or both govern radical attacks. Also, our results from bonding descriptors show that Si—Si bonds can be formed via the radical mechanism between two Si atoms, and formations of Si—O and O—O bonds are possible when the O content is high. These results conform with experimental findings and can help experimentalists design appropriate clusters to synthesize Si nanowires with high yields. The approach established in this work could be generalized and applied to study reactivity properties for other systems.
Influence of chirality on the thermal and electric properties of the columnar mesophase exhibited by homomeric dipeptides
Authors: Parthasarathi Srividhya , Shankar Rao D. S. , Prabhu Rashmi , Yelamaggad C. V. , Krishna Prasad S.
Published: October 2017

We present the first investigation of the influence of chirality on the thermal and electric properties in a biologically important homomeric dipeptide that exhibits a hexagonal columnar liquid crystal mesophase. The peptide employed has two chiral centres, and thus the two possible enantiopures are the (R,R) and (S,S) forms having opposite chirality. The measurements reported the span of the binary phase space between these two enantiopures. Any point in the binary diagram is identified by the enantiomeric excess Xee (the excess content of the R,R enantiopure over its S,S counterpart). We observe that the magnitude of Xee plays a pivotal role in governing the properties as evidenced by X-ray diffraction (XRD), electric polarization (Ps), dielectric relaxation spectroscopy (DRS) measurements, and the isotropic-columnar transition temperature. For example, XRD shows that while other features pointing to a hexagonal columnar phase remain the same, additional short-range ordering, indicating correlated discs within the column, is present for the enantiopures (Xee = ±1) but not for the racemate (Xee = 0). Similarly, an electric-field driven switching whose profile suggests the phase structure to be antiferroelectric is seen over the entire binary space, but the magnitude is dependent on Xee; interestingly the polarization direction is axial, i.e., along the column axis. DRS studies display two dielectric modes over a limited temperature range and one mode (mode 2) connected with the antiferroelectric nature of the columnar structure covering the entire mesophase. The relaxation frequency and the thermal behaviour of mode 2 are strongly influenced by Xee. The most attractive effect of chirality is its influence on the polar order, a measure of which is the magnitude of the axial polarization. This result can be taken to be a direct evidence of the manifestation of molecular recognition and the delicate interplay between chiral perturbations and the magnitude of the polar order, a feature attractive from the viewpoint of devices based on, e.g., remnant polarization—a currently hot topic. To add further dimension to the work, the DRS measurements are also extended to elevated pressures.
Single neural adaptive controller and neural network identifier based on PSO algorithm for spherical actuators with 3D magnet array
Authors: Yan Liang , Zhang Lu , Zhu Bo , Zhang Jingying , Jiao Zongxia
Published: October 2017

Permanent magnet spherical actuator (PMSA) is a multi-variable featured and inter-axis coupled nonlinear system, which unavoidably compromises its motion control implementation. Uncertainties such as external load and friction torque of ball bearing and manufacturing errors also influence motion performance significantly. Therefore, the objective of this paper is to propose a controller based on a single neural adaptive (SNA) algorithm and a neural network (NN) identifier optimized with a particle swarm optimization (PSO) algorithm to improve the motion stability of PMSA with three-dimensional magnet arrays. The dynamic model and computed torque model are formulated for the spherical actuator, and a dynamic decoupling control algorithm is developed. By utilizing the global-optimization property of the PSO algorithm, the NN identifier is trained to avoid locally optimal solution and achieve high-precision compensations to uncertainties. The employment of the SNA controller helps to reduce the effect of compensation errors and convert the system to a stable one, even if there is difference between the compensations and uncertainties due to external disturbances. A simulation model is established, and experiments are conducted on the research prototype to validate the proposed control algorithm. The amplitude of the parameter perturbation is set to 5%, 10%, and 15%, respectively. The strong robustness of the proposed hybrid algorithm is validated by the abundant simulation data. It shows that the proposed algorithm can effectively compensate the influence of uncertainties and eliminate the effect of inter-axis couplings of the spherical actuator.
Landau damping in Kaniadakis and Tsallis distributed electron plasmas
Authors: López Rodrigo A. , Navarro Roberto E. , Pons Sebastian I. , Araneda Jaime A.
Published: October 2017

The damping arrest and saturation stages in the evolution of the electric field amplitude are characteristic imprint of the nonlinear Landau damping. Scaling laws for the wave amplitudes and times and critical parameters which separate the monotonic damping from nondamping regimes are well known for Maxwellian and Tsallis-like plasmas. Here, the properties of electrostatic waves in unmagnetized, collisionless, and non-Maxwellian electron plasmas are studied by taking into account the α-deformed Kaniadakis distribution and compared with results using the q-Tsallis formalism. It is checked that the damping arrest and saturation characteristics scale as power-laws for the α-Kaniadakis, similarly as for the q-Tsallis parameter, indicating that a universal behaviour exists for the transition between linear and non-linear regimes. It is shown that the damping of electrostatic waves is much weaker when using Kaniadakis distributions, even in situations where this distribution exhibits more enhanced high-velocity tails. Furthermore, it is observed that in cases where the Tsallis distribution damps out completely the initial perturbation, the equivalent Kaniadakis distributed plasmas still support particle trapping, or even if wider Kaniadakis distributions are used. This important signature may provide a new tool to diagnose the nature of the distribution function and its relation to wave measurements in laboratory and space plasmas.
Highly conducting leakage-free electrolyte for SrCoOx-based non-volatile memory device
Authors: Katase Takayoshi , Suzuki Yuki , Ohta Hiromichi
Published: October 2017

The electrochemical switching of SrCoOx-based non-volatile memory with a thin-film-transistor structure was examined by using liquid-leakage-free electrolytes with different conductivities (σ) as the gate insulator. We first examined leakage-free water, which is incorporated in the amorphous (a-) 12CaO·7Al2O3 film with a nanoporous structure (Calcium Aluminate with Nanopore), but the electrochemical oxidation/reduction of the SrCoOx layer required the application of a high gate voltage (Vg) up to 20 V for a very long current-flowing-time (t) ∼40 min, primarily due to the low σ [2.0 × 10−8 S cm−1 at room temperature (RT)] of leakage-free water. We then controlled the σ of the leakage-free electrolyte, infiltrated in the a-NaxTaO3 film with a nanopillar array structure, from 8.0 × 10−8 S cm−1 to 2.5 × 10−6 S cm−1 at RT by changing the x = 0.01–1.0. As the result, the t, required for the metallization of the SrCoOx layer under small Vg = –3 V, becomes two orders of magnitude shorter with increase of the σ of the a-NaxTaO3 leakage-free electrolyte. These results indicate that the ion migration in the leakage-free electrolyte is the rate-determining step for the electrochemical switching, compared to the other electrochemical process, and the high σ of the leakage-free electrolyte is the key factor for the development of the non-volatile SrCoOx-based electro-magnetic phase switching device.
Combination of conductive filaments and Schottky behavior in multifunctional Sn1−xCuxO2−δ memristor
Authors: Mei Fang , Shen Hui , Li Yang , Li Liben , Zang Guozhong , Zhou Min , Ti Ruixia , Yang Dianyuan , Huang Fengzhen , Lu Xiaomei , Zhu Jinsong
Published: October 2017

Resistive switching behaviors of SnO2 films are largely improved by Cu acceptor doping. At a suitable Cu2+ concentration, a high ON/OFF resistance ratio (104), good endurance (104) and long retention (104 s) are achieved in the Cu/SnO2:Cu/Pt sandwich structure with the modulation of carriers and oxygen vacancies. As a memristor, the resistive switching can be triggered by one pulse or a train of pulses, and the latter mode could simulate the long-term potentiation of biological synapses. Moreover, the multi-resistance states during the reset process demonstrate a combination of abrupt and incremental resistive switching. The peculiar conductive behavior of the devices is considered to result from the cooperation of conductive filaments and Schottky barrier, with the oxygen vacancies serving as the bridge. These studies are significant for higher density storage and cognitive computing in future.
Importance of free-living and particle-associated bacteria for the growth of the harmful dinoflagellate Prorocentrum minimum: evidence in culture stages
Authors: Park Bum Soo , Guo Ruoyu , Lim Weol-Ae , Ki Jang-Seu
Published: October 2017

The marine dinoflagellate Prorocentrum minimum is the cause of harmful algal blooms and may grow in association with co-occurring bacteria as ectosymbiotic, endosymbiotic and free-living forms. In the present study we investigated the bacterial community composition of both free-living bacteria (FLB) and particle-associated bacteria (PAB) in the lag, exponential and stationary growth stages of P. minimum using pyrosequencing. Metagenomics, hierarchical cluster and non-metric multidimensional scaling analyses revealed that FLB and PAB had significantly different bacterial community compositions. The PAB community had greater taxonomic richness and diversity than the FLB community. In addition, the shared bacteria identified were clearly dominant in both the FLB (≥98.2%) and PAB (≥89.9%) communities. Among shared bacteria, the genera Seohaeicola (P. minimum operational taxonomic unit (OTU) #1) and Roseovarius (P. minimum OTU #6), belonging to the Roseobacter clade, were predominant in FLB (42–57%) and PAB (11–14%) communities respectively. In the PAB community, the Marinobacter clade (P. minimum OTU #13 and #15) was also a dominant taxon. Interestingly, in response to the growth of P. minimum, the proportion of the Roseobacter clade increased gradually, whereas the genus Marinobacter decreased in both the FLB and PAB communities. These results suggest that Roseobacter and Marinobacter clades are intimately associated with host dinoflagellate.
Effect of melatonin on bovine theca cells in vitro
Authors: Feng T. , Schutz L. F. , Morrell B. C. , Perego M. C. , Spicer L. J.
Published: October 2017

Melatonin affects granulosa cell function in several species but its function in theca cells is less clear, particularly in monotocous animals. Thus, the objectives of this study were to determine the effects of melatonin on theca cell steroidogenesis, gene expression and cell proliferation in a monotocous species, namely cattle. Ovaries were collected from a local bovine abattoir, from which theca cells were isolated from large (8–22 mm) follicles and treated with various hormones in serum-free medium for 24 h or 48 h. Melatonin caused a dose-dependent inhibition (P < 0.05) of LH+insulin-like growth factor 1 (IGF1)-induced androstenedione and progesterone production. Also, melatonin inhibited (P < 0.05) LH+IGF1-induced expression of steroidogenic acute regulatory protein (StAR) mRNA (via real-time polymerase chain reaction) in theca cells, but it had no effect (P > 0.10) on cytochrome P450 11A1 (CYP11A1) and cytochrome P450 17A1 (CYP17A1) mRNA abundance. In LH+IGF1-treated theca cells, melatonin decreased caspase 3 (CASP3) mRNA to levels similar to those observed in LH-treated theca cells. In contrast, melatonin increased (P < 0.05) the number of bovine theca cells in both LH- and LH+IGF1-treated cultures. In conclusion, melatonin may act as an endocrine regulator of ovarian function in cattle by stimulating theca cell proliferation and inhibiting differentiation via inhibition of hormone-induced steroidogenesis.
FOXO1 opposition of CD8+T cell effector programming confers early memory properties and phenotypic diversity
Authors: Delpoux Arnaud , Lai Chen-Yen , Hedrick Stephen M. , Doedens Andrew L.
Published: October 2017

Significance

Acute infection with intracellular pathogen results in the expansion and effector differentiation of pathogen-specific CD8+T cells, most of which die after pathogen clearance. The factors and steps controlling CD8+T cell differentiation in response to acute infection are not fully understood. We find FOXO1 and TCF7 drive postinfection immune memory characteristics in cells expressing low TIM3, where TCF7 actively down-regulates the cytotoxic molecule GZMB and reduces terminally differentiated KLRG1higheffector abundance. We further report the creation of a continuum of CD8+T cell phenotypes, ranging from terminal effector cells to long-lived immune-memory cells, dependent on FOXO1 and TCF7. We conclude FOXO1 and TCF7 are essential to oppose cytotoxic/terminal differentiation programs and enable full phenotypic diversity of postinfection CD8+T cells.
Mechanics dictate where and how freshwater planarians fission
Authors: Malinowski Paul T. , Cochet-Escartin Olivier , Kaj Kelson J. , Ronan Edward , Groisman Alexander , Diamond Patrick H. , Collins Eva-Maria S.
Published: October 2017

Significance

How planarians reproduce by ripping themselves into a head and a tail piece, which subsequently regenerate into two new worms, is a centuries-old biomechanics problem. Michael Faraday contemplated how this feat can be achieved in the 1800s, but it remained unanswered because it is experimentally difficult to observe planarians “doing it.” We recorded
Dugesia japonica
planarians in the act and developed a physical model that captures pivotal steps of their reproduction dynamics. The model reproduces experimental time scales and rupture stresses without fit parameters. The key to rupture is a local reduction of the animal’s cross-sectional area, which greatly amplifies the stresses exerted by the planarian’s musculature and enables rupture at substrate stresses in the pascal range.
A peptide extension dictates IgM assembly
Authors: Pasalic Dzana , Weber Benedikt , Giannone Chiara , Anelli Tiziana , Müller Roger , Fagioli Claudio , Felkl Manuel , John Christine , Mossuto Maria Francesca , Becker Christian F. W. , Sitia Roberto , Buchner Johannes
Published: October 2017

Significance

How protein assemblies with complex topologies are formed is an important question in structural biology. An intriguing example is IgM, a complex of over 1,200 kDa consisting of six antibody subunits (or five in the presence of the J-chain protein). These are arranged in a ring-like structure connected by disulfide bonds. Here, we show that in vitro and in cell culture, a short peptide extension of the IgM heavy chain is sufficient to steer the formation of the hexameric complex. The formation of a disulfide bond triggers conformational changes in the peptide extensions, which involve specific hydrophobic residues. Our study reveals the redox-controlled assembly of a large protein complex via structural rearrangements in a peptide as a design principle.
Rapid evolution of hosts begets species diversity at the cost of intraspecific diversity
Authors: Frickel Jens , Theodosiou Loukas , Becks Lutz
Published: October 2017

Significance

The interactions between ecological and evolutionary processes on the same timescale have been suggested as an important driver for the maintenance of diversity within populations. Nothing is, however, known about how this interaction alters coexistence of species and how coexistence, in return, affects diversity within populations. Here we report an experiment directly testing how and when eco-evolutionary dynamics alter coexistence of competing consumers (predator and parasite) and how coexistence, in return, changes diversity within the shared resource population. We found a switch from diversity at the within-population level to diversity at the species level. Stunningly, these dynamics were mostly driven by indirect interactions and effects that continued for many generations, even after the initial causal process had stopped.
Metamorphosis is induced by food absence rather than a critical weight in the solitary bee,Osmia lignaria
Authors: Helm Bryan R. , Rinehart Joseph P. , Yocum George D. , Greenlee Kendra J. , Bowsher Julia H.
Published: October 2017

Significance

In this study, we characterize the developmental mechanisms shaping body size in the solitary bee pollinator,Osmia lignaria. This study manipulates larval development in a solitary bee to understand how developmental mechanisms shape adult body size. We based our approach on the insect body size model that postulates a critical weight is necessary for normal metamorphosis. However, our study identified food absence as a cue for metamorphosis in this species, rather than a “critical weight.” These data directly challenge the ubiquity of critical weights and offer insights about context dependency of metamorphic regulation. Developmental mechanisms shape size variation in solitary bees, which will have strong effects on their capabilities as pollinators.
Cell volume change through water efflux impacts cell stiffness and stem cell fate
Authors: Guo Ming , Pegoraro Adrian F. , Mao Angelo , Zhou Enhua H. , Arany Praveen R. , Han Yulong , Burnette Dylan T. , Jensen Mikkel H. , Kasza Karen E. , Moore Jeffrey R. , Mackintosh Frederick C. , Fredberg Jeffrey J. , Mooney David J. , Lippincott-Schwartz Jennifer , Weitz David A.
Published: October 2017

Significance

Cell volume is thought to be a well-controlled cellular characteristic, increasing as a cell grows, while macromolecular density is maintained. We report that cell volume can also change in response to external physical cues, leading to water influx/efflux, which causes significant changes in subcellular macromolecular density. This is observed when cells spread out on a substrate: Cells reduce their volume and increase their molecular crowding due to an accompanying water efflux. Exploring this phenomenon further, we removed water from mesenchymal stem cells through osmotic pressure and found this was sufficient to alter their differentiation pathway. Based on these results, we suggest cells chart different differentiation and behavioral pathways by sensing/altering their cytoplasmic volume and density through changes in water influx/efflux.
Lipidomics reveals diurnal lipid oscillations in human skeletal muscle persisting in cellular myotubes cultured in vitro
Authors: Loizides-Mangold Ursula , Perrin Laurent , Vandereycken Bart , Betts James A. , Walhin Jean-Philippe , Templeman Iain , Chanon Stéphanie , Weger Benjamin D. , Durand Christine , Robert Maud , Paz Montoya Jonathan , Moniatte Marc , Karagounis Leonidas G. , Johnston Jonathan D. , Gachon Frédéric , Lefai Etienne , Riezman Howard , Dibner Charna
Published: October 2017

Significance

Our experiments provide the analysis of lipid metabolite circadian oscillations in a cellular system synchronized in vitro, suggesting cell-autonomous diurnal changes in lipid profiles independent of feeding. Moreover, our work represents a comprehensive comparison between the lipid composition of human skeletal muscle derived from sedentary healthy adults, receiving hourly isocaloric solutions, and human primary skeletal myotubes cultured in vitro. A substantial number of lipid metabolites, in particular membrane lipids, exhibited oscillatory patterns in muscle tissue and in myotube cells, where they were blunted upon cell-autonomous clock disruption. As lipid oscillations in skeletal muscle membrane lipids may impact on insulin signaling and on the development of insulin resistance, studying the temporal lipid composition of human muscle is therefore of utmost importance.
Granulocyte-colony–stimulating factor (G-CSF) signaling in spinal microglia drives visceral sensitization following colitis
Authors: Basso Lilian , Lapointe Tamia K. , Iftinca Mircea , Marsters Candace , Hollenberg Morley D. , Kurrasch Deborah M. , Altier Christophe
Published: October 2017

Significance

Visceral pain is a debilitating type of pain that afflicts adults and children. Major challenges exist in developing analgesics due to the limited understanding of the mechanisms that mediate visceral nociception. Using a model of colitis, we have identified the granulocyte-colony–stimulating factor (G-CSF) as an essential mediator of central sensitization that leads to visceral hypersensitivity, even after the resolution of inflammation. We demonstrate that G-CSF acting on spinal microglia activates a signaling platform that causes hyperexcitability of sensory neurons. We found that ablating microglia or blocking the G-CSF receptor prevents visceral sensitization. Our work establishes a microglial signaling mechanism in the transition to chronic visceral pain and likely other forms of persistent pain associated with chronic inflammatory diseases.
Butyrylcholinesterase gene transfer in obese mice prevents postdieting body weight rebound by suppressing ghrelin signaling
Authors: Chen Vicky Ping , Gao Yang , Geng Liyi , Brimijoin Stephen
Published: October 2017

Significance

Obesity is a major public health problem affecting physical and emotional well-being. Although lifestyle-based programs can help with weight loss, avoiding weight regain is nearly impossible because of persistent hormonal adaptations. Here, in mouse models, we explored a more effective strategy using viral gene transfer of butyrylcholinesterase (BChE) to control the appetite-mediating hormone acyl-ghrelin. We found that a single injection of BChE vector led to a lifetime high enzyme expression and lower circulating acyl-ghrelin. This same treatment suppressed postdieting hyperphagia, corrected metabolic lesions, and lowered weight regain. This outcome confirms the impact of the BChE-ghrelin axis on body weight and indicates that BChE gene transfer could be a successful strategy for long-term control of obesity and the “metabolic syndrome.”
Chemical substitutions in the selectivity filter of potassium channels do not rule out constricted-like conformations for C-type inactivation
Authors: Li Jing , Ostmeyer Jared , Boulanger Eliot , Rui Huan , Perozo Eduardo , Roux Benoît
Published: October 2017

Significance

After opening in response to a specific stimulus, some potassium channels undergo C-type inactivation. Crystal structures of KcsA have revealed that the selectivity filter constricts under conditions associated with C-type inactivation. Functional studies based on semisynthetic KcsA channels with either D-ala77 or amide-to-ester backbone substitutions provide important observations arguing against the constricted conformation of the selectivity filter as the molecular basis of C-type inactivation. In this study, molecular dynamics simulations based on atomic models of the KcsA channel are performed to clarify the impact of these chemical modifications on the conformation of the selectivity filter. The results support the notion that the constricted conformation of the selectivity filter, indeed, corresponds to the functional C-type inactivated state of the KcsA channel.
Kinesin rotates unidirectionally and generates torque while walking on microtubules
Authors: Ramaiya Avin , Roy Basudev , Bugiel Michael , Schäffer Erik
Published: October 2017

Significance

Given the importance of cytoskeletal motor proteins, we asked whether translational motors rotate while walking along their tracks. Using an optical tweezers-based approach, we simultaneously measured translation, force, rotation, and torque of a kinesin motor with molecular resolution. We found that the gait followed a rotary stepping mechanism that generates torque and spins cargo. Thus, during walking, the motor “tail (and organelle) will tend to wind up like the rubber band of a toy airplane,” as Joe Howard hypothesized in 1996. To determine the overall motor efficiency, our measurements also point to the importance of accounting for rotational work. Apart from other cytoskeletal motors, the technique may be applied to molecular machines such as DNA motors and rotary engines like the ATP synthase.
Miscoding-induced stalling of substrate translocation on the bacterial ribosome
Authors: Alejo Jose L. , Blanchard Scott C.
Published: October 2017

Significance

Using single-molecule FRET imaging, we show that programmed base-pair mismatches between the peptidyl-tRNA anticodon and the mRNA codon dramatically prolong elongation factor G (EF-G)–catalyzed translocation. Mismatched peptidyl-tRNA–mRNA pairing within the pretranslocation complex specifically inhibits peptidyl-tRNA engagement of the small subunit P site, a rate-limiting process in translocation characterized by large-scale, intramolecular conformational changes within the EF-G(GDP)–bound ribosome complex. Consistent with the E site being vacant during this period, we find that elongation factor P (EF-P) can rescue this translocation defect. These findings reveal an unexpected relationship between tRNA decoding at the A site and translocation, and suggest an alternative mode of action for miscoding-inducing drugs as well as a novel function of EF-P in the cell to rescue ribosomes stalled by miscoding errors.
Physical proximity of chromatin to nuclear pores prevents harmful R loop accumulation contributing to maintain genome stability
Authors: García-Benítez Francisco , Gaillard Hélène , Aguilera Andrés
Published: October 2017

Significance

During transcription, the mRNA may hybridize back with its template DNA, forming a structure called R loop. These structures have been associated with genome instability and human disease. Using budding yeast as a model organism to screen for new genes preventing R loops, we identified
MLP1
and subsequently showed that the nuclear basket protein Mlp1/2 has a role in preventing R loop formation and genome instability in yeast. Our work indicates that R loops are formed in the nucleoplasm and that proximity of transcribed chromatin to the nuclear pore constrains R loop formation. Our study opens additional perspectives to understand the role of RNA in the control of genome integrity as a function of nuclear location.
Discovery of an O-mannosylation pathway selectively serving cadherins and protocadherins
Authors: Larsen Ida Signe Bohse , Narimatsu Yoshiki , Joshi Hiren Jitendra , Siukstaite Lina , Harrison Oliver J. , Brasch Julia , Goodman Kerry M. , Hansen Lars , Shapiro Lawrence , Honig Barry , Vakhrushev Sergey Y. , Clausen Henrik , Halim Adnan
Published: October 2017

Significance

The large superfamily of cadherins serve essential roles in cell–cell interactions and guidance. The extracellular cadherin (EC) domains responsible for the biological functions are decorated with O-linked mannose glycans, but the functions of these O-glycans are poorly understood. Here we describe an O-mannosylation pathway orchestrated by four homologous
TMTC1–4
genes that is dedicated selectively to the cadherin superfamily. Mutations in the
TMTC3
gene cause cobblestone lissencephaly, demonstrating the importance of this type of O-mannosylation.
Rewiring a Rab regulatory network reveals a possible inhibitory role for the vesicle tether, Uso1
Authors: Yuan Hua , Davis Saralin , Ferro-Novick Susan , Novick Peter
Published: October 2017

Significance

Members of the Rab family act as molecular switches to control distinct stages of vesicular traffic into and out of a eukaryotic cell. Many Rabs are linked to the adjacent Rab by their regulators, generating circuits that direct transport along the pathway. We have rewired one such regulatory circuit by exploiting a chimeric Rab that acts early on the pathway but can be activated by a regulator that is situated late on the pathway. Expression of this chimeric Rab leads to a block late on the pathway. Our findings confirm the importance of Rabs in establishing membrane identity.
Unexpected source of Fukushima-derived radiocesium to the coastal ocean of Japan
Authors: Sanial Virginie , Buesseler Ken O. , Charette Matthew A. , Nagao Seiya
Published: October 2017

Significance

Five years after the Fukushima Dai-ichi Nuclear Power Plant accident, the highest radiocesium (
137
Cs) activities outside of the power plant site were observed in brackish groundwater underneath sand beaches. We hypothesize that the radiocesium was deposited on mineral surfaces in the days and weeks after the accident through wave- and tide-driven exchange of seawater through the beach face. As seawater radiocesium concentrations decreased, this radiocesium reentered the ocean via submarine groundwater discharge, at a rate on par with direct discharge from the power plant and river runoff. This new unanticipated pathway for the storage and release of radionuclides to ocean should be taken into account in the management of coastal areas where nuclear power plants are situated.
Systems-level identification of PKA-dependent signaling in epithelial cells
Authors: Isobe Kiyoshi , Jung Hyun Jun , Yang Chin-Rang , Claxton J’Neka , Sandoval Pablo , Burg Maurice B. , Raghuram Viswanathan , Knepper Mark A.
Published: October 2017

Significance

Maintenance of homeostasis is dependent on intercellular communication via secreted hormones that bind G protein-coupled receptors. Many of these receptors activate an enzyme called protein kinase A (PKA) that modifies cell function by covalently attaching phosphate groups to proteins. To comprehensively identify PKA substrates, we used genome editing (CRISPR-Cas9) to delete PKA from kidney epithelial cells followed by large-scale mass spectrometry to measure phosphorylation changes throughout the proteome; 229 PKA target sites were identified, many previously unrecognized. Surprisingly, PKA deletion caused seemingly paradoxical phosphorylation increases at many sites, indicating secondary activation of one or more mitogen-activated kinases. The data, coupled with transcriptomics and standard proteomics, identified a signaling network that explains the effects of PKA that regulate cellular functions.
Projections of white and black older adults without living kin in the United States, 2015 to 2060
Authors: Verdery Ashton M. , Margolis Rachel
Published: October 2017

Significance

Family members provide the majority of social support for most older adults, but not all individuals have living family. Those without living close kin report higher rates of loneliness and experience elevated risks of chronic diseases and nursing facility placement. How the population of older adults without living family, the kinless population, will change in the coming decades merits consideration. Historical racial differences and recent variation in demographic rates imply unequal burdens of kinlessness for white and black Americans. By projecting the US population using demographic microsimulation, we find increases in lacking kin similar in magnitude to projected increases in other important population health burdens such as diabetes and Alzheimer’s dementia. Increasing kinlessness may represent a growing population health concern.
Molecular mechanisms and structural features of cardiomyopathy-causing troponin T mutants in the tropomyosin overlap region
Authors: Gangadharan Binnu , Sunitha Margaret S. , Mukherjee Souhrid , Chowdhury Ritu Roy , Haque Farah , Sekar Narendrakumar , Sowdhamini Ramanathan , Spudich James A. , Mercer John A.
Published: October 2017

Significance

Mutations in genes encoding sarcomeric proteins are the major cause of primary inherited cardiomyopathies. Troponin T (TnT), encoded by
TNNT2
, harbors most of its pathogenic mutants at TNT1 (residues ∼80–180 of TnT). TNT1 is known to interact with tropomyosin (Tm). In this study, we have analyzed TNT1 mutants using in vitro and in silico methods and correlated the results. We also found a striking correlation between binding affinities for Tm and changes in the calcium sensitivity of regulated actomyosin ATPase activities within residues 92–144. These data are consistent with reducing or increasing the affinity of TnT for Tm as the primary cause of cardiomyopathy for mutations in this region, suggesting a smaller Tm binding region.
Super-swelled lyotropic single crystals
Authors: Kim Hojun , Song Ziyuan , Leal Cecilia
Published: October 2017

Significance

Lipids self-assemble in water into diverse polycrystalline mesophases. The swelling capacity of these superstructures is finite, specific, and traditionally dictated by lipid composition. Bicontinuous cubic phases have tremendous potential in drug delivery and protein crystallization. However, limited swelling caps unit cells at dimensions too small to encapsulate many drugs and most proteins. In this work, we discovered that bicontinuous cubic phase swelling is not solely determined by lipid composition. Self-assembly conditions yield stable unit cell sizes fourfold larger than usual. Unexpectedly, these conditions also dictate mesophase ordering resulting in X-ray and electron microscopy diffraction patterns that do not conform to polycrystallinity. Instead, macroscale super-swelled single crystals are encountered. This discovery highlights insights in understanding swelling and ordering of self-assembled materials.
Assortative mating and persistent reproductive isolation in hybrids
Authors: Schumer Molly , Powell Daniel L. , Delclós Pablo J. , Squire Mattie , Cui Rongfeng , Andolfatto Peter , Rosenthal Gil G.
Published: October 2017

Significance

Understanding the processes that generate or breakdown reproductive isolation between species is essential to understanding evolution. Assortative mating mediates reproductive isolation between species, but its dynamics in natural populations are poorly understood. Here we show that strong assortative mating maintains reproductive isolation in a natural hybrid population following an initial breakdown when the hybrid population formed, and strongly shaped the genetic structure of this population over ∼25 generations. Intriguingly, although in the wild these mate preferences result in nearly 100% of matings occurring between similar genotypes, this barrier breaks down in the laboratory. Our results highlight the importance of assortative mating in shaping hybrid population evolution and imply that short-term breakdown in assortative mating can have long-term evolutionary consequences.