bluuebunny/crossref_metadata_2025 huggingface dataset:
Sound radiation by supersonic unstable modes in hypersonic blunt cone boundary layers. I. Linear stability theory
Authors: Knisely Carleton P. , Zhong Xiaolin
Published: February 2019

There has been renewed interest in supersonic modes in hypersonic boundary layers, which have been previously thought to be insignificant due to their smaller amplitudes than Mack’s traditional second mode. Supersonic modes are associated with an unstable second mode synchronizing with the slow acoustic spectrum, causing sound to radiate outwards from the boundary layer. Because supersonic modes have not been observed experimentally, the majority of previous investigations either relied on Linear Stability Theory (LST) to study supersonic modes on a flat plate or observed them in the context of other research objectives. This two-part study uses a combined LST and Direct Numerical Simulation (DNS) approach to investigate the mechanism of supersonic modes in Mach 5 flow over a blunt cold-wall cone with thermochemical nonequilibrium effects. Paper I focuses on LST with new shock boundary conditions, whereas Paper II [C.P. Knisely and X. Zhong, “Sound radiation by supersonic unstable modes in hypersonic blunt cone boundary layers. II. Direct numerical simulation,” Phys. Fluids 31, 024104 (2019)] focuses on DNS with the overall goal of investigating the impact of supersonic modes on transition. LST results indicate that supersonic modes exist in the flow with wall-to-free-stream temperature ratio Tw/T∞ = 0.2 and create an abnormal growth pattern. However, supersonic modes were not shown to exist using LST in the case with Tw/T∞ = 0.667. Subsequent DNS analysis in Paper II shows supersonic modes in the Tw/T∞ = 0.667 case, although they are significantly weaker than the second mode and are unlikely to lead to transition. Understanding the mechanism of supersonic modes can yield more accurate transition location predictions leading to improved estimates for drag and heat transfer to the vehicle.
Photo-dissociation of naphthalene dimer cations stored in a compact electrostatic ion storage ring
Authors: Bernard J. , Al-Mogeeth A. , Allouche A.-R. , Chen L. , Montagne G. , Martin S.
Published: February 2019

Naphthalene dimer cations [C10H8]2+ have been produced by using an electron cyclotron resonance plasma ion source and stored in a compact electrostatic ion storage ring. We show that the radiative cooling of these cations is much slower than the isolated monomer naphthalene cations. We also report on photo-dissociation studies in the gas phase of naphthalene dimer cations at high internal energy. The dissociation energy is estimated to 0.5 eV in close agreement with previous measurements but a factor of 2 smaller than recent (density functional theory (DFT) and ab initio) theoretical studies. As uncertainties on theory as well as on the experiment cannot be as large as this difference, we conclude that this discrepancy may be due to temperature effects with possible isomerization. As an interpretation of the photo-dissociation spectrum of naphthalene dimer cations, we propose a tentative simple analytical model based on effective Morse potentials. These effective potentials are expected to “average” temperature effects that would apparently result in a smaller energy difference between the fundamental and dissociation states due to the twisting vibration modes of the naphthalene dimer cations.
The effect of Coulomb repulsion on the space-time resolution limits for ultrafast electron diffraction
Authors: Ischenko A. A. , Kochikov I. V. , Miller R. J. Dwayne
Published: February 2019

The development of electron sources capable of temporal resolution on the order of 1 ps or less raises a number of questions associated with the estimation of the physical meaning and accuracy of the dynamic parameters based on the analysis of time-dependent scattering intensity. The use of low brightness ultrashort pulses with few electrons leads to the necessity for increasing the total exposure time and lengthening the time of data acquisition, with attendant problems with the limited sample. The sample restrictions can be mitigated by increasing the charge per pulse, i.e., by going to high brightness sources. Increasing in the number of electrons, however, is limited by the Coulomb repulsion between them, which leads on one hand to distortion of the diffraction pattern and on the other hand to an increase in the duration of the pulse. An analytical technique for estimating the deformation of the diffraction pattern caused by the Coulomb repulsion of the electrons in electron bunches with duration of less than 10 ps and the influence of this effect on the accuracy of determination of the interatomic distances is developed for the non-relativistic and relativistic regimes for electron energies.
Plasma flows generated by an annular thermionic cathode in a large magnetized plasma
Authors: Jin S. , Poulos M. J. , Van Compernolle B. , Morales G. J.
Published: February 2019

A LaB6 thermionic emitter of annular shape is used in the Large Plasma Device at the University of California, Los Angeles to create off-axis heating conditions for various transport studies. Since the emitter is biased relative to a distant anode, which is many collision lengths away, the entire magnetized plasma develops a self-consistent, potential structure that simultaneously generates transverse and axial flows with shear. This study uses swept Langmuir probe techniques and Mach probes to map the flow patterns and their dependence on bias and plasma parameters. By implementing additional biasing configurations, it is possible to control the magnitude of the flows and their shear strength. The experimental measurements, including the self-consistent currents, are compared to predictions of a model that incorporates the boundary conditions associated with thermionic injection, combined with a Braginskii transport code for the electron temperature.
Effect of InAs quantum dots capped with GaAs on atomic-scale ordering in Ga0.5In0.5P
Authors: Su P.-Y. , Liu H. , Kawabata R. M. S. , Weiner E. C. , Jakomin R. , Pires M. P. , King R. R. , Souza P. L. , Ponce F. A.
Published: February 2019

The CuPt ordering of the group III elements in GaxIn1-xP (x ≃ 0.5) has been observed to vary during growth by metalorganic vapor-phase epitaxy of InAs quantum dots capped with GaAs in a GaInP matrix. While ordering is not affected by the insertion of a GaAs layer, the growth of InAs quantum dots capped with GaAs results in ordered, partially ordered, or fully disordered GaInP. We show that the degree of ordering depends on the deposition time of the InAs quantum dots and on the thickness of the GaAs capping layer. Our results indicate that disordered GaInP occurs in the presence of excess indium at the growth surface, which results from the growth of strained InAs quantum dots. Ordering resumes when the excess indium is consumed. Cathodoluminescence, scanning transmission electron microscopy, and atomic force microscopy are used in this study to correlate the electronic properties and the microstructure of the thin films.
Ordering in clusters of uniaxial anisotropic particles during homogeneous nucleation and growth
Authors: Nozawa Takuma , Brumby Paul E. , Ayuba Sho , Yasuoka Kenji
Published: February 2019

The nucleation process of anisotropic particles often differs from that of their spherically symmetric counterparts. Despite a large body of work on the structure of droplets of anisotropic particles, their formation process remains poorly understood. In this study, homogeneous nucleation of uniaxial anisotropic particles was studied. Through structural analysis of cluster development and the formation free energy during the nucleation stage, it was revealed that the nucleation of uniaxial particles begins from highly ordered states. There is, however, a marked decrease in orientational order within the cluster before critical nucleus size is attained. Further investigation on variations in the molecular interactions demonstrates how droplet elongation and the direction of the nematic ordering director relative to the axis of elongation can both be controlled according to the nature of the molecular anisotropy.
Transport of neutral solutes in a viscoelastic solvent through a porous microchannel
Authors: Gaikwad Harshad Sanjay , Baghel Prashant , Sarma Rajkumar , Mondal Pranab Kumar
Published: February 2019

We study the effect of viscoelasticity on the transportation of neutral solutes through a porous microchannel. The underlying transport phenomenon, modelled using the simplified Phan-Thien-Tanner constitutive equation, is actuated by the combined influence of pressure gradient and electroosmosis. Here, we obtain the closed form solution for the velocity distribution inside the flow domain and calculate the concentration profiles of the neutral solutes within the mass transport boundary layer by invoking the similarity solution approach. To establish the efficacy of viscoelastic solvents in the transportation of neutral solutes, which may find relevance in transdermal drug delivery applications, here we show the variations in the local solute concentration, the length averaged solute concentration at the wall, and the Sherwood number with the viscoelastic parameter. The present study infers that the shear-thinning nature of the viscoelastic fluid enhances the convective mass transfer as well as the permeation rate in the porous membranes. A complex interplay between the fluid rheology and the porous structure of the walls influenced by the electrochemistry at the interfacial scale modulates the mass transfer boundary layer of neutral solutes, implicating an effective method of mass transport in transdermal drug delivery applications.
eGFRD in all dimensions
Authors: Sokolowski Thomas R. , Paijmans Joris , Bossen Laurens , Miedema Thomas , Wehrens Martijn , Becker Nils B. , Kaizu Kazunari , Takahashi Koichi , Dogterom Marileen , ten Wolde Pieter Rein
Published: February 2019

Biochemical reactions often occur at low copy numbers but at once in crowded and diverse environments. Space and stochasticity therefore play an essential role in biochemical networks. Spatial-stochastic simulations have become a prominent tool for understanding how stochasticity at the microscopic level influences the macroscopic behavior of such systems. While particle-based models guarantee the level of detail necessary to accurately describe the microscopic dynamics at very low copy numbers, the algorithms used to simulate them typically imply trade-offs between computational efficiency and biochemical accuracy. eGFRD (enhanced Green’s Function Reaction Dynamics) is an exact algorithm that evades such trade-offs by partitioning the N-particle system into M ≤ N analytically tractable one- and two-particle systems; the analytical solutions (Green’s functions) then are used to implement an event-driven particle-based scheme that allows particles to make large jumps in time and space while retaining access to their state variables at arbitrary simulation times. Here we present “eGFRD2,” a new eGFRD version that implements the principle of eGFRD in all dimensions, thus enabling efficient particle-based simulation of biochemical reaction-diffusion processes in the 3D cytoplasm, on 2D planes representing membranes, and on 1D elongated cylinders representative of, e.g., cytoskeletal tracks or DNA; in 1D, it also incorporates convective motion used to model active transport. We find that, for low particle densities, eGFRD2 is up to 6 orders of magnitude faster than conventional Brownian dynamics. We exemplify the capabilities of eGFRD2 by simulating an idealized model of Pom1 gradient formation, which involves 3D diffusion, active transport on microtubules, and autophosphorylation on the membrane, confirming recent experimental and theoretical results on this system to hold under genuinely stochastic conditions.
Perpendicular magnetic anisotropy and spin mixing conductance in polycrystalline europium iron garnet thin films
Authors: Bauer J. J. , Rosenberg E. R. , Ross C. A.
Published: February 2019

Polycrystalline single-phase europium iron garnet films (EuIG, Eu3Fe5O12, a ferrimagnetic insulator), with thicknesses from 25 to 50 nm and roughness <1 nm, have been grown on various substrates using pulsed laser deposition followed by a rapid thermal anneal. The films are under strain that originates primarily from thermal mismatch and leads to a magnetoelastic anisotropy that dominates the net anisotropy. EuIG grown on quartz (0001) demonstrated perpendicular magnetic anisotropy (PMA) attributed to the in-plane (IP) compressive thermal mismatch strain, whereas films on (11 2¯ 0) quartz, Si, fused silica, and yttria-stabilized zirconia exhibited an IP easy axis due to tensile strain, consistent with the positive magnetostriction of polycrystalline EuIG. For the PMA EuIG, the saturation magnetization was close to that of bulk EuIG, and the out-of-plane coercivity ranged from 600 to 900 Oe, depending on the film thickness. Spin transport measurements on Pt/EuIG/quartz heterostructures gave an anomalous Hall effect-like spin Hall magnetoresistance similar to that of Pt/epitaxial single crystal EuIG. These results show that high quality polycrystalline garnets can be grown with PMA making them useful for applications in spintronic devices.
Sound radiation by supersonic unstable modes in hypersonic blunt cone boundary layers. II. Direct numerical simulation
Authors: Knisely Carleton P. , Zhong Xiaolin
Published: February 2019

Supersonic modes, previously thought to be insignificant due to their smaller amplitude than Mack’s traditional second mode, occur in hypersonic boundary layers when a disturbance travels supersonically with respect to the mean flow outside the boundary layer, causing outward-radiating acoustic waves. Very few previous studies perform Direct Numerical Simulation (DNS) of supersonic modes and instead rely on Linear Stability Theory (LST). This combined LST and DNS study investigates supersonic modes in Mach 5 flow over a blunt cold-wall cone. An LST analysis was performed in Paper I [C. P. Knisely and X. Zhong, “Sound radiation by supersonic unstable modes in hypersonic blunt cone boundary layers. I. Linear stability theory,” Phys. Fluids 31, 024103 (2019)], whereas DNS is the focus of Paper II. The overall goal is to determine the mechanism of supersonic modes and the conditions under which they exist. Compared to previous pure LST studies, DNS provides the advantage of making fewer limiting assumptions and can resolve interactions between modes. The results here indicate the excitation of supersonic modes via modal interactions not resolved with LST, suggesting the inadequacy of pure LST analyses concerning supersonic modes. Unsteady DNS results verified supersonic modes in the flow with wall-to-free-stream temperature ratio Tw/T∞ = 0.2, lending credence to the modes’ physical existence. However in the case of Tw/T∞ = 0.667, sound radiation was also found in DNS while LST predicted a stable supersonic mode. The mechanism for supersonic modes is attributed to a modal interaction between mode F1, mode S, and the slow acoustic spectrum. Therefore, it is necessary to perform combined LST and DNS studies of supersonic modes to reliably predict their presence and impact on transition to turbulence.
Bismuth-induced band-tail states in GaAsBi probed by photoluminescence
Authors: Yan Bing , Chen Xiren , Zhu Liangqing , Pan Wenwu , Wang Lijuan , Yue Li , Zhang Xiaolei , Han Li , Liu Feng , Wang Shumin , Shao Jun
Published: February 2019

Band-tail states in semiconductors reflect the effects of material growth and/or treatment, affect the performance of optoelectronic applications, and are hence a well-concerned issue. Dilute-Bi GaAs is considered very competitive though the role of Bi is yet to be well clarified. We in this letter investigate the effect of Bi incorporation on the band-tail states in GaAs1−xBix by excitation power- and magnetic field-dependent photoluminescence (PL) measurements at low temperatures. Three PL features are identified from a broad PL peak, which blue-shift monotonically with the increase in excitation power. None of the PL features correlate with single Bi-content free-exciton recombination, and band-tail filling rather than the donor-acceptor pair process is responsible for the power-induced blueshift. The density of band-tail states gets enhanced with the increase in the Bi incorporation level and affects the determination of Bi-induced bandgap reduction. The results indicate that joint analysis of excitation- and magneto-PL may serve as a good probe for band-tail states in semiconductors.
R
(
p
,
q
)
-deformed conformal Virasoro algebra
Authors: Hounkonnou Mahouton Norbert , Melong Fridolin
Published: February 2019

This paper addresses an R(p,q)-deformed conformal Virasoro algebra with an arbitrary conformal dimension Δ. Well-known deformations constructed in the literature are deduced as particular cases. Then, the special case of the conformal dimension Δ = 1 is elucidated for its interesting properties. The R(p,q)− KdV equation, associated with the deformed Virasoro algebra, is also derived and discussed. Finally, the (p, q)-deformed energy-momentum tensor, consistent with the central extension term, is computed and analyzed.
Influence of bonded interactions on structural phases of flexible polymers
Authors: Qi Kai , Liewehr Benjamin , Koci Tomas , Pattanasiri Busara , Williams Matthew J. , Bachmann Michael
Published: February 2019

We introduce a novel coarse-grained bead-spring model for flexible polymers to systematically examine the effects of an adjusted bonded potential on the formation and stability of structural macrostates in a thermal environment. The density of states obtained in advanced replica-exchange Monte Carlo simulations is analyzed by employing the recently developed generalized microcanonical inflection-point analysis method, which enables the identification of diverse structural phases and the construction of a suitably parameterized hyperphase diagram. It reveals that icosahedral phases dominate for polymers with asymmetric and narrow bond potentials, whereas polymers with symmetric and more elastic bonds tend to form amorphous structures with non-icosahedral cores. We also observe a hierarchy in the freezing transition behavior associated with the formation of the surface layer after nucleation.
Analyses based on statistical thermodynamics for large difference between thermophilic rhodopsin and xanthorhodopsin in terms of thermostability
Authors: Yasuda Satoshi , Hayashi Tomohiko , Kajiwara Yuta , Murata Takeshi , Kinoshita Masahiro
Published: February 2019

Although the two membrane proteins, thermophilic rhodopsin (TR) and xanthorhodopsin (XR), share a high similarity in amino-acid sequence and an almost indistinguishable three-dimensional structure, TR is much more thermostable than XR. This is counterintuitive also because TR possesses only a smaller number of intramolecular hydrogen bonds (HBs) than XR. Here we investigate physical origins of the remarkable difference between XR and TR in the stability. Our free-energy function (FEF) is improved so that not only the portion within the transmembrane (TM) region but also the extracellular and intracellular portions within the water-immersed (WI) regions can be considered in assessing the stability. The assessment is performed on the basis of the FEF change upon protein folding, which is calculated for the crystal structure of XR or TR. Since the energetics within the TM region is substantially different from that within the WI regions, we determine the TM and WI portions of XR or TR by analyzing the distribution of water molecules using all-atom molecular dynamics simulations. The energetic component of the FEF change consists of a decrease in energy arising from the formation of intramolecular HBs and an increase in energy caused by the break of protein-water HBs referred to as “energetic dehydration penalty.” The entropic component is a gain of the translational, configurational entropies of hydrocarbon groups within the lipid bilayer and of water molecules. The entropic component is calculated using the integral equation theory combined with our morphometric approach. The energetic one is estimated by a simple but physically reasonable method. We show that TR is much more stable than XR for the following reasons: The decrease in energy within the TM region is larger, and the energetic dehydration penalty within the WI regions is smaller, leading to higher energetic stabilization, and tighter packing of side chains accompanying the association of seven helices confers higher entropic stabilization on TR.
A universal mechanism for plasma blob formation
Authors: Bisai N. , Banerjee Santanu , Sen Abhijit
Published: February 2019

The formation of a density blob in the boundary region of a tokamak plasma is widely believed to be due to the presence of poloidal velocity shear that differentially breaks off a radially elongated streamer structure. However, blobs have also been experimentally detected in the absence of poloidal velocity shear. We ascribe the formation of such blobs to the differential stretching of the streamer arising from a radial velocity shear and thereby present a unified picture of the breaking mechanism that takes into account both the processes in a synergistic manner. Our universal condition for blob formation is validated from detailed numerical simulations of the edge turbulence in a typical L-mode scenario.
Fractional models with singular and non-singular kernels for energy efficient buildings
Authors: Bas Erdal , Acay Bahar , Ozarslan Ramazan
Published: February 2019

In the current study, we investigate and analyze the fractional version of the heating and cooling model for buildings with energy efficiency. We apply the Caputo fractional derivative, Caputo-Fabrizio, and Atangana-Baleanu in the Caputo sense in the analysis and investigation of the governing model. We derive some novel analytical solutions by means of Laplace’s transform. Simulation analysis is carried out in order to shed more light on the physical features of the governing models. To believe the results obtained, the fractional order has been allowed to vary between (0,1], whereupon the physical observations match those obtained in the classical case, but the fractional model has persisted all the memory effects making the model much more suitable when presented in the structure of fractional derivatives.
Analytical solutions of Hristov diffusion equations with non-singular fractional derivatives
Authors: Sene Ndolane
Published: February 2019

Analytical solutions of the first and second model of Hristov fractional diffusion equations based on the non-singular Atangana-Baleanu derivative have been developed. The solutions are based on an integral method based on the consequent application of the Fourier and Laplace transforms. Particular cases of Hristov fractional diffusion equations considering operators with orders converging to unity have been analyzed, too.
Towards generation of millihertz-linewidth laser light with 10−18 frequency instability via four-wave mixing
Authors: Jin Li , Hang Chao , Jiang Yanyi , Zhu Chengjie , Zheng Zhan , Yao Yuan , Huang Guoxiang , Ma Longsheng
Published: February 2019

Laser light with spectral purity and frequency stability is pursued in precision spectroscopy and precision measurements. We propose a scheme to generate millihertz-linewidth laser light with a frequency instability of 10−18 via optical four-wave mixing in alkaline-earth atoms. We show that the linewidth of the mixing laser light is ultimately limited by the natural linewidth of the atomic transition rather than by the linewidth of the input lasers. The frequency stability of the mixing laser light depends largely on the intensity stability of the input lasers. It is possible to generate a millihertz-linewidth laser light with a frequency instability of 10−18 and a power of 10−12 W when the input lasers with a relative intensity instability of 10−4 and a spectral width of 1 Hz interact with strontium (Sr) atoms with a density of 1 × 1011 cm−3.
On the choice of coordinates in anharmonic theoretical vibrational spectroscopy: Harmonic vs. anharmonic coupling in vibrational configuration interaction
Authors: Panek Paweł T. , Hoeske Adrian A. , Jacob Christoph R.
Published: February 2019

By a suitable choice of coordinates, the computational effort required for calculations of anharmonic vibrational spectra can be reduced significantly. By using suitable localized-mode coordinates obtained from an orthogonal transformation of the conventionally used normal-mode coordinates, anharmonic couplings between modes can be significantly reduced. However, such a transformation introduces harmonic couplings between the localized modes. To elucidate the role of these harmonic couplings, we consider the vibrational self-consistent field (VSCF)/vibrational configuration interaction (VCI) calculations for both few-mode model systems and for ethene as a molecular test case. We show that large harmonic couplings can result in significant errors in localized-mode L-VSCF/L-VCI calculations and study the convergence with respect to the size of the VCI excitation space. To further elucidate the errors introduced by harmonic couplings, we discuss the connection between L-VSCF/L-VCI and vibrational exciton models. With the help of our results, we propose an algorithm for the localization of normal modes in suitable subsets that are chosen to strictly limit the errors introduced by the harmonic couplings while still leading to maximally localized modes.
Achieving panorama using singular metamaterials
Authors: Tan Qingze , Zhu Rongrong , Zheng Bin , Shen Lian , Ruan Yi , Wang Huaping
Published: February 2019

Panoramic lens (PL) can help us to achieve a wide-angle field of view. The design of PL was proposed conceptually, but until now it remains unrealized. Metamaterials are synthetic materials with some unusual electromagnetic properties which cannot be found in nature. Herein, a PL design based on singular metamaterials is proposed, which can confine the light of all directions into the visual angle of human eyes. An equivalent model with simplified parameters, as well as the real structure, is presented, and furthermore, the improvement in the field of view is proved with simulation results. Our method provides a practical way to achieve PL which may discover utility in applications such as panoramic images and virtual reality.
Coulomb blockade from the shell of an InP-InAs core-shell nanowire with a triangular cross section
Authors: Göransson D. J. O. , Heurlin M. , Dalelkhan B. , Abay S. , Messing M. E. , Maisi V. F. , Borgström M. T. , Xu H. Q.
Published: February 2019

We report on growth of InP-InAs core-shell nanowires and demonstration of the formation of single quantum structures, which show the Coulomb blockade effect, over entire lengths of the nanowires. The core-shell nanowires are grown by a selective area growth technique via metal-organic vapor phase epitaxy. The as-grown core-shell nanowires are found to be of wurtzite crystals. The InP cores have a hexagonal cross section, while the InAs shells are grown preferentially on specific {11¯00} facets, leading to the formation of the core-shell nanowires with an overall triangular cross section. The grown core-shell nanowires are transferred onto a Si/SiO2 substrate and then contacted by several narrow metal electrodes. Low-temperature transport measurements show the Coulomb-blockade effect. We analyze the measured gate capacitance and single electron charging energy of the devices and demonstrate that a quantum structure which shows the Coulomb blockade effect of a many-electron quantum dot is formed over the full length of a single core-shell nanowire and consists of the entire InAs shell in the nanowire.
Manipulation of magnetization in Pd(100) ultrathin films with quantum well structure using modification of Schottky barrier potentials
Authors: Tanabe Hidetake , Sakuragi Shunsuke , Sato Tetsuya
Published: February 2019

The magnetization of Pd(100) ultrathin films that show ferromagnetism due to quantum well states was manipulated by changing the quantum well state with an applied bias voltage. The voltage dependence of the magnetic moment of Pd/SrTiO3−x/Ti/Au intrinsically depends on the Pd film thickness. The induced change in the magnetic moment is due to the modulation of the phase shift at the interface between the Pd thin film and the semiconductor SrTiO3−x substrate.
Stable isotope trends in gilgaied Vertosols – variability between mounds and depressions and implications for sampling
Authors: Biggs A. J. W. , Oudyn F. , King T. , Harris M.
Published: February 2019

Stable isotopes (2H and 18O) are widely used in ecohydrological studies in Australia but their trends in Vertosols with microtopography (gilgai) is unknown. An understanding of short-distance variations in stable isotopes is important for designing cost-effective, sound sampling strategies in ecohydrological studies, but the knowledge can also further inform our understanding of infiltration and drainage processes in these soils. A comparison of mounds and depressions in sites with large and small gilgai revealed surprisingly little variation in stable isotope profiles between gilgai components or in relation to gilgai size. Variations in cracking, surface conditions, surface cover, solar radiation and wooded vegetation patterns could have potentially contributed to large variations in stable isotope profiles throughout the sites but the influence of these appears to have been minor and constrained to the upper 0.3m. Despite cracks being present to depths up to 1.5m, few samples are needed below 0.6m depth to characterise the isotope signature of the subsoil. Comparison of isotope profiles in closely spaced cores suggested that one core can sufficiently capture the profile trend, although bulking of multiple cores is recommended to minimise the likelihood of sampling error.
DNA helicase RecQ1 regulates mutually exclusive expression of virulence genes inPlasmodium falciparumvia heterochromatin alteration
Authors: Li Zhou , Yin Shigang , Sun Maoxin , Cheng Xiu , Wei Jieqiong , Gilbert Nicolas , Miao Jun , Cui Liwang , Huang Zhenghui , Dai Xueyu , Jiang Lubin
Published: February 2019

ThePlasmodium falciparum vargene family encodes ∼60 surface antigens by which parasites escape the host immune responses via clonal expression ofvargenes. However, the mechanism controlling this mutual exclusivity, associated with alterations in chromatin assembly, is not understood. Here, we determined how expression of thevargene family is regulated by two RecQ DNA helicase family members, PfRecQ1 and PfWRN, inP. falciparum. Through genetic manipulation, we found that the completevarrepertoire was silenced onPfRecQ1knockout, whereas their expression did not show noticeable changes whenPfWRNwas knocked out. More important, mutually exclusive expression ofvargenes could be rescued by complementation of PfRecQ1. In addition, knocking out either of these two helicase genes changed the perinuclear cluster distribution of subtelomeres and subtelomericvargenes. Whereas deletion ofPfRecQ1increased the heterochromatin mark trimethylated (H3K9me3) at the transcription start site (TSS) of thevargeneupsC1, that deletion had no effect on the global distribution of H3K9me3 over gene bodies, including those for thevargenes. ChIP-seq assay showed that PfRecQ1 was enriched globally at the TSSs of all genes, whereas PfWRN-enriched regions occurred at the gene bodies of thevargene family, but not of other genes or at TSSs of all genes. OnPfRecQ1deletion, theupsC1 vargene moved from the active perinuclear transcription region to a silenced region of theupsCtype. These findings imply that PfRecQ1, but not PfWRN, is essential for maintaining the clonal expression ofvargenes.
ERK2 regulates epithelial-to-mesenchymal plasticity through DOCK10-dependent Rac1/FoxO1 activation
Authors: Shin Sejeong , Buel Gwen R. , Nagiec Michal J. , Han Min-Joon , Roux Philippe P. , Blenis John , Yoon Sang-Oh
Published: February 2019

ERK is a key coordinator of the epithelial-to-mesenchymal transition (EMT) in that a variety of EMT-inducing factors activate signaling pathways that converge on ERK to regulate EMT transcription programs. However, the mechanisms by which ERK controls the EMT program are not well understood. Through an analysis of the global changes of gene expression mediated by ERK2, we identified the transcription factor FoxO1 as a potential mediator of ERK2-induced EMT, and thus we investigated the mechanism by which ERK2 regulates FoxO1. Additionally, our analysis revealed that ERK2 induced the expression of Dock10, a Rac1/Cdc42 GEF, during EMT. We demonstrate that the activation of the Rac1/JNK signaling axis downstream of Dock10 leads to an increase in FoxO1 expression and EMT. Taken together, our study uncovers mechanisms by which epithelial cells acquire less proliferative but more migratory mesenchymal properties and reveals potential therapeutic targets for cancers evolving into a metastatic disease state.
Presynaptic SNAP-25 regulates retinal waves and retinogeniculate projection via phosphorylation
Authors: Hsiao Yu-Tien , Shu Wen-Chi , Chen Pin-Chun , Yang Hui-Ju , Chen Hsin-Yo , Hsu Sheng-Ping , Huang Yi-Ting , Yang Cheng-Chang , Chen Yen-Ju , Yu Ni-Yen , Liou Shih-Yuan , Chiang Ning , Huang Chien-Ting , Cheng Tzu-Lin , Cheung Lam-Yan , Lin Yu-Chun , Lu Juu-Chin , Wang Chih-Tien
Published: February 2019

Significance

Patterned spontaneous activity can modify the structure and function of neural circuits during development, such as retinal waves essential for establishing functional visual circuits. Retinal waves are initiated by presynaptic release, further inducing temporally synchronized oscillations of PKA activity. However, the PKA substrate regulating visual circuit refinement remains elusive. Here, we describe a biological mechanism in which PKA-mediated SN25 phosphorylation in presynaptic retinal neurons down-regulates synaptic strength and retinal waves during development. These changes in wave spatiotemporal patterns can further induce global effects on visual circuit refinement, i.e., the eye-specific segregation of retinogeniculate projection. Therefore, by switching the phosphorylation state by PKA, SN25 in wave-initiating neurons can regulate the plasticity of retinal circuit activity and sculpt developing visual circuits.
Abnormal glycogen storage in tuberous sclerosis complex caused by impairment of mTORC1-dependent and -independent signaling pathways
Authors: Pal Rituraj , Xiong Yan , Sardiello Marco
Published: February 2019

Significance

Tuberous sclerosis complex (TSC) is a genetic disease characterized by tumor formation in multiple organs. The identification of dysregulated cellular processes in TSC is necessary for the selection of possible therapeutic interventions. The current models place impaired mTORC1 signaling at the core of TSC pathogenesis. In this study, we identify an mTORC1-independent pathway that drives excess glycogen storage in TSC via impaired autophagic degradation of glycogen caused by defects in the autophagy-lysosome system. Importantly, we find that the combined use of mTORC1 and Akt pharmacological inhibitors restore glycogen homeostasis. Our findings uncouple mTORC1-dependent from mTORC1-independent processes that are dysregulated in TSC and pinpoint multiple pharmacologically actionable entry points that could be leveraged to develop a therapeutic treatment.
Metabolic preference of nitrate over oxygen as an electron acceptor in foraminifera from the Peruvian oxygen minimum zone
Authors: Glock Nicolaas , Roy Alexandra-Sophie , Romero Dennis , Wein Tanita , Weissenbach Julia , Revsbech Niels Peter , Høgslund Signe , Clemens David , Sommer Stefan , Dagan Tal
Published: February 2019

Significance

Foraminifera are able to respire nitrate instead of oxygen, a rare ability amongst eukaryotes. Here, we show that benthic foraminifera from the Peruvian oxygen minimum zone are not just facultative anaerobes by switching to nitrate respiration when oxygen is depleted but that denitrification is their preferred respiration pathway. Their metabolic adaptations allow some species to grow larger than predicted by cell physiology of aerobic organisms due to oxygen limitation. Finally, we formulate, from our observations, mathematical equations to predict the amount of foraminiferal denitrification using their cell volume. Nitrate is an important macronutrient, and denitrification is the main oceanic nitrate sink. Our equations will help to constrain biogeochemical models for marine nitrate cycling.
Structure–function characterization of an insecticidal protein GNIP1Aa, a member of an MACPF and β-tripod families
Authors: Zaitseva Jelena , Vaknin Daniel , Krebs Christian , Doroghazi James , Milam Sara L. , Balasubramanian Deepa , Duck Nicholas B. , Freigang Joerg
Published: February 2019

The crystal structure of the Gram-negative insecticidal protein, GNIP1Aa, has been solved at 2.5-Å resolution. The protein consists of two structurally distinct domains, a MACPF (membrane attack complex/PerForin) and a previously uncharacterized type of domain. GNIP1Aa is unique in being a prokaryotic MACPF member to have both its structure and function identified. It was isolated from a
Chromobacterium piscinae
strain and is specifically toxic to
Diabrotica virgifera virgifera
larvae upon feeding. In members of the MACPF family, the MACPF domain has been shown to be important for protein oligomerization and formation of transmembrane pores, while accompanying domains define the specificity of the target of the toxicity. In GNIP1Aa the accompanying C-terminal domain has a unique fold composed of three pseudosymmetric subdomains with shared sequence similarity, a feature not obvious from the initial sequence examination. Our analysis places this domain into a protein family, named here β-tripod. Using mutagenesis, we identified functionally important regions in the β-tripod domain, which may be involved in target recognition.
Structural basis for antiarrhythmic drug interactions with the human cardiac sodium channel
Authors: Nguyen Phuong T. , DeMarco Kevin R. , Vorobyov Igor , Clancy Colleen E. , Yarov-Yarovoy Vladimir
Published: February 2019

Significance

Voltage-gated sodium channels play a central role in cellular excitability and are key targets for drug development. Recent breakthroughs in high-resolution cryo-electron microscopy protein structure determination, Rosetta computational protein structure modeling, and multimicrosecond molecular dynamics simulations are empowering advances in structural biology to study the atomistic details of channel−drug interactions. We used Rosetta structural computational modeling and molecular dynamics simulations to study the interactions of antiarrhythmic and local anesthetic drugs with cardiac sodium channel. Our results provide crucial atomic-scale mechanistic insights into the channel–drug interactions, necessary for the rational design of novel modulators of the human cardiac sodium channel to be used for the treatment of cardiac arrhythmias.
Involvement of ERK1/2-mediated ELK1/CHOP/DR5 pathway in 6-(methylsulfinyl)hexyl isothiocyanate-induced apoptosis of colorectal cancer cells
Authors: Yano Satoshi , Wu Shusong , Sakao Kozue , Hou De-Xing
Published: February 2019

6-(Methylsulfinyl)hexyl isothiocyanate (6-MSITC) is a major bioactive compound in Wasabi. Although 6-MSITC is reported to have cancer chemopreventive activities in rat model, the molecular mechanism is unclear. In this study, we investigated the anticancer mechanisms using two types of human colorectal cancer cells (HCT116 p53+/+ and p53−/−). 6-MSITC caused cell cycle arrest in G2/M phase and induced apoptosis in both types of cells in the same fashion. Signaling data revealed that the activation of ERK1/2, rather than p53, is recruited for 6-MSITC-induced apoptosis. 6-MSITC stimulated ERK1/2 phosphorylation, and then activated ERK1/2 signaling including ELK1 phosphorylation, and upregulation of C/EBP homologous protein (CHOP) and death receptor 5 (DR5). The MEK1/2 inhibitor U0126 blocked all of these molecular events induced by 6-MSITC, and enhanced the cell viability in both types of cells in the same manner. These results indicated that ERK1/2-mediated ELK1/CHOP/DR5 pathway is involved in 6-MSITC-induced apoptosis in colorectal cancer cells.

Abbreviations: CHOP: C/EBP homologous protein; DR5: death receptor 5; ELK1: ETS transcription factor; ERK1/2: extracellular signal-regulated kinase 1/2; JNK: Jun-N-terminal kinase; MAPK: mitogen-activated protein kinase; MEK1/2: MAP/ERK kinase 1/2; 6-MSITC: 6-(methylsulfinyl)hexyl isothiocyanate; MTT: 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide; PARP: poly(ADP-ribose) polymerase.
Mitotic chromosome alignment ensures mitotic fidelity by promoting interchromosomal compaction during anaphase
Authors: Fonseca Cindy L. , Malaby Heidi L.H. , Sepaniac Leslie A. , Martin Whitney , Byers Candice , Czechanski Anne , Messinger Dana , Tang Mary , Ohi Ryoma , Reinholdt Laura G. , Stumpff Jason
Published: February 2019

Chromosome alignment at the equator of the mitotic spindle is a highly conserved step during cell division; however, its importance to genomic stability and cellular fitness is not understood. Normal mammalian somatic cells lacking KIF18A function complete cell division without aligning chromosomes. These alignment-deficient cells display normal chromosome copy numbers in vitro and in vivo, suggesting that chromosome alignment is largely dispensable for maintenance of euploidy. However, we find that loss of chromosome alignment leads to interchromosomal compaction defects during anaphase, abnormal organization of chromosomes into a single nucleus at mitotic exit, and the formation of micronuclei in vitro and in vivo. These defects slow cell proliferation and are associated with impaired postnatal growth and survival in mice. Our studies support a model in which the alignment of mitotic chromosomes promotes proper organization of chromosomes into a single nucleus and continued proliferation by ensuring that chromosomes segregate as a compact mass during anaphase.
Tumoral EHF predicts the efficacy of anti-PD1 therapy in pancreatic ductal adenocarcinoma
Authors: Liu Jing , Jiang Wenna , Zhao Kaili , Wang Hongwei , Zhou Tianxing , Bai Weiwei , Wang Xiuchao , Zhao Tiansuo , Huang Chongbiao , Gao Song , Qin Tai , Yu Wenwen , Yang Bo , Li Xin , Fu Danqi , Tan Wei , Yang Shengyu , Ren He , Hao Jihui
Published: February 2019

Pancreatic ductal adenocarcinoma (PDAC) is a highly immune-suppressive tumor with a low response rate to single checkpoint blockade therapy. ETS homologous factor (EHF) is a tumor suppressor in PDAC. Here, we report a novel function of EHF in pancreatic cancer immune microenvironment editing and efficacy prediction for anti-PD1 therapy. Our findings support that the deficiency of tumoral EHF induced the accumulation of regulatory T (T reg) cells and myeloid-derived suppressor cells (MDSCs) and a decrease in the number of tumor-infiltrating CD8+ T cells. Mechanistically, EHF deficiency induced the conversion and expansion of T reg cells and MDSCs through inhibiting tumor TGFβ1 and GM-CSF secretion. EHF suppressed the transcription of TGFB1 and CSF2 by directly binding to their promoters. Mice bearing EHF overexpression tumors exhibited significantly better response to anti-PD1 therapy than those with control tumors. Our findings delineate the immunosuppressive mechanism of EHF deficiency in PDAC and highlight that EHF overexpression may improve PDAC checkpoint immunotherapy.
EDA fibronectin–TLR4 axis sustains megakaryocyte expansion and inflammation in bone marrow fibrosis
Authors: Malara Alessandro , Gruppi Cristian , Abbonante Vittorio , Cattaneo Daniele , De Marco Luigi , Massa Margherita , Iurlo Alessandra , Gianelli Umberto , Balduini Carlo L. , Tira Maria E. , Muro Andrès F. , Chauhan Anil K. , Rosti Vittorio , Barosi Giovanni , Balduini Alessandra
Published: February 2019

The fibronectin EDA isoform (EDA FN) is instrumental in fibrogenesis but, to date, its expression and function in bone marrow (BM) fibrosis have not been explored. We found that mice constitutively expressing the EDA domain (EIIIA+/+), but not EDA knockout mice, are more prone to develop BM fibrosis upon treatment with the thrombopoietin (TPO) mimetic romiplostim (TPOhigh). Mechanistically, EDA FN binds to TLR4 and sustains progenitor cell proliferation and megakaryopoiesis in a TPO-independent fashion, inducing LPS-like responses, such as NF-κB activation and release of profibrotic IL-6. Pharmacological inhibition of TLR4 or TLR4 deletion in TPOhigh mice abrogated Mk hyperplasia, BM fibrosis, IL-6 release, extramedullary hematopoiesis, and splenomegaly. Finally, developing a novel ELISA assay, we analyzed samples from patients affected by primary myelofibrosis (PMF), a well-known pathological situation caused by altered TPO signaling, and found that the EDA FN is increased in plasma and BM biopsies of PMF patients as compared with healthy controls, correlating with fibrotic phase.
Leaf heteroblasty in Passiflora edulis as revealed by metabolic profiling and expression analyses of the microRNAs miR156 and miR172
Authors: Silva Priscila O , Batista Diego S , Cavalcanti João Henrique F , Koehler Andréa D , Vieira Lorena M , Fernandes Amanda M , Barrera-Rojas Carlos Hernan , Ribeiro Dimas M , Nogueira Fabio T S , Otoni Wagner C
Published: February 2019

Background and Aims

Juvenile-to-adult phase transition is marked by changes in leaf morphology, mostly due to the temporal development of the shoot apical meristem, a phenomenon known as heteroblasty. Sugars and microRNA-controlled modules are components of the heteroblastic process in Arabidopsis thaliana leaves. However, our understanding about their roles during phase-changing in other species, such as Passiflora edulis, remains limited. Unlike Arabidopsis, P. edulis (a semi-woody perennial climbing vine) undergoes remarkable changes in leaf morphology throughout juvenile-to-adult transition. Nonetheless, the underlying molecular mechanisms are unknown.

Methods

Here we evaluated the molecular mechanisms underlying the heteroblastic process by analysing the temporal expression of microRNAs and targets in leaves as well as the leaf metabolome during P. edulis development.

Key Results

Metabolic profiling revealed a unique composition of metabolites associated with leaf heteroblasty. Increasing levels of glucose and α-trehalose were observed during juvenile-to-adult phase transition. Accumulation of microRNA156 (miR156) correlated with juvenile leaf traits, whilst miR172 transcript accumulation was associated with leaf adult traits. Importantly, glucose may mediate adult leaf characteristics during de novo shoot organogenesis by modulating miR156-targeted PeSPL9 expression levels at early stages of shoot development.

Conclusions

Altogether, our results suggest that specific sugars may act as co-regulators, along with two microRNAs, leading to leaf morphological modifications throughout juvenile-to-adult phase transition in P. edulis.