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Sample records for polarization dependence revealed

  1. Polarization-dependent Imaging Contrast (PIC) mapping reveals nanocrystal orientation patterns in carbonate biominerals

    Energy Technology Data Exchange (ETDEWEB)

    Gilbert, Pupa U.P.A., E-mail: pupa@physics.wisc.edu [University of Wisconsin-Madison, Departments of Physics and Chemistry, Madison, WI 53706 (United States)

    2012-10-15

    Highlights: Black-Right-Pointing-Pointer Nanocrystal orientation shown by Polarization-dependent Imaging Contrast (PIC) maps. Black-Right-Pointing-Pointer PIC-mapping of carbonate biominerals reveals their ultrastructure at the nanoscale. Black-Right-Pointing-Pointer The formation mechanisms of biominerals is discovered by PIC-mapping using PEEM. -- Abstract: Carbonate biominerals are one of the most interesting systems a physicist can study. They play a major role in the CO{sub 2} cycle, they master templation, self-assembly, nanofabrication, phase transitions, space filling, crystal nucleation and growth mechanisms. A new imaging modality was introduced in the last 5 years that enables direct observation of the orientation of carbonate single crystals, at the nano- and micro-scale. This is Polarization-dependent Imaging Contrast (PIC) mapping, which is based on X-ray linear dichroism, and uses PhotoElectron Emission spectroMicroscopy (PEEM). Here we present PIC-mapping results from biominerals, including the nacre and prismatic layers of mollusk shells, and sea urchin teeth. We describe various PIC-mapping approaches, and show that these lead to fundamental discoveries on the formation mechanisms of biominerals.

  2. Frequency dependent polarization in blazars

    International Nuclear Information System (INIS)

    Bjoernsson, C.I.

    1984-10-01

    It is argued that the intrinsic frequency dependent polarization in blazars finds its most straightforward explanations in terms of a single rather than a multicomponent sourcemodel. In order to reproduce the observations, under the assumption that the emission mechanism is optically thin synchrotron radiation, both a well ordered magnetic field and an electron distribution with a sharp break or cuttoff are necessary. Non-uniform pitch angle distribution and/or environments where synchrotron losses are important are both conducive to producing strong frequency dependent polarization. Reasons are put forth as to why such conditions ar expected to occur in blazars. Two specific models are discussed in detail and it is shown that they are both able to produce strong frequency dependent polarization, even when the spectral index changes by a small amount only. (orig.)

  3. Venus's southern polar vortex reveals precessing circulation.

    Science.gov (United States)

    Luz, D; Berry, D L; Piccioni, G; Drossart, P; Politi, R; Wilson, C F; Erard, S; Nuccilli, F

    2011-04-29

    Initial images of Venus's south pole by the Venus Express mission have shown the presence of a bright, highly variable vortex, similar to that at the planet's north pole. Using high-resolution infrared measurements of polar winds from the Venus Express Visible and Infrared Thermal Imaging Spectrometer (VIRTIS) instrument, we show the vortex to have a constantly varying internal structure, with a center of rotation displaced from the geographic south pole by ~3 degrees of latitude and that drifts around the pole with a period of 5 to 10 Earth days. This is indicative of a nonsymmetric and varying precession of the polar atmospheric circulation with respect to the planetary axis.

  4. Plasmonic vortex generator without polarization dependence

    Science.gov (United States)

    Wang, Han; Liu, Lixia; Liu, Chunxiang; Li, Xing; Wang, Shuyun; Xu, Qing; Teng, Shuyun

    2018-03-01

    In view of the limitations of vortex generators with polarization dependence at present, we propose a plasmonic vortex generator composed of rectangular holes etched in silver film, in which the optical vortex can be generated under arbitrary linearly polarized light illumination. Two sets of rectangular holes are arranged equidistantly on a circle and rotate in postulate directions. Theoretical analysis provides the design principle for the vortex generator, and numerical simulations give guidance on designating the vortex generator parameters. Experimental measurements verify the performance of the proposed vortex generator. Moreover, two alternative structures for the generation of a plasmonic vortex are also provided in this paper. The resulting perfect vortex, compact structure and flexible illumination conditions will lead to wide applications of this plasmonic vortex generator.

  5. Polarization-Dependent Multi-Functional Metamaterial as Polarization Filter, Transparent Wall and Circular Polarizer using Ring-Cross Resonator

    Directory of Open Access Journals (Sweden)

    Z. Zhang

    2017-09-01

    Full Text Available We propose a polarization-dependent multi-functional metamaterial using ring-cross resonator. Based on the analysis of surface current distributions induced by different polarized incidence, we demonstrate that the proposed metamaterial serves as a polarization filter, a transparent wall and a circular polarizer under different polarization normal incidence. Additionally, parameter analyses on the control of resonance are discussed to complementally explain the physical origin. Simulated results show that the proposed metamaterial functions as a polarization filter eliminating the x-polarization wave at 10.1 GHz and y-polarization wave at 14.3 GHz, a transparent wall transmitting both x-polarized and y-polarized incident waves at 12.6 GHz, and a broadband circular polarizer converting the +45° polarized (-45° polarized incident wave to the left (right handed circularly polarized wave from 10.8 to 12.8 GHz, respectively. Measured results agree well with the simulation and validate the performance of the proposed multifunctional metamaterial.

  6. Scale dependence and small x behaviour of polarized parton distributions

    CERN Document Server

    Ball, R D; Ridolfi, G; Forte, S; Ridolfi, G

    1995-01-01

    We discuss perturbative evolution of the polarized structure function g_1 in the (x,Q^2) plane, with special regard to the small-x region. We determine g_1 in terms of polarized quark and gluon distributions using coefficient functions to order alpha_s. At small x g_1 then displays substantial scale dependence, which necessarily implies a corresponding scale dependence in the large-x region. This scale dependence has significant consequences for the extraction of the first moment from the experimental data, reducing its value while increasing the error. Conversely, the scale dependence may be used to constrain the size of the polarized gluon distribution.

  7. Polarization-dependent aluminum metasurface operating at 450 nm

    DEFF Research Database (Denmark)

    Højlund-Nielsen, Emil; Zhu, Xiaolong; Carstensen, Marcus S

    2015-01-01

    We report on a polarization-dependent plasmonic aluminum-based high-density metasurface operating at blue wavelengths. The fabricated sub-wavelength structures, tailored in size and geometry, possess strong, localized, plasmonic resonances able to control linear polarization. Best performance...

  8. Polarization-dependent electromagnetic responses in an A-shape metasurface.

    Science.gov (United States)

    Zhang, Ning; Xu, Quan; Li, Shaoxian; Ouyang, Chunmei; Zhang, Xueqian; Li, Yanfeng; Gu, Jianqiang; Tian, Zhen; Han, Jiaguang; Zhang, Weili

    2017-08-21

    We numerically and experimentally demonstrate polarization-dependent terahertz responses in a proposed metasurface of A-shape resonators. With the horizontal polarization incidence, the observed transmission window is formed by two resonance dips, corresponding to the inductive-capacitive resonance at the lower frequency and the high-order antisymmetric resonance at a higher frequency, respectively. When the incident wave is perpendicularly polarized, the transmission window arises from the plasmon-induced transparency spectral response. The origin of the polarization-sensitive resonance properties is revealed by mapping the electric field and terahertz-induced surface current in the proposed metamaterials. Moreover, the influence of the geometry of the A-shape microstructures on the transmission spectra is analyzed. These polarization-dependent metamaterials may provide more degrees of freedom in tuning the electromagnetic responses, thus offering a path toward robust metamaterials design.

  9. The wavelength dependence of polarization in NGC 2023

    International Nuclear Information System (INIS)

    Rolph, C. D.; Scarrott, S. M.

    1989-01-01

    NGC 2023 is a bright reflection nebula illuminated by the central star HD37903. At 2 microns the nebula is seen solely by reflected light from the central star but in the NIR there is excess radiation that is supposed to arise from thermal emission from a population of small grains (Sellgren, 1984). The unexpectedly high surface brightness at R and I wavelengths has led to the suggestion that even at these wavelengths there is a significant contribution from this thermal emission process (Witt, Schild, and Kraiman, 1984). If the nebula is seen by reflected starlight then this radiation will be linearly polarized. The level of polarization depends on the scattering geometry, grain size distribution, etc., and is typically 20 to 40 percent for nebulae such as NGC 1999 which is morphologically similar to NGC 2023. If, in any waveband, there is a contribution of radiation from emission processes this radiation will be unpolarized and will serve to dilute the scattered radiation to give a lower level of observed polarization. A study of the wavelength dependence of polarization in nebulae in which there may be thermal emission from grains will indicate the contribution from this process to the total luminosity. Polarization maps were produced in BVRI wavebands for the NGC 2023 nebulosity which confirm that at all wavelengths it is a reflection nebula illuminated by a central star. The wavelength dependence of polarization at representative points in the nebula and in a scatter plot of polarization in V and I wavebands at all points at which measurements are given. Results indicate that throughout the nebula there is a general trend for the level of polarization to increase with wavelength and that maximum levels of polarization occur at the longest wavelengths. No evidence is seen in the data for any significant contribution from the thermal emission from grains in the BVRI luminosity of NGC 2023

  10. Modelling polarization dependent absorption: The vectorial Lambert-Beer law

    Science.gov (United States)

    Franssens, G.

    2014-07-01

    The scalar Lambert-Beer law, describing the absorption of unpolarized light travelling through a linear non-scattering medium, is simple, well-known, and mathematically trivial. However, when we take the polarization of light into account and consider a medium with polarization dependent absorption, we now need a Vectorial Lambert-Beer Law (VLBL) to quantify this interaction. Such a generalization of the scalar Lambert-Beer law appears not to be readily available. A careful study of this topic reveals that it is not a trivial problem. We will see that the VLBL is not and cannot be a straightforward vectorized version of its scalar counterpart. The aim of the work is to present the general form of the VLBL and to explain how it arises. A reasonable starting point to derive the VLBL is the Vectorial Radiative Transfer Equation (VRTE), which models the absorption and scattering of (partially) polarized light travelling through a linear medium. When we turn off scattering, the VRTE becomes an infinitesimal model for the VLBL holding in the medium. By integrating this equation, we expect to find the VLBL. Surprisingly, this is not the end of the story. It turns out that light propagation through a medium with polarization-dependent absorption is mathematically not that trivial. The trickiness behind the VLBL can be understood in the following terms. The matrix in the VLBL, relating any input Stokes vector to the corresponding output Stokes vector, must necessarily be a Mueller matrix. The subset of invertible Mueller matrices forms a Lie group. It is known that this Lie group contains the ortho-chronous Lorentz group as a subgroup. The group manifold of this subgroup has a (well-known) non-trivial topology. Consequently, the manifold of the Lie group of Mueller matrices also has (at least the same, but likely a more general) non-trivial topology (the full extent of which is not yet known). The type of non-trivial topology, possessed by the manifold of (invertible

  11. Angle-dependent rotation of calcite in elliptically polarized light

    Science.gov (United States)

    Herne, Catherine M.; Cartwright, Natalie A.; Cattani, Matthew T.; Tracy, Lucas A.

    2017-08-01

    Calcite crystals trapped in an elliptically polarized laser field exhibit intriguing rotational motion. In this paper, we show measurements of the angle-dependent motion, and discuss how the motion of birefringent calcite can be used to develop a reliable and efficient process for determining the polarization ellipticity and orientation of a laser mode. The crystals experience torque in two ways: from the transfer of spin angular momentum (SAM) from the circular polarization component of the light, and from a torque due to the linear polarization component of the light that acts to align the optic axis of the crystal with the polarization axis of the light. These torques alternatingly compete with and amplify each other, creating an oscillating rotational crystal velocity. We model the behavior as a rigid body in an angle-dependent torque. We experimentally demonstrate the dependence of the rotational velocity on the angular orientation of the crystal by placing the crystals in a sample solution in our trapping region, and observing their behavior under different polarization modes. Measurements are made by acquiring information simultaneously from a quadrant photodiode collecting the driving light after it passes through the sample region, and by imaging the crystal motion onto a camera. We finish by illustrating how to use this model to predict the ellipticity of a laser mode from rotational motion of birefringent crystals.

  12. Polarized light modulates light-dependent magnetic compass orientation in birds

    Science.gov (United States)

    Muheim, Rachel; Sjöberg, Sissel; Pinzon-Rodriguez, Atticus

    2016-01-01

    Magnetoreception of the light-dependent magnetic compass in birds is suggested to be mediated by a radical-pair mechanism taking place in the avian retina. Biophysical models on magnetic field effects on radical pairs generally assume that the light activating the magnetoreceptor molecules is nondirectional and unpolarized, and that light absorption is isotropic. However, natural skylight enters the avian retina unidirectionally, through the cornea and the lens, and is often partially polarized. In addition, cryptochromes, the putative magnetoreceptor molecules, absorb light anisotropically, i.e., they preferentially absorb light of a specific direction and polarization, implying that the light-dependent magnetic compass is intrinsically polarization sensitive. To test putative interactions between the avian magnetic compass and polarized light, we developed a spatial orientation assay and trained zebra finches to magnetic and/or overhead polarized light cues in a four-arm “plus” maze. The birds did not use overhead polarized light near the zenith for sky compass orientation. Instead, overhead polarized light modulated light-dependent magnetic compass orientation, i.e., how the birds perceive the magnetic field. Birds were well oriented when tested with the polarized light axis aligned parallel to the magnetic field. When the polarized light axis was aligned perpendicular to the magnetic field, the birds became disoriented. These findings are the first behavioral evidence to our knowledge for a direct interaction between polarized light and the light-dependent magnetic compass in an animal. They reveal a fundamentally new property of the radical pair-based magnetoreceptor with key implications for how birds and other animals perceive the Earth’s magnetic field. PMID:26811473

  13. Polarization dependence of Na* + Na* associative ionization revisited

    NARCIS (Netherlands)

    Meijer, H.A.J.; Meulen, H.P. v.d.; Morgenstern, R.; Hertel, I.V.; Meyer, E.; Witte, R.

    1986-01-01

    The dependence of the associative ionization process Na 3 2P3/2 + Na 3 2P3/2 → Na2+ + e- on the polarization of the laser light used for Na excitation was independently investigated in Utrecht and Berlin. The purpose of this paper is to clarify discrepancies between two other earlier experimental

  14. Characterization of a magnetic trap by polarization dependent Zeeman spectroscopy

    DEFF Research Database (Denmark)

    Nielsen, Carsten Vandel; Lyngsøe, Jens Kristian; Thorseth, Anders

    2008-01-01

    This paper demonstrates a detailed experimental study of our cloverleaf magnetic trap for sodium atoms. By using polarization dependent Zeeman spectroscopy of our atomic beam, passing the magnetic trap region, we have determined important trap parameters such as gradients, their curvatures...

  15. Polarization dependent switching of asymmetric nanorings with a circular field

    Directory of Open Access Journals (Sweden)

    Nihar R. Pradhan

    2016-01-01

    Full Text Available We experimentally investigated the switching from onion to vortex states in asymmetric cobalt nanorings by an applied circular field. An in-plane field is applied along the symmetric or asymmetric axis of the ring to establish domain walls (DWs with symmetric or asymmetric polarization. A circular field is then applied to switch from the onion state to the vortex state, moving the DWs in the process. The asymmetry of the ring leads to different switching fields depending on the location of the DWs and direction of applied field. For polarization along the asymmetric axis, the field required to move the DWs to the narrow side of the ring is smaller than the field required to move the DWs to the larger side of the ring. For polarization along the symmetric axis, establishing one DW in the narrow side and one on the wide side, the field required to switch to the vortex state is an intermediate value.

  16. Constraints on cosmological birefringence energy dependence from CMB polarization data

    International Nuclear Information System (INIS)

    Gubitosi, G.; Paci, F.

    2013-01-01

    We study the possibility of constraining the energy dependence of cosmological birefringence by using CMB polarization data. We consider four possible behaviors, characteristic of different theoretical scenarios: energy-independent birefringence motivated by Chern-Simons interactions of the electromagnetic field, linear energy dependence motivated by a 'Weyl' interaction of the electromagnetic field, quadratic energy dependence, motivated by quantum gravity modifications of low-energy electrodynamics, and inverse quadratic dependence, motivated by Faraday rotation generated by primordial magnetic fields. We constrain the parameters associated to each kind of dependence and use our results to give constraints on the models mentioned. We forecast the sensitivity that Planck data will be able to achieve in this respect

  17. Spin dependence studies with the ZGS polarized proton beam

    International Nuclear Information System (INIS)

    Wicklund, A.B.

    1977-01-01

    Selected results are summarized of recent measurements using a polarized proton beam at the Argonne ZGS. The polarized target asymmetry and the beam-target spin correlation are measured in pp→pp at 6 and 12 GeV/c. Asymmetry is slowly varying with energy while spin correlation increases considerably from 6 to 12 GeV/c. The polarized parameters in pp→pp and pn→pn elastic scattering are compared. The data show that pp and pn polarizations tend to approach mirror symmetry as the energy increases. The effective mass spectrometer has been used to study the pp→pπ + n, pn→pπ - p reactions from 2 to 6 GeV/c. For small -t values (-t 2 ) these reactions are dominated by π exchange. At large -t values other mechanisms besides π-exchange become important. The 3-body diffraction dissociation reactions have been measured at 6 GeV/c with hydrogen and deuterium targets. The reactions are pp→pπ + π - (p); pd→pπ + π - (p+n). Comparison of hydrogen and deuterium cross section reveals a considerable coherent contribution of deuterium, which has an approximately 20% larger cross section per nucleon than hydrogen

  18. Imaging of Polarization-dependent Photocurrent in Graphene Photodevices

    Science.gov (United States)

    Kim, Minjung; Yoon, Duhee; Ang Yoon, Ho; Lee, Sang Wook; Cheong, Hyeonsik

    2012-02-01

    Recently, a metal-graphene-metal photodetector for high-speed optical communications was reported. In addition, a graphene-based photodetector was reported to be able to absorb broadband light owing to the unique band structure of graphene [Mueller et al., Nature Photonics 4, 297 (2010)]. We investigated the polarization dependence of the photocurrent generated in metal-graphene-metal junctions. The graphene photodevice was fabricated by depositing Pd/Au and Ti/Au electrodes on single-layer graphene samples. When the polarization of incident laser beam is rotated with respect to the metal-graphene-metal junction, the photocurrent is significantly modulated. In addition, we measured the exact positions where the photocurrent is generated by measuring the photocurrent and Raman images of the graphene photodevices simultaneously.

  19. Observation of interface dependent spin polarized photocurrents in InAs/GaSb superlattice

    Energy Technology Data Exchange (ETDEWEB)

    Li, Yuan, E-mail: liyuan12@semi.ac.cn; Liu, Yu; Zhu, Laipan; Qin, Xudong; Wu, Qing; Huang, Wei; Chen, Yonghai, E-mail: yhchen@semi.ac.cn [Key Laboratory of Semiconductor Materials Science, Institute of Semiconductors, Chinese Academy of Sciences, 100083 Beijing (China); Niu, Zhichuan; Xiang, Wei; Hao, Hongyue [The State Key Laboratory of Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, 100083 Beijing (China)

    2015-05-11

    In this letter, we investigated the spin polarized photocurrents excited by mid-infrared radiation and near-infrared radiation, respectively, in InAs/GaSb type II superlattices with different kinds of interfaces. By periodically varying the polarization state of the radiation, we analyzed Rashba-type and Dresselhaus-type spin polarized photocurrents, which present different features depending on the interface types and excitation conditions. Under mid-infrared excitation, the ratio of Rashba-type and Dresselhaus-type spin polarized photocurrents of the superlattice with InSb-like interface is obviously larger than that of the superlattice with GaAs-like interface, the ratio of the superlattice with alternate interface is in the middle. Whereas under near-infrared excitation, the ratios of the three superlattices are nearly the same. Further researches reveal the synactic effects of interface dependent strain and asymmetric interface potential on the spin splitting. Besides, the polarized Raman spectroscopies of these structures were also analyzed.

  20. Observation of interface dependent spin polarized photocurrents in InAs/GaSb superlattice

    International Nuclear Information System (INIS)

    Li, Yuan; Liu, Yu; Zhu, Laipan; Qin, Xudong; Wu, Qing; Huang, Wei; Chen, Yonghai; Niu, Zhichuan; Xiang, Wei; Hao, Hongyue

    2015-01-01

    In this letter, we investigated the spin polarized photocurrents excited by mid-infrared radiation and near-infrared radiation, respectively, in InAs/GaSb type II superlattices with different kinds of interfaces. By periodically varying the polarization state of the radiation, we analyzed Rashba-type and Dresselhaus-type spin polarized photocurrents, which present different features depending on the interface types and excitation conditions. Under mid-infrared excitation, the ratio of Rashba-type and Dresselhaus-type spin polarized photocurrents of the superlattice with InSb-like interface is obviously larger than that of the superlattice with GaAs-like interface, the ratio of the superlattice with alternate interface is in the middle. Whereas under near-infrared excitation, the ratios of the three superlattices are nearly the same. Further researches reveal the synactic effects of interface dependent strain and asymmetric interface potential on the spin splitting. Besides, the polarized Raman spectroscopies of these structures were also analyzed

  1. Brucella Dysregulates Monocytes and Inhibits Macrophage Polarization through LC3-Dependent Autophagy

    Directory of Open Access Journals (Sweden)

    Yang Wang

    2017-06-01

    Full Text Available Brucellosis is caused by infection with Brucella species and exhibits diverse clinical manifestations in infected humans. Monocytes and macrophages are not only the first line of defense against Brucella infection but also a main reservoir for Brucella. In the present study, we examined the effects of Brucella infection on human peripheral monocytes and monocyte-derived polarized macrophages. We showed that Brucella infection led to an increase in the proportion of CD14++CD16− monocytes and the expression of the autophagy-related protein LC3B, and the effects of Brucella-induced monocytes are inhibited after 6 weeks of antibiotic treatment. Additionally, the production of IL-1β, IL-6, IL-10, and TNF-α from monocytes in patients with brucellosis was suppressed through the LC3-dependent autophagy pathway during Brucella infection. Moreover, Brucella infection inhibited macrophage polarization. Consistently, the addition of 3-MA, an inhibitor of LC3-related autophagy, partially restored macrophage polarization. Intriguingly, we also found that the upregulation of LC3B expression by rapamycin and heat-killed Brucella in vitro inhibits M2 macrophage polarization, which can be reversed partially by 3-MA. Taken together, these findings reveal that Brucella dysregulates monocyte and macrophage polarization through LC3-dependent autophagy. Thus, targeting this pathway may lead to the development of new therapeutics against Brucellosis.

  2. Polarization-angle dependence of photoluminescence intensity of ordered GaInP{sub 2} layers: observation of polarization memory

    Energy Technology Data Exchange (ETDEWEB)

    Prutskij, T.; Brito-Orta, R. [Instituto de Ciencias, BUAP, Puebla (Mexico); Pelosi, C. [IMEM/CNR, Parma (Italy)

    2008-09-15

    We compare measured and calculated polarization-angle dependencies of the intensity of the photoluminescence emission from MOVPE-grown GaInP{sub 2} layers with different ordering parameters. We measured the polarization-angle dependencies of the emission propagating along the [001],[110] and [1 anti 10] directions at room temperature. Symmetry considerations were used to calculate the dependence of the relative intensity of the PL emission which was linearly polarized along different directions and to estimate the value of the valence-band splitting by fitting the measured dependencies with calculated curves. An intriguing influence of the polarization of the exciting beam on the relative amount of the polarized PL emission was observed in the emission from the (110) plane. (copyright 2008 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  3. Polarized Trafficking of AQP2 Revealed in Three Dimensional Epithelial Culture.

    Directory of Open Access Journals (Sweden)

    William L Rice

    Full Text Available In renal collecting duct (CD principal cells (PCs, vasopressin (VP acts through its receptor, V2R, to increase intracellular cAMP leading to phosphorylation and apical membrane accumulation of the water channel aquaporin 2 (AQP2. The trafficking and function of basolaterally located AQP2 is, however, poorly understood. Here we report the successful application of a 3-dimensional Madin-Darby canine kidney (MDCK epithelial model to study polarized AQP2 trafficking. This model recapitulates the luminal architecture of the CD and bi-polarized distribution of AQP2 as seen in kidney. Without stimulation, AQP2 is located in the subapical and basolateral regions. Treatment with VP, forskolin (FK, or 8-(4-Chlorophenylthio-2'-O-methyladenosine 3',5'-cyclic monophosphate monosodium hydrate (CPT-cAMP leads to translocation of cytosolic AQP2 to the apical membrane, but not to the basolateral membrane. Treating cells with methyl-β-cyclodextrin (mβCD to acutely block endocytosis causes accumulation of AQP2 on the basolateral membrane, but not on the apical membrane. Our data suggest that AQP2 may traffic differently at the apical and basolateral domains in this 3D epithelial model. In addition, application of a panel of phosphorylation specific AQP2 antibodies reveals the polarized, subcellular localization of differentially phosphorylated AQP2 at S256, S261, S264 and S269 in the 3D culture model, which is consistent with observations made in the CDs of VP treated animals, suggesting the preservation of phosphorylation dependent regulatory mechanism of AQP2 trafficking in this model. Therefore we have established a 3D culture model for the study of trafficking and regulation of both the apical and basolaterally targeted AQP2. The new model will enable further characterization of the complex mechanism regulating bi-polarized trafficking of AQP2 in vitro.

  4. Temperature-Dependent Polarization in Field-Effect Transport and Photovoltaic Measurements of Methylammonium Lead Iodide.

    Science.gov (United States)

    Labram, John G; Fabini, Douglas H; Perry, Erin E; Lehner, Anna J; Wang, Hengbin; Glaudell, Anne M; Wu, Guang; Evans, Hayden; Buck, David; Cotta, Robert; Echegoyen, Luis; Wudl, Fred; Seshadri, Ram; Chabinyc, Michael L

    2015-09-17

    While recent improvements in the reported peak power conversion efficiency (PCE) of hybrid organic-inorganic perovskite solar cells have been truly astonishing, there are many fundamental questions about the electronic behavior of these materials. Here we have studied a set of electronic devices employing methylammonium lead iodide ((MA)PbI3) as the active material and conducted a series of temperature-dependent measurements. Field-effect transistor, capacitor, and photovoltaic cell measurements all reveal behavior consistent with substantial and strongly temperature-dependent polarization susceptibility in (MA)PbI3 at temporal and spatial scales that significantly impact functional behavior. The relative PCE of (MA)PbI3 photovoltaic cells is observed to reduce drastically with decreasing temperature, suggesting that such polarization effects could be a prerequisite for high-performance device operation.

  5. Solar polar magnetic field dependency of geomagnetic activity semiannual variation indicated in the Aa index

    Science.gov (United States)

    Oh, Suyeon; Yi, Yu

    2018-01-01

    Three major hypotheses have been proposed to explain the well-known semiannual variation of geomagnetic activity, maxima at equinoxes and minima at solstices. This study examined whether the seasonal variation of equinoctial geomagnetic activity is different in periods of opposite solar magnetic polarity in order to understand the contribution of the interplanetary magnetic field (IMF) in the Sun-Earth connection. Solar magnetic polarity is parallel to the Earth's polarity in solar minimum years of odd/even cycles but antiparallel in solar minimum years of even/odd cycles. The daily mean of the aa, Aa indices during each solar minimum was compared for periods when the solar magnetic polarity remained in opposite dipole conditions. The Aa index values were used for each of the three years surrounding the solar minimum years of the 14 solar cycles recorded since 1856. The Aa index reflects seasonal variation in geomagnetic activity, which is greater at the equinoxes than at the solstices. The Aa index reveals solar magnetic polarity dependency in which the geomagnetic activity is stronger in the antiparallel solar magnetic polarity condition than in the parallel one. The periodicity in semiannual variation of the Aa index is stronger in the antiparallel solar polar magnetic field period than in the parallel period. Additionally, we suggest the favorable IMF condition of the semiannual variation in geomagnetic activity. The orientation of IMF toward the Sun in spring and away from the Sun in fall mainly contributes to the semiannual variation of geomagnetic activity in both antiparallel and parallel solar minimum years.

  6. Polarization dependent asymmetric magneto-resistance features in nanocrystalline diamond films

    International Nuclear Information System (INIS)

    Bhattacharyya, Somnath; Churochkin, Dmitry

    2014-01-01

    Polar angle-dependence of magneto-resistance (AMR) in heavily nitrogen-incorporated ultra-nanocrystalline diamond (UNCD) films is recorded by applying high magnetic fields, which shows strong anisotropic features at low temperatures. The temperature-dependence of MR and AMR can reveal transport in the weak-localization regime, which is explained by using a superlattice model for arbitrary values of disorder and angles. While a propagative Fermi surface model explains the negative MR features for low degree of disorder the azimuthal angle-dependent MR shows field dependent anisotropy due to the aligned conducting channels on the layers normal to film growth direction. The analysis of MR and AMR can extract the temperature dependence of dephasing time with respect to the elastic scattering time which not only establishes quasi-two dimensional features in this system but also suggests a potential application in monitoring the performance of UNCD based quantum devices.

  7. Measuring polarization dependent dispersion of non-polarizing beam splitter cubes with spectrally resolved white light interferometry

    Science.gov (United States)

    Csonti, K.; Hanyecz, V.; Mészáros, G.; Kovács, A. P.

    2017-06-01

    In this work we have measured the group-delay dispersion of an empty Michelson interferometer for s- and p-polarized light beams applying two different non-polarizing beam splitter cubes. The interference pattern appearing at the output of the interferometer was resolved with two different spectrometers. It was found that the group-delay dispersion of the empty interferometer depended on the polarization directions in case of both beam splitter cubes. The results were checked by inserting a glass plate in the sample arm of the interferometer and similar difference was obtained for the two polarization directions. These results show that to reach high precision, linearly polarized white light beam should be used and the residual dispersion of the empty interferometer should be measured at both polarization directions.

  8. Polarization-dependent single-beam laser-induced grating-like effects on titanium films

    International Nuclear Information System (INIS)

    Camacho-Lopez, Santiago; Evans, Rodger; Escobar-Alarcon, Luis; Camacho-Lopez, Miguel A.; Camacho-Lopez, Marco A.

    2008-01-01

    In this paper we present results on polarization-dependent laser-induced effects on titanium (Ti) thin films. We irradiated the titanium films, in ambient air, using a nanosecond Nd:YAG laser (532 nm, 9 ns pulse duration, 10 Hz). Using a series of pulses of fluence well below the ablation threshold, it was possible to form grating-like structures, whose grooves run parallel to the linear polarization of the incident beam. No grating-like structures were obtained when circularly polarized light was used. Our results revealed the remarkable formation of tiny (100 nm and even smaller diameter) craters, which self-arrange quasi-periodically along the ridges (never on the valleys) of the grating-like structure. Optical and scanning electron microscopy were used to study the laser-induced changes on the surface of the titanium films. Micro-Raman spectroscopy was used to analyze the irradiated areas on the titanium films. The Raman analysis demonstrated that the grooves in the grating-like structure, build up from the laser-induced oxidation of titanium. This is the first time, to the best of our knowledge, that periodic surface structures are reported to be induced below the ablation threshold regime, with the grooves made of crystalline metal oxide, in this case TiO 2 in the well-known Rutile phase. The laser irradiated areas on the film acquired selective (upon recording polarization) holographic reflectance

  9. Polarization-dependent single-beam laser-induced grating-like effects on titanium films

    Energy Technology Data Exchange (ETDEWEB)

    Camacho-Lopez, Santiago [Departamento de Optica, Centro de Investigacion Cientifica y de Educacion Superior de Ensenada, Km 107 Carretera Tijuana-Ensenada, Ensenada, Baja California 22860 (Mexico)], E-mail: camachol@cicese.mx; Evans, Rodger [Departamento de Optica, Centro de Investigacion Cientifica y de Educacion Superior de Ensenada, Km 107 Carretera Tijuana-Ensenada, Ensenada, Baja California 22860 (Mexico); Escobar-Alarcon, Luis [Departamento de Fisica, Instituto Nacional de Investigaciones Nucleares, Apdo. Postal 18-1027, Mexico DF 11801 (Mexico); Camacho-Lopez, Miguel A. [Facultad de Medicina, Universidad Autonoma del Estado de Mexico, Paseo Tollocan s/n, esq. Jesus Carranza, Toluca, Estado de Mexico 50120 (Mexico); Camacho-Lopez, Marco A. [Facultad de Quimica, Universidad Autonoma del Estado de Mexico, Tollocan s/n, esq. Paseo Colon, Toluca, Estado de Mexico, 50110 (Mexico)

    2008-12-30

    In this paper we present results on polarization-dependent laser-induced effects on titanium (Ti) thin films. We irradiated the titanium films, in ambient air, using a nanosecond Nd:YAG laser (532 nm, 9 ns pulse duration, 10 Hz). Using a series of pulses of fluence well below the ablation threshold, it was possible to form grating-like structures, whose grooves run parallel to the linear polarization of the incident beam. No grating-like structures were obtained when circularly polarized light was used. Our results revealed the remarkable formation of tiny (100 nm and even smaller diameter) craters, which self-arrange quasi-periodically along the ridges (never on the valleys) of the grating-like structure. Optical and scanning electron microscopy were used to study the laser-induced changes on the surface of the titanium films. Micro-Raman spectroscopy was used to analyze the irradiated areas on the titanium films. The Raman analysis demonstrated that the grooves in the grating-like structure, build up from the laser-induced oxidation of titanium. This is the first time, to the best of our knowledge, that periodic surface structures are reported to be induced below the ablation threshold regime, with the grooves made of crystalline metal oxide, in this case TiO{sub 2} in the well-known Rutile phase. The laser irradiated areas on the film acquired selective (upon recording polarization) holographic reflectance.

  10. Polarization-dependent diffraction in all-dielectric, twisted-band structures

    Energy Technology Data Exchange (ETDEWEB)

    Kardaś, Tomasz M.; Jagodnicka, Anna; Wasylczyk, Piotr, E-mail: pwasylcz@fuw.edu.pl [Photonic Nanostructure Facility, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warszawa (Poland)

    2015-11-23

    We propose a concept for light polarization management: polarization-dependent diffraction in all-dielectric microstructures. Numerical simulations of light propagation show that with an appropriately configured array of twisted bands, such structures may exhibit zero birefringence and at the same time diffract two circular polarizations with different efficiencies. Non-birefringent structures as thin as 3 μm have a significant difference in diffraction efficiency for left- and right-hand circular polarizations. We identify the structural parameters of such twisted-band matrices for optimum performance as circular polarizers.

  11. Scale dependence and small-x behaviour of polarized parton distributions

    International Nuclear Information System (INIS)

    Ball, R.D.; Forte, S.; Ridolfi, G.

    1995-01-01

    We discuss perturbative evolution of the polarized structure function g 1 in the (x, Q 2 ) plane, with special regard to the small-x region. We determine g 1 in terms of polarized quark and gluon distributions using coefficient functions to order α s . At small x g 1 then displays substantial scale dependence, which necessarily implies a corresponding scale dependence in the large-x region. This scale dependence has significant consequences for the extraction of the first moment from the experimental data, reducing its value while increasing the error. Conversely, the scale dependence may be used to constrain the size of the polarized gluon distribution. ((orig.))

  12. Polarization Dependence Suppression of Optical Fiber Grating Sensor in a π-Shifted Sagnac Loop Interferometer

    Directory of Open Access Journals (Sweden)

    Jaebum Son

    2010-04-01

    Full Text Available In the sensing applications of optical fiber grating, it is necessary to reduce the transmission-type polarization dependence to isolate the sensing parameter. It is experimentally shown that the polarization-dependent spectrum of acousto-optic long-period fiber grating sensors can be suppressed in the transmission port of a π-shifted Sagnac loop interferometer. General expressions for the transmittance and reflectance are derived for transmission-type, reflection-type, and partially reflecting/transmitting-type polarization-dependent optical devices. The compensation of polarization dependence through the counter propagation in the Sagnac loop interferometer is quantitatively measured for a commercial in-line polarizer and an acousto-optic long-period fiber grating sensor.

  13. Polarization-Dependent Measurements of Molecular Super Rotors with Oriented Angular Momenta

    Science.gov (United States)

    Murray, Matthew J.; Toro, Carlos; Liu, Qingnan; Mullin, Amy S.

    2014-05-01

    Controlling molecular motion would enable manipulation of energy flow between molecules. Here we have used an optical centrifuge to investigate energy transfer between molecular super rotors with oriented angular momenta. The polarizable electron cloud of the molecules interacts with the electric field of linearly polarized light that angularly accelerates over the time of the optical pulse. This process drives molecules into high angular momentum states that are oriented with the optical field and have energies far from equilibrium. High resolution transient IR spectroscopy reveals the dynamics of collisional energy transfer for these super excited rotors. The results of this study leads to a more fundamental understanding of energy balance in non-equilibrium environments and the physical and chemical properties of gases in a new regime of energy states. Results will be presented for several super rotor species including carbon monoxide, carbon dioxide, and acetylene. Polarization-dependent measurements reveal the extent to which the super rotors maintain spatial orientation of high angular momentum states.

  14. In vivo polarization dependant Second and Third harmonic generation imaging of Caenorhabditis elegans pharyngeal muscles

    Science.gov (United States)

    Filippidis, G.; Troulinaki, K.; Fotakis, C.; Tavernarakis, N.

    2009-07-01

    In this study Second and Third harmonic generation (SHG-THG) imaging measurements were performed to the pharyngeal muscles of the nematode Caenorhabditis elegans, in vivo with linearly polarized laser beam. Complementary information about the anatomy of the pharynx and the morphology of the anterior part of the worm were extracted. THG signals proved to have no dependence on incident light polarization, while SHG images are highly sensitive to the changes of the incident linearly polarized light.

  15. Polarized bow shocks reveal features of the winds and environments of massive stars

    Science.gov (United States)

    Shrestha, Manisha

    2018-01-01

    Massive stars strongly affect their surroundings through their energetic stellar winds and deaths as supernovae. The bow shock structures created by fast-moving massive stars contain important information about the winds and ultimate fates of these stars as well as their local interstellar medium (ISM). Since bow shocks are aspherical, the light scattered in the dense shock material becomes polarized. Analyzing this polarization reveals details of the bow shock geometry as well as the composition, velocity, density, and albedo of the scattering material. With these quantities, we can constrain the properties of the stellar wind and thus the evolutionary state of the star, as well as the dust composition of the local ISM.In my dissertation research, I use a Monte Carlo radiative transfer code that I optimized to simulate the polarization signatures produced by both resolved and unresolved stellar wind bow shocks (SWBS) illuminated by a central star and by shock emission. I derive bow shock shapes and densities from published analytical calculations and smooth particle hydrodynamic (SPH) models. In the case of the analytical SWBS and electron scattering, I find that higher optical depths produce higher polarization and position angle rotations at specific viewing angles compared to theoretical predictions for low optical depths. This is due to the geometrical properties of the bow shock combined with multiple scattering effects. For dust scattering, the polarization signature is strongly affected by wavelength, dust grain properties, and viewing angle. The behavior of the polarization as a function of wavelength in these cases can distinguish among different dust models for the local ISM. In the case of SPH density structures, I investigate how the polarization changes as a function of the evolutionary phase of the SWBS. My dissertation compares these simulations with polarization data from Betelgeuse and other massive stars with bow shocks. I discuss the

  16. Polarization Dependence of Surface Enhanced Raman Scattering on a Single Dielectric Nanowire

    Directory of Open Access Journals (Sweden)

    Hua Qi

    2012-01-01

    Full Text Available Our measurements of surface enhanced Raman scattering (SERS on Ga2O3 dielectric nanowires (NWs core/silver composites indicate that the SERS enhancement is highly dependent on the polarization direction of the incident laser light. The polarization dependence of the SERS signal with respect to the direction of a single NW was studied by changing the incident light angle. Further investigations demonstrate that the SERS intensity is not only dependent on the direction and wavelength of the incident light, but also on the species of the SERS active molecule. The largest signals were observed on an NW when the incident 514.5 nm light was polarized perpendicular to the length of the NW, while the opposite phenomenon was observed at the wavelength of 785 nm. Our theoretical simulations of the polarization dependence at 514.5 nm and 785 nm are in good agreement with the experimental results.

  17. Flatland Position-Dependent-Mass: Polar Coordinates, Separability and Exact Solvability

    Science.gov (United States)

    Mazharimousavi, S. Habib; Mustafa, Omar

    2010-10-01

    The kinetic energy operator with position-dependent-mass in plane polar coordinates is obtained. The separability of the corresponding Schrödinger equation is discussed. A hypothetical toy model is reported and two exactly solvable examples are studied.

  18. Wavelength Dependence of the Polarization Singularities in a Two-Mode Optical Fiber

    Directory of Open Access Journals (Sweden)

    V. V. G. Krishna Inavalli

    2012-01-01

    Full Text Available We present here an experimental demonstration of the wavelength dependence of the polarization singularities due to linear combination of the vector modes excited directly in a two-mode optical fiber. The coherent superposition of the vector modes excited by linearly polarized Gaussian beam as offset skew rays propagated in a helical path inside the fiber results in the generation of phase singular beams with edge dislocation in the fiber output. The polarization character of these beams is found to change dramatically with wavelength—from left-handed elliptically polarized edge dislocation to right-handed elliptically polarized edge-dislocation through disclinations. The measured behaviour is understood as being due to intermodal dispersion of the polarization corrections to the propagating vector modes, as the wavelength of the input beam is scanned.

  19. Dependence of extinction cross-section on incident polarization state and particle orientation

    International Nuclear Information System (INIS)

    Yang Ping; Wendisch, Manfred; Bi Lei; Kattawar, George; Mishchenko, Michael; Hu, Yongxiang

    2011-01-01

    This note reports on the effects of the polarization state of an incident quasi-monochromatic parallel beam of radiation and the orientation of a hexagonal ice particle with respect to the incident direction on the extinction process. When the incident beam is aligned with the six-fold rotational symmetry axis, the extinction is independent of the polarization state of the incident light. For other orientations, the extinction cross-section for linearly polarized light can be either larger or smaller than its counterpart for an unpolarized incident beam. Therefore, the attenuation of a quasi-monochromatic radiation beam by an ice cloud depends on the polarization state of the beam if ice crystals within the cloud are not randomly oriented. Furthermore, a case study of the extinction of light by a quartz particle is also presented to illustrate the dependence of the extinction cross-section on the polarization state of the incident light.

  20. Polarization-state-dependent attenuation and amplification in a columnar thin film

    Science.gov (United States)

    Mackay, Tom G.; Lakhtakia, Akhlesh

    2017-12-01

    We numerically investigated the plane-wave reflection-transmission characteristics of a columnar thin film (CTF) whose columns are made from a dissipative material but whose void regions are filled with an active material. By computing the reflectances and transmittances, we found that the CTF can simultaneously amplify s-polarized incident light and attenuate p-polarized incident light, or vice versa. This polarization-state-dependent attenuation and amplification phenomenon depends upon the angle of incidence and the thickness of the CTF.

  1. Polarization dependent nanostructuring of silicon with femtosecond vortex pulse

    Directory of Open Access Journals (Sweden)

    M. G. Rahimian

    2017-08-01

    Full Text Available We fabricated conical nanostructures on silicon with a tip dimension of ∼ 70 nm using a single twisted femtosecond light pulse carrying orbital angular momentum (ℓ=±1. The height of the nano-cone, encircled by a smooth rim, increased from ∼ 350 nm to ∼ 1 μm with the pulse energy and number of pulses, whereas the apex angle remained constant. The nano-cone height was independent of the helicity of the twisted light; however, it is reduced for linear polarization compared to circular at higher pulse energies. Fluid dynamics simulations show nano-cones formation when compressive forces arising from the radial inward motion of the molten material push it perpendicular to the surface and undergo re-solidification. Simultaneously, the radial outward motion of the molten material re-solidifies after reaching the cold boundary to form a rim. Overlapping of two irradiated spots conforms to the fluid dynamics model.

  2. Temperature dependence of the photoluminescence polarization of ordered III-V semiconductor alloys

    International Nuclear Information System (INIS)

    Prutskij, T.; Makarov, N.; Attolini, G.

    2016-01-01

    We studied the linear polarization of the photoluminescence (PL) emission of atomically ordered GaInAsP and GaInP alloys with different ordering parameters in the temperature range from 10 to 300 K. The epitaxial layers of these alloys were grown on GaAs and Ge (001) substrates by metal organic vapor phase epitaxy. The polarization of the PL emission propagating along different crystallographic axes depends on the value of biaxial strain in the layer and changes with temperature. We calculated the PL polarization patterns for different propagation directions as a function of biaxial strain using an existing model developed for ternary atomically ordered III-V alloys. Comparing the calculated PL polarization patterns with those obtained experimentally, we separated the variation of the PL polarization due to change of biaxial strain with temperature.

  3. A Polarization-Dependent Frequency-Selective Metamaterial Absorber with Multiple Absorption Peaks

    Directory of Open Access Journals (Sweden)

    Guangsheng Deng

    2017-06-01

    Full Text Available A polarization-dependent, frequency-selective metamaterial (MM absorber based on a single-layer patterned resonant structure intended for F frequency band is proposed. The design, fabrication, and measurement for the proposed absorber are presented. The absorber’s absorption properties at resonant frequencies have unique characteristics of a single-band, dual-band, or triple-band absorption for different polarization of the incident wave. The calculated surface current distributions and power loss distribution provide further understanding of physical mechanism of resonance absorption. Moreover, a high absorption for a wide range of TE-polarized oblique incidence was achieved. Hence, the MM structure realized on a highly flexible polyimide film, makingthe absorber suitable for conformal geometry applications. The proposed absorber has great potential in the development of polarization detectors and polarizers.

  4. Polarization and collision velocity dependence of associative ionization in cold Na (3p)-Na(3p) collisions

    NARCIS (Netherlands)

    Meijer, H.A.J.

    1990-01-01

    We studied the polarization dependence of the associative ionization (AI) process Na(3p) + Na(3p) → Na2+ at collision velocities between 100 and 700 m/s (5 and 200 K), using linearly and circularly polarized light for the excitation. We found that the polarization dependence varies strongly in the

  5. Magnetization-dependent viscosity in brute-force-polarized liquid 3He

    DEFF Research Database (Denmark)

    Vermeulen, G.A.; Schuhl, A.; Joffrin, J.

    1988-01-01

    A new method to measure the magnetization dependence of the viscosity in polarized liquid He3 is presented. The magnetization is obtained by "brute-force polarization" at 45 mK in magnetic fields up to 11 T; it is subsequently destroyed by saturation of the NMR signal. Our result, a relative...... increase of the viscosity of (31.5)×10-3 at 3.9% polarization and a pressure of 30 bars, disagrees with a prediction based on the "nearly metamagnetic" model....

  6. Spin dependent fragmentation functions for heavy flavor baryons and single heavy hyperon polarization

    CERN Document Server

    Goldstein, G R

    2001-01-01

    Spin dependent fragmentation functions for heavy flavor quarks to fragment into heavy baryons are calculated in a quark-diquark model. The production of intermediate spin 1/2 and 3/2 excited states is explicity included. $\\Lambda_b$ , $\\Lambda_c$ and $\\Xi_c$ production rate and polarization at LEP energies are calculated and, where possible, compared with experiment. A different approach, also relying on a heavy quark-diquark model, is proposed for the small momentum transfer inclusive production of polarized heavy flavor hyperons. The predicted $\\Lambda_c$ polarization is roughly in agreement with experiment.

  7. Anisotropic optical response of optically opaque elastomers with conductive fillers as revealed by terahertz polarization spectroscopy

    Science.gov (United States)

    Okano, Makoto; Watanabe, Shinichi

    2016-01-01

    Elastomers are one of the most important materials in modern society because of the inherent viscoelastic properties due to their cross-linked polymer chains. Their vibration-absorbing and adhesive properties are especially useful and thus utilized in various applications, for example, tires in automobiles and bicycles, seismic dampers in buildings, and seals in a space shuttle. Thus, the nondestructive inspection of their internal states such as the internal deformation is essential in safety. Generally, industrial elastomers include various kinds of additives, such as carbon blacks for reinforcing them. The additives make most of them opaque in a wide spectral range from visible to mid-infrared, resulting in that the nondestructive inspection of the internal deformation is quite difficult. Here, we demonstrate transmission terahertz polarization spectroscopy as a powerful technique for investigating the internal optical anisotropy in optically opaque elastomers with conductive additives, which are transparent only in the terahertz frequency region. The internal deformation can be probed through the polarization changes inside the material due to the anisotropic dielectric response of the conductive additives. Our study about the polarization-dependent terahertz response of elastomers with conductive additives provides novel knowledge for in situ, nondestructive evaluation of their internal deformation. PMID:28008942

  8. Polarization dependent micro-structuring of silicon with a femtosecond laser

    International Nuclear Information System (INIS)

    Al-Khazraji, H.; Bhardwaj, V.R.

    2015-01-01

    Highlights: • We demonstrate polarization sensitive rim formation around an ablation crater in silicon. • In n-type and intrinsic silicon, the rim height asymmetry is along laser polarization. • In p-type silicon, the rim height asymmetry is perpendicular to laser polarization. • Field enhancement during light-plasma interaction causes asymmetric energy deposition. • Motion of the molten material from the ablation center causes asymmetric rim formation. - Abstract: We experimentally demonstrate formation of a sub-micron rim around femtosecond laser ablated crater on silicon whose height and width were sensitive to laser polarization. Except for circularly polarized light we show that the rim height and width were asymmetric – larger along the direction of the laser polarization for n-type and intrinsic silicon, while in p-type silicon the asymmetry was perpendicular. Polarization dependent rim formation is attributed to the transient light–plasma interaction that gives rise to local-field enhancements resulting in an asymmetric electron density and energy deposition. Picoseconds later when the electron energy is transferred to the lattice, the asymmetry is retained in the temperature distribution within the interaction region. The temperature distribution eventually leads to non-symmetric radial outward fluid motion of a thin layer of molten material from the centre of the ablation crater that subsequently re-solidifies on a nanosecond timescale.

  9. Frequency-Dependent Solvent Impedance and Colloid Microelectrophoresis Measurements in Partially Polar Solvents.

    Science.gov (United States)

    Hayden, Edward; Aljabal, Zena; Yethiraj, Anand

    2017-05-16

    We carry out frequency-dependent solvent impedance measurements and alternating current (ac) colloid microelectrophoresis experiments in partially polar solvents in the low-frequency regime (0.25 Hz ≤ f ≤ 10 Hz). Solvent electrode polarization effects are quantified first in partially polar solvent mixtures containing bromocyclohexane (CHB). We find that the polarization capacitance from electrode polarization exhibits a clear power law behavior C p = C p0 f -m with power law exponent m = 0.25 ± 0.04. Once we account for electrode polarization effects, we are able to obtain quantitative mobilities in the low-frequency regime from our ac microelectrophoresis measurements; for these measurements, we use poly(methyl methacrylate colloids that are gravitationally confined to a plane while suspended in a low-polar solvent mixture of cis-trans decahydronapthalene and CHB. We find that the dimensionless electrophoretic mobility is constant, consistent with expectations for frequencies below the ion-diffusion frequency, and has a value E = 1.6 ± 0.4.

  10. On the temperature dependence of the spontaneous polarization of lithium niobate and lithium tantalate

    International Nuclear Information System (INIS)

    Ismailzade, I.G.; Ismailov, R.M.

    1980-01-01

    The temperature dependence of spontaneous polarization Psub(s)(T) of LiNbO 3 and LiTaO 3 ferroelectrics is studied by the precision X-ray diffraction method up to the Curie temperature - 1140 and 650 deg C, respectively. It is shown that for LiTaO 3 a deviation from continuous variation of spontaneous polarization with temperature is observed, expressing itself more disticntly at temperatures corresponding to intermediate ferroelectric phase transitions. The Psub(s)(T) obtained has whown that up to 210 deg C the value of LiNbO 3 spontaneous polarization practically remains constant and it decreases with the temperature increase, and near the phase transition temperature (transition of the first order) Psub(s)(T) is 40% of spontaneous polarization at room temperature. As in the case of lithium tantalate stepwise changes of Psub(s)(T) for LiNbO 3 are observed

  11. Polarization-dependent interfacial coupling modulation of ferroelectric photovoltaic effect in PZT-ZnO heterostructures

    Science.gov (United States)

    Pan, Dan-Feng; Bi, Gui-Feng; Chen, Guang-Yi; Zhang, Hao; Liu, Jun-Ming; Wang, Guang-Hou; Wan, Jian-Guo

    2016-03-01

    Recently, ferroelectric perovskite oxides have drawn much attention due to potential applications in the field of solar energy conversion. However, the power conversion efficiency of ferroelectric photovoltaic effect currently reported is far below the expectable value. One of the crucial problems lies in the two back-to-back Schottky barriers, which are formed at the ferroelectric-electrode interfaces and blocking most of photo-generated carriers to reach the outside circuit. Herein, we develop a new approach to enhance the ferroelectric photovoltaic effect by introducing the polarization-dependent interfacial coupling effect. Through inserting a semiconductor ZnO layer with spontaneous polarization into the ferroelectric ITO/PZT/Au film, a p-n junction with strong polarization-dependent interfacial coupling effect is formed. The power conversion efficiency of the heterostructure is improved by nearly two orders of magnitude and the polarization modulation ratio is increased about four times. It is demonstrated that the polarization-dependent interfacial coupling effect can give rise to a great change in band structure of the heterostructure, not only producing an aligned internal electric field but also tuning both depletion layer width and potential barrier height at PZT-ZnO interface. This work provides an efficient way in developing highly efficient ferroelectric-based solar cells and novel optoelectronic memory devices.

  12. Polarization dependence of two-photon transition intensities in rare-earth doped crystals

    Energy Technology Data Exchange (ETDEWEB)

    Le Nguyen, An-Dien [Univ. of California, Berkeley, CA (United States)

    1996-05-01

    A polarization dependence technique has been developed as a tool to investigate phonon scattering (PS), electronic Raman scattering (ERS), and two-photon absorption (TPA) transition intensities in vanadate and phosphate crystals. A general theory for the polarization dependence (PD) of two-photon transition intensities has been given. Expressions for the polarization dependent behavior of two-photon transition intensities have been tabulated for the 32 crystallographic point groups. When the wavefunctions for the initial and final states of a rare-earth doped in crystals are known, explicit PD expressions with no unknown parameters can be obtained. A spectroscopic method for measuring and interpreting phonon and ERS intensities has been developed to study PrVO4, NdVO4, ErVO4, and TmVO4 crystals. Relative phonon intensities with the polarization of the incident and scattered light arbitrarily varied were accurately predicted and subsequently used for alignment and calibration in ERS measurements in these systems for the first time. Since ERS and PS intensities generally follow different polarization curves as a function of polar angles, the two can be uniquely identified by comparing their respective polarization behavior. The most crucial application of the technique in ERS spectroscopy is the establishment of a stringent test for the Axe theory. For the first time, the F1/F2 ratio extracted from the experimental fits of the ERS intensities were compared with those predicted by theories which include both the second- and third-order contributions. Relatively good agreement between the fitted values of F1/F2 and the predicted values using the second-order theory has been found.

  13. High-Efficiency Dielectric Metasurfaces for Polarization-Dependent Terahertz Wavefront Manipulation

    KAUST Repository

    Zhang, Huifang

    2017-11-30

    Recently, metasurfaces made up of dielectric structures have drawn enormous attentions in the optical and infrared regimes due to their high efficiency and designing freedom in manipulating light propagation. Such advantages can also be introduced to terahertz frequencies where efficient functional devices are still lacking. Here, polarization-dependent all-silicon terahertz dielectric metasurfaces are proposed and experimentally demonstrated. The metasurfaces are composed of anisotropic rectangular-shaped silicon pillars on silicon substrate. Each metasurface holds dual different functions depending on the incident polarizations. Furthermore, to suppress the reflection loss and multireflection effect in practical applications, a high-performance polarization-independent antireflection silicon pillar array is also proposed, which can be patterned at the other side of the silicon substrate. Such all-silicon dielectric metasurfaces are easy to fabricate and can be very promising in developing next-generation efficient, compact, and low-cost terahertz functional devices.

  14. Polarization-dependent transverse-stress sensing based on photonic crystal fiber with gold-coated air-holes

    Science.gov (United States)

    Liu, Hai; Zhu, Chenghao; Wang, Yan; Tan, Ce; Li, Hongwei; Cheng, Deqiang

    2017-05-01

    A transverse-stress sensor with polarization filtering function based on a specially designed photonic crystal fiber (PCF) is proposed. Four ultralarge side-holes are introduced into the cladding layer, and two of them are gold-coated to enhance the stress sensitivity. The finite element method is applied to study the polarization-dependent wavelength-selective sensing characteristics at the optical communication wavelength. Results reveal that the sensor can achieve a high sensitivity in either direction that can be divided into an x-direction component and a y-direction component. Combining the advantages of side-hole structure and surface plasmon resonance technology, the proposed sensor is believed to be an excellent candidate for the transverse-stress measurement.

  15. Development of an in situ polarization-dependent total-reflection fluorescence XAFS measurement system.

    Science.gov (United States)

    Chun, W J; Tanizawa, Y; Shido, T; Iwasawa, Y; Nomura, M; Asakura, K

    2001-03-01

    An in situ polarization-dependent total-reflection fluorescence X-ray absorption fine structure (PTRF-XAFS) spectroscopy system has been developed, which enables PTRF-XAFS experiments to be performed in three different orientations at various temperatures (273-600 K) and pressures (10(-10) approximately 760 torr). The system consists of a measurement chamber and a preparation chamber. The measurement chamber has a high-precision six-axis goniometer and a multielement solid-state detector. Using a transfer chamber, also operated under ultra-high-vacuum conditions, the sample can be transferred to the measurement chamber from the preparation chamber, which possesses low-energy electron diffraction, Auger electron spectroscopy and X-ray photoelectron spectroscopy facilities, as well as a sputtering gun and an annealing system. The in situ PTRF-EXAFS for Cu species on TiO2 (110) has been measured in three different orientations, revealing anisotropic growth of Cu under the influence of the TiO2 (110) surface.

  16. arXiv Black hole superradiance and polarization-dependent bending of light

    CERN Document Server

    Plascencia, Alexis D.

    2017-01-01

    An inhomogeneous pseudo-scalar field configuration behaves like an optically active medium. Consequently, if a light ray passes through an axion cloud surrounding a Kerr black hole, it may experience a polarization-dependent bending. We explore the size and relevance of such effect considering both the QCD axion and a generic axion-like particle.

  17. Intensity-dependent change in polarization state of light in normal ...

    Indian Academy of Sciences (India)

    Intensity-dependent change in polarization state of light in normal incidence on an isotropic nonlinear Kerr medium. Hari Prakash Devendra K ... Devendra K Singh2. Department of Physics, University of Allahabad, Allahabad 211 002, India; Department of Physics, Udai Pratap Autonomous College, Varanasi 221 002, India ...

  18. Flatland Position-Dependent-Mass: Polar Coordinates, Separability and Exact Solvability

    Directory of Open Access Journals (Sweden)

    Omar Mustafa

    2010-10-01

    Full Text Available The kinetic energy operator with position-dependent-mass in plane polar coordinates is obtained. The separability of the corresponding Schrödinger equation is discussed. A hypothetical toy model is reported and two exactly solvable examples are studied.

  19. Revealing the large extra dimension effective interaction at an e+e- collider with polarized beams

    International Nuclear Information System (INIS)

    Pankov, A. A.; Tsytrinov, A. V.; Paver, N.

    2007-01-01

    Several types of new physics scenarios are represented by contactlike effective interactions. An example is the exchange of nonstandard quanta of very large mass scales, beyond the kinematical limit for direct production set by the available collider energy. This kind of interactions can be revealed only through deviations of observables from the standard model predictions. If such deviations were observed, the relevant source should be identified among the possible models that could explain them. Here, we assess the expected 'identification reach' on the ADD model of gravity in large compactified extra dimensions, against the compositeness-inspired four-fermion contact interaction. As basic observables we take the differential cross sections for fermion-pair production at a 0.5-1 TeV electron-positron linear collider with both beams longitudinally polarized. For the four-fermion contact interaction, we assume a general linear combination of the individual models with definite chiralities, with arbitrary coupling constants. In this sense, the estimated identification reach on the ADD model can be considered as 'model independent'. In the analysis, we give estimates also for the expected ''discovery reaches'' on the various scenarios. We emphasize the substantial role of beams polarization in enhancing the sensitivity to the contactlike interactions under consideration

  20. Polarization-dependent responses of fluorescent indicators partitioned into myelinated axons

    Science.gov (United States)

    Micu, Ileana; Brideau, Craig; Stys, Peter K.

    2012-02-01

    Myelination, i.e. the wrapping of axons in multiple layers of lipid-rich membrane, is a unique phenomenon in the nervous systems of both vertebrates and invertebrates, that greatly increases the speed and efficiency of signal transmission. In turn, disruption of axo-myelinic integrity underlies disability in numerous clinical disorders. The dependence of myelin physiology on nanometric organization of its lamellae makes it difficult to accurately study this structure in the living state. We expected that fluorescent probes might become highly oriented when partitioned into the myelin sheath, and in turn, this anisotropy could be interrogated by controlling the polarization state of the exciting laser field used for 2-photon excited fluorescence (TPEF). Live ex vivo myelinated rodent axons were labeled with a series of lipohilic and hydrophilic fluorescenct probes, and TPEF images acquired while laser polarization was varied at the sample over a broad range of ellipticities and orientations of the major angle [see Brideau, Micu & Stys, abstract this meeting]. We found that most probes exhibited strong dependence on both the major angle of polarization, and perhaps more surprisingly, on ellipticity as well. Lipophilic vs. hydrophilic probes exhibited distinctly different behavior. We propose that polarization-dependent TPEF microscopy represents a powerful tool for probing the nanostructural architecture of both myelin and axonal cytoskeleton in a domain far below the resolution limit of visible light microscopy. By selecting probes with different sizes and physicochemical properties, distinct aspects of cellular nanoarchitecture can be accurately interrogated in real-time in living tissue.

  1. Saturn's north polar cyclone and hexagon at depth revealed by Cassini/VIMS

    Science.gov (United States)

    Baines, K.H.; Momary, T.W.; Fletcher, L.N.; Showman, A.P.; Roos-Serote, M.; Brown, R.H.; Buratti, B.J.; Clark, R.N.; Nicholson, P.D.

    2009-01-01

    A high-speed cyclonic vortex centered on the north pole of Saturn has been revealed by the visual-infrared mapping spectrometer (VIMS) onboard the Cassini-Huygens Orbiter, thus showing that the tropospheres of both poles of Saturn are occupied by cyclonic vortices with winds exceeding 135 m/s. High-spatial-resolution (~200 km per pixel) images acquired predominantly under night-time conditions during Saturn's polar winter-using a thermal wavelength of 5.1 ??m to obtain time-lapsed imagery of discrete, deep-seated (>2.1-bar) cloud features viewed in silhouette against Saturn's internally generated thermal glow-show a classic cyclonic structure, with prograde winds exceeding 135 m/s at its maximum near 88.3?? (planetocentric) latitude, and decreasing to Saturn indicates that cyclonic circulation may be an important dynamical style in planets with significant atmospheres. ?? 2009 Elsevier Ltd. All rights reserved.

  2. Polarization Dependent Dynamics of CO2 Trapped in AN Optical Centrifuge

    Science.gov (United States)

    Toro, Carlos; Echebiri, Geraldine; Liu, Qingnan; Mullin, Amy S.

    2012-06-01

    An optical centrifuge (Yuan {et al}. {PNAS} 2011, 108, 6872) has been employed to prepare carbon dioxide molecules in very high rotational states (``hot'' rotors, J ˜220) in order to investigate how collisions relax ensembles of molecules with an overall angular momentum that is spatially oriented. We have performed polarization-dependent high resolution transient IR absorption measurements to study the spatial dependence of the relaxation dynamics. Our results show that the net angular momentum of the initially centrifuged molecules persists for at least 10 gas kinetic collisions and that the translational energy distributions are dependent on the probe orientation and polarization. These studies indicate that the centrifuged molecules tend to maintain the orientation of their initial angular momentum for the first set of collisions and that relatively large changes in J are involved in the first collisions.

  3. Laser damage resistance of RbTiOPO(4): evidence of polarization dependent anisotropy.

    Science.gov (United States)

    Wagner, F R; Hildenbrand, A; Natoli, J Y; Commandré, M; Théodore, F; Albrecht, H

    2007-10-17

    Nanosecond-laser induced damage of RbTiOPO(4) crystals (RTP) has been studied at 1064 nm as a function of propagation direction and polarization orientation. A significant difference in the Laser Induced Damage Threshold (LIDT) was observed for x-cut and y-cut crystals in Pockels cell configuration, where the light propagation direction is along the x and y axes of the crystal respectively. In Pockels cell configuration the polarization is oriented at 45? with respect to the z-axis of the crystal. Experiments with the polarization oriented parallel to the principal axes of the crystal pointed out the importance of the polarization direction for the LIDT whereas the propagation direction did not significantly influence the LIDT. Comparison of the experimental data with a simple model reveals the influence of frequency doubling on the LIDT in Pockels cell configuration. In the case of the y-cut Pockels cell, the generation of frequency doubled light causes an LIDT below the LIDT of x and z-polarized light at the fundamental wavelength.

  4. Crystal fields of porphyrins and phthalocyanines from polarization-dependent 2p-to-3d multiplets

    DEFF Research Database (Denmark)

    Johnson, Phillip S.; García Lastra, Juan Maria; Kennedy, Colton K.

    2014-01-01

    Polarization-dependent X-ray absorption spectroscopy is combined with density functional calculations and atomic multiplet calculations to determine the crystal field parameters 10Dq, Ds, and Dt of transition metal phthalocyanines and octaethylporphyrins (Mn, Fe, Co, Ni). The polarization depende...

  5. Quantum-well exciton dipolar interaction: Polarization-dependence and Z-LT splitting

    International Nuclear Information System (INIS)

    Nguyen Ba An.

    1996-12-01

    We calculate the exciton dipolar interaction in a semiconductor quantum well. The explicit polarization-dependence, i.e, the dependence on both the exciton dipole moment μ-vector and its inplane wavevector k-vector is derived. The obtained results for the three modes (L, T and Z modes) of the long-range part of the dipolar interaction satisfy the polarization sum rule for any parameters. In the long wavelength limit there is a Z-LT splitting which decreases as the well width increases reflecting a crossover from strict 2D to quasi-2D. A rough crossover from quasi-2D to 3D is also described. (author). 18 refs, 4 figs

  6. Improved geophysical excitations constrained by polar motion observations and GRACE/SLR time-dependent gravity

    Directory of Open Access Journals (Sweden)

    Wei Chen

    2017-11-01

    Full Text Available At seasonal and intraseasonal time scales, polar motions are mainly excited by angular momentum fluctuations due to mass redistributions and relative motions in the atmosphere, oceans, and continental water, snow, and ice, which are usually provided by various global atmospheric, oceanic, and hydrological models (some with meteorological observations assimilated; e.g., NCEP, ECCO, ECMWF, OMCT and LSDM etc.. Unfortunately, these model outputs are far from perfect and have notable discrepancies with respect to polar motion observations, due to non-uniform distributions of meteorological observatories, as well as theoretical approximations and non-global mass conservation in these models. In this study, the LDC (Least Difference Combination method is adopted to obtain some improved atmospheric, oceanic, and hydrological/crospheric angular momentum (AAM, OAM and HAM/CAM, respectively functions and excitation functions (termed as the LDCgsm solutions. Various GRACE (Gravity Recovery and Climate Experiment and SLR (Satellite Laser Ranging geopotential data are adopted to correct the non-global mass conservation problem, while polar motion data are used as general constraints. The LDCgsm solutions can reveal not only periodic fluctuations but also secular trends in AAM, OAM and HAM/CAM, and are in better agreement with polar motion observations, reducing the unexplained excitation to the level of about 5.5 mas (standard derivation value; about 1/5–1/4 of those corresponding to the original model outputs.

  7. Revealing Fundamental Interactions: the Role of Polarized Positrons and Electrons at the Linear Collider

    Energy Technology Data Exchange (ETDEWEB)

    Moortgat-Pick, G.; /CERN /Durham U., IPPP; Abe, T.; Alexander, G.; Ananthanarayan, B.; Babich, A.A.; Bharadwaj, V.; Barber, D.; Bartl, A.; Brachmann, A.; Chen, S.; Clarke,; Clendenin, J.E.; Dainton, J.; Desch, K.; Diehl, M.; Dobos, B.; Dorland, T.; Eberl, H.; Ellis, John R.; Flottman, K.; Frass, H.; /CERN /Durham U., IPPP /Colorado U. /Tel-Aviv

    2005-07-06

    The proposed International Linear Collider (ILC) is well-suited for discovering physics beyond the Standard Model and for precisely unraveling the structure of the underlying physics. The physics return can be maximized by the use of polarized beams. This report shows the paramount role of polarized beams and summarizes the benefits obtained from polarizing the positron beam, as well as the electron beam. The physics case for this option is illustrated explicitly by analyzing reference reactions in different physics scenarios. The results show that positron polarization, combined with the clean experimental environment provided by the linear collider, allows to improve strongly the potential of searches for new particles and the identification of their dynamics, which opens the road to resolve shortcomings of the Standard Model. The report also presents an overview of possible designs for polarizing both beams at the ILC, as well as for measuring their polarization.

  8. The Role of polarized positrons and electrons in revealing fundamental interactions at the linear collider

    Energy Technology Data Exchange (ETDEWEB)

    Moortgat-Pick, G.; /CERN /Durham U., IPPP; Abe, T.; Alexander, G.; Ananthanarayan, B.; Babich, A.A.; Bharadwaj, V.; Barber, D.; Bartl, A.; Brachmann, A.; Chen, S.; Clarke,; Clendenin, J.E.; Dainton, J.; Desch, K.; Diehl, M.; Dobos, B.; Dorland, T.; Eberl, H.; Ellis, John R.; Flottman, K.; Frass, H.; /CERN /Durham U., IPPP /Colorado U. /Tel-Aviv

    2005-07-01

    The proposed International Linear Collider (ILC) is well-suited for discovering physics beyond the Standard Model and for precisely unraveling the structure of the underlying physics. The physics return can be maximized by the use of polarized beams. This report shows the paramount role of polarized beams and summarizes the benefits obtained from polarizing the positron beam, as well as the electron beam. The physics case for this option is illustrated explicitly by analyzing reference reactions in different physics scenarios. The results show that positron polarization, combined with the clean experimental environment provided by the linear collider, allows to improve strongly the potential of searches for new particles and the identification of their dynamics, which opens the road to resolve shortcomings of the Standard Model. The report also presents an overview of possible designs for polarizing both beams at the ILC, as well as for measuring their polarization.

  9. Morphology-dependent space charge polarization and dielectric relaxation of CdO nanomorphotypes

    Directory of Open Access Journals (Sweden)

    Paulose Thomas

    2016-12-01

    Full Text Available A versatile approach signifying the morphology-dependent dielectric polarization and relaxation mechanisms of cadmium oxide (CdO nanosphere, nanoflakes and nanoparallelepiped morphotypes as a function of frequency and temperature is presented. Variation of dielectric property is observed due to the changes of space charge/interfacial polarization resulting from the variations of surface to volume ratio of nanomorphology. Accordingly, colossal dielectric constant value has been observed in CdO nanosphere having larger surface to volume ratio. The order of dielectric constant (dc values observed for the present nanomorphologies is: dc of sphere > dc of flakes > dc of parallelepiped resembles the order of surface to volume ratios of the present morphologies respectively. The experimental data of complex impedance values are numerically fitted using theoretical models which provide the information of role of grain resistance on dielectric polarization and Cole–Cole type mechanism of dielectric relaxation process. The activation energies for electron transport are found to be 0.087eV for spheres, 0.074eV for flakes and 0.067 for parallelepiped nanomorphotypes of CdO. The dielectric and impedance spectroscopic analysis of the present material opens up wide scope for morphology-dependent tuning of nanomaterials for electrical applications.

  10. Effect of Stabilization Heat Treatment on Time-Dependent Polarization Losses in Sintered Nd-Fe-B Permanent Magnets

    Directory of Open Access Journals (Sweden)

    Tuominen S.

    2013-01-01

    Full Text Available Some companies in the motor and generator industry utilizing sintered NdFeB magnets have adopted pre-ageing heat treatment in order to improve the stability of the magnets. The parameters of this stabilization heat treatment are based mainly on assumptions rather than on any published research results. In this work, the effects of pre-ageing treatment on the time-dependent polarization losses of two different types of commercial sintered NdFeB magnets were studied. The material showing the squarer J(H curve did not benefit from the pre-ageing treatment, since it seems to be stable under a certain critical temperature. In contrast, a stabilizing effect was observed in the material showing rounder J(H curve. After the stabilization heat treatment, the polarization of the magnets was found to be at lower level, but unchanged over a certain period of time. The length of this period depends on the temperature and the duration of the pre-ageing treatment. In addition, our analysis reveals that the stabilization heat treatment performed in an open circuit condition does not stabilize the magnet uniformly.

  11. How to measure a complete set of polarization-dependent differential cross sections in a scattering experiment with aligned reagents?

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Fengyan, E-mail: fengyanwang@fudan.edu.cn, E-mail: kliu@po.iams.sinica.edu.tw [Institute of Atomic and Molecular Sciences, Academia Sinica, P. O. Box 23-166, Taipei 10617, Taiwan (China); Department of Chemistry, Fudan University, Shanghai 200433 (China); Lin, Jui-San; Liu, Kopin, E-mail: fengyanwang@fudan.edu.cn, E-mail: kliu@po.iams.sinica.edu.tw [Institute of Atomic and Molecular Sciences, Academia Sinica, P. O. Box 23-166, Taipei 10617, Taiwan (China)

    2014-02-28

    Polarization-dependent differential cross section (PDDCS) is one of the three-vector correlations (k, k{sup ′}, j) in molecular collisions, which provides the most detailed insights into the steric requirements of chemical reactions, i.e., how the reactivity depends on the polarization of reagents. Only quite recently has such quantity been fully realized experimentally in the study of the reaction of the aligned CHD{sub 3}(v{sub 1} = 1, |jK〉 = |10〉) molecules with Cl({sup 2}P{sub 3/2}) atoms. Theoretically, PDDCS is a relatively new concept; experimental realization of the theoretical construct requires some careful considerations that are not readily available in the literature. Here, we present the “know-how” behind the full PDDCS measurements to fill the gaps and to provide a clear roadmap for future applications. To make the connection apparent between the methodology presented here and the stereodynamics revealed in previous reports, the same Cl + aligned CHD{sub 3} reaction is used for illustration.

  12. How to measure a complete set of polarization-dependent differential cross sections in a scattering experiment with aligned reagents?

    International Nuclear Information System (INIS)

    Wang, Fengyan; Lin, Jui-San; Liu, Kopin

    2014-01-01

    Polarization-dependent differential cross section (PDDCS) is one of the three-vector correlations (k, k ′ , j) in molecular collisions, which provides the most detailed insights into the steric requirements of chemical reactions, i.e., how the reactivity depends on the polarization of reagents. Only quite recently has such quantity been fully realized experimentally in the study of the reaction of the aligned CHD 3 (v 1 = 1, |jK〉 = |10〉) molecules with Cl( 2 P 3/2 ) atoms. Theoretically, PDDCS is a relatively new concept; experimental realization of the theoretical construct requires some careful considerations that are not readily available in the literature. Here, we present the “know-how” behind the full PDDCS measurements to fill the gaps and to provide a clear roadmap for future applications. To make the connection apparent between the methodology presented here and the stereodynamics revealed in previous reports, the same Cl + aligned CHD 3 reaction is used for illustration

  13. Polarization-dependent X-ray absorption spectroscopy of MnWO{sub 4}

    Energy Technology Data Exchange (ETDEWEB)

    Hollmann, Nils; Hu, Zhiwei; Tjeng, Liu Hao [II. Physikalisches Institut, Universitaet zu Koeln (Germany); Bohaty, Ladislav; Becker-Bohaty, Petra [Kristallographisches Institut, Universitaet zu Koeln (Germany); Tanaka, Arata [Department of Quantum Matter, Hiroshima University (Japan)

    2008-07-01

    Multiferroic materials which combine magnetism and ferroelectricity currently attract considerable attention. One of the recently discovered multiferroic materials is MnWO{sub 4} (Huebnerite). It belongs to the group of multiferroics where a spontaneous electric polarization is caused by a spiral magnetic structure with a spin rotation axis not coinciding with the propagation vector. To investigate the details of this astonishing combination of electronic and magnetic properties, we look at the electronic structure with the use of polarization-dependent X-ray absorption spectroscopy on single crystals of MnWO{sub 4}. The analysis of the experimental data on the L-edge of Mn is done by a configuration interaction calculation and is discussed.

  14. Anisotropies in cortical tension reveal the physical basis of polarizing cortical flows

    NARCIS (Netherlands)

    Mayer, M.; Depken, S.M.; Bois, J.S.; Julicher, M.; Grill, S.W.

    2010-01-01

    Asymmetric cell divisions are essential for the development of multicellular organisms. To proceed, they require an initially symmetric cell to polarize. In Caenorhabditis elegans zygotes, anteroposterior polarization is facilitated by a large-scale flow of the actomyosin cortex, which directs the

  15. Polarization-basis tracking scheme for quantum key distribution using revealed sifted key bits

    Science.gov (United States)

    Ding, Yu-Yang; Chen, Wei; Chen, Hua; Wang, Chao; li, Ya-Ping; Wang, Shuang; Yin, Zhen-Qiang; Guo, Guang-Can; Han, Zheng-Fu

    2017-03-01

    Calibration of the polarization basis between the transmitter and receiver is an important task in quantum key distribution (QKD). An effective polarization-basis tracking scheme will decrease the quantum bit error rate (QBER) and improve the efficiency of a polarization encoding QKD system. In this paper, we proposed a polarization-basis tracking scheme using only unveiled sifted key bits while performing error correction by legitimate users, rather than introducing additional reference light or interrupting the transmission of quantum signals. A polarization-encoding fiber BB84 QKD prototype was developed to examine the validity of this scheme. An average QBER of 2.32% and a standard derivation of 0.87% have been obtained during 24 hours of continuous operation.

  16. Nuclear genomic sequences reveal that polar bears are an old and distinct bear lineage.

    Science.gov (United States)

    Hailer, Frank; Kutschera, Verena E; Hallström, Björn M; Klassert, Denise; Fain, Steven R; Leonard, Jennifer A; Arnason, Ulfur; Janke, Axel

    2012-04-20

    Recent studies have shown that the polar bear matriline (mitochondrial DNA) evolved from a brown bear lineage since the late Pleistocene, potentially indicating rapid speciation and adaption to arctic conditions. Here, we present a high-resolution data set from multiple independent loci across the nuclear genomes of a broad sample of polar, brown, and black bears. Bayesian coalescent analyses place polar bears outside the brown bear clade and date the divergence much earlier, in the middle Pleistocene, about 600 (338 to 934) thousand years ago. This provides more time for polar bear evolution and confirms previous suggestions that polar bears carry introgressed brown bear mitochondrial DNA due to past hybridization. Our results highlight that multilocus genomic analyses are crucial for an accurate understanding of evolutionary history.

  17. Neurobiological signatures of alcohol dependence revealed by protein profiling.

    Directory of Open Access Journals (Sweden)

    Giorgio Gorini

    Full Text Available Alcohol abuse causes dramatic neuroadaptations in the brain, which contribute to tolerance, dependence, and behavioral modifications. Previous proteomic studies in human alcoholics and animal models have identified candidate alcoholism-related proteins. However, recent evidences suggest that alcohol dependence is caused by changes in co-regulation that are invisible to single protein-based analysis. Here, we analyze global proteomics data to integrate differential expression, co-expression networks, and gene annotations to unveil key neurobiological rearrangements associated with the transition to alcohol dependence modeled by a Chronic Intermittent Ethanol (CIE, two-bottle choice (2BC paradigm. We analyzed cerebral cortices (CTX and midbrains (MB from male C57BL/6J mice subjected to a CIE, 2BC paradigm, which induces heavy drinking and represents one of the best available animal models for alcohol dependence and relapse drinking. CIE induced significant changes in protein levels in dependent mice compared with their non-dependent controls. Multiple protein isoforms showed region-specific differential regulation as a result of post-translational modifications. Our integrative analysis identified modules of co-expressed proteins that were highly correlated with CIE treatment. We found that modules most related to the effects of CIE treatment coordinate molecular imbalances in endocytic- and energy-related pathways, with specific proteins involved, such as dynamin-1. The qRT-PCR experiments validated both differential and co-expression analyses, and the correspondence among our data and previous genomic and proteomic studies in humans and rodents substantiates our findings. The changes identified above may play a key role in the escalation of ethanol consumption associated with dependence. Our approach to alcohol addiction will advance knowledge of brain remodeling mechanisms and adaptive changes in response to drug abuse, contribute to

  18. Genetic dissection reveals two separate retinal substrates for polarization vision in Drosophila.

    Science.gov (United States)

    Wernet, Mathias F; Velez, Mariel M; Clark, Damon A; Baumann-Klausener, Franziska; Brown, Julian R; Klovstad, Martha; Labhart, Thomas; Clandinin, Thomas R

    2012-01-10

    Linearly polarized light originates from atmospheric scattering or surface reflections and is perceived by insects, spiders, cephalopods, crustaceans, and some vertebrates. Thus, the neural basis underlying how this fundamental quality of light is detected is of broad interest. Morphologically unique, polarization-sensitive ommatidia exist in the dorsal periphery of many insect retinas, forming the dorsal rim area (DRA). However, much less is known about the retinal substrates of behavioral responses to polarized reflections. Drosophila exhibits polarotactic behavior, spontaneously aligning with the e-vector of linearly polarized light, when stimuli are presented either dorsally or ventrally. By combining behavioral experiments with genetic dissection and ultrastructural analyses, we show that distinct photoreceptors mediate the two behaviors: inner photoreceptors R7+R8 of DRA ommatidia are necessary and sufficient for dorsal polarotaxis, whereas ventral responses are mediated by combinations of outer and inner photoreceptors, both of which manifest previously unknown features that render them polarization sensitive. Drosophila uses separate retinal pathways for the detection of linearly polarized light emanating from the sky or from shiny surfaces. This work establishes a behavioral paradigm that will enable genetic dissection of the circuits underlying polarization vision. Copyright © 2012 Elsevier Ltd. All rights reserved.

  19. Maxwell-Wagner polarization and frequency-dependent injection at aqueous electrical interfaces.

    Science.gov (United States)

    Desmond, Mitchell; Mavrogiannis, Nicholas; Gagnon, Zachary

    2012-11-02

    We demonstrate a new type of alternating current (ac) interfacial polarization and frequency-dependent fluid displacement phenomenon at a liquid-liquid electrical interface. Two fluid streams--one with a greater electrical conductivity and the other a greater dielectric constant--are made to flow side by side in a microfluidic channel. An ac electric field is applied perpendicular to the interface formed between the liquid lamellae, and fluid is observed to displace across the liquid-liquid interface. The direction and magnitude of this displacement is frequency dependent. At low ac frequency, below the interfacial inverse charge relaxation time, the high-conductivity fluid displaces into the high-dielectric stream. At high frequency the direction of liquid displacement reverses, and the high-dielectric stream injects into the high-conductivity stream. The interfacial crossover frequency where the liquid displacement direction reverses is dependent on differences in electrical properties between the two fluid streams, and is well explained by Maxwell-Wagner polarization mechanics.

  20. Revealing the Cosmic Web-dependent Halo Bias

    Science.gov (United States)

    Yang, Xiaohu; Zhang, Youcai; Lu, Tianhuan; Wang, Huiyuan; Shi, Feng; Tweed, Dylan; Li, Shijie; Luo, Wentao; Lu, Yi; Yang, Lei

    2017-10-01

    Halo bias is the one of the key ingredients of the halo models. It was shown at a given redshift to be only dependent, to the first order, on the halo mass. In this study, four types of cosmic web environments—clusters, filaments, sheets, and voids—are defined within a state-of-the-art high-resolution N-body simulation. Within these environments, we use both halo-dark matter cross correlation and halo-halo autocorrelation functions to probe the clustering properties of halos. The nature of the halo bias differs strongly between the four different cosmic web environments described here. With respect to the overall population, halos in clusters have significantly lower biases in the {10}11.0˜ {10}13.5 {h}-1 {M}⊙ mass range. In other environments, however, halos show extremely enhanced biases up to a factor 10 in voids for halos of mass ˜ {10}12.0 {h}-1 {M}⊙ . Such a strong cosmic web environment dependence in the halo bias may play an important role in future cosmological and galaxy formation studies. Within this cosmic web framework, the age dependency of halo bias is found to be only significant in clusters and filaments for relatively small halos ≲ {10}12.5 {h}-1 {M}⊙ .

  1. Measurements of polarization-dependent angle-resolved light scattering from individual microscopic samples using Fourier transform light scattering

    Science.gov (United States)

    Jung, JaeHwang; Kim, Jinhyung; Seo, Min-Kyo; Park, YongKeun

    2018-03-01

    We present a method to measure the vector-field light scattering of individual microscopic objects. The polarization-dependent optical field images are measured with quantitative phase imaging at the sample plane, and then numerically propagated to the far-field plane. This approach allows the two-dimensional polarization-dependent angle-resolved light scattered patterns from individual object to be obtained with high precision and sensitivity. Using this method, we present the measurements of the polarization-dependent light scattering of a liquid crystal droplet and individual silver nanowires over scattering angles of 50{\\deg}. In addition, the spectroscopic extension of the polarization-dependent angle-resolved light scattering is demonstrated using wavelength-scanning illumination.

  2. Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears

    DEFF Research Database (Denmark)

    Liu, Shiping; Lorenzen, Eline D.; Fumagalli, Matteo

    2014-01-01

    Polar bears are uniquely adapted to life in the High Arctic and have undergone drastic physiological changes in response to Arctic climates and a hyperlipid diet of primarily marine mammal prey. We analyzed 89 complete genomes of polar bear and brown bear using population genomic modeling and show...... that the species diverged only 479-343 thousand years BP. We find that genes on the polar bear lineage have been under stronger positive selection than in brown bears; nine of the top 16 genes under strong positive selection are associated with cardiomyopathy and vascular disease, implying important reorganization...... of the cardiovascular system. One of the genes showing the strongest evidence of selection, APOB, encodes the primary lipoprotein component of low-density lipoprotein (LDL); functional mutations in APOB may explain how polar bears are able to cope with life-long elevated LDL levels that are associated with high risk...

  3. Anatomical Reconstruction and Functional Imaging Reveal an Ordered Array of Skylight Polarization Detectors in Drosophila.

    Science.gov (United States)

    Weir, Peter T; Henze, Miriam J; Bleul, Christiane; Baumann-Klausener, Franziska; Labhart, Thomas; Dickinson, Michael H

    2016-05-11

    Many insects exploit skylight polarization as a compass cue for orientation and navigation. In the fruit fly, Drosophila melanogaster, photoreceptors R7 and R8 in the dorsal rim area (DRA) of the compound eye are specialized to detect the electric vector (e-vector) of linearly polarized light. These photoreceptors are arranged in stacked pairs with identical fields of view and spectral sensitivities, but mutually orthogonal microvillar orientations. As in larger flies, we found that the microvillar orientation of the distal photoreceptor R7 changes in a fan-like fashion along the DRA. This anatomical arrangement suggests that the DRA constitutes a detector for skylight polarization, in which different e-vectors maximally excite different positions in the array. To test our hypothesis, we measured responses to polarized light of varying e-vector angles in the terminals of R7/8 cells using genetically encoded calcium indicators. Our data confirm a progression of preferred e-vector angles from anterior to posterior in the DRA, and a strict orthogonality between the e-vector preferences of paired R7/8 cells. We observed decreased activity in photoreceptors in response to flashes of light polarized orthogonally to their preferred e-vector angle, suggesting reciprocal inhibition between photoreceptors in the same medullar column, which may serve to increase polarization contrast. Together, our results indicate that the polarization-vision system relies on a spatial map of preferred e-vector angles at the earliest stage of sensory processing. The fly's visual system is an influential model system for studying neural computation, and much is known about its anatomy, physiology, and development. The circuits underlying motion processing have received the most attention, but researchers are increasingly investigating other functions, such as color perception and object recognition. In this work, we investigate the early neural processing of a somewhat exotic sense, called

  4. Frequency Dependent Polarization Analysis of Ambient Seismic Noise Recorded at Broadband Seismometers

    Science.gov (United States)

    Koper, K.; Hawley, V.

    2010-12-01

    Analysis of ambient seismic noise is becoming increasingly relevant to modern seismology. Advances in computational speed and storage have made it feasible to analyze years and even decades of continuous seismic data in short amounts of time. Therefore, it is now possible to perform longitudinal studies of station performance in order to identify degradation or mis-installation of seismic equipment. Long-term noise analysis also provides insight into the evolution of the ocean wave climate, specifically whether the frequency and intensity of storms have changed as global temperatures have changed. Here we present a new approach to polarization analysis of seismic noise recorded by three-component seismometers. Essentially, eigen-decomposition of the 3-by-3 Hermitian spectral matrix associated with a sliding window of data is applied to yield various polarization attributes as a function of time and frequency. This in turn yields fundamental information about the composition of seismic noise, such as the extent to which it is polarized, its mode of propagation, and the direction from which it arrives at the seismometer. The polarization attributes can be viewed as function of time or binned over 2D frequency-time space to deduce regularities in the ambient noise that are unbiased by transient signals from earthquakes and explosions. We applied the algorithm to continuous data recorded in 2009 by the seismic station SLM, located in central North America. A rich variety of noise sources was observed. At low frequencies (3 Hz), Rayleigh-type energy was again dominant, in the form of Rg waves created by nearby cultural activities. Analysis of the time dependence of noise power shows that a frequency range of at least 0.02-1.0 Hz (much larger than the microseism band) is sensitive to annual, meteorologically induced sources of noise. We are currently applying our technique to selected seismometers from USArray and the University of Utah Seismic Network.

  5. Laboratory measurements for the wavelength dependence of the linear polarization with the PROGRA2 instruments

    Science.gov (United States)

    Renard, Jean-Baptiste; Hadamcik, Edith; Levasseur-Regourd, Anny-Chantal; Carrasco, Nathalie; Couté, Benoit; Duverger, Vincent; Guerrini, Vincent

    2017-04-01

    Clouds of solid particles are present in many regions of the Solar System (comets, interplanetary dust cloud, planetary atmospheres). These clouds can be remotely studied by the light they scatter. There is a need for a data base of the light scattered by a large variety of samples at different wavelengths to interpret such measurements. The PROGRA2 instruments are used for this purpose. The PROGRA2 instruments, PROGRA2-VIS and PROGRA2-IR, are imaging polarimeters with a rotating arm to change the phase angle (angle between directions of illumination and observation). They allow to retrieve the complete polarization phase function between 10° and 165°. The light sources are at around 550 and 650 nm for PROGRA2-VIS, and 1000 and 1500 nm for PROGRA2-IR. The detectors are cameras, with a spatial resolution between 20 and 40 micrometers per pixel (PROGRA2-IR uses now new high sensitivity cameras). Measurements are conducted in the laboratory by an air draught technique for grains smaller than about 20 micrometers (which can be included in porous aggregates), and during parabolic flights on-board the A300 ZeroG and now the A310 ZeroG for larger grains; these flights campaigns are funded by the French and European Space Agencies. Hundreds of scattering phase functions have been obtained since 20 years, for a large number of samples (sands, silicon carbide, basalt, volcanic ashes, lunar and Martian simulants, tholins, meteoritic material, black carbon, carbonaceous compounds, …); the main results are available at www.icare.univ-lille1.fr/progra2/. Several samples have been already studied by the two instruments, showing a large diversity of wavelength dependences, from close-to-zero dependence for yellow and ocher sand grains to high dependence for silicon carbide and anthracite grains. These variations should be related to the wavelength dependence of the real and imaginary parts of the refractive index of the particles. We present a summary of the main results of

  6. Fish introductions reveal the temperature dependence of species interactions.

    Science.gov (United States)

    Hein, Catherine L; Öhlund, Gunnar; Englund, Göran

    2014-01-22

    A major area of current research is to understand how climate change will impact species interactions and ultimately biodiversity. A variety of environmental conditions are rapidly changing owing to climate warming, and these conditions often affect both the strength and outcome of species interactions. We used fish distributions and replicated fish introductions to investigate environmental conditions influencing the coexistence of two fishes in Swedish lakes: brown trout (Salmo trutta) and pike (Esox lucius). A logistic regression model of brown trout and pike coexistence showed that these species coexist in large lakes (more than 4.5 km(2)), but not in small, warm lakes (annual air temperature more than 0.9-1.5°C). We then explored how climate change will alter coexistence by substituting climate scenarios for 2091-2100 into our model. The model predicts that brown trout will be extirpated from approximately half of the lakes where they presently coexist with pike and from nearly all 9100 lakes where pike are predicted to invade. Context dependency was critical for understanding pike-brown trout interactions, and, given the widespread occurrence of context-dependent species interactions, this aspect will probably be critical for accurately predicting climate impacts on biodiversity.

  7. Spin-polarization dependent carrier recombination dynamics and spin relaxation mechanism in asymmetrically doped (110) n-GaAs quantum wells

    Science.gov (United States)

    Teng, Lihua; Jiang, Tianran; Wang, Xia; Lai, Tianshu

    2018-05-01

    Carrier recombination and electron spin relaxation dynamics in asymmetric n-doped (110) GaAs/AlGaAs quantum wells are investigated with time-resolved pump-probe spectroscopy. The experiment results reveal that the measured carrier recombination time depends strongly on the polarization of pump pulse. With the same pump photon flux densities, the recombination time of spin-polarized carriers is always longer than that of the spin-balanced carriers except at low pump photon flux densities, this anomaly originates from the polarization-sensitive nonlinear absorption effect. Differing from the traditional views, in the low carrier density regime, the D'yakonov-Perel' (DP) mechanism can be more important than the Bir-Aronov-Pikus (BAP) mechanism, since the DP mechanism takes effect, the spin relaxation time in (110) GaAs QWs is shortened obviously via asymmetric doping.

  8. Competition and coexistence of polar and non-polar states in Sr1-x Ca x TiO3: an investigation using pressure dependent Raman spectroscopy

    Science.gov (United States)

    Tyagi, Shekhar; Sharma, Gaurav; Sathe, Vasant G.

    2018-03-01

    The competition and cooperation between ferroelectric and anti-ferro-distortion (AFD) instabilities are studied using pressure dependent Raman spectroscopy on polycrystalline powder samples of Sr1-x Ca x TiO3(x  =  0.0, 0.06, 0.25, 0.35). For x  =  0.0 composition, a broad polar mode is detected in the Raman spectra above 6 GPa, while for x  =  0.06 composition, the polar modes appear well above 9 GPa where the AFD modes showed strong suppression. In x  =  0.25 and 0.35 composition, the application of small pressure resulted in the appearance of strong AFD modes suppressing the polar modes. At elevated pressures, re-entrant polar modes are observed along with the broad AFD modes and some new peaks are also observed, signifying the lowering of local symmetry. The reappearance of polar modes is found to be related to pressure induced symmetry disorder at local level, suggesting its electronic origin. The re-entrant polar modes observed at higher pressure values are found to be significantly broad and asymmetric in nature, signifying the development of ferroelectric micro regions/nano domains coexisting with AFD. The lower symmetry at local length scale provides a conducive atmosphere for coexisting AFD and FE instabilities.

  9. Polarization-Dependent Photoinduced Bias-Stress Effect in Single-Crystal Organic Field-Effect Transistors.

    Science.gov (United States)

    Choi, Hyun Ho; Najafov, Hikmet; Kharlamov, Nikolai; Kuznetsov, Denis V; Didenko, Sergei I; Cho, Kilwon; Briseno, Alejandro L; Podzorov, Vitaly

    2017-10-04

    Photoinduced charge transfer between semiconductors and gate dielectrics can occur in organic field-effect transistors (OFETs) operating under illumination, leading to a pronounced bias-stress effect in devices that are normally stable while operating in the dark. Here, we report an observation of a polarization-dependent photoinduced bias-stress effect in two prototypical single-crystal OFETs, based on rubrene and tetraphenylbis(indolo{1,2-a})quinolin. We find that the decay rate of the source-drain current in these OFETs under illumination is a periodic function of the polarization angle of incident photoexcitation with respect to the crystal axes, with a periodicity of π. The angular positions of maxima and minima of the bias-stress rate match those of the optical absorption coefficient of the corresponding crystals. The analysis of the effect shows that it stems from a charge transfer of "hot" holes, photogenerated in the crystal within a very short thermalization length (≪μm) from the semiconductor-dielectric interface. The observed phenomenon is a type of intrinsic structure-property relationship, revealing how molecular packing affects parameter drift in organic transistors under illumination. We also demonstrate that a photoinduced charge transfer in OFETs can be used for recording rewritable accumulation channels with an optically defined geometry and resolution, which can be used in a number of potential applications.

  10. A chemical-genetic strategy reveals distinct temporal requirements for SAD-1 kinase in neuronal polarization and synapse formation

    Directory of Open Access Journals (Sweden)

    Shokat Kevan M

    2008-09-01

    Full Text Available Abstract Background Neurons assemble into a functional network through a sequence of developmental processes including neuronal polarization and synapse formation. In Caenorhabditis elegans, the serine/threonine SAD-1 kinase is essential for proper neuronal polarity and synaptic organization. To determine if SAD-1 activity regulates the establishment or maintenance of these neuronal structures, we examined its temporal requirements using a chemical-genetic method that allows for selective and reversible inactivation of its kinase activity in vivo. Results We generated a PP1 analog-sensitive variant of SAD-1. Through temporal inhibition of SAD-1 kinase activity we show that its activity is required for the establishment of both neuronal polarity and synaptic organization. However, while SAD-1 activity is needed strictly when neurons are polarizing, the temporal requirement for SAD-1 is less stringent in synaptic organization, which can also be re-established during maintenance. Conclusion This study reports the first temporal analysis of a neural kinase activity using the chemical-genetic system. It reveals that neuronal polarity and synaptic organization have distinct temporal requirements for SAD-1.

  11. Quantitative flux analysis reveals folate-dependent NADPH production

    Science.gov (United States)

    Fan, Jing; Ye, Jiangbin; Kamphorst, Jurre J.; Shlomi, Tomer; Thompson, Craig B.; Rabinowitz, Joshua D.

    2014-06-01

    ATP is the dominant energy source in animals for mechanical and electrical work (for example, muscle contraction or neuronal firing). For chemical work, there is an equally important role for NADPH, which powers redox defence and reductive biosynthesis. The most direct route to produce NADPH from glucose is the oxidative pentose phosphate pathway, with malic enzyme sometimes also important. Although the relative contribution of glycolysis and oxidative phosphorylation to ATP production has been extensively analysed, similar analysis of NADPH metabolism has been lacking. Here we demonstrate the ability to directly track, by liquid chromatography-mass spectrometry, the passage of deuterium from labelled substrates into NADPH, and combine this approach with carbon labelling and mathematical modelling to measure NADPH fluxes. In proliferating cells, the largest contributor to cytosolic NADPH is the oxidative pentose phosphate pathway. Surprisingly, a nearly comparable contribution comes from serine-driven one-carbon metabolism, in which oxidation of methylene tetrahydrofolate to 10-formyl-tetrahydrofolate is coupled to reduction of NADP+ to NADPH. Moreover, tracing of mitochondrial one-carbon metabolism revealed complete oxidation of 10-formyl-tetrahydrofolate to make NADPH. As folate metabolism has not previously been considered an NADPH producer, confirmation of its functional significance was undertaken through knockdown of methylenetetrahydrofolate dehydrogenase (MTHFD) genes. Depletion of either the cytosolic or mitochondrial MTHFD isozyme resulted in decreased cellular NADPH/NADP+ and reduced/oxidized glutathione ratios (GSH/GSSG) and increased cell sensitivity to oxidative stress. Thus, although the importance of folate metabolism for proliferating cells has been long recognized and attributed to its function of producing one-carbon units for nucleic acid synthesis, another crucial function of this pathway is generating reducing power.

  12. Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears.

    Science.gov (United States)

    Liu, Shiping; Lorenzen, Eline D; Fumagalli, Matteo; Li, Bo; Harris, Kelley; Xiong, Zijun; Zhou, Long; Korneliussen, Thorfinn Sand; Somel, Mehmet; Babbitt, Courtney; Wray, Greg; Li, Jianwen; He, Weiming; Wang, Zhuo; Fu, Wenjing; Xiang, Xueyan; Morgan, Claire C; Doherty, Aoife; O'Connell, Mary J; McInerney, James O; Born, Erik W; Dalén, Love; Dietz, Rune; Orlando, Ludovic; Sonne, Christian; Zhang, Guojie; Nielsen, Rasmus; Willerslev, Eske; Wang, Jun

    2014-05-08

    Polar bears are uniquely adapted to life in the High Arctic and have undergone drastic physiological changes in response to Arctic climates and a hyper-lipid diet of primarily marine mammal prey. We analyzed 89 complete genomes of polar bear and brown bear using population genomic modeling and show that the species diverged only 479-343 thousand years BP. We find that genes on the polar bear lineage have been under stronger positive selection than in brown bears; nine of the top 16 genes under strong positive selection are associated with cardiomyopathy and vascular disease, implying important reorganization of the cardiovascular system. One of the genes showing the strongest evidence of selection, APOB, encodes the primary lipoprotein component of low-density lipoprotein (LDL); functional mutations in APOB may explain how polar bears are able to cope with life-long elevated LDL levels that are associated with high risk of heart disease in humans. Copyright © 2014 Elsevier Inc. All rights reserved.

  13. Low-Mach-number turbulence in interstellar gas revealed by radio polarization gradients.

    Science.gov (United States)

    Gaensler, B M; Haverkorn, M; Burkhart, B; Newton-McGee, K J; Ekers, R D; Lazarian, A; McClure-Griffiths, N M; Robishaw, T; Dickey, J M; Green, A J

    2011-10-05

    The interstellar medium of the Milky Way is multiphase, magnetized and turbulent. Turbulence in the interstellar medium produces a global cascade of random gas motions, spanning scales ranging from 100 parsecs to 1,000 kilometres (ref. 4). Fundamental parameters of interstellar turbulence such as the sonic Mach number (the speed of sound) have been difficult to determine, because observations have lacked the sensitivity and resolution to image the small-scale structure associated with turbulent motion. Observations of linear polarization and Faraday rotation in radio emission from the Milky Way have identified unusual polarized structures that often have no counterparts in the total radiation intensity or at other wavelengths, and whose physical significance has been unclear. Here we report that the gradient of the Stokes vector (Q, U), where Q and U are parameters describing the polarization state of radiation, provides an image of magnetized turbulence in diffuse, ionized gas, manifested as a complex filamentary web of discontinuities in gas density and magnetic field. Through comparison with simulations, we demonstrate that turbulence in the warm, ionized medium has a relatively low sonic Mach number, M(s) ≲ 2. The development of statistical tools for the analysis of polarization gradients will allow accurate determinations of the Mach number, Reynolds number and magnetic field strength in interstellar turbulence over a wide range of conditions.

  14. GBT Detection of Polarization-Dependent HI Absorption and HI Outflows in Local ULIRGs and Quasars

    Science.gov (United States)

    Teng, Stacy H.; Veilleux, Sylvain; Baker, Andrew J.

    2013-01-01

    We present the results of a 21-cm HI survey of 27 local massive gas-rich late-stage mergers and merger remnants with the Green Bank Telescope (GBT). These remnants were selected from the Quasar/ULIRG Evolution Study (QUEST) sample of ultraluminous infrared galaxies (ULIRGs; L(sub 8 - 1000 micron) > 10(exp 12) solar L) and quasars; our targets are all bolometrically dominated by active galactic nuclei (AGN) and sample the later phases of the proposed ULIRG-to-quasar evolutionary sequence. We find the prevalence of HI absorption (emission) to be 100% (29%) in ULIRGs with HI detections, 100% (88%) in FIR-strong quasars, and 63% (100%) in FIR-weak quasars. The absorption features are associated with powerful neutral outflows that change from being mainly driven by star formation in ULIRGs to being driven by the AGN in the quasars. These outflows have velocities that exceed 1500 km/s in some cases. Unexpectedly, we find polarization-dependent HI absorption in 57% of our spectra (88% and 63% of the FIR-strong and FIR-weak quasars, respectively). We attribute this result to absorption of polarized continuum emission from these sources by foreground HI clouds. About 60% of the quasars displaying polarized spectra are radio-loud, far higher than the approx 10% observed in the general AGN population. This discrepancy suggests that radio jets play an important role in shaping the environments in these galaxies. These systems may represent a transition phase in the evolution of gas-rich mergers into "mature" radio galaxies.

  15. Brown and polar bear Y chromosomes reveal extensive male-biased gene flow within brother lineages.

    Science.gov (United States)

    Bidon, Tobias; Janke, Axel; Fain, Steven R; Eiken, Hans Geir; Hagen, Snorre B; Saarma, Urmas; Hallström, Björn M; Lecomte, Nicolas; Hailer, Frank

    2014-06-01

    Brown and polar bears have become prominent examples in phylogeography, but previous phylogeographic studies relied largely on maternally inherited mitochondrial DNA (mtDNA) or were geographically restricted. The male-specific Y chromosome, a natural counterpart to mtDNA, has remained underexplored. Although this paternally inherited chromosome is indispensable for comprehensive analyses of phylogeographic patterns, technical difficulties and low variability have hampered its application in most mammals. We developed 13 novel Y-chromosomal sequence and microsatellite markers from the polar bear genome and screened these in a broad geographic sample of 130 brown and polar bears. We also analyzed a 390-kb-long Y-chromosomal scaffold using sequencing data from published male ursine genomes. Y chromosome evidence support the emerging understanding that brown and polar bears started to diverge no later than the Middle Pleistocene. Contrary to mtDNA patterns, we found 1) brown and polar bears to be reciprocally monophyletic sister (or rather brother) lineages, without signals of introgression, 2) male-biased gene flow across continents and on phylogeographic time scales, and 3) male dispersal that links the Alaskan ABC islands population to mainland brown bears. Due to female philopatry, mtDNA provides a highly structured estimate of population differentiation, while male-biased gene flow is a homogenizing force for nuclear genetic variation. Our findings highlight the importance of analyzing both maternally and paternally inherited loci for a comprehensive view of phylogeographic history, and that mtDNA-based phylogeographic studies of many mammals should be reevaluated. Recent advances in sequencing technology render the analysis of Y-chromosomal variation feasible, even in nonmodel organisms. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e

  16. Polarization-dependent Goos-Hänchen shift at a graded dielectric interface

    Science.gov (United States)

    Löffler, W.; van Exter, M. P.; 't Hooft, G. W.; Eliel, E. R.; Hermans, K.; Broer, D. J.; Woerdman, J. P.

    2010-09-01

    We examine the polarization differential Goos-Hänchen beam shift upon total internal reflection, for a graded-index dielectric interface. We find a generic scaling law where the magnitude of this shift depends solely on the product of wavelength and gradient steepness. The analytic results are extended using transmission matrix calculations in cases where the assumptions made to allow analytical treatment might become questionable. Two important cases in this category are: (i) incident angle close to the critical angle and (ii) gradients with an overall thickness of the order of a wavelength. We demonstrate this effect experimentally using a polymer-blend sample with a gradual refractive-index transition induced by diffusion.

  17. Polarization dependent behavior of CdS around the first and second LO-phonon modes

    Energy Technology Data Exchange (ETDEWEB)

    Frausto-Reyes, C., E-mail: cfraus@cio.mx [Centro de Investigaciones en Optica AC, Unidad Aguascalientes, Prolong., Constitucion 607, Fracc. Reserva Loma Bonita, CP 20200, Apartado Postal 507, Ags. (Mexico); Molina-Contreras, J.R., E-mail: rmolina@correo.ita.mx [Departamento de Ingenieria Electrica y Electronica, Instituto Tecnologico de Aguascalientes, Av. Lopez Mateos 1081 Oriente, Fracc. Bonna Gens, CP 20256, Aguascalientes, Ags. (Mexico); Lopez-Alvarez, Y.F. [Departamento de Ingenieria Electrica y Electronica, Instituto Tecnologico de Aguascalientes, Av. Lopez Mateos 1081 Oriente, Fracc. Bonna Gens, CP 20256, Aguascalientes, Ags. (Mexico); Medel-Ruiz, C.I.; Perez Ladron de Guevara, H. [Universidad de Guadalajara, Centro Universitario de los Lagos, Av. Enrique Diaz de Leon s/n, Fracc. Paseos de la Montana, CP 47460, Lagos de Moreno, Jal. (Mexico); Ortiz-Morales, M. [Centro de Investigaciones en Optica AC, Unidad Aguascalientes, Prolong., Constitucion 607, Fracc. Reserva Loma Bonita, CP 20200, Apartado Postal 507, Ags. (Mexico)

    2010-10-25

    The present work report studies on resonant Raman experimental line shape for CdS around the first and second LO-phonon modes. The application of our method to the study of LO-phonon modes of CdS suggests that the scattered intensity is dominated by the surface and dependent on polarization. Results showed that the Raman spectra for CdS, roughly fall into three groups: a broad line-wing with apparent maxima around 194 cm{sup -1} in the range of 140 and 240 cm{sup -1} which can be ascribed to overtone scattering from acoustic phonons; a band near the 1LO phonon mode which can be attributed to a combination of one-phonon scattering and peak acoustic phonon and finally, a band near the 2LO phonon mode which can be attributed to a combination of two-phonon scattering and peak acoustic phonon.

  18. On the angular dependence and scattering model of polar mesospheric summer echoes at VHF

    Science.gov (United States)

    Sommer, Svenja; Stober, Gunter; Chau, Jorge L.

    2016-01-01

    We present measurements of the angular dependence of polar mesospheric summer echoes (PMSE) with the Middle Atmosphere Alomar Radar System in Northern Norway (69.30° N, 16.04° E). Our results are based on multireceiver and multibeam observations using beam pointing directions with off-zenith angles up to 25° as well as on spatial correlation analysis (SCA) from vertical beam observations. We consider a beam filling effect at the upper and lower boundaries of PMSE in tilted beams, which determines the effective mean angle of arrival. Comparing the average power of the vertical beam to the oblique beams suggests that PMSE are mainly not as aspect sensitive as in contrast to previous studies. However, from SCA, times of enhanced correlation are found, indicating aspect sensitivity or a localized scattering mechanism. Our results suggest that PMSE consist of nonhomogeneous isotropic scattering and previously reported aspect sensitivity values might have been influenced by the inhomogeneous nature of PMSE.

  19. Comment on `The azimuthal dependence of surface wave polarization in a slightly anisotropic medium' by T. Tanimoto

    Science.gov (United States)

    Maupin, Valérie

    2004-10-01

    This comment points out that the simple azimuthal dependence of the polarization anomalies derived in a recent paper by Tanimoto may not be valid for the Love wave fundamental mode in oceanic or tectonic regions as a result of strong coupling with the first Rayleigh wave overtone. More generally, I also point out the fact that polarization anomalies reflect partly the anisotropy away from the station and that this usually complicates the azimuthal pattern observed at single stations.

  20. Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change

    Science.gov (United States)

    Miller, Webb; Schuster, Stephan C.; Welch, Andreanna J.; Ratan, Aakrosh; Bedoya-Reina, Oscar C.; Zhao, Fangqing; Kim, Hie Lim; Burhans, Richard C.; Drautz, Daniela I.; Wittekindt, Nicola E.; Tomsho, Lynn P.; Ibarra-Laclette, Enrique; Herrera-Estrella, Luis; Peacock, Elizabeth; Farley, Sean; Sage, George K.; Rode, Karyn D.; Obbard, Martyn E.; Montiel, Rafael; Bachmann, Lutz; Ingólfsson, Ólafur; Aars, Jon; Mailund, Thomas; Wiig, Øystein; Talbot, Sandra L.; Lindqvist, Charlotte

    2012-01-01

    Polar bears (PBs) are superbly adapted to the extreme Arctic environment and have become emblematic of the threat to biodiversity from global climate change. Their divergence from the lower-latitude brown bear provides a textbook example of rapid evolution of distinct phenotypes. However, limited mitochondrial and nuclear DNA evidence conflicts in the timing of PB origin as well as placement of the species within versus sister to the brown bear lineage. We gathered extensive genomic sequence data from contemporary polar, brown, and American black bear samples, in addition to a 130,000- to 110,000-y old PB, to examine this problem from a genome-wide perspective. Nuclear DNA markers reflect a species tree consistent with expectation, showing polar and brown bears to be sister species. However, for the enigmatic brown bears native to Alaska's Alexander Archipelago, we estimate that not only their mitochondrial genome, but also 5–10% of their nuclear genome, is most closely related to PBs, indicating ancient admixture between the two species. Explicit admixture analyses are consistent with ancient splits among PBs, brown bears and black bears that were later followed by occasional admixture. We also provide paleodemographic estimates that suggest bear evolution has tracked key climate events, and that PB in particular experienced a prolonged and dramatic decline in its effective population size during the last ca. 500,000 years. We demonstrate that brown bears and PBs have had sufficiently independent evolutionary histories over the last 4–5 million years to leave imprints in the PB nuclear genome that likely are associated with ecological adaptation to the Arctic environment.

  1. Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change.

    Science.gov (United States)

    Miller, Webb; Schuster, Stephan C; Welch, Andreanna J; Ratan, Aakrosh; Bedoya-Reina, Oscar C; Zhao, Fangqing; Kim, Hie Lim; Burhans, Richard C; Drautz, Daniela I; Wittekindt, Nicola E; Tomsho, Lynn P; Ibarra-Laclette, Enrique; Herrera-Estrella, Luis; Peacock, Elizabeth; Farley, Sean; Sage, George K; Rode, Karyn; Obbard, Martyn; Montiel, Rafael; Bachmann, Lutz; Ingólfsson, Olafur; Aars, Jon; Mailund, Thomas; Wiig, Oystein; Talbot, Sandra L; Lindqvist, Charlotte

    2012-09-04

    Polar bears (PBs) are superbly adapted to the extreme Arctic environment and have become emblematic of the threat to biodiversity from global climate change. Their divergence from the lower-latitude brown bear provides a textbook example of rapid evolution of distinct phenotypes. However, limited mitochondrial and nuclear DNA evidence conflicts in the timing of PB origin as well as placement of the species within versus sister to the brown bear lineage. We gathered extensive genomic sequence data from contemporary polar, brown, and American black bear samples, in addition to a 130,000- to 110,000-y old PB, to examine this problem from a genome-wide perspective. Nuclear DNA markers reflect a species tree consistent with expectation, showing polar and brown bears to be sister species. However, for the enigmatic brown bears native to Alaska's Alexander Archipelago, we estimate that not only their mitochondrial genome, but also 5-10% of their nuclear genome, is most closely related to PBs, indicating ancient admixture between the two species. Explicit admixture analyses are consistent with ancient splits among PBs, brown bears and black bears that were later followed by occasional admixture. We also provide paleodemographic estimates that suggest bear evolution has tracked key climate events, and that PB in particular experienced a prolonged and dramatic decline in its effective population size during the last ca. 500,000 years. We demonstrate that brown bears and PBs have had sufficiently independent evolutionary histories over the last 4-5 million years to leave imprints in the PB nuclear genome that likely are associated with ecological adaptation to the Arctic environment.

  2. Orientation and thickness dependence of magnetization at the interfacesof highly spin-polarized manganite thin films

    Energy Technology Data Exchange (ETDEWEB)

    Chopdekar, Rajesh V.; Arenholz, Elke; Suzuki, Y.

    2008-08-18

    We have probed the nature of magnetism at the surface of (001), (110) and (111)-oriented La{sub 0.7}Sr{sub 0.3}MnO{sub 3} thin films. The spin polarization of La{sub 0.7}Sr{sub 0.3}MnO{sub 3} thin films is not intrinsically suppressed at all surfaces and interfaces but is highly sensitive to both the epitaxial strain state as well as the substrate orientation. Through the use of soft x-ray spectroscopy, the magnetic properties of (001), (110) and (111)-oriented La{sub 0.7}Sr{sub 0.3}MnO{sub 3}/SrTiO{sub 3} interfaces have been investigated and compared to bulk magnetometry and resistivity measurements. The magnetization of (110) and (111)-oriented La{sub 0.7}Sr{sub 0.3}MnO{sub 3}/SrTiO{sub 3} interfaces are more bulk-like as a function of thickness whereas the magnetization at the (001)-oriented La{sub 0.7}Sr{sub 0.3}MnO{sub 3}/SrTiO{sub 3} interface is suppressed significantly below a layer thickness of 20 nm. Such findings are correlated with the biaxial strain state of the La{sub 0.7}Sr{sub 0.3}MnO{sub 3} films; for a given film thickness it is the tetragonal distortion of (001) La{sub 0.7}Sr{sub 0.3}MnO{sub 3} that severely impacts the magnetization, whereas the trigonal distortion for (111)-oriented films and monoclinic distortion for (110)-oriented films have less of an impact. These observations provide evidence that surface magnetization and thus spin polarization depends strongly on the crystal surface orientation as well as epitaxial strain.

  3. The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation

    Energy Technology Data Exchange (ETDEWEB)

    Blanc, Guillaume; Agarkova, Irina; Grimwood, Jane; Kuo, Alan; Brueggeman, Andrew; Dunigan, David D.; Gurnon, James; Ladunga, Istvan; Lindquist, Erika; Lucas, Susan; Pangilinan, Jasmyn; Proschold, Thomas; Salamov, Asaf; Schmutz, Jeremy; Weeks, Donald; Tamada, Takashi; Lomsadze, Alexandre; Borodovsky, Mark; Claverie, Jean-Michel; Grigoriev, Igor V.; Van Etten, James L.

    2012-02-13

    Background Little is known about the mechanisms of adaptation of life to the extreme environmental conditions encountered in polar regions. Here we present the genome sequence of a unicellular green alga from the division chlorophyta, Coccomyxa subellipsoidea C-169, which we will hereafter refer to as C-169. This is the first eukaryotic microorganism from a polar environment to have its genome sequenced. Results The 48.8 Mb genome contained in 20 chromosomes exhibits significant synteny conservation with the chromosomes of its relatives Chlorella variabilis and Chlamydomonas reinhardtii. The order of the genes is highly reshuffled within synteny blocks, suggesting that intra-chromosomal rearrangements were more prevalent than inter-chromosomal rearrangements. Remarkably, Zepp retrotransposons occur in clusters of nested elements with strictly one cluster per chromosome probably residing at the centromere. Several protein families overrepresented in C. subellipsoidae include proteins involved in lipid metabolism, transporters, cellulose synthases and short alcohol dehydrogenases. Conversely, C-169 lacks proteins that exist in all other sequenced chlorophytes, including components of the glycosyl phosphatidyl inositol anchoring system, pyruvate phosphate dikinase and the photosystem 1 reaction center subunit N (PsaN). Conclusions We suggest that some of these gene losses and gains could have contributed to adaptation to low temperatures. Comparison of these genomic features with the adaptive strategies of psychrophilic microbes suggests that prokaryotes and eukaryotes followed comparable evolutionary routes to adapt to cold environments.

  4. Polarized Line Formation in Arbitrary Strength Magnetic Fields Angle-averaged and Angle-dependent Partial Frequency Redistribution

    Energy Technology Data Exchange (ETDEWEB)

    Sampoorna, M.; Nagendra, K. N. [Indian Institute of Astrophysics, Koramangala, Bengaluru 560 034 (India); Stenflo, J. O., E-mail: sampoorna@iiap.res.in, E-mail: knn@iiap.res.in, E-mail: stenflo@astro.phys.ethz.ch [Institute of Astronomy, ETH Zurich, CH-8093 Zurich (Switzerland)

    2017-08-01

    Magnetic fields in the solar atmosphere leave their fingerprints in the polarized spectrum of the Sun via the Hanle and Zeeman effects. While the Hanle and Zeeman effects dominate, respectively, in the weak and strong field regimes, both these effects jointly operate in the intermediate field strength regime. Therefore, it is necessary to solve the polarized line transfer equation, including the combined influence of Hanle and Zeeman effects. Furthermore, it is required to take into account the effects of partial frequency redistribution (PRD) in scattering when dealing with strong chromospheric lines with broad damping wings. In this paper, we present a numerical method to solve the problem of polarized PRD line formation in magnetic fields of arbitrary strength and orientation. This numerical method is based on the concept of operator perturbation. For our studies, we consider a two-level atom model without hyperfine structure and lower-level polarization. We compare the PRD idealization of angle-averaged Hanle–Zeeman redistribution matrices with the full treatment of angle-dependent PRD, to indicate when the idealized treatment is inadequate and what kind of polarization effects are specific to angle-dependent PRD. Because the angle-dependent treatment is presently computationally prohibitive when applied to realistic model atmospheres, we present the computed emergent Stokes profiles for a range of magnetic fields, with the assumption of an isothermal one-dimensional medium.

  5. All-optical clocked flip-flops and random access memory cells using the nonlinear polarization rotation effect of low-polarization-dependent semiconductor optical amplifiers

    Science.gov (United States)

    Wang, Yongjun; Liu, Xinyu; Tian, Qinghua; Wang, Lina; Xin, Xiangjun

    2018-03-01

    Basic configurations of various all-optical clocked flip-flops (FFs) and optical random access memory (RAM) based on the nonlinear polarization rotation (NPR) effect of low-polarization-dependent semiconductor optical amplifiers (SOA) are proposed. As the constituent elements, all-optical logic gates and all-optical SR latches are constructed by taking advantage of the SOA's NPR switch. Different all-optical FFs (AOFFs), including SR-, D-, T-, and JK-types as well as an optical RAM cell were obtained by the combination of the proposed all-optical SR latches and logic gates. The effectiveness of the proposed schemes were verified by simulation results and demonstrated by a D-FF and 1-bit RAM cell experimental system. The proposed all-optical clocked FFs and RAM cell are significant to all-optical signal processing.

  6. Polarization-dependent transverse-stress sensing characters of the gold-coated and liquid crystal filled photonic crystal fiber based on Surface Plasmon Resonance

    Science.gov (United States)

    Liu, Hai; Zhu, Chenghao; Wang, Yan; Tan, Ce; Li, Hongwei

    2018-03-01

    A transverse-stress sensor with enhanced sensitivity based on nematic liquid crystal (NLC) filled photonic crystal fiber (PCF) is proposed and analyzed by using the finite element method (FEM). The central hole of the PCF is infiltrated with NLC material with an adjustable rotation angle to achieve the polarization-dependent wavelength-selective sensing. And the combined use of side-hole structure and Surface Plasmon Resonance (SPR) technology enhanced the transverse-stress sensitivity enormously. Results reveal that the sensor can achieve a high sensitivity based on the polarization filter characteristic at special wavelengths. Besides that, the temperature and the transverse-stress in either direction can be effectively discriminated through dual-parameter demodulation method by adjusting the rotation angle of the NLC to introduce a new degree of freedom for sensing.

  7. Polarization-dependent Character of 1x3 Beam Splitter Using Self-Imaging Phenomena in Air-Slab PhCW

    DEFF Research Database (Denmark)

    Zhang, Min; Malureanu, Radu; Kristensen, Martin

    2010-01-01

    A 1x3 beam splitter in PhCWs using multi-mode interference (MMI) based on self-imaging principle is investigated. The 1x3 splitter is polarization-dependent. The total TE-polarized transmission of the 1x3 splitter is almost equal to the corresponding length of W1 PhCW. The TE-polarized input power...

  8. Polarized angular dependent light scattering from plasmonic nanoparticles: Modeling, measurements, and biomedical applications

    Science.gov (United States)

    Fu, Kun

    Several significant applications have been realized for light scattering in biomedical imaging. In order to improve imaging results with light scattering-based techniques, a variety of nanoparticles have been investigated as contrast agents, including gold nanoshells. As a method for studying the optical properties of plasmonic gold nanoparticles used as contrast agents for molecular imaging, we developed an automated goniometer instrumentation system. This system, which allows us to specifically study polarized angular-dependent light scattering of plasmonic nanoparticles, allowed us to perform a series of theoretical and experimental step-wise studies. The basic optical properties of the following gold nanoparticles were progressively investigated: (1) bare nanoshells at multipolar plasmonic resonances, (2) nanoshells with PEG modifications, (3) surface-textured nanoshells and (4) immunotargeted nanoshells (nanoshell-antibody bioconjugates) for cancer imaging. Based on the results from these studies, a new technique was developed to quantitatively measure the number of immunotargeted nanoparticles that bind to HER2-positive SKBR3 human breast cancer cells. Preliminary studies of determining the minimal incubation time of immunotargeted nanoshells with SKBR3 cells were also carried out to evaluate the potential clinical application of using gold nanoshells intraoperatively. We, therefore, anticipate that our findings will provide the theoretical groundwork required for further studies aimed at optimizing the application of plasmonic nanoparticles in scattering-based optical imaging techniques.

  9. Dependence of polar effect on parameters of coaxial plasma-erosive switches

    International Nuclear Information System (INIS)

    Bystritskij, V.M.; Ivanov, I.B.; Krasik, Ya.E.; Ryzhakin, N.N.; Sinebryukhov, A.A.; Tolmacheva, V.G.

    1988-01-01

    The results of experimental investigations and numerical simulation of the polar effect in a coaxial plasma-erosive switch (PES) established in a circuit of a strong-current nanosecond accelerator are presented. PES characteristics (energy losses, impedance, rate of its increase, etc.) are investigated depending on mutual direction of accelerator current and plasma flow as well as on the cathode radius in the PES region. It is experimentally shown that the magnetic fields near the cathode determined by this electrode radius influences mainly on PES characteristics. Mutual direction of accelerator current and plasma flow is the second significance factor influencing on PES characteristics. The optimal mode of PES operation is realized when providing the less with respect to the positive electrode, cathode radius and coinciding in direction accelerator current and plasma flow. Numerical simulation of dynamic processes in coaxial PES for different ratios of cathode and anode radii and mutual directions of accelerator current and plasma flow gives qualitative agreement with the experimental results

  10. Orientation-dependent chemistry and band-bending of Ti on polar ZnO surfaces.

    Science.gov (United States)

    Borghetti, Patrizia; Mouchaal, Younes; Dai, Zongbei; Cabailh, Gregory; Chenot, Stéphane; Lazzari, Rémi; Jupille, Jacques

    2017-04-19

    Orientation-dependent reactivity and band-bending are evidenced upon Ti deposition (1-10 Å) on polar ZnO(0001)-Zn and ZnO(0001[combining macron])-O surfaces. At the onset of the Ti deposition, a downward band-bending was observed on ZnO(0001[combining macron])-O while no change occurred on ZnO(0001)-Zn. Combining this with the photoemission analysis of the Ti 2p core level and Zn L 3 (L 2 )M 45 M 45 Auger transition, it is established that the Ti/ZnO reaction is of the form Ti + 2ZnO → TiO 2 + 2Zn on ZnO(0001)-Zn and Ti + yZnO → TiZn x O y + (y - x)Zn on ZnO(0001[combining macron])-O. Consistently, upon annealing thicker Ti adlayers, the metallic zinc is removed to leave ZnO(0001)-Zn surfaces covered with a TiO 2 -like phase and ZnO(0001[combining macron])-O surfaces covered with a defined (Ti, Zn, O) compound. Finally, a difference in the activation temperature between the O-terminated (500 K) and Zn-terminated (700 K) surfaces is observed, which is tentatively explained by different electric fields in the space charge layer at ZnO surfaces.

  11. Retrieval of Polar Stratospheric Cloud Microphysical Properties from Lidar Measurements: Dependence on Particle Shape Assumptions

    Science.gov (United States)

    Reichardt, J.; Reichardt, S.; Yang, P.; McGee, T. J.; Bhartia, P. K. (Technical Monitor)

    2001-01-01

    A retrieval algorithm has been developed for the microphysical analysis of polar stratospheric cloud (PSC) optical data obtained using lidar instrumentation. The parameterization scheme of the PSC microphysical properties allows for coexistence of up to three different particle types with size-dependent shapes. The finite difference time domain (FDTD) method has been used to calculate optical properties of particles with maximum dimensions equal to or less than 2 mu m and with shapes that can be considered more representative of PSCs on the scale of individual crystals than the commonly assumed spheroids. Specifically. these are irregular and hexagonal crystals. Selection of the optical parameters that are input to the inversion algorithm is based on a potential data set such as that gathered by two of the lidars on board the NASA DC-8 during the Stratospheric Aerosol and Gas Experiment 0 p (SAGE) Ozone Loss Validation experiment (SOLVE) campaign in winter 1999/2000: the Airborne Raman Ozone and Temperature Lidar (AROTEL) and the NASA Langley Differential Absorption Lidar (DIAL). The 0 microphysical retrieval algorithm has been applied to study how particle shape assumptions affect the inversion of lidar data measured in leewave PSCs. The model simulations show that under the assumption of spheroidal particle shapes, PSC surface and volume density are systematically smaller than the FDTD-based values by, respectively, approximately 10-30% and approximately 5-23%.

  12. Polarization modeling and predictions for DKIST part 3: focal ratio and thermal dependencies of spectral polarization fringes and optic retardance

    Science.gov (United States)

    Harrington, David M.; Sueoka, Stacey R.

    2018-01-01

    Data products from high spectral resolution astronomical polarimeters are often limited by fringes. Fringes can skew derived magnetic field properties from spectropolarimetric data. Fringe removal algorithms can also corrupt the data if the fringes and object signals are too similar. For some narrow-band imaging polarimeters, fringes change the calibration retarder properties and dominate the calibration errors. Systems-level engineering tools for polarimetric instrumentation require accurate predictions of fringe amplitudes, periods for transmission, diattenuation, and retardance. The relevant instabilities caused by environmental, thermal, and optical properties can be modeled and mitigation tools developed. We create spectral polarization fringe amplitude and temporal instability predictions by applying the Berreman calculus and simple interferometric calculations to optics in beams of varying F/ number. We then apply the formalism to superachromatic six-crystal retarders in converging beams under beam thermal loading in outdoor environmental conditions for two of the world's largest observatories: the 10-m Keck telescope and the Daniel K. Inouye Solar Telescope (DKIST). DKIST will produce a 300-W optical beam, which has imposed stringent requirements on the large diameter six-crystal retarders, dichroic beamsplitters, and internal optics. DKIST retarders are used in a converging beam with F/ ratios between 8 and 62. The fringe spectral periods, amplitudes, and thermal models of retarder behavior assisted DKIST optical designs and calibration plans with future application to many astronomical spectropolarimeters. The Low Resolution Imaging Spectrograph with polarimetry instrument at Keck also uses six-crystal retarders in a converging F / 13 beam in a Cassegrain focus exposed to summit environmental conditions providing observational verification of our predictions.

  13. Temperature dependence of cross-effect dynamic nuclear polarization in rotating solids

    DEFF Research Database (Denmark)

    Geiger, Michel-Andreas; Orwick-Rydmark, Marcella; Märker, Katharina

    2016-01-01

    Dynamic nuclear polarization exploits electron spin polarization to boost signal-to-noise in magic-angle-spinning (MAS) NMR, creating new opportunities in materials science, structural biology, and metabolomics studies. Since protein NMR spectra recorded under DNP conditions can show improved...

  14. Large-Scale Phosphoproteomics Reveals Shp-2 Phosphatase-Dependent Regulators of Pdgf Receptor Signaling

    DEFF Research Database (Denmark)

    Batth, Tanveer S; Papetti, Moreno; Pfeiffer, Anamarija

    2018-01-01

    of Pdgfr pTyr signaling. Application of a recently introduced allosteric Shp-2 inhibitor revealed global regulation of the Pdgf-dependent tyrosine phosphoproteome, which significantly impaired cell migration. In addition, we present a list of hundreds of Shp-2-dependent targets and putative substrates...

  15. Energy and polarization dependence of resonant inelastic X-ray scattering in Nd2CuO4

    International Nuclear Information System (INIS)

    Hill, J.P.; Kao, C.C.; Haemaelaeinen, K.

    1998-01-01

    The authors report the energy and polarization dependence of resonant inelastic x-ray scattering from Nd 2 CuO 4 . An energy loss feature at ∼6 eV is observed in the vicinity of the Cu K-edge. Numerical calculations based on the Anderson impurity model identify this as a charge transfer excitation to the anti-bonding state. The incident polarization is shown to select the intermediate states participating in the resonance process. Resonances are observed at 8,990 eV and 9,000 eV with the incident polarization perpendicular and parallel to the CuO planes, respectively. In contrast to the single-site model calculations, no resonances are observed associated with the 1s3d 10 L intermediate states, suggesting non-local effects play a role

  16. Polarity-Dependent Isomerization of an Unsymmetrical Overcrowded Ethylene Promoted by Zwitterionic Contribution in the Twisted Isomer.

    Science.gov (United States)

    Hirao, Yasukazu; Nagamachi, Nobuhiro; Hosoi, Katsuma; Kubo, Takashi

    2018-03-02

    The twisted form of bianthrone is known as a metastable state provided by a photo-induced or thermal-induced isomerization of the folded form, and thus prevents the isolation and the detailed analysis of its electronic structure. In this study, an unsymmetrical bianthrone (2), consisting of the electron-withdrawing anthrone and electron-donating acridane, have been synthesized and shown to exhibit a solvent-polarity-dependent isomerization reaction between the folded and twisted isomers. With increasing the polarity of the solvent, 2 showed an isomerization reaction from the folded form to the twisted form. The stabilization of the twisted isomer in polar solvents can be interpreted as proof of its relatively large zwitterionic character. The DMF solution of 2 displayed paramagnetically-broadened NMR signals from the thermally populated triplet state resulting from rotation of the weakened ethylenic double bond of the twisted isomer. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Polarization-dependent atomic dipole traps behind a circular aperture for neutral-atom quantum computing

    International Nuclear Information System (INIS)

    Gillen-Christandl, Katharina; Copsey, Bert D.

    2011-01-01

    The neutral-atom quantum computing community has successfully implemented almost all necessary steps for constructing a neutral-atom quantum computer. We present computational results of a study aimed at solving the remaining problem of creating a quantum memory with individually addressable sites for quantum computing. The basis of this quantum memory is the diffraction pattern formed by laser light incident on a circular aperture. Very close to the aperture, the diffraction pattern has localized bright and dark spots that can serve as red-detuned or blue-detuned atomic dipole traps. These traps are suitable for quantum computing even for moderate laser powers. In particular, for moderate laser intensities (∼100 W/cm 2 ) and comparatively small detunings (∼1000-10 000 linewidths), trap depths of ∼1 mK and trap frequencies of several to tens of kilohertz are achieved. Our results indicate that these dipole traps can be moved by tilting the incident laser beams without significantly changing the trap properties. We also explored the polarization dependence of these dipole traps. We developed a code that calculates the trapping potential energy for any magnetic substate of any hyperfine ground state of any alkali-metal atom for any laser detuning much smaller than the fine-structure splitting for any given electric field distribution. We describe details of our calculations and include a summary of different notations and conventions for the reduced matrix element and how to convert it to SI units. We applied this code to these traps and found a method for bringing two traps together and apart controllably without expelling the atoms from the trap and without significant tunneling probability between the traps. This approach can be scaled up to a two-dimensional array of many pinholes, forming a quantum memory with single-site addressability, in which pairs of atoms can be brought together and apart for two-qubit gates for quantum computing.

  18. Calcium-dependent protein kinases regulate polarized tip growth in pollen tubes.

    Science.gov (United States)

    Myers, Candace; Romanowsky, Shawn M; Barron, Yoshimi D; Garg, Shilpi; Azuse, Corinn L; Curran, Amy; Davis, Ryan M; Hatton, Jasmine; Harmon, Alice C; Harper, Jeffrey F

    2009-08-01

    Calcium signals are critical for the regulation of polarized growth in many eukaryotic cells, including pollen tubes and neurons. In plants, the regulatory pathways that code and decode Ca(2+) signals are poorly understood. In Arabidopsis thaliana, genetic evidence presented here indicates that pollen tube tip growth involves the redundant activity of two Ca(2+)-dependent protein kinases (CPKs), isoforms CPK17 and -34. Both isoforms appear to target to the plasma membrane, as shown by imaging of CPK17-yellow fluorescent protein (YFP) and CPK34-YFP in growing pollen tubes. Segregation analyses from two independent sets of T-DNA insertion mutants indicate that a double disruption of CPK17 and -34 results in an approximately 350-fold reduction in pollen transmission efficiency. The near sterile phenotype of homozygous double mutants could be rescued through pollen expression of a CPK34-YFP fusion. In contrast, a transgene rescue was blocked by mutations engineered to disrupt the Ca(2+)-activation mechanism of CPK34 (CPK34-YFP-E465A,E500A), providing in vivo evidence linking Ca(2+) activation to a biological function of a CPK. While double mutant pollen tubes displayed normal morphology, relative growth rates for the most rapidly growing tubes were reduced by more than three-fold compared with wild type. In addition, while most mutant tubes appeared to grow far enough to reach ovules, the vast majority (>90%) still failed to locate and fertilize ovules. Together, these results provide genetic evidence that CPKs are essential to pollen fitness, and support a mechanistic model in which CPK17 and -34 transduce Ca(2+) signals to increase the rate of pollen tube tip growth and facilitate a response to tropism cues.

  19. Temperature dependence measurements and structural characterization of trimethyl ammonium ionic liquids with a highly polar solvent.

    Science.gov (United States)

    Attri, Pankaj; Venkatesu, Pannuru; Hofman, T

    2011-08-25

    We report the synthesis and characterization of a series of an ammonium ionic liquids (ILs) containing acetate, dihydrogen phosphate, and hydrogen sulfate anions with a common cation. To characterize the thermophysical properties of these newly synthesized ILs with the highly polar solvent N,N-dimethylformamide (DMF), precise measurements such as densities (ρ) and ultrasonic sound velocities (u) over the whole composition range have been performed at atmospheric pressure and over wide temperature ranges (25-50 °C). The excess molar volume (V(E)) and the deviation in isentropic compressibilities (Δκ(s)) were predicted using these temperature dependence properties as a function of the concentration of ILs. The Redlich-Kister polynomial was used to correlate the results. The ILs investigated in the present study included trimethylammonium acetate [(CH(3))(3)NH][CH(3)COO] (TMAA), trimethylammonium dihydrogen phosphate [(CH(3))(3)NH][H(2)PO(4)] (TMAP), and trimethylammonium hydrogen sulfate [(CH(3))(3)NH][HSO(4)] (TMAS). The intermolecular interactions and structural effects were analyzed on the basis of the measured and the derived properties. In addition, the hydrogen bonding between ILs and DMF has been demonstrated using semiempirical calculations with help of Hyperchem 7. A qualitative analysis of the results is discussed in terms of the ion-dipole, ion-pair interactions, and hydrogen bonding between ILs and DMF molecules and their structural factors. The influence of the anion of the protic IL, namely, acetate (CH(3)COO), dihydrogen phosphate (H(2)PO(4)), and hydrogen sulfate (HSO(4)), on the thermophysical properties is also provided. © 2011 American Chemical Society

  20. Low-frequency (0.7-7.4 mHz geomagnetic field fluctuations at high latitude: frequency dependence of the polarization pattern

    Directory of Open Access Journals (Sweden)

    L. Cafarella

    2001-06-01

    Full Text Available A statistical analysis of the polarization pattern of low-frequency geomagnetic field fluctuations (0.7-7.4 mHz covering the entire 24-h interval was performed at the Antarctic station Terra Nova Bay (80.0°S geomagnetic latitude throughout 1997 and 1998. The results show that the polarization pattern exhibits a frequency dependence, as can be expected from the frequency dependence of the latitude where the coupling between the magnetospheric compressional mode and the field line resonance takes place. The polarization analysis of single pulsation events shows that wave packets with different polarization sense, depending on frequency, can be simultaneously observed.

  1. Depth enhancement of multi-layer light field display using polarization dependent internal reflection.

    Science.gov (United States)

    Jo, Na-Young; Lim, Hong-Gi; Lee, Sung-Keun; Kim, Yong-Soo; Park, Jae-Hyeung

    2013-12-02

    A technique to enhance the depth range of the multi-layer light field three-dimensional display is proposed. A set of the optical plates are stacked in front of the conventional multi-layer light field display, creating additional internal reflection for one polarization state. By switching between two orthogonal polarization states in synchronization with the displayed three-dimensional images, the depth range of the display can be doubled. The proposed method is verified experimentally, confirming its feasibility.

  2. Metagenomic analysis reveals that modern microbialites and polar microbial mats have similar taxonomic and functional potential

    Directory of Open Access Journals (Sweden)

    Richard Allen White III

    2015-09-01

    Full Text Available Within the subarctic climate of Clinton Creek, Yukon, Canada, lies an abandoned and flooded open-pit asbestos mine that harbors rapidly growing microbialites. To understand their formation we completed a metagenomic community profile of the microbialites and their surrounding sediments. Assembled metagenomic data revealed that bacteria within the phylum Proteobacteria numerically dominated this system, although the relative abundances of taxa within the phylum varied among environments. Bacteria belonging to Alphaproteobacteria and Gammaproteobacteria were dominant in the microbialites and sediments, respectively. The microbialites were also home to many other groups associated with microbialite formation including filamentous cyanobacteria and dissimilatory sulfate-reducing Deltaproteobacteria, consistent with the idea of a shared global microbialite microbiome. Other members were present that are typically not associated with microbialites including Gemmatimonadetes and iron-oxidizing Betaproteobacteria, which participate in carbon metabolism and iron cycling. Compared to the sediments, the microbialite microbiome has significantly more genes associated with photosynthetic processes (e.g., photosystem II reaction centers, carotenoid and chlorophyll biosynthesis and carbon fixation (e.g., CO dehydrogenase. The Clinton Creek microbialite communities had strikingly similar functional potentials to non-lithifying microbial mats from the Canadian High Arctic and Antarctica, but are functionally distinct, from non-lithifying mats or biofilms from Yellowstone. Clinton Creek microbialites also share metabolic genes (R2 0.900. These metagenomic profiles from an anthropogenic microbialite-forming ecosystem provide context to microbialite formation on a human-relevant timescale.

  3. Attention-dependent modulation of cortical taste circuits revealed by Granger causality with signal-dependent noise.

    Directory of Open Access Journals (Sweden)

    Qiang Luo

    2013-10-01

    Full Text Available We show, for the first time, that in cortical areas, for example the insular, orbitofrontal, and lateral prefrontal cortex, there is signal-dependent noise in the fMRI blood-oxygen level dependent (BOLD time series, with the variance of the noise increasing approximately linearly with the square of the signal. Classical Granger causal models are based on autoregressive models with time invariant covariance structure, and thus do not take this signal-dependent noise into account. To address this limitation, here we describe a Granger causal model with signal-dependent noise, and a novel, likelihood ratio test for causal inferences. We apply this approach to the data from an fMRI study to investigate the source of the top-down attentional control of taste intensity and taste pleasantness processing. The Granger causality with signal-dependent noise analysis reveals effects not identified by classical Granger causal analysis. In particular, there is a top-down effect from the posterior lateral prefrontal cortex to the insular taste cortex during attention to intensity but not to pleasantness, and there is a top-down effect from the anterior and posterior lateral prefrontal cortex to the orbitofrontal cortex during attention to pleasantness but not to intensity. In addition, there is stronger forward effective connectivity from the insular taste cortex to the orbitofrontal cortex during attention to pleasantness than during attention to intensity. These findings indicate the importance of explicitly modeling signal-dependent noise in functional neuroimaging, and reveal some of the processes involved in a biased activation theory of selective attention.

  4. Modulation of human macrophage activity by Ascaris antigens is dependent on macrophage polarization state

    DEFF Research Database (Denmark)

    Almeida, Sara; Nejsum, Peter; Williams, Andrew R.

    2018-01-01

    Parasitic worms (helminths) are known to actively modulate host immune responses and inflammation. The aim of this study was to investigate if adult body fluid (ABF) from the helminth Ascaris suum has immunomodulatory effects on different subtypes of human monocyte-derived macrophages (Mɸ) in vitro....... Mɸs were exposed to A. suum ABF at different stages of their differentiation and/or polarization. Mɸ were first differentiated from monocytes into either uncommitted (M-), classically activated (M(GM-CSF)) or alternatively activated (M(M-CSF)) phenotypes and then stimulated with lipopolysaccharide...... Mɸ to either type 1 or type 2 Mɸ, monocytes were differentiated with human serum into (M-)s and then polarized by IFN-γ/LPS or IL-4 treatment in the presence of ABF. Under these conditions, ABF did not modulate cytokine secretion but did reduce CD80 expression in IFNγ/LPS-polarized cells but not IL-4...

  5. Planck intermediate results. XXII. Frequency dependence of thermal emission from Galactic dust in intensity and polarization

    DEFF Research Database (Denmark)

    Cardoso, J. F.; Delabrouille, J.; Ganga, K.

    2015-01-01

    of the cosmic microwave background. We use a mask that focuses our analysis on the diffuse interstellar medium at intermediate Galactic latitudes. We determine the spectral indices of dust emission in intensity and polarization between 100 and 353 GHz, for each sky patch. Both indices are found to be remarkably......)% from 353 to 70 GHz. We discuss this result within the context of existing dust models. The decrease in p could indicate differences in polarization efficiency among components of interstellar dust (e.g., carbon versus silicate grains). Our observational results provide inputs to quantify and optimize...

  6. Polarity-dependence of the defect formation in c-axis oriented ZnO by the irradiation of an 8 MeV proton beam

    Science.gov (United States)

    Koike, Kazuto; Yano, Mitsuaki; Gonda, Shun-ichi; Uedono, Akira; Ishibashi, Shoji; Kojima, Kazunobu; Chichibu, Shigefusa F.

    2018-04-01

    The polarity dependence of the radiation hardness of single-crystalline ZnO bulk crystals is studied by irradiating the Zn-polar and O-polar c-planes with an 8 MeV proton beam up to the fluence of 4.2 × 1016 p/cm2. To analyze the hardness, radiation-induced defects were evaluated using positron annihilation (PA) analysis, and the recovery by post-annealing was examined using continuous-wave photoluminescence (PL) and time-resolved photoluminescence (TRPL) measurements. It was suggested by the PA and PL analyses that the major defects in both polarities were VZnVO divacancies. While the PA data did not show the clear dependence on the polarity, the PL and TRPL results showed that the Zn-polar c-plane had a little higher radiation tolerance than that of the O-polar c-plane, which was consistent with the result that the increase in the electrical resistance by proton beam irradiation was smaller for the former one. Considering these results in total, the polarity dependence is considered to be not so large, but the Zn-polar c-plane has a little higher tolerance than that of the O-polar one.

  7. Temperature dependent polarization reversal mechanism in 0.94(Bi1/2Na1/2)TiO3-0.06Ba(Zr0.02Ti0.98)O3 relaxor ceramics

    Science.gov (United States)

    Glaum, Julia; Simons, Hugh; Hudspeth, Jessica; Acosta, Matias; Daniels, John E.

    2015-12-01

    The temperature at which the electric field induced long-range ordered ferroelectric state undergoes transition into the short-range ordered relaxor state, TF-R, is commonly defined by the onset of strong dispersion of the dielectric permittivity. However, this combined macroscopic property and structural investigation of the polarization reversal process in the prototypical lead-free relaxor 0.94(Bi1/2Na1/2)TiO3-0.06Ba(Zr0.02Ti0.98)O3 reveals that an applied electric field can trigger depolarization and onset of relaxor-like behavior well below TF-R. The polarization reversal process can as such be described as a combination of (1) ferroelectric domain switching and (2) a reversible phase transition between two polar ferroelectric states mediated by a non-polar relaxor state. Furthermore, the threshold fields of the second, mediated polarization reversal mechanism depend strongly on temperature. These results are concomitant with a continuous ferroelectric to relaxor transition occurring over a broad temperature range, during which mixed behavior is observed. The nature of polarization reversal can be illustrated in electric-field-temperature (E-T) diagrams showing the electric field amplitudes associated with different polarization reversal processes. Such diagrams are useful tools for identifying the best operational temperature regimes for a given composition in actuator applications.

  8. "Depend on, Rely on, Count on": Economic Subjectivities Aboard "The Polar Express"

    Science.gov (United States)

    Saltmarsh, Sue

    2009-01-01

    Christmas literature and film produced for children is an important, albeit under-researched, site for the production of cultural values and norms. This paper analyses Chris Van Allsburg's 1985 picture book "The Polar Express", the 2004 Warner Brothers feature film of the same title, the film's official website, and resources for teachers…

  9. Drosophila tensin plays an essential role in cell migration and planar polarity formation during oogenesis by mediating integrin-dependent extracellular signals to actin organization.

    Science.gov (United States)

    Cha, In Jun; Lee, Jang Ho; Cho, Kyoung Sang; Lee, Sung Bae

    2017-03-11

    Oogenesis in Drosophila involves very dynamic cellular changes such as cell migration and polarity formation inside an ovary during short period. Previous studies identified a number of membrane-bound receptors directly receiving certain types of extracellular inputs as well as intracellular signalings to be involved in the regulation of these dynamic cellular changes. However, yet our understanding on exactly how these receptor-mediated extracellular inputs lead to dynamic cellular changes remains largely unclear. Here, we identified Drosophila tensin encoded by blistery (by) as a novel regulator of cell migration and planar polarity formation and characterized the genetic interaction between tensin and integrin during oogenesis. Eggs from by mutant showed decreased hatching rate and morphological abnormality, a round-shape, compared to the wild-type eggs. Further analyses revealed that obvious cellular defects such as defective border cell migration and planar polarity formation might be primarily associated with the decreased hatching rate and the round-shape phenotype of by mutant eggs, respectively. Moreover, by mutation also induced marked defects in F-actin organization closely associated with both cell migration and planar polarity formation during oogenesis of Drosophila. Notably, all these defective phenotypes observed in by mutant eggs became much severer by reduced level of integrin, indicative of a close functional association between integrin and tensin during oogenesis. Collectively, our findings suggest that tensin acts as a crucial regulator of dynamic cellular changes during oogenesis by bridging integrin-dependent extracellular signals to intracellular cytoskeletal organization. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. Impedance of vapor feed direct methanol fuel cells--polarization dependence of elementary processes at the anode

    International Nuclear Information System (INIS)

    Fukunaga, Hiroshi; Ishida, Tomohiro; Teranishi, Nozomu; Arai, Chikao; Yamada, Koichi

    2004-01-01

    Membrane electrode assemblies of direct methanol fuel cells (DMFCs) with different catalyst and ionomer loading were prepared. Anode performance and impedance spectra were measured to clarify the characteristics of vapor feed DMFCs (VF-DMFCs). The impedance spectra were deconvolved into three semi-circles with different time constants, each showing a different dependence on the anodic polarization. The middle-frequency range arc decreased as the anodic polarization increased, indicating that this process represents the oxidation reaction of methanol. The high-frequency range arc showed little dependence on the anodic polarization, but increased with the thickness of the electrode, indicating that this process might be related to proton conduction through the electrode. The low-frequency range arc was observed only when the methanol concentration was low, in contrast to liquid feed DMFCs (LF-DMFCs), for which the removal of the product gas presents a large resistance. A simpler design can therefore be used for a VF-DMFC, giving it an advantage over an LF-DMFC. A decreasing ionomer to catalyst ratio (I/C) caused the interfacial conductivity (σ E ) to increase, but it intensively decreased when I/C was below 0.25. Thus, the connection of the catalysts is important for the anode's performance

  11. Dependence of model-simulated response to ozone depletion on stratospheric polar vortex climatology

    Science.gov (United States)

    Lin, Pu; Paynter, David; Polvani, Lorenzo; Correa, Gustavo J. P.; Ming, Yi; Ramaswamy, V.

    2017-06-01

    We contrast the responses to ozone depletion in two climate models: Community Atmospheric Model version 3 (CAM3) and Geophysical Fuild Dynamics Laboratory (GFDL) AM3. Although both models are forced with identical ozone concentration changes, the stratospheric cooling simulated in CAM3 is 30% stronger than in AM3 in annual mean, and twice as strong in December. We find that this difference originates from the dynamical response to ozone depletion, and its strength can be linked to the timing of the climatological springtime polar vortex breakdown. This mechanism is further supported by a variant of the AM3 simulation in which the southern stratospheric zonal wind climatology is nudged to be CAM3-like. Given that the delayed breakdown of the southern polar vortex is a common bias among many climate models, previous model-based assessments of the forced responses to ozone depletion may have been somewhat overestimated.

  12. Real-time photonic sampling with improved signal-to-noise and distortion ratio using polarization-dependent modulators

    Science.gov (United States)

    Liang, Dong; Zhang, Zhiyao; Liu, Yong; Li, Xiaojun; Jiang, Wei; Tan, Qinggui

    2018-04-01

    A real-time photonic sampling structure with effective nonlinearity suppression and excellent signal-to-noise ratio (SNR) performance is proposed. The key points of this scheme are the polarization-dependent modulators (P-DMZMs) and the sagnac loop structure. Thanks to the polarization sensitive characteristic of P-DMZMs, the differences between transfer functions of the fundamental signal and the distortion become visible. Meanwhile, the selection of specific biases in P-DMZMs is helpful to achieve a preferable linearized performance with a low noise level for real-time photonic sampling. Compared with the quadrature-biased scheme, the proposed scheme is capable of valid nonlinearity suppression and is able to provide a better SNR performance even in a large frequency range. The proposed scheme is proved to be effective and easily implemented for real time photonic applications.

  13. Polarization dependence of the spin-density-wave excitations in single-domain chromium

    Energy Technology Data Exchange (ETDEWEB)

    Boeni, P. [Paul Scherrer Inst. (PSI), Villigen (Switzerland); Roessli, B. [Institut Max von Laue - Paul Langevin, 75 - Paris (France); Sternlieb, B.J. [Brookhaven (United States); Lorenzo, E. [Centre National de la Recherche Scientifique (CNRS), 38 - Grenoble (France); Werner, S.A. [Missouri (United States)

    1997-09-01

    A polarized neutron scattering experiment has been performed with a single-Q, single domain sample of chromium in a magnetic field of 4 T. It is confirmed that the longitudinal fluctuations are enhanced for small energy transfers and that the spin wave modes with {delta}S parallel to Q and {delta}S perpendicular to Q are similar. (author) 2 figs., 1 tab., 2 refs.

  14. Carrier and polarization dynamics in monolayer MoS2: temperature and power dependence

    Science.gov (United States)

    Urbaszek, Bernhard; Lagarde, D.; Bouet, L.; Amand, T.; Marie, X.; Zhu, C. R.; Liu, B. L.; Tan, P. H.

    2014-03-01

    In monolayer (ML) MoS2 optical transitions across the direct bandgap are governed by chiral selection rules, allowing optical k-valley initialization. Here we present the first time resolved photoluminescence (PL) polarization measurements in MoS2 MLs, providing vital information on the electron valley dynamics. Using quasi-resonant excitation of the A-exciton transitions, we can infer that the PL decays within τ ~= 4ps. The PL polarization of Pc ~ 60 % remains nearly constant in time for experiments from 4K - 300K, a necessary condition for the success of future Valley Hall experiments. τ does not vary significantly over this temperature range. This is surprising when considering the decrease of Pc in continuous wave experiments when going from 4K to 300K reported in the literature. By tuning the laser following the shift of the A-exciton resonance with temperature we are able to recover at 300K ~ 80 % of the polarization observed at 4K. For pulsed laser excitation, we observe a decrease of Pc with increasing laser power at all temperatures.

  15. Deletion analysis of AGD1 reveals domains crucial for plasma membrane recruitment and function in root hair polarity.

    Science.gov (United States)

    Yoo, Cheol-Min; Naramoto, Satoshi; Sparks, J Alan; Khan, Bibi Rafeiza; Nakashima, Jin; Fukuda, Hiroo; Blancaflor, Elison B

    2018-01-29

    AGD1, a plant ACAP-type ADP-ribosylation factor-GTPase activating protein (ARF-GAP), functions in specifying root hair polarity in Arabidopsis thaliana To better understand how AGD1 modulates root hair growth, we generated full-length and domain-deleted AGD1-green fluorescent protein (GFP) constructs, and followed their localization during root hair development. AGD1-GFP localized to the cytoplasm and was recruited to specific regions of the root hair plasma membrane (PM). Distinct PM AGD1-GFP signal was first detected along the site of root hair bulge formation. The construct continued to mark the PM at the root hair apical dome, but only during periods of reduced growth. During rapid tip growth, AGD1-GFP labeled the PM of the lateral flanks and dissipated from the apical-most PM. Deletion analysis and a single domain GFP fusion revealed that the pleckstrin homology (PH) domain is the minimal unit required for recruitment of AGD1 to the PM. Our results indicate that differential recruitment of AGD1 to specific PM domains is an essential component of the membrane trafficking machinery that facilitates root hair developmental phase transitions and responses to changes in the root microenvironment. © 2018. Published by The Company of Biologists Ltd.

  16. Polarized light microscopy reveals physiological and drug-induced changes in surfactant membrane assembly in alveolar type II pneumocytes.

    Science.gov (United States)

    Haller, Thomas; Cerrada, Alejandro; Pfaller, Kristian; Braubach, Peter; Felder, Edward

    2018-01-06

    In alveolar type II (AT II) cells, pulmonary surfactant (PS) is synthetized, stored and exocytosed from lamellar bodies (LBs), specialized large secretory organelles. By applying polarization microscopy (PM), we confirm a specific optical anisotropy of LBs, which indicates a liquid-crystalline mesophase of the stored surfactant phospholipids (PL) and an unusual case of a radiation-symmetric, spherocrystalline organelle. Evidence is shown that the degree of anisotropy is dependent on the amount of lipid layers and their degree of hydration, but unaffected by acutely modulating vital cell parameters like intravesicular pH or cellular energy supply. In contrast, physiological factors that perturb this structure include osmotic cell volume changes and LB exocytosis. In addition, we found two pharmaceuticals, Amiodarone and Ambroxol, both of which severely affect the liquid-crystalline order. Our study shows that PM is an easy, very sensitive, but foremost non-invasive and label-free method able to collect important structural information of PS assembly in live AT II cells which otherwise would be accessible by destructive or labor intense techniques only. This may open new approaches to dynamically investigate LB biosynthesis - the incorporation, folding and packing of lipid membranes - or the initiation of pathological states that manifest in altered LB structures. Due to the observed drug effects, we further suggest that PM provides an appropriate way to study unspecific drug interactions with alveolar cells and even drug-membrane interactions in general. Copyright © 2018 Elsevier B.V. All rights reserved.

  17. Temperature dependence of low-frequency polarized Raman scattering spectra in TlInS{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Paucar, Raul; Wakita, Kazuki [Electronics and Computer Engineering, Chiba Institute of Technology, Chiba (Japan); Shim, YongGu; Mimura, Kojiro [Graduate School of Engineering, Osaka Prefecture University, Osaka (Japan); Alekperov, Oktay; Mamedov, Nazim [Institute of Physics, Azerbaijan National Academy of Sciences, Baku (Azerbaijan)

    2017-06-15

    In this work, we examined phase transitions in the layered ternary thallium chalcogenide TlInS{sub 2} by studying the temperature dependence of polarized Raman spectra with the aid of the Raman confocal microscope system. The Raman spectra were measured over the temperature range of 77-320 K (which includes the range of successive phase transitions) in the low-frequency region of 35-180 cm{sup -1}. The optical phonons that showed strong temperature dependence were identified as interlayer vibrations related to phase transitions, while the phonons that showed weak temperature dependence were identified as intralayer vibrations. (copyright 2017 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  18. Quantitative analysis with advanced compensated polarized light microscopy on wavelength dependence of linear birefringence of single crystals causing arthritis

    Science.gov (United States)

    Takanabe, Akifumi; Tanaka, Masahito; Taniguchi, Atsuo; Yamanaka, Hisashi; Asahi, Toru

    2014-07-01

    To improve our ability to identify single crystals causing arthritis, we have developed a practical measurement system of polarized light microscopy called advanced compensated polarized light microscopy (A-CPLM). The A-CPLM system is constructed by employing a conventional phase retardation plate, an optical fibre and a charge-coupled device spectrometer in a polarized light microscope. We applied the A-CPLM system to measure linear birefringence (LB) in the visible region, which is an optical anisotropic property, for tiny single crystals causing arthritis, i.e. monosodium urate monohydrate (MSUM) and calcium pyrophosphate dihydrate (CPPD). The A-CPLM system performance was evaluated by comparing the obtained experimental data using the A-CPLM system with (i) literature data for a standard sample, MgF2, and (ii) experimental data obtained using an established optical method, high-accuracy universal polarimeter, for the MSUM. The A-CPLM system was found to be applicable for measuring the LB spectra of the single crystals of MSUM and CPPD, which cause arthritis, in the visible regions. We quantitatively reveal the large difference in LB between MSUM and CPPD crystals. These results demonstrate the usefulness of the A-CPLM system for distinguishing the crystals causing arthritis.

  19. Dual gene activation and knockout screen reveals directional dependencies in genetic networks. | Office of Cancer Genomics

    Science.gov (United States)

    Understanding the direction of information flow is essential for characterizing how genetic networks affect phenotypes. However, methods to find genetic interactions largely fail to reveal directional dependencies. We combine two orthogonal Cas9 proteins from Streptococcus pyogenes and Staphylococcus aureus to carry out a dual screen in which one gene is activated while a second gene is deleted in the same cell. We analyze the quantitative effects of activation and knockout to calculate genetic interaction and directionality scores for each gene pair.

  20. Polarization-dependent NEXAFS study of adsorption of long-chain surfactants on mechanically milled iron powder

    Energy Technology Data Exchange (ETDEWEB)

    Syugaev, A.V., E-mail: syual@mail.ru; Maratkanova, A.N.

    2014-08-15

    Highlights: • Plate-like particles modified with surfactant molecules were obtained under high-energy ball milling. • Adsorption layers were studied with polarization-dependent NEXAFS spectroscopy. • For the first time, arrangement of surfactants molecules on the powdered metal surface has been determined. • Tails of surfactant molecules (C-F/C-H) are shown to be oriented perpendicular to the particle surface. • Arrangement of carboxylate groups on the particle surfaces is discussed. - Abstract: In this work we have demonstrated the possibility of using the polarization-dependent NEXAFS spectra to study the structure of organic layers at the surface of powdered materials with plate-like shaped particles. The polarization dependence of the NEXAFS spectra may be easily obtained by just changing the angle between the X-ray beam direction and the substrate onto which the powder particles are set. For the first time, we have carried out a detailed study of the surfactant layers (n-perfluorononanoic and stearic acid), which are formed at the surface of iron plate-like particles under mechanical milling of iron powder with an addition of corresponding surfactants. The surfactant molecules are predominantly oriented perpendicular to the surface of the mechanically milled particles. Such orientation is similar to the arrangement of the molecules in the layers formed under equilibrium conditions, e.g. deposition from solutions. The changes in the chemical environment occurring in the molecule tails (defluorination or dehydrogenation) under mechanochemical treatment, do not result in a significant change in the molecular orientation and disordering of the adsorbed layer.

  1. Polarization-dependent in-line quasi-Michelson interferometer based on PM-PCF reflection.

    Science.gov (United States)

    Du, Yanying; Qiao, Xueguang; Rong, Qiangzhou; Zhang, Jing; Feng, Dingyi; Wang, Ruohui; Sun, Hao; Hu, Manli; Feng, Zhongyao

    2013-05-20

    An in-line fiber quasi-Michelson interferometer (IFQMI) working on reflection is proposed and experimentally demonstrated. The sensing head is fabricated by splicing a section of polarization-maintaining photonic crystal fiber (PM-PCF) with a lead-in single mode fiber (SMF). Some cladding modes are excited into the PM-PCF via the mismatch-core splicing interface between PM-PCF and SMF. Besides, two orthogonal polarized-modes are formed due to the inherent multiholes cladding structure of the PM-PCF. A well-defined interference pattern is obtained as the result of cladding-orthogonal modes interference. The IFQMI with 20 cm long PM-PCF is proposed for strain and torsion measurements. A strain sensitivity of -1.3 pm/με and a torsion sensitivity of -19.17 pm/deg are obtained, respectively. The proposed device with 10 cm long PM-PCF exhibits a considered temperature sensitivity of 9.9 pm/°C. The IFQMI has a compact structure and small size, making it a good candidate for multiparameter measurements.

  2. The phenomenology of optically pumped 13C NMR in diamond at 7.05 T: Room temperature polarization, orientation dependence, and the effect of defect concentration on polarization dynamics

    Science.gov (United States)

    Scott, Eric; Drake, Melanie; Reimer, Jeffrey A.

    2016-03-01

    Room temperature optical illumination of NV- imbibed single crystal diamonds with a 532 nm laser produces 13C polarization enhancements up to 200 times greater than that of the thermal equilibrium value at 7.05 T. We report high field NV- mediated 13C polarization as a function of the number and type (NV- and P1) of defects in commercially available diamonds. Surprisingly, both positive and negative 13C polarizations are observed depending on the orientation of the crystal with respect to the external magnetic field and the electric field vector of the optical illumination. The data reported herein cannot be explained by a previously proposed mechanism.

  3. Segment polarity gene expression in a myriapod reveals conserved and diverged aspects of early head patterning in arthropods.

    Science.gov (United States)

    Janssen, Ralf

    2012-09-01

    Arthropods show two kinds of developmental mode. In the so-called long germ developmental mode (as exemplified by the fly Drosophila), all segments are formed almost simultaneously from a preexisting field of cells. In contrast, in the so-called short germ developmental mode (as exemplified by the vast majority of arthropods), only the anterior segments are patterned similarly as in Drosophila, and posterior segments are added in a single or double segmental periodicity from a posterior segment addition zone (SAZ). The addition of segments from the SAZ is controlled by dynamic waves of gene activity. Recent studies on a spider have revealed that a similar dynamic process, involving expression of the segment polarity gene (SPG) hedgehog (hh), is involved in the formation of the anterior head segments. The present study shows that in the myriapod Glomeris marginata the early expression of hh is also in a broad anterior domain, but this domain corresponds only to the ocular and antennal segment. It does not, like in spiders, represent expression in the posterior adjacent segment. In contrast, the anterior hh pattern is conserved in Glomeris and insects. All investigated myriapod SPGs and associated factors are expressed with delay in the premandibular (tritocerebral) segment. This delay is exclusively found in insects and myriapods, but not in chelicerates, crustaceans and onychophorans. Therefore, it may represent a synapomorphy uniting insects and myriapods (Atelocerata hypothesis), contradicting the leading opinion that suggests a sister relationship of crustaceans and insects (Pancrustacea hypothesis). In Glomeris embryos, the SPG engrailed is first expressed in the mandibular segment. This feature is conserved in representatives of all arthropod classes suggesting that the mandibular segment may have a special function in anterior patterning.

  4. The Hanle effect in a random magnetic field. Dependence of the polarization on statistical properties of the magnetic field

    Science.gov (United States)

    Frisch, H.; Anusha, L. S.; Sampoorna, M.; Nagendra, K. N.

    2009-07-01

    Context: The Hanle effect is used to determine weak turbulent magnetic fields in the solar atmosphere, usually assuming that the angular distribution is isotropic, the magnetic field strength constant, and that micro-turbulence holds, i.e. that the magnetic field correlation length is much less than a photon mean free path. Aims: To examine the sensitivity of turbulent magnetic field measurements to these assumptions, we study the dependence of Hanle effect on the magnetic field correlation length, its angular, and strength distributions. Methods: We introduce a fairly general random magnetic field model characterized by a correlation length and a magnetic field vector distribution. Micro-turbulence is recovered when the correlation length goes to zero and macro-turbulence when it goes to infinity. Radiative transfer equations are established for the calculation of the mean Stokes parameters and they are solved numerically by a polarized approximate lambda iteration method. Results: We show that optically thin spectral lines and optically very thick ones are insensitive to the correlation length of the magnetic field, while spectral lines with intermediate optical depths (around 10-100) show some sensitivity to this parameter. The result is interpreted in terms of the mean number of scattering events needed to create the surface polarization. It is shown that the single-scattering approximation holds good for thin and thick lines but may fail for lines with intermediate thickness. The dependence of the polarization on the magnetic field vector probability density function (PDF) is examined in the micro-turbulent limit. A few PDFs with different angular and strength distributions, but equal mean value of the magnetic field, are considered. It is found that the polarization is in general quite sensitive to the shape of the magnetic field strength PDF and somewhat to the angular distribution. Conclusions: The mean field derived from Hanle effect analysis of

  5. Polarized dependence of nonlinear susceptibility in a single layer graphene system in infrared region

    Energy Technology Data Exchange (ETDEWEB)

    Solookinejad, G., E-mail: ghsolooki@gmail.com

    2016-09-15

    In this study, the linear and nonlinear susceptibility of a single-layer graphene nanostructure driven by a weak probe light and an elliptical polarized coupling field is discussed theoretically. The Landau levels of graphene can be separated in infrared or terahertz regions under the strong magnetic field. Therefore, by using the density matrix formalism in quantum optic, the linear and nonlinear susceptibility of the medium can be derived. It is demonstrated that by adjusting the elliptical parameter, one can manipulate the linear and nonlinear absorption as well as Kerr nonlinearity of the medium. It is realized that the enhanced Kerr nonlinearity can be possible with zero linear absorption and nonlinear amplification at some values of elliptical parameter. Our results may be having potential applications in quantum information science based on Nano scales devices.

  6. The enzymes of biotin dependent CO2 metabolism: What structures reveal about their reaction mechanisms

    Science.gov (United States)

    Waldrop, Grover L; Holden, Hazel M; Maurice, Martin St

    2012-01-01

    Biotin is the major cofactor involved in carbon dioxide metabolism. Indeed, biotin-dependent enzymes are ubiquitous in nature and are involved in a myriad of metabolic processes including fatty acid synthesis and gluconeogenesis. The cofactor, itself, is composed of a ureido ring, a tetrahydrothiophene ring, and a valeric acid side chain. It is the ureido ring that functions as the CO2 carrier. A complete understanding of biotin-dependent enzymes is critically important for translational research in light of the fact that some of these enzymes serve as targets for anti-obesity agents, antibiotics, and herbicides. Prior to 1990, however, there was a dearth of information regarding the molecular architectures of biotin-dependent enzymes. In recent years there has been an explosion in the number of three-dimensional structures reported for these proteins. Here we review our current understanding of the structures and functions of biotin-dependent enzymes. In addition, we provide a critical analysis of what these structures have and have not revealed about biotin-dependent catalysis. PMID:22969052

  7. Solvent dependency of the UV-Vis spectrum of indenoisoquinolines: role of keto-oxygens as polarity interaction probes.

    Directory of Open Access Journals (Sweden)

    Andrea Coletta

    Full Text Available Indenoisoquinolines are the most promising non-campthotecins topoisomerase IB inhibitors. We present an integrated experimental/computational investigation of the UV-Vis spectra of the IQNs parental compound (NSC314622 and two of its derivatives (NSC724998 and NSC725776 currently undergoing Phase I clinical trials. In all the three compounds a similar dependence of the relative absorption intensities at 270 nm and 290 nm on solvent polarity is found. The keto-oxygens in positions 5 and 11 of the molecular scaffold of the molecule are the principal chromophores involved in this dependence. Protic interactions on these sites are also found to give rise to absorptions at wavelength <250 nm observed in water solution, due to the stabilization of highly polarized tautomers of the molecule. These results suggest that the keto-oxygens are important polarizable groups that can act as useful interactors with the molecular receptor, providing at the same time an useful fingerprint for the monitoring of the drug binding to topoisomerase IB.

  8. Crystal structure of NAD+-dependent Peptoniphilus asaccharolyticus glutamate dehydrogenase reveals determinants of cofactor specificity.

    Science.gov (United States)

    Oliveira, Tânia; Panjikar, Santosh; Carrigan, John B; Hamza, Muaawia; Sharkey, Michael A; Engel, Paul C; Khan, Amir R

    2012-02-01

    Glutamate dehydrogenases (EC 1.4.1.2-4) catalyse the oxidative deamination of l-glutamate to α-ketoglutarate using NAD(P) as a cofactor. The bacterial enzymes are hexamers and each polypeptide consists of an N-terminal substrate-binding (Domain I) followed by a C-terminal cofactor-binding segment (Domain II). The reaction takes place at the junction of the two domains, which move as rigid bodies and are presumed to narrow the cleft during catalysis. Distinct signature sequences in the nucleotide-binding domain have been linked to NAD(+) vs. NADP(+) specificity, but they are not unambiguous predictors of cofactor preferences. Here, we have determined the crystal structure of NAD(+)-specific Peptoniphilus asaccharolyticus glutamate dehydrogenase in the apo state. The poor quality of native crystals was resolved by derivatization with selenomethionine, and the structure was solved by single-wavelength anomalous diffraction methods. The structure reveals an open catalytic cleft in the absence of substrate and cofactor. Modeling of NAD(+) in Domain II suggests that a hydrophobic pocket and polar residues contribute to nucleotide specificity. Mutagenesis and isothermal titration calorimetry studies of a critical glutamate at the P7 position of the core fingerprint confirms its role in NAD(+) binding. Finally, the cofactor binding site is compared with bacterial and mammalian enzymes to understand how the amino acid sequences and three-dimensional structures may distinguish between NAD(+) vs. NADP(+) recognition. Copyright © 2011 Elsevier Inc. All rights reserved.

  9. Dynamic nuclear spin polarization

    Energy Technology Data Exchange (ETDEWEB)

    Stuhrmann, H.B. [GKSS-Forschungszentrum Geesthacht GmbH (Germany)

    1996-11-01

    Polarized neutron scattering from dynamic polarized targets has been applied to various hydrogenous materials at different laboratories. In situ structures of macromolecular components have been determined by nuclear spin contrast variation with an unprecedented precision. The experiments of selective nuclear spin depolarisation not only opened a new dimension to structural studies but also revealed phenomena related to propagation of nuclear spin polarization and the interplay of nuclear polarisation with the electronic spin system. The observation of electron spin label dependent nuclear spin polarisation domains by NMR and polarized neutron scattering opens a way to generalize the method of nuclear spin contrast variation and most importantly it avoids precontrasting by specific deuteration. It also likely might tell us more about the mechanism of dynamic nuclear spin polarisation. (author) 4 figs., refs.

  10. Epitope-dependent mechanisms of CD27 neutralization revealed by X-ray crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Obmolova, Galina; Teplyakov, Alexey; Malia, Thomas J.; Wunderler, Nicole; Kwok, Deborah; Barone, Linda; Sweet, Raymond; Ort, Tatiana; Scully, Michael; Gilliland, Gary L. (Janssen)

    2017-03-01

    CD27 is a T and B cell co-stimulatory protein of the TNF receptor superfamily dependent on the availability of the TNF-like ligand CD70. Two anti-CD27 neutralizing monoclonal antibodies were obtained from mouse hybridoma and subsequently humanized and optimized for binding the target. The two antibodies are similar in terms of their CD27-binding affinity and ability to block NF-κB signaling, however their clearance rates in monkeys are very different. The pharmacokinetics profiles could be epitope dependent. To identify the epitopes, we determined the crystal structure of the ternary complex between CD27 and the Fab fragments of these non-competing antibodies. The structure reveals the binding modes of the antibodies suggesting that their mechanisms of action are distinctly different and provides a possible explanation of the in vivo data.

  11. Weak antilocalization effect in exfoliated black phosphorus revealed by temperature- and angle-dependent magnetoconductivity

    KAUST Repository

    Hou, Zhipeng

    2018-01-10

    Recently, there have been increasingly debates on whether there exists a surface resonance state (SRS) in black phosphorus (BP), as suggested by recent angle-resolved photoemission spectroscopy (ARPES) results. To resolve this issue, we have performed temperature- and angle-dependent magnetoconductivity measurements on exfoliated, high-quality BP single crystals. A pronounced weak-antilocalization (WAL) effect was observed within a narrow temperature range of 8 - 16 K, with the electrical current flowing parallel to the cleaved ac-plane (along the a- or c-axis) and the magnetic field along the b-axis. The angle-dependent magnetoconductivity and the Hikami-Larkin-Nagaoka (HLN) model-fitted results have revealed that the observed WAL effect shows surface-bulk coherent features, which supports the existence of SRS in black phosphorus.

  12. Polarization-dependent optical characterization of poly(phenylquinoxaline) thin films

    Science.gov (United States)

    Ksianzou, V.; Velagapudi, R. K.; Grimm, B.; Schrader, S.

    2006-09-01

    Linear optical properties of two types of poly(phenylquinoxaline) (PPQ) are studied by multiwavelength prism coupling technique and optical absorption spectroscopy. Surface roughness measurements are done using atomic force microscopy. PPQs form smooth films of high optical quality having refractive indices above 1.7 in the visible and near infrared spectral ranges. Enhanced birefringence of Δn ˜0.04 has been observed in both PPQ films prepared by spin coating. Sellmeier coefficients are derived for the wavelength range starting from 0.532to1.064μm for both TE and TM polarizations. Quantum chemical calculations both on the semiempirical and on the ab initio level are carried out in order to calculate the first-order molecular polarizability tensors of the polymer repeat units. From the obtained tensor elements, theoretical values for both the average refractive indices and the maximum expectable birefringence are calculated. Based on these values a more detailed interpretation of the experimental findings is carried out. The dispersion of refractive index is quantified by the value of Abbe's constant (νd). In our case the value νd≈11 indicates high dispersion in the visible spectral range. The imaginary part k of the complex refractive index n*=n-ik reaches values of k ⩽10-3 in the wavelength range from 0.5to1μm.

  13. A Density-Dependent Switch Drives Stochastic Clustering and Polarization of Signaling Molecules

    Science.gov (United States)

    Jilkine, Alexandra; Angenent, Sigurd B.; Wu, Lani F.; Altschuler, Steven J.

    2011-01-01

    Positive feedback plays a key role in the ability of signaling molecules to form highly localized clusters in the membrane or cytosol of cells. Such clustering can occur in the absence of localizing mechanisms such as pre-existing spatial cues, diffusional barriers, or molecular cross-linking. What prevents positive feedback from amplifying inevitable biological noise when an un-clustered “off” state is desired? And, what limits the spread of clusters when an “on” state is desired? Here, we show that a minimal positive feedback circuit provides the general principle for both suppressing and amplifying noise: below a critical density of signaling molecules, clustering switches off; above this threshold, highly localized clusters are recurrently generated. Clustering occurs only in the stochastic regime, suggesting that finite sizes of molecular populations cannot be ignored in signal transduction networks. The emergence of a dominant cluster for finite numbers of molecules is partly a phenomenon of random sampling, analogous to the fixation or loss of neutral mutations in finite populations. We refer to our model as the “neutral drift polarity model.” Regulating the density of signaling molecules provides a simple mechanism for a positive feedback circuit to robustly switch between clustered and un-clustered states. The intrinsic ability of positive feedback both to create and suppress clustering is a general mechanism that could operate within diverse biological networks to create dynamic spatial organization. PMID:22102805

  14. Polarization dependent Pd deposition structure on LiNbO3 {0001} surface

    Science.gov (United States)

    Kim, Seungchul; Rappe, Andrew M.

    2011-03-01

    We investigate effects of polarization orientation on atomic structure of palladium deposited on lithium niobate (LiNb O3) {0001} surface, using density functional theory (DFT) and kinetic Monte Carlo (kMC) simulations. Adsorption, diffusion, aggregation and clustering process -- include geometries, paths and energies -- of Pd clusters were calculated from DFT simulations. It has been observed that energy barriers of Pd motions on the negatively poled (c-) surface are much larger than those on the positively poled surface (c+), which indicates the Pd motions on the c- surface are much slower than that of c+ surface. We demonstrate, using kMC with kinetic parameters from DFT, very slow motion of Pd on c- surface leads dispersed small clusters or atoms while fast motion on c+ surface leads large clusters, indicating larger Pd-covered area on c- surface than c+ after Pd deposition. This work has been supported by US-DOE (grant DE-FG02-07ER15920), and by AROSR (FA9550-07-1-0397). Computational support was provided by HPCMO of the US-DoD.

  15. A density-dependent switch drives stochastic clustering and polarization of signaling molecules.

    Directory of Open Access Journals (Sweden)

    Alexandra Jilkine

    2011-11-01

    Full Text Available Positive feedback plays a key role in the ability of signaling molecules to form highly localized clusters in the membrane or cytosol of cells. Such clustering can occur in the absence of localizing mechanisms such as pre-existing spatial cues, diffusional barriers, or molecular cross-linking. What prevents positive feedback from amplifying inevitable biological noise when an un-clustered "off" state is desired? And, what limits the spread of clusters when an "on" state is desired? Here, we show that a minimal positive feedback circuit provides the general principle for both suppressing and amplifying noise: below a critical density of signaling molecules, clustering switches off; above this threshold, highly localized clusters are recurrently generated. Clustering occurs only in the stochastic regime, suggesting that finite sizes of molecular populations cannot be ignored in signal transduction networks. The emergence of a dominant cluster for finite numbers of molecules is partly a phenomenon of random sampling, analogous to the fixation or loss of neutral mutations in finite populations. We refer to our model as the "neutral drift polarity model." Regulating the density of signaling molecules provides a simple mechanism for a positive feedback circuit to robustly switch between clustered and un-clustered states. The intrinsic ability of positive feedback both to create and suppress clustering is a general mechanism that could operate within diverse biological networks to create dynamic spatial organization.

  16. GREEN BANK TELESCOPE DETECTION OF POLARIZATION-DEPENDENT H I ABSORPTION AND H I OUTFLOWS IN LOCAL ULIRGs AND QUASARS

    Energy Technology Data Exchange (ETDEWEB)

    Teng, Stacy H. [Observational Cosmology Laboratory, NASA Goddard Space Flight Center, Greenbelt, MD 20771 (United States); Veilleux, Sylvain [Department of Astronomy, University of Maryland, College Park, MD 20742 (United States); Baker, Andrew J., E-mail: stacy.h.teng@nasa.gov [Department of Physics and Astronomy, Rutgers, State University of New Jersey, Piscataway, NJ 08854 (United States)

    2013-03-10

    We present the results of a 21 cm H I survey of 27 local massive gas-rich late-stage mergers and merger remnants with the Robert C. Byrd Green Bank Telescope. These remnants were selected from the Quasar/ULIRG Evolution Study sample of ultraluminous infrared galaxies (ULIRGs; L{sub 8{sub -{sub 1000{sub {mu}m}}}} > 10{sup 12} L{sub Sun }) and quasars; our targets are all bolometrically dominated by active galactic nuclei (AGNs) and sample the later phases of the proposed ULIRG-to-quasar evolutionary sequence. We find the prevalence of H I absorption (emission) to be 100% (29%) in ULIRGs with H I detections, 100% (88%) in FIR-strong quasars, and 63% (100%) in FIR-weak quasars. The absorption features are associated with powerful neutral outflows that change from being mainly driven by star formation in ULIRGs to being driven by the AGN in the quasars. These outflows have velocities that exceed 1500 km s{sup -1} in some cases. Unexpectedly, we find polarization-dependent H I absorption in 57% of our spectra (88% and 63% of the FIR-strong and FIR-weak quasars, respectively). We attribute this result to absorption of polarized continuum emission from these sources by foreground H I clouds. About 60% of the quasars displaying polarized spectra are radio-loud, far higher than the {approx}10% observed in the general AGN population. This discrepancy suggests that radio jets play an important role in shaping the environments in these galaxies. These systems may represent a transition phase in the evolution of gas-rich mergers into ''mature'' radio galaxies.

  17. Large-Scale Phosphoproteomics Reveals Shp-2 Phosphatase-Dependent Regulators of Pdgf Receptor Signaling

    Directory of Open Access Journals (Sweden)

    Tanveer S. Batth

    2018-03-01

    Full Text Available Despite its low cellular abundance, phosphotyrosine (pTyr regulates numerous cell signaling pathways in health and disease. We applied comprehensive phosphoproteomics to unravel differential regulators of receptor tyrosine kinase (RTK-initiated signaling networks upon activation by Pdgf-ββ, Fgf-2, or Igf-1 and identified more than 40,000 phosphorylation sites, including many phosphotyrosine sites without additional enrichment. The analysis revealed RTK-specific regulation of hundreds of pTyr sites on key signaling molecules. We found the tyrosine phosphatase Shp-2 to be the master regulator of Pdgfr pTyr signaling. Application of a recently introduced allosteric Shp-2 inhibitor revealed global regulation of the Pdgf-dependent tyrosine phosphoproteome, which significantly impaired cell migration. In addition, we present a list of hundreds of Shp-2-dependent targets and putative substrates, including Rasa1 and Cortactin with increased pTyr and Gab1 and Erk1/2 with decreased pTyr. Our study demonstrates that large-scale quantitative phosphoproteomics can precisely dissect tightly regulated kinase-phosphatase signaling networks.

  18. Constraints on direction-dependent cosmic birefringence from Planck polarization data

    Science.gov (United States)

    Contreras, Dagoberto; Boubel, Paula; Scott, Douglas

    2017-12-01

    Cosmic birefringence is the process that rotates the plane of polarization by an amount, α, as photons propagate through free space. Such an effect arises in parity-violating extensions to the electromagnetic sector, such as the Chern-Simons term common in axion models, quintessence models, or Lorentz-violating extensions to the standard model. Most studies consider the monopole of this rotation, but it is also possible for the effect to have spatial anisotropies. Paying particular attention to large scales, we implement a novel pixel-based method to extract the spherical harmonics for L 30. Our results are consistent with no detection and we set 95 % upper limits on the amplitude of a scale-invariant power spectrum of L(L+1)CL/2π<[2.2 (stat.)±0.7 (syst.)]×10-5=[0.07 (stat.)±0.02 (syst.)] deg2, on par with previous constraints. This implies specific limits on the dipole and quadrupole amplitudes to be √C1/4π lesssim 0.o2 and √C2/4π lesssim 0.o1, at 95 % CL, respectively, improving previous constraints by an order of magnitude. We further constrain a model independent M=0 quadrupole in an arbitrary direction to be α20 = 0.o02 ± 0.o21, with an unconstrained direction. However, we find an excess of dipolar power with an amplitude √3C1/4π = 0.o32±0.o10 (stat.)±0.o08 (syst.)], in the direction (l,b)=(295o,17o)±(22o,17o) (stat.)±(5o,16o) (syst.), larger than 1.4 % of simulations with no birefringence. We attribute part of this signal to the contamination of residual foregrounds not accounted for in our simulations, although this should be further investigated.

  19. The spin-dependent structure function $g_1(x)$ of the proton from polarized deep-inelastic muon scattering

    CERN Document Server

    Adeva, B; Arvidson, A; Badelek, B; Bardin, G; Baum, G; Berglund, P; Betev, L; Birsa, R; De Botton, N R; Bradamante, Franco; Bravar, A; Bressan, A; Bültmann, S; Burtin, E; Crabb, D; Cranshaw, J; Çuhadar-Dönszelmann, T; Dalla Torre, S; Van Dantzig, R; Derro, B R; Deshpande, A A; Dhawan, S K; Dulya, C M; Eichblatt, S; Fasching, D; Feinstein, F; Fernández, C; Forthmann, S; Frois, Bernard; Gallas, A; Garzón, J A; Gilly, H; Giorgi, M A; Görtz, S; Gracia, G; De Groot, N; Haft, K; Von Harrach, D; Hasegawa, T; Hautle, P; Hayashi, N; Heusch, C A; Horikawa, N; Hughes, V W; Igo, G; Ishimoto, S; Iwata, T; Kabuss, E M; Kageya, T; Karev, A G; Ketel, T; Kiryluk, J; Kiselev, Yu F; Krivokhizhin, V G; Kröger, W; Kukhtin, V V; Kurek, K; Kyynäräinen, J; Lamanna, M; Landgraf, U; Le Goff, J M; Lehár, F; de Lesquen, A; Lichtenstadt, J; Litmaath, M; Magnon, A; Mallot, G K; Marie, F; Martin, A; Martino, J; Matsuda, T; Mayes, B W; McCarthy, J S; Medved, K S; Meyer, W T; Van Middelkoop, G; Miller, D; Miyachi, Y; Mori, K; Moromisato, J H; Nassalski, J P; Naumann, Lutz; Niinikoski, T O; Oberski, J; Ogawa, A; Grosse-Perdekamp, M; Pereira, H; Perrot-Kunne, F; Peshekhonov, V D; Pinsky, L; Platchkov, S K; Pló, M; Pose, D; Postma, H; Pretz, J; Puntaferro, R; Rädel, G; Rijllart, A; Reicherz, G; Rodríguez, M; Rondio, Ewa; Roscherr, B; Sabo, I; Saborido, J; Sandacz, A; Savin, I A; Schiavon, R P; Schiller, A; Sichtermann, E P; Simeoni, F; Smirnov, G I; Staude, A; Steinmetz, A; Stiegler, U; Stuhrmann, H B; Szleper, M; Tessarotto, F; Thers, D; Tlaczala, W; Tripet, A; Ünel, G; Velasco, M; Vogt, J; Voss, Rüdiger; Whitten, C; Windmolders, R; Wislicki, W; Witzmann, A; Ylöstalo, J; Zanetti, A M; Zaremba, K

    1997-01-01

    We present a new measurement of the virtual photon proton asymmetry $A_1^{\\rm p}$ from deep inelastic scattering of polarized muons on polarized protons in the kinematic range $0.0008 1$ GeV$^{2}$. A perturbative QCD evolution in next-to-leading order is used to determine $g_1^{\\rm p}(x)$ at a constant $Q^2$. At $Q^{2} = 10$ GeV$^{2}$ we find, in the measured range, $\\int_{0.003}^{0.7} g_{1}^{\\rm p}(x){\\rm d}x = 0.139 \\pm 0.006~({\\rm stat})\\pm 0.008~({\\rm syst)} \\pm 0.006~({\\rm evol})$. The value of the first moment $\\Gamma_{1}^{\\rm p} = \\int_{0}^{1} g_{1}^{\\rm p}(x){\\rm d}x$ of $g_{1}^{\\rm p}$ depends on the approach used to describe the behaviour of $g_{1}^{\\rm p}$ at low $x$. We find that the Ellis-Jaffe sum rule is violated. With our published result for $\\Gamma_{1}^{\\rm d}$ we confirm the Bjorken sum rule with an accuracy of $\\approx 15\\%$ at the one standard deviation level.

  20. The spin-dependent structure function $g_{1}(x)$ of the deuteron from polarized deep-inelastic muon scattering

    CERN Document Server

    Adams, D; Adeva, B; Akdogan, T; Arik, E; Arvidson, A; Badelek, B; Ballintijn, M K; Bardin, Dimitri Yuri; Bardin, G; Baum, G; Berglund, P; Betev, L; Bird, I G; Birsa, R; Björkholm, P; Bonner, B E; De Botton, N R; Boutemeur, M; Bradamante, Franco; Bravar, A; Bressan, A; Bültmann, S; Burtin, E; Cavata, C; Crabb, D; Cranshaw, J; Çuhadar-Dönszelmann, T; Dalla Torre, S; Van Dantzig, R; Derro, B R; Deshpande, A A; Dhawan, S K; Dulya, C M; Dyring, A; Eichblatt, S; Faivre, Jean-Claude; Fasching, D; Feinstein, F; Fernández, C; Frois, Bernard; Gallas, A; Garzón, J A; Gaussiran, T; Giorgi, M A; von Goeler, E; Gómez, F; Gracia, G; De Groot, N; Grosse-Perdekamp, M; Von Harrach, D; Hasegawa, T; Hautle, P; Hayashi, N; Heusch, C A; Horikawa, N; Hughes, V W; Igo, G; Ishimoto, S; Iwata, T; Kabuss, E M; Kageya, T; Kalinovskaya, L V; Karev, A G; Kessler, H J; Ketel, T; Kiryluk, J; Kishi, A; Kiselev, Yu F; Klostermann, L; Krämer, Dietrich; Krivokhizhin, V G; Kröger, W; Kukhtin, V V; Kurek, K; Kyynäräinen, J; Lamanna, M; Landgraf, U; Le Goff, J M; Lehár, F; de Lesquen, A; Lichtenstadt, J; Lindqvist, T; Litmaath, M; Loewe, M; Magnon, A; Mallot, G K; Marie, F; Martin, A; Martino, J; Matsuda, T; Mayes, B W; McCarthy, J S; Medved, K S; Van Middelkoop, G; Miller, D; Mori, K; Moromisato, J H; Nagaitsev, A P; Nassalski, J P; Naumann, Lutz; Niinikoski, T O; Oberski, J; Ogawa, A; Ozben, C; Parks, D P; Perrot-Kunne, F; Peshekhonov, V D; Piegaia, R; Pinsky, L; Platchkov, S K; Pló, M; Polec, J; Pose, D; Postma, H; Pretz, J; Puntaferro, R; Pussieux, T; Pyrlik, J; Rädel, G; Rijllart, A; Roberts, J B; Rock, S E; Rodríguez, M; Rondio, Ewa; Rosado, A; Sabo, I; Saborido, J; Sandacz, A; Savin, I A; Schiavon, R P; Schüler, K P; Seitz, R; Semertzidis, Y K; Sever, F; Shanahan, P; Sichtermann, E P; Simeoni, F; Smirnov, G I; Staude, A; Steinmetz, A; Steigler, U; Stuhrmann, H B; Szleper, M; Teichert, K M; Tessarotto, F; Tlaczala, W; Trentalange, S; Tripet, A; Ünel, G; Velasco, M; Vogt, J; Voss, Rüdiger; Weinstein, R; Whitten, C; Windmolders, R; Willumeit, R; Wislicki, W; Witzmann, A; Yañez, A; Ylöstalo, J; Zanetti, A M; Zaremba, K; Zhao, J

    1997-01-01

    We present a new measurement of the spin-dependent structure function $g_{1}^{\\rm d}$ of the deuteron from deep inelastic scattering of 190 GeV polarized muons on polarized deuterons. The results are combined with our previous measurements of $g_{1}^{\\rm d}$. A perturbative QCD evolution in next-to-leading order is used to compute $g_{1}^{\\rm d}(x)$ at a constant $Q^{2}$. At $Q^{2} = 10$ GeV$^{2}$, we obtain a first moment $\\Gamma_{1}^{\\rm d} = \\int_{0}^{1} g_{1}^{\\rm d}{\\rm d}x = 0.041 \\pm 0.008$, a flavour-singlet axial charge of the nucleon $a_{0} = 0.30 \\pm 0.08$, and an axial charge of the strange quark $a_{s} = -0.09 \\pm 0.03$. Using our earlier determination of $\\Gamma_{1}^{\\rm p}$, we obtain $\\Gamma_1^{\\rm p} - \\Gamma_1^{\\rm n} = 0.183 \\pm 0.035$ at $Q^2 = 10\\,\\mbox{GeV}^2$. This result is in agreement with the Bjorken sum rule which predicts $\\Gamma_1^{\\rm p} - \\Gamma_1^{\\rm n} = 0.186 \\pm 0.002$ at the same $Q^2$.

  1. Mammalian diaphanous-related formin 1 regulates GSK3β-dependent microtubule dynamics required for T cell migratory polarization.

    Directory of Open Access Journals (Sweden)

    Baoxia Dong

    Full Text Available The mammalian diaphanous-related formin (mDia1, a Rho-regulated cytoskeletal modulator, has been shown to promote T lymphocyte chemotaxis and interaction with antigen presenting cells, but the mechanisms underpinning mDia1 roles in these processes have not been defined. Here we show that mDia1(-/- T cells exhibit impaired lymphocyte function-associated antigen 1 (LFA-1-mediated T cell adhesion, migration and in vivo trafficking. These defects are associated with impaired microtubule (MT polarization and stabilization, altered MT dynamics and reduced peripheral clustering of the MT plus-end-protein, adenomatous polyposis coli (APC in migrating T cells following LFA-1-engagement. Loss of mDia1 also leads to impaired inducible inactivation of the glycogen synthase kinase (GSK 3β as well as hyperphosphorylation and reduced levels of APC in migrating T cells. These findings identify essential roles for the mDia1 formin in modulating GSK3β-dependent MT contributions to induction of T-cell polarity, adhesion and motility.

  2. RNAi screen reveals an Abl kinase-dependent host cell pathway involved in Pseudomonas aeruginosa internalization.

    Directory of Open Access Journals (Sweden)

    Julia F Pielage

    2008-03-01

    Full Text Available Internalization of the pathogenic bacterium Pseudomonas aeruginosa by non-phagocytic cells is promoted by rearrangements of the actin cytoskeleton, but the host pathways usurped by this bacterium are not clearly understood. We used RNAi-mediated gene inactivation of approximately 80 genes known to regulate the actin cytoskeleton in Drosophila S2 cells to identify host molecules essential for entry of P. aeruginosa. This work revealed Abl tyrosine kinase, the adaptor protein Crk, the small GTPases Rac1 and Cdc42, and p21-activated kinase as components of a host signaling pathway that leads to internalization of P. aeruginosa. Using a variety of complementary approaches, we validated the role of this pathway in mammalian cells. Remarkably, ExoS and ExoT, type III secreted toxins of P. aeruginosa, target this pathway by interfering with GTPase function and, in the case of ExoT, by abrogating P. aeruginosa-induced Abl-dependent Crk phosphorylation. Altogether, this work reveals that P. aeruginosa utilizes the Abl pathway for entering host cells and reveals unexpected complexity by which the P. aeruginosa type III secretion system modulates this internalization pathway. Our results furthermore demonstrate the applicability of using RNAi screens to identify host signaling cascades usurped by microbial pathogens that may be potential targets for novel therapies directed against treatment of antibiotic-resistant infections.

  3. Polarization-dependent spectra in the photoassociative ionization of cold atoms in a bright sodium beam

    International Nuclear Information System (INIS)

    Ramirez-Serrano, Jaime; DeGraffenreid, William; Weiner, John

    2002-01-01

    We report measurements of cold photoassociative ionization (PAI) spectra obtained from collisions within a slow, bright Na atomic beam. A high-brightness atom flux, obtained by optical cooling and focusing of the atom beam, permits a high degree of alignment and orientation of binary collisions with respect to the laboratory atom-beam axis. The results reveal features of PAI spectra not accessible in conventional magneto-optical trap studies. We take advantage of this high degree of alignment to selectively excite autoionizing doubly excited states of specific symmetry

  4. Vertebrate kidney tubules elongate using a planar cell polarity-dependent, rosette-based mechanism of convergent extension.

    Science.gov (United States)

    Lienkamp, Soeren S; Liu, Kun; Karner, Courtney M; Carroll, Thomas J; Ronneberger, Olaf; Wallingford, John B; Walz, Gerd

    2012-12-01

    Cystic kidney diseases are a global public health burden, affecting over 12 million people. Although much is known about the genetics of kidney development and disease, the cellular mechanisms driving normal kidney tubule elongation remain unclear. Here, we used in vivo imaging to show for the first time that mediolaterally oriented cell intercalation is fundamental to vertebrate kidney morphogenesis. Unexpectedly, we found that kidney tubule elongation is driven in large part by a myosin-dependent, multicellular rosette-based mechanism, previously only described in Drosophila melanogaster. In contrast to findings in Drosophila, however, non-canonical Wnt and planar cell polarity (PCP) signaling is required to control rosette topology and orientation during vertebrate kidney tubule elongation. These data resolve long-standing questions concerning the role of PCP signaling in the developing kidney and, moreover, establish rosette-based intercalation as a deeply conserved cellular engine for epithelial morphogenesis.

  5. Direct transverse load profile determination using the polarization-dependent loss spectral response of a chirped fiber Bragg grating.

    Science.gov (United States)

    Descamps, Frédéric; Bette, Sébastien; Kinet, Damien; Caucheteur, Christophe

    2016-06-01

    The determination of stress profiles created by transverse loads was proved to be important in different domains, such as structural health monitoring and biomechanics, and, more specifically, in the prostheses domain. In this paper, we report an original method to estimate the transverse load profile from the polarization-dependent loss (PDL) spectrum of a chirped fiber Bragg grating (CFBG). This method makes use of the relationship between the integration of the PDL of a CFBG, and the force profile has the advantage of not requiring any iterative method to estimate the transverse load profile. The relationship linking the integration of the PDL and the force profile is demonstrated using an analytical approximation of the transmission spectrum of CFBGs. The validity of this method for the determination of non-uniform load profiles is then shown using a numerical analysis. An experimental demonstration is finally reported using a 48 mm-long CFBG subject to different step transverse load profiles.

  6. In vitro biomonitoring in polar extracts of solid phase matrices reveals the presence of unknown compounds with estrogenic activity

    NARCIS (Netherlands)

    Legler, J.; Leonards, P.E.G.; Spenkelink, A.; Murk, A.J.

    2003-01-01

    Determination of estrogenic activity has so far mainly concentrated on the assessment of compounds in surface water and effluent. This study is one of the first to biomonitor (xeno-)estrogens in sediment, suspended particulate matter and aquatic organisms. The relatively polar acetone extracts from

  7. Low temporal variation in the intact polar lipid composition of North Sea coastal marine water reveals limited chemotaxonomic value

    NARCIS (Netherlands)

    Brandsma, J.; Hopmans, E.C.; Philippart, C.J.M.; Veldhuis, M.J.W.; Schouten, S.; Sinninghe Damsté, J.S.S.

    2012-01-01

    Temporal variations in the abundance and composition of intact polar lipids (IPLs) in North Sea coastal marine water were assessed over a one-year seasonal cycle, and compared with environmental parameters and the microbial community composition. Sulfoquinovosyldiacylglycerol (SQDG) was the most

  8. Determination of scattering coefficient considering wavelength and absorption dependence of anisotropy factor measured by polarized beam for biological tissues

    Science.gov (United States)

    Fukutomi, D.; Ishii, K.; Awazu, K.

    2015-12-01

    Anisotropy factor g, one of the optical properties of biological tissues, is the most important parameter to accurately determine scattering coefficient μs in the inverse Monte Carlo (iMC) simulation. It has been reported that g has wavelength and absorption dependence, however, there are few attempts in order to calculate μs of biological tissue considering the wavelength and absorption dependence of g. In this study, the scattering angular distributions of biological tissue phantoms were measured in order to determine g by using goniometric measurements with three polarization conditions at strongly and weakly absorbing wavelengths of hemoglobin. Then, optical properties, especially, μs were measured by integrating sphere measurements and iMC simulation in order to confirm the influence of measured g on optical properties in comparison of with general value of g (0.9) for soft biological tissue. Consequently, it was found that μs was overestimated at strongly absorbing wavelength, however, μs was underestimated at weakly absorbing wavelength if the g was not considered its wavelength and absorption dependence.

  9. Predicting invasive species impacts: a community module functional response approach reveals context dependencies.

    Science.gov (United States)

    Paterson, Rachel A; Dick, Jaimie T A; Pritchard, Daniel W; Ennis, Marilyn; Hatcher, Melanie J; Dunn, Alison M

    2015-03-01

    Predatory functional responses play integral roles in predator-prey dynamics, and their assessment promises greater understanding and prediction of the predatory impacts of invasive species. Other interspecific interactions, however, such as parasitism and higher-order predation, have the potential to modify predator-prey interactions and thus the predictive capability of the comparative functional response approach. We used a four-species community module (higher-order predator; focal native or invasive predators; parasites of focal predators; native prey) to compare the predatory functional responses of native Gammarus duebeni celticus and invasive Gammarus pulex amphipods towards three invertebrate prey species (Asellus aquaticus, Simulium spp., Baetis rhodani), thus, quantifying the context dependencies of parasitism and a higher-order fish predator on these functional responses. Our functional response experiments demonstrated that the invasive amphipod had a higher predatory impact (lower handling time) on two of three prey species, which reflects patterns of impact observed in the field. The community module also revealed that parasitism had context-dependent influences, for one prey species, with the potential to further reduce the predatory impact of the invasive amphipod or increase the predatory impact of the native amphipod in the presence of a higher-order fish predator. Partial consumption of prey was similar for both predators and occurred increasingly in the order A. aquaticus, Simulium spp. and B. rhodani. This was associated with increasing prey densities, but showed no context dependencies with parasitism or higher-order fish predator. This study supports the applicability of comparative functional responses as a tool to predict and assess invasive species impacts incorporating multiple context dependencies. © 2014 The Authors. Journal of Animal Ecology © 2014 British Ecological Society.

  10. Temperature Dependence of the Inhibition of Positronium by Chlorine- Substituted Hydrocarbons in Non-Polar Liquids

    DEFF Research Database (Denmark)

    Wikander, G.; Mogensen, O.E.; Pedersen, Niels Jørgen

    1984-01-01

    Positron annihilation lifetime spectra were measured for solutions of 1,2,3,5-C6H2Cl4 in hexane, toluene, m-xylene and mesitylene, CCl4 in hexane and toluene, and C2HCl3 in n-hexane for concentrations below 1 M and at various temperatures between −30°C and 67°C. The Ps inhibition by C6H2Cl4...... was roughly 14 times stronger at −30°C than at 67°C in toluene, m-xylene, and mesitylene, while that of CCl4 displayed hardly any temperature dependence in hexane and toluene. Previously, the Ps inhibition by C6H2Cl4 in various liquids at 20°C was explained by a competition between electron pick off...

  11. Scattering of polarized 7Li by 120Sn and projectile-target spin-dependent interactions

    International Nuclear Information System (INIS)

    Sakuragi, Y.; Yahiro, M.; Kamimura, M.; Tanifuji, M.

    1986-07-01

    Scattering of 7 Li by 120 Sn targets at E lab = 44 MeV is investigated in the coupled-channel frame by taking account of the projectile virtual excitations to the lowest three excited states. Calculations are performed by the cluster-folding (CF) interactions and the double-folding (DF) one. Both interactions reproduce very well the expeimental data on the cross section, the vector analyzing power, the second-rank tensor ones and the third-rank tensor one in elastic and projectile inelastic scattering, although some differences are found between the CF results and the DF ones. In the calculation, the virtual excitations of the projectile are important for most of the analyzing powers and the spin-orbit interaction is indispensable for the vector analyzing power. These features are in contrast to those in 7 Li - 58 Ni scattering at 20 MeV and are interpreted as over-Coulomb-barrier effects. The scattering amplitudes and the analyzing powers are investigated by the invariant amplitude method, which provides a key connecting the spin-dependent interactions to the analyzing powers. The method proposes an important relationship between the tensor analyzing powers, which is useful in analyses of both theoretical and experimental results. Finally, it is found that in the elastic scattering the second-rank tensor analyzing powers are proportional to the strength of the second-rank tensor interaction and the vector and third-rank tensor analyzing powers to the square or cube of the strength of this interaction, while in the inelastic scattering the cross section is proportional to the square of the strength of the tensor interaction, other quantities being weakly dependent on the strength. (author)

  12. Mesoscale Mapping of Mouse Cortex Reveals Frequency-Dependent Cycling between Distinct Macroscale Functional Modules.

    Science.gov (United States)

    Vanni, Matthieu P; Chan, Allen W; Balbi, Matilde; Silasi, Gergely; Murphy, Timothy H

    2017-08-02

    Connectivity mapping based on resting-state activity in mice has revealed functional motifs of correlated activity. However, the rules by which motifs organize into larger functional modules that lead to hemisphere wide spatial-temporal activity sequences is not clear. We explore cortical activity parcellation in head-fixed, quiet awake GCaMP6 mice from both sexes by using mesoscopic calcium imaging. Spectral decomposition of spontaneous cortical activity revealed the presence of two dominant frequency modes (domain such as intrahemispheric reflections of sensory and motor cortices. In contrast, higher frequency activity >1 Hz yielded two larger clusters of coactivated areas with an enlarged default mode network-like posterior region. We suggest that the apparent constrained structure for intra-areal cortical activity flow could be exploited in future efforts to normalize activity in diseases of the nervous system. SIGNIFICANCE STATEMENT Increasingly, functional connectivity mapping of spontaneous activity is being used to reveal the organization of the brain. However, because the brain operates across multiple space and time domains a more detailed understanding of this organization is necessary. We used in vivo wide-field calcium imaging of the indicator GCaMP6 in head-fixed, awake mice to characterize the organization of spontaneous cortical activity at different spatiotemporal scales. Correlation analysis defines the presence of two to three superclusters of activity that span traditionally defined functional territories and were frequency dependent. This work helps define the rules for how different cortical areas interact in time and space. We provide a framework necessary for future studies that explore functional reorganization of brain circuits in disease models. Copyright © 2017 the authors 0270-6474/17/377513-21$15.00/0.

  13. Mitochondrial Sirtuin Network Reveals Dynamic SIRT3-Dependent Deacetylation in Response to Membrane Depolarization.

    Science.gov (United States)

    Yang, Wen; Nagasawa, Koji; Münch, Christian; Xu, Yingjie; Satterstrom, Kyle; Jeong, Seungmin; Hayes, Sebastian D; Jedrychowski, Mark P; Vyas, F Sejal; Zaganjor, Elma; Guarani, Virginia; Ringel, Alison E; Gygi, Steven P; Harper, J Wade; Haigis, Marcia C

    2016-11-03

    Mitochondrial sirtuins, SIRT3-5, are NAD + -dependent deacylases and ADP-ribosyltransferases that are critical for stress responses. However, a comprehensive understanding of sirtuin targets, regulation of sirtuin activity, and the relationships between sirtuins remains a key challenge in mitochondrial physiology. Here, we employ systematic interaction proteomics to elucidate the mitochondrial sirtuin protein interaction landscape. This work reveals sirtuin interactions with numerous functional modules within mitochondria, identifies candidate sirtuin substrates, and uncovers a fundamental role for sequestration of SIRT3 by ATP synthase in mitochondrial homeostasis. In healthy mitochondria, a pool of SIRT3 binds ATP synthase, but upon matrix pH reduction with concomitant loss of mitochondrial membrane potential, SIRT3 dissociates. This release correlates with rapid deacetylation of matrix proteins, and SIRT3 is required for recovery of membrane potential. In vitro reconstitution experiments, as well as analysis of CRISPR/Cas9-engineered cells, indicate that pH-dependent SIRT3 release requires H135 in the ATP5O subunit of ATP synthase. Our SIRT3-5 interaction network provides a framework for discovering novel biological functions regulated by mitochondrial sirtuins. Copyright © 2016 Elsevier Inc. All rights reserved.

  14. Role of quantum-confined stark effect on bias dependent photoluminescence of N-polar GaN/InGaN multi-quantum disk amber light emitting diodes

    Science.gov (United States)

    Tangi, Malleswararao; Mishra, Pawan; Janjua, Bilal; Prabaswara, Aditya; Zhao, Chao; Priante, Davide; Min, Jung-Wook; Ng, Tien Khee; Ooi, Boon S.

    2018-03-01

    We study the impact of quantum-confined stark effect (QCSE) on bias dependent micro-photoluminescence emission of the quantum disk (Q-disk) based nanowires light emitting diodes (NWs-LED) exhibiting the amber colored emission. The NWs are found to be nitrogen polar (N-polar) verified using KOH wet chemical etching and valence band spectrum analysis of high-resolution X-ray photoelectron spectroscopy. The crystal structure and quality of the NWs were investigated by high-angle annular dark field - scanning transmission electron microscopy. The LEDs were fabricated to acquire the bias dependent micro-photoluminescence spectra. We observe a redshift and a blueshift of the μPL peak in the forward and reverse bias conditions, respectively, with reference to zero bias, which is in contrast to the metal-polar InGaN well-based LEDs in the literature. Such opposite shifts of μPL peak emission observed for N-polar NWs-LEDs, in our study, are due to the change in the direction of the internal piezoelectric field. The quenching of PL intensity, under the reverse bias conditions, is ascribed to the reduction of electron-hole overlap. Furthermore, the blueshift of μPL emission with increasing excitation power reveals the suppression of QCSE resulting from the photo-generated carriers. Thereby, our study confirms the presence of QCSE for NWs-LEDs from both bias and power dependent μPL measurements. Thus, this study serves to understand the QCSE in N-polar InGaN Q-disk NWs-LEDs and other related wide-bandgap nitride nanowires, in general.

  15. Role of quantum-confined stark effect on bias dependent photoluminescence of N-polar GaN/InGaN multi-quantum disk amber light emitting diodes

    KAUST Repository

    Tangi, Malleswararao

    2018-03-09

    We study the impact of quantum-confined stark effect (QCSE) on bias dependent micro-photoluminescence emission of the quantum disk (Q-disk) based nanowires light emitting diodes (NWs-LED) exhibiting the amber colored emission. The NWs are found to be nitrogen polar (N-polar) verified using KOH wet chemical etching and valence band spectrum analysis of high-resolution X-ray photoelectron spectroscopy. The crystal structure and quality of the NWs were investigated by high-angle annular dark field - scanning transmission electron microscopy. The LEDs were fabricated to acquire the bias dependent micro-photoluminescence spectra. We observe a redshift and a blueshift of the μPL peak in the forward and reverse bias conditions, respectively, with reference to zero bias, which is in contrast to the metal-polar InGaN well-based LEDs in the literature. Such opposite shifts of μPL peak emission observed for N-polar NWs-LEDs, in our study, are due to the change in the direction of the internal piezoelectric field. The quenching of PL intensity, under the reverse bias conditions, is ascribed to the reduction of electron-hole overlap. Furthermore, the blueshift of μPL emission with increasing excitation power reveals the suppression of QCSE resulting from the photo-generated carriers. Thereby, our study confirms the presence of QCSE for NWs-LEDs from both bias and power dependent μPL measurements. Thus, this study serves to understand the QCSE in N-polar InGaN Q-disk NWs-LEDs and other related wide-bandgap nitride nanowires, in general.

  16. Interface-induced chiral domain walls, spin spirals and skyrmions revealed by spin-polarized scanning tunneling microscopy.

    Science.gov (United States)

    von Bergmann, Kirsten; Kubetzka, André; Pietzsch, Oswald; Wiesendanger, Roland

    2014-10-01

    The spin textures of ultra-thin magnetic layers exhibit surprising variety. The loss of inversion symmetry at the interface of the magnetic layer and substrate gives rise to the so-called Dzyaloshinskii-Moriya interaction which favors non-collinear spin arrangements with unique rotational sense. Here we review the application of spin-polarized scanning tunneling microscopy to such systems, which has led to the discovery of interface-induced chiral domain walls and spin spirals. Recently, different interface-driven skyrmion lattices have been found, and the writing as well as the deleting of individual skyrmions based on local spin-polarized current injection has been demonstrated. These interface-induced non-collinear magnetic states offer new exciting possibilities to study fundamental magnetic interactions and to tailor material properties for spintronic applications.

  17. Polarization Effects in Graded AlGaN Nanolayers Revealed by Current-Sensing and Kelvin Probe Microscopy.

    Science.gov (United States)

    Lytvyn, Petro M; Kuchuk, Andrian V; Mazur, Yuriy I; Li, Chen; Ware, Morgan E; Wang, Zhiming M; Kladko, Vasyl P; Belyaev, Alexander E; Salamo, Gregory J

    2018-02-21

    We experimentally demonstrate that the conductivity of graded Al x Ga 1-x N increases as a function of the magnitude of the Al concentration gradient (%Al/nm) due to polarization doping effects, without the use of impurity dopants. Using three up/down-graded Al x Ga 1-x N nanolayers with Al gradients ranging from ∼0.16 to ∼0.28%Al/nm combined in one structure, the effects of polarization engineering for localized electric fields and current transport were investigated. Cross-sectional Kelvin probe force microscopy and conductive atomic force microscopy were used to directly probe the electrical properties of the films with spatial resolution along the thickness of the growth. The experimental profiles of the built-in electric fields and the spreading current found in the graded layers are shown to be consistent with simulations of the field distribution as well as of the electron and hole densities. Finally, it was directly observed that for gradients less than 0.28%Al/nm the native n-type donors still limit polarization-induced hole doping, making p-type conductivity still a challenge due to background impurities and defects.

  18. Polarization Dependent Bulk-sensitive Valence Band Photoemission Spectroscopy and Density Functional Theory Calculations: Part I. 3d Transition Metals

    Science.gov (United States)

    Ueda, Shigenori; Hamada, Ikutaro

    2017-12-01

    The X-ray polarization dependent valence band HAXPES spectra of 3d transition metals (TMs) of Ti-Zn were measured to investigate the orbital resolved electronic structures by utilizing that the fact the photoionization cross-section of the atomic orbitals strongly depends on the experimental geometry. We have calculated the HAXPES spectra, which correspond to the cross-section weighted densities of states (CSW-DOSs), where the DOSs were obtained by the density functional theory calculations, and we have determined the relative photoionization cross-sections of the 4s and 4p orbitals to the 3d orbital in the 3d TMs. The experimentally obtained bulk-sensitive 3d and 4s DOSs were good agreement with the calculated DOSs in Ti, V, Cr, and Cu. In contrast, the deviations between the experimental and calculated 3d DOSs for Mn, Fe, Co, Ni were found, suggesting that the electron correlation plays an important role in the electronic structures for these materials.

  19. DISTRIBUTION AND MIGRATION OF POLAR BEARS, PACIFIC WALRUSES AND GRAY WHALES DEPENDING ON ICE CONDITIONS IN THE RUSSIAN ARCTIC (17th Symposium on Polar Biology)

    OpenAIRE

    Stanislav, BELIKOV; Andrei, BOLTUNOV; Yuri, GORBUNOV

    1996-01-01

    This report presents a review of available data concerning the influence of ice cover on distribution, density and migration of three species of marine mammals inhabiting the Russian Arctic. Association of marine mammals with ice cover is as follows: (1) the polar bear is distributed in ice zone in the whole year, (2) the walrus is associated with the ice zone only in summer, and (3) the gray whale inhabits the southern area of the ice zone.

  20. Probabilistic Inference: Task Dependency and Individual Differences of Probability Weighting Revealed by Hierarchical Bayesian Modeling.

    Science.gov (United States)

    Boos, Moritz; Seer, Caroline; Lange, Florian; Kopp, Bruno

    2016-01-01

    Cognitive determinants of probabilistic inference were examined using hierarchical Bayesian modeling techniques. A classic urn-ball paradigm served as experimental strategy, involving a factorial two (prior probabilities) by two (likelihoods) design. Five computational models of cognitive processes were compared with the observed behavior. Parameter-free Bayesian posterior probabilities and parameter-free base rate neglect provided inadequate models of probabilistic inference. The introduction of distorted subjective probabilities yielded more robust and generalizable results. A general class of (inverted) S-shaped probability weighting functions had been proposed; however, the possibility of large differences in probability distortions not only across experimental conditions, but also across individuals, seems critical for the model's success. It also seems advantageous to consider individual differences in parameters of probability weighting as being sampled from weakly informative prior distributions of individual parameter values. Thus, the results from hierarchical Bayesian modeling converge with previous results in revealing that probability weighting parameters show considerable task dependency and individual differences. Methodologically, this work exemplifies the usefulness of hierarchical Bayesian modeling techniques for cognitive psychology. Theoretically, human probabilistic inference might be best described as the application of individualized strategic policies for Bayesian belief revision.

  1. Probabilistic inference: Task dependency and individual differences of probability weighting revealed by hierarchical Bayesian modelling

    Directory of Open Access Journals (Sweden)

    Moritz eBoos

    2016-05-01

    Full Text Available Cognitive determinants of probabilistic inference were examined using hierarchical Bayesian modelling techniques. A classic urn-ball paradigm served as experimental strategy, involving a factorial two (prior probabilities by two (likelihoods design. Five computational models of cognitive processes were compared with the observed behaviour. Parameter-free Bayesian posterior probabilities and parameter-free base rate neglect provided inadequate models of probabilistic inference. The introduction of distorted subjective probabilities yielded more robust and generalizable results. A general class of (inverted S-shaped probability weighting functions had been proposed; however, the possibility of large differences in probability distortions not only across experimental conditions, but also across individuals, seems critical for the model’s success. It also seems advantageous to consider individual differences in parameters of probability weighting as being sampled from weakly informative prior distributions of individual parameter values. Thus, the results from hierarchical Bayesian modelling converge with previous results in revealing that probability weighting parameters show considerable task dependency and individual differences. Methodologically, this work exemplifies the usefulness of hierarchical Bayesian modelling techniques for cognitive psychology. Theoretically, human probabilistic inference might be best described as the application of individualized strategic policies for Bayesian belief revision.

  2. Sleep-Dependent Memory Consolidation and Incremental Sentence Comprehension: Computational Dependencies during Language Learning as Revealed by Neuronal Oscillations.

    Science.gov (United States)

    Cross, Zachariah R; Kohler, Mark J; Schlesewsky, Matthias; Gaskell, M G; Bornkessel-Schlesewsky, Ina

    2018-01-01

    We hypothesize a beneficial influence of sleep on the consolidation of the combinatorial mechanisms underlying incremental sentence comprehension. These predictions are grounded in recent work examining the effect of sleep on the consolidation of linguistic information, which demonstrate that sleep-dependent neurophysiological activity consolidates the meaning of novel words and simple grammatical rules. However, the sleep-dependent consolidation of sentence-level combinatorics has not been studied to date. Here, we propose that dissociable aspects of sleep neurophysiology consolidate two different types of combinatory mechanisms in human language: sequence-based (order-sensitive) and dependency-based (order-insensitive) combinatorics. The distinction between the two types of combinatorics is motivated both by cross-linguistic considerations and the neurobiological underpinnings of human language. Unifying this perspective with principles of sleep-dependent memory consolidation, we posit that a function of sleep is to optimize the consolidation of sequence-based knowledge (the when ) and the establishment of semantic schemas of unordered items (the what ) that underpin cross-linguistic variations in sentence comprehension. This hypothesis builds on the proposal that sleep is involved in the construction of predictive codes, a unified principle of brain function that supports incremental sentence comprehension. Finally, we discuss neurophysiological measures (EEG/MEG) that could be used to test these claims, such as the quantification of neuronal oscillations, which reflect basic mechanisms of information processing in the brain.

  3. Sleep-Dependent Memory Consolidation and Incremental Sentence Comprehension: Computational Dependencies during Language Learning as Revealed by Neuronal Oscillations

    Directory of Open Access Journals (Sweden)

    Zachariah R. Cross

    2018-01-01

    Full Text Available We hypothesize a beneficial influence of sleep on the consolidation of the combinatorial mechanisms underlying incremental sentence comprehension. These predictions are grounded in recent work examining the effect of sleep on the consolidation of linguistic information, which demonstrate that sleep-dependent neurophysiological activity consolidates the meaning of novel words and simple grammatical rules. However, the sleep-dependent consolidation of sentence-level combinatorics has not been studied to date. Here, we propose that dissociable aspects of sleep neurophysiology consolidate two different types of combinatory mechanisms in human language: sequence-based (order-sensitive and dependency-based (order-insensitive combinatorics. The distinction between the two types of combinatorics is motivated both by cross-linguistic considerations and the neurobiological underpinnings of human language. Unifying this perspective with principles of sleep-dependent memory consolidation, we posit that a function of sleep is to optimize the consolidation of sequence-based knowledge (the when and the establishment of semantic schemas of unordered items (the what that underpin cross-linguistic variations in sentence comprehension. This hypothesis builds on the proposal that sleep is involved in the construction of predictive codes, a unified principle of brain function that supports incremental sentence comprehension. Finally, we discuss neurophysiological measures (EEG/MEG that could be used to test these claims, such as the quantification of neuronal oscillations, which reflect basic mechanisms of information processing in the brain.

  4. PH-DEPENDENT PROTON PERMEABILITY OF THE PLASMA-MEMBRANE IN A REGULATING MECHANISM OF POLAR TRANSPORT THROUGH THE SUBMERGED LEAVES OF POTAMOGETON-LUCENS

    NARCIS (Netherlands)

    MIEDEMA, H; PRINS, HBA

    Recently it has been hypothesized that light-induced polarity in leaves of the submerged angiosperms Potamogeton and Elodea results in part from a pH-dependent change in the permeability of the plasma membrane for protons. It is assumed that the proton permeability increases at high pH. In this

  5. Investigation of photon detection probability dependence of SPADnet-I digital photon counter as a function of angle of incidence, wavelength and polarization

    Energy Technology Data Exchange (ETDEWEB)

    Játékos, Balázs, E-mail: jatekosb@eik.bme.hu; Ujhelyi, Ferenc; Lőrincz, Emőke; Erdei, Gábor

    2015-01-01

    SPADnet-I is a prototype, fully digital, high spatial and temporal resolution silicon photon counter, based on standard CMOS imaging technology, developed by the SPADnet consortium. Being a novel device, the exact dependence of photon detection probability (PDP) of SPADnet-I was not known as a function of angle of incidence, wavelength and polarization of the incident light. Our targeted application area of this sensor is next generation PET detector modules, where they will be used along with LYSO:Ce scintillators. Hence, we performed an extended investigation of PDP in a wide range of angle of incidence (0° to 80°), concentrating onto a 60 nm broad wavelength interval around the characteristic emission peak (λ=420 nm) of the scintillator. In the case where the sensor was optically coupled to a scintillator, our experiments showed a notable dependence of PDP on angle, polarization and wavelength. The sensor has an average PDP of approximately 30% from 0° to 60° angle of incidence, where it starts to drop rapidly. The PDP turned out not to be polarization dependent below 30°. If the sensor is used without a scintillator (i.e. the light source is in air), the polarization dependence is much less expressed, it begins only from 50°.

  6. Optical polarization tractography revealed significant fiber disarray in skeletal muscles of a mouse model for Duchenne muscular dystrophy.

    Science.gov (United States)

    Wang, Y; Zhang, K; Wasala, N B; Duan, D; Yao, G

    2015-02-01

    Optical polarization tractography (OPT) was recently developed to visualize tissue fiber architecture with cellular-level resolution and accuracy. In this study, we explored the feasibility of using OPT to study muscle disease in the mdx4cv mouse model of Duchenne muscular dystrophy. The freshly dissected tibialis anterior muscles of mdx4cv and normal mice were imaged. A "fiber disarray index" (FDI) was developed to quantify the myofiber disorganization. In necrotic muscle regions of the mdx4cv mice, the FDI was significantly elevated and can be used to segment the 3D necrotic regions for assessing the overall muscle damage. These results demonstrated the OPT's capability for imaging microscopic fiber alternations in muscle research.

  7. Intracellular CHO Cell Metabolite Profiling Reveals Steady-State Dependent Metabolic Fingerprints in Perfusion Culture.

    Science.gov (United States)

    Karst, Daniel J; Steinhoff, Robert F; Kopp, Marie R G; Serra, Elisa; Soos, Miroslav; Zenobi, Renato; Morbidelli, Massimo

    2017-07-01

    Perfusion cell culture processes allow the steady-state culture of mammalian cells at high viable cell density, which is beneficial for overall product yields and homogeneity of product quality in the manufacturing of therapeutic proteins. In this study, the extent of metabolic steady state and the change of the metabolite profile between different steady states of an industrial Chinese hamster ovary (CHO) cell line producing a monoclonal antibody (mAb) was investigated in stirred tank perfusion bioreactors. Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) of daily cell extracts revealed more than a hundred peaks, among which 76 metabolites were identified by tandem MS (MS/MS) and high resolution Fourier transform ion cyclotron resonance (FT-ICR) MS. Nucleotide ratios (Uridine (U)-ratio, nucleotide triphosphate (NTP)-ratio and energy charge (EC)) and multivariate analysis of all features indicated a consistent metabolite profile for a stable culture performed at 40 × 10 6 cells/mL over 26 days of culture. Conversely, the reactor was operated continuously so as to reach three distinct steady states one after the other at 20, 60, and 40 × 10 6 cells/mL. In each case, a stable metabolite profile was achieved after an initial transient phase of approximately three days at constant cell density when varying between these set points. Clear clustering according to cell density was observed by principal component analysis, indicating steady-state dependent metabolite profiles. In particular, varying levels of nucleotides, nucleotide sugar, and lipid precursors explained most of the variance between the different cell density set points. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:879-890, 2017. © 2016 American Institute of Chemical Engineers.

  8. Two-day Planetary Wave Impact on Austral Polar Mesopause Temperatures: as Revealed by a January Diminution in PMSE above Davis, Antarctica

    Science.gov (United States)

    Morris, R. J.; Klekociuk, A. R.; Murphy, D. J.; Holdsworth, D. A.

    2008-12-01

    A new characteristic of the austral summer polar mesopause as revealed by ground MST radar charged ice- aerosol echoes and satellite MLS temperature is reported, that is plausibly linked to the low-latitude easterly wind jet. Four consecutive seasons of polar mesosphere summer echoes (PMSE) and mesosphere temperature observations above Davis, Antarctica (geographic: 68.6°S; 78.0°N) exhibit an annual mid-January diminution in PMSE occurrence rate that is correlated with a simultaneous mesopause warming by several degrees. Interestingly, the corresponding mesosphere meridional wind field changes from equatorward to a poleward flow at these times. Although displaying some inter-annual variation in the peak onset time, the mid-January mesopause warming correlates with the peak in the line-of-sight meridional wind and temperature enhancements (both poleward and in altitude) associated with the low-latitude 2-day planetary wave (PW). Periodogram analyses of PMSE and Aura MLS temperatures show the dominance of 5- day PWs throughout the austral summer coupled with pronounced 2-day PWs evident from early January to mid-February. Zonal spectral analyses of Aura MLS temperature records reveal the high-latitude 2-day PWs have zonal wavenumber (s) with both westward (s = -2, -3) and eastward (s = 2, 3) spectral features consistent with the periodogram results. Our polar observations support the evolution of a myriad of prodigy PWs spawned from the westward 2-day PW (s = -3) activity, originating from the low-latitude easterly jet, albeit not previously linked to the reported mid-January diminution of PMSE at southern latitudes.

  9. Spectral dependence of backscattering coefficient of mixed phase clouds over West Africa measured with two-wavelength Raman polarization lidar: Features attributed to ice-crystals corner reflection

    Science.gov (United States)

    Veselovskii, I.; Goloub, P.; Podvin, T.; Tanre, D.; Ansmann, A.; Korenskiy, M.; Borovoi, A.; Hu, Q.; Whiteman, D. N.

    2017-11-01

    The existing models predict that corner reflection (CR) of laser radiation by simple ice crystals of perfect shape, such as hexagonal columns or plates, can provide a significant contribution to the ice cloud backscattering. However in real clouds the CR effect may be suppressed due to crystal deformation and surface roughness. In contrast to the extinction coefficient, which is spectrally independent, consideration of diffraction associated with CR results in a spectral dependence of the backscattering coefficient. Thus measuring the spectral dependence of the cloud backscattering coefficient, the contribution of CR can be identified. The paper presents the results of profiling of backscattering coefficient (β) and particle depolarization ratio (δ) of ice and mixed-phase clouds over West Africa by means of a two-wavelength polarization Mie-Raman lidar operated at 355 nm and 532 nm during the SHADOW field campaign. The lidar observations were performed at a slant angle of 43 degree off zenith, thus CR from both randomly oriented crystals and oriented plates could be analyzed. For the most of the observations the cloud backscatter color ratio β355/β532 was close to 1.0, and no spectral features that might indicate the presence of CR of randomly oriented crystals were revealed. Still, in two measurement sessions we observed an increase of backscatter color ratio to a value of nearly 1.3 simultaneously with a decrease of the spectral depolarization ratio δ355/δ532 ratio from 1.0 to 0.8 inside the layers containing precipitating ice crystals. We attribute these changes in optical properties to corner reflections by horizontally oriented ice plates.

  10. The nature of hydrogen-bonding interactions in nonsteroidal anti-inflammatory drugs revealed by polarized IR spectroscopy

    Science.gov (United States)

    Hachuła, Barbara

    2018-01-01

    The influence of hydrogen-bonding interactions in the solid phase on the IR spectroscopic pattern of the νOsbnd H band of nonsteroidal anti-inflammatory drugs (NSAIDs) was studied experimentally by IR spectroscopy with the use of polarized light at two temperatures (293 K and 77 K) and in isotopic dilution. The neat and deuterated crystals of (S)-naproxen ((S)-NPX), (R)-flurbiprofen ((R)-FBP), (RS)-flurbiprofen ((RS)-FBP) and (RS)-ketoprofen ((RS)-KTP) were obtained by melt crystallization between the two squeezed CaF2 plates. The vibrational spectra of selected α-aryl propionic acid derivatives (2APAs) reflected the characteristics of their hydrogen-bond networks, i.e., 2APAs were characterized by the chain ((S)-NPX, (R)-FBP) and by dimeric ((RS)-FBP, (RS)-KTP) arrangement of hydrogen bonds in the crystal lattice. Spectroscopic results showed that the interchain (through-space) exciton coupling, between two laterally-spaced hydrogen bonds, dominates in the crystals of four NSAIDs. The same exciton coupled hydrogen bonds were also responsible for the H/D isotopic recognition mechanism in the crystalline spectra of deuterated 2APAs. The presented spectral results may help to predict the hydrogen bond motifs in the crystalline NSAIDs, which structures are not yet known, based on their IR spectra of hydrogen bond in the crystals.

  11. Laser polarization dependence of proton emission from a thin foil target irradiated by a 70 fs, intense laser pulse

    International Nuclear Information System (INIS)

    Fukumi, A.; Nishiuchi, M.; Daido, H.; Li, Z.; Sagisaka, A.; Ogura, K.; Orimo, S.; Kado, M.; Hayashi, Y.; Mori, M.; Bulanov, S.V.; Esirkepov, T.; Nemoto, K.; Oishi, Y.; Nayuki, T.; Fujii, T.; Noda, A.; Nakamura, S.

    2005-01-01

    A study of proton emission from a 3-μm-thick Ta foil target irradiated by p-, s-, and circularly polarized laser pulses with respect to the target plane has been carried out. Protons with energies up to 880 keV were observed in the target normal direction under the irradiation by the p-polarized laser pulse, which yielded the highest efficiency for proton emission. In contrast, s- and circularly polarized laser pulses gave the maximum energies of 610 and 680 keV, respectively. The difference in the maximum energy between the p- and s-polarized cases was associated with the difference between the sheath fields estimated from electron spectra

  12. Extensive sampling of polar bears (Ursus maritimus) in the Northwest Passage (Canadian Arctic Archipelago) reveals population differentiation across multiple spatial and temporal scales.

    Science.gov (United States)

    Campagna, Leonardo; Van Coeverden de Groot, Peter J; Saunders, Brenda L; Atkinson, Stephen N; Weber, Diana S; Dyck, Markus G; Boag, Peter T; Lougheed, Stephen C

    2013-09-01

    As global warming accelerates the melting of Arctic sea ice, polar bears (Ursus maritimus) must adapt to a rapidly changing landscape. This process will necessarily alter the species distribution together with population dynamics and structure. Detailed knowledge of these changes is crucial to delineating conservation priorities. Here, we sampled 361 polar bears from across the center of the Canadian Arctic Archipelago spanning the Gulf of Boothia (GB) and M'Clintock Channel (MC). We use DNA microsatellites and mitochondrial control region sequences to quantify genetic differentiation, estimate gene flow, and infer population history. Two populations, roughly coincident with GB and MC, are significantly differentiated at both nuclear (F ST = 0.01) and mitochondrial (ΦST = 0.47; F ST = 0.29) loci, allowing Bayesian clustering analyses to assign individuals to either group. Our data imply that the causes of the mitochondrial and nuclear genetic patterns differ. Analysis of mtDNA reveals the matrilineal structure dates at least to the Holocene, and is common to individuals throughout the species' range. These mtDNA differences probably reflect both genetic drift and historical colonization dynamics. In contrast, the differentiation inferred from microsatellites is only on the scale of hundreds of years, possibly reflecting contemporary impediments to gene flow. Taken together, our data suggest that gene flow is insufficient to homogenize the GB and MC populations and support the designation of GB and MC as separate polar bear conservation units. Our study also provide a striking example of how nuclear DNA and mtDNA capture different aspects of a species demographic history.

  13. Kinome analysis reveals nongenomic glucocorticoid receptor-dependent inhibition of insulin signaling

    NARCIS (Netherlands)

    Löwenberg, Mark; Tuynman, Jurriaan; Scheffer, Meike; Verhaar, Auke; Vermeulen, Louis; van Deventer, Sander; Hommes, Daniel; Peppelenbosch, Maikel

    2006-01-01

    Glucocorticoids (GCs) are powerful immunosuppressive agents that control genomic effects through GC receptor (GR)-dependent transcriptional changes. A common complication of GC therapy is insulin resistance, but the underlying molecular mechanism remains obscure. Evidence is increasing for rapid

  14. Kinome analysis reveals nongenomic glucocorticoid receptor-dependent inhibition of insulin signaling

    NARCIS (Netherlands)

    Loewenberg, M; Tuynman, J; Scheffer, M; Verhaar, A; Vermeulen, L; van Deventer, S; Hommes, D; Peppelenbosch, M

    Glucocorticoids (GCs) are powerful immunosuppressive agents that control genomic effects through GC receptor (GR)-dependent transcriptional changes. A common complication of GC therapy is insulin resistance, but the underlying molecular mechanism remains obscure. Evidence is increasing for rapid

  15. Correlative STED and Atomic Force Microscopy on Live Astrocytes Reveals Plasticity of Cytoskeletal Structure and Membrane Physical Properties during Polarized Migration

    Directory of Open Access Journals (Sweden)

    Nathalie Rouach

    2017-04-01

    Full Text Available The plasticity of the cytoskeleton architecture and membrane properties is important for the establishment of cell polarity, adhesion and migration. Here, we present a method which combines stimulated emission depletion (STED super-resolution imaging and atomic force microscopy (AFM to correlate cytoskeletal structural information with membrane physical properties in live astrocytes. Using STED compatible dyes for live cell imaging of the cytoskeleton, and simultaneously mapping the cell surface topology with AFM, we obtain unprecedented detail of highly organized networks of actin and microtubules in astrocytes. Combining mechanical data from AFM with optical imaging of actin and tubulin further reveals links between cytoskeleton organization and membrane properties. Using this methodology we illustrate that scratch-induced migration induces cytoskeleton remodeling. The latter is caused by a polarization of actin and microtubule elements within astroglial cell processes, which correlates strongly with changes in cell stiffness. The method opens new avenues for the dynamic probing of the membrane structural and functional plasticity of living brain cells. It is a powerful tool for providing new insights into mechanisms of cell structural remodeling during physiological or pathological processes, such as brain development or tumorigenesis.

  16. Efficient three-photon luminescence with strong polarization dependence from a scintillating silicate glass co-doped with Gd3+ and Tb3+.

    Science.gov (United States)

    Li, Guang-Can; Zhang, Cheng-Yun; Deng, Hai-Dong; Liu, Guang-Yin; Lan, Sheng; Qian, Qi-; Yang, Zhong-Min; Gopal, Achanta Venu

    2013-03-11

    Efficient three-photon luminescence (3PL) from a scintillating silicate glass co-doped with Gd(3+) and Tb(3+) was generated by using a focused femtosecond laser beam at 800 nm. Four emission bands centered at 496, 541, 583, and 620 nm were identified as the electronic transitions between the energy levels of Tb(3+) followed by three-photon absorption (3PA) in Gd(3+) and Tb(3+) and the resonant energy transfer from Gd(3+) to Tb(3+). More interestingly, a strong polarization dependence of the 3PL was observed and it is ascribed to the polarization dependent 3PA in Gd(3+) and Tb(3+) and/or the angular distribution of photogenerated electrons in the glass.

  17. Virtually naked: virtual environment reveals sex-dependent nature of skin disclosure.

    Directory of Open Access Journals (Sweden)

    Anna M Lomanowska

    Full Text Available The human tendency to reveal or cover naked skin reflects a competition between the individual propensity for social interactions related to sexual appeal and interpersonal touch versus climatic, environmental, physical, and cultural constraints. However, due to the ubiquitous nature of these constraints, isolating on a large scale the spontaneous human tendency to reveal naked skin has remained impossible. Using the online 3-dimensional virtual world of Second Life, we examined spontaneous human skin-covering behavior unhindered by real-world climatic, environmental, and physical variables. Analysis of hundreds of avatars revealed that virtual females disclose substantially more naked skin than virtual males. This phenomenon was not related to avatar hypersexualization as evaluated by measurement of sexually dimorphic body proportions. Furthermore, analysis of skin-covering behavior of a population of culturally homogeneous avatars indicated that the propensity of female avatars to reveal naked skin persisted despite explicit cultural norms promoting less revealing attire. These findings have implications for further understanding how sex-specific aspects of skin disclosure influence human social interactions in both virtual and real settings.

  18. Exploring the entrance of proton pathways in cytochrome c oxidase from Paracoccus denitrificans: surface charge, buffer capacity and redox-dependent polarity changes at the internal surface.

    Science.gov (United States)

    Kirchberg, Kristina; Michel, Hartmut; Alexiev, Ulrike

    2013-03-01

    Cytochrome c oxidase (CcO), the terminal oxidase of cellular respiration, reduces molecular oxygen to water. The mechanism of proton pumping as well as the coupling of proton and electron transfer is still not understood in this redox-linked proton pump. Eleven residues at the aqueous-exposed surfaces of CcO from Paracoccus denitrificans have been exchanged to cysteines in a two-subunit base variant to yield single reactive cysteine variants. These variants are designed to provide unique labeling sites for probes to be used in spectroscopic experiments investigating the mechanism of proton pumping in CcO. To this end we have shown that all cysteine variants are enzymatically active. Cysteine positions at the negative (N-) side of the membrane are located close to the entrance of the D- and K-proton transfer pathways that connect the N-side with the catalytic oxygen reduction site. Labeling of the pH-indicator dye fluorescein to these sites allowed us to determine the surface potential at the cytoplasmic CcO surface, which corresponds to a surface charge density of -0.5 elementary charge/1000Å(2). In addition, acid-base titrations revealed values of CcO buffer capacity. Polarity measurements of the label environment at the N-side provided (i) site-specific values indicative of a hydrophilic and a more hydrophobic environment dependent on the label position, and (ii) information on a global change to a more apolar environment upon reduction of the enzyme. Thus, the redox state of the copper and heme centers inside the hydrophobic interior of CcO affect the properties at the cytoplasmic surface. Copyright © 2012 Elsevier B.V. All rights reserved.

  19. Beta4 integrin-dependent formation of polarized three-dimensionalarchitecture confers resistance to apoptosis in normal and malignantmammary epithelium

    Energy Technology Data Exchange (ETDEWEB)

    Weaver, Valerie M.; Lelievre, Sophie; Lakins, Johnathon N.; Chrenek, Micah A.; Jones, Jonathan C.R.; Giancotti, Filippo; Werb, Zena; Bissell, Mina J.

    2002-08-27

    Tumor cells can evade chemotherapy by acquiring resistanceto apoptosis. We investigated the molecular mechanism whereby malignantand nonmalignant mammary epithelial cells become insensitive toapoptosis. We show that regardless of growth status formation ofpolarized, three-dimensional structures driven by basement membraneconfers protection to apoptosis in both nonmalignant and malignantmammary epithelial cells. By contrast, irrespective of their malignantstatus, nonpolarized structures are sensitive to induction of apoptosis.Resistance to apoptosis requires ligation of beta4 integrins, whichregulates tissue polarity, hemidesmosome formation and NFkB activation.Expression of beta4 integrin that lacks the hemidesmosome targetingdomain interferes with tissue polarity and NFkB activation and permitsapoptosis. These results indicate that integrin-induced polarity maydrive tumor cell resistance to apoptosis-inducing agents via effects onNFkB.

  20. Sleep slow-wave activity reveals developmental changes in experience-dependent plasticity.

    Science.gov (United States)

    Wilhelm, Ines; Kurth, Salomé; Ringli, Maya; Mouthon, Anne-Laure; Buchmann, Andreas; Geiger, Anja; Jenni, Oskar G; Huber, Reto

    2014-09-10

    Experience-dependent plasticity, the ability of the brain to constantly adapt to an ever-changing environment, has been suggested to be highest during childhood and to decline thereafter. However, empirical evidence for this is rather scarce. Slow-wave activity (SWA; EEG activity of 1-4.5 Hz) during deep sleep can be used as a marker of experience-dependent plasticity. For example, performing a visuomotor adaptation task in adults increased SWA during subsequent sleep over a locally restricted region of the right parietal cortex, which is known to be involved in visuomotor adaptation. Here, we investigated whether local experience-dependent changes in SWA vary as a function of brain maturation. Three age groups (children, adolescents, and adults) participated in a high-density EEG study with two conditions (baseline and adaptation) of a visuomotor learning task. Compared with the baseline condition, sleep SWA was increased after visuomotor adaptation in a cluster of eight electrodes over the right parietal cortex. The local boost in SWA was highest in children. Baseline SWA in the parietal cluster and right parietal gray matter volume, which both indicate region-specific maturation, were significantly correlated with the local increase in SWA. Our findings indicate that processes of brain maturation favor experience-dependent plasticity and determine how sensitive a specific brain region is for learning experiences. Moreover, our data confirm that SWA is a highly sensitive tool to map maturational differences in experience-dependent plasticity. Copyright © 2014 the authors 0270-6474/14/3412568-08$15.00/0.

  1. Laser polarization dependent and magnetically control of group velocity in a dielectric medium doped with nanodiamond nitrogen vacancy centers

    Energy Technology Data Exchange (ETDEWEB)

    Asadpour, Seyyed Hossein; Rahimpour Soleimani, H., E-mail: Rahimpour@guilan.ac.ir

    2014-03-01

    In this paper, group velocity control of Gaussian beam in a dielectric medium doped with nanodiamond nitrogen vacancy (NV) centers under optical excitation is discussed. The shape of transmitted and reflected pulses from dielectric can be tuned by changing the intensity of magnetic field and polarization of the control beam. The effect of intensity of control beam on group velocity is also investigated.

  2. Visualization of Excitonic Structure in the Fenna-Matthews-OlsonPhotosynthetic Complex by Polarization-Dependent Two-DimensionalElectronic Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Department of Chemistry, The University of Chicago; Department of Biology, Department of Chemistry, Washington University; Fleming, Graham; Read, Elizabeth L.; Schlau-Cohen, Gabriela S.; Engel, Gregory S.; Wen, Jianzhong; Blankenship, Robert E.; Fleming, Graham R.

    2008-05-26

    Photosynthetic light-harvesting proceeds by the collection and highly efficient transfer of energy through a network of pigment-protein complexes. Inter-chromophore electronic couplings and interactions between pigments and the surrounding protein determine energy levels of excitonic states and dictate the mechanism of energy flow. The excitonic structure (orientation of excitonic transition dipoles) of pigment-protein complexes is generally deduced indirectly from x-ray crystallography in combination with predictions of transition energies and couplings in the chromophore site basis. Here, we demonstrate that coarse-grained excitonic structural information in the form of projection angles between transition dipole moments can be obtained from polarization-dependent two-dimensional electronic spectroscopy of an isotropic sample, particularly when the nonrephasing or free polarization decay signal rather than the photon echo signal is considered. The method provides an experimental link between atomic and electronic structure and accesses dynamical information with femtosecond time resolution. In an investigation of the Fenna-Matthews-Olson complex from green sulfur bacteria, energy transfer connecting two particular exciton states in the protein is isolated as being the primary contributor to a cross peak in the nonrephasing 2D spectrum at 400 fs under a specific sequence of polarized excitation pulses. The results suggest the possibility of designing experiments using combinations of tailored polarization sequencesto separate and monitor individual relaxation pathways.

  3. Structures of apicomplexan calcium-dependent protein kinases reveal mechanism of activation by calcium

    Energy Technology Data Exchange (ETDEWEB)

    Wernimont, Amy K; Artz, Jennifer D.; Jr, Patrick Finerty; Lin, Yu-Hui; Amani, Mehrnaz; Allali-Hassani, Abdellah; Senisterra, Guillermo; Vedadi, Masoud; Tempel, Wolfram; Mackenzie, Farrell; Chau, Irene; Lourido, Sebastian; Sibley, L. David; Hui, Raymond (Toronto); (WU-MED)

    2010-09-21

    Calcium-dependent protein kinases (CDPKs) have pivotal roles in the calcium-signaling pathway in plants, ciliates and apicomplexan parasites and comprise a calmodulin-dependent kinase (CaMK)-like kinase domain regulated by a calcium-binding domain in the C terminus. To understand this intramolecular mechanism of activation, we solved the structures of the autoinhibited (apo) and activated (calcium-bound) conformations of CDPKs from the apicomplexan parasites Toxoplasma gondii and Cryptosporidium parvum. In the apo form, the C-terminal CDPK activation domain (CAD) resembles a calmodulin protein with an unexpected long helix in the N terminus that inhibits the kinase domain in the same manner as CaMKII. Calcium binding triggers the reorganization of the CAD into a highly intricate fold, leading to its relocation around the base of the kinase domain to a site remote from the substrate binding site. This large conformational change constitutes a distinct mechanism in calcium signal-transduction pathways.

  4. Movement reveals scale dependence in habitat selection of a large ungulate

    Science.gov (United States)

    Northrup, Joseph; Anderson, Charles R.; Hooten, Mevin B.; Wittemyer, George

    2016-01-01

    Ecological processes operate across temporal and spatial scales. Anthropogenic disturbances impact these processes, but examinations of scale dependence in impacts are infrequent. Such examinations can provide important insight to wildlife–human interactions and guide management efforts to reduce impacts. We assessed spatiotemporal scale dependence in habitat selection of mule deer (Odocoileus hemionus) in the Piceance Basin of Colorado, USA, an area of ongoing natural gas development. We employed a newly developed animal movement method to assess habitat selection across scales defined using animal-centric spatiotemporal definitions ranging from the local (defined from five hour movements) to the broad (defined from weekly movements). We extended our analysis to examine variation in scale dependence between night and day and assess functional responses in habitat selection patterns relative to the density of anthropogenic features. Mule deer displayed scale invariance in the direction of their response to energy development features, avoiding well pads and the areas closest to roads at all scales, though with increasing strength of avoidance at coarser scales. Deer displayed scale-dependent responses to most other habitat features, including land cover type and habitat edges. Selection differed between night and day at the finest scales, but homogenized as scale increased. Deer displayed functional responses to development, with deer inhabiting the least developed ranges more strongly avoiding development relative to those with more development in their ranges. Energy development was a primary driver of habitat selection patterns in mule deer, structuring their behaviors across all scales examined. Stronger avoidance at coarser scales suggests that deer behaviorally mediated their interaction with development, but only to a degree. At higher development densities than seen in this area, such mediation may not be possible and thus maintenance of sufficient

  5. Characterization of KCNQ1 atrial fibrillation mutations reveals distinct dependence on KCNE1

    Science.gov (United States)

    Chan, Priscilla J.; Osteen, Jeremiah D.; Xiong, Dazhi; Bohnen, Michael S.; Doshi, Darshan; Sampson, Kevin J.; Marx, Steven O.; Karlin, Arthur

    2012-01-01

    The IKs potassium channel, critical to control of heart electrical activity, requires assembly of α (KCNQ1) and β (KCNE1) subunits. Inherited mutations in either IKs channel subunit are associated with cardiac arrhythmia syndromes. Two mutations (S140G and V141M) that cause familial atrial fibrillation (AF) are located on adjacent residues in the first membrane-spanning domain of KCNQ1, S1. These mutations impair the deactivation process, causing channels to appear constitutively open. Previous studies suggest that both mutant phenotypes require the presence of KCNE1. Here we found that despite the proximity of these two mutations in the primary protein structure, they display different functional dependence in the presence of KCNE1. In the absence of KCNE1, the S140G mutation, but not V141M, confers a pronounced slowing of channel deactivation and a hyperpolarizing shift in voltage-dependent activation. When coexpressed with KCNE1, both mutants deactivate significantly slower than wild-type KCNQ1/KCNE1 channels. The differential dependence on KCNE1 can be correlated with the physical proximity between these positions and KCNE1 as shown by disulfide cross-linking studies: V141C forms disulfide bonds with cysteine-substituted KCNE1 residues, whereas S140C does not. These results further our understanding of the structural relationship between KCNE1 and KCNQ1 subunits in the IKs channel, and provide mechanisms for understanding the effects on channel deactivation underlying these two atrial fibrillation mutations. PMID:22250012

  6. First measurement of the polarization observable E and helicity-dependent cross sections in single π0 photoproduction from quasi-free nucleons

    Directory of Open Access Journals (Sweden)

    M. Dieterle

    2017-07-01

    Full Text Available The double-polarization observable E and the helicity-dependent cross sections σ1/2 and σ3/2 have been measured for the first time for single π0 photoproduction from protons and neutrons bound in the deuteron at the electron accelerator facility MAMI in Mainz, Germany. The experiment used a circularly polarized photon beam and a longitudinally polarized deuterated butanol target. The reaction products, recoil nucleons and decay photons from the π0 meson were detected with the Crystal Ball and TAPS electromagnetic calorimeters. Effects from nuclear Fermi motion were removed by a kinematic reconstruction of the π0N final state. A comparison to data measured with a free proton target showed that the absolute scale of the cross sections is significantly modified by nuclear final-state interaction (FSI effects. However, there is no significant effect on the asymmetry E since the σ1/2 and σ3/2 components appear to be influenced in a similar way. Thus, the best approximation of the two helicity-dependent cross sections for the free neutron is obtained by combining the asymmetry E measured with quasi-free neutrons and the unpolarized cross section corrected for FSI effects under the assumption that the FSI effects are similar for neutrons and protons.

  7. Density-dependent home-range size revealed by spatially explicit capture–recapture

    Science.gov (United States)

    Efford, M.G.; Dawson, Deanna K.; Jhala, Y.V.; Qureshi, Q.

    2016-01-01

    The size of animal home ranges often varies inversely with population density among populations of a species. This fact has implications for population monitoring using spatially explicit capture–recapture (SECR) models, in which both the scale of home-range movements σ and population density D usually appear as parameters, and both may vary among populations. It will often be appropriate to model a structural relationship between population-specific values of these parameters, rather than to assume independence. We suggest re-parameterizing the SECR model using kp = σp √Dp, where kp relates to the degree of overlap between home ranges and the subscript p distinguishes populations. We observe that kp is often nearly constant for populations spanning a range of densities. This justifies fitting a model in which the separate kp are replaced by the single parameter k and σp is a density-dependent derived parameter. Continuous density-dependent spatial variation in σ may also be modelled, using a scaled non-Euclidean distance between detectors and the locations of animals. We illustrate these methods with data from automatic photography of tigers (Panthera tigris) across India, in which the variation is among populations, from mist-netting of ovenbirds (Seiurus aurocapilla) in Maryland, USA, in which the variation is within a single population over time, and from live-trapping of brushtail possums (Trichosurus vulpecula) in New Zealand, modelling spatial variation within one population. Possible applications and limitations of the methods are discussed. A model in which kp is constant, while density varies, provides a parsimonious null model for SECR. The parameter k of the null model is a concise summary of the empirical relationship between home-range size and density that is useful in comparative studies. We expect deviations from this model, particularly the dependence of kp on covariates, to be biologically interesting.

  8. A Broad RNA Virus Survey Reveals Both miRNA Dependence and Functional Sequestration

    DEFF Research Database (Denmark)

    Scheel, Troels K H; Luna, Joseph M; Liniger, Matthias

    2016-01-01

    , critically depended on the interaction of cellular miR-17 and let-7 with the viral 3' UTR. Unlike canonical miRNA interactions, miR-17 and let-7 binding enhanced pestivirus translation and RNA stability. miR-17 sequestration by pestiviruses conferred reduced AGO binding and functional de...... immunoprecipitation (CLIP) of the Argonaute (AGO) proteins to characterize strengths and specificities of miRNA interactions in the context of 15 different RNA virus infections, including several clinically relevant pathogens. Notably, replication of pestiviruses, a major threat to milk and meat industries...

  9. Proteome analysis reveals an energy-dependent central process for Populus×canadensis seed germination.

    Science.gov (United States)

    Zhang, Hong; Zhou, Ke-Xin; Wang, Wei-Qing; Liu, Shu-Jun; Song, Song-Quan

    2017-06-01

    Poplar (Populus×canadensis) seeds rapidly germinated in darkness at 10, 15, and 20°C and reached 50% seed germination after about 22, 4.5, and 3.5h, respectively. Germination of poplar seeds was markedly inhibited by abscisic acid (ABA) at 50μM and cycloheximide (CHX) at 100μM, and these inhibitive roles were temperature-dependent. In the present study, mature poplar seeds were used to investigate the differentially changed proteome of seeds germinating in water, ABA, and CHX. A total of 130 protein spots showed a significant change (1.5-fold increase/decrease, Pgermination of poplar seeds is closely related with the increase in those proteins involved in amino acid and lipid metabolism, the tricarboxylic acid cycle and pentose phosphate pathway, protein synthesis and destination, cell defense and rescue, and degradation of storage proteins. ABA and CHX inhibit the germination of poplar seeds by decreasing the protein abundance associated with protein proteolysis, protein folding, and storage proteins. We conclude that poplar seed germination is an energy-dependent active process, and is accompanied by increasing amino acid activation, protein synthesis and destination, as well as cell defense and rescue, and degradation of storage proteins. Copyright © 2017 Elsevier GmbH. All rights reserved.

  10. Chromosome conformation maps in fission yeast reveal cell cycle dependent sub nuclear structure.

    Science.gov (United States)

    Grand, Ralph S; Pichugina, Tatyana; Gehlen, Lutz R; Jones, M Beatrix; Tsai, Peter; Allison, Jane R; Martienssen, Robert; O'Sullivan, Justin M

    2014-11-10

    Successful progression through the cell cycle requires spatial and temporal regulation of gene transcript levels and the number, positions and condensation levels of chromosomes. Here we present a high resolution survey of genome interactions in Schizosaccharomyces pombe using synchronized cells to investigate cell cycle dependent changes in genome organization and transcription. Cell cycle dependent interactions were captured between and within S. pombe chromosomes. Known features of genome organization (e.g. the clustering of telomeres and retrotransposon long terminal repeats (LTRs)) were observed throughout the cell cycle. There were clear correlations between transcript levels and chromosomal interactions between genes, consistent with a role for interactions in transcriptional regulation at specific stages of the cell cycle. In silico reconstructions of the chromosome organization within the S. pombe nuclei were made by polymer modeling. These models suggest that groups of genes with high and low, or differentially regulated transcript levels have preferred positions within the S. pombe nucleus. We conclude that the S. pombe nucleus is spatially divided into functional sub-nuclear domains that correlate with gene activity. The observation that chromosomal interactions are maintained even when chromosomes are fully condensed in M phase implicates genome organization in epigenetic inheritance and bookmarking. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  11. NMR-Based Metabonomic Investigation of Heat Stress in Myotubes Reveals a Time-Dependent Change in the Metabolites

    DEFF Research Database (Denmark)

    Straadt, Ida K; Young, Jette F; Bross, Peter

    2010-01-01

    NMR-based metabonomics was applied to elucidate the time-dependent stress responses in mouse myotubes after heat exposure of either 42 or 45 degrees C for 1 h. Principal component analysis (PCA) revealed that the gradual time-dependent changes in metabolites contributing to the clustering...... and separation of the control samples from the different time points after heat stress primarily are in the metabolites glucose, leucine, lysine, phenylalanine, creatine, glutamine, and acetate. In addition, PC scores revealed a maximum change in metabolite composition 4 h after the stress exposure; thereafter......, samples returned toward control samples, however, without reaching the control samples even 10 h after stress. The results also indicate that the myotubes efficiently regulate the pH level by release of lactate to the culture medium at a heat stress level of 42 degrees C, which is a temperature level...

  12. Anharmonic onsets in polypeptides revealed by neutron scattering: experimental evidences and quantitative description of energy resolution dependence.

    Science.gov (United States)

    Schiró, Giorgio

    2013-01-01

    Neutron scattering measurements on protein powders reveal two deviations from harmonic dynamics at low temperature, whose molecular origin, physical nature and biological relevance are still matter of discussion. In this study we present a new experimental and theoretical approach to evidence the resolution dependence of anharmonic onsets: the use of strategically selected homomeric polypeptides allows revealing the exact resolution dependence; a two-site energy landscape model, where resolution effects are explicitly taken into account, is able to interpret quantitatively the experimental data in terms of energy landscape parameters. The energetic description provided by this analysis, together with recent experimental evidences obtained on chemically and structurally different peptide systems, allows us to connect the protein/water energy landscape structure with the two-wells water interaction potential proposed to explain the low-density→high-density liquid-liquid transition observed in supercooled water. Copyright © 2013 Elsevier B.V. All rights reserved.

  13. Polarization dependence of the magnetic fluctuations in the weak itinerant ferromagnet MnSi below T{sub c}

    Energy Technology Data Exchange (ETDEWEB)

    Boeni, P.; Tixier, S. [Paul Scherrer Inst. (PSI), Villigen (Switzerland); Endoh, Y. [Tohoku Univ., Sendai (Japan); Roessli, B. [Institut Max von Laue - Paul Langevin, 75 - Paris (France); Shirane, G. [Brookhaven (United States)

    1997-09-01

    The dispersion of the spin-flip and non-spin-flip excitations in the weak itinerant ferromagnet MnSi have been measured in the ferromagnetic phase using inelastic polarized neutron scattering. Spin wave excitations are well defined at energy transfers as large as 7 meV. The cross section of the non-spin-flip excitations is compatible with a quasielastic response function. (author) 2 figs., 3 refs.

  14. Dependence of InGaN solar cell performance on polarization-induced electric field and carrier lifetime

    International Nuclear Information System (INIS)

    Yang Jing; Zhao De-Gang; Jiang De-Sheng; Liu Zong-Shun; Chen Ping; Li Liang; Wu Liang-Liang; Le Ling-Cong; Li Xiao-Jing; He Xiao-Guang; Yang Hui; Wang Hui; Zhu Jian-Jun; Zhang Shu-Ming; Zhang Bao-Shun

    2013-01-01

    The effects of Mg-induced net acceptor doping concentration and carrier lifetime on the performance of a p—i—n InGaN solar cell are investigated. It is found that the electric field induced by spontaneous and piezoelectric polarization in the i-region could be totally shielded when the Mg-induced net acceptor doping concentration is sufficiently high. The polarization-induced potential barriers are reduced and the short circuit current density is remarkably increased from 0.21 mA/cm 2 to 0.95 mA/cm 2 by elevating the Mg doping concentration. The carrier lifetime determined by defect density of i-InGaN also plays an important role in determining the photovoltaic properties of solar cell. The short circuit current density severely degrades, and the performance of InGaN solar cell becomes more sensitive to the polarization when carrier lifetime is lower than the transit time. This study demonstrates that the crystal quality of InGaN absorption layer is one of the most important challenges in realizing high efficiency InGaN solar cells. (interdisciplinary physics and related areas of science and technology)

  15. Spin-dependent energy distribution of B-hadrons from polarized top decays considering the azimuthal correlation rate

    Directory of Open Access Journals (Sweden)

    S.M. Moosavi Nejad

    2016-04-01

    Full Text Available Basically, the energy distribution of bottom-flavored hadrons produced through polarized top quark decays t(↑→W++b(→Xb, is governed by the unpolarized rate and the polar and the azimuthal correlation functions which are related to the density matrix elements of the decay t(↑→bW+. Here we present, for the first time, the analytical expressions for the O(αs radiative corrections to the differential azimuthal decay rates of the partonic process t(↑→b+W+ in two helicity systems, which are needed to study the azimuthal distribution of the energy spectrum of the hadrons produced in polarized top decays. These spin-momentum correlations between the top quark spin and its decay product momenta will allow the detailed studies of the top decay mechanism. Our predictions of the hadron energy distributions also enable us to deepen our knowledge of the hadronization process and to test the universality and scaling violations of the bottom-flavored meson fragmentation functions.

  16. The viscoelastic properties of chromatin and the nucleoplasm revealed by scale-dependent protein mobility

    Science.gov (United States)

    Erdel, Fabian; Baum, Michael; Rippe, Karsten

    2015-02-01

    The eukaryotic cell nucleus harbours the DNA genome that is organized in a dynamic chromatin network and embedded in a viscous crowded fluid. This environment directly affects enzymatic reactions and target search processes that access the DNA sequence information. However, its physical properties as a reaction medium are poorly understood. Here, we exploit mobility measurements of differently sized inert green fluorescent tracer proteins to characterize the viscoelastic properties of the nuclear interior of a living human cell. We find that it resembles a viscous fluid on small and large scales but appears viscoelastic on intermediate scales that change with protein size. Our results are consistent with simulations of diffusion through polymers and suggest that chromatin forms a random obstacle network rather than a self-similar structure with fixed fractal dimensions. By calculating how long molecules remember their previous position in dependence on their size, we evaluate how the nuclear environment affects search processes of chromatin targets.

  17. Intravital imaging reveals p53-dependent cancer cell death induced by phototherapy via calcium signaling

    Science.gov (United States)

    Missiroli, Sonia; Poletti, Federica; Ramirez, Fabian Galindo; Morciano, Giampaolo; Morganti, Claudia; Pandolfi, Pier Paolo; Mammano, Fabio; Pinton, Paolo

    2015-01-01

    One challenge in biology is signal transduction monitoring in a physiological context. Intravital imaging techniques are revolutionizing our understanding of tumor and host cell behaviors in the tumor environment. However, these deep tissue imaging techniques have not yet been adopted to investigate the second messenger calcium (Ca2+). In the present study, we established conditions that allow the in vivo detection of Ca2+ signaling in three-dimensional tumor masses in mouse models. By combining intravital imaging and a skinfold chamber technique, we determined the ability of photodynamic cancer therapy to induce an increase in intracellular Ca2+ concentrations and, consequently, an increase in cell death in a p53-dependent pathway. PMID:25544762

  18. Plant root transcriptome profiling reveals a strain-dependent response during Azospirillum-rice cooperation.

    Science.gov (United States)

    Drogue, Benoît; Sanguin, Hervé; Chamam, Amel; Mozar, Michael; Llauro, Christel; Panaud, Olivier; Prigent-Combaret, Claire; Picault, Nathalie; Wisniewski-Dyé, Florence

    2014-01-01

    Cooperation involving Plant Growth-Promoting Rhizobacteria results in improvements of plant growth and health. While pathogenic and symbiotic interactions are known to induce transcriptional changes for genes related to plant defense and development, little is known about the impact of phytostimulating rhizobacteria on plant gene expression. This study aims at identifying genes significantly regulated in rice roots upon Azospirillum inoculation, considering possible favored interaction between a strain and its original host cultivar. Genome-wide analyzes of Oryza sativa japonica cultivars Cigalon and Nipponbare were performed, by using microarrays, seven days post-inoculation with Azospirillum lipoferum 4B (isolated from Cigalon) or Azospirillum sp. B510 (isolated from Nipponbare) and compared to the respective non-inoculated condition. A total of 7384 genes were significantly regulated, which represent about 16% of total rice genes. A set of 34 genes is regulated by both Azospirillum strains in both cultivars, including a gene orthologous to PR10 of Brachypodium, and these could represent plant markers of Azospirillum-rice interactions. The results highlight a strain-dependent response of rice, with 83% of the differentially expressed genes being classified as combination-specific. Whatever the combination, most of the differentially expressed genes are involved in primary metabolism, transport, regulation of transcription and protein fate. When considering genes involved in response to stress and plant defense, it appears that strain B510, a strain displaying endophytic properties, leads to the repression of a wider set of genes than strain 4B. Individual genotypic variations could be the most important driving force of rice roots gene expression upon Azospirillum inoculation. Strain-dependent transcriptional changes observed for genes related to auxin and ethylene signaling highlight the complexity of hormone signaling networks in the Azospirillum

  19. Plant root transcriptome profiling reveals a strain-dependent response during Azospirillum-rice cooperation

    Directory of Open Access Journals (Sweden)

    Benoît eDrogue

    2014-11-01

    Full Text Available Cooperation involving Plant Growth-Promoting Rhizobacteria results in improvements of plant growth and health. While pathogenic and symbiotic interactions are known to induce transcriptional changes for genes related to plant defence and development, little is known about the impact of phytostimulating rhizobacteria on plant gene expression. This study aims at identifying genes significantly regulated in rice roots upon Azospirillum inoculation, considering possible favored interaction between a strain and its original host cultivar. Genome-wide analyses of Oryza sativa japonica cultivars Cigalon and Nipponbare were performed, by using microarrays, seven days post inoculation with A. lipoferum 4B (isolated from Cigalon or Azospirillum sp. B510 (isolated from Nipponbare and compared to the respective non-inoculated condition. A total of 7,384 genes were significantly regulated, which represent about 16 % of total rice genes. A set of 34 genes is regulated by both Azospirillum strains in both cultivars, including a gene orthologous to PR10 of Brachypodium, and these could represent plant markers of Azospirillum-rice interactions. The results highlight a strain-dependent response of rice, with 83 % of the differentially expressed genes being classified as combination-specific. Whatever the combination, most of the differentially expressed genes are involved in primary metabolism, transport, regulation of transcription and protein fate. When considering genes involved in response to stress and plant defence, it appears that strain B510, a strain displaying endophytic properties, leads to the repression of a wider set of genes than strain 4B. Individual genotypic variations could be the most important driving force of rice roots gene expression upon Azospirillum inoculation. Strain-dependent transcriptional changes observed for genes related to auxin and ethylene signalling highlight the complexity of hormone signalling networks in the Azospirillum

  20. Sine wave electropermeabilization reveals the frequency-dependent response of the biological membranes.

    Science.gov (United States)

    García-Sánchez, Tomás; Merla, Caterina; Fontaine, Jessica; Muscat, Adeline; Mir, Lluis M

    2018-02-02

    The permeabilization of biological membranes by electric fields, known as electroporation, has been traditionally performed with square electric pulses. These signals distribute the energy applied to cells in a wide frequency band. This paper investigates the use of sine waves, which are narrow band signals, to provoke electropermeabilization and the frequency dependence of this phenomenon. Single bursts of sine waves at different frequencies in the range from 8 kHz-130 kHz were applied to cells in vitro. Electroporation was studied in the plasma membrane and the internal organelles membrane using calcium as a permeabilization marker. Additionally, a double-shell electrical model was simulated to give a theoretical framework to our results. The electroporation efficiency shows a low pass filter frequency dependence for both the plasma membrane and the internal organelles membrane. The mismatch between the theoretical response and the observed behavior for the internal organelles membrane is explained by a two-step permeabilization process: first the permeabilization of the external membrane and afterwards that of the internal membranes. The simulations in the model confirm this two-step hypothesis when a variable plasma membrane conductivity is considered in the analysis. This study demonstrates how the use of narrow-band signals as sine waves is a suitable method to perform electroporation in a controlled manner. We suggest that the use of this type of signals could bring a simplification in the investigations of the very complex phenomenon of electroporation, thus representing an interesting option in future fundamental studies. Copyright © 2018 Elsevier B.V. All rights reserved.

  1. Sapling growth rates reveal conspecific negative density dependence in a temperate forest.

    Science.gov (United States)

    Ramage, Benjamin S; Johnson, Daniel J; Gonzalez-Akre, Erika; McShea, William J; Anderson-Teixeira, Kristina J; Bourg, Norman A; Clay, Keith

    2017-10-01

    Local tree species diversity is maintained in part by conspecific negative density dependence (CNDD). This pervasive mechanism occurs in a variety of forms and ecosystems, but research to date has been heavily skewed toward tree seedling survival in tropical forests. To evaluate CNDD more broadly, we investigated how sapling growth rates were affected by conspecific adult neighbors in a fully mapped 25.6 ha temperate deciduous forest. We examined growth rates as a function of the local adult tree neighborhood (via spatial autoregressive modeling) and compared the spatial positioning of faster-growing and slower-growing saplings with respect to adult conspecific and heterospecific trees (via bivariate point pattern analysis). In addition, to determine whether CNDD-driven variation in growth rates leaves a corresponding spatial signal, we extended our point pattern analysis to a static, growth-independent comparison of saplings and the next larger size class. We found that negative conspecific effects on sapling growth were most prevalent. Five of the nine species that were sufficiently abundant for analysis exhibited CNDD, while only one species showed evidence of a positive conspecific effect, and one or two species, depending on the analysis, displayed heterospecific effects. There was general agreement between the autoregressive models and the point pattern analyses based on sapling growth rates, but point pattern analyses based on single-point-in-time size classes yielded results that differed markedly from the other two approaches. Our work adds to the growing body of evidence that CNDD is an important force in temperate forests, and demonstrates that this process extends to sapling growth rates. Further, our findings indicate that point pattern analyses based solely on size classes may fail to detect the process of interest (e.g., neighborhood-driven variation in growth rates), in part due to the confounding of tree size and age.

  2. RNA-seq transcriptional profiling of Leishmania amazonensis reveals an arginase-dependent gene expression regulation.

    Directory of Open Access Journals (Sweden)

    Juliana Ide Aoki

    2017-10-01

    Full Text Available Leishmania is a protozoan parasite that alternates its life cycle between the sand-fly vector and the mammalian host. This alternation involves environmental changes and leads the parasite to dynamic modifications in morphology, metabolism, cellular signaling and regulation of gene expression to allow for a rapid adaptation to new conditions. The L-arginine pathway in L. amazonensis is important during the parasite life cycle and interferes in the establishment and maintenance of the infection in mammalian macrophages. Host arginase is an immune-regulatory enzyme that can reduce the production of nitric oxide by activated macrophages, directing the availability of L-arginine to the polyamine pathway, resulting in parasite replication. In this work, we performed transcriptional profiling to identify differentially expressed genes in L. amazonensis wild-type (La-WT versus L. amazonensis arginase knockout (La-arg- promastigotes and axenic amastigotes.A total of 8253 transcripts were identified in La-WT and La-arg- promastigotes and axenic amastigotes, about 60% of them codifying hypothetical proteins and 443 novel transcripts, which did not match any previously annotated genes. Our RNA-seq data revealed that 85% of genes were constitutively expressed. The comparison of transcriptome and metabolome data showed lower levels of arginase and higher levels of glutamate-5-kinase in La-WT axenic amastigotes compared to promastigotes. The absence of arginase activity in promastigotes increased the levels of pyrroline 5-carboxylate reductase, but decreased the levels of arginosuccinate synthase, pyrroline 5-carboxylate dehydrogenase, acetylornithine deacetylase and spermidine synthase transcripts levels. These observations can explain previous metabolomic data pointing to the increase of L-arginine, citrulline and L-glutamate and reduction of aspartate, proline, ornithine and putrescine. Altogether, these results indicate that arginase activity is important

  3. Active nuclear transcriptome analysis reveals inflammasome-dependent mechanism for early neutrophil response to Mycobacterium marinum.

    Science.gov (United States)

    Kenyon, Amy; Gavriouchkina, Daria; Zorman, Jernej; Napolitani, Giorgio; Cerundolo, Vincenzo; Sauka-Spengler, Tatjana

    2017-07-26

    The mechanisms governing neutrophil response to Mycobacterium tuberculosis remain poorly understood. In this study we utilise biotagging, a novel genome-wide profiling approach based on cell type-specific in vivo biotinylation in zebrafish to analyse the initial response of neutrophils to Mycobacterium marinum, a close genetic relative of M. tuberculosis used to model tuberculosis. Differential expression analysis following nuclear RNA-seq of neutrophil active transcriptomes reveals a significant upregulation in both damage-sensing and effector components of the inflammasome, including caspase b, NLRC3 ortholog (wu: fb15h11) and il1β. Crispr/Cas9-mediated knockout of caspase b, which acts by proteolytic processing of il1β, results in increased bacterial burden and less infiltration of macrophages to sites of mycobacterial infection, thus impairing granuloma development. We also show that a number of immediate early response genes (IEGs) are responsible for orchestrating the initial neutrophil response to mycobacterial infection. Further perturbation of the IEGs exposes egr3 as a key transcriptional regulator controlling il1β transcription.

  4. Single-Molecule Imaging Reveals Topology Dependent Mutual Relaxation of Polymer Chains

    KAUST Repository

    Abadi, Maram

    2015-08-24

    The motion and relaxation of linear and cyclic polymers under entangled conditions are investigated by means of a newly developed single-molecule tracking technique, cumulative-area (CA) tracking. CA tracking enables simultaneous quantitative characterization of the diffusion mode, diffusion rate, and relaxation time that have been impossible with a widely used conventional single-molecule localization and tracking method, by analyzing cumulative areas occupied by the moving molecule. Using the novel approach, we investigate the motion and relaxation of entangled cyclic polymers, which have been an important but poorly understood question. Fluorescently labeled 42 kbp linear or cyclic tracer dsDNAs in concentrated solutions of unlabeled linear or cyclic DNAs are used as model systems. We show that CA tracking can explicitly distinguish topology-dependent diffusion mode, rate, and relaxation time, demonstrating that the method provides an invaluable tool for characterizing topological interaction between the entangled chains. We further demonstrate that the current models proposed for the entanglement between cyclic polymers which are based on cyclic chains moving through an array of fixed obstacles cannot correctly describe the motion of the cyclic chain under the entangled conditions. Our results rather suggest the mutual relaxation of the cyclic chains, which underscore the necessity of developing a new model to describe the motion of cyclic polymer under the entangled conditions based on the mutual interaction of the chains.

  5. Genome-wide analysis reveals a cell cycle–dependent mechanism controlling centromere propagation

    Science.gov (United States)

    Erhardt, Sylvia; Mellone, Barbara G.; Betts, Craig M.; Zhang, Weiguo; Karpen, Gary H.; Straight, Aaron F.

    2008-01-01

    Centromeres are the structural and functional foundation for kinetochore formation, spindle attachment, and chromosome segregation. In this study, we isolated factors required for centromere propagation using genome-wide RNA interference screening for defects in centromere protein A (CENP-A; centromere identifier [CID]) localization in Drosophila melanogaster. We identified the proteins CAL1 and CENP-C as essential factors for CID assembly at the centromere. CID, CAL1, and CENP-C coimmunoprecipitate and are mutually dependent for centromere localization and function. We also identified the mitotic cyclin A (CYCA) and the anaphase-promoting complex (APC) inhibitor RCA1/Emi1 as regulators of centromere propagation. We show that CYCA is centromere localized and that CYCA and RCA1/Emi1 couple centromere assembly to the cell cycle through regulation of the fizzy-related/CDH1 subunit of the APC. Our findings identify essential components of the epigenetic machinery that ensures proper specification and propagation of the centromere and suggest a mechanism for coordinating centromere inheritance with cell division. PMID:19047461

  6. Genome-wide analysis reveals a cell cycle-dependent mechanism controlling centromere propagation.

    Science.gov (United States)

    Erhardt, Sylvia; Mellone, Barbara G; Betts, Craig M; Zhang, Weiguo; Karpen, Gary H; Straight, Aaron F

    2008-12-01

    Centromeres are the structural and functional foundation for kinetochore formation, spindle attachment, and chromosome segregation. In this study, we isolated factors required for centromere propagation using genome-wide RNA interference screening for defects in centromere protein A (CENP-A; centromere identifier [CID]) localization in Drosophila melanogaster. We identified the proteins CAL1 and CENP-C as essential factors for CID assembly at the centromere. CID, CAL1, and CENP-C coimmunoprecipitate and are mutually dependent for centromere localization and function. We also identified the mitotic cyclin A (CYCA) and the anaphase-promoting complex (APC) inhibitor RCA1/Emi1 as regulators of centromere propagation. We show that CYCA is centromere localized and that CYCA and RCA1/Emi1 couple centromere assembly to the cell cycle through regulation of the fizzy-related/CDH1 subunit of the APC. Our findings identify essential components of the epigenetic machinery that ensures proper specification and propagation of the centromere and suggest a mechanism for coordinating centromere inheritance with cell division.

  7. Recombinant VSV G proteins reveal a novel raft-dependent endocytic pathway in resorbing osteoclasts

    International Nuclear Information System (INIS)

    Mulari, Mika T.K.; Nars, Martin; Laitala-Leinonen, Tiina; Kaisto, Tuula; Metsikkoe, Kalervo; Sun Yi; Vaeaenaenen, H. Kalervo

    2008-01-01

    Transcytotic membrane flow delivers degraded bone fragments from the ruffled border to the functional secretory domain, FSD, in bone resorbing osteoclasts. Here we show that there is also a FSD-to-ruffled border trafficking pathway that compensates for the membrane loss during the matrix uptake process and that rafts are essential for this ruffled border-targeted endosomal pathway. Replacing the cytoplasmic tail of the vesicular stomatitis virus G protein with that of CD4 resulted in partial insolubility in Triton X-100 and retargeting from the peripheral non-bone facing plasma membrane to the FSD. Recombinant G proteins were subsequently endosytosed and delivered from the FSD to the peripheral fusion zone of the ruffled border, which were both rich in lipid rafts as suggested by viral protein transport analysis and visualizing the rafts with fluorescent recombinant cholera toxin. Cholesterol depletion by methyl-β-cyclodextrin impaired the ruffled border-targeted vesicle trafficking pathway and inhibited bone resorption dose-dependently as quantified by measuring the CTX and TRACP 5b secreted to the culture medium and by measuring the resorbed area visualized with a bi-phasic labeling method using sulpho-NHS-biotin and WGA-lectin. Thus, rafts are vital for membrane recycling from the FSD to the late endosomal/lysosomal ruffled border and bone resorption

  8. Dependence of black fragment azimuthal and projected angular distributions on polar angle in silicon-emulsion collisions at 4.5A GeV/c

    International Nuclear Information System (INIS)

    Liu Fuhu; Abd Allah, Nabil N.; Singh, B.K.

    2004-01-01

    The experimental results of dependence of black fragment azimuth (φ) and projected angle (ψ) distributions on polar angle θ in silicon-emulsion collisions at 4.5A GeV/c (the Dubna momentum) are reported. There are two regions of enhancement around φ=±90 deg. for different θ ranges. These enhancements are due to directed (v 1 ) and elliptic (v 2 ) flows. The v 1 and v 2 dependence of values on θ shows that the directed flow is weak and the elliptic flow is strong in these collisions. A multisource ideal gas model is used to describe the experimental results of dependence. The Monte Carlo calculated results are approximately in agreement with the experimental data

  9. Metabarcoding Reveals Seasonal and Temperature-Dependent Succession of Zooplankton Communities in the Red Sea

    Directory of Open Access Journals (Sweden)

    Laura Casas

    2017-08-01

    Full Text Available Very little is known about the composition and the annual cycle of zooplankton assemblages in the Red Sea, a confined water body characterized by a high biodiversity and endemism but at the same time one of the most understudied areas in the world in terms of marine biodiversity. This high diversity together with the lack of references for several of the groups poses a problem in obtaining basic information on zooplankton seasonal patterns. In the present work, we used high throughput sequencing to examine the temporal and spatial distribution of the zooplankton communities inhabiting the epipelagic zone in the central Red Sea. The analysis of zooplankton assemblages collected at two sites—coastal and offshore—twice a month at several depth strata by using MANTA, Bongo and WP2 nets provides baseline information of the seasonal patterns of the zooplankton community over 1 year. We show that the seasonal fluctuation of zooplankton communities living in the upper 100 m of the water column is driven mainly by the annual changes in seawater temperature. The 18S rRNA gene was used for metabarcoding of zooplankton assemblages revealing 630 metazoan OTUs (97% similarity in five phyla, highlighting the richness of the Red Sea community. During colder months, communities were characterized by lower richness and higher biomass than communities found during the hot season. Throughout the year the zooplankton communities were dominated by the class Maxillopoda, mainly represented by copepods and class Hydrozoa. The rise in the water temperature favors the appearance of classes Malacostraca, Cephalopoda, Gastropoda, and Saggitoidea. The present study provides essential baseline information for future monitoring and improves our knowledge of the marine ecosystem in the Red Sea while reporting the main environmental variable structuring zooplankton assemblages in this region.

  10. Metabarcoding Reveals Seasonal and Temperature-Dependent Succession of Zooplankton Communities in the Red Sea

    KAUST Repository

    Casas, Laura

    2017-08-02

    Very little is known about the composition and the annual cycle of zooplankton assemblages in the Red Sea, a confined water body characterized by a high biodiversity and endemism but at the same time one of the most understudied areas in the world in terms of marine biodiversity. This high diversity together with the lack of references for several of the groups poses a problem in obtaining basic information on zooplankton seasonal patterns. In the present work, we used high throughput sequencing to examine the temporal and spatial distribution of the zooplankton communities inhabiting the epipelagic zone in the central Red Sea. The analysis of zooplankton assemblages collected at two sites—coastal and offshore—twice a month at several depth strata by using MANTA, Bongo and WP2 nets provides baseline information of the seasonal patterns of the zooplankton community over 1 year. We show that the seasonal fluctuation of zooplankton communities living in the upper 100 m of the water column is driven mainly by the annual changes in seawater temperature. The 18S rRNA gene was used for metabarcoding of zooplankton assemblages revealing 630 metazoan OTUs (97% similarity) in five phyla, highlighting the richness of the Red Sea community. During colder months, communities were characterized by lower richness and higher biomass than communities found during the hot season. Throughout the year the zooplankton communities were dominated by the class Maxillopoda, mainly represented by copepods and class Hydrozoa. The rise in the water temperature favors the appearance of classes Malacostraca, Cephalopoda, Gastropoda, and Saggitoidea. The present study provides essential baseline information for future monitoring and improves our knowledge of the marine ecosystem in the Red Sea while reporting the main environmental variable structuring zooplankton assemblages in this region.

  11. Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production.

    Science.gov (United States)

    Wu, Gary D; Compher, Charlene; Chen, Eric Z; Smith, Sarah A; Shah, Rachana D; Bittinger, Kyle; Chehoud, Christel; Albenberg, Lindsey G; Nessel, Lisa; Gilroy, Erin; Star, Julie; Weljie, Aalim M; Flint, Harry J; Metz, David C; Bennett, Michael J; Li, Hongzhe; Bushman, Frederic D; Lewis, James D

    2016-01-01

    The consumption of an agrarian diet is associated with a reduced risk for many diseases associated with a 'Westernised' lifestyle. Studies suggest that diet affects the gut microbiota, which subsequently influences the metabolome, thereby connecting diet, microbiota and health. However, the degree to which diet influences the composition of the gut microbiota is controversial. Murine models and studies comparing the gut microbiota in humans residing in agrarian versus Western societies suggest that the influence is large. To separate global environmental influences from dietary influences, we characterised the gut microbiota and the host metabolome of individuals consuming an agrarian diet in Western society. Using 16S rRNA-tagged sequencing as well as plasma and urinary metabolomic platforms, we compared measures of dietary intake, gut microbiota composition and the plasma metabolome between healthy human vegans and omnivores, sampled in an urban USA environment. Plasma metabolome of vegans differed markedly from omnivores but the gut microbiota was surprisingly similar. Unlike prior studies of individuals living in agrarian societies, higher consumption of fermentable substrate in vegans was not associated with higher levels of faecal short chain fatty acids, a finding confirmed in a 10-day controlled feeding experiment. Similarly, the proportion of vegans capable of producing equol, a soy-based gut microbiota metabolite, was less than that was reported in Asian societies despite the high consumption of soy-based products. Evidently, residence in globally distinct societies helps determine the composition of the gut microbiota that, in turn, influences the production of diet-dependent gut microbial metabolites. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

  12. Suppressing an anti-inflammatory cytokine reveals a strong age-dependent survival cost in mice.

    Directory of Open Access Journals (Sweden)

    Virginia Belloni

    Full Text Available BACKGROUND: The central paradigm of ecological immunology postulates that selection acts on immunity as to minimize its cost/benefit ratio. Costs of immunity may arise because the energetic requirements of the immune response divert resources that are no longer available for other vital functions. In addition to these resource-based costs, mis-directed or over-reacting immune responses can be particularly harmful for the host. In spite of the potential importance of immunopathology, most studies dealing with the evolution of the immune response have neglected such non resource-based costs. To keep the immune response under control, hosts have evolved regulatory pathways that should be considered when studying the target of the selection pressures acting on immunity. Indeed, variation in regulation may strongly modulate the negative outcome of immune activation, with potentially important fitness consequences. METHODOLOGY/PRINCIPAL FINDINGS: Here, we experimentally assessed the survival costs of reduced immune regulation by inhibiting an anti-inflammatory cytokine (IL-10 with anti-IL-10 receptor antibodies (anti-IL-10R in mice that were either exposed to a mild inflammation or kept as control. The experiment was performed on young (3 months and old (15 months individuals, as to further assess the age-dependent cost of suppressing immune regulation. IL-10 inhibition induced high mortality in old mice exposed to the mild inflammatory insult, whereas no mortality was observed in young mice. However, young mice experienced a transitory lost in body mass when injected with the anti-IL-10R antibodies, showing that the treatment was to a lesser extent also costly for young individuals. CONCLUSIONS: These results suggest a major role of immune regulation that deserves attention when investigating the evolution of immunity, and indicate that the capacity to down-regulate the inflammatory response is crucial for late survival and longevity.

  13. Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production

    Science.gov (United States)

    Wu, Gary D; Compher, Charlene; Chen, Eric Z; Smith, Sarah A; Shah, Rachana D; Bittinger, Kyle; Chehoud, Christel; Albenberg, Lindsey G; Nessel, Lisa; Gilroy, Erin; Star, Julie; Weljie, Aalim M; Flint, Harry J; Metz, David C; Bennett, Michael J; Li, Hongzhe; Bushman, Frederic D; Lewis, James D

    2015-01-01

    Objective The consumption of an agrarian diet is associated with a reduced risk for many diseases associated with a ‘Westernised’ lifestyle. Studies suggest that diet affects the gut microbiota, which subsequently influences the metabolome, thereby connecting diet, microbiota and health. However, the degree to which diet influences the composition of the gut microbiota is controversial. Murine models and studies comparing the gut microbiota in humans residing in agrarian versus Western societies suggest that the influence is large. To separate global environmental influences from dietary influences, we characterised the gut microbiota and the host metabolome of individuals consuming an agrarian diet in Western society. Design and results Using 16S rRNA-tagged sequencing as well as plasma and urinary metabolomic platforms, we compared measures of dietary intake, gut microbiota composition and the plasma metabolome between healthy human vegans and omnivores, sampled in an urban USA environment. Plasma metabolome of vegans differed markedly from omnivores but the gut microbiota was surprisingly similar. Unlike prior studies of individuals living in agrarian societies, higher consumption of fermentable substrate in vegans was not associated with higher levels of faecal short chain fatty acids, a finding confirmed in a 10-day controlled feeding experiment. Similarly, the proportion of vegans capable of producing equol, a soy-based gut microbiota metabolite, was less than that was reported in Asian societies despite the high consumption of soy-based products. Conclusions Evidently, residence in globally distinct societies helps determine the composition of the gut microbiota that, in turn, influences the production of diet-dependent gut microbial metabolites. PMID:25431456

  14. Replication origin-flanking roadblocks reveal origin-licensing dynamics and altered sequence dependence.

    Science.gov (United States)

    Warner, Megan D; Azmi, Ishara F; Kang, Sukhyun; Zhao, Yanding; Bell, Stephen P

    2017-12-29

    In eukaryotes, DNA replication initiates from multiple origins of replication for timely genome duplication. These sites are selected by origin licensing, during which the core enzyme of the eukaryotic DNA replicative helicase, the Mcm2-7 (minichromosome maintenance) complex, is loaded at each origin. This origin licensing requires loading two Mcm2-7 helicases around origin DNA in a head-to-head orientation. Current models suggest that the origin-recognition complex (ORC) and cell-division cycle 6 (Cdc6) proteins recognize and encircle origin DNA and assemble an Mcm2-7 double-hexamer around adjacent double-stranded DNA. To test this model and assess the location of Mcm2-7 initial loading, we placed DNA-protein roadblocks at defined positions adjacent to the essential ORC-binding site within Saccharomyces cerevisiae origin DNA. Roadblocks were made either by covalent cross-linking of the HpaII methyltransferase to DNA or through binding of a transcription activator-like effector (TALE) protein. Contrary to the sites of Mcm2-7 recruitment being precisely defined, only single roadblocks that inhibited ORC-DNA binding showed helicase loading defects. We observed inhibition of helicase loading without inhibition of ORC-DNA binding only when roadblocks were placed on both sides of the origin to restrict sliding of a helicase-loading intermediate. Consistent with a sliding helicase-loading intermediate, when either one of the flanking roadblocks was eliminated, the remaining roadblock had no effect on helicase loading. Interestingly, either origin-flanking nucleosomes or roadblocks resulted in helicase loading being dependent on an additional origin sequence known to be a weaker ORC-DNA-binding site. Together, our findings support a model in which sliding helicase-loading intermediates increase the flexibility of the DNA sequence requirements for origin licensing. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  15. Multiple sweet receptors and transduction pathways revealed in knockout mice by temperature dependence and gurmarin sensitivity.

    Science.gov (United States)

    Ohkuri, Tadahiro; Yasumatsu, Keiko; Horio, Nao; Jyotaki, Masafumi; Margolskee, Robert F; Ninomiya, Yuzo

    2009-04-01

    Sweet taste transduction involves taste receptor type 1, member 2 (T1R2), taste receptor type 1, member 3 (T1R3), gustducin, and TRPM5. Because knockout (KO) mice lacking T1R3, gustducin's Galpha subunit (Galphagust), or TRPM5 exhibited greatly reduced, but not abolished responses of the chorda tympani (CT) nerve to sweet compounds, it is likely that multiple sweet transduction pathways exist. That gurmarin (Gur), a sweet taste inhibitor, inhibits some but not all mouse CT responses to sweet compounds supports the existence of multiple sweet pathways. Here, we investigated Gur inhibition of CT responses to sweet compounds as a function of temperature in KO mice lacking T1R3, Galphagust, or TRPM5. In T1R3-KO mice, responses to sucrose and glucose were Gur sensitive (GS) and displayed a temperature-dependent increase (TDI). In Galphagust-KO mice, responses to sucrose and glucose were Gur-insensitive (GI) and showed a TDI. In TRPM5-KO mice, responses to glucose were GS and showed a TDI. All three KO mice exhibited no detectable responses to SC45647, and their responses to saccharin displayed neither GS nor a TDI. For all three KO mice, the lingual application of pronase, another sweet response inhibitor, almost fully abolished responses to sucrose and glucose but did not affect responses to saccharin. These results provide evidence for 1) the existence of multiple transduction pathways underlying responses to sugars: a T1R3-independent GS pathway for sucrose and glucose, and a TRPM5-independent temperature sensitive GS pathway for glucose; 2) the requirement for Galphagust in GS sweet taste responses; and 3) the existence of a sweet independent pathway for saccharin, in mouse taste cells on the anterior tongue.

  16. Single-molecule diffusometry reveals the nucleotide-dependent oligomerization pathways of Nicotiana tabacum Rubisco activase

    Science.gov (United States)

    Wang, Quan; Serban, Andrew J.; Wachter, Rebekka M.; Moerner, W. E.

    2018-03-01

    Oligomerization plays an important role in the function of many proteins, but a quantitative picture of the oligomer distribution has been difficult to obtain using existing techniques. Here we describe a method that combines sub-stoichiometric labeling and recently developed single-molecule diffusometry to measure the size distribution of oligomers under equilibrium conditions in solution, one molecule at a time. We use this technique to characterize the oligomerization behavior of Nicotiana tabacum (Nt) Rubisco activase (Nt-Rca), a chaperone-like AAA-plus ATPase essential in regulating carbon fixation during photosynthesis. We directly observed monomers, dimers, and a tetramer/hexamer mixture and extracted their fractional abundance as a function of protein concentration. We show that the oligomerization pathway of Nt-Rca is nucleotide dependent: ATPγS binding strongly promotes tetramer/hexamer formation from dimers and results in a preferred tetramer/hexamer population for concentrations in the 1-10 μM range. Furthermore, we directly observed dynamic assembly and disassembly processes of single complexes in real time and from there estimated the rate of subunit exchange to be ˜0.1 s-1 with ATPγS. On the other hand, ADP binding destabilizes Rca complexes by enhancing the rate of subunit exchange by >2 fold. These observations provide a quantitative starting point to elucidate the structure-function relations of Nt-Rca complexes. We envision the method to fill a critical gap in defining and quantifying protein assembly pathways in the small-oligomer regime.

  17. Spin-dependent scattering and the spin polarization of a diffusive current in partly disordered L10 epitaxial FePd

    International Nuclear Information System (INIS)

    Seemann, K M; Hickey, M C; Baltz, V; Hickey, B J; Marrows, C H

    2010-01-01

    We report magnetic domain wall (DW) resistance in epitaxial films of FePd. When equal numbers of Fe and Pd atoms are present, this material forms an ordered structure with alternating crystal planes of Fe and Pd. We prepared films enriched with Pd to varying degrees, gradually degrading this structure. As might be expected, this increased the electrical resistivity of the films by introducing extra defects that can scatter electrons. However, unexpectedly, the additional resistance arising from the ∼10 nm thick DWs rose as a proportion of the overall resistivity, roughly doubling when halving the degree of chemical ordering-as determined from x-ray diffraction measurements-within the films. These data can be used to infer a rise in the spin polarization of the current flowing in the layers when extra Pd atoms are introduced. On the other hand, a separate measurement of spin polarization using a superconducting point contact technique that is insensitive to electron scattering revealed no changes as extra Pd was introduced. We conclude that Pd atoms scatter electrons of one spin far more strongly than the other, suggesting a possible means of producing highly spin-polarized currents for use in spintronic devices.

  18. Polarization extension mechanism revealed through dynamic ferroelectric hysteresis and electric field driven structural distortions in lead free Na0.5Bi0.5TiO3 ceramic

    Science.gov (United States)

    Karthik, T.; Asthana, Saket

    2017-09-01

    The electric field amplitude (E o) dependent dynamic ferroelectric hysteresis and polarization current density curves measured at room temperature for Na0.5Bi0.5TiO3 (NBT), showed three different stages of polarization reversal mechanism. The scaling relationship confirmed the dominance of domain wall motion at Stage I (i.e. upto E o  <  35 kV cm-1), followed by domain switching at Stage II (35 kV cm-1  <  E o  <  60 kV cm-1). Interestingly, a unique behaviour with two sub stages was observed in Stage III (60 kV cm-1  <  E o  <  90 kV cm-1), with two distinct switching mechanisms viz., polarization rotation at Stage III-A and polarization extension at Stage III-B. X-ray diffraction analysis based on the Rietveld refined atomic positional co-ordinates, in electrically poled system strongly favors the polarization extension mechanism proposed at Stage III-B. The measured E o-dependent longitudinal piezoelectric response (d 33 and g33) values match closely with our proposed polarization reversal mechanism.

  19. Spin-polarized relativistic linear-muffin-tin-orbital method: Volume-dependent electronic structure and magnetic moment of plutonium

    International Nuclear Information System (INIS)

    Solovyev, I.V.; Liechtenstein, A.I.; Gubanov, V.A.; Antropov, V.P.; Andersen, O.K.

    1991-01-01

    The linear-muffin-tin-orbital method is generalized to the case of relativistic and spin-polarized self-consistent band calculations. Our formalism is analogous to the standard orthogonal--linear-muffin-tin-orbital formalism, except that the potential functions and the potential parameters are now matrices. The method is used to perform density-functional calculations for fcc plutonium with different atomic volumes. The formation of spin and orbital magnetic moments, as well as the changes in the energy bands for volume changes corresponding to the α-δ transition, are investigated. The calculated magnetic moments agree quite well with the experimental ones

  20. Functional Definition of Progenitors Versus Mature Endothelial Cells Reveals Key SoxF-Dependent Differentiation Process.

    Science.gov (United States)

    Patel, Jatin; Seppanen, Elke J; Rodero, Mathieu P; Wong, Ho Yi; Donovan, Prudence; Neufeld, Zoltan; Fisk, Nicholas M; Francois, Mathias; Khosrotehrani, Kiarash

    2017-02-21

    During adult life, blood vessel formation is thought to occur via angiogenic processes involving branching from existing vessels. An alternate proposal suggests that neovessels form from endothelial progenitors able to assemble the intimal layers. We here aimed to define vessel-resident endothelial progenitors in vivo in a variety of tissues in physiological and pathological situations such as normal aorta, lungs, and wound healing, tumors, and placenta, as well. Based on protein expression levels of common endothelial markers using flow cytometry, 3 subpopulations of endothelial cells could be identified among VE-Cadherin+ and CD45- cells. Lineage tracing by using Cdh5cre ERt2 /Rosa-YFP reporter strategy demonstrated that the CD31-/loVEGFR2lo/intracellular endothelial population was indeed an endovascular progenitor (EVP) of an intermediate CD31intVEGFR2lo/intracellular transit amplifying (TA) and a definitive differentiated (D) CD31hiVEGFR2hi/extracellular population. EVP cells arose from vascular-resident beds that could not be transferred by bone marrow transplantation. Furthermore, EVP displayed progenitor-like status with a high proportion of cells in a quiescent cell cycle phase as assessed in wounds, tumors, and aorta. Only EVP cells and not TA and D cells had self-renewal capacity as demonstrated by colony-forming capacity in limiting dilution and by transplantation in Matrigel plugs in recipient mice. RNA sequencing revealed prominent gene expression differences between EVP and D cells. In particular, EVP cells highly expressed genes related to progenitor function including Sox9 , Il33 , Egfr , and Pdfgrα. Conversely, D cells highly expressed genes related to differentiated endothelium including Ets1&2 , Gata2 , Cd31 , Vwf , and Notch . The RNA sequencing also pointed to an essential role of the Sox18 transcription factor. The role of SOX18 in the differentiation process was validated by using lineage-tracing experiments based on S ox18Cre ERt2 /Rosa

  1. Modeling optical and UV polarization of AGNs. IV. Polarization timing

    Science.gov (United States)

    Rojas Lobos, P. A.; Goosmann, R. W.; Marin, F.; Savić, D.

    2018-03-01

    Context. Optical observations cannot resolve the structure of active galactic nuclei (AGN), and a unified model for AGN was inferred mostly from indirect methods, such as spectroscopy and variability studies. Optical reverberation mapping allowed us to constrain the spatial dimension of the broad emission line region and thereby to measure the mass of supermassive black holes. Recently, reverberation was also applied to the polarized signal emerging from different AGN components. In principle, this should allow us to measure the spatial dimensions of the sub-parsec reprocessing media. Aim. We conduct numerical modeling of polarization reverberation and provide theoretical predictions for the polarization time lag induced by different AGN components. The model parameters are adjusted to the observational appearance of the Seyfert 1 galaxy NGC 4151. Methods: We modeled scattering-induced polarization and tested different geometries for the circumnuclear dust component. Our tests included the effects of clumpiness and different dust prescriptions. To further extend the model, we also explored the effects of additional ionized winds stretched along the polar direction, and of an equatorial scattering ring that is responsible for the polarization angle observed in pole-on AGN. The simulations were run using a time-dependent version of the STOKES code. Results: Our modeling confirms the previously found polarization characteristics as a function of the observer`s viewing angle. When the dust adopts a flared-disk geometry, the lags reveal a clear difference between type 1 and type 2 AGN. This distinction is less clear for a torus geometry where the time lag is more sensitive to the geometry and optical depth of the inner surface layers of the funnel. The presence of a scattering equatorial ring and ionized outflows increased the recorded polarization time lags, and the polar outflows smooths out dependence on viewing angle, especially for the higher optical depth of the

  2. Two-Photon Polarization Dependent Spectroscopy in Chirality: A Novel Experimental-Theoretical Approach to Study Optically Active Systems

    Directory of Open Access Journals (Sweden)

    Florencio E. Hernández

    2011-04-01

    Full Text Available Many phenomena, including life itself and its biochemical foundations are fundamentally rooted in chirality. Combinatorial methodologies for catalyst discovery and optimization remain an invaluable tool for gaining access to enantiomerically pure compounds in the development of pharmaceuticals, agrochemicals, and flavors. Some exotic metamaterials exhibiting negative refractive index at optical frequencies are based on chiral structures. Chiroptical activity is commonly quantified in terms of circular dichroism (CD and optical rotatory dispersion (ORD. However, the linear nature of these effects limits their application in the far and near-UV region in highly absorbing and scattering biological systems. In order to surmount this barrier, in recent years we made important advancements on a novel non linear, low-scatter, long-wavelength CD approach called two-photon absorption circular dichroism (TPACD. Herein we present a descriptive analysis of the optics principles behind the experimental measurement of TPACD, i.e., the double L-scan technique, and its significance using pulsed lasers. We also make an instructive examination and discuss the reliability of our theoretical-computational approach, which uses modern analytical response theory, within a Time-Dependent Density Functional Theory (TD-DFT approach. In order to illustrate the potential of this novel spectroscopic tool, we first present the experimental and theoretical results obtained in C2-symmetric, axially chiral R-(+-1,1'-bi(2-naphthol, R-BINOL, a molecule studied at the beginning of our investigation in this field. Next, we reveal some preliminary results obtained for (R-3,3′-diphenyl-2,2′-bi-1-naphthol, R-VANOL, and (R-2,2′-diphenyl-3,3′-(4-biphenanthrol, R-VAPOL. This family of optically active compounds has been proven to be a suitable model for the structure-property relationship study of TPACD, because its members are highly conjugated yet photo-stable, and easily

  3. Polarization Optics

    OpenAIRE

    Fressengeas, Nicolas

    2010-01-01

    The physics of polarization optics *Polarized light propagation *Partially polarized light; DEA; After a brief introduction to polarization optics, this lecture reviews the basic formalisms for dealing with it: Jones Calculus for totally polarized light and Stokes parameters associated to Mueller Calculus for partially polarized light.

  4. Quantitative cell polarity imaging defines leader-to-follower transitions during collective migration and the key role of microtubule-dependent adherens junction formation.

    Science.gov (United States)

    Revenu, Céline; Streichan, Sebastian; Donà, Erika; Lecaudey, Virginie; Hufnagel, Lars; Gilmour, Darren

    2014-03-01

    The directed migration of cell collectives drives the formation of complex organ systems. A characteristic feature of many migrating collectives is a 'tissue-scale' polarity, whereby 'leader' cells at the edge of the tissue guide trailing 'followers' that become assembled into polarised epithelial tissues en route. Here, we combine quantitative imaging and perturbation approaches to investigate epithelial cell state transitions during collective migration and organogenesis, using the zebrafish lateral line primordium as an in vivo model. A readout of three-dimensional cell polarity, based on centrosomal-nucleus axes, allows the transition from migrating leaders to assembled followers to be quantitatively resolved for the first time in vivo. Using live reporters and a novel fluorescent protein timer approach, we investigate changes in cell-cell adhesion underlying this transition by monitoring cadherin receptor localisation and stability. This reveals that while cadherin 2 is expressed across the entire tissue, functional apical junctions are first assembled in the transition zone and become progressively more stable across the leader-follower axis of the tissue. Perturbation experiments demonstrate that the formation of these apical adherens junctions requires dynamic microtubules. However, once stabilised, adherens junction maintenance is microtubule independent. Combined, these data identify a mechanism for regulating leader-to-follower transitions within migrating collectives, based on the relocation and stabilisation of cadherins, and reveal a key role for dynamic microtubules in this process.

  5. Assessment Of Mold-Design Dependent Textures In CIM-Components By Polarized Light Optical Texture Analysis (PLOTA)

    International Nuclear Information System (INIS)

    Kern, Frank; Rauch, Johannes; Gadow, Rainer

    2007-01-01

    By thermoplastic ceramic injection moulding (CIM) ceramic components of high complexity can be produced in a large number of items at low dimensional tolerances. The cost advantage by the high degree of automation leads to an economical mass-production. The structure of injection-moulded components is determined by the form filling behaviour and viscosity of the feedstock, the machine parameters, the design of the mold and the gate design. With an adapted mold- and gate-design CIM-components without textures are possible. The ''Polarized Light Optical Texture analysis'' (PLOTA) makes it possible to inspect the components and detect and quantify the textures produced by a new mold. Based on the work of R. Fischer (2004) the PLOTA procedure was improved by including the possibility to measure the inclination angle and thus describe the orientation of the grains in three dimensions. Sampled thin sections of ceramic components are analysed under the polarization microscope and are brought in diagonal position. Pictures are taken with a digital camera. The pictures are converted in the L*a*b*- colour space and the crystals color values a* and b* in the picture are measured. The color values are compared with the values of a quartz wedge, which serves as universal standard. From the received values the inclination angle can be calculated relative to the microscope axis. It is possible to use the received data quantitatively e.g. for the FEM supported simulation of texture-conditioned divergences of mechanical values. Thus the injection molding parameters can be optimized to obtain improved mechanical properties

  6. The interplanetary magnetic field By-dependent field-aligned current in the dayside polar cap under quiet conditions

    International Nuclear Information System (INIS)

    Yamauchi, M.; Araki, T.

    1989-01-01

    Spatial distribution and temporal variation of the interplanetary magnetic field (IMF) B y -dependent cusp region field-aligned currents (FACs) during quiet periods were studied by use of magnetic data observed by Magsat. The analysis was made for 11 events (each event lasts more than one and a half days) when the IMF B y component was steadily large and B x was relatively small (|B z | y |). Results of the analysis of total 62 half-day periods for the IMF B y -dependent cusp region FAC are summarized as follows: (1) the IMF B y -dependent cusp region FAC is located at around 86 degree-87 degree invariant latitude local noon, which is more poleward than the location of the IMF B z -dependent cusp region FAC; (2) the current density of this FAC is greater than previous studies (≥ 4 μA/m 2 for IMF B y = 6 nT); (3) there are two time scales for the IMF B y -dependent cusp region FAC to appear: the initial rise of the current is on a short time scale, ∼ 10 min, and it is followed by a gradual increase on a time scale of several hours to a half day; (4) the seasonal change of this FAC is greater than that of the nightside region 1 or region 2 FACs; (5) the IMF B z -dependent cusp region FAC is not well observed around the cusp when the IMF B y -dependent cusp region FAC is intense

  7. Low-cost fabrication and polar-dependent switching uniformity of memory devices using alumina interfacial layer and Ag nanoparticle monolayer

    Directory of Open Access Journals (Sweden)

    Peng Xia

    2017-11-01

    Full Text Available A facile and low-cost process was developed for fabricating write-once-read-many-times (WORM Cu/Ag NPs/Alumina/Al memory devices, where the alumina passivation layer formed naturally in air at room temperature, whereas the Ag nanoparticle monolayer was in situ prepared through thermal annealing of a 4.5 nm Ag film in air at 150°C. The devices exhibit irreversible transition from initial high resistance (OFF state to low resistance (ON state, with ON/OFF ratio of 107, indicating the introduction of Ag nanoparticle monolayer greatly improves ON/OFF ratio by four orders of magnitude. The uniformity of threshold voltages exhibits a polar-dependent behavior, and a narrow range of threshold voltages of 0.40 V among individual devices was achieved upon the forward voltage. The memory device can be regarded as two switching units connected in series. The uniform alumina interfacial layer and the non-uniform distribution of local electric fields originated from Ag nanoparticles might be responsible for excellent switching uniformity. Since silver ions in active layer can act as fast ion conductor, a plausible mechanism relating to the formation of filaments sequentially among the two switching units connected in series is suggested for the polar-dependent switching behavior. Furthermore, we demonstrate both alumina layer and Ag NPs monolayer play essential roles in improving switching parameters based on comparative experiments.

  8. Low-cost fabrication and polar-dependent switching uniformity of memory devices using alumina interfacial layer and Ag nanoparticle monolayer

    Science.gov (United States)

    Xia, Peng; Li, Luman; Wang, Pengfei; Gan, Ying; Xu, Wei

    2017-11-01

    A facile and low-cost process was developed for fabricating write-once-read-many-times (WORM) Cu/Ag NPs/Alumina/Al memory devices, where the alumina passivation layer formed naturally in air at room temperature, whereas the Ag nanoparticle monolayer was in situ prepared through thermal annealing of a 4.5 nm Ag film in air at 150°C. The devices exhibit irreversible transition from initial high resistance (OFF) state to low resistance (ON) state, with ON/OFF ratio of 107, indicating the introduction of Ag nanoparticle monolayer greatly improves ON/OFF ratio by four orders of magnitude. The uniformity of threshold voltages exhibits a polar-dependent behavior, and a narrow range of threshold voltages of 0.40 V among individual devices was achieved upon the forward voltage. The memory device can be regarded as two switching units connected in series. The uniform alumina interfacial layer and the non-uniform distribution of local electric fields originated from Ag nanoparticles might be responsible for excellent switching uniformity. Since silver ions in active layer can act as fast ion conductor, a plausible mechanism relating to the formation of filaments sequentially among the two switching units connected in series is suggested for the polar-dependent switching behavior. Furthermore, we demonstrate both alumina layer and Ag NPs monolayer play essential roles in improving switching parameters based on comparative experiments.

  9. Angle and Polarization Dependent Fluorescence EXAFS Measurements on Al-doped Single Crystal V_2O3 Above and Below the Transition Temperature

    Science.gov (United States)

    Müller, O.; Pfalzer, P.; Schramme, M.; Urbach, J.-P.; Klemm, M.; Horn, S.; Frenkel, A. I.; Denboer, M. L.

    1998-03-01

    We present angle and polarisation dependent flourescence EXAFS measured on Al-doped single crystal V_2O3 below and above the structural phase transition from monoclinic to trigonal. Strong self-absorption distorted the spectra; this was corrected by using the procedure described by Tröger et al. (L. Tröger, D. Arvantis, K. Baberschke, H. Michaelis, U. Grimm, and E. Zschech, Phys. Rev. B,.46), 3238 (1992), generalized to the Lytle detector employed in our work. The spectra show pronounced dependence on the angle between the threefold symmetry axes and the polarization of the incident photons, making it possible to measure the local atomic distances in different directions. We compare our results with the measurements of Frenkel et al. (A. I. Frenkel, E. A. Stern, and F. A. Chudnovsky, Sol. State Comm.102), 637 (1997) on pure V_2O3 They found that locally the monoclinic distortion persists in the trigonal metallic phase.

  10. Resonant inelastic X-ray spectroscopy of atoms and simple molecules: Satellite features and dependence on energy detuning and photon polarization

    Energy Technology Data Exchange (ETDEWEB)

    Žitnik, M., E-mail: matjaz.zitnik@ijs.si [Jožef Stefan Institute, P.O. Box 3000, SI-1001 Ljubljana (Slovenia); University of Ljubljana, Faculty of Mathematics and Physics, Jadranska 21, SI-1000 Ljubljana (Slovenia); Kavčič, M.; Bohinc, R.; Bučar, K.; Mihelič, A. [Jožef Stefan Institute, P.O. Box 3000, SI-1001 Ljubljana (Slovenia); Cao, W. [Research Centre for Molecular Materials, University of Oulu, P.O. Box 3000, FIN-90014 Oulu (Finland); Guillemin, R.; Journel, L.; Marchenko, T.; Carniato, S.; Kawerk, E. [Sorbonne Universités, UPMC Univ Paris 06, UMR 7614, Laboratoire de Chimie Physique Matière et Rayonnement, F-75005 Paris (France); CNRS, UMR 7614, Laboratoire de Chimie Physique Matière et Rayonnement, F-75005 Paris (France); Piancastelli, M.N. [Sorbonne Universités, UPMC Univ Paris 06, UMR 7614, Laboratoire de Chimie Physique Matière et Rayonnement, F-75005 Paris (France); CNRS, UMR 7614, Laboratoire de Chimie Physique Matière et Rayonnement, F-75005 Paris (France); Department of Physics and Astronomy, Uppsala University, P.O. Box 516, 75120 Uppsala (Sweden); Simon, M. [Sorbonne Universités, UPMC Univ Paris 06, UMR 7614, Laboratoire de Chimie Physique Matière et Rayonnement, F-75005 Paris (France); CNRS, UMR 7614, Laboratoire de Chimie Physique Matière et Rayonnement, F-75005 Paris (France)

    2015-10-15

    We summarize recent results dealing with high resolution (resonant) X-ray spectroscopy of atomic and molecular targets in the tender X-ray energy region. We comment on advantages, new possibilities and problems related to RIXS spectroscopy with respect to the standard photoabsorption technique, where scanning the probe energy is the only option. In particular, three research areas are covered: X-ray emission mediated by energy dependent photoabsorption to multi-electron excited states, the Cl K core-hole clock studies exemplified by systematic study of chloro(fluoro)-hydrocarbon targets and the polarization dependent X-ray emission studies. Due to its spectral selectivity and simultaneous detection capability, high resolution wavelength dispersive X-ray spectroscopy has the capability to resolve structural and dynamical properties of matter within new instrumentation frontiers.

  11. Effect of atomic vibrations in XANES: polarization-dependent damping of the fine structure at the Cu K-edge of (creat)2CuCl4.

    Science.gov (United States)

    Šipr, Ondřej; Vackář, Jiří; Kuzmin, Alexei

    2016-11-01

    Polarization-dependent damping of the fine structure in the Cu K-edge spectrum of creatinium tetrachlorocuprate [(creat) 2 CuCl 4 ] in the X-ray absorption near-edge structure (XANES) region is shown to be due to atomic vibrations. These vibrations can be separated into two groups, depending on whether the respective atoms belong to the same molecular block; individual molecular blocks can be treated as semi-rigid entities while the mutual positions of these blocks are subject to large mean relative displacements. The effect of vibrations can be efficiently included in XANES calculations by using the same formula as for static systems but with a modified free-electron propagator which accounts for fluctuations in interatomic distances.

  12. Study of temperature dependent local structure by polarized Cu K-edge EXAFS measurements on La sub 2 sub - sub x Sr sub x CuO sub 4 (x=0.105, 0.13, 0.20)

    CERN Document Server

    Saini, N L; Bianconi, A; Oyanagi, H; Ito, T; Oka, K

    2003-01-01

    We have studied temperature dependent local structure of superconducting La sub 2 sub - sub x Sr sub x CuO sub 4 (0.105, 0.13, 0.20) single crystals by Cu K-edge extended x-ray absorption fine structure (EXAFS) measurements with polarization parallel to the in-plane Cu-O bonds. We find that, while underdoped crystals (x=0.105, 0.13) show anomalous temperature dependence, similar to the case of optimally doped system (x=0.15), overdoped crystal (x=0.20) does not reveal such anomaly. Correlated Debye-Waller factor (DWF) of the Cu-O bonds (distance broadening) has been used as an order parameter to determine characteristic local displacements in the CuO sub 2 plane. The amplitude of temperature dependent step-like increase in the DWF at low temperature decreases with increasing doping. It has been discussed that decreasing electron-lattice interaction with increasing doping, shown by angle resolved photoemission measurements, is closely related to the evolving anomalous local CuO sub 2 distortion and charge inho...

  13. Meta-analysis reveals host-dependent nitrogen recycling as a mechanism of symbiont control in Aiptasia

    KAUST Repository

    Cui, Guoxin

    2018-02-22

    The metabolic symbiosis with photosynthetic algae of the genus Symbiodinium allows corals to thrive in the oligotrophic environments of tropical seas. Many aspects of this relationship have been investigated using transcriptomic analyses in the emerging model organism Aiptasia. However, previous studies identified thousands of putatively symbiosis-related genes, making it difficult to disentangle symbiosis-induced responses from undesired experimental parameters. Using a meta-analysis approach, we identified a core set of 731 high-confidence symbiosis-associated genes that reveal host-dependent recycling of waste ammonium and amino acid synthesis as central processes in this relationship. Combining transcriptomic and metabolomic analyses, we show that symbiont-derived carbon enables host recycling of ammonium into nonessential amino acids. We propose that this provides a regulatory mechanism to control symbiont growth through a carbon-dependent negative feedback of nitrogen availability to the symbiont. The dependence of this mechanism on symbiont-derived carbon highlights the susceptibility of this symbiosis to changes in carbon translocation, as imposed by environmental stress.

  14. Polyglutamine- and temperature-dependent conformational rigidity in mutant huntingtin revealed by immunoassays and circular dichroism spectroscopy.

    Directory of Open Access Journals (Sweden)

    Valentina Fodale

    Full Text Available In Huntington's disease, expansion of a CAG triplet repeat occurs in exon 1 of the huntingtin gene (HTT, resulting in a protein bearing>35 polyglutamine residues whose N-terminal fragments display a high propensity to misfold and aggregate. Recent data demonstrate that polyglutamine expansion results in conformational changes in the huntingtin protein (HTT, which likely influence its biological and biophysical properties. Developing assays to characterize and measure these conformational changes in isolated proteins and biological samples would advance the testing of novel therapeutic approaches aimed at correcting mutant HTT misfolding. Time-resolved Förster energy transfer (TR-FRET-based assays represent high-throughput, homogeneous, sensitive immunoassays widely employed for the quantification of proteins of interest. TR-FRET is extremely sensitive to small distances and can therefore provide conformational information based on detection of exposure and relative position of epitopes present on the target protein as recognized by selective antibodies. We have previously reported TR-FRET assays to quantify HTT proteins based on the use of antibodies specific for different amino-terminal HTT epitopes. Here, we investigate the possibility of interrogating HTT protein conformation using these assays.By performing TR-FRET measurements on the same samples (purified recombinant proteins or lysates from cells expressing HTT fragments or full length protein at different temperatures, we have discovered a temperature-dependent, reversible, polyglutamine-dependent conformational change of wild type and expanded mutant HTT proteins. Circular dichroism spectroscopy confirms the temperature and polyglutamine-dependent change in HTT structure, revealing an effect of polyglutamine length and of temperature on the alpha-helical content of the protein.The temperature- and polyglutamine-dependent effects observed with TR-FRET on HTT proteins represent a simple

  15. ddRADseq reveals determinants for temperature-dependent sex reversal in Nile tilapia on LG23.

    Science.gov (United States)

    Wessels, Stephan; Krause, Ina; Floren, Claudia; Schütz, Ekkehard; Beck, Jule; Knorr, Christoph

    2017-07-14

    In Nile tilapia sex determination is governed by a male heterogametic system XX/XY either on LG1 or LG23. The latter carries a Y-specific duplicate of the amh gene, which is a testis-determining factor. Allelic variants in the amh gene demonstrated to be major triggers for autosomal and temperature-dependent sex reversal. Further, QTL on LG23 and LG20 show a temperature-responsiveness with influence on the phenotypic sex relative to the sex chromosomes. Here we present a ddRADseq based approach to identify genomic regions that show unusual large differentiation in terms of fixation index (F ST ) between temperature-treated pseudomales and non-masculinized females using a comparative genome-scan. Genome-wide associations were identified for the temperature-dependent sex using a genetically all-female population devoid of amh-ΔY. Twenty-two thousand three hundred ninety-two SNPs were interrogated for the comparison of temperature-treated pseudomales and females, which revealed the largest differentiation on LG23. Outlier F ST -values (0.35-0.44) were determined for six SNPs in the genomic interval (9,190,077-11,065,693) harbouring the amh gene (9,602,693-9,605,808), exceeding the genome-wide low F ST of 0.013. Association analysis with a set of 9104 selected SNPs confirmed that the same genomic region on LG23 exerts a significant effect on the temperature-dependent sex. This study highlights the role of LG23 in sex determination, harbouring major determinants for temperature-dependent sex reversal in Nile tilapia. Furthermore F ST outlier detection proves a powerful tool for detection of sex-determining regions in fish genomes.

  16. A chemo-mechanical free-energy-based approach to model durotaxis and extracellular stiffness-dependent contraction and polarization of cells.

    Science.gov (United States)

    Shenoy, Vivek B; Wang, Hailong; Wang, Xiao

    2016-02-06

    We propose a chemo-mechanical model based on stress-dependent recruitment of myosin motors to describe how the contractility, polarization and strain in cells vary with the stiffness of their surroundings and their shape. A contractility tensor, which depends on the distribution of myosin motors, is introduced to describe the chemical free energy of the cell due to myosin recruitment. We explicitly include the contributions to the free energy that arise from mechanosensitive signalling pathways (such as the SFX, Rho-Rock and MLCK pathways) through chemo-mechanical coupling parameters. Taking the variations of the total free energy, which consists of the chemical and mechanical components, in accordance with the second law of thermodynamics provides equations for the temporal evolution of the active stress and the contractility tensor. Following this approach, we are able to recover the well-known Hill relation for active stresses, based on the fundamental principles of irreversible thermodynamics rather than phenomenology. We have numerically implemented our free energy-based approach to model spatial distribution of strain and contractility in (i) cells supported by flexible microposts, (ii) cells on two-dimensional substrates, and (iii) cells in three-dimensional matrices. We demonstrate how the polarization of the cells and the orientation of stress fibres can be deduced from the eigenvalues and eigenvectors of the contractility tensor. Our calculations suggest that the chemical free energy of the cell decreases with the stiffness of the extracellular environment as the cytoskeleton polarizes in response to stress-dependent recruitment of molecular motors. The mechanical energy, which includes the strain energy and motor potential energy, however, increases with stiffness, but the overall energy is lower for cells in stiffer environments. This provides a thermodynamic basis for durotaxis, whereby cells preferentially migrate towards stiffer regions of the

  17. Next-to-leading order corrections to the spin-dependent energy spectrum of hadrons from polarized top quark decay in the general two Higgs doublet model

    Directory of Open Access Journals (Sweden)

    S. Mohammad Moosavi Nejad

    2017-08-01

    Full Text Available In recent years, searches for the light and heavy charged Higgs bosons have been done by the ATLAS and the CMS collaborations at the Large Hadron Collider (LHC in proton–proton collision. Nevertheless, a definitive search is a program that still has to be carried out at the LHC. The experimental observation of charged Higgs bosons would indicate physics beyond the Standard Model. In the present work, we study the scaled-energy distribution of bottom-flavored mesons (B inclusively produced in polarized top quark decays into a light charged Higgs boson and a massless bottom quark at next-to-leading order in the two-Higgs-doublet model; t(↑→bH+→BH++X. This spin-dependent energy distribution is studied in a specific helicity coordinate system where the polarization vector of the top quark is measured with respect to the direction of the Higgs momentum. The study of these energy distributions could be considered as a new channel to search for the charged Higgs bosons at the LHC. For our numerical analysis and phenomenological predictions, we restrict ourselves to the unexcluded regions of the MSSM mH+−tan⁡β parameter space determined by the recent results of the CMS [13] and ATLAS [14] collaborations.

  18. The response of mammalian cells to UV-light reveals Rad54-dependent and independent pathways of homologous recombination

    DEFF Research Database (Denmark)

    Eppink, Berina; Tafel, Agnieszka A; Hanada, Katsuhiro

    2011-01-01

    with lesions in replicating DNA. The core HR protein in mammalian cells is the strand exchange protein RAD51, which is aided by numerous proteins, including RAD54. We used RAD54 as a cellular marker for HR to study the response of mammalian embryonic stem (ES) cells to UV irradiation. In contrast to yeast, ES......Ultraviolet (UV) radiation-induced DNA lesions can be efficiently repaired by nucleotide excision repair (NER). However, NER is less effective during replication of UV-damaged chromosomes. In contrast, translesion DNA synthesis (TLS) and homologous recombination (HR) are capable of dealing....... We demonstrate using chromosome fiber analysis at the individual replication fork level, that HR activity is important for the restart of DNA replication after induction of DNA damage by UV-light in NER-deficient cells. Furthermore, our data reveal RAD54-dependent and -independent contributions of HR...

  19. Portable ultrahigh-vacuum sample storage system for polarization-dependent total-reflection fluorescence x-ray absorption fine structure spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Watanabe, Yoshihide, E-mail: e0827@mosk.tytlabs.co.jp; Nishimura, Yusaku F.; Suzuki, Ryo; Beniya, Atsushi; Isomura, Noritake [Toyota Central R& D Labs., Inc., Yokomichi 41-1, Nagakute, Aichi 480-1192 (Japan); Uehara, Hiromitsu; Asakura, Kiyotaka; Takakusagi, Satoru [Catalysis Research Center, Hokkaido University, Kita 21-10, Sapporo, Hokkaido 001-0021 (Japan); Nimura, Tomoyuki [AVC Co., Ltd., Inada 1450-6, Hitachinaka, Ibaraki 312-0061 (Japan)

    2016-03-15

    A portable ultrahigh-vacuum sample storage system was designed and built to investigate the detailed geometric structures of mass-selected metal clusters on oxide substrates by polarization-dependent total-reflection fluorescence x-ray absorption fine structure spectroscopy (PTRF-XAFS). This ultrahigh-vacuum (UHV) sample storage system provides the handover of samples between two different sample manipulating systems. The sample storage system is adaptable for public transportation, facilitating experiments using air-sensitive samples in synchrotron radiation or other quantum beam facilities. The samples were transferred by the developed portable UHV transfer system via a public transportation at a distance over 400 km. The performance of the transfer system was demonstrated by a successful PTRF-XAFS study of Pt{sub 4} clusters deposited on a TiO{sub 2}(110) surface.

  20. Exoproteome Analysis of the Seaweed Pathogen Nautella italica R11 Reveals Temperature-Dependent Regulation of RTX-Like Proteins

    Directory of Open Access Journals (Sweden)

    Melissa Gardiner

    2017-06-01

    Full Text Available Climate fluctuations have been linked to an increased prevalence of disease in seaweeds, including the red alga Delisea pulchra, which is susceptible to a bleaching disease caused by the bacterium Nautella italica R11 under elevated seawater temperatures. To further investigate the role of temperature in the induction of disease by N. italica R11, we assessed the effect of temperature on the expression of the extracellular proteome (exoproteome in this bacterium. Label-free quantitative mass spectrometry was used to identify 207 proteins secreted into supernatant fraction, which is equivalent to 5% of the protein coding genes in the N. italica R11 genome. Comparative analysis demonstrated that expression of over 30% of the N. italica R11 exoproteome is affected by temperature. The temperature-dependent proteins include traits that could facilitate the ATP-dependent transport of amino acid and carbohydrate, as well as several uncharacterized proteins. Further, potential virulence determinants, including two RTX-like proteins, exhibited significantly higher expression in the exoproteome at the disease inducing temperature of 24°C relative to non-inducing temperature (16°C. This is the first study to demonstrate that temperature has an influence exoproteome expression in a macroalgal pathogen. The results have revealed several temperature regulated candidate virulence factors that may have a role in macroalgal colonization and invasion at elevated sea-surface temperatures, including novel RTX-like proteins.

  1. Quantitative time-course metabolomics in human red blood cells reveal the temperature dependence of human metabolic networks.

    Science.gov (United States)

    Yurkovich, James T; Zielinski, Daniel C; Yang, Laurence; Paglia, Giuseppe; Rolfsson, Ottar; Sigurjónsson, Ólafur E; Broddrick, Jared T; Bordbar, Aarash; Wichuk, Kristine; Brynjólfsson, Sigurður; Palsson, Sirus; Gudmundsson, Sveinn; Palsson, Bernhard O

    2017-12-01

    The temperature dependence of biological processes has been studied at the levels of individual biochemical reactions and organism physiology ( e.g. basal metabolic rates) but has not been examined at the metabolic network level. Here, we used a systems biology approach to characterize the temperature dependence of the human red blood cell (RBC) metabolic network between 4 and 37 °C through absolutely quantified exo- and endometabolomics data. We used an Arrhenius-type model ( Q 10 ) to describe how the rate of a biochemical process changes with every 10 °C change in temperature. Multivariate statistical analysis of the metabolomics data revealed that the same metabolic network-level trends previously reported for RBCs at 4 °C were conserved but accelerated with increasing temperature. We calculated a median Q 10 coefficient of 2.89 ± 1.03, within the expected range of 2-3 for biological processes, for 48 individual metabolite concentrations. We then integrated these metabolomics measurements into a cell-scale metabolic model to study pathway usage, calculating a median Q 10 coefficient of 2.73 ± 0.75 for 35 reaction fluxes. The relative fluxes through glycolysis and nucleotide metabolism pathways were consistent across the studied temperature range despite the non-uniform distributions of Q 10 coefficients of individual metabolites and reaction fluxes. Together, these results indicate that the rate of change of network-level responses to temperature differences in RBC metabolism is consistent between 4 and 37 °C. More broadly, we provide a baseline characterization of a biochemical network given no transcriptional or translational regulation that can be used to explore the temperature dependence of metabolism. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  2. Signals involved in the early TH1/TH2 polarization of an immune response depending on the type of antigen.

    Science.gov (United States)

    Bellinghausen, I; Brand, U; Enk, A H; Knop, J; Saloga, J

    1999-02-01

    The early production of distinct cytokines by epidermal cells (ECs) in response to antigen exposure may govern the development of TH1 -like immune responses, such as contact sensitivity, or TH2 -like immune responses, such as IgE-dependent allergies of the immediate type, depending on the type of antigen. The aim of this study was to compare the signals induced by protein allergens with those induced by haptens in ECs and subsequently in local draining lymph node cells (LNCs) or splenocytes. BALB/c mice were primed in vivo with the protein allergens ovalbumin or birch pollen or the haptens 2, 4-dinitrofluorobenzene or trinitrochlorbenzene, respectively, and cytokine and immunoglobulin secretions of responding splenocytes were measured by ELISA after in vitro coculture with ECs. Induction of cytokine mRNA expression in ECs and LNCs was analyzed by reverse transcriptase-PCR. In the presence of protein allergens, ECs enhance the induction of a TH2 immune response (IL-4 and IgE production of splenocytes), whereas a TH1 immune response (IFN-gamma and IgG2a production) was only induced in the context of haptens. Heat inactivation of ovalbumin did not diminish the development of a TH2 immune response. One direct effect of antigen on ECs was the earlier expression of IL-10 mRNA after stimulation with protein allergens (30 minutes) than with haptens (2 hours) in vitro. By using an in vivo approach, sensitization of the skin with trinitrochlorbenzene, but not with ovalbumin, resulted in an early induction of IL-1beta, IL-12p40, and IFN-gamma mRNA in LNCs, whereas IL-18 was induced by both. These data indicate that the type of antigen strongly influences the type of immune response by eliciting distinct signals already in the epithelium.

  3. Potentiodynamic polarization analysis of silver-palladium alloys in chloride solutions

    Science.gov (United States)

    Sastri, S.; Vaidyanathan, T. K.; Mukherjee, K.

    1982-02-01

    A comprehensive anodic potentiodynamic polarization analysis of Ag-Pd binary alloys in chloride solutions has revealed composition dependent active-passive polarization profiles. The results are interpreted in terms of the transition metal properties of Pd and the electron donor acceptor theory of passivation.

  4. Airborne Laser Polarization Sensor

    Science.gov (United States)

    Kalshoven, James, Jr.; Dabney, Philip

    1991-01-01

    Instrument measures polarization characteristics of Earth at three wavelengths. Airborne Laser Polarization Sensor (ALPS) measures optical polarization characteristics of land surface. Designed to be flown at altitudes of approximately 300 m to minimize any polarizing or depolarizing effects of intervening atmosphere and to look along nadir to minimize any effects depending on look angle. Data from measurements used in conjunction with data from ground surveys and aircraft-mounted video recorders to refine mathematical models used in interpretation of higher-altitude polarimetric measurements of reflected sunlight.

  5. Revealing kinetics and state-dependent binding properties of IKur-targeting drugs that maximize atrial fibrillation selectivity

    Science.gov (United States)

    Ellinwood, Nicholas; Dobrev, Dobromir; Morotti, Stefano; Grandi, Eleonora

    2017-09-01

    The KV1.5 potassium channel, which underlies the ultra-rapid delayed-rectifier current (IKur) and is predominantly expressed in atria vs. ventricles, has emerged as a promising target to treat atrial fibrillation (AF). However, while numerous KV1.5-selective compounds have been screened, characterized, and tested in various animal models of AF, evidence of antiarrhythmic efficacy in humans is still lacking. Moreover, current guidelines for pre-clinical assessment of candidate drugs heavily rely on steady-state concentration-response curves or IC50 values, which can overlook adverse cardiotoxic effects. We sought to investigate the effects of kinetics and state-dependent binding of IKur-targeting drugs on atrial electrophysiology in silico and reveal the ideal properties of IKur blockers that maximize anti-AF efficacy and minimize pro-arrhythmic risk. To this aim, we developed a new Markov model of IKur that describes KV1.5 gating based on experimental voltage-clamp data in atrial myocytes from patient right-atrial samples in normal sinus rhythm. We extended the IKur formulation to account for state-specificity and kinetics of KV1.5-drug interactions and incorporated it into our human atrial cell model. We simulated 1- and 3-Hz pacing protocols in drug-free conditions and with a [drug] equal to the IC50 value. The effects of binding and unbinding kinetics were determined by examining permutations of the forward (kon) and reverse (koff) binding rates to the closed, open, and inactivated states of the KV1.5 channel. We identified a subset of ideal drugs exhibiting anti-AF electrophysiological parameter changes at fast pacing rates (effective refractory period prolongation), while having little effect on normal sinus rhythm (limited action potential prolongation). Our results highlight that accurately accounting for channel interactions with drugs, including kinetics and state-dependent binding, is critical for developing safer and more effective pharmacological anti

  6. Evolutionary divergence of plant borate exporters and critical amino acid residues for the polar localization and boron-dependent vacuolar sorting of AtBOR1

    KAUST Repository

    Wakuta, Shinji

    2015-01-24

    Boron (B) is an essential micronutrient for plants but is toxic when accumulated in excess. The plant BOR family encodes plasma membrane-localized borate exporters (BORs) that control translocation and homeostasis of B under a wide range of conditions. In this study, we examined the evolutionary divergence of BORs among terrestrial plants and showed that the lycophyte Selaginella moellendorffii and angiosperms have evolved two types of BOR (clades I and II). Clade I includes AtBOR1 and homologs previously shown to be involved in efficient transport of B under conditions of limited B availability. AtBOR1 shows polar localization in the plasma membrane and high-B-induced vacuolar sorting, important features for efficient B transport under low-B conditions, and rapid down-regulation to avoid B toxicity. Clade II includes AtBOR4 and barley Bot1 involved in B exclusion for high-B tolerance. We showed, using yeast complementation and B transport assays, that three genes in S. moellendorffii, SmBOR1 in clade I and SmBOR3 and SmBOR4 in clade II, encode functional BORs. Furthermore, amino acid sequence alignments identified an acidic di-leucine motif unique in clade I BORs. Mutational analysis of AtBOR1 revealed that the acidic di-leucine motif is required for the polarity and high-B-induced vacuolar sorting of AtBOR1. Our data clearly indicated that the common ancestor of vascular plants had already acquired two types of BOR for low- and high-B tolerance, and that the BOR family evolved to establish B tolerance in each lineage by adapting to their environments. © The Author 2015. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists.

  7. Lattice dynamics approach to determine the dependence of the time-of-flight of transversal polarized acoustic waves on external stress

    Science.gov (United States)

    Tarar, K. S.; Pluta, M.; Amjad, U.; Grill, W.

    2011-04-01

    Based on the lattice dynamics approach the dependence of the time-of-flight (TOF) on stress has been modeled for transversal polarized acoustic waves. The relevant dispersion relation is derived from the appropriate mass-spring model together with the dependencies on the restoring forces including the effect of externally applied stress. The lattice dynamics approach can also be interpreted as a discrete and strictly periodic lumped circuit. In that case the modeling represents a finite element approach. In both cases the properties relevant for wavelengths large with respect to the periodic structure can be derived from the respective limit relating also to low frequencies. The model representing a linear chain with stiffness to shear and additional stiffness introduced by extensional stress is presented and compared to existing models, which so far represent each only one of the effects treated here in combination. For a string this effect is well known from musical instruments. The counteracting effects are discussed and compared to experimental results.

  8. RAP-PCR fingerprinting reveals time-dependent expression of development-related genes following differentiation process of Bacillus thuringiensis.

    Science.gov (United States)

    Huang, Tianpei; Yu, Xiaomin; Gelbič, Ivan; Guan, Xiong

    2015-09-01

    Gene expression profiles are important data to reveal the functions of genes putatively involved in crucial biological processes. RNA arbitrarily primed polymerase chain reaction (RAP-PCR) and specifically primed reverse transcription polymerase chain reaction (RT-PCR) were combined to screen differentially expressed genes following development of a commercial Bacillus thuringiensis subsp. kurstaki strain 8010 (serotype 3a3b). Six differentially expressed transcripts (RAP1 to RAP6) were obtained. RAP1 encoded a putative triple helix repeat-containing collagen or an exosporium protein H related to spore pathogenicity. RAP2 was homologous to a ClpX protease and an ATP-dependent protease La (LonB), which likely acted as virulence factors. RAP3 was homologous to a beta subunit of propionyl-CoA carboxylase required for the development of Myxococcus xanthus. RAP4 had homology to a quinone oxidoreductase involved in electron transport and ATP formation. RAP5 showed significant homology to a uridine kinase that mediates phosphorylation of uridine and azauridine. RAP6 shared high sequence identity with 3-methyl-2-oxobutanoate-hydroxymethyltransferase (also known as ketopantoate hydroxymethyltransferase or PanB) involved in the operation of the tricarboxylic acid cycle. The findings described here would help to elucidate the molecular mechanisms underlying the differentiation process of B. thuringiensis and unravel novel pathogenic genes.

  9. Signatures of Nucleotide Analog Incorporation by an RNA-Dependent RNA Polymerase Revealed Using High-Throughput Magnetic Tweezers

    Directory of Open Access Journals (Sweden)

    David Dulin

    2017-10-01

    Full Text Available RNA viruses pose a threat to public health that is exacerbated by the dearth of antiviral therapeutics. The RNA-dependent RNA polymerase (RdRp holds promise as a broad-spectrum, therapeutic target because of the conserved nature of the nucleotide-substrate-binding and catalytic sites. Conventional, quantitative, kinetic analysis of antiviral ribonucleotides monitors one or a few incorporation events. Here, we use a high-throughput magnetic tweezers platform to monitor the elongation dynamics of a prototypical RdRp over thousands of nucleotide-addition cycles in the absence and presence of a suite of nucleotide analog inhibitors. We observe multiple RdRp-RNA elongation complexes; only a subset of which are competent for analog utilization. Incorporation of a pyrazine-carboxamide nucleotide analog, T-1106, leads to RdRp backtracking. This analysis reveals a mechanism of action for this antiviral ribonucleotide that is corroborated by cellular studies. We propose that induced backtracking represents a distinct mechanistic class of antiviral ribonucleotides.

  10. Polarization Diversity DPSK Demodulator on the Silicon-on-Insulator Platform with Simple Fabrication

    DEFF Research Database (Denmark)

    Ding, Yunhong; Huang, Bo; Ou, Haiyan

    2013-01-01

    We demonstrate a novel polarization diversity DPSK demodulator on the SOI platform with low polarization dependent loss (1.6 dB) and low polarization dependent extinction ratio (<3 dB). System experiments verify the low polarization dependency....

  11. Collar temperature sensor data reveal long-term patterns in southern Beaufort Sea polar bear den distribution on pack ice and land

    Science.gov (United States)

    Olson, Jay W; Rode, Karyn D.; Eggett, Dennis L.; Smith, T.S.; Wilson, R. R.; Durner, George M.; Fischbach, Anthony; Atwood, Todd C.; Douglas, David

    2017-01-01

    In response to a changing climate, many species alter habitat use. Polar bears Ursus maritimus in the southern Beaufort Sea have increasingly used land for maternal denning. To aid in detecting denning behavior, we developed an objective method to identify polar bear denning events using temperature sensor data collected by satellite-linked transmitters deployed on adult females between 1985 and 2013. We then applied this method to determine whether southern Beaufort Sea polar bears have continued to increase land denning with recent sea-ice loss and examined whether sea-ice conditions affect the distribution of dens between pack-ice and coastal substrates. Because land use in summer and autumn has also increased, we examined potential associations between summering substrate and denning substrate. Statistical process control methods applied to temperature-sensor data identified denning events with 94.5% accuracy in comparison to direct observations (n = 73) and 95.7% accuracy relative to subjective classifications based on temperature, location, and activity sensor data (n = 116). We found an increase in land-based denning during the study period. The frequency of land denning was directly related to the distance that sea ice retreated from the coast. Among females that denned, all 14 that summered on land subsequently denned there, whereas 29% of the 69 bears summering on ice denned on land. These results suggest that denning on land may continue to increase with further loss of sea ice. While the effects that den substrate have on nutrition, energetics, and reproduction are unclear, more polar bears denning onshore will likely increase human-bear interactions.

  12. Transcriptional response of zebrafish embryos exposed to neurotoxic compounds reveals a muscle activity dependent hspb11 expression.

    Directory of Open Access Journals (Sweden)

    Nils Klüver

    Full Text Available Acetylcholinesterase (AChE inhibitors are widely used as pesticides and drugs. Their primary effect is the overstimulation of cholinergic receptors which results in an improper muscular function. During vertebrate embryonic development nerve activity and intracellular downstream events are critical for the regulation of muscle fiber formation. Whether AChE inhibitors and related neurotoxic compounds also provoke specific changes in gene transcription patterns during vertebrate development that allow them to establish a mechanistic link useful for identification of developmental toxicity pathways has, however, yet not been investigated. Therefore we examined the transcriptomic response of a known AChE inhibitor, the organophosphate azinphos-methyl (APM, in zebrafish embryos and compared the response with two non-AChE inhibiting unspecific control compounds, 1,4-dimethoxybenzene (DMB and 2,4-dinitrophenol (DNP. A highly specific cluster of APM induced gene transcripts was identified and a subset of strongly regulated genes was analyzed in more detail. The small heat shock protein hspb11 was found to be the most sensitive induced gene in response to AChE inhibitors. Comparison of expression in wildtype, ache and sop(fixe mutant embryos revealed that hspb11 expression was dependent on the nicotinic acetylcholine receptor (nAChR activity. Furthermore, modulators of intracellular calcium levels within the whole embryo led to a transcriptional up-regulation of hspb11 which suggests that elevated intracellular calcium levels may regulate the expression of this gene. During early zebrafish development, hspb11 was specifically expressed in muscle pioneer cells and Hspb11 morpholino-knockdown resulted in effects on slow muscle myosin organization. Our findings imply that a comparative toxicogenomic approach and functional analysis can lead to the identification of molecular mechanisms and specific marker genes for potential neurotoxic compounds.

  13. Nucleic Acid-Dependent Conformational Changes in CRISPR-Cas9 Revealed by Site-Directed Spin Labeling.

    Science.gov (United States)

    Vazquez Reyes, Carolina; Tangprasertchai, Narin S; Yogesha, S D; Nguyen, Richard H; Zhang, Xiaojun; Rajan, Rakhi; Qin, Peter Z

    2017-06-01

    In a type II clustered regularly interspaced short palindromic repeats (CRISPR) system, RNAs that are encoded at the CRISPR locus complex with the CRISPR-associated (Cas) protein Cas9 to form an RNA-guided nuclease that cleaves double-stranded DNAs at specific sites. In recent years, the CRISPR-Cas9 system has been successfully adapted for genome engineering in a wide range of organisms. Studies have indicated that a series of conformational changes in Cas9, coordinated by the RNA and the target DNA, direct the protein into its active conformation, yet details on these conformational changes, as well as their roles in the mechanism of function of Cas9, remain to be elucidated. Here, nucleic acid-dependent conformational changes in Streptococcus pyogenes Cas9 (SpyCas9) were investigated using the method of site-directed spin labeling (SDSL). Single nitroxide spin labels were attached, one at a time, at one of the two native cysteine residues (Cys80 and Cys574) of SpyCas9, and the spin-labeled proteins were shown to maintain their function. X-band continuous-wave electron paramagnetic resonance spectra of the nitroxide attached at Cys80 revealed conformational changes of SpyCas9 that are consistent with a large-scale domain re-arrangement upon binding to its RNA partner. The results demonstrate the use of SDSL to monitor conformational changes in CRISPR-Cas9, which will provide key information for understanding the mechanism of CRISPR function.

  14. Fluorescent Protein-Based Ca2+ Sensor Reveals Global, Divalent Cation-Dependent Conformational Changes in Cardiac Troponin C.

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    Myriam A Badr

    Full Text Available Cardiac troponin C (cTnC is a key effector in cardiac muscle excitation-contraction coupling as the Ca2+ sensing subunit responsible for controlling contraction. In this study, we generated several FRET sensors for divalent cations based on cTnC flanked by a donor fluorescent protein (CFP and an acceptor fluorescent protein (YFP. The sensors report Ca2+ and Mg2+ binding, and relay global structural information about the structural relationship between cTnC's N- and C-domains. The sensors were first characterized using end point titrations to decipher the response to Ca2+ binding in the presence or absence of Mg2+. The sensor that exhibited the largest responses in end point titrations, CTV-TnC, (Cerulean, TnC, and Venus was characterized more extensively. Most of the divalent cation-dependent FRET signal originates from the high affinity C-terminal EF hands. CTV-TnC reconstitutes into skinned fiber preparations indicating proper assembly of troponin complex, with only ~0.2 pCa unit rightward shift of Ca2+-sensitive force development compared to WT-cTnC. Affinity of CTV-TnC for divalent cations is in agreement with known values for WT-cTnC. Analytical ultracentrifugation indicates that CTV-TnC undergoes compaction as divalent cations bind. C-terminal sites induce ion-specific (Ca2+ versus Mg2+ conformational changes in cTnC. Our data also provide support for the presence of additional, non-EF-hand sites on cTnC for Mg2+ binding. In conclusion, we successfully generated a novel FRET-Ca2+ sensor based on full length cTnC with a variety of cellular applications. Our sensor reveals global structural information about cTnC upon divalent cation binding.

  15. Processing-Dependent and Clonal Contamination Patterns of Listeria monocytogenes in the Cured Ham Food Chain Revealed by Genetic Analysis.

    Science.gov (United States)

    Morganti, Marina; Scaltriti, Erika; Cozzolino, Paolo; Bolzoni, Luca; Casadei, Gabriele; Pierantoni, Marco; Foni, Emanuela; Pongolini, Stefano

    2016-02-01

    The quantitative and qualitative patterns of environmental contamination by Listeria monocytogenes were investigated in the production chain of dry-cured Parma ham. Standard arrays of surfaces were sampled in processing facilities during a single visit per plant in the three compartments of the food chain, i.e., ham production (19 plants) and postproduction, which was divided into deboning (43 plants) and slicing (25 plants) steps. The numbers of sampled surfaces were 384 in ham production, with 25 positive for L. monocytogenes, and 1,084 in postproduction, with 83 positives. Statistical analysis of the prevalence of contaminated surfaces showed that in ham production, contamination was higher at the beginning of processing and declined significantly toward the end, while in postproduction, prevalence rose toward the end of processing. Prevalence was higher in the deboning facilities than in slicing facilities and was dependent on the type of surface (floor/drainage > clothing > equipment). The qualitative pattern of contamination was investigated through an analysis of the survey isolates and a set of isolates derived from routine monitoring, including longitudinal isolations. Pulsed-field gel electrophoresis (PFGE) and whole-genome single-nucleotide polymorphism (SNP) analysis revealed a remarkable clonality of L. monocytogenes within plants, with the detection of 16 plant-specific clones out of 17 establishments with multiple isolates. Repeated detections of clonal isolates >6 months apart were also observed. Six was the maximum number of between-isolate differences in core SNPs observed within these clones. Based on the same six-SNP threshold, three clusters of clonal isolates, shared by six establishments, were also identified. The spread of L. monocytogenes within and between plants, as indicated by its clonal behavior, is a matter of concern for the hygienic management of establishments. Copyright © 2016, American Society for Microbiology. All Rights

  16. Transcranial direct current stimulation (tDCS) reveals a dissociation between SNARC and MARC effects: Implication for the polarity correspondence account.

    Science.gov (United States)

    Di Rosa, Elisa; Bardi, Lara; Umiltà, Carlo; Masina, Fabio; Forgione, Margherita; Mapelli, Daniela

    2017-08-01

    The concept of stimulus response compatibility (SRC) refers to the existence of a privileged association between a specific stimulus feature and a specific response feature. Two examples of SRC are the Spatial Numerical Association of Response Codes (SNARC) and the Markedness Association of Response Codes (MARC) effects. According to the polarity correspondence principle, these two SRC effects occur because of a match between the most salient dimensions of stimulus and response. Specifically, the SNARC effect would be caused by a match between right-sided responses and large numbers, while a match between right-sided responses and even numbers would give rise to the MARC effect. The aim of the present study was to test the validity of the polarity correspondence principle in explaining these two SRC effects. To this end, we applied transcranial direct current stimulation (tDCS) over left and right posterior parietal cortex (PPC), which is thought to be the neural basis of salience processing, during a parity judgement task. Results showed that cathodal tDCS over the PPC significantly reduced the MARC effect but did not affect the SNARC effect, suggesting a dissociation between the two effects. That is, the MARC would rely on a salience processing mechanism, whereas the SNARC would not. Despite this interpretation is in need of further experimental confirmations (i.e., testing different tasks or using different tDCS montages), our results suggest that the polarity correspondence principle can be a plausible explanation only for the MARC effect but not for the SNARC effect. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Polar Heat Flow on Io

    Science.gov (United States)

    Veeder, G. J.; Matson, D. L.; Johnson, T. V.; Davies, A. G.; Blaney, D. L.

    2003-01-01

    Recently, Galileo spacecraft data have revealed Io's polar regions to be much warmer than previously expected. This unexpected development came from Photo-Polarimeter Radiometer (PPR) data which show that the minimum night temperatures are in the range of 90-95 K virtually everywhere on Io. The minimum night temperatures show no dependence upon latitude and, when away from the sunset terminator, they show no dependence upon time of night. This is indeed bizarre behavior for surface units which generally had been assumed to be passive with respect to Io's pervasive volcanism. Night temperatures of 90-95 K at high, polar latitudes are particularly hard to explain. Even assuming infinite thermal inertia, at these latitudes there is insufficient sunlight to support these warm night temperatures. Thus, through the process of elimination of other possibilities, we come to the conclusion that these surfaces are volcanically heated. Taking previously passive units and turning them into new sources of heat flow is a radical departure from previous thermophysical model paradigms. However, the geological interpretation is straight forward. We are simply seeing the effect of old, cool lava flows which cover most of the surface of Io but yet have some heat to radiate. Under these new constraints, we have taken on the challenge of formulating a physical model which quantitatively reproduces all of the observations of Io's thermal emission. In the following we introduce a new parametric model which suffices to identify a previously unrecognized polar component of Io's heat flow.

  18. Full-Field Calcium K-Edge X-ray Absorption Near-Edge Structure Spectroscopy on Cortical Bone at the Micron-Scale: Polarization Effects Reveal Mineral Orientation.

    Science.gov (United States)

    Hesse, Bernhard; Salome, Murielle; Castillo-Michel, Hiram; Cotte, Marine; Fayard, Barbara; Sahle, Christoph J; De Nolf, Wout; Hradilova, Jana; Masic, Admir; Kanngießer, Birgit; Bohner, Marc; Varga, Peter; Raum, Kay; Schrof, Susanne

    2016-04-05

    Here, we show results on X-ray absorption near edge structure spectroscopy in both transmission and X-ray fluorescence full-field mode (FF-XANES) at the calcium K-edge on human bone tissue in healthy and diseased conditions and for different tissue maturation stages. We observe that the dominating spectral differences originating from different tissue regions, which are well pronounced in the white line and postedge structures are associated with polarization effects. These polarization effects dominate the spectral variance and must be well understood and modeled before analyzing the very subtle spectral variations related to the bone tissue variations itself. However, these modulations in the fine structure of the spectra can potentially be of high interest to quantify orientations of the apatite crystals in highly structured tissue matrices such as bone. Due to the extremely short wavelengths of X-rays, FF-XANES overcomes the limited spatial resolution of other optical and spectroscopic techniques exploiting visible light. Since the field of view in FF-XANES is rather large the acquisition times for analyzing the same region are short compared to, for example, X-ray diffraction techniques. Our results on the angular absorption dependence were verified by both site-matched polarized Raman spectroscopy, which has been shown to be sensitive to the orientation of bone building blocks and by mathematical simulations of the angular absorbance dependence. As an outlook we further demonstrate the polarization based assessment of calcium-containing crystal orientation and specification of calcium in a beta-tricalcium phosphate (β-Ca3(PO4)2 scaffold implanted into ovine bone. Regarding the use of XANES to assess chemical properties of Ca in human bone tissue our data suggest that neither the anatomical site (tibia vs jaw) nor pathology (healthy vs necrotic jaw bone tissue) affected the averaged spectral shape of the XANES spectra.

  19. Measurement of inclusive quasielastic scattering of polarized electrons from polarized 3He

    International Nuclear Information System (INIS)

    Woodward, C.E.; Beise, E.J.; Belz, J.E.; Carr, R.W.; Filippone, B.W.; Lorenzon, W.B.; McKeown, R.D.; Mueller, B.; O'Neill, T.G.; Dodson, G.; Dow, K.; Farkhondeh, M.; Kowalski, S.; Lee, K.; Makins, N.; Milner, R.; Thompson, A.; Tieger, D.; van den Brand, J.; Young, A.; Yu, X.; Zumbro, J.

    1990-01-01

    We report a measurement of the asymmetry in spin-dependent quasielastic scattering of longitudinally polarized electrons from a polarized 3 He gas target. This measurement represents the first demonstration of a new method for studying electromagnetic nuclear structure: the scattering of polarized electrons from a polarized nuclear target. The measured asymmetry is in good agreement with a Faddeev calculation and supports the picture of spin-dependent quasielastic scattering from polarized 3 He as predominantly scattering from a polarized neutron

  20. Optically polarized 3He

    Science.gov (United States)

    Gentile, T. R.; Nacher, P. J.; Saam, B.; Walker, T. G.

    2018-01-01

    This article reviews the physics and technology of producing large quantities of highly spin-polarized 3He nuclei using spin-exchange (SEOP) and metastability-exchange (MEOP) optical pumping. Both technical developments and deeper understanding of the physical processes involved have led to substantial improvements in the capabilities of both methods. For SEOP, the use of spectrally narrowed lasers and K-Rb mixtures has substantially increased the achievable polarization and polarizing rate. For MEOP nearly lossless compression allows for rapid production of polarized 3He and operation in high magnetic fields has likewise significantly increased the pressure at which this method can be performed, and revealed new phenomena. Both methods have benefitted from development of storage methods that allow for spin-relaxation times of hundreds of hours, and specialized precision methods for polarimetry. SEOP and MEOP are now widely applied for spin-polarized targets, neutron spin filters, magnetic resonance imaging, and precision measurements. PMID:29503479

  1. Optically polarized 3He

    Science.gov (United States)

    Gentile, T. R.; Nacher, P. J.; Saam, B.; Walker, T. G.

    2017-10-01

    This article reviews the physics and technology of producing large quantities of highly spin-polarized 3He nuclei using spin-exchange (SEOP) and metastability-exchange (MEOP) optical pumping. Both technical developments and deeper understanding of the physical processes involved have led to substantial improvements in the capabilities of both methods. For SEOP, the use of spectrally narrowed lasers and K-Rb mixtures has substantially increased the achievable polarization and polarizing rate. For MEOP nearly lossless compression allows for rapid production of polarized 3He and operation in high magnetic fields has likewise significantly increased the pressure at which this method can be performed, and revealed new phenomena. Both methods have benefitted from development of storage methods that allow for spin-relaxation times of hundreds of hours, and specialized precision methods for polarimetry. SEOP and MEOP are now widely applied for spin-polarized targets, neutron spin filters, magnetic resonance imaging, and precision measurements.

  2. Morning and evening-type differences in slow waves during NREM sleep reveal both trait and state-dependent phenotypes.

    Directory of Open Access Journals (Sweden)

    Valérie Mongrain

    Full Text Available Brain recovery after prolonged wakefulness is characterized by increased density, amplitude and slope of slow waves (SW, <4 Hz during non-rapid eye movement (NREM sleep. These SW comprise a negative phase, during which cortical neurons are mostly silent, and a positive phase, in which most neurons fire intensively. Previous work showed, using EEG spectral analysis as an index of cortical synchrony, that Morning-types (M-types present faster dynamics of sleep pressure than Evening-types (E-types. We thus hypothesized that single SW properties will also show larger changes in M-types than in E-types in response to increased sleep pressure. SW density (number per minute and characteristics (amplitude, slope between negative and positive peaks, frequency and duration of negative and positive phases were compared between chronotypes for a baseline sleep episode (BL and for recovery sleep (REC after two nights of sleep fragmentation. While SW density did not differ between chronotypes, M-types showed higher SW amplitude and steeper slope than E-types, especially during REC. SW properties were also averaged for 3 NREM sleep periods selected for their decreasing level of sleep pressure (first cycle of REC [REC1], first cycle of BL [BL1] and fourth cycle of BL [BL4]. Slope was significantly steeper in M-types than in E-types in REC1 and BL1. SW frequency was consistently higher and duration of positive and negative phases constantly shorter in M-types than in E-types. Our data reveal that specific properties of cortical synchrony during sleep differ between M-types and E-types, although chronotypes show a similar capacity to generate SW. These differences may involve 1 stable trait characteristics independent of sleep pressure (i.e., frequency and durations likely linked to the length of silent and burst-firing phases of individual neurons, and 2 specific responses to increased sleep pressure (i.e., slope and amplitude expected to depend on the synchrony

  3. Retinofugal Projections from Melanopsin-Expressing Retinal Ganglion Cells Revealed by Intraocular Injections of Cre-Dependent Virus.

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    Anton Delwig

    Full Text Available To understand visual functions mediated by intrinsically photosensitive melanopsin-expressing retinal ganglion cells (mRGCs, it is important to elucidate axonal projections from these cells into the brain. Initial studies reported that melanopsin is expressed only in retinal ganglion cells within the eye. However, recent studies in Opn4-Cre mice revealed Cre-mediated marker expression in multiple brain areas. These discoveries complicate the use of melanopsin-driven genetic labeling techniques to identify retinofugal projections specifically from mRGCs. To restrict labeling to mRGCs, we developed a recombinant adeno-associated virus (AAV carrying a Cre-dependent reporter (human placental alkaline phosphatase that was injected into the vitreous of Opn4-Cre mouse eyes. The labeling observed in the brain of these mice was necessarily restricted specifically to retinofugal projections from mRGCs in the injected eye. We found that mRGCs innervate multiple nuclei in the basal forebrain, hypothalamus, amygdala, thalamus and midbrain. Midline structures tended to be bilaterally innervated, whereas the lateral structures received mostly contralateral innervation. As validation of our approach, we found projection patterns largely corresponded with previously published results; however, we have also identified a few novel targets. Our discovery of projections to the central amygdala suggests a possible direct neural pathway for aversive responses to light in neonates. In addition, projections to the accessory optic system suggest that mRGCs play a direct role in visual tracking, responses that were previously attributed to other classes of retinal ganglion cells. Moreover, projections to the zona incerta raise the possibility that mRGCs could regulate visceral and sensory functions. However, additional studies are needed to investigate the actual photosensitivity of mRGCs that project to the different brain areas. Also, there is a concern of "overlabeling

  4. Precision Polarization of Neutrons

    Science.gov (United States)

    Martin, Elise; Barron-Palos, Libertad; Couture, Aaron; Crawford, Christopher; Chupp, Tim; Danagoulian, Areg; Estes, Mary; Hona, Binita; Jones, Gordon; Klein, Andi; Penttila, Seppo; Sharma, Monisha; Wilburn, Scott

    2009-05-01

    Determining polarization of a cold neutron beam to high precision is required for the next generation neutron decay correlation experiments at the SNS, such as the proposed abBA and PANDA experiments. Precision polarimetry measurements were conducted at Los Alamos National Laboratory with the goal of determining the beam polarization to the level of 10-3 or better. The cold neutrons from FP12 were polarized using optically polarized ^3He gas as a spin filter, which has a highly spin-dependent absorption cross section. A second ^ 3He spin filter was used to analyze the neutron polarization after passing through a resonant RF spin rotator. A discussion of the experiment and results will be given.

  5. Study on the thermal structure of the Venusian polar atmosphere

    Science.gov (United States)

    Takamura, M.; Taguchi, M.; Fukuhara, T.; Kouyama, T.; Imamura, T.; Sato, T. M.; Futaguchi, M.; Yamada, T.; Nakamura, M.; Iwagami, N.; Suzuki, M.; Ueno, M.; Sato, M.; Hashimoto, G. L.; Takagi, S.

    2017-12-01

    The Venus atmosphere exhibits characteristic thermal features called `polar dipoles' and `polar collars' in both polar regions. The polar dipole which locates around the center of the polar region is warmer than mid-latitudes and the polar collar surrounding the polar dipole is colder than the other regions at the same altitude. These features were revealed by infrared observations of Venus by the previous missions. The previous observations showed that shapes of the polar dipoles can be characterized by three patterns which are the zonal wave numbers of 0-2, and that they change with time. The rotation periods of polar dipoles were determined to be 2.5 and 2.8-3.2 Earth days for the southern and northern polar regions, respectively. It has not been clear that the difference and variability in the rotation period is due to just a temporal variation, influence of solar activity, or other reasons. Sato et al. compared the appearances of both polar hot regions by a ground-based observation, rotation of the hot regions is synchronized between the northern and southern hemispheres. However, rotation periods of the northern and southern polar dipoles have not yet been directly compared. The Japanese Venus orbiter Akatsuki is a planetary meteorological satellite aiming at understanding the atmosphere dynamics of Venus. The Longwave Infrared Camera (LIR), observes thermal emission from the cloud top ( 65km). Akatsuki is in an equatorial orbit, which is suitable for simultaneous observations of both northern and southern polar regions. Rotation periods of polar vortices were derived using the LIR data by tracking a zonal position of maximum temperature. The rotation periods of polar vortices of southern and northern hemispheres are determined to be 3.0 - 8.2 and 1.6 - 5.5 Earth days, respectively (Fig.1). These rotation periods of southern polar vortex are longer than the values observed in the past. As a next step, we will derive rotation periods of the polar vortices for

  6. Arabidopsis AIP1-2 restricted by WER-mediated patterning modulates planar polarity.

    Science.gov (United States)

    Kiefer, Christian S; Claes, Andrea R; Nzayisenga, Jean-Claude; Pietra, Stefano; Stanislas, Thomas; Hüser, Anke; Ikeda, Yoshihisa; Grebe, Markus

    2015-01-01

    The coordination of cell polarity within the plane of the tissue layer (planar polarity) is crucial for the development of diverse multicellular organisms. Small Rac/Rho-family GTPases and the actin cytoskeleton contribute to planar polarity formation at sites of polarity establishment in animals and plants. Yet, upstream pathways coordinating planar polarity differ strikingly between kingdoms. In the root of Arabidopsis thaliana, a concentration gradient of the phytohormone auxin coordinates polar recruitment of Rho-of-plant (ROP) to sites of polar epidermal hair initiation. However, little is known about cytoskeletal components and interactions that contribute to this planar polarity or about their relation to the patterning machinery. Here, we show that ACTIN7 (ACT7) represents a main actin isoform required for planar polarity of root hair positioning, interacting with the negative modulator ACTIN-INTERACTING PROTEIN1-2 (AIP1-2). ACT7, AIP1-2 and their genetic interaction are required for coordinated planar polarity of ROP downstream of ethylene signalling. Strikingly, AIP1-2 displays hair cell file-enriched expression, restricted by WEREWOLF (WER)-dependent patterning and modified by ethylene and auxin action. Hence, our findings reveal AIP1-2, expressed under control of the WER-dependent patterning machinery and the ethylene signalling pathway, as a modulator of actin-mediated planar polarity. © 2015. Published by The Company of Biologists Ltd.

  7. Solvent Dependence of (14)N Nuclear Magnetic Resonance Chemical Shielding Constants as a Test of the Accuracy of the Computed Polarization of Solute Electron Densities by the Solvent.

    Science.gov (United States)

    Ribeiro, Raphael F; Marenich, Aleksandr V; Cramer, Christopher J; Truhlar, Donald G

    2009-09-08

    Although continuum solvation models have now been shown to provide good quantitative accuracy for calculating free energies of solvation, questions remain about the accuracy of the perturbed solute electron densities and properties computed from them. Here we examine those questions by applying the SM8, SM8AD, SMD, and IEF-PCM continuum solvation models in combination with the M06-L density functional to compute the (14)N magnetic resonance nuclear shieldings of CH3CN, CH3NO2, CH3NCS, and CH3ONO2 in multiple solvents, and we analyze the dependence of the chemical shifts on solvent dielectric constant. We examine the dependence of the computed chemical shifts on the definition of the molecular cavity (both united-atom models and models based on superposed individual atomic spheres) and three kinds of treatments of the electrostatics, namely the generalized Born approximation with the Coulomb field approximation, the generalized Born model with asymmetric descreening, and models based on approximate numerical solution schemes for the nonhomogeneous Poisson equation. Our most systematic analyses are based on the computation of relative (14)N chemical shifts in a series of solvents, and we compare calculated shielding constants relative to those in CCl4 for various solvation models and density functionals. While differences in the overall results are found to be reasonably small for different solvation models and functionals, the SMx models SM8, and SM8AD, using the same cavity definitions (which for these models means the same atomic radii) as those employed for the calculation of free energies of solvation, exhibit the best agreement with experiment for every functional tested. This suggests that in addition to predicting accurate free energies of solvation, the SM8 and SM8AD generalized Born models also describe the solute polarization in a manner reasonably consistent with experimental (14)N nuclear magnetic resonance spectroscopy. Models based on the

  8. Polarization fluctuations in stationary light beams

    International Nuclear Information System (INIS)

    Shevchenko, A.; Setaelae, T.; Kaivola, M.; Friberg, A.T.; Royal Institute of Technology , Department of Microelectronics and Applied Physics; Sweden)

    2009-01-01

    For stationary beams the degree of polarization contains only limited information on time dependent polarization. Two approaches towards assessing a beams polarization dynamics, one based on Poincare and the other on Jones vector formalism, are described leading to the notion of polarization time. Specific examples of partially temporally coherent electromagnetic beams are discussed. (Author)

  9. Integration of miRNA and protein profiling reveals coordinated neuroadaptations in the alcohol-dependent mouse brain.

    Directory of Open Access Journals (Sweden)

    Giorgio Gorini

    Full Text Available The molecular mechanisms underlying alcohol dependence involve different neurochemical systems and are brain region-dependent. Chronic Intermittent Ethanol (CIE procedure, combined with a Two-Bottle Choice voluntary drinking paradigm, represents one of the best available animal models for alcohol dependence and relapse drinking. MicroRNAs, master regulators of the cellular transcriptome and proteome, can regulate their targets in a cooperative, combinatorial fashion, ensuring fine tuning and control over a large number of cellular functions. We analyzed cortex and midbrain microRNA expression levels using an integrative approach to combine and relate data to previous protein profiling from the same CIE-subjected samples, and examined the significance of the data in terms of relative contribution to alcohol consumption and dependence. MicroRNA levels were significantly altered in CIE-exposed dependent mice compared with their non-dependent controls. More importantly, our integrative analysis identified modules of coexpressed microRNAs that were highly correlated with CIE effects and predicted target genes encoding differentially expressed proteins. Coexpressed CIE-relevant proteins, in turn, were often negatively correlated with specific microRNA modules. Our results provide evidence that microRNA-orchestrated translational imbalances are driving the behavioral transition from alcohol consumption to dependence. This study represents the first attempt to combine ex vivo microRNA and protein expression on a global scale from the same mammalian brain samples. The integrative systems approach used here will improve our understanding of brain adaptive changes in response to drug abuse and suggests the potential therapeutic use of microRNAs as tools to prevent or compensate multiple neuroadaptations underlying addictive behavior.

  10. Polarization developments

    International Nuclear Information System (INIS)

    Prescott, C.Y.

    1993-07-01

    Recent developments in laser-driven photoemission sources of polarized electrons have made prospects for highly polarized electron beams in a future linear collider very promising. This talk discusses the experiences with the SLC polarized electron source, the recent progress with research into gallium arsenide and strained gallium arsenide as a photocathode material, and the suitability of these cathode materials for a future linear collider based on the parameters of the several linear collider designs that exist

  11. Transcriptome profiling reveals the regulatory mechanism underlying pollination dependent and parthenocarpic fruit set mainly mediated by auxin and gibberellin.

    Science.gov (United States)

    Tang, Ning; Deng, Wei; Hu, Guojian; Hu, Nan; Li, Zhengguo

    2015-01-01

    Fruit set is a key process for crop production in tomato which occurs after successful pollination and fertilization naturally. However, parthenocarpic fruit development can be uncoupled from fertilization triggered by exogenous auxin or gibberellins (GAs). Global transcriptome knowledge during fruit initiation would help to characterize the molecular mechanisms by which these two hormones regulate pollination-dependent and -independent fruit set. In this work, digital gene expression tag profiling (DGE) technology was applied to compare the transcriptomes from pollinated and 2, 4-D/GA3-treated ovaries. Activation of carbohydrate metabolism, cell division and expansion as well as the down-regulation of MADS-box is a comprehensive regulatory pathway during pollination-dependent and parthenocarpic fruit set. The signaling cascades of auxin and GA are significantly modulated. The feedback regulations of Aux/IAAs and DELLA genes which functioned to fine-tune auxin and GA response respectively play fundamental roles in triggering fruit initiation. In addition, auxin regulates GA synthesis via up-regulation of GA20ox1 and down-regulation of KNOX. Accordingly, the effect of auxin on fruit set is mediated by GA via ARF2 and IAA9 down-regulation, suggesting that both pollination-dependent and parthenocarpic fruit set depend on the crosstalk between auxin and GA. This study characterizes the transcriptomic features of ovary development and more importantly unravels the integral roles of auxin and GA on pollination-dependent and parthenocarpic fruit set.

  12. Transcriptome profiling reveals the regulatory mechanism underlying pollination dependent and parthenocarpic fruit set mainly mediated by auxin and gibberellin.

    Directory of Open Access Journals (Sweden)

    Ning Tang

    Full Text Available Fruit set is a key process for crop production in tomato which occurs after successful pollination and fertilization naturally. However, parthenocarpic fruit development can be uncoupled from fertilization triggered by exogenous auxin or gibberellins (GAs. Global transcriptome knowledge during fruit initiation would help to characterize the molecular mechanisms by which these two hormones regulate pollination-dependent and -independent fruit set.In this work, digital gene expression tag profiling (DGE technology was applied to compare the transcriptomes from pollinated and 2, 4-D/GA3-treated ovaries. Activation of carbohydrate metabolism, cell division and expansion as well as the down-regulation of MADS-box is a comprehensive regulatory pathway during pollination-dependent and parthenocarpic fruit set. The signaling cascades of auxin and GA are significantly modulated. The feedback regulations of Aux/IAAs and DELLA genes which functioned to fine-tune auxin and GA response respectively play fundamental roles in triggering fruit initiation. In addition, auxin regulates GA synthesis via up-regulation of GA20ox1 and down-regulation of KNOX. Accordingly, the effect of auxin on fruit set is mediated by GA via ARF2 and IAA9 down-regulation, suggesting that both pollination-dependent and parthenocarpic fruit set depend on the crosstalk between auxin and GA.This study characterizes the transcriptomic features of ovary development and more importantly unravels the integral roles of auxin and GA on pollination-dependent and parthenocarpic fruit set.

  13. FRET ratiometric probes reveal the chiral-sensitive cysteine-dependent H2S production and regulation in living cells

    Science.gov (United States)

    Wei, Lv; Yi, Long; Song, Fanbo; Wei, Chao; Wang, Bai-Fan; Xi, Zhen

    2014-04-01

    Hydrogen sulfide (H2S) is an endogenously produced gaseous signalling molecule with multiple biological functions. In order to visualize and quantify the endogenous in situ production of H2S in living cells, here we developed two new sulphide ratiometric probes (SR400 and SR550) based on fluorescence resonance energy transfer (FRET) strategy for live capture of H2S. The FRET-based probes show excellent selectivity toward H2S in a high thiol background under physiological buffer. The probe can be used to in situ visualize cysteine-dependent H2S production in a chiral-sensitive manner in living cells. The ratiometric imaging studies indicated that D-Cys induces more H2S production than that of L-Cys in mitochondria of human embryonic kidney 293 cells (HEK293). The cysteine mimics propargylglycine (PPG) has also been found to inhibit the cysteine-dependent endogenous H2S production in a chiral-sensitive manner in living cells. D-PPG inhibited D-Cys-dependent H2S production more efficiently than L-PPG, while, L-PPG inhibited L-Cys-dependent H2S production more efficiently than D-PPG. Our bioimaging studies support Kimura's discovery of H2S production from D-cysteine in mammalian cells and further highlight the potential of D-cysteine and its derivatives as an alternative strategy for classical H2S-releasing drugs.

  14. MouseTmem135mutation reveals a mechanism involving mitochondrial dynamics that leads to age-dependent retinal pathologies.

    Science.gov (United States)

    Lee, Wei-Hua; Higuchi, Hitoshi; Ikeda, Sakae; Macke, Erica L; Takimoto, Tetsuya; Pattnaik, Bikash R; Liu, Che; Chu, Li-Fang; Siepka, Sandra M; Krentz, Kathleen J; Rubinstein, C Dustin; Kalejta, Robert F; Thomson, James A; Mullins, Robert F; Takahashi, Joseph S; Pinto, Lawrence H; Ikeda, Akihiro

    2016-11-15

    While the aging process is central to the pathogenesis of age-dependent diseases, it is poorly understood at the molecular level. We identified a mouse mutant with accelerated aging in the retina as well as pathologies observed in age-dependent retinal diseases, suggesting that the responsible gene regulates retinal aging, and its impairment results in age-dependent disease. We determined that a mutation in the transmembrane 135 ( Tmem135 ) is responsible for these phenotypes. We observed localization of TMEM135 on mitochondria, and imbalance of mitochondrial fission and fusion in mutant Tmem135 as well as Tmem135 overexpressing cells, indicating that TMEM135 is involved in the regulation of mitochondrial dynamics. Additionally, mutant retina showed higher sensitivity to oxidative stress. These results suggest that the regulation of mitochondrial dynamics through TMEM135 is critical for protection from environmental stress and controlling the progression of retinal aging. Our study identified TMEM135 as a critical link between aging and age-dependent diseases.

  15. A Systematic Analysis of Factors Localized to Damaged Chromatin Reveals PARP-Dependent Recruitment of Transcription Factors

    Directory of Open Access Journals (Sweden)

    Lior Izhar

    2015-06-01

    Full Text Available Localization to sites of DNA damage is a hallmark of DNA damage response (DDR proteins. To identify DDR factors, we screened epitope-tagged proteins for localization to sites of chromatin damaged by UV laser microirradiation and found >120 proteins that localize to damaged chromatin. These include the BAF tumor suppressor complex and the amyotrophic lateral sclerosis (ALS candidate protein TAF15. TAF15 contains multiple domains that bind damaged chromatin in a poly-(ADP-ribose polymerase (PARP-dependent manner, suggesting a possible role as glue that tethers multiple PAR chains together. Many positives were transcription factors; > 70% of randomly tested transcription factors localized to sites of DNA damage, and of these, ∼90% were PARP dependent for localization. Mutational analyses showed that localization to damaged chromatin is DNA-binding-domain dependent. By examining Hoechst staining patterns at damage sites, we see evidence of chromatin decompaction that is PARP dependent. We propose that PARP-regulated chromatin remodeling at sites of damage allows transient accessibility of DNA-binding proteins.

  16. Deciphering the onychophoran 'segmentation gene cascade': Gene expression reveals limited involvement of pair rule gene orthologs in segmentation, but a highly conserved segment polarity gene network.

    Science.gov (United States)

    Janssen, Ralf; Budd, Graham E

    2013-10-01

    The hallmark of the arthropods is their segmented body, although origin of segmentation, however, is unresolved. In order to shed light on the origin of segmentation we investigated orthologs of pair rule genes (PRGs) and segment polarity genes (SPGs) in a member of the closest related sister-group to the arthropods, the onychophorans. Our gene expression data analysis suggests that most of the onychophoran PRGs do not play a role in segmentation. One possible exception is the even-skipped (eve) gene that is expressed in the posterior end of the onychophoran where new segments are likely patterned, and is also expressed in segmentation-gene typical transverse stripes in at least a number of newly formed segments. Other onychophoran PRGs such as runt (run), hairy/Hes (h/Hes) and odd-skipped (odd) do not appear to have a function in segmentation at all. Onychophoran PRGs that act low in the segmentation gene cascade in insects, however, are potentially involved in segment-patterning. Most obvious is that from the expression of the pairberry (pby) gene ortholog that is expressed in a typical SPG-pattern. Since this result suggested possible conservation of the SPG-network we further investigated SPGs (and associated factors) such as Notum in the onychophoran. We find that the expression patterns of SPGs in arthropods and the onychophoran are highly conserved, suggesting a conserved SPG-network in these two clades, and indeed also in an annelid. This may suggest that the common ancestor of lophotrochozoans and ecdysozoans was already segmented utilising the same SPG-network, or that the SPG-network was recruited independently in annelids and onychophorans/arthropods. © 2013 Elsevier Inc. All rights reserved.

  17. Polarization, political

    NARCIS (Netherlands)

    Wojcieszak, M.; Mazzoleni, G.; Barnhurst, K.G.; Ikeda, K.; Maia, R.C.M.; Wessler, H.

    2015-01-01

    Polarization has been studied in three different forms: on a social, group, and individual level. This entry first focuses on the undisputed phenomenon of elite polarization (i.e., increasing adherence of policy positions among the elites) and also outlines different approaches to assessing mass

  18. Unoccupied density of states of La2–xSrxNiO4+δ studied by polarization-dependent x-ray-absorption spectroscopy and bremsstrahlung isochromat spectroscopy

    NARCIS (Netherlands)

    Kuiper, P.; Elp, J. van; Sawatzky, G.A.; Fujimori, A.; Hosoya, S.; Leeuw, D.M. de

    1991-01-01

    Oxygen 1s x-ray-absorption measurements of La2–xSrxNiO4+δ (0≤x≤1.15) are presented, together with O 1s polarization-dependent x-ray absorption on single-crystal La1.85Sr0.15NiO4. It is concluded that the charge-compensating holes have mainly oxygen 2p character. The Ni 3d9 final states reached

  19. Effects of solution crowding on actin polymerization reveal the energetic basis for nucleotide-dependent filament stability

    OpenAIRE

    Frederick, Kendra B.; Sept, David; De La Cruz, Enrique M.

    2008-01-01

    Actin polymerization is a fundamental cellular process involved in cell structure maintenance, force generation, and motility. Phosphate release from filament subunits following ATP hydrolysis destabilizes the filament lattice and increases the critical concentration (Cc) for assembly. The structural differences between ATP- and ADP-actin are still debated, as well as the energetic factors that underlie nucleotide-dependent filament stability, particularly under crowded intracellular conditio...

  20. Selective inhibition reveals cyclin-dependent kinase 2 as another kinase that phosphorylates the androgen receptor at serine 81

    Czech Academy of Sciences Publication Activity Database

    Jorda, Radek; Bučková, Zuzana; Řezníčková, Eva; Bouchal, J.; Kryštof, Vladimír

    2018-01-01

    Roč. 1865, č. 2 (2018), s. 354-363 ISSN 0167-4889 R&D Projects: GA MŠk(CZ) LO1204; GA MŠk(CZ) LO1304 Institutional support: RVO:61389030 Keywords : Androgen receptor * Cyclin-dependent kinase * Inhibitor * Phosphorylation * Serine 81 Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Biochemistry and molecular biology Impact factor: 4.521, year: 2016

  1. Polarization holography

    DEFF Research Database (Denmark)

    Nikolova, L.; Ramanujam, P.S.

    Current research into holography is concerned with applications in optically storing, retrieving, and processing information. Polarization holography has many unique properties compared to conventional holography. It gives results in high efficiency, achromaticity, and special polarization...... properties. This books reviews the research carried out in this field over the last 15 years. The authors provide basic concepts in polarization and the propagation of light through anisotropic materials, before presenting a sound theoretical basis for polarization holography. The fabrication...... and characterization of azobenzene based materials, which remain the most efficient for the purpose, is described in detail. This is followed by a description of other materials that are used in polarization holography. An in-depth description of various applications, including display holography and optical storage...

  2. Effects of solution crowding on actin polymerization reveal the energetic basis for nucleotide-dependent filament stability.

    Science.gov (United States)

    Frederick, Kendra B; Sept, David; De La Cruz, Enrique M

    2008-05-02

    Actin polymerization is a fundamental cellular process involved in cell structure maintenance, force generation, and motility. Phosphate release from filament subunits following ATP hydrolysis destabilizes the filament lattice and increases the critical concentration (C(c)) for assembly. The structural differences between ATP- and ADP-actin are still debated, as well as the energetic factors that underlie nucleotide-dependent filament stability, particularly under crowded intracellular conditions. Here, we investigate the effect of crowding agents on ATP- and ADP-actin polymerization and find that ATP-actin polymerization is largely unaffected by solution crowding, while crowding agents lower the C(c) of ADP-actin in a concentration-dependent manner. The stabilities of ATP- and ADP-actin filaments are comparable in the presence of physiological amounts (approximately 30% w/v) and types (sorbitol) of low molecular weight crowding agents. Crowding agents act to stabilize ADP-F-actin by slowing subunit dissociation. These observations suggest that nucleotide hydrolysis and phosphate release per se do not introduce intrinsic differences in the in vivo filament stability. Rather, the preferential disassembly of ADP-actin filaments in cells is driven through interactions with regulatory proteins. Interpretation of the experimental data according to osmotic stress theory implicates water as an allosteric regulator of actin activity and hydration as the molecular basis for nucleotide-dependent filament stability.

  3. Trophic calculations reveal the mechanism of population-level variation in mercury concentrations between marine ecosystems: Case studies of two polar seabirds

    International Nuclear Information System (INIS)

    Brasso, Rebecka L.; Polito, Michael J.

    2013-01-01

    Highlights: • Ecosystem-specific baseline and consumer δ 15 N paired for population-specific trophic level. • Source of population-level variation in mercury exposure identified in two seabirds. • High mercury and trophic position suggests trophic driver of population-level variation. • Trophic similarities, differing mercury reveals geographic differences in bioavailability. -- Abstract: The incorporation of quantitative trophic level analysis in ecotoxicological studies provides explanatory power to identify the factors, trophic or environmental, driving population-level variation in mercury exposure at large geographic scales. In the Antarctic marine ecosystem, mercury concentrations and stable isotope values in Adélie penguins (Pygoscelis adeliae) were compared between the Antarctic Peninsula and the Ross Sea. Correcting tissue δ 15 N values for baseline δ 15 N values revealed population-level differences in trophic position which contributes to differences in mercury. Data from Thick-billed murres (Uria lomvia) were synthesized from published values from Baffin Bay and Svalbard to demonstrate the utility of baseline δ 15 N values in identifying differences in environmental mercury exposure independent of diet. Here, we demonstrate the importance of calculating population-specific trophic level data to uncover the source of variation in mercury concentrations between geographically distinct populations of marine predators

  4. A High-Throughput Technique Reveals the Load- and Site Density-Dependent Kinetics of E-Selectin

    Science.gov (United States)

    Snook, Jeremy H.; Guilford, William H.

    2013-01-01

    The kinetics of bond rupture between receptors and ligand are critically dependent on applied mechanical force. Force spectroscopy of single receptor-ligand pairs to measure kinetics is a laborious and time-consuming process that is generally performed using individual force probes and making one measurement at a time when typically hundreds of measurements are needed. A high-throughput approach is thus desirable. We report here a magnetic bond puller that provides high-throughput measurements of single receptor-ligand bond kinetics. Electromagnets are used to apply pN tensile and compressive forces to receptor-coated magnetic microspheres while monitoring their contact with a ligand-coated surface. Bond lifetimes and the probability of forming a bond are measured via videomicroscopy, and the data are used to determine the load dependent rates of bond rupture and bond formation. The approach is simple, customizable, relatively inexpensive, and can make dozens of kinetic measurements simultaneously. We used the device to investigate how compressive and tensile forces affect the rates of formation and rupture, respectively, of bonds between E-selectin and sialyl Lewisa (sLea), a sugar on P-selectin glycoprotein ligand-1 to which selectins bind. We confirmed earlier findings of a load-dependent rate of bond formation between these two molecules, and that they form a catch-slip bond like other selectin family members. We also make the novel observation of an “ideal” bond in a highly multivalent system of this receptor-ligand pair. PMID:24511329

  5. Analysis of the molecular networks in androgen dependent and independent prostate cancer revealed fragile and robust subsystems.

    Directory of Open Access Journals (Sweden)

    Ryan Tasseff

    Full Text Available Androgen ablation therapy is currently the primary treatment for metastatic prostate cancer. Unfortunately, in nearly all cases, androgen ablation fails to permanently arrest cancer progression. As androgens like testosterone are withdrawn, prostate cancer cells lose their androgen sensitivity and begin to proliferate without hormone growth factors. In this study, we constructed and analyzed a mathematical model of the integration between hormone growth factor signaling, androgen receptor activation, and the expression of cyclin D and Prostate-Specific Antigen in human LNCaP prostate adenocarcinoma cells. The objective of the study was to investigate which signaling systems were important in the loss of androgen dependence. The model was formulated as a set of ordinary differential equations which described 212 species and 384 interactions, including both the mRNA and protein levels for key species. An ensemble approach was chosen to constrain model parameters and to estimate the impact of parametric uncertainty on model predictions. Model parameters were identified using 14 steady-state and dynamic LNCaP data sets taken from literature sources. Alterations in the rate of Prostatic Acid Phosphatase expression was sufficient to capture varying levels of androgen dependence. Analysis of the model provided insight into the importance of network components as a function of androgen dependence. The importance of androgen receptor availability and the MAPK/Akt signaling axes was independent of androgen status. Interestingly, androgen receptor availability was important even in androgen-independent LNCaP cells. Translation became progressively more important in androgen-independent LNCaP cells. Further analysis suggested a positive synergy between the MAPK and Akt signaling axes and the translation of key proliferative markers like cyclin D in androgen-independent cells. Taken together, the results support the targeting of both the Akt and MAPK

  6. Functional gene profiling through metaRNAseq approach reveals diet-dependent variation in rumen microbiota of buffalo (Bubalus bubalis).

    Science.gov (United States)

    Hinsu, Ankit T; Parmar, Nidhi R; Nathani, Neelam M; Pandit, Ramesh J; Patel, Anand B; Patel, Amrutlal K; Joshi, Chaitanya G

    2017-04-01

    Recent advances in next generation sequencing technology have enabled analysis of complex microbial community from genome to transcriptome level. In the present study, metatranscriptomic approach was applied to elucidate functionally active bacteria and their biological processes in rumen of buffalo (Bubalus bubalis) adapted to different dietary treatments. Buffaloes were adapted to a diet containing 50:50, 75:25 and 100:0 forage to concentrate ratio, each for 6 weeks, before ruminal content sample collection. Metatranscriptomes from rumen fiber adherent and fiber-free active bacteria were sequenced using Ion Torrent PGM platform followed by annotation using MG-RAST server and CAZYmes (Carbohydrate active enzymes) analysis toolkit. In all the samples Bacteroidetes was the most abundant phylum followed by Firmicutes. Functional analysis using KEGG Orthology database revealed Metabolism as the most abundant category at level 1 within which Carbohydrate metabolism was dominating. Diet treatments also exerted significant differences in proportion of enzymes involved in metabolic pathways for VFA production. Carbohydrate Active Enzyme(CAZy) analysis revealed the abundance of genes encoding glycoside hydrolases with the highest representation of GH13 CAZy family in all the samples. The findings provide an overview of the activities occurring in the rumen as well as active bacterial population and the changes occurring through different dietary treatments. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Fungal diversity in adult date palm (Phoenix dactylifera L.) revealed by culture-dependent and culture-independent approaches.

    Science.gov (United States)

    Ben Chobba, Ines; Elleuch, Amine; Ayadi, Imen; Khannous, Lamia; Namsi, Ahmed; Cerqueira, Frederique; Drira, Noureddine; Gharsallah, Néji; Vallaeys, Tatiana

    2013-12-01

    Endophytic flora plays a vital role in the colonization and survival of host plants, especially in harsh environments, such as arid regions. This flora may, however, contain pathogenic species responsible for various troublesome host diseases. The present study is aimed at investigating the diversity of both cultivable and non-cultivable endophytic fungal floras in the internal tissues (roots and leaves) of Tunisian date palm trees (Phoenix dactylifera). Accordingly, 13 isolates from both root and leaf samples, exhibiting distinct colony morphology, were selected from potato dextrose agar (PDA) medium and identified by a sequence match search wherein their 18S-28S internal transcribed spacer (ITS) sequences were compared to those available in public databases. These findings revealed that the cultivable root and leaf isolates fell into two groups, namely Nectriaceae and Pleosporaceae. Additionally, total DNA from palm roots and leaves was further extracted and ITS fragments were amplified. Restriction fragment length polymorphism (RFLP) analysis of the ITS from 200 fungal clones (leaves: 100; roots: 100) using HaeIII restriction enzyme revealed 13 distinct patterns that were further sequenced and led to the identification of Alternaria, Cladosporium, Davidiella (Cladosporium teleomorph), Pythium, Curvularia, and uncharacterized fungal endophytes. Both approaches confirmed that while the roots were predominantly colonized by Fusaria (members of the Nectriaceae family), the leaves were essentially colonized by Alternaria (members of the Pleosporaceae family). Overall, the findings of the present study constitute, to the authors' knowledge, the first extensive report on the diversity of endophytic fungal flora associated with date palm trees (P. dactylifera).

  8. Small RNA Deep Sequencing Reveals Role for Arabidopsis thaliana RNA-Dependent RNA Polymerases in Viral siRNA Biogenesis

    OpenAIRE

    Qi, Xiaopeng; Bao, Forrest Sheng; Xie, Zhixin

    2009-01-01

    RNA silencing functions as an important antiviral defense mechanism in a broad range of eukaryotes. In plants, biogenesis of several classes of endogenous small interfering RNAs (siRNAs) requires RNA-dependent RNA Polymerase (RDR) activities. Members of the RDR family proteins, including RDR1and RDR6, have also been implicated in antiviral defense, although a direct role for RDRs in viral siRNA biogenesis has yet to be demonstrated. Using a crucifer-infecting strain of Tobacco Mosaic Virus (T...

  9. PEPPo: Using a Polarized Electron Beam to Produce Polarized Positrons

    Energy Technology Data Exchange (ETDEWEB)

    Adeyemi, Adeleke H. [Hampton Univ., Hampton, VA (United States); et al.

    2015-09-01

    Polarized positron beams have been identified as either an essential or a significant ingredient for the experimental program of both the present and next generation of lepton accelerators (JLab, Super KEK B, ILC, CLIC). An experiment demonstrating a new method for producing polarized positrons has been performed at the Continuous Electron Beam Accelerator Facility at Jefferson Lab. The PEPPo (Polarized Electrons for Polarized Positrons) concept relies on the production of polarized e⁻/e⁺ pairs from the bremsstrahlung radiation of a longitudinally polarized electron beam interacting within a high-Z conversion target. PEPPo demonstrated the effective transfer of spin-polarization of an 8.2 MeV/c polarized (P~85%) electron beam to positrons produced in varying thickness tungsten production targets, and collected and measured in the range of 3.1 to 6.2 MeV/c. In comparison to other methods this technique reveals a new pathway for producing either high-energy or thermal polarized positron beams using a relatively low polarized electron beam energy (~10MeV) .This presentation will describe the PEPPo concept, the motivations of the experiment and high positron polarization achieved.

  10. Appearance of differentiated cells derived from polar body nuclei in the silkworm, Bombyx mori

    Directory of Open Access Journals (Sweden)

    Hiroki eSakai

    2013-09-01

    Full Text Available AbstractIn Bombyx mori, polar body nuclei are observed until 9h after egg lying, however, the fate of polar body nuclei remains unclear. To examine the fate of polar body nuclei, we employed a mutation of serosal cell pigmentation, pink-eyed white egg (pe. The heterozygous pe/+pe females produced black serosal cells in white eggs, while pe/pe females did not produce black serosal cells in white eggs. These results suggest that the appearance of black serosal cells in white eggs depends on the genotype (pe/ +pe of the mother. Because the polar body nuclei had +pe genes in the white eggs laid by a pe/ +pe female, polar body nuclei participate in development and differentiate into functional cell (serosal cells. Analyses of serosal cells pigmentation indicated that approximately 30% of the eggs contained polar-body-nucleus-derived cells. These results demonstrate that polar-body-nucleus-derived cells appeared at a high frequency under natural conditions. Approximately 80% of polar-body-nucleus-derived cells appeared near the anterior pole and the dorsal side, which is opposite to where embryogenesis occurs. The number of cells derived from the polar body nuclei was very low. Approximately 26 % of these eggs contained only one black serosal cell. PCR-based analysis revealed that the polar-body-nucleus-derived cells disappeared in late embryonic stages (stage 25. Overall, polar-body-nuclei-derived cells were unlikely to contribute to embryos.

  11. Strain dependence on polarization properties of AlGaN and AlGaN-based ultraviolet lasers grown on AlN substrates

    Energy Technology Data Exchange (ETDEWEB)

    Bryan, Zachary, E-mail: zabryan@ncsu.edu; Bryan, Isaac; Sitar, Zlatko; Collazo, Ramón [Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695 (United States); Mita, Seiji [HexaTech, Inc., 991 Aviation Pkwy., Suite 800, Morrisville, North Carolina 27560 (United States); Tweedie, James [Adroit Materials, 2054 Kildaire Farm Rd., Suite 205, Cary, North Carolina 27518 (United States)

    2015-06-08

    Since the band ordering in AlGaN has a profound effect on the performance of UVC light emitting diodes (LEDs) and even determines the feasibility of surface emitting lasers, the polarization properties of emitted light from c-oriented AlGaN and AlGaN-based laser structures were studied over the whole composition range, as well as various strain states, quantum confinements, and carrier densities. A quantitative relationship between the theoretical valence band separation, determined using k•p theory, and the experimentally measured degree of polarization is presented. Next to composition, strain was found to have the largest influence on the degree of polarization while all other factors were practically insignificant. The lowest crossover point from the transverse electric to transverse magnetic polarized emission of 245 nm was found for structures pseudomorphically grown on AlN substrates. This finding has significant implications toward the efficiency and feasibility of surface emitting devices below this wavelength.

  12. Polar Bears

    Science.gov (United States)

    Amstrup, Steven C.; Douglas, David C.; Reynolds, Patricia E.; Rhode, E.B.

    2002-01-01

    Polar bears (Ursus maritimus) are hunted throughout most of their range. In addition to hunting polar bears of the Beaufort Sea region are exposed to mineral and petroleum extraction and related human activities such as shipping road-building, and seismic testing (Stirling 1990).Little was known at the start of this project about how polar bears move about in their environment, and although it was understood that many bears travel across political borders, the boundaries of populations had not been delineated (Amstrup 1986, Amstrup et al. 1986, Amstrup and DeMaster 1988, Garner et al. 1994, Amstrup 1995, Amstrup et al. 1995, Amstrup 2000).As human populations increase and demands for polar bears and other arctic resources escalate, managers must know the sizes and distributions of the polar bear populations. Resource managers also need reliable estimates of breeding rates, reproductive intervals, litter sizes, and survival of young and adults.Our objectives for this research were 1) to determine the seasonal and annual movements of polar bears in the Beaufort Sea, 2) to define the boundaries of the population(s) using this region, 3) to determine the size and status of the Beaufort Sea polar bear population, and 4) to establish reproduction and survival rates (Amstrup 2000).

  13. Mutational analysis of the mycobacteriophage BPs promoter PR reveals context-dependent sequences for mycobacterial gene expression.

    Science.gov (United States)

    Oldfield, Lauren M; Hatfull, Graham F

    2014-10-01

    The PR promoter of mycobacteriophage BPs directs early lytic gene expression and is under the control of the BPs repressor, gp33. Reporter gene fusions showed that PR has modest activity in an extrachromosomal context but has activity that is barely detectable in an integrated context, even in the absence of its repressor. Mutational dissection of PR showed that it uses a canonical -10 hexamer recognized by SigA, and mutants with mutations to the sequence 5'-TATAMT had the greatest activities. It does not contain a 5'-TGN-extended -10 sequence, although mutants with mutations creating an extended -10 sequence had substantially increased promoter activity. Mutations in the -35 hexamer also influenced promoter activity but were strongly context dependent, and similar substitutions in the -35 hexamer differentially affected promoter activity, depending on the -10 and extended -10 motifs. This warrants caution in the construction of synthetic promoters or the bioinformatic prediction of promoter activity. Combinations of mutations throughout PR generated a calibrated series of promoters for expression of stably integrated recombinant genes in both Mycobacterium smegmatis and M. tuberculosis, with maximal promoter activity being more than 2-fold that of the strong hsp60 promoter. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  14. Structures of Asymmetric ClpX Hexamers Reveal Nucleotide-Dependent Motions in a AAA+ Protein-Unfolding Machine

    Energy Technology Data Exchange (ETDEWEB)

    Glynn, Steven E.; Martin, Andreas; Nager, Andrew R.; Baker, Tania A.; Sauer, Robert T.; MIT

    2010-02-02

    ClpX is a AAA+ machine that uses the energy of ATP binding and hydrolysis to unfold native proteins and translocate unfolded polypeptides into the ClpP peptidase. The crystal structures presented here reveal striking asymmetry in ring hexamers of nucleotide-free and nucleotide-bound ClpX. Asymmetry arises from large changes in rotation between the large and small AAA+ domains of individual subunits. These differences prevent nucleotide binding to two subunits, generate a staggered arrangement of ClpX subunits and pore loops around the hexameric ring, and provide a mechanism for coupling conformational changes caused by ATP binding or hydrolysis in one subunit to flexing motions of the entire ring. Our structures explain numerous solution studies of ClpX function, predict mechanisms for pore elasticity during translocation of irregular polypeptides, and suggest how repetitive conformational changes might be coupled to mechanical work during the ATPase cycle of ClpX and related molecular machines.

  15. Fungal diversity in adult date palm (Phoenix dactylifera L.) revealed by culture-dependent and culture-independent approaches*

    Science.gov (United States)

    Ben Chobba, Ines; Elleuch, Amine; Ayadi, Imen; Khannous, Lamia; Namsi, Ahmed; Cerqueira, Frederique; Drira, Noureddine; Gharsallah, Néji; Vallaeys, Tatiana

    2013-01-01

    Endophytic flora plays a vital role in the colonization and survival of host plants, especially in harsh environments, such as arid regions. This flora may, however, contain pathogenic species responsible for various troublesome host diseases. The present study is aimed at investigating the diversity of both cultivable and non-cultivable endophytic fungal floras in the internal tissues (roots and leaves) of Tunisian date palm trees (Phoenix dactylifera). Accordingly, 13 isolates from both root and leaf samples, exhibiting distinct colony morphology, were selected from potato dextrose agar (PDA) medium and identified by a sequence match search wherein their 18S–28S internal transcribed spacer (ITS) sequences were compared to those available in public databases. These findings revealed that the cultivable root and leaf isolates fell into two groups, namely Nectriaceae and Pleosporaceae. Additionally, total DNA from palm roots and leaves was further extracted and ITS fragments were amplified. Restriction fragment length polymorphism (RFLP) analysis of the ITS from 200 fungal clones (leaves: 100; roots: 100) using HaeIII restriction enzyme revealed 13 distinct patterns that were further sequenced and led to the identification of Alternaria, Cladosporium, Davidiella (Cladosporium teleomorph), Pythium, Curvularia, and uncharacterized fungal endophytes. Both approaches confirmed that while the roots were predominantly colonized by Fusaria (members of the Nectriaceae family), the leaves were essentially colonized by Alternaria (members of the Pleosporaceae family). Overall, the findings of the present study constitute, to the authors’ knowledge, the first extensive report on the diversity of endophytic fungal flora associated with date palm trees (P. dactylifera). PMID:24302709

  16. In situ visualization of Li/Ag2VP2O8 batteries revealing rate-dependent discharge mechanism

    Science.gov (United States)

    Kirshenbaum, Kevin; Bock, David C.; Lee, Chia-Ying; Zhong, Zhong; Takeuchi, Kenneth J.; Marschilok, Amy C.; Takeuchi, Esther S.

    2015-01-01

    The functional capacity of a battery is observed to decrease, often quite dramatically, as discharge rate demands increase. These capacity losses have been attributed to limited ion access and low electrical conductivity, resulting in incomplete electrode use. A strategy to improve electronic conductivity is the design of bimetallic materials that generate a silver matrix in situ during cathode reduction. Ex situ x-ray absorption spectroscopy coupled with in situ energy-dispersive x-ray diffraction measurements on intact lithium/silver vanadium diphosphate (Li/Ag2VP2O8) electrochemical cells demonstrate that the metal center preferentially reduced and its location in the bimetallic cathode are rate-dependent, affecting cell impedance. This work illustrates that spatial imaging as a function of discharge rate can provide needed insights toward improving realizable capacity of bimetallic cathode systems.

  17. Mg2+ dependence of 70 S ribosomal protein flexibility revealed by hydrogen/deuterium exchange and mass spectrometry.

    Science.gov (United States)

    Yamamoto, Tatsuya; Shimizu, Yoshihiro; Ueda, Takuya; Shiro, Yoshitsugu

    2010-02-19

    The ribosome from Escherichia coli requires a specific concentration of Mg(2+) to maintain the 70 S complex formation and allow protein synthesis, and then the structure must be stable and flexible. How does the ribosome acquire these conflicting factors at the same time? Here, we investigated the hydrogen/deuterium exchange of 52 proteins in the 70 S ribosome, which controlled stability and flexibility under various Mg(2+) concentrations, using mass spectrometry. Many proteins exhibited a sigmoidal curve for Mg(2+) concentration dependence, incorporating more deuterium at lower Mg(2+) concentration. By comparing deuterium incorporation with assembly, we have discovered a typical mechanism of complexes for acquiring both stability and flexibility at the same time. In addition, we got information of the localization of flexibility in ribosomal function by the analysis of related proteins with stalk protein, tRNA, mRNA, and nascent peptide, and demonstrate the relationship between structure, assembly, flexibility, and function of the ribosome.

  18. The role of Ca2+-dependent K+- channels at the rat corticostriatal synapses revealed by paired pulse stimulation.

    Science.gov (United States)

    Robles Gómez, Angel A; Vega, Ana V; Gónzalez-Sandoval, Carolina; Barral, Jaime

    2018-02-01

    Potassium channels play an important role in modulating synaptic activity both at presynaptic and postsynaptic levels. We have shown before that presynaptically located K V and K IR channels modulate the strength of corticostriatal synapses in rat brain, but the role of other types of potassium channels at these synapses remains largely unknown. Here, we show that calcium-dependent potassium channels BK-type but not SK-type channels are located presynaptically in corticostriatal synapses. We stimulated cortical neurons in rat brain slices and recorded postsynaptic excitatory potentials (EPSP) in medium spiny neurons (MSN) in dorsal neostriatum. By using a paired pulse protocol, we induced synaptic facilitation before applying either BK- or SK-specific toxins. Thus, we found that blockage of BK Ca with iberiotoxin (10 nM) reduces synaptic facilitation and increases the amplitude of the EPSP, while exposure to SK-blocker apamin (100 nM) has no effect. Additionally, we induced train action potentials on striatal MSN by current injection before and after the exposure to K Ca toxins. We found that the action potential becomes broader when the MSN is exposed to iberiotoxin, although it has no impact on frequency. In contrast, exposure to apamin results in loss of afterhyperpolarization phase and an increase of spike frequency. Therefore, we concluded that postsynaptic SK channels are involved in afterhyperpolarization and modulation of spike frequency while the BK channels are involved on the late repolarization phase of the action potential. Altogether, our results show that calcium-dependent potassium channels modulate both input towards and output from the striatum. © 2017 Wiley Periodicals, Inc.

  19. Faecal egg counts from field experiment reveal density dependence in helminth fecundity: Strongyloides robustus infecting grey squirrels (Sciurus carolinensis).

    Science.gov (United States)

    Romeo, Claudia; Wauters, L A; Cauchie, S; Martinoli, A; Matthysen, E; Saino, N; Ferrari, N

    2014-09-01

    Investigation of endo-macroparasite infections in living animals relies mostly on indirect methods aimed to detect parasite eggs in hosts' faeces. However, faecal flotation does not provide quantitative information on parasite loads, whereas faecal egg count (FEC) techniques may not give reliable estimates of parasite intensity, since egg production may be affected by density-dependent effects on helminth fecundity. We addressed this issue using Eastern grey squirrels (Sciurus carolinensis) and their gastrointestinal nematode Strongyloides robustus to assess the performance of coprological techniques and to investigate factors affecting parasite fecundity. We compared results of gut examination, flotation and McMaster FECs in 65 culled grey squirrels. Sensitivity and specificity of flotation were 81.2% (Confidence Interval, CI 54.3-95.9%) and 85.7% (CI 72.7-94.1%), respectively, resulting in low positive predictive values when infection prevalence is low. Individual parasite fecundity (no. of eggs/adult female worm) was negatively affected by S. robustus intensity, leading to a non-linear relationship between parasite load and eggs/gram of faeces (EPG). As a consequence, whereas flotation may be a valid method to perform the first screening of infection status, FECs are not a reliable method to estimate S. robustus intensity, since diverse values of EPG may correspond to the same number of parasites. Neither the amount of analysed faeces nor the season had any effect on EPG, indicating that the observed reduction in helminth fecundity is likely caused exclusively by density-dependent processes such as competition among worms or host immune response.

  20. Climate Drives Polar Bear Origins

    Science.gov (United States)

    In their provocative analysis of northern bears (“Nuclear genomic sequences reveal that polar bears are an old and distinct bear lineage,” Reports, 20 April, p. 344), F. Hailer et al. use independent nuclear loci to show that polar bears originated during the middle Pleistocene, rather than during t...

  1. Single-molecule imaging reveals topological isomer-dependent diffusion by 4-armed star and dicyclic 8-shaped polymers

    KAUST Repository

    Habuchi, Satoshi

    2015-04-21

    Diffusion dynamics of topological isomers of polymer molecules was investigated at the single-molecule level in a melt state by employing the fluorophore-incorporated 4-armed star and the corresponding doubly-cyclized, 8-shaped poly(THF) chains. While the single-molecule fluorescence imaging experiment revealed that the diffusion of the 4-armed star polymer was described by a single Gaussian distribution, the diffusion of the 8-shaped polymer exhibited a double Gaussian distribution behaviour. We reasoned that the two 8-shaped polymeric isomers have distinct diffusion modes in the melt state, although ensemble-averaged experimental methods cannot detect differences in overall conformational state of the isomers. The single-molecule experiments suggested that one of the 8-shaped polymeric isomer, having the horizontally oriented form, causes an efficient threading with the linear matrix chains which leads to the slower diffusion compared with the corresponding 4-armed star polymer, while the other 8-shaped polymeric isomer, having the vertically oriented form, displayed faster diffusion by the suppression of effective threading with the linear matrix chains due to its contracted chain conformation.

  2. A pan-European epidemiological study reveals honey bee colony survival depends on beekeeper education and disease control.

    Science.gov (United States)

    Jacques, Antoine; Laurent, Marion; Ribière-Chabert, Magali; Saussac, Mathilde; Bougeard, Stéphanie; Budge, Giles E; Hendrikx, Pascal; Chauzat, Marie-Pierre

    2017-01-01

    Reports of honey bee population decline has spurred many national efforts to understand the extent of the problem and to identify causative or associated factors. However, our collective understanding of the factors has been hampered by a lack of joined up trans-national effort. Moreover, the impacts of beekeeper knowledge and beekeeping management practices have often been overlooked, despite honey bees being a managed pollinator. Here, we established a standardised active monitoring network for 5 798 apiaries over two consecutive years to quantify honey bee colony mortality across 17 European countries. Our data demonstrate that overwinter losses ranged between 2% and 32%, and that high summer losses were likely to follow high winter losses. Multivariate Poisson regression models revealed that hobbyist beekeepers with small apiaries and little experience in beekeeping had double the winter mortality rate when compared to professional beekeepers. Furthermore, honey bees kept by professional beekeepers never showed signs of disease, unlike apiaries from hobbyist beekeepers that had symptoms of bacterial infection and heavy Varroa infestation. Our data highlight beekeeper background and apicultural practices as major drivers of honey bee colony losses. The benefits of conducting trans-national monitoring schemes and improving beekeeper training are discussed.

  3. A pan-European epidemiological study reveals honey bee colony survival depends on beekeeper education and disease control.

    Directory of Open Access Journals (Sweden)

    Antoine Jacques

    Full Text Available Reports of honey bee population decline has spurred many national efforts to understand the extent of the problem and to identify causative or associated factors. However, our collective understanding of the factors has been hampered by a lack of joined up trans-national effort. Moreover, the impacts of beekeeper knowledge and beekeeping management practices have often been overlooked, despite honey bees being a managed pollinator. Here, we established a standardised active monitoring network for 5 798 apiaries over two consecutive years to quantify honey bee colony mortality across 17 European countries. Our data demonstrate that overwinter losses ranged between 2% and 32%, and that high summer losses were likely to follow high winter losses. Multivariate Poisson regression models revealed that hobbyist beekeepers with small apiaries and little experience in beekeeping had double the winter mortality rate when compared to professional beekeepers. Furthermore, honey bees kept by professional beekeepers never showed signs of disease, unlike apiaries from hobbyist beekeepers that had symptoms of bacterial infection and heavy Varroa infestation. Our data highlight beekeeper background and apicultural practices as major drivers of honey bee colony losses. The benefits of conducting trans-national monitoring schemes and improving beekeeper training are discussed.

  4. Analyses in zebrafish embryos reveal that nanotoxicity profiles are dependent on surface-functionalization controlled penetrance of biological membranes.

    Science.gov (United States)

    Paatero, Ilkka; Casals, Eudald; Niemi, Rasmus; Özliseli, Ezgi; Rosenholm, Jessica M; Sahlgren, Cecilia

    2017-08-21

    Mesoporous silica nanoparticles (MSNs) are extensively explored as drug delivery systems, but in depth understanding of design-toxicity relationships is still scarce. We used zebrafish (Danio rerio) embryos to study toxicity profiles of differently surface functionalized MSNs. Embryos with the chorion membrane intact, or dechoroniated embryos, were incubated or microinjected with amino (NH 2 -MSNs), polyethyleneimine (PEI-MSNs), succinic acid (SUCC-MSNs) or polyethyleneglycol (PEG-MSNs) functionalized MSNs. Toxicity was assessed by viability and cardiovascular function. NH 2 -MSNs, SUCC-MSNs and PEG-MSNs were well tolerated, 50 µg/ml PEI-MSNs induced 100% lethality 48 hours post fertilization (hpf). Dechoroniated embryos were more sensitive and 10 µg/ml PEI-MSNs reduced viability to 5% at 96hpf. Sensitivity to PEG- and SUCC-, but not NH 2 -MSNs, was also enhanced. Typically cardiovascular toxicity was evident prior to lethality. Confocal microscopy revealed that PEI-MSNs penetrated into the embryos whereas PEG-, NH2- and SUCC-MSNs remained aggregated on the skin surface. Direct exposure of inner organs by microinjecting NH 2 -MSNs and PEI-MSNs demonstrated that the particles displayed similar toxicity indicating that functionalization affects the toxicity profile by influencing penetrance through biological barriers. The data emphasize the need for careful analyses of toxicity mechanisms in relevant models and constitute an important knowledge step towards the development of safer and sustainable nanotherapies.

  5. Structural Basis for Flip-Flop Action of Thiamin Pyrophosphate-Dependent Enzymes Revealed by Human Pyruvate Dehydrogenase

    Science.gov (United States)

    Dominiak, Paulina; Ciszak, Ewa M.; Korotchkina, Lioubov; Sidhu, Sukhdeep; Patel, Mulchand

    2003-01-01

    Thiamin pyrophosphate (TPP), the biologically active form of vitamin BI, is a cofactor of enzymes catalyzing reactions involving the cleavage of a carbon-carbon bond adjacent to an oxo group. TPP-dependent enzymes show a common mechanism of TPP activation by: (1) forming the ionic N-H...O(sup -) hydrogen bonding between the N1' atom of the aminopirymidine ring of the coenzyme and intrinsic gamma-carboxylate group of glutamate and (2) imposing an "active" V-conformation that brings the N4' atom of the aminopirymidine to the distance required for the intramolecular C-H.. .N hydrogen bonding with the thiazolium C2 atom. Within these two hydrogen bonds that rapidly exchange protons, protonation of the N1' atom is strictly coordinated with the deprotonation of the 4' -amino group and eventually abstraction of the proton from C2. The human pyruvate dehydrogenase Elp, component of human pyruvate dehydrogenase complex, catalyzes the irreversible decarboxylation of the pyruvate followed by the reductive acetylation of the lipoyl group of dihydrolipoyl acyltransferase. Elp is alpha(sub 2)beta(sub2)-heterotetrameric with a molecular mass of I54 kDa, which has two catalytic sites, each providing TPP and magnesium ion as cofactors and each formed on the interface between the PP and PYR domains. The dynamic nonequivalence of two otherwise chemically equivalent catalytic sites has been observed and the flip-flop mechanism was suggested, according to which two active sites affect each other and in which different steps of the catalytic reaction are performed in each of the sites at any given moment. Based on specific futures of human pyruvate dehydrogenase including rigid and flexible connections between domains that bind the cofactor we propose a mechanistic model for the flip-flop action of this enzyme. We postulate that the dynamic protein environment drives the exchange of tautomers in the 4' -aminopyrimidine ring of the cofactor through a concerted shuttl-like motion of

  6. Meta-Analysis Reveals Significant Association of the 3'-UTR VNTR in SLC6A3 with Alcohol Dependence.

    Science.gov (United States)

    Ma, Yunlong; Fan, Rongli; Li, Ming D

    2016-07-01

    Although many studies have analyzed the association of 3'-untranslated region variable-number tandem repeat (VNTR) polymorphism in SLC6A3 with alcohol dependence (AD), the results remain controversial. This study aimed to determine whether this variant indeed has any genetic effect on AD by integrating 17 reported studies with 5,929 participants included. The A9-dominant genetic model that considers A9-repeat and non-A9 repeat as 2 genotypes and compared their frequencies in alcoholics with that in controls was adopted. Considering the potential influence of ethnicity, differences in diagnostic criteria of AD, and alcoholic subgroups, stratified meta-analyses were conducted. There existed no evidence for the presence of heterogeneity among the studied samples, indicating the results under the fixed-effects model are acceptable. We found a significant association of VNTR A9 genotypes with AD in all ethnic populations (pooled odds ratio [OR] 1.12; 95% confidence interval [CI] 1.00, 1.25; p = 0.045) and the Caucasian population (pooled OR 1.15; 95% CI 1.01, 1.31; p = 0.036). We also found VNTR A9 genotypes to be significantly associated with alcoholism as defined by the DSM-IV criteria (pooled OR 1.18; 95% CI 1.03, 1.36; p = 0.02). Further, we found a significant association between VNTR A9 genotypes and alcoholism associated with alcohol withdrawal seizure or delirium tremens (pooled OR 1.55; 95% CI 1.24, 1.92; p = 1.0 × 10(-4) ). In all these meta-analyses, no evidence of publication bias was detected. We concluded that the VNTR polymorphism has an important role in the etiology of AD, and individuals with at least 1 A9 allele are more likely to be dependent on alcohol than persons carrying the non-A9 allele. Copyright © 2016 by the Research Society on Alcoholism.

  7. Cygnus X-1: Discovery of variable circular polarization

    International Nuclear Information System (INIS)

    Michalsky, J.J.; Swedlund, J.B.; Stokes, R.A.

    1975-01-01

    HDE 226868, the optical counterpart of Cyg X-1, has been observed for circular polarization during 1974. Observations in five colors suggest that circular polarization results from an interstellar effect. Measurements of the blue polarization reveal circular polarization variations synchronous with the 5)./sub /6 orbital period. The circular polarization variation appears to be similar to the blue intensity variation

  8. Conformational dynamics of L-lysine, L-arginine, L-ornithine binding protein reveals ligand-dependent plasticity.

    Science.gov (United States)

    Silva, Daniel-Adriano; Domínguez-Ramírez, Lenin; Rojo-Domínguez, Arturo; Sosa-Peinado, Alejandro

    2011-07-01

    The molecular basis of multiple ligand binding affinity for amino acids in periplasmic binding proteins (PBPs) and in the homologous domain for class C G-protein coupled receptors is an unsolved question. Here, using unrestrained molecular dynamic simulations, we studied the ligand binding mechanism present in the L-lysine, L-arginine, L-ornithine binding protein. We developed an analysis based on dihedral angles for the description of the conformational changes upon ligand binding. This analysis has an excellent correlation with each of the two main movements described by principal component analysis (PCA) and it's more convenient than RMSD measurements to describe the differences in the conformational ensembles observed. Furthermore, an analysis of hydrogen bonds showed specific interactions for each ligand studied as well as the ligand interaction with the aromatic residues Tyr-14 and Phe-52. Using uncharged histidine tautomers, these interactions are not observed. On the basis of these results, we propose a model in which hydrogen bond interactions place the ligand in the correct orientation to induce a cation-π interaction with Tyr-14 and Phe-52 thereby stabilizing the closed state. Our results also show that this protein adopts slightly different closed conformations to make available specific hydrogen bond interactions for each ligand thus, allowing a single mechanism to attain multiple ligand specificity. These results shed light on the experimental evidence for ligand-dependent conformational plasticity not explained by the previous crystallographic data. Copyright © 2011 Wiley-Liss, Inc.

  9. Structural Basis for Flip-Flop Action of Thiamin-Dependent Enzymes Revealed by Crystal Structure of Human Pyruvate Dehydrogenase

    Science.gov (United States)

    Ciszak, Ewa; Korotchkina, Lioubov G.; Dominiak, Paulina M.; Sidhu, Sukdeep; Patel, Mulchand S.

    2003-01-01

    The biologically active derivative of vitamin B1; thiamin pyrophosphate; is used as cofactor by many enzymes that perform a wide range of catalytic functions in the pathways of energy production. In alpha2beta2-heterotetrameric human pyruvate dehydrogenase, the first catalytic component enzyme of human pyruvate dehydrogenase complex, this cofactor is used to cleave the C(sup alpha)-C(=0) bond of pyruvate followed by reductive acetyl transfer to lipoyl-dihydrolipoamide acetyltransferase, the second catalytic component of the complex. The dynamic nonequivalence of two, otherwise chemically equivalent, catalytic sites have puzzled researchers from earlier functional studies of this enzyme. In order to gain insight into the mechanism of action of this enzyme, we determined the crystal structure of the holoform of human pyruvate dehydrogenase at 1.958, resolution. We propose a kinetic model for the flip-flop action of this enzyme through the concerted approx. 2A, shuttle-like motion of the heterodimers. The similarity of thiamin pyrophosphate binding in human pyruvate dehydrogenase and other functionally related enzymes suggests this newly defined mechanism of shuttle-like motion of domains to be common for the family of thiamin pyrophosphate-dependent enzymes.

  10. Analysis of hydroxycinnamic acid degradation in Agrobacterium fabrum reveals a coenzyme A-dependent, beta-oxidative deacetylation pathway.

    Science.gov (United States)

    Campillo, Tony; Renoud, Sébastien; Kerzaon, Isabelle; Vial, Ludovic; Baude, Jessica; Gaillard, Vincent; Bellvert, Floriant; Chamignon, Cécile; Comte, Gilles; Nesme, Xavier; Lavire, Céline; Hommais, Florence

    2014-06-01

    The soil- and rhizosphere-inhabiting bacterium Agrobacterium fabrum (genomospecies G8 of the Agrobacterium tumefaciens species complex) is known to have species-specific genes involved in ferulic acid degradation. Here, we characterized, by genetic and analytical means, intermediates of degradation as feruloyl coenzyme A (feruloyl-CoA), 4-hydroxy-3-methoxyphenyl-β-hydroxypropionyl-CoA, 4-hydroxy-3-methoxyphenyl-β-ketopropionyl-CoA, vanillic acid, and protocatechuic acid. The genes atu1416, atu1417, and atu1420 have been experimentally shown to be necessary for the degradation of ferulic acid. Moreover, the genes atu1415 and atu1421 have been experimentally demonstrated to be essential for this degradation and are proposed to encode a phenylhydroxypropionyl-CoA dehydrogenase and a 4-hydroxy-3-methoxyphenyl-β-ketopropionic acid (HMPKP)-CoA β-keto-thiolase, respectively. We thus demonstrated that the A. fabrum hydroxycinnamic degradation pathway is an original coenzyme A-dependent β-oxidative deacetylation that could also transform p-coumaric and caffeic acids. Finally, we showed that this pathway enables the metabolism of toxic compounds from plants and their use for growth, likely providing the species an ecological advantage in hydroxycinnamic-rich environments, such as plant roots or decaying plant materials.

  11. Pathogenesis of POLR1C-dependent Type 3 Treacher Collins Syndrome revealed by a zebrafish model.

    Science.gov (United States)

    Lau, Marco Chi Chung; Kwong, Ernest Man Lok; Lai, Keng Po; Li, Jing-Woei; Ho, Jeff Cheuk Hin; Chan, Ting-Fung; Wong, Chris Kong Chu; Jiang, Yun-Jin; Tse, William Ka Fai

    2016-06-01

    Treacher Collins Syndrome (TCS) is a rare congenital birth disorder (1 in 50,000 live births) characterized by severe craniofacial defects, including the downward slanting palpebral fissures, hypoplasia of the facial bones, and cleft palate (CP). Over 90% of patients with TCS have a mutation in the TCOF1 gene. However, some patients exhibit mutations in two new causative genes, POLR1C and POLR1D, which encode subunits of RNA polymerases I and III, that affect ribosome biogenesis. In this study, we examine the role of POLR1C in TCS using zebrafish as a model system. Our data confirmed that polr1c is highly expressed in the facial region, and dysfunction of this gene by knockdown or knock-out resulted in mis-expression of neural crest cells during early development that leads to TCS phenotype. Next generation sequencing and bioinformatics analysis of the polr1c mutants further demonstrated the up-regulated p53 pathway and predicted skeletal disorders. Lastly, we partially rescued the TCS facial phenotype in the background of p53 mutants, which supported the hypothesis that POLR1C-dependent type 3 TCS is associated with the p53 pathway. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. Dissection of TALE-dependent gene activation reveals that they induce transcription cooperatively and in both orientations

    Science.gov (United States)

    Streubel, Jana; Baum, Heidi; Grau, Jan; Stuttman, Johannes; Boch, Jens

    2017-01-01

    Plant-pathogenic Xanthomonas bacteria inject transcription activator-like effector proteins (TALEs) into host cells to specifically induce transcription of plant genes and enhance susceptibility. Although the DNA-binding mode is well-understood it is still ambiguous how TALEs initiate transcription and whether additional promoter elements are needed to support this. To systematically dissect prerequisites for transcriptional initiation the activity of one TALE was compared on different synthetic Bs4 promoter fragments. In addition, a large collection of artificial TALEs spanning the OsSWEET14 promoter was compared. We show that the presence of a TALE alone is not sufficient to initiate transcription suggesting the requirement of additional supporting promoter elements. At the OsSWEET14 promoter TALEs can initiate transcription from various positions, in a synergistic manner of multiple TALEs binding in parallel to the promoter, and even by binding in reverse orientation. TALEs are known to shift the transcriptional start site, but our data show that this shift depends on the individual position of a TALE within a promoter context. Our results implicate that TALEs function like classical enhancer-binding proteins and initiate transcription in both orientations which has consequences for in planta target gene prediction and design of artificial activators. PMID:28301511

  13. Small angle neutron scattering reveals pH-dependent conformational changes in Trichoderma reesei cellobiohydrolase I: implications for enzymatic activity.

    Science.gov (United States)

    Pingali, Sai Venkatesh; O'Neill, Hugh M; McGaughey, Joseph; Urban, Volker S; Rempe, Caroline S; Petridis, Loukas; Smith, Jeremy C; Evans, Barbara R; Heller, William T

    2011-09-16

    Cellobiohydrolase I (Cel7A) of the fungus Trichoderma reesei (now classified as an anamorph of Hypocrea jecorina) hydrolyzes crystalline cellulose to soluble sugars, making it of key interest for producing fermentable sugars from biomass for biofuel production. The activity of the enzyme is pH-dependent, with its highest activity occurring at pH 4-5. To probe the response of the solution structure of Cel7A to changes in pH, we measured small angle neutron scattering of it in a series of solutions having pH values of 7.0, 6.0, 5.3, and 4.2. As the pH decreases from 7.0 to 5.3, the enzyme structure remains well defined, possessing a spatial differentiation between the cellulose binding domain and the catalytic core that only changes subtly. At pH 4.2, the solution conformation of the enzyme changes to a structure that is intermediate between a properly folded enzyme and a denatured, unfolded state, yet the secondary structure of the enzyme is essentially unaltered. The results indicate that at the pH of optimal activity, the catalytic core of the enzyme adopts a structure in which the compact packing typical of a fully folded polypeptide chain is disrupted and suggest that the increased range of structures afforded by this disordered state plays an important role in the increased activity of Cel7A through conformational selection.

  14. Individual differences in context-dependent effects reveal common mechanisms underlying the direction aftereffect and direction repulsion.

    Science.gov (United States)

    McGovern, David P; Walsh, Kevin S; Bell, Jason; Newell, Fiona N

    2017-12-01

    Both spatial and temporal context influence our perception of visual stimuli. For instance, both nearby moving stimuli and recently viewed motion can lead to biases in the perceived direction of a moving stimulus. Due to similarities in the spatial tuning properties of these spatial and temporal context-dependent effects, it is often assumed that they share a functional goal in motion processing and arise from common neural mechanisms. However, the psychophysical evidence concerning this assumption is inconsistent. Here we used an individual differences approach to examine the relationship between different effects of contextual modulation on perception. We reasoned that if measures of contextual modulation share a common underlying mechanism, they should exhibit a strong positive correlation across participants. To test this hypothesis, estimates of the direction aftereffect, direction repulsion, the tilt aftereffect and contrast adaptation were obtained from 54 healthy participants. Our results show pronounced interindividual differences in the effect sizes of all four tasks. Furthermore, there was a strong positive correlation between the estimates of the direction aftereffect and direction repulsion. This correlation was also evident in the threshold elevations that accompanied these repulsive biases in perceived direction. While the effects of contrast adaptation did not correlate with any of the other tasks, there was a weak, but non-significant, correlation between the direction and tilt aftereffects. These results provide evidence for common mechanisms underlying the direction aftereffect and direction repulsion. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Single particle tracking of internalized metallic nanoparticles reveals heterogeneous directed motion after clathrin dependent endocytosis in mouse chromaffin cells

    Science.gov (United States)

    Gabriel, Manuela; Moya-Díaz, José; Gallo, Luciana I.; Marengo, Fernando D.; Estrada, Laura C.

    2018-01-01

    Most accepted single particle tracking methods are able to obtain high-resolution trajectories for relatively short periods of time. In this work we apply a straightforward combination of single-particle tracking microscopy and metallic nanoparticles internalization on mouse chromaffin cells to unveil the intracellular trafficking mechanism of metallic-nanoparticle-loaded vesicles (MNP-V) complexes after clathrin dependent endocytosis. We found that directed transport is the major route of MNP-Vs intracellular trafficking after stimulation (92.6% of the trajectories measured). We then studied the MNP-V speed at each point along the trajectory, and found that the application of a second depolarization stimulus during the tracking provokes an increase in the percentage of low-speed trajectory points in parallel with a decrease in the number of high-speed trajectory points. This result suggests that stimulation may facilitate the compartmentalization of internalized MNPs in a more restricted location such as was already demonstrated in neuronal and neuroendocrine cells (Bronfman et al 2003 J. Neurosci. 23 3209-20). Although further experiments will be required to address the mechanisms underlying this transport dynamics, our studies provide quantitative evidence of the heterogeneous behavior of vesicles mobility after endocytosis in chromaffin cells highlighting the potential of MNPs as alternative labels in optical microscopy to provide new insights into the vesicles dynamics in a wide variety of cellular environments.

  16. Cell-Type-Specific Circuit Connectivity of Hippocampal CA1 Revealed through Cre-Dependent Rabies Tracing

    Directory of Open Access Journals (Sweden)

    Yanjun Sun

    2014-04-01

    Full Text Available We developed and applied a Cre-dependent, genetically modified rabies-based tracing system to map direct synaptic connections to specific CA1 neuron types in the mouse hippocampus. We found common inputs to excitatory and inhibitory CA1 neurons from CA3, CA2, the entorhinal cortex (EC, the medial septum (MS, and, unexpectedly, the subiculum. Excitatory CA1 neurons receive inputs from both cholinergic and GABAergic MS neurons, whereas inhibitory neurons receive a great majority of inputs from GABAergic MS neurons. Both cell types also receive weaker input from glutamatergic MS neurons. Comparisons of inputs to CA1 PV+ interneurons versus SOM+ interneurons showed similar strengths of input from the subiculum, but PV+ interneurons received much stronger input than SOM+ neurons from CA3, the EC, and the MS. Thus, rabies tracing identifies hippocampal circuit connections and maps how the different input sources to CA1 are distributed with different strengths on each of its constituent cell types.

  17. Polarization of Bremsstrahlung

    International Nuclear Information System (INIS)

    Miller, J.

    1957-01-01

    The numerical results for the polarization of Bremsstrahlung are presented. The multiple scattering of electrons in the target is taken into account. The angular-and photon energy dependences are seen on the curves for an incident 25 MeV electron energy. (Author) [fr

  18. Polar Lipids Analysis of Cultured Phytoplankton Reveals Significant Inter-taxa Changes, Low Influence of Growth Stage, and Usefulness in Chemotaxonomy.

    Science.gov (United States)

    Cañavate, José Pedro; Armada, Isabel; Hachero-Cruzado, Ismael

    2017-05-01

    The high lipid diversity of microalgae has been used to taxonomically differentiate phytoplankton taxa at the class level. However, important lipids such as phospholipids (PL) and betaine lipids (BL) with potential chemotaxonomy application in phytoplankton ecology have been scarcely studied. The chemotaxonomy value of PL and BL depends on their intraspecific extent of variation as microalgae respond to external changing factors. To determine such effects, lipid class changes occurring at different growth stages in 15 microalgae from ten different classes were analyzed. BL occurred in 14 species and were the less affected lipids by growth stage with diacylglyceryl-hydroxymethyl-N,N,N-trimethyl-b-alanine (DGTA) showing the highest stability. PL were more influenced by growth stage with phosphatidylcholine (PC), phosphatidylglycerol (PG), and phosphatidyletanolamine (PE) declining towards older culture stages in some species. Glycolipids were the more common lipids, and no evident age-related variability pattern could be associated to taxonomic diversity. Selecting BL and PL as descriptor variables optimally distinguished microalgae taxonomic variability at all growth stages. Principal coordinate analysis arranged species through a main tendency from diacylglyceryl-hydroxymethyl-N,N,N-trimethyl-b-alanine (DGCC) containing species (mainly dinoflagellates and haptophytes) to DGTA or PC containing species (mainly cryptophytes). Two diatom classes with similar fatty acid profiles could be distinguished from their respective content in DGTA (Bacillariophyceae) or DGCC (Mediophyceae). In green lineage classes (Trebouxiophyceae, Porphyridophyceae, and Chlorodendrophyceae), PC was a better descriptor than BL. BL and PL explained a higher proportion of microalgae taxonomic variation than did fatty acids and played a complementary role as lipid markers.

  19. Comparative genomic analysis reveals species-dependent complexities that explain difficulties with microsatellite marker development in molluscs.

    Science.gov (United States)

    McInerney, C E; Allcock, A L; Johnson, M P; Bailie, D A; Prodöhl, P A

    2011-01-01

    Reliable population DNA molecular markers are difficult to develop for molluscs, the reasons for which are largely unknown. Identical protocols for microsatellite marker development were implemented in three gastropods. Success rates were lower for Gibbula cineraria compared to Littorina littorea and L. saxatilis. Comparative genomic analysis of 47.2 kb of microsatellite containing sequences (MCS) revealed a high incidence of cryptic repetitive DNA in their flanking regions. The majority of these were novel, and could be grouped into DNA families based upon sequence similarities. Significant inter-specific variation in abundance of cryptic repetitive DNA and DNA families was observed. Repbase scans show that a large proportion of cryptic repetitive DNA was identified as transposable elements (TEs). We argue that a large number of TEs and their transpositional activity may be linked to differential rates of DNA multiplication and recombination. This is likely to be an important factor explaining inter-specific variation in genome stability and hence microsatellite marker development success rates. Gastropods also differed significantly in the type of TEs classes (autonomous vs non-autonomous) observed. We propose that dissimilar transpositional mechanisms differentiate the TE classes in terms of their propensity for transposition, fixation and/or silencing. Consequently, the phylogenetic conservation of non-autonomous TEs, such as CvA, suggests that dispersal of these elements may have behaved as microsatellite-inducing elements. Results seem to indicate that, compared to autonomous, non-autonomous TEs maybe have a more active role in genome rearrangement processes. The implications of the findings for genomic rearrangement, stability and marker development are discussed.

  20. Polarization-dependent X-ray-absorption spectroscopy of $RNi_{2} B_{2}$ C (R=Er $\\to$ Lu) Reduced Ni-3d occupancy in $YbNi_{2} B_{2} C$

    CERN Document Server

    Mazumdar, C; Von Lips, H; Golden, M S; Fink, J; Canfield, P C; Kaindl, G

    2001-01-01

    We present here the results of polarization-dependent X-ray- absorption near-edge structure (XANES) studies at the B-K, C-K, and Ni-L/sub 3/ thresholds of single-crystalline borocarbide compounds RNi/sub 2/B/sub 2/C (with R=Er to Lu) using bulk-sensitive fluorescence yield technique. The Ni-L/sub 3/ XANES spectrum for YbNi /sub 2/B/sub 2/C with photon polarization parallel to the ab plane is significantly more intense than in analogous spectra of other members of this series. This indicates a reduced Ni-3d occupancy in the Ni /sub 2/B/sub 2/ layer in YbNi/sub 2/B/sub 2/C, a fact that might be responsible for the absence of superconductivity in this material. (26 refs).

  1. Real-time cell toxicity profiling of Tox21 10K compounds reveals cytotoxicity dependent toxicity pathway linkage.

    Directory of Open Access Journals (Sweden)

    Jui-Hua Hsieh

    Full Text Available Cytotoxicity is a commonly used in vitro endpoint for evaluating chemical toxicity. In support of the U.S. Tox21 screening program, the cytotoxicity of ~10K chemicals was interrogated at 0, 8, 16, 24, 32, & 40 hours of exposure in a concentration dependent fashion in two cell lines (HEK293, HepG2 using two multiplexed, real-time assay technologies. One technology measures the metabolic activity of cells (i.e., cell viability, glo while the other evaluates cell membrane integrity (i.e., cell death, flor. Using glo technology, more actives and greater temporal variations were seen in HEK293 cells, while results for the flor technology were more similar across the two cell types. Chemicals were grouped into classes based on their cytotoxicity kinetics profiles and these classes were evaluated for their associations with activity in the Tox21 nuclear receptor and stress response pathway assays. Some pathways, such as the activation of H2AX, were associated with the fast-responding cytotoxicity classes, while others, such as activation of TP53, were associated with the slow-responding cytotoxicity classes. By clustering pathways based on their degree of association to the different cytotoxicity kinetics labels, we identified clusters of pathways where active chemicals presented similar kinetics of cytotoxicity. Such linkages could be due to shared underlying biological processes between pathways, for example, activation of H2AX and heat shock factor. Others involving nuclear receptor activity are likely due to shared chemical structures rather than pathway level interactions. Based on the linkage between androgen receptor antagonism and Nrf2 activity, we surmise that a subclass of androgen receptor antagonists cause cytotoxicity via oxidative stress that is associated with Nrf2 activation. In summary, the real-time cytotoxicity screen provides informative chemical cytotoxicity kinetics data related to their cytotoxicity mechanisms, and with our

  2. Insertional mutagenesis and deep profiling reveals gene hierarchies and a Myc/p53-dependent bottleneck in lymphomagenesis.

    Directory of Open Access Journals (Sweden)

    Camille A Huser

    2014-02-01

    Full Text Available Retroviral insertional mutagenesis (RIM is a powerful tool for cancer genomics that was combined in this study with deep sequencing (RIM/DS to facilitate a comprehensive analysis of lymphoma progression. Transgenic mice expressing two potent collaborating oncogenes in the germ line (CD2-MYC, -Runx2 develop rapid onset tumours that can be accelerated and rendered polyclonal by neonatal Moloney murine leukaemia virus (MoMLV infection. RIM/DS analysis of 28 polyclonal lymphomas identified 771 common insertion sites (CISs defining a 'progression network' that encompassed a remarkably large fraction of known MoMLV target genes, with further strong indications of oncogenic selection above the background of MoMLV integration preference. Progression driven by RIM was characterised as a Darwinian process of clonal competition engaging proliferation control networks downstream of cytokine and T-cell receptor signalling. Enhancer mode activation accounted for the most efficiently selected CIS target genes, including Ccr7 as the most prominent of a set of chemokine receptors driving paracrine growth stimulation and lymphoma dissemination. Another large target gene subset including candidate tumour suppressors was disrupted by intragenic insertions. A second RIM/DS screen comparing lymphomas of wild-type and parental transgenics showed that CD2-MYC tumours are virtually dependent on activation of Runx family genes in strong preference to other potent Myc collaborating genes (Gfi1, Notch1. Ikzf1 was identified as a novel collaborating gene for Runx2 and illustrated the interface between integration preference and oncogenic selection. Lymphoma target genes for MoMLV can be classified into (a a small set of master regulators that confer self-renewal; overcoming p53 and other failsafe pathways and (b a large group of progression genes that control autonomous proliferation in transformed cells. These findings provide insights into retroviral biology, human cancer

  3. Transcriptomic Analysis Of Purified Embryonic Neural Stem Cells From Zebrafish Embryos Reveals Signalling Pathways Involved In Glycine-dependent Neurogenesis

    Directory of Open Access Journals (Sweden)

    Eric eSAMARUT

    2016-03-01

    Full Text Available How is the initial set of neurons correctly established during the development of the vertebrate central nervous system? In the embryo, glycine and GABA are depolarizing due the immature chloride gradient, which is only reversed to become hyperpolarizing later in post-natal development. We previously showed that glycine regulates neurogenesis via paracrine signalling that promotes calcium transients in neural stem cells (NSCs and their differentiation into interneurons within the spinal cord of the zebrafish embryo. However, the subjacent molecular mechanisms are not yet understood. Our previous work suggests that early neuronal progenitors were not differentiating correctly in the developing spinal cord. As a result, we aimed at identifying the downstream molecular mechanisms involved specifically in NSCs during glycine-dependent embryonic neurogenesis. Using a gfap:GFP transgenic line, we successfully purified NSCs by fluorescence-activated cell sorting (FACS from whole zebrafish embryos and in embryos in which the glycine receptor was knocked down. The strength of this approach is that it focused on the NSC population while tackling the biological issue in an in vivo context in whole zebrafish embryos. After sequencing the transcriptome by RNA-sequencing, we analyzed the genes whose expression was changed upon disruption of glycine signalling and we confirmed the differential expression by independent RTqPCR assay. While over a thousand genes showed altered expression levels, through pathway analysis we identified 14 top candidate genes belonging to five different canonical signalling pathways (signalling by calcium, TGF-beta, sonic hedgehog, Wnt and p53-related apoptosis that are likely to mediate the promotion of neurogenesis by glycine.

  4. Evf2 lncRNA/BRG1/DLX1 interactions reveal RNA-dependent inhibition of chromatin remodeling.

    Science.gov (United States)

    Cajigas, Ivelisse; Leib, David E; Cochrane, Jesse; Luo, Hao; Swyter, Kelsey R; Chen, Sean; Clark, Brian S; Thompson, James; Yates, John R; Kingston, Robert E; Kohtz, Jhumku D

    2015-08-01

    Transcription-regulating long non-coding RNAs (lncRNAs) have the potential to control the site-specific expression of thousands of target genes. Previously, we showed that Evf2, the first described ultraconserved lncRNA, increases the association of transcriptional activators (DLX homeodomain proteins) with key DNA enhancers but represses gene expression. In this report, mass spectrometry shows that the Evf2-DLX1 ribonucleoprotein (RNP) contains the SWI/SNF-related chromatin remodelers Brahma-related gene 1 (BRG1, SMARCA4) and Brahma-associated factor (BAF170, SMARCC2) in the developing mouse forebrain. Evf2 RNA colocalizes with BRG1 in nuclear clouds and increases BRG1 association with key DNA regulatory enhancers in the developing forebrain. While BRG1 directly interacts with DLX1 and Evf2 through distinct binding sites, Evf2 directly inhibits BRG1 ATPase and chromatin remodeling activities. In vitro studies show that both RNA-BRG1 binding and RNA inhibition of BRG1 ATPase/remodeling activity are promiscuous, suggesting that context is a crucial factor in RNA-dependent chromatin remodeling inhibition. Together, these experiments support a model in which RNAs convert an active enhancer to a repressed enhancer by directly inhibiting chromatin remodeling activity, and address the apparent paradox of RNA-mediated stabilization of transcriptional activators at enhancers with a repressive outcome. The importance of BRG1/RNA and BRG1/homeodomain interactions in neurodevelopmental disorders is underscored by the finding that mutations in Coffin-Siris syndrome, a human intellectual disability disorder, localize to the BRG1 RNA-binding and DLX1-binding domains. © 2015. Published by The Company of Biologists Ltd.

  5. Whole transcriptome analysis reveals differential gene expression profile reflecting macrophage polarization in response to influenza A H5N1 virus infection.

    Science.gov (United States)

    Zhang, Na; Bao, Yun-Juan; Tong, Amy Hin-Yan; Zuyderduyn, Scott; Bader, Gary D; Malik Peiris, J S; Lok, Si; Lee, Suki Man-Yan

    2018-02-23

    Avian influenza A H5N1 virus can cause lethal disease in humans. The virus can trigger severe pneumonia and lead to acute respiratory distress syndrome. Data from clinical, in vitro and in vivo suggest that virus-induced cytokine dysregulation could be a contributory factor to the pathogenesis of human H5N1 disease. However, the precise mechanism of H5N1 infection eliciting the unique host response are still not well understood. To obtain a better understanding of the molecular events at the earliest time points, we used RNA-Seq to quantify and compare the host mRNA and miRNA transcriptomes induced by the highly pathogenic influenza A H5N1 (A/Vietnam/3212/04) or low virulent H1N1 (A/Hong Kong/54/98) viruses in human monocyte-derived macrophages at 1-, 3-, and 6-h post infection. Our data reveals that two macrophage populations corresponding to M1 (classically activated) and M2 (alternatively activated) macrophage subtypes respond distinctly to H5N1 virus infection when compared to H1N1 virus or mock infection, a distinction that could not be made from previous microarray studies. When this confounding variable is considered in our statistical model, a clear set of dysregulated genes and pathways emerges specifically in H5N1 virus-infected macrophages at 6-h post infection, whilst was not found with H1N1 virus infection. Furthermore, altered expression of genes in these pathways, which have been previously implicated in viral host response, occurs specifically in the M1 subtype. We observe a significant up-regulation of genes in the RIG-I-like receptor signaling pathway. In particular, interferons, and interferon-stimulated genes are broadly affected. The negative regulators of interferon signaling, the suppressors of cytokine signaling, SOCS-1 and SOCS-3, were found to be markedly up-regulated in the initial round of H5N1 virus replication. Elevated levels of these suppressors could lead to the eventual suppression of cellular antiviral genes, contributing to

  6. Genetically encoded pH-indicators reveal activity-dependent cytosolic acidification of Drosophila motor nerve termini in vivo

    Science.gov (United States)

    Rossano, Adam J; Chouhan, Amit K; Macleod, Gregory T

    2013-01-01

    All biochemical processes, including those underlying synaptic function and plasticity, are pH sensitive. Cytosolic pH (pHcyto) shifts are known to accompany nerve activity in situ, but technological limitations have prevented characterization of such shifts in vivo. Genetically encoded pH-indicators (GEpHIs) allow for tissue-specific in vivo measurement of pH. We expressed three different GEpHIs in the cytosol of Drosophila larval motor neurons and observed substantial presynaptic acidification in nerve termini during nerve stimulation in situ. SuperEcliptic pHluorin was the most useful GEpHI for studying pHcyto shifts in this model system. We determined the resting pH of the nerve terminal cytosol to be 7.30 ± 0.02, and observed a decrease of 0.16 ± 0.01 pH units when the axon was stimulated at 40 Hz for 4 s. Realkalinization occurred upon cessation of stimulation with a time course of 20.54 ± 1.05 s (τ). The chemical pH-indicator 2′,7′-bis-(2-carboxyethyl)-5-(and-6)-carboxyfluorescein corroborated these changes in pHcyto. Bicarbonate-derived buffering did not contribute to buffering of acid loads from short (≤4 s) trains of action potentials but did buffer slow (∼60 s) acid loads. The magnitude of cytosolic acid transients correlated with cytosolic Ca2+ increase upon stimulation, and partial inhibition of the plasma membrane Ca2+-ATPase, a Ca2+/H+ exchanger, attenuated pHcyto shifts. Repeated stimulus trains mimicking motor patterns generated greater cytosolic acidification (∼0.30 pH units). Imaging through the cuticle of intact larvae revealed spontaneous pHcyto shifts in presynaptic termini in vivo, similar to those seen in situ during fictive locomotion, indicating that presynaptic pHcyto shifts cannot be dismissed as artifacts of ex vivo preparations. PMID:23401611

  7. Quantitative DNA methylation analyses reveal stage dependent DNA methylation and association to clinico-pathological factors in breast tumors

    International Nuclear Information System (INIS)

    Klajic, Jovana; Tost, Jörg; Kristensen, Vessela N; Fleischer, Thomas; Dejeux, Emelyne; Edvardsen, Hege; Warnberg, Fredrik; Bukholm, Ida; Lønning, Per Eystein; Solvang, Hiroko; Børresen-Dale, Anne-Lise

    2013-01-01

    Aberrant DNA methylation of regulatory genes has frequently been found in human breast cancers and correlated to clinical outcome. In the present study we investigate stage specific changes in the DNA methylation patterns in order to identify valuable markers to understand how these changes affect breast cancer progression. Quantitative DNA methylation analyses of 12 candidate genes ABCB1, BRCCA1, CDKN2A, ESR1, GSTP1, IGF2, MGMT, HMLH1, PPP2R2B, PTEN, RASSF1A and FOXC1 was performed by pyrosequencing a series of 238 breast cancer tissue samples from DCIS to invasive tumors stage I to IV. Significant differences in methylation levels between the DCIS and invasive stage II tumors were observed for six genes RASSF1A, CDKN2A, MGMT, ABCB1, GSTP1 and FOXC1. RASSF1A, ABCB1 and GSTP1 showed significantly higher methylation levels in late stage compared to the early stage breast carcinoma. Z-score analysis revealed significantly lower methylation levels in DCIS and stage I tumors compared with stage II, III and IV tumors. Methylation levels of PTEN, PPP2R2B, FOXC1, ABCB1 and BRCA1 were lower in tumors harboring TP53 mutations then in tumors with wild type TP53. Z-score analysis showed that TP53 mutated tumors had significantly lower overall methylation levels compared to tumors with wild type TP53. Methylation levels of RASSF1A, PPP2R2B, GSTP1 and FOXC1 were higher in ER positive vs. ER negative tumors and methylation levels of PTEN and CDKN2A were higher in HER2 positive vs. HER2 negative tumors. Z-score analysis also showed that HER2 positive tumors had significantly higher z-scores of methylation compared to the HER2 negative tumors. Univariate survival analysis identifies methylation status of PPP2R2B as significant predictor of overall survival and breast cancer specific survival. In the present study we report that the level of aberrant DNA methylation is higher in late stage compared with early stage of invasive breast cancers and DCIS for genes mentioned above

  8. Novel and unexpected bacterial diversity in an arsenic-rich ecosystem revealed by culture-dependent approaches

    Directory of Open Access Journals (Sweden)

    Delavat François

    2012-09-01

    . The isolated bacteria may be part of the rare biosphere which remained previously undetected due to molecular biases. No matter their current ecological relevance, the exploration of the full diversity remains crucial to decipher the function and dynamic of any community. This work also underlines the importance to associate culture-dependent and -independent approaches to gain an integrative view of the community function. Reviewers This paper was reviewed by Sándor Pongor, Eugene V. Koonin and Brett Baker (nominated by Purificacion Lopez-Garcia.

  9. Computer modeling reveals that modifications of the histone tail charges define salt-dependent interaction of the nucleosome core particles.

    Science.gov (United States)

    Yang, Ye; Lyubartsev, Alexander P; Korolev, Nikolay; Nordenskiöld, Lars

    2009-03-18

    Coarse-grained Langevin molecular dynamics computer simulations were conducted for systems that mimic solutions of nucleosome core particles (NCPs). The NCP was modeled as a negatively charged spherical particle representing the complex of DNA and the globular part of the histones combined with attached strings of connected charged beads modeling the histone tails. The size, charge, and distribution of the tails relative to the core were built to match real NCPs. Three models of NCPs were constructed to represent different extents of covalent modification on the histone tails: (nonmodified) recombinant (rNCP), acetylated (aNCP), and acetylated and phosphorylated (paNCP). The simulation cell contained 10 NCPs in a dielectric continuum with explicit mobile counterions and added salt. The NCP-NCP interaction is decisively dependent on the modification state of the histone tails and on salt conditions. Increasing the monovalent salt concentration (KCl) from salt-free to physiological concentration leads to NCP aggregation in solution for rNCP, whereas NCP associates are observed only occasionally in the system of aNCPs. In the presence of divalent salt (Mg(2+)), rNCPs form dense stable aggregates, whereas aNCPs form aggregates less frequently. Aggregates are formed via histone-tail bridging and accumulation of counterions in the regions of NCP-NCP contacts. The paNCPs do not show NCP-NCP interaction upon addition of KCl or in the presence of Mg(2+). Simulations for systems with a gradual substitution of K(+) for Mg(2+), to mimic the Mg(2+) titration of an NCP solution, were performed. The rNCP system showed stronger aggregation that occurred at lower concentrations of added Mg(2+), compared to the aNCP system. Additional molecular dynamics simulations performed with a single NCP in the simulation cell showed that detachment of the tails from the NCP core was modest under a wide range of salt concentrations. This implies that salt-induced tail dissociation of the

  10. Detection of Pol IV/RDR2-dependent transcripts at the genomic scale in Arabidopsis reveals features and regulation of siRNA biogenesis

    Science.gov (United States)

    Li, Shaofang; Vandivier, Lee E.; Tu, Bin; Gao, Lei; Won, So Youn; Li, Shengben; Zheng, Binglian; Gregory, Brian D.

    2015-01-01

    Twenty-four-nucleotide small interfering (si)RNAs are central players in RNA-directed DNA methylation (RdDM), a process that establishes and maintains DNA methylation at transposable elements to ensure genome stability in plants. The plant-specific RNA polymerase IV (Pol IV) is required for siRNA biogenesis and is believed to transcribe RdDM loci to produce primary transcripts that are converted to double-stranded RNAs (dsRNAs) by RDR2 to serve as siRNA precursors. Yet, no such siRNA precursor transcripts have ever been reported. Here, through genome-wide profiling of RNAs in genotypes that compromise the processing of siRNA precursors, we were able to identify Pol IV/RDR2-dependent transcripts from tens of thousands of loci. We show that Pol IV/RDR2-dependent transcripts correspond to both DNA strands, whereas the RNA polymerase II (Pol II)-dependent transcripts produced upon derepression of the loci are derived primarily from one strand. We also show that Pol IV/RDR2-dependent transcripts have a 5′ monophosphate, lack a poly(A) tail at the 3′ end, and contain no introns; these features distinguish them from Pol II-dependent transcripts. Like Pol II-transcribed genic regions, Pol IV-transcribed regions are flanked by A/T-rich sequences depleted in nucleosomes, which highlights similarities in Pol II- and Pol IV-mediated transcription. Computational analysis of siRNA abundance from various mutants reveals differences in the regulation of siRNA biogenesis at two types of loci that undergo CHH methylation via two different DNA methyltransferases. These findings begin to reveal features of Pol IV/RDR2-mediated transcription at the heart of genome stability in plants. PMID:25414514

  11. Robust reflective ghost imaging against different partially polarized thermal light

    Science.gov (United States)

    Li, Hong-Guo; Wang, Yan; Zhang, Rui-Xue; Zhang, De-Jian; Liu, Hong-Chao; Li, Zong-Guo; Xiong, Jun

    2018-03-01

    We theoretically study the influence of degree of polarization (DOP) of thermal light on the contrast-to-noise ratio (CNR) of the reflective ghost imaging (RGI), which is a novel and indirect imaging modality. An expression for the CNR of RGI with partially polarized thermal light is carefully derived, which suggests a weak dependence of CNR on the DOP, especially when the ratio of the object size to the speckle size of thermal light has a large value. Different from conventional imaging approaches, our work reveals that RGI is much more robust against the DOP of the light source, which thereby has advantages in practical applications, such as remote sensing.

  12. Fractal analysis of polar bear hairs

    Directory of Open Access Journals (Sweden)

    Wang Qing-Li

    2015-01-01

    Full Text Available Hairs of a polar bear (Ursus maritimus are of superior properties such as the excellent thermal protection. Why do polar bears can resist such cold environment? The paper concludes that its fractal porosity plays an important role, and its fractal dimensions are very close to the golden mean, 1.618, revealing the possible optimal structure of polar bear hair.

  13. Fourier transform analysis of rabbit detrusor autonomous contractions reveals length dependent increases in tone and slow wave development at long lengths.

    Science.gov (United States)

    Byrne, Michael D; Klausner, Adam P; Speich, John E; Southern, Jordan B; Habibi, Joseph R; Ratz, Paul H

    2013-07-01

    Bladder wall muscle (detrusor) develops low amplitude rhythmic contractions. Low amplitude rhythmic contraction activity is increased in detrusor from patients with overactive bladder. In this in vitro study we used fast Fourier transforms to assess the length dependence of low amplitude rhythmic contraction components. Rabbit detrusor strips were placed in a muscle bath between 2 clips to adjust length and record isometric tension. Tissues stretched from 70% to 130% of a reference muscle length at 10% increments were allowed to develop low amplitude rhythmic contractions at each length for 20 minutes. Low amplitude rhythmic contraction data were analyzed using fast Fourier transforms and represented by a frequency rather than a time spectrum. Based on fast Fourier transform analysis summarized by signal peaks within specific frequency ranges, rabbit low amplitude rhythmic contraction waveforms were divided into 1 tonic and 2 phasic components, defined as A0 + A1F1 + A2F2, where A0 is a length dependent basal tonic component that increases linearly, A1F1 is a slow wave with a length dependent specific amplitude (A1) and a length independent constant frequency (F1) of approximately 11.2 Hz, and A2F2 is a fast wave with a length dependent amplitude (A2) and frequency (F2) of approximately 0.03 Hz. Fast Fourier transform analysis revealed that rabbit low amplitude rhythmic contractions consist of a basal tonic component plus 2 phasic components. The amplitude of all 3 components was length dependent. The frequency of the fast component was not length dependent and the slow component was absent at short muscle lengths, developing only at muscle lengths beyond that producing a maximum active contraction. Copyright © 2013 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

  14. Polarization properties of below-threshold harmonics from aligned molecules H2+ in linearly polarized laser fields.

    Science.gov (United States)

    Dong, Fulong; Tian, Yiqun; Yu, Shujuan; Wang, Shang; Yang, Shiping; Chen, Yanjun

    2015-07-13

    We investigate the polarization properties of below-threshold harmonics from aligned molecules in linearly polarized laser fields numerically and analytically. We focus on lower-order harmonics (LOHs). Our simulations show that the ellipticity of below-threshold LOHs depends strongly on the orientation angle and differs significantly for different harmonic orders. Our analysis reveals that this LOH ellipticity is closely associated with resonance effects and the axis symmetry of the molecule. These results shed light on the complex generation mechanism of below-threshold harmonics from aligned molecules.

  15. On the nature of IMF polarity dependent asymmetries in solar wind plasma properties during the minimum of sunspot cycles 23 and 24

    Science.gov (United States)

    Pereira, B. Felix; Philip, Bijoy John; Girish, T. E.

    2016-03-01

    The monthly solar wind speed and density observed near 1 AU in IMF sectors of opposite magnetic polarity are studied during the minimum of sunspot cycles 23 and 24. During sunspot minima, the IMF is pointing away from the sun (Away sector) in the north of the Heliospheric Current Sheet (HCS) and pointing towards the sun (Toward sector) in the south of HCS during odd sunspot cycles and the same process is reversed during the even cycles. During this period, the solar wind plasma parameters (number density and speed) show a systematic month to month variation with solar wind number density decreases and velocity increases from equator to poles (heliomagnetic latitudinal organization) only in 'Away' IMF sectors compared to 'Toward' IMF sectors. This feature is particularly more evident for low speed solar wind and happens in a helio-hemisphere with a larger polar coronal hole. The association of the above phenomena with north-south asymmetry in coronal and solar wind flow characteristics will be discussed.

  16. Monitoring the distributed impact wave on a concrete slab due to the traffic based on polarization dependence on stimulated Brillouin scattering

    International Nuclear Information System (INIS)

    Bao Xiaoyi; Zhang Chunshu; Li Wenhai; Eisa, M; El-Gamal, S; Benmokrane, B

    2008-01-01

    For the first time to our knowledge, distributed impact waves due to the highway traffic on concrete slabs reinforced with FRP bars are monitored in real time using stimulated Brillouin scattering. The impact wave is caused by the traffic passing on the highway pavement at high speed (>100 km h −1 ), which induced pressure on the concrete slabs, and in turn created a local birefringence change, leading to variation of the local state of polarization change (SOP). The pump and probe waves of the stimulated Brillouin scattering 'see' the SOP change and react with a decrease of the Brillouin gain or loss signal, when the pump and probe waves have the same input polarization state. The frequency difference between the pump and probe waves are locked at the static-strain-related Brillouin frequency. Optical fiber was embedded throughout the concrete pavement continuously reinforced with FRP bars in Highway 40 East, Montréal, Quebec to detect impact waves caused by cars and trucks passing on these pavements at a sampling rate of 10 kHz. A spatial resolution of 2 m was used over a sensing length of 300 m

  17. The Bochum Polarized Target

    International Nuclear Information System (INIS)

    Reicherz, G.; Goertz, S.; Harmsen, J.; Heckmann, J.; Meier, A.; Meyer, W.; Radtke, E.

    2001-01-01

    The Bochum 'Polarized Target' group develops the target material 6 LiD for the COMPASS experiment at CERN. Several different materials like alcohols, alcanes and ammonia are under investigation. Solid State Targets are polarized in magnetic fields higher than B=2.5T and at temperatures below T=1K. For the Dynamic Nuclear Polarization process, paramagnetic centers are induced chemically or by irradiation with ionizing beams. The radical density is a critical factor for optimization of polarization and relaxation times at adequate magnetic fields and temperatures. In a high sensitive EPR--apparatus, an evaporator and a dilution cryostat with a continuous wave NMR--system, the materials are investigated and optimized. To improve the polarization measurement, the Liverpool NMR-box is modified by exchanging the fixed capacitor for a varicap diode which not only makes the tuning very easy but also provides a continuously tuned circuit. The dependence of the signal area upon the circuit current is measured and it is shown that it follows a linear function

  18. Political polarization

    OpenAIRE

    Dixit, Avinash K.; Weibull, Jörgen W.

    2007-01-01

    Failures of government policies often provoke opposite reactions from citizens; some call for a reversal of the policy, whereas others favor its continuation in stronger form. We offer an explanation of such polarization, based on a natural bimodality of preferences in political and economic contexts and consistent with Bayesian rationality.

  19. Political polarization.

    Science.gov (United States)

    Dixit, Avinash K; Weibull, Jörgen W

    2007-05-01

    Failures of government policies often provoke opposite reactions from citizens; some call for a reversal of the policy, whereas others favor its continuation in stronger form. We offer an explanation of such polarization, based on a natural bimodality of preferences in political and economic contexts and consistent with Bayesian rationality.

  20. Polarization-Directed Surface Plasmon Polariton Launching

    Energy Technology Data Exchange (ETDEWEB)

    Gong, Yu; Joly, Alan G.; El-Khoury, Patrick Z.; Hess, Wayne P.

    2017-01-05

    The relative intensities of propagating surface plasmons (PSPs) simultaneously launched from opposing edges of a symmetric trench structure etched into a silver thin film may be controllably varied by tuning the linear polarization of the driving field. This is demonstrated through transient multiphoton photoemission electron microscopy measurements performed using a pair of spatially separated phase-locked femtosecond pulses. Our measurements are rationalized using finite-difference time domain simulations, which reveal that the coupling efficiency into the PSP modes is inversely proportional to the magnitude of the localized surface plasmon fields excited at the trench edges. Additional experiments on single step edges also show asymmetric PSP launching with respect to polarization, analogous to the trench results. Our combined experimental and computational results allude to the interplay between localized and propagating surface plasmon modes in the trench; strong coupling to the localized modes at the edges correlates to weak coupling to the PSP modes. Simultaneous excitation of the electric fields localized at both edges of the trench results in complex interactions between the right- and left-side PSP modes with Fabry-Perot and cylindrical modes. This results in a trench width-dependent PSP intensity ratio using otherwise identical driving fields. A systematic exploration of polarization directed PSP launching from a series of trench structures reveals an optimal PSP contrast ratio of 4.2 using a 500 nm-wide trench.

  1. Dynamic trapping of a polarization rotation vector soliton in a fiber laser.

    Science.gov (United States)

    Liu, Meng; Luo, Ai-Ping; Luo, Zhi-Chao; Xu, Wen-Cheng

    2017-01-15

    Ultrafast fiber laser, as a dissipative nonlinear optical system, plays an important role in investigating various nonlinear phenomena and soliton dynamics. Vector features of solitons, including polarization locked and polarization rotation vector solitons (PRVSs), are interesting nonlinear dynamics in ultrafast fiber lasers. Herein, we experimentally reveal the trapping characteristics of PRVSs for the first time, to the best of our best knowledge. We show that, for the conventional soliton trapping in the ultrafast fiber laser, the soliton central wavelengths of the two polarization components are constant at the laser output port. However, it is found that the dynamic trapping can be observed for the PRVS. That is, the peak frequencies along the two orthogonal polarization directions are dynamically alternating, depending on the relative intensities of the two polarization components. The obtained results would further unveil the physical mechanism of PRVSs.

  2. Revealing mechanisms of selective, concentration-dependent potentials of 4-hydroxy-2-nonenal to induce apoptosis in cancer cells through inactivation of membrane-associated catalase.

    Science.gov (United States)

    Bauer, Georg; Zarkovic, Neven

    2015-04-01

    Tumor cells generate extracellular superoxide anions and are protected against superoxide anion-mediated intercellular apoptosis-inducing signaling by the expression of membrane-associated catalase. 4-Hydroxy-2-nonenal (4-HNE), a versatile second messenger generated during lipid peroxidation, has been shown to induce apoptosis selectively in malignant cells. The findings described in this paper reveal the strong, concentration-dependent potential of 4-HNE to specifically inactivate extracellular catalase of tumor cells both indirectly and directly and to consequently trigger apoptosis in malignant cells through superoxide anion-mediated intercellular apoptosis-inducing signaling. Namely, 4-HNE caused apoptosis selectively in NOX1-expressing tumor cells through inactivation of their membrane-associated catalase, thus reactivating subsequent intercellular signaling through the NO/peroxynitrite and HOCl pathways, followed by the mitochondrial pathway of apoptosis. Concentrations of 4-HNE of 1.2 µM and higher directly inactivated membrane-associated catalase of tumor cells, whereas at lower concentrations, 4-HNE triggered a complex amplificatory pathway based on initial singlet oxygen formation through H2O2 and peroxynitrite interaction. Singlet-oxygen-dependent activation of the FAS receptor and caspase-8 increased superoxide anion generation by NOX1 and amplification of singlet oxygen generation, which allowed singlet-oxygen-dependent inactivation of catalase. 4-HNE and singlet oxygen cooperate in complex autoamplificatory loops during this process. The finding of these novel anticancer pathways may be useful for understanding the role of 4-HNE in the control of malignant cells and for the optimization of ROS-dependent therapeutic approaches including antioxidant treatments. Copyright © 2015 Elsevier Inc. All rights reserved.

  3. Polarized advanced fuel reactors

    International Nuclear Information System (INIS)

    Kulsrud, R.M.

    1987-07-01

    The d- 3 He reaction has the same spin dependence as the d-t reaction. It produces no neutrons, so that if the d-d reactivity could be reduced, it would lead to a neutron-lean reactor. The current understanding of the possible suppression of the d-d reactivity by spin polarization is discussed. The question as to whether a suppression is possible is still unresolved. Other advanced fuel reactions are briefly discussed. 11 refs

  4. Voltage-dependent conformational changes in human Ca2+- and voltage-activated K+ channel, revealed by voltage-clamp fluorometry

    Science.gov (United States)

    Savalli, Nicoletta; Kondratiev, Andrei; Toro, Ligia; Olcese, Riccardo

    2006-01-01

    Large conductance voltage- and Ca2+-activated K+ (BKCa) channels regulate important physiological processes such as neurotransmitter release and vascular tone. BKCa channels possess a voltage sensor mainly represented by the S4 transmembrane domain. Changes in membrane potential displace the voltage sensor, producing a conformational change that leads to channel opening. By site-directed fluorescent labeling of residues in the S3–S4 region and by using voltage clamp fluorometry, we have resolved the conformational changes the channel undergoes during activation. The voltage dependence of these conformational changes (detected as changes in fluorescence emission, fluorescence vs. voltage curves) always preceded the channel activation curves, as expected for protein rearrangements associated to the movement of the voltage sensor. Extremely slow conformational changes were revealed by fluorescent labeling of position 202, elicited by a mutual interaction of the fluorophore with the adjacent tryptophan 203. PMID:16895996

  5. Voltage-dependent conformational changes in human Ca(2+)- and voltage-activated K(+) channel, revealed by voltage-clamp fluorometry.

    Science.gov (United States)

    Savalli, Nicoletta; Kondratiev, Andrei; Toro, Ligia; Olcese, Riccardo

    2006-08-15

    Large conductance voltage- and Ca(2+)-activated K(+) (BK(Ca)) channels regulate important physiological processes such as neurotransmitter release and vascular tone. BK(Ca) channels possess a voltage sensor mainly represented by the S4 transmembrane domain. Changes in membrane potential displace the voltage sensor, producing a conformational change that leads to channel opening. By site-directed fluorescent labeling of residues in the S3-S4 region and by using voltage clamp fluorometry, we have resolved the conformational changes the channel undergoes during activation. The voltage dependence of these conformational changes (detected as changes in fluorescence emission, fluorescence vs. voltage curves) always preceded the channel activation curves, as expected for protein rearrangements associated to the movement of the voltage sensor. Extremely slow conformational changes were revealed by fluorescent labeling of position 202, elicited by a mutual interaction of the fluorophore with the adjacent tryptophan 203.

  6. Neutron diffraction reveals hydrogen bonds critical for cGMP-selective activation: insights for cGMP-dependent protein kinase agonist design.

    Science.gov (United States)

    Huang, Gilbert Y; Gerlits, Oksana O; Blakeley, Matthew P; Sankaran, Banumathi; Kovalevsky, Andrey Y; Kim, Choel

    2014-11-04

    High selectivity of cyclic-nucleotide binding (CNB) domains for cAMP and cGMP are required for segregating signaling pathways; however, the mechanism of selectivity remains unclear. To investigate the mechanism of high selectivity in cGMP-dependent protein kinase (PKG), we determined a room-temperature joint X-ray/neutron (XN) structure of PKG Iβ CNB-B, a domain 200-fold selective for cGMP over cAMP, bound to cGMP (2.2 Å), and a low-temperature X-ray structure of CNB-B with cAMP (1.3 Å). The XN structure directly describes the hydrogen bonding interactions that modulate high selectivity for cGMP, while the structure with cAMP reveals that all these contacts are disrupted, explaining its low affinity for cAMP.

  7. Optical properties of InN nanocolumns: Electron accumulation at InN non-polar surfaces and dependence on the growth conditions

    Energy Technology Data Exchange (ETDEWEB)

    Segura-Ruiz, J.; Cantarero, A. [Materials Science Institute, University of Valencia (Spain); Garro, N. [Materials Science Institute, University of Valencia (Spain); Fundacio General de la Universitat de Valencia, Valencia (Spain); Iikawa, F. [Instituto de Fisica ' ' Gleb Wataghin' ' , UNICAMP, Campinas-SP (Brazil); Denker, C.; Malindretos, J.; Rizzi, A. [IV. Physikalisches Institut, Georg-August Universitaet Goettingen (Germany)

    2009-06-15

    InN nanocolumns grown by plasma-assisted molecular beam epitaxy have been studied by photoluminescence (PL) and photoluminescence excitation (PLE). The PL peak energy was red-shifted with respect to the PLE onset and both energies were higher than the low temperature band-gap reported for InN. PL and PLE experiments for different excitation and detection energies indicated that the PL peaks were homogeneously broadened. This overall phenomenology has been attributed to the effects of an electron accumulation layer present at the non-polar surfaces of the InN nanocolumns. Variations in the growth conditions modify the edge of the PLE spectra and the PL peak energies evidencing that the density of free electrons can be somehow controlled by the growth parameters. It was observed that In-BEP and substrate temperature leading to shorter In diffusion lengths diminished the effects of the electron accumulation layer on the optical properties. (copyright 2009 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  8. Optical properties of InN nanocolumns: Electron accumulation at InN non-polar surfaces and dependence on the growth conditions

    International Nuclear Information System (INIS)

    Segura-Ruiz, J.; Cantarero, A.; Garro, N.; Iikawa, F.; Denker, C.; Malindretos, J.; Rizzi, A.

    2009-01-01

    InN nanocolumns grown by plasma-assisted molecular beam epitaxy have been studied by photoluminescence (PL) and photoluminescence excitation (PLE). The PL peak energy was red-shifted with respect to the PLE onset and both energies were higher than the low temperature band-gap reported for InN. PL and PLE experiments for different excitation and detection energies indicated that the PL peaks were homogeneously broadened. This overall phenomenology has been attributed to the effects of an electron accumulation layer present at the non-polar surfaces of the InN nanocolumns. Variations in the growth conditions modify the edge of the PLE spectra and the PL peak energies evidencing that the density of free electrons can be somehow controlled by the growth parameters. It was observed that In-BEP and substrate temperature leading to shorter In diffusion lengths diminished the effects of the electron accumulation layer on the optical properties. (copyright 2009 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  9. Schrodinger-Poisson Modeling of AlxGa1-xN/GaN Heterostructures Employing Tailored Depth-Dependent Aluminum Concentration for Polarization Grading

    Science.gov (United States)

    Calame, Jeffrey; Chernyavskiy, Igor; Ancona, Mario; Meyer, David

    Polarization-gradient profiling of AlxGa1-xN/GaN heterostructures in the vertical (depth) direction, achieved by deliberate spatial tailoring of the aluminum concentration profile, can be used to control the spatial structure of the conducting electron gas in high electron mobility transistors. In particular, the typical two-dimensional electron gas of abrupt heterostructures can exhibit a more three-dimensional distribution in graded structures. This offers the possibility of improved device linearity through deliberate vertical heterostructure engineering, which can minimize or compensate for various scattering mechanisms that contribute to nonlinearity. Schrodinger-Poisson modeling (i.e., the Hartree approximation) is used to study the electron density profiles that result from such deliberate grading, and how those profiles evolve with the application of biasing vertical electric fields across the heterostructure. Implications of the results on device linearity will be discussed. Comparisons between the electron density profiles predicted by the Schrodinger-Poisson modeling and those obtained by density-gradient theory will be made in selected examples. Work supported by the U.S. Office of Naval Research.

  10. Cytokine-dependent and–independent gene expression changes and cell cycle block revealed in Trypanosoma cruzi-infected host cells by comparative mRNA profiling

    Directory of Open Access Journals (Sweden)

    Burleigh Barbara A

    2009-05-01

    Full Text Available Abstract Background The requirements for growth and survival of the intracellular pathogen Trypanosoma cruzi within mammalian host cells are poorly understood. Transcriptional profiling of the host cell response to infection serves as a rapid read-out for perturbation of host physiology that, in part, reflects adaptation to the infective process. Using Affymetrix oligonucleotide array analysis we identified common and disparate host cell responses triggered by T. cruzi infection of phenotypically diverse human cell types. Results We report significant changes in transcript abundance in T. cruzi-infected fibroblasts, endothelial cells and smooth muscle cells (2852, 2155 and 531 genes respectively; fold-change ≥ 2, p-value T. cruzi-infected fibroblasts and endothelial cells transwell plates were used to distinguish cytokine-dependent and -independent gene expression profiles. This approach revealed the induction of metabolic and signaling pathways involved in cell proliferation, amino acid catabolism and response to wounding as common themes in T. cruzi-infected cells. In addition, the downregulation of genes involved in mitotic cell cycle and cell division predicted that T. cruzi infection may impede host cell cycle progression. The observation of impaired cytokinesis in T. cruzi-infected cells, following nuclear replication, confirmed this prediction. Conclusion Metabolic pathways and cellular processes were identified as significantly altered at the transcriptional level in response to T. cruzi infection in a cytokine-independent manner. Several of these alterations are supported by previous studies of T. cruzi metabolic requirements or effects on the host. However, our methods also revealed a T. cruzi-dependent block in the host cell cycle, at the level of cytokinesis, previously unrecognized for this pathogen-host cell interaction.

  11. Widespread spin polarization effects in photoemission from topological insulators

    Energy Technology Data Exchange (ETDEWEB)

    Jozwiak, C.; Chen, Y. L.; Fedorov, A. V.; Analytis, J. G.; Rotundu, C. R.; Schmid, A. K.; Denlinger, J. D.; Chuang, Y.-D.; Lee, D.-H.; Fisher, I. R.; Birgeneau, R. J.; Shen, Z.-X.; Hussain, Z.; Lanzara, A.

    2011-06-22

    High-resolution spin- and angle-resolved photoemission spectroscopy (spin-ARPES) was performed on the three-dimensional topological insulator Bi{sub 2}Se{sub 3} using a recently developed high-efficiency spectrometer. The topological surface state's helical spin structure is observed, in agreement with theoretical prediction. Spin textures of both chiralities, at energies above and below the Dirac point, are observed, and the spin structure is found to persist at room temperature. The measurements reveal additional unexpected spin polarization effects, which also originate from the spin-orbit interaction, but are well differentiated from topological physics by contrasting momentum and photon energy and polarization dependencies. These observations demonstrate significant deviations of photoelectron and quasiparticle spin polarizations. Our findings illustrate the inherent complexity of spin-resolved ARPES and demonstrate key considerations for interpreting experimental results.

  12. Non-density dependent pollen dispersal of Shorea maxwelliana (Dipterocarpaceae revealed by a Bayesian mating model based on paternity analysis in two synchronized flowering seasons.

    Directory of Open Access Journals (Sweden)

    Shinsuke Masuda

    Full Text Available Pollinator syndrome is one of the most important determinants regulating pollen dispersal in tropical tree species. It has been widely accepted that the reproduction of tropical forest species, especially dipterocarps that rely on insects with weak flight for their pollination, is positively density-dependent. However differences in pollinator syndrome should affect pollen dispersal patterns and, consequently, influence genetic diversity via the mating process. We examined the pollen dispersal pattern and mating system of Shorea maxwelliana, the flowers of which are larger than those of Shorea species belonging to section Mutica which are thought to be pollinated by thrips (weak flyers. A Bayesian mating model based on the paternity of seeds collected from mother trees during sporadic and mass flowering events revealed that the estimated pollen dispersal kernel and average pollen dispersal distance were similar for both flowering events. This evidence suggests that the putative pollinators - small beetles and weevils - effectively contribute to pollen dispersal and help to maintain a high outcrossing rate even during sporadic flowering events. However, the reduction in pollen donors during a sporadic event results in a reduction in effective pollen donors, which should lead to lower genetic diversity in the next generation derived from seeds produced during such an event. Although sporadic flowering has been considered less effective for outcrossing in Shorea species that depend on thrips for their pollination, effective pollen dispersal by the small beetles and weevils ensures outcrossing during periods of low flowering tree density, as occurs in a sporadic flowering event.

  13. A Conserved Pattern of Primer-Dependent Transcription Initiation in Escherichia coli and Vibrio cholerae Revealed by 5' RNA-seq.

    Directory of Open Access Journals (Sweden)

    Sergey Y Druzhinin

    2015-07-01

    Full Text Available Transcription initiation that involves the use of a 2- to ~4-nt oligoribonucleotide primer, "primer-dependent initiation," (PDI has been shown to be widely prevalent at promoters of genes expressed during the stationary phase of growth in Escherichia coli. However, the extent to which PDI impacts E. coli physiology, and the extent to which PDI occurs in other bacteria is not known. Here we establish a physiological role for PDI in E. coli as a regulatory mechanism that modulates biofilm formation. We further demonstrate using high-throughput sequencing of RNA 5' ends (5' RNA-seq that PDI occurs in the pathogenic bacterium Vibrio cholerae. A comparative global analysis of PDI in V. cholerae and E. coli reveals that the pattern of PDI is strikingly similar in the two organisms. In particular, PDI is detected in stationary phase, is not detected in exponential phase, and is preferentially apparent at promoters carrying the sequence T-1A+1 or G-1G+1 (where position +1 corresponds to the position of de novo initiation. Our findings demonstrate a physiological role for PDI and suggest PDI may be widespread among Gammaproteobacteria. We propose that PDI in both E. coli and V. cholerae occurs though a growth phase-dependent process that leads to the preferential generation of the linear dinucleotides 5´-UA-3´ and 5´-GG-3´.

  14. A Conserved Pattern of Primer-Dependent Transcription Initiation in Escherichia coli and Vibrio cholerae Revealed by 5' RNA-seq.

    Science.gov (United States)

    Druzhinin, Sergey Y; Tran, Ngat T; Skalenko, Kyle S; Goldman, Seth R; Knoblauch, Jared G; Dove, Simon L; Nickels, Bryce E

    2015-07-01

    Transcription initiation that involves the use of a 2- to ~4-nt oligoribonucleotide primer, "primer-dependent initiation," (PDI) has been shown to be widely prevalent at promoters of genes expressed during the stationary phase of growth in Escherichia coli. However, the extent to which PDI impacts E. coli physiology, and the extent to which PDI occurs in other bacteria is not known. Here we establish a physiological role for PDI in E. coli as a regulatory mechanism that modulates biofilm formation. We further demonstrate using high-throughput sequencing of RNA 5' ends (5' RNA-seq) that PDI occurs in the pathogenic bacterium Vibrio cholerae. A comparative global analysis of PDI in V. cholerae and E. coli reveals that the pattern of PDI is strikingly similar in the two organisms. In particular, PDI is detected in stationary phase, is not detected in exponential phase, and is preferentially apparent at promoters carrying the sequence T-1A+1 or G-1G+1 (where position +1 corresponds to the position of de novo initiation). Our findings demonstrate a physiological role for PDI and suggest PDI may be widespread among Gammaproteobacteria. We propose that PDI in both E. coli and V. cholerae occurs though a growth phase-dependent process that leads to the preferential generation of the linear dinucleotides 5´-UA-3´ and 5´-GG-3´.

  15. Parallel pigment and transcriptomic analysis of four barley albina and xantha mutants reveals the complex network of the chloroplast-dependent metabolism.

    Science.gov (United States)

    Campoli, Chiara; Caffarri, Stefano; Svensson, Jan T; Bassi, Roberto; Stanca, A Michele; Cattivelli, Luigi; Crosatti, Cristina

    2009-09-01

    We investigated the pigment composition and the transcriptome of albina (alb-e ( 16 ) and alb-f ( 17 )) and xantha (xan-s ( 46 ) and xan-b ( 12 )) barley mutants to provide an overall transcriptional picture of genes whose expression is interconnected with chloroplast activities and to search for candidate genes associated with the mutations. Beside those encoding plastid-localized proteins, more than 3,000 genes involved in non-chloroplast localized metabolism were up-/down-regulated in the mutants revealing the network of chloroplast-dependent metabolic pathways. The alb-e ( 16 ) mutant was characterized by overaccumulation of protoporphyrin IX upon ALA (5-amino levulinic acid) feeding and down-regulation of the gene encoding one subunit of Mg-chelatase, suggesting a block of the chlorophyll biosynthetic pathway before Mg-protoporphyrin IX biosynthesis, while alb-f ( 17 ) overaccumulated Mg-protoporphyrin IX and repressed PorA expression, without alterations in Mg-chelatase mRNA level. The alb-f ( 17 )mutant also showed overexpression of several genes involved in phytochrome and in phytochrome-dependent pathways. The results indicate that the down-regulation of Lhcb genes in alb-e ( 16 ) cannot be mediated by the accumulation of Mg-protoporphyrin IX. After ALA treatment, xan-s ( 46 ) showed overaccumulation of Mg-protoporphyrin IX, while the relative porphyrin composition of xan-b ( 12 ) was similar to wild type. The transcripts encoding the components of several mitochondrial metabolic pathways were up-regulated in albina/xantha leaves to compensate for the absence of active chloroplasts. The mRNAs encoding gun3, gun4, and gun5 barley homologous genes showed significant expression variations and were used to search for co-expressed genes across all samples. These analyses provide additional evidences on a chloroplast-dependent covariation of large sets of nuclear genes.

  16. The calcium-dependent protein kinase 3 of toxoplasma influences basal calcium levels and functions beyond egress as revealed by quantitative phosphoproteome analysis.

    Directory of Open Access Journals (Sweden)

    Moritz Treeck

    2014-06-01

    Full Text Available Calcium-dependent protein kinases (CDPKs are conserved in plants and apicomplexan parasites. In Toxoplasma gondii, TgCDPK3 regulates parasite egress from the host cell in the presence of a calcium-ionophore. The targets and the pathways that the kinase controls, however, are not known. To identify pathways regulated by TgCDPK3, we measured relative phosphorylation site usage in wild type and TgCDPK3 mutant and knock-out parasites by quantitative mass-spectrometry using stable isotope-labeling with amino acids in cell culture (SILAC. This revealed known and novel phosphorylation events on proteins predicted to play a role in host-cell egress, but also a novel function of TgCDPK3 as an upstream regulator of other calcium-dependent signaling pathways, as we also identified proteins that are differentially phosphorylated prior to egress, including proteins important for ion-homeostasis and metabolism. This observation is supported by the observation that basal calcium levels are increased in parasites where TgCDPK3 has been inactivated. Most of the differential phosphorylation observed in CDPK3 mutants is rescued by complementation of the mutants with a wild type copy of TgCDPK3. Lastly, the TgCDPK3 mutants showed hyperphosphorylation of two targets of a related calcium-dependent kinase (TgCDPK1, as well as TgCDPK1 itself, indicating that this latter kinase appears to play a role downstream of TgCDPK3 function. Overexpression of TgCDPK1 partially rescues the egress phenotype of the TgCDPK3 mutants, reinforcing this conclusion. These results show that TgCDPK3 plays a pivotal role in regulating tachyzoite functions including, but not limited to, egress.

  17. The Calcium-Dependent Protein Kinase 3 of Toxoplasma Influences Basal Calcium Levels and Functions beyond Egress as Revealed by Quantitative Phosphoproteome Analysis

    Science.gov (United States)

    Treeck, Moritz; Sanders, John L.; Gaji, Rajshekhar Y.; LaFavers, Kacie A.; Child, Matthew A.; Arrizabalaga, Gustavo; Elias, Joshua E.; Boothroyd, John C.

    2014-01-01

    Calcium-dependent protein kinases (CDPKs) are conserved in plants and apicomplexan parasites. In Toxoplasma gondii, TgCDPK3 regulates parasite egress from the host cell in the presence of a calcium-ionophore. The targets and the pathways that the kinase controls, however, are not known. To identify pathways regulated by TgCDPK3, we measured relative phosphorylation site usage in wild type and TgCDPK3 mutant and knock-out parasites by quantitative mass-spectrometry using stable isotope-labeling with amino acids in cell culture (SILAC). This revealed known and novel phosphorylation events on proteins predicted to play a role in host-cell egress, but also a novel function of TgCDPK3 as an upstream regulator of other calcium-dependent signaling pathways, as we also identified proteins that are differentially phosphorylated prior to egress, including proteins important for ion-homeostasis and metabolism. This observation is supported by the observation that basal calcium levels are increased in parasites where TgCDPK3 has been inactivated. Most of the differential phosphorylation observed in CDPK3 mutants is rescued by complementation of the mutants with a wild type copy of TgCDPK3. Lastly, the TgCDPK3 mutants showed hyperphosphorylation of two targets of a related calcium-dependent kinase (TgCDPK1), as well as TgCDPK1 itself, indicating that this latter kinase appears to play a role downstream of TgCDPK3 function. Overexpression of TgCDPK1 partially rescues the egress phenotype of the TgCDPK3 mutants, reinforcing this conclusion. These results show that TgCDPK3 plays a pivotal role in regulating tachyzoite functions including, but not limited to, egress. PMID:24945436

  18. Dependence of matrix effect on ionization polarity during LC-ESI-MS analysis of derivatized amino acids in some natural samples.

    Science.gov (United States)

    Oldekop, Maarja-Liisa; Rebane, Riin; Herodes, Koit

    2017-10-01

    Matrix effect, the influence of co-eluting components on the ionization efficiency of the analyte, affects the trueness and precision of the LC-ESI-MS analysis. Derivatization can reduce or eliminate matrix effect, for example, diethyl ethoxymethylenemalonate (DEEMM) derivatives have shown less matrix effect compared to other derivatives. Moreover, the use of negative ion mode can further reduce matrix effect. In order to investigate the combination of derivatization and different ionization modes, an LC-ESI-MS/MS method using alternating positive/negative ion mode was developed and validated. The analyses in positive and negative ion modes had comparable limit of quantitation values. The influence of ESI polarity on matrix effect was investigated during the analysis of 22 DEEMM-derivatized amino acids in herbal extracts and honeys. Sample dilution approach was used for the evaluation of the presence of matrix effect. Altogether, 4 honeys and 11 herbal extracts were analyzed, and the concentrations of 22 amino acids in the samples are presented. In the positive ion mode, matrix effect was observed for several amino acid derivatives and the matrix effect was stronger in honey samples compared to the herbal extracts. The negative ion mode was free from matrix effect, with only few exceptions in honeys (average relative standard deviation over all analytes and matrices was 8%; SD = 7%). The matrix effect was eliminated in the positive ion mode by sample dilution and agreement between concentrations from the two ion modes was achieved for most amino acids. In conclusion, it was shown that the combination of derivatization and negative ion mode can be a powerful tool for minimizing matrix effect in more complicated applications.

  19. Study of the polarization dependence of the photoelectric effect in the soft X-ray band - A focal plane photoelectric stellar X-ray polarimeter for the Spectrum-X-Gamma mission

    International Nuclear Information System (INIS)

    Heckler, A.; Blaer, A.; Kaaret, P.; Novick, R.

    1989-01-01

    An experimental study of the polarization dependence of the photoelectric effect in cesium iodide in the soft X-ray band was started (Heckler et al., 1989). At a grazing angle of 10 degrees and a photon energy of 2.6 keV, it is found that the photoelectric yield from a thin layer of evaporated cesium iodide varies by 12.4 percent as the polarization vector of the incident X-ray beam is rotated about the line-of-sight. The rotation angle corresponding to the maximum photoyield is displaced by 16 degrees from the normal to the photocathode. This modulation and phase shift are in good agreement with the results recently reported by Fraser, et al. (1989) It is shown that a focal plane stellar X-ray polarimeter based on this photoelectric effect will be substantially more efficient than convential X-ray polarimeters such as those based on either Bragg reflection or scattering from low atomic number targets. 7 refs

  20. Strategic Polarization.

    Science.gov (United States)

    Kalai, Adam; Kalai, Ehud

    2001-08-01

    In joint decision making, similarly minded people may take opposite positions. Consider the example of a marriage in which one spouse gives generously to charity while the other donates nothing. Such "polarization" may misrepresent what is, in actuality, a small discrepancy in preferences. It may be that the donating spouse would like to see 10% of their combined income go to charity each year, while the apparently frugal spouse would like to see 8% donated. A simple game-theoretic analysis suggests that the spouses will end up donating 10% and 0%, respectively. By generalizing this argument to a larger class of games, we provide strategic justification for polarization in many situations such as debates, shared living accommodations, and disciplining children. In some of these examples, an arbitrarily small disagreement in preferences leads to an arbitrarily large loss in utility for all participants. Such small disagreements may also destabilize what, from game-theoretic point of view, is a very stable equilibrium. Copyright 2001 Academic Press.

  1. Linear and non-linear dependencies between copy number aberrations and mRNA expression reveal distinct molecular pathways in breast cancer

    Directory of Open Access Journals (Sweden)

    Frigessi Arnoldo

    2011-05-01

    Full Text Available Abstract Background Elucidating the exact relationship between gene copy number and expression would enable identification of regulatory mechanisms of abnormal gene expression and biological pathways of regulation. Most current approaches either depend on linear correlation or on nonparametric tests of association that are insensitive to the exact shape of the relationship. Based on knowledge of enzyme kinetics and gene regulation, we would expect the functional shape of the relationship to be gene dependent and to be related to the gene regulatory mechanisms involved. Here, we propose a statistical approach to investigate and distinguish between linear and nonlinear dependences between DNA copy number alteration and mRNA expression. Results We applied the proposed method to DNA copy numbers derived from Illumina 109 K SNP-CGH arrays (using the log R values and expression data from Agilent 44 K mRNA arrays, focusing on commonly aberrated genomic loci in a collection of 102 breast tumors. Regression analysis was used to identify the type of relationship (linear or nonlinear, and subsequent pathway analysis revealed that genes displaying a linear relationship were overall associated with substantially different biological processes than genes displaying a nonlinear relationship. In the group of genes with a linear relationship, we found significant association to canonical pathways, including purine and pyrimidine metabolism (for both deletions and amplifications as well as estrogen metabolism (linear amplification and BRCA-related response to damage (linear deletion. In the group of genes displaying a nonlinear relationship, the top canonical pathways were specific pathways like PTEN and PI13K/AKT (nonlinear amplification and Wnt(B and IL-2 signalling (nonlinear deletion. Both amplifications and deletions pointed to the same affected pathways and identified cancer as the top significant disease and cell cycle, cell signaling and cellular

  2. Ca(2+-dependent regulation of the Ca(2+ concentration in the myometrium mitochondria. II. Ca(2+ effects on mitochondria membranes polarization and [Ca(2+](m

    Directory of Open Access Journals (Sweden)

    L. G. Babich

    2017-06-01

    Full Text Available It is known that Ca2+ accumulation in the mitochondria undergoes complex regulation by Ca2+ itself. But the mechanisms of such regulation are still discussed. In this paper we have shown that Ca ions directly or indirectly regulate the level of myometrium mitochondria membranes polarization. The additions of 100 µM Ca2+ were accompanied by depolarization of the mitochondria membranes. The following experiments were designed to study the impact of Ca2+ on the myometrium mitochondria [Ca2+]m. Isolated myometrium mitochondria were preincubated without or with 10 μM Са2+ followed by 100 μM Са2+ addition. Experiments were conducted in three mediums: without ATP and Mg2+ (0-medium, in the presence of 3 mM Mg2+ (Mg-medium and 3 mM Mg2+ + 3 mM ATP (Mg,ATP-medium. It was shown that the effects of 10 μM Са2+ addition were different in different mediums, namely in 0- and Mg-medium the [Ca2+]m values increased, whereas in Mg,ATP-medium statistically reliable changes were not registered. Preincubation of mitochondria with 10 μM Са2+ did not affect the [Ca2+]m value after the addition of 100 μM Са2+. The [Ca2+]m values after 100 μM Са2+ addition were the same in 0- and Mg,ATP-mediums and somewhat lower in Mg-medium. Preliminary incubation of mitochondria with 10 μM Са2+ in 0- and Mg-mediums reduced changes of Fluo 4 normalized fluorescence values that were induced by 100 μM Са2+ additions, but in Mg,ATP-medium such differences were not recorded. It is concluded that Са2+ exchange in myometrium mitochondria is regulated by the concentration of Ca ions as in the external medium, so in the matrix of mitochondria. The medium composition had a significant impact on the [Са2+]m values in the absence of exogenous cation. It is suggested that light increase of [Са2+]m before the addition of 100 μM Са2+ may have a positive effect on the functional activity of the mitochondria.

  3. Polarization memory of white luminescence of Ag nanoclusters dispersed in glass host.

    Science.gov (United States)

    Kuznetsov, A S; Tikhomirov, V K; Moshchalkov, V V

    2012-09-10

    A mechanism for white luminescence of Ag nanoclusters dispersed in oxyfluoride glass host has been revealed by studying a temperature dependence of its polarization memory. The spectral dependence of the polarization memory indicates the presence of a variety of Ag nanoclusters, particularly emitting in the blue, green and red. Temperature activated intercluster energy transfer has been found responsible for white luminescence. The means for increasing luminescence quantum yield have been suggested. This efficient white luminescence may be used in highly demanded devices, such as luminescent lamps, displays, color phosphors for LEDs, photovoltaic devices based on down shifting of solar spectrum.

  4. Few-body experiments with polarized beams and polarized targets

    International Nuclear Information System (INIS)

    Simmons, J.E.

    1983-01-01

    A survey is presented concerning recent polarization experiments in the elastic p-d, p- 3 He, and p- 4 He systems. Mention is made of selected neutron experiments. The nominal energy range is 10 to 1000 MeV. Recent results and interpretations of the p-d system near 10 MeV are discussed. New experiments on the energy dependence of back angle p-d tensor polarization are discussed with respect to resolution of discrepancies and difficulty of theoretical interpretation. Progress is noted concerning multiple scattering interpretation of forward p-d deuteron polarization. Some new results are presented concerning the p- 3 He system and higher energy p- 4 He polarization experiments. 52 references

  5. Mutational analysis of Sep-tRNA:Cys-tRNA synthase reveals critical residues for tRNA-dependent cysteine formation.

    Science.gov (United States)

    Helgadóttir, Sunna; Sinapah, Sylvie; Söll, Dieter; Ling, Jiqiang

    2012-01-02

    In methanogenic archaea, Sep-tRNA:Cys-tRNA synthase (SepCysS) converts Sep-tRNA(Cys) to Cys-tRNA(Cys). The mechanism of tRNA-dependent cysteine formation remains unclear due to the lack of functional studies. In this work, we mutated 19 conserved residues in Methanocaldococcus jannaschii SepCysS, and employed an in vivo system to determine the activity of the resulting variants. Our results show that three active-site cysteines (Cys39, Cys42 and Cys247) are essential for SepCysS activity. In addition, combined with structural modeling, our mutational and functional analyses also reveal multiple residues that are important for the binding of PLP, Sep and tRNA. Our work thus represents the first systematic functional analysis of conserved residues in archaeal SepCysSs, providing insights into the catalytic and substrate binding mechanisms of this poorly characterized enzyme. Copyright © 2011 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  6. Transcriptomic Profiling and H3K27me3 Distribution Reveal Both Demethylase-Dependent and Independent Regulation of Developmental Gene Transcription in Cell Differentiation.

    Science.gov (United States)

    Kang, Sung Chul; Kim, Se Kye; Chai, Jin Choul; Kim, Sun Hwa; Won, Kyoung-Jae; Lee, Young Seek; Jung, Kyoung Hwa; Chai, Young Gyu

    2015-01-01

    The removal of histone H3 trimethylation at lysine residue 27 (H3K27me3) plays a critical role in the transcriptional initiation of developmental genes. The H3K27me3-specific KDM6 demethylases JMJD3 and UTX are responsible for the transcriptional initiation of various developmental genes, but some genes are expressed in a KDM6 demethylase-independent manner. To address the role of H3K27me3 in the retinoic acid (RA)-induced differentiation of the human carcinoma NCCIT cell line, we inhibited JMJD3 and UTX using the H3K27me3 demethylase inhibitor GSK-J4. The commitment of JMJD3/UTX-inhibited cells to a specific fate was delayed, and transcriptome profiling also revealed the differential expression of genes related to cell fate specification in demethylase-inactivated cells; the expression levels of RA metabolism and HOX family genes significantly decreased. We observed a weak correlation between H3K27me3 enrichment and transcriptional repression in the control and JMJD/UTX-inhibited cells, except for a few sets of developmental genes that are indispensable for cell fate specification. Taken together, these results provide the H3K27me3 landscape of a differentiating cell line and suggest that both demethylase-dependent and demethylase-independent transcriptional regulation play a role in early differentiation and developmental gene expression activated by H3K27me3 demethylation.

  7. Large-Scale Analysis of CRISPR/Cas9 Cell-Cycle Knockouts Reveals the Diversity of p53-Dependent Responses to Cell-Cycle Defects.

    Science.gov (United States)

    McKinley, Kara L; Cheeseman, Iain M

    2017-02-27

    Defining the genes that are essential for cellular proliferation is critical for understanding organismal development and identifying high-value targets for disease therapies. However, the requirements for cell-cycle progression in human cells remain incompletely understood. To elucidate the consequences of acute and chronic elimination of cell-cycle proteins, we generated and characterized inducible CRISPR/Cas9 knockout human cell lines targeting 209 genes involved in diverse cell-cycle processes. We performed single-cell microscopic analyses to systematically establish the effects of the knockouts on subcellular architecture. To define variations in cell-cycle requirements between cultured cell lines, we generated knockouts across cell lines of diverse origins. We demonstrate that p53 modulates the phenotype of specific cell-cycle defects through distinct mechanisms, depending on the defect. This work provides a resource to broadly facilitate robust and long-term depletion of cell-cycle proteins and reveals insights into the requirements for cell-cycle progression. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. Precessing deuteron polarization

    International Nuclear Information System (INIS)

    Sitnik, I.M.; Volkov, V.I.; Kirillov, D.A.; Piskunov, N.M.; Plis, Yu.A.

    2002-01-01

    The feasibility of the acceleration in the Nuclotron of deuterons polarized in the horizontal plane is considered. This horizontal polarization is named precessing polarization. The effects of the main magnetic field and synchrotron oscillations are included. The precessing polarization is supposed to be used in studying the polarization parameters of the elastic dp back-scattering and other experiments

  9. Structure-dependent degradation of polar compounds in weathered oils observed by atmospheric pressure photo-ionization hydrogen/deuterium exchange ultrahigh resolution mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Islam, Ananna; Kim, Donghwi [Kyungpook National University, Department of Chemistry, Daegu 702-701 (Korea, Republic of); Yim, Un Hyuk; Shim, Won Joon [Oil and POPs Research Group, Korea Institute of Ocean Science and Technology, KIOST, Geoje 656-834 (Korea, Republic of); Kim, Sunghwan, E-mail: sunghwank@knu.ac.kr [Kyungpook National University, Department of Chemistry, Daegu 702-701 (Korea, Republic of); Green Nano Center, Department of Chemistry, Daegu 702-701 (Korea, Republic of)

    2015-10-15

    Highlights: • We examined source crude oil and weathered oils from M/V Hebei accident. • APPI hydrogen/deuterium exchange ultrahigh mass spectrometry was applied. • N{sub 1} class compounds with 2° and/or 3° amine decrease in larger scale than pyridines. • Preferential degradation of nitrogen-containing compounds was confirmed. • Significant increase in S{sub 1}O{sub 1} compounds was observed as the weathering proceeds. - Abstract: The resin fractions of fresh mixtures of three oils spilled during the M/V Hebei Spirit oil spill, as well as weathered oils collected at weathering stages II and IV from the oil spill site were analyzed and compared by atmospheric pressure photo-ionization hydrogen/deuterium exchange mass spectrometry (HDX MS). The significantly decreased abundance of N{sup +}· and [N − H + D]{sup +} ions suggested that secondary and tertiary amine-containing compounds were preferentially degraded during the early stage of weathering. [N + H]{sup +} and [N + D]{sup +} ions previously attributed to pyridine-type compounds degraded more slowly than secondary and tertiary amine-containing compounds. The preferential degradation of nitrogen-containing compounds was confirmed by photo-degradation experiments using 15 standard compounds. In addition, significant increases of [S{sub 1}O{sub 1} + H]{sup +} and [S{sub 1}O{sub 1} + D]{sup +} ions with higher DBE values were observed from fresh oil mixtures as compared to stages II and IV samples, and that could be linked with the decrease of higher DBE compounds of the S{sub 1} class. This study presented convincing arguments and evidence demonstrating that secondary and tertiary amines were more vulnerable to photo-degradation than compounds containing pyridine, and hence, preferential degradation depending on chemical structures must be considered in the production of hazardous or toxic components.

  10. Structure-dependent degradation of polar compounds in weathered oils observed by atmospheric pressure photo-ionization hydrogen/deuterium exchange ultrahigh resolution mass spectrometry

    International Nuclear Information System (INIS)

    Islam, Ananna; Kim, Donghwi; Yim, Un Hyuk; Shim, Won Joon; Kim, Sunghwan

    2015-01-01

    Highlights: • We examined source crude oil and weathered oils from M/V Hebei accident. • APPI hydrogen/deuterium exchange ultrahigh mass spectrometry was applied. • N 1 class compounds with 2° and/or 3° amine decrease in larger scale than pyridines. • Preferential degradation of nitrogen-containing compounds was confirmed. • Significant increase in S 1 O 1 compounds was observed as the weathering proceeds. - Abstract: The resin fractions of fresh mixtures of three oils spilled during the M/V Hebei Spirit oil spill, as well as weathered oils collected at weathering stages II and IV from the oil spill site were analyzed and compared by atmospheric pressure photo-ionization hydrogen/deuterium exchange mass spectrometry (HDX MS). The significantly decreased abundance of N + · and [N − H + D] + ions suggested that secondary and tertiary amine-containing compounds were preferentially degraded during the early stage of weathering. [N + H] + and [N + D] + ions previously attributed to pyridine-type compounds degraded more slowly than secondary and tertiary amine-containing compounds. The preferential degradation of nitrogen-containing compounds was confirmed by photo-degradation experiments using 15 standard compounds. In addition, significant increases of [S 1 O 1 + H] + and [S 1 O 1 + D] + ions with higher DBE values were observed from fresh oil mixtures as compared to stages II and IV samples, and that could be linked with the decrease of higher DBE compounds of the S 1 class. This study presented convincing arguments and evidence demonstrating that secondary and tertiary amines were more vulnerable to photo-degradation than compounds containing pyridine, and hence, preferential degradation depending on chemical structures must be considered in the production of hazardous or toxic components

  11. Polare maskuliniteter

    Directory of Open Access Journals (Sweden)

    Marit Anne Hauan

    2012-05-01

    Full Text Available In this paper my aim is to read and understand the journal of Gerrit de Veer from the last journey of William Barents to the Arctic Regions in 1596 and the journal of captain Junge on his hunting trip from Tromsø to Svalbard in 1834.It is nearly 240 years between this to voyages. The first journal is known as the earliest report from the arctic era. Gerrit de Veer adds instructive copper engravings to his text and give us insight in the crews meeting with this new land. Captain Junges journal is found together with his dead crew in a house in a fjord nearby Ny-Ålesund and has no drawings, but word. Both of these journals may be read as sources of the knowledge and understanding of the polar region. They might also unveil the ideas of how to deal with and survive under the challenges that is given. In addition one can ask if the sources can tell us more about how men describe their challenges. Can the way they expressed themselves in the journals give us an understanding of masculinity? And not least help us to create good questions of the change in the ideas of masculinities which is said to follow the change in understanding of the wilderness.

  12. Geomagnetic polarity transitions

    Science.gov (United States)

    Merrill, Ronald T.; McFadden, Phillip L.

    1999-05-01

    The top of Earth's liquid outer core is nearly 2900 km beneath Earth's surface, so we will never be able to observe it directly. This hot, dense, molten iron-rich body is continuously in motion and is the source of Earth's magnetic field. One of the most dynamic manifestations at Earth's surface of this fluid body is, perhaps, a reversal of the geomagnetic field. Unfortunately, the most recent polarity transition occurred at about 780 ka, so we have never observed a transition directly. It seems that a polarity transition spans many human lifetimes, so no human will ever witness the phenomenon in its entirety. Thus we are left with the tantalizing prospect that paleomagnetic records of polarity transitions may betray some of the secrets of the deep Earth. Certainly, if there are systematics in the reversal process and they can be documented, then this will reveal substantial information about the nature of the lowermost mantle and of the outer core. Despite their slowness on a human timescale, polarity transitions occur almost instantaneously on a geological timescale. This rapidity, together with limitations in the paleomagnetic recording process, prohibits a comprehensive description of any reversal transition both now and into the foreseeable future, which limits the questions that may at this stage be sensibly asked. The natural model for the geomagnetic field is a set of spherical harmonic components, and we are not able to obtain a reliable model for even the first few harmonic terms during a transition. Nevertheless, it is possible, in principle, to make statements about the harmonic character of a geomagnetic polarity transition without having a rigorous spherical harmonic description of one. For example, harmonic descriptions of recent geomagnetic polarity transitions that are purely zonal can be ruled out (a zonal harmonic does not change along a line of latitude). Gleaning information about transitions has proven to be difficult, but it does seem

  13. Suppressor analysis reveals a role for SecY in the SecA2-dependent protein export pathway of Mycobacteria.

    Science.gov (United States)

    Ligon, Lauren S; Rigel, Nathan W; Romanchuk, Artur; Jones, Corbin D; Braunstein, Miriam

    2013-10-01

    All bacteria use the conserved Sec pathway to transport proteins across the cytoplasmic membrane, with the SecA ATPase playing a central role in the process. Mycobacteria are part of a small group of bacteria that have two SecA proteins: the canonical SecA (SecA1) and a second, specialized SecA (SecA2). The SecA2-dependent pathway exports a small subset of proteins and is required for Mycobacterium tuberculosis virulence. The mechanism by which SecA2 drives export of proteins across the cytoplasmic membrane remains poorly understood. Here we performed suppressor analysis on a dominant negative secA2 mutant (secA2 K129R) of the model mycobacterium Mycobacterium smegmatis to better understand the pathway used by SecA2 to export proteins. Two extragenic suppressor mutations were identified as mapping to the promoter region of secY, which encodes the central component of the canonical Sec export channel. These suppressor mutations increased secY expression, and this effect was sufficient to alleviate the secA2 K129R phenotype. We also discovered that the level of SecY protein was greatly diminished in the secA2 K129R mutant, but at least partially restored in the suppressors. Furthermore, the level of SecY in a suppressor strongly correlated with the degree of suppression. Our findings reveal a detrimental effect of SecA2 K129R on SecY, arguing for an integrated system in which SecA2 works with SecY and the canonical Sec translocase to export proteins.

  14. Magic angle spinning NMR reveals sequence-dependent structural plasticity, dynamics, and the spacer peptide 1 conformation in HIV-1 capsid protein assemblies.

    Science.gov (United States)

    Han, Yun; Hou, Guangjin; Suiter, Christopher L; Ahn, Jinwoo; Byeon, In-Ja L; Lipton, Andrew S; Burton, Sarah; Hung, Ivan; Gor'kov, Peter L; Gan, Zhehong; Brey, William; Rice, David; Gronenborn, Angela M; Polenova, Tatyana

    2013-11-27

    A key stage in HIV-1 maturation toward an infectious virion requires sequential proteolytic cleavage of the Gag polyprotein leading to the formation of a conical capsid core that encloses the viral RNA genome and a small complement of proteins. The final step of this process involves severing the SP1 peptide from the CA-SP1 maturation intermediate, which triggers the condensation of the CA protein into the capsid shell. The details of the overall mechanism, including the conformation of the SP1 peptide in CA-SP1, are still under intense debate. In this report, we examine tubular assemblies of CA and the CA-SP1 maturation intermediate using magic angle spinning (MAS) NMR spectroscopy. At magnetic fields of 19.9 T and above, outstanding quality 2D and 3D MAS NMR spectra were obtained for tubular CA and CA-SP1 assemblies, permitting resonance assignments for subsequent detailed structural characterization. Dipolar- and scalar-based correlation experiments unequivocally indicate that SP1 peptide is in a random coil conformation and mobile in the assembled CA-SP1. Analysis of two CA protein sequence variants reveals that, unexpectedly, the conformations of the SP1 tail, the functionally important CypA loop, and the loop preceding helix 8 are modulated by residue variations at distal sites. These findings provide support for the role of SP1 as a trigger of the disassembly of the immature CA capsid for its subsequent de novo reassembly into mature cores and establish the importance of sequence-dependent conformational plasticity in CA assembly.

  15. Absence of RIP140 reveals a pathway regulating glut4-dependent glucose uptake in oxidative skeletal muscle through UCP1-mediated activation of AMPK.

    Directory of Open Access Journals (Sweden)

    Asmaà Fritah

    Full Text Available Skeletal muscle constitutes the major site of glucose uptake leading to increased removal of glucose from the circulation in response to insulin. Type 2 diabetes and obesity are often associated with insulin resistance that can be counteracted by exercise or the use of drugs increasing the relative proportion of oxidative fibers. RIP140 is a transcriptional coregulator with a central role in metabolic tissues and we tested the effect of modulating its level of expression on muscle glucose and lipid metabolism in two mice models. Here, we show that although RIP140 protein is expressed at the same level in both oxidative and glycolytic muscles, it inhibits both fatty acid and glucose utilization in a fiber-type dependent manner. In RIP140-null mice, fatty acid utilization increases in the extensor digitorum longus and this is associated with elevated expression of genes implicated in fatty acid binding and transport. In the RIP140-null soleus, depletion of RIP140 leads to increased GLUT4 trafficking and glucose uptake with no change in Akt activity. AMPK phosphorylation/activity is inhibited in the soleus of RIP140 transgenic mice and increased in RIP140-null soleus. This is associated with increased UCP1 expression and mitochondrial uncoupling revealing the existence of a signaling pathway controlling insulin-independent glucose uptake in the soleus of RIP140-null mice. In conclusion, our findings reinforce the participation of RIP140 in the maintenance of energy homeostasis by acting as an inhibitor of energy production and particularly point to RIP140 as a promising therapeutic target in the treatment of insulin resistance.

  16. Polarization Spectra of Extrasolar Giant Planets

    NARCIS (Netherlands)

    Stam, D.M.

    2004-01-01

    We present simulated spectra of the flux and degree of polarization of starlight that is reflected by extrasolar giant planets (EGPs). In particular the polarization depends strongly on the structure of the planetary atmosphere, and appears to be a valuable tool for the characterization of EGPs.

  17. Polarization-independent, differential-phase-shift, quantum-key distribution system using upconversion detectors.

    Science.gov (United States)

    Iwai, Yuki; Honjo, Toshimori; Inoue, Kyo; Kamada, Hidehiko; Nishida, Yoshiki; Tadanaga, Osamu; Asobe, Masaki

    2009-05-15

    We propose and demonstrate a polarization-independent, differential-phase-shift, quantum-key distribution system with upconversion detectors. Even though the detectors have polarization dependency, use of alternative polarization modulation and a two-bit delay interferometer achieves polarization-insensitive operation. In an experiment, sifted key bits were polarization-independently generated over 50 km fiber.

  18. Polarity of translation boundaries in antiferroelectric PbZrO{sub 3}

    Energy Technology Data Exchange (ETDEWEB)

    Wei, Xian-Kui, E-mail: xiankui.wei@epfl.ch [Ceramics Laboratory, EPFL–Swiss Federal Institute of Technology, Lausanne 1015 (Switzerland); Peter Grünberg Institute and Ernst Ruska Center for Microscopy and Spectroscopy with Electrons, Research Center Jülich, 52425 Jülich (Germany); Jia, Chun-Lin [Peter Grünberg Institute and Ernst Ruska Center for Microscopy and Spectroscopy with Electrons, Research Center Jülich, 52425 Jülich (Germany); International Centre of Dielectric Research, The School of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an 710049 (China); Roleder, Krystian [Institute of Physics, University of Silesia, Katowice 40007 (Poland); Setter, Nava [Ceramics Laboratory, EPFL–Swiss Federal Institute of Technology, Lausanne 1015 (Switzerland)

    2015-02-15

    Graphical abstract: Strain-free rigid model and aberration-corrected transmission electron microscopes are used to investigate the polarity of translation boundaries in antiferroelectric PbZrO{sub 3}. - Highlights: • Domain boundaries in antiferroelectric PbZrO{sub 3} show polar and antipolar property. • The antiphase boundary can split into “sub-domains”. • Polarization reversal possibly exists inside the translation boundaries. • Thermal treatment can alter morphology and density of the translation boundaries. - Abstract: The polarity of translation boundaries (TBs) in antiferroelectric PbZrO{sub 3} is investigated. We show that previous experimentally reported polar property of R{sub III-1} type TB can be well approximated by a strain-free rigid model. Based on this, the modeling investigation suggests that there are two additional polar TBs, three antipolar-like TBs and one antipolar antiphase boundary. High-resolution scanning-transmission-electron-microscopy study reveals that the straight R{sub III-1} type TB can split into “sub-domains” with possible polarization reversal, suggesting the occurrence of ferroic orders at the TBs. In addition, dependence of morphology and density of the TBs on thermal treatments is discussed according to our results.

  19. Charge transport in non-polar and semi-polar III-V nitride heterostructures

    International Nuclear Information System (INIS)

    Konar, Aniruddha; Verma, Amit; Fang, Tian; Zhao, Pei; Jana, Raj; Jena, Debdeep

    2012-01-01

    Compared to the intense research focus on the optical properties, the transport properties in non-polar and semi-polar III-nitride semiconductors remain relatively unexplored to date. The purpose of this paper is to discuss charge-transport properties in non-polar and semi-polar orientations of GaN in a comparative fashion to what is known for transport in polar orientations. A comprehensive approach is adopted, starting from an investigation of the differences in the electronic bandstructure along different polar orientations of GaN. The polarization fields along various orientations are then discussed, followed by the low-field electron and hole mobilities. A number of scattering mechanisms that are specific to non-polar and semi-polar GaN heterostructures are identified, and their effects are evaluated. Many of these scattering mechanisms originate due to the coupling of polarization with disorder and defects in various incarnations depending on the crystal orientation. The effect of polarization orientation on carrier injection into quantum-well light-emitting diodes is discussed. This paper ends with a discussion of orientation-dependent high-field charge-transport properties including velocity saturation, instabilities and tunneling transport. Possible open problems and opportunities are also discussed. (paper)

  20. Polarized electron sources

    Energy Technology Data Exchange (ETDEWEB)

    Prepost, R. [Univ. of Wisconsin, Madison, WI (United States)

    1994-12-01

    The fundamentals of polarized electron sources are described with particular application to the Stanford Linear Accelerator Center. The SLAC polarized electron source is based on the principle of polarized photoemission from Gallium Arsenide. Recent developments using epitaxially grown, strained Gallium Arsenide cathodes have made it possible to obtain electron polarization significantly in excess of the conventional 50% polarization limit. The basic principles for Gallium and Arsenide polarized photoemitters are reviewed, and the extension of the basic technique to strained cathode structures is described. Results from laboratory measurements of strained photocathodes as well as operational results from the SLAC polarized source are presented.

  1. Polarization Observations of the Fermi blazars

    Science.gov (United States)

    Rani, Bindu; S. Jorstad, A. P. Marscher (BU, USA), K. Sokolovsky (IAASARS, Greece), I. Agudo (CSIC, Spain)

    2018-01-01

    Ever since the revolutionary discovery by the Fermi mission that active galactic nuclei (AGN) produce copious amounts of high-energy emission, its origin has remained elusive. Using high-frequency radio interferometry (VLBI) polarization imaging, we could probe the magnetic field topology of the compact high-energy emission regions in blazars. A case study for blazar 3C 279 reveals presence of multiple gamma-ray emission regions. The observed anti-correlation between gamma-ray flux and percentage polarization at optical bands challenges the current high-energy emission models. In addition to the turbulent component responsible for gamma-ray flares, our analysis suggests the presence of a steady polarized component having with its polarization direction aligned along the jet axis. The steady polarized component could possibly be the toroidal component of the helical magnetic field. To better understand the acceleration processes in jets, high-energy polarization missions are of great importance.

  2. Polarized electroluminescence from silicon nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    Bagraev, Nikolay; Danilovsky, Eduard; Gets, Dmitry; Klyachkin, Leonid; Kudryavtsev, Andrey; Kuzmin, Roman; Malyarenko, Anna [Ioffe Physical-Technical Institute, 194021 St. Petersburg (Russian Federation); Mashkov, Vladimir [St. Petersburg State Polytechnical University, 195251 St. Petersburg (Russian Federation)

    2012-05-15

    We present the first findings of the circularly polarized electroluminescence (CPEL) from silicon nanostructures which are the p-type ultra-narrow silicon quantum well (Si-QW) confined by {delta}-barriers heavily doped with boron. The CPEL dependences on the forward current and lateral electric field show the circularly polarized light emission which appears to be caused by the exciton recombination through the negative-U dipole boron centers at the Si-QW-{delta}-barriers interface with the assistance of phosphorus donors. (copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  3. Quantitative in vivo Analyses Reveal Calcium-dependent Phosphorylation Sites and Identifies a Novel Component of the Toxoplasma Invasion Motor Complex

    Science.gov (United States)

    Nebl, Thomas; Prieto, Judith Helena; Kapp, Eugene; Smith, Brian J.; Williams, Melanie J.; Yates, John R.; Cowman, Alan F.; Tonkin, Christopher J.

    2011-01-01

    Apicomplexan parasites depend on the invasion of host cells for survival and proliferation. Calcium-dependent signaling pathways appear to be essential for micronemal release and gliding motility, yet the target of activated kinases remains largely unknown. We have characterized calcium-dependent phosphorylation events during Toxoplasma host cell invasion. Stimulation of live tachyzoites with Ca2+-mobilizing drugs leads to phosphorylation of numerous parasite proteins, as shown by differential 2-DE display of 32[P]-labeled protein extracts. Multi-dimensional Protein Identification Technology (MudPIT) identified ∼546 phosphorylation sites on over 300 Toxoplasma proteins, including 10 sites on the actomyosin invasion motor. Using a Stable Isotope of Amino Acids in Culture (SILAC)-based quantitative LC-MS/MS analyses we monitored changes in the abundance and phosphorylation of the invasion motor complex and defined Ca2+-dependent phosphorylation patterns on three of its components - GAP45, MLC1 and MyoA. Furthermore, calcium-dependent phosphorylation of six residues across GAP45, MLC1 and MyoA is correlated with invasion motor activity. By analyzing proteins that appear to associate more strongly with the invasion motor upon calcium stimulation we have also identified a novel 15-kDa Calmodulin-like protein that likely represents the MyoA Essential Light Chain of the Toxoplasma invasion motor. This suggests that invasion motor activity could be regulated not only by phosphorylation but also by the direct binding of calcium ions to this new component. PMID:21980283

  4. Photoemission of Bi_{2}Se_{3} with Circularly Polarized Light: Probe of Spin Polarization or Means for Spin Manipulation?

    Directory of Open Access Journals (Sweden)

    J. Sánchez-Barriga

    2014-03-01

    Full Text Available Topological insulators are characterized by Dirac-cone surface states with electron spins locked perpendicular to their linear momenta. Recent theoretical and experimental work implied that this specific spin texture should enable control of photoelectron spins by circularly polarized light. However, these reports questioned the so far accepted interpretation of spin-resolved photoelectron spectroscopy. We solve this puzzle and show that vacuum ultraviolet photons (50–70 eV with linear or circular polarization indeed probe the initial-state spin texture of Bi_{2}Se_{3} while circularly polarized 6-eV low-energy photons flip the electron spins out of plane and reverse their spin polarization, with its sign determined by the light helicity. Our photoemission calculations, taking into account the interplay between the varying probing depth, dipole-selection rules, and spin-dependent scattering effects involving initial and final states, explain these findings and reveal proper conditions for light-induced spin manipulation. Our results pave the way for future applications of topological insulators in optospintronic devices.

  5. Geographical Income Polarization

    DEFF Research Database (Denmark)

    Azhar, Hussain; Jonassen, Anders Bruun

    inter municipal income inequality. Counter factual simulations show that rising property prices to a large part explain the rise in polarization. One side-effect of polarization is tendencies towards a parallel polarization of residence location patterns, where low skilled individuals tend to live......In this paper we estimate the degree, composition and development of geographical income polarization based on data at the individual and municipal level in Denmark from 1984 to 2002. Rising income polarization is reconfirmed when applying new polarization measures, the driving force being greater...

  6. Electron Beam Polarization Measurement Using Touschek Lifetime Technique

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Changchun; /Duke U., DFELL; Li, Jingyi; /Duke U., DFELL; Mikhailov, Stepan; /Duke U., DFELL; Popov, Victor; /Duke U., DFELL; Wu, Wenzhong; /Duke U., DFELL; Wu, Ying; /Duke U., DFELL; Chao, Alex; /SLAC; Xu, Hong-liang; /Hefei, NSRL; Zhang, Jian-feng; /Hefei, NSRL

    2012-08-24

    Electron beam loss due to intra-beam scattering, the Touschek effect, in a storage ring depends on the electron beam polarization. The polarization of an electron beam can be determined from the difference in the Touschek lifetime compared with an unpolarized beam. In this paper, we report on a systematic experimental procedure recently developed at Duke FEL laboratory to study the radiative polarization of a stored electron beam. Using this technique, we have successfully observed the radiative polarization build-up of an electron beam in the Duke storage ring, and determined the equilibrium degree of polarization and the time constant of the polarization build-up process.

  7. Complex microbiota of a Chinese "Fen" liquor fermentation starter (Fen-Daqu), revealed by culture-dependent and culture-independent methods

    NARCIS (Netherlands)

    Zheng, X.; Zheng, Y.; Han, B.; Zwietering, M.H.; Samson, R.A.; Boekhout, T.; Nout, M.J.R.

    2012-01-01

    Daqu is a traditional fermentation starter that is used for Chinese liquor production. Although partly mechanized, its manufacturing process has remained traditional. We investigated the microbial diversity of Fen-Daqu, a starter for light-flavour liquor, using combined culture-dependent and

  8. Polarization and ellipticity of high-order harmonics from aligned molecules generated by linearly polarized intense laser pulses

    International Nuclear Information System (INIS)

    Le, Anh-Thu; Lin, C. D.; Lucchese, R. R.

    2010-01-01

    We present theoretical calculations for polarization and ellipticity of high-order harmonics from aligned N 2 , CO 2 , and O 2 molecules generated by linearly polarized lasers. Within the rescattering model, the two polarization amplitudes of the harmonics are determined by the photo-recombination amplitudes for photons emitted with polarization parallel or perpendicular to the direction of the same returning electron wave packet. Our results show clear species-dependent polarization states, in excellent agreement with experiments. We further note that the measured polarization ellipse of the harmonic furnishes the needed parameters for a 'complete' experiment in molecules.

  9. Quantitative in vivo analyses reveal calcium-dependent phosphorylation sites and identifies a novel component of the Toxoplasma invasion motor complex.

    Directory of Open Access Journals (Sweden)

    Thomas Nebl

    2011-09-01

    Full Text Available Apicomplexan parasites depend on the invasion of host cells for survival and proliferation. Calcium-dependent signaling pathways appear to be essential for micronemal release and gliding motility, yet the target of activated kinases remains largely unknown. We have characterized calcium-dependent phosphorylation events during Toxoplasma host cell invasion. Stimulation of live tachyzoites with Ca²⁺-mobilizing drugs leads to phosphorylation of numerous parasite proteins, as shown by differential 2-DE display of ³²[P]-labeled protein extracts. Multi-dimensional Protein Identification Technology (MudPIT identified ∼546 phosphorylation sites on over 300 Toxoplasma proteins, including 10 sites on the actomyosin invasion motor. Using a Stable Isotope of Amino Acids in Culture (SILAC-based quantitative LC-MS/MS analyses we monitored changes in the abundance and phosphorylation of the invasion motor complex and defined Ca²⁺-dependent phosphorylation patterns on three of its components--GAP45, MLC1 and MyoA. Furthermore, calcium-dependent phosphorylation of six residues across GAP45, MLC1 and MyoA is correlated with invasion motor activity. By analyzing proteins that appear to associate more strongly with the invasion motor upon calcium stimulation we have also identified a novel 15-kDa Calmodulin-like protein that likely represents the MyoA Essential Light Chain of the Toxoplasma invasion motor. This suggests that invasion motor activity could be regulated not only by phosphorylation but also by the direct binding of calcium ions to this new component.

  10. Switching the response of metasurfaces in polarization standing waves

    OpenAIRE

    Fang, X.; MacDonald, K.F.; Zheludev, N.I.

    2015-01-01

    We demonstrate experimentally that standing waves of polarization, as opposed to intensity, can be engaged to coherently control light-matter interactions in planar photonic nanostructures, presenting unique opportunities for all-optical data processing and polarization-dependent molecular spectroscopy. Such waves, formed by counter-propagating (linear or circular) orthogonally polarized beams can, for example, uniquely detect polarization conversion, planar chirality and related asymmetric t...

  11. Polarized Light Corridor Demonstrations.

    Science.gov (United States)

    Davies, G. R.

    1990-01-01

    Eleven demonstrations of light polarization are presented. Each includes a brief description of the apparatus and the effect demonstrated. Illustrated are strain patterns, reflection, scattering, the Faraday Effect, interference, double refraction, the polarizing microscope, and optical activity. (CW)

  12. RNA-sequencing of a mouse-model of spinal muscular atrophy reveals tissue-wide changes in splicing of U12-dependent introns

    DEFF Research Database (Denmark)

    Doktor, Thomas Koed; Hua, Yimin; Andersen, Henriette Skovgaard

    2016-01-01

    unknown. It is likely that aberrant splicing of genes expressed in motor neurons is involved in SMA pathogenesis, but increasing evidence indicates that pathologies also exist in other tissues. We present here a comprehensive RNA-seq study that covers multiple tissues in an SMA mouse model. We show...... elevated U12-intron retention in all examined tissues from SMA mice, and that U12-dependent intron retention is induced upon siRNA knock-down of SMN in HeLa cells. Furthermore, we show that retention of U12-dependent introns is mitigated by ASO treatment of SMA mice and that many transcriptional changes......Spinal Muscular Atrophy (SMA) is a neuromuscular disorder caused by insufficient levels of the Survival of Motor Neuron (SMN) protein. SMN is expressed ubiquitously and functions in RNA processing pathways that include trafficking of mRNA and assembly of snRNP complexes. Importantly, SMA severity...

  13. Polarized Moessbauer transitions

    International Nuclear Information System (INIS)

    Barb, D.

    1975-01-01

    Theoretical aspects of the emission, absorption and scattering of polarized gamma rays are reviewed for a general case of combined magnetic and electric hyperfine interactions; various possibilities of obtaining polarized gamma sources are described and examples are given of the applications of Moessbauer spectroscopy with polarized gamma rays in solving problems of solid state physics. (A.K.)

  14. Polarization Induced Changes in LSM Thin Film Electrode Composition Observed by In Operando Raman Spectroscopy and TOF-SIMS

    DEFF Research Database (Denmark)

    McIntyre, Melissa D.; Traulsen, Marie Lund; Norrman, Kion

    2015-01-01

    electrical polarizations. Raman spectra recorded during polarization showed shifts in spectral intensities that were both reversible and dependent on the applied potential. Spectral changes were assigned to changes in the LSM electronic structure that resulted from changing oxide concentrations in the near......Polarization induced changes in LSM electrode composition were investigated by utilizing in operando Raman spectroscopy and post mortem TOF-SIMS depth profiling. Experiments were conducted on cells with 160 nm thick (La0.85Sr0.15)0.9MnO3±δ thin film electrodes in 10% O2 at 700 °C under various......-surface region. Ex situ TOF-SIMS depth profiles were recorded through the LSM electrodes and revealed distinct compositional changes throughout the electrodes. The electrode elements and impurities separated into well-defined layers that were more stratified for stronger applied polarizations. The mechanism...

  15. Aspartic acid substitutions in monoamine oxidase-A reveal both catalytic-dependent and -independent influences on cell viability and proliferation.

    Science.gov (United States)

    Wei, Zelan; Satram-Maharaj, Tamara; Chaharyn, Bradley; Kuski, Kelly; Pennington, Paul R; Cao, Xia; Chlan, Jennifer; Mousseau, Darrell D

    2012-11-01

    Post-translational influences could underlie the ambiguous roles of monoamine oxidase-A (MAO-A) in pathologies such as depression, cancer and Alzheimer disease. In support of this, we recently demonstrated that the Ca²⁺-sensitive component of MAO-A catalytic activity is inhibited by a pro-survival p38 (MAPK)-dependent mechanism. We substituted three aspartic acid (D) residues in human MAO-A that reside in putative Ca²⁺-binding motifs and overexpressed the individual proteins in the human HEK293 cell line. We assayed the overexpressed proteins for catalytic activity and for their influence on cell viability (using MTT conversion and trypan blue exclusion) and proliferation/DNA synthesis [using bromodeoxyuridine (BrdU) incorporation]. Innate MAO-A catalytic activity (and the capacity for generating hydrogen peroxide) was unaffected by the D61A substitution, but inhibited moderately or completely by the D248A and D328G substitutions, respectively. The Ca²⁺-sensitive activities of wild-type and D248A MAO-A proteins were enhanced by treatment with the selective p38(MAPK) inhibitor, SB203580, but was completely abrogated by the D61A substitution. Monoamine oxidase-A(D61A) was toxic to cells and exerted no effect on cell proliferation, while MAO-A(D248A) was generally comparable to wild-type MAO-A. As expected, the catalytic-dead MAO-A(D328G) was not cytotoxic, but unexpectedly enhanced both MTT conversion and BrdU staining. Variant-dependent changes in Bax and Bcl-2/Bcl-XL protein expression were observed. A different pattern of effects in N2-a cells suggests cell line-dependent roles for MAO-A. A catalytic-dependent mechanism influences MAO-A-mediated cytotoxicity, whereas a catalytic-independent mechanism contributes to proliferation. Context-dependent inputs by either mechanism could underlie the ambiguous pathological contributions of MAO-A.

  16. Nonlinear optical responses to circularly polarized lights of the surface state of a topological insulator

    Science.gov (United States)

    Misawa, Tetsuro; Yokoyama, Takehito; Murakami, Shuichi

    2012-02-01

    Recent photoelectron spectroscopy experiments have revealed the presence of the Dirac cone on the surface of the topological insulator and its spin-splitting due to the spin-orbit interaction. In general, on spin-orbit coupled systems, electric fields induce spin polarizations as linear and nonlinear responses. Here we investigate the inverse Faraday effect on the surface of the topological insulator. The inverse Faraday effect is a non-linear optical effect where a circularly polarized light induces a dc spin polarization. We employ the Keldysh Green's function method to calculate the induced spin polarization and discuss its frequency dependence. In particular, in the low frequency limit, our analytical result gives the spin polarization proportional to the frequency and the square of the lifetime. As for the finite frequency regime, we employ numerical methods to discuss the resonance due to interband transitions. We also discuss the photogalvanic effect, where an illumination of a circular polarized light generates the dc charge current. Lastly, we evaluate those quantities with realistic parameters.[4pt] [1] T. Misawa, T. Yokoyama, S. Murakami, Phys. Rev. B84, 165407 (2011).

  17. Polarized semi-inclusive deep-inelastic scattering on transversely and longitudinally polarized nucleons at HERMES

    International Nuclear Information System (INIS)

    Hommes, B.

    2005-01-01

    The HERMES experiment has measured double spin asymmetries in the cross section for deep-inelastic scattering of longitudinal polarized positrons off longitudinal polarized hydrogen and deuterium targets. From these asymmetries, based on inclusive and semi-inclusive measurements, polarized quark distributions were extracted as a function of x. Single-spin azimuthal asymmetries in semi-inclusive pion production were measured by the HERMES experiment for the first time, with a transversely polarized hydrogen target. Two different sine-dependencies were extracted which can be related to the quark transversity distribution h q 1 (x) and the Sivers function (Author)

  18. Physics results from polarized DIS

    International Nuclear Information System (INIS)

    Ramsey, G. P.

    1998-01-01

    We have extracted polarized nucleon distributions from recent data at CERN, SLAC and DESY. The flavor-dependent valence and sea quark spin distributions are determined for each experiment. We take into account possible differences in the up and down sea distributions, and assume that the strange sea contribution is suppressed by mass effects. Physics results determined from different experiments are compared, including higher order corrections

  19. Physics results from polarized DIS.

    Energy Technology Data Exchange (ETDEWEB)

    Ramsey, G. P.

    1998-03-23

    We have extracted polarized nucleon distributions from recent data at CERN, SLAC and DESY. The flavor-dependent valence and sea quark spin distributions are determined for each experiment. We take into account possible differences in the up and down sea distributions, and assume that the strange sea contribution is suppressed by mass effects. Physics results determined from different experiments are compared, including higher order corrections.

  20. Polarization Monitoring of the Lens System JVAS B0218+357

    Directory of Open Access Journals (Sweden)

    Andrew Biggs

    2017-10-01

    Full Text Available Monitoring of the lens system JVAS B0218+357 with the Fermi Gamma-ray Space Telescope measured a different time delay to that derived from radio observations. We have re-analysed three months of archival Very Large Array data to produce variability curves with an average sampling of one epoch per day in total flux, polarized flux and polarization position angle (PPA at 15, 8.4 and 5 GHz. The variability is particularly strong in polarized flux. Dense sampling and improved subtraction of the Einstein ring has allowed us to produce superior variability curves and a preliminary analysis has resulted in a time delay (11.5 days which agrees well with the γ -ray value. Both images of 0218+357 are subject to strong Faraday rotation and depolarization as a result of the radio waves passing through the interstellar medium of the spiral lens galaxy. Our data reveal frequency-dependent variations in the PPA that are different in each image and which must therefore result from variable Faraday rotation in the lens galaxy on timescales of a few days. Our analysis has revealed systematic errors in the polarization position angle measurements that strongly correlate with hour angle. Although we have been able to correct for these, we caution that all VLA polarization observations are potentially affected.

  1. Voltage-Dependent Rhythmogenic Property of Respiratory Pre-Bötzinger Complex Glutamatergic, Dbx1-Derived, and Somatostatin-Expressing Neuron Populations Revealed by Graded Optogenetic Inhibition.

    Science.gov (United States)

    Koizumi, Hidehiko; Mosher, Bryan; Tariq, Mohammad F; Zhang, Ruli; Koshiya, Naohiro; Smith, Jeffrey C

    2016-01-01

    The rhythm of breathing in mammals, originating within the brainstem pre-Bötzinger complex (pre-BötC), is presumed to be generated by glutamatergic neurons, but this has not been directly demonstrated. Additionally, developmental expression of the transcription factor Dbx1 or expression of the neuropeptide somatostatin (Sst), has been proposed as a marker for the rhythmogenic pre-BötC glutamatergic neurons, but it is unknown whether these other two phenotypically defined neuronal populations are functionally equivalent to glutamatergic neurons with regard to rhythm generation. To address these problems, we comparatively investigated, by optogenetic approaches, the roles of pre-BötC glutamatergic, Dbx1-derived, and Sst-expressing neurons in respiratory rhythm generation in neonatal transgenic mouse medullary slices in vitro and also more intact adult perfused brainstem-spinal cord preparations in situ. We established three different triple-transgenic mouse lines with Cre-driven Archaerhodopsin-3 (Arch) expression selectively in glutamatergic, Dbx1-derived, or Sst-expressing neurons for targeted photoinhibition. In each line, we identified subpopulations of rhythmically active, Arch-expressing pre-BötC inspiratory neurons by whole-cell recordings in medullary slice preparations in vitro, and established that Arch-mediated hyperpolarization of these inspiratory neurons was laser power dependent with equal efficacy. By site- and population-specific graded photoinhibition, we then demonstrated that inspiratory frequency was reduced by each population with the same neuronal voltage-dependent frequency control mechanism in each state of the respiratory network examined. We infer that enough of the rhythmogenic pre-BötC glutamatergic neurons also have the Dbx1 and Sst expression phenotypes, and thus all three phenotypes share the same voltage-dependent frequency control property.

  2. Voltage-Dependent Rhythmogenic Property of Respiratory Pre-Bötzinger Complex Glutamatergic, Dbx1-Derived, and Somatostatin-Expressing Neuron Populations Revealed by Graded Optogenetic Inhibition123

    Science.gov (United States)

    Koizumi, Hidehiko; Mosher, Bryan; Tariq, Mohammad F.; Zhang, Ruli

    2016-01-01

    Abstract The rhythm of breathing in mammals, originating within the brainstem pre-Bötzinger complex (pre-BötC), is presumed to be generated by glutamatergic neurons, but this has not been directly demonstrated. Additionally, developmental expression of the transcription factor Dbx1 or expression of the neuropeptide somatostatin (Sst), has been proposed as a marker for the rhythmogenic pre-BötC glutamatergic neurons, but it is unknown whether these other two phenotypically defined neuronal populations are functionally equivalent to glutamatergic neurons with regard to rhythm generation. To address these problems, we comparatively investigated, by optogenetic approaches, the roles of pre-BötC glutamatergic, Dbx1-derived, and Sst-expressing neurons in respiratory rhythm generation in neonatal transgenic mouse medullary slices in vitro and also more intact adult perfused brainstem-spinal cord preparations in situ. We established three different triple-transgenic mouse lines with Cre-driven Archaerhodopsin-3 (Arch) expression selectively in glutamatergic, Dbx1-derived, or Sst-expressing neurons for targeted photoinhibition. In each line, we identified subpopulations of rhythmically active, Arch-expressing pre-BötC inspiratory neurons by whole-cell recordings in medullary slice preparations in vitro, and established that Arch-mediated hyperpolarization of these inspiratory neurons was laser power dependent with equal efficacy. By site- and population-specific graded photoinhibition, we then demonstrated that inspiratory frequency was reduced by each population with the same neuronal voltage-dependent frequency control mechanism in each state of the respiratory network examined. We infer that enough of the rhythmogenic pre-BötC glutamatergic neurons also have the Dbx1 and Sst expression phenotypes, and thus all three phenotypes share the same voltage-dependent frequency control property. PMID:27275007

  3. Emission polarization study on quartz and calcite.

    Science.gov (United States)

    Vincent, R. K.

    1972-01-01

    Calculation of the spectral emission polarization of quartz and calcite polished plates for observation angles of 20 and 70 deg by the substitution of complex index of refraction values for each mineral into Fresnel's equations. The emission polarization is shown to be quite wavelength-dependent, demonstrating that selected narrow or medium-width spectral bands exhibit a significantly higher percentage of polarization than a broad spectral band for these two minerals. Field measurements with a broadband infrared radiometer yield polarizations on the order of 2% for a coarse-grained granite rock and beach sand (both quartz-rich). This implies that a more sensitive detector with a selected medium-width filter may be capable of measuring emission polarization accurately enough to make this parameter useful as a remote sensing tool for discrimination among rocks on the basis of texture.

  4. A note on polarized light from magnetars

    Energy Technology Data Exchange (ETDEWEB)

    Capparelli, L.M.; Damiano, A.; Polosa, A.D. [Sapienza Universita di Roma, Dipartimento di Fisica, Rome (Italy); INFN, Rome (Italy); Maiani, L. [CERN, Theory Department, Geneva (Switzerland)

    2017-11-15

    In a recent paper it is claimed that vacuum birefringence has been experimentally observed for the first time by measuring the degree of polarization of visible light from a magnetar candidate, a neutron star with a magnetic field presumably as large as B ∝ 10{sup 13} G. The role of such a strong magnetic field is twofold. First, the surface of the star emits, at each point, polarized light with linear polarization correlated with the orientation of the magnetic field. Depending on the relative orientation of the magnetic axis of the star with the direction to the distant observer, a certain degree of polarization should be visible. Second, the strong magnetic field in the vacuum surrounding the star could enhance the effective degree of polarization observed: vacuum birefringence. We compare experimental data and theoretical expectations concluding that the conditions to support a claim of strong evidence of vacuum birefringence effects are not met. (orig.)

  5. Arabidopsis Pol II-Dependent in Vitro Transcription System Reveals Role of Chromatin for Light-Inducible rbcS Gene Transcription1

    Science.gov (United States)

    Ido, Ayaka; Iwata, Shinya; Iwata, Yuka; Igarashi, Hisako; Hamada, Takahiro; Sonobe, Seiji; Sugiura, Masahiro; Yukawa, Yasushi

    2016-01-01

    In vitro transcription is an essential tool to study the molecular mechanisms of transcription. For over a decade, we have developed an in vitro transcription system from tobacco (Nicotiana tabacum)-cultured cells (BY-2), and this system supported the basic activities of the three RNA polymerases (Pol I, Pol II, and Pol III). However, it was not suitable to study photosynthetic genes, because BY-2 cells have lost their photosynthetic activity. Therefore, Arabidopsis (Arabidopsis thaliana) in vitro transcription systems were developed from green and etiolated suspension cells. Sufficient in vitro Pol II activity was detected after the minor modification of the nuclear soluble extracts preparation method; removal of vacuoles from protoplasts and L-ascorbic acid supplementation in the extraction buffer were particularly effective. Surprisingly, all four Arabidopsis Rubisco small subunit (rbcS-1A, rbcS-1B, rbcS-2B, and rbcS-3B) gene members were in vitro transcribed from the naked DNA templates without any light-dependent manner. However, clear light-inducible transcriptions were observed using chromatin template of rbcS-1A gene, which was prepared with a human nucleosome assembly protein 1 (hNAP1) and HeLa histones. This suggested that a key determinant of light-dependency through the rbcS gene transcription was a higher order of DNA structure (i.e. chromatin). PMID:26662274

  6. Transcriptome analysis of cyclic AMP-dependent protein kinase A–regulated genes reveals the production of the novel natural compound fumipyrrole by Aspergillus fumigatus

    Science.gov (United States)

    Macheleidt, Juliane; Scherlach, Kirstin; Neuwirth, Toni; Schmidt-Heck, Wolfgang; Straßburger, Maria; Spraker, Joseph; Baccile, Joshua A.; Schroeder, Frank C.; Keller, Nancy P.; Hertweck, Christian; Heinekamp, Thorsten; Brakhage, Axel A.

    2015-01-01

    Summary Aspergillus fumigatus is an opportunistic human pathogenic fungus causing life-threatening infections in immunocompromised patients. Adaptation to different habitats and also virulence of the fungus depends on signal perception and transduction by modules such as the cyclic AMP-dependent protein kinase A (PKA) pathway. Here, by transcriptome analysis, 632 differentially regulated genes of this important signaling cascade were identified, including 23 putative transcriptional regulators. The highest upregulated transcription factor gene was located in a previously unknown secondary metabolite gene cluster, which we named fmp, encoding an incomplete nonribosomal peptide synthetase, FmpE. Overexpression of the regulatory gene fmpR using the TetOn system led to the specific expression of the other six genes of the fmp cluster. Metabolic profiling of wild type and fmpR overexpressing strain by HPLC-DAD and HPLCHRESI-MS and structure elucidation by NMR led to identification of 5-benzyl-1H-pyrrole-2-carboxylic acid, which we named fumipyrrole. Fumipyrrole was not described as natural product yet. Chemical synthesis of fumipyrrole confirmed its structure. Interestingly, deletion of fmpR or fmpE led to reduced growth and sporulation of the mutant strains. Although fmp cluster genes were transcribed in infected mouse lungs, deletion of fmpR resulted in wild-type virulence in a murine infection model. PMID:25582336

  7. Positional cloning reveals strain-dependent expression of Trim16 to alter susceptibility to bleomycin-induced pulmonary fibrosis in mice.

    Directory of Open Access Journals (Sweden)

    Anguel N Stefanov

    Full Text Available Pulmonary fibrosis is a disease of significant morbidity, with no effective therapeutics and an as yet incompletely defined genetic basis. The chemotherapeutic agent bleomycin induces pulmonary fibrosis in susceptible C57BL/6J mice but not in mice of the C3H/HeJ strain, and this differential strain response has been used in prior studies to map bleomycin-induced pulmonary fibrosis susceptibility loci named Blmpf1 and Blmpf2. In this study we isolated the quantitative trait gene underlying Blmpf2 initially by histologically phenotyping the bleomycin-induced lung disease of sublines of congenic mice to reduce the linkage region to 13 genes. Of these genes, Trim16 was identified to have strain-dependent expression in the lung, which we determined was due to sequence variation in the promoter. Over-expression of Trim16 by plasmid injection increased pulmonary fibrosis, and bronchoalveolar lavage levels of both interleukin 12/23-p40 and neutrophils, in bleomycin treated B6.C3H-Blmpf2 subcongenic mice compared to subcongenic mice treated with bleomycin only, which follows the C57BL/6J versus C3H/HeJ strain difference in these traits. In summary we demonstrate that genetic variation in Trim16 leads to its strain-dependent expression, which alters susceptibility to bleomycin-induced pulmonary fibrosis in mice.

  8. Optically pumped electron spin polarized targets for use in the production of polarized ion beams

    International Nuclear Information System (INIS)

    Anderson, L.W.

    1979-01-01

    The production of relatively dense electron spin polarized alkali metal vapor targets by optical pumping with intense cw dye lasers is discussed. The target density and electron spin polarization depend on the dye laser intensity and bandwidth, the magnetic field at the target, and the electron spin depolarization time. For example in a magnetic field of 1.5 x 10 3 G, and using 1 W dye laser with a bandwidth of 10 10 Hz one can construct an electron spin polarized Na vapor target with a target thickness of 1.6 x 10 13 atoms/cm 2 and an average electron spin polarization of about 90% even though the Na atoms are completely depolarized at every wall collision. Possible uses of the electron spin polarized targets for the production of intense beams of polarized H - or 3 He - ions are discussed. (orig.)

  9. The Physics of Polarization

    Science.gov (United States)

    Landi Degl'Innocenti, Egidio

    2015-10-01

    The introductory lecture that has been delivered at this Symposium is a condensed version of an extended course held by the author at the XII Canary Island Winter School from November 13 to November 21, 2000. The full series of lectures can be found in Landi Degl'Innocenti (2002). The original reference is organized in 20 Sections that are here itemized: 1. Introduction, 2. Description of polarized radiation, 3. Polarization and optical devices: Jones calculus and Muller matrices, 4. The Fresnel equations, 5. Dichroism and anomalous dispersion, 6. Polarization in everyday life, 7. Polarization due to radiating charges, 8. The linear antenna, 9. Thomson scattering, 10. Rayleigh scattering, 11. A digression on Mie scattering, 12. Bremsstrahlung radiation, 13. Cyclotron radiation, 14. Synchrotron radiation, 15. Polarization in spectral lines, 16. Density matrix and atomic polarization, 17. Radiative transfer and statistical equilibrium equations, 18. The amplification condition in polarized radiative transfer, and 19. Coupling radiative transfer and statistical equilibrium equations.

  10. Polarization digital holographic microscopy using low-cost liquid crystal polarization rotators

    Science.gov (United States)

    Dovhaliuk, Rostyslav Yu

    2018-02-01

    Polarization imaging methods are actively used to study anisotropic objects. A number of methods and systems, such as imaging polarimeters, were proposed to measure the state of polarization of light that passed through the object. Digital holographic and interferometric approaches can be used to quantitatively measure both amplitude and phase of a wavefront. Using polarization modulation optics, the measurement capabilities of such interference-based systems can be extended to measure polarization-dependent parameters, such as phase retardation. Different kinds of polarization rotators can be used to alternate the polarization of a reference beam. Liquid crystals are used in a rapidly increasing number of different optoelectronic devices. Twisted nematic liquid crystals are widely used as amplitude modulators in electronic displays and light valves or shutter glass. Such devices are of particular interest for polarization imaging, as they can be used as polarization rotators, and due to large-scale manufacturing have relatively low cost. A simple Mach-Zehnder polarized holographic setup that uses modified shutter glass as a polarization rotator is demonstrated. The suggested approach is experimentally validated by measuring retardation of quarter-wave film.

  11. Evaluation of Waveform Structure Features on Time Domain Target Recognition under Cross Polarization

    Science.gov (United States)

    Selver, M. A.; Seçmen, M.; Zoral, E. Y.

    2016-08-01

    Classification of aircraft targets from scattered electromagnetic waves is a challenging application, which suffers from aspect angle dependency. In order to eliminate the adverse effects of aspect angle, various strategies were developed including the techniques that rely on extraction of several features and design of suitable classification systems to process them. Recently, a hierarchical method, which uses features that take advantage of waveform structure of the scattered signals, is introduced and shown to have effective results. However, this approach has been applied to the special cases that consider only a single planar component of electric field that cause no-cross polarization at the observation point. In this study, two small scale aircraft models, Boeing-747 and DC-10, are selected as the targets and various polarizations are used to analyse the cross-polarization effects on system performance of the aforementioned method. The results reveal the advantages and the shortcomings of using waveform structures in time-domain target identification.

  12. Genome-Wide Analysis of Chromatin States Reveals Distinct Mechanisms of Sex-Dependent Gene Regulation in Male and Female Mouse Liver

    Science.gov (United States)

    Sugathan, Aarathi

    2013-01-01

    Chromatin state maps were developed to elucidate sex differences in chromatin structure and their impact on sex-differential chromatin accessibility and sex-biased gene expression in mouse liver. Genes in active, inactive, and poised chromatin states exhibited differential responsiveness to ligand-activated nuclear receptors and distinct enrichments for functional gene categories. Sex-biased genes were clustered by chromatin environments and mapped to DNase-hypersensitive sites (DHS) classified by sex bias in chromatin accessibility and enhancer modifications. Results were integrated with genome-wide binding data for five transcription factors implicated in growth hormone-regulated, sex-biased liver gene expression, leading to the following findings. (i) Sex-biased DHS, but not sex-biased genes, are frequently characterized by sex-differential chromatin states, indicating distal regulation. (ii) Trimethylation of histone H3 at K27 (H3K27me3) is a major sex-biased repressive mark at highly female-biased but not at highly male-biased genes. (iii) FOXA factors are associated with sex-dependent chromatin opening at male-biased but not female-biased regulatory sites. (iv) Sex-biased STAT5 binding is enriched at sex-biased DHS marked as active enhancers and preferentially targets sex-biased genes with sex-differences in local chromatin marks. (v) The male-biased repressor BCL6 preferentially targets female-biased genes and regulatory sites in a sex-independent chromatin state. (vi) CUX2, a female-specific repressor of male-biased genes, also activates strongly female-biased genes, in association with loss of H3K27me3 marks. Chromatin states are thus a major determinant of sex-biased chromatin accessibility and gene expression, with FOXA pioneer factors proposed to confer sex-dependent chromatin opening and STAT5, but not BCL6, regulating sex-biased genes by binding to sites in a sex-biased chromatin state. PMID:23836885

  13. Suomi National Polar-Orbiting Partnership Visible Infrared Imaging Radiometer Suite Polarization Sensitivity Analysis

    Science.gov (United States)

    Sun, Junqiang; Xiong, Xiaoxiong; Waluschka, Eugene; Wang, Menghua

    2016-01-01

    The Visible Infrared Imaging Radiometer Suite (VIIRS) is one of five instruments onboard the Suomi National Polar-Orbiting Partnership (SNPP) satellite that launched from Vandenberg Air Force Base, California, on October 28, 2011. It is a whiskbroom radiometer that provides +/-56.28deg scans of the Earth view. It has 22 bands, among which 14 are reflective solar bands (RSBs). The RSBs cover a wavelength range from 410 to 2250 nm. The RSBs of a remote sensor are usually sensitive to the polarization of incident light. For VIIRS, it is specified that the polarization factor should be smaller than 3% for 410 and 862 nm bands and 2.5% for other RSBs for the scan angle within +/-45deg. Several polarization sensitivity tests were performed prelaunch for SNPP VIIRS. The first few tests either had large uncertainty or were less reliable, while the last one was believed to provide the more accurate information about the polarization property of the instrument. In this paper, the measured data in the last polarization sensitivity test are analyzed, and the polarization factors and phase angles are derived from the measurements for all the RSBs. The derived polarization factors and phase angles are band, detector, and scan angle dependent. For near-infrared bands, they also depend on the half-angle mirror side. Nevertheless, the derived polarization factors are all within the specification, although the strong detector dependence of the polarization parameters was not expected. Compared to the Moderate Resolution Imaging Spectroradiometer on both Aqua and Terra satellites, the polarization effect on VIIRS RSB is much smaller.

  14. Polarization phenomena in quantum chromodynamics

    Energy Technology Data Exchange (ETDEWEB)

    Brodsky, S.J. [Stanford Univ., CA (United States)

    1994-12-01

    The author discusses a number of interrelated hadronic spin effects which test fundamental features of perturbative and nonperturbative QCD. For example, the anomalous magnetic moment of the proton and the axial coupling g{sub A} on the nucleon are shown to be related to each other for fixed proton radius, independent of the form of the underlying three-quark relativistic quark wavefunction. The renormalization scale and scheme ambiguities for the radiative corrections to the Bjorken sum rule for the polarized structure functions can be eliminated by using commensurate scale relations with other observables. Other examples include (a) new constraints on the shape and normalization of the polarized quark and gluon structure functions of the proton at large and small x{sub bj}; (b) consequences of the principle of hadron retention in high x{sub F} inclusive reactions; (c) applications of hadron helicity conservation to high momentum transfer exclusive reactions; and (d) the dependence of nuclear structure functions and shadowing on virtual photon polarization. The author also discusses the implications of a number of measurements which are in striking conflict with leading-twist perturbative QCD predictions, such as the extraordinarily large spin correlation A{sub NN} observed in large angle proton-proton scattering, the anomalously large {rho}{pi} branching ratio of the J/{psi}, and the rapidly changing polarization dependence of both J/{psi} and continuum lepton pair hadroproduction observed at large x{sub F}. The azimuthal angular dependence of the Drell-Yan process is shown to be highly sensitive to the projectile distribution amplitude, the fundamental valence light-cone wavefunction of the hadron.

  15. Maris polarization in neutron-rich nuclei

    Science.gov (United States)

    Shubhchintak; Bertulani, C. A.; Aumann, T.

    2018-03-01

    We present a theoretical study of the Maris polarization effect and its application in quasi-free reactions to assess information on the structure of exotic nuclei. In particular, we explore the dependence of the polarization effect on neutron excess and neutron-skin thickness. We discuss the uncertainties in the calculations of triple differential cross sections and of analyzing powers due the choices of various nucleon-nucleon interactions and optical potentials and the limitations of the method. Our study implies that polarization variables in (p, 2p) reactions in inverse kinematics can be an effective probe of single-particle structure of nuclei in radioactive-beam facilities.

  16. Projective geometry for polarization in geometric quantization

    International Nuclear Information System (INIS)

    Campbell, P.; Dodson, C.T.J.

    1976-12-01

    It is important to know the extent to which the procedure of geometric quantization depends on a choice of polarization of the symplectic manifold that is the classical phase space. Published results have so far been restricted to real and transversal polarizations. Here we also consider these cases by presenting a formulation in terms of projective geometry. It turns out that there is a natural characterization of real transversal polarizations and maps among them using projective concepts. We give explicit constructions for Rsup(2n)

  17. On the thermal properties of polarized nuclear matter

    International Nuclear Information System (INIS)

    Hassan, M.Y.M.; Montasser, S.S.; Ramadan, S.

    1979-08-01

    The thermal properties of polarized nuclear matter are calculated using Skyrme III interaction modified by Dabrowski for polarized nuclear matter. The temperature dependence of the volume, isospin, spin and spin isospin pressure and energies are determined. The temperature, isospin, spin and spin isospin dependence of the equilibrium Fermi momentum is also discussed. (author)

  18. Current density functional theory for optical spectra : A polarization functional

    NARCIS (Netherlands)

    Boeij, P.L. de; Kootstra, F.; Berger, J.A.; Leeuwen, R. van; Snijders, J.G.

    2001-01-01

    In this paper we present a new approach to calculate optical spectra, which for the first time uses a polarization dependent functional within current density functional theory (CDFT), which was proposed by Vignale and Kohn. This polarization dependent functional includes exchange-correlation (xc)

  19. Advantages of polarization experiments at RHIC

    International Nuclear Information System (INIS)

    Underwood, D.G.

    1990-01-01

    We point out various spin experiments that could be done if the polarized beam option is pursued at RHIC. The advantages of RHIC for investigating several current and future physics problems are discussed. In particular, the gluon spin dependent structure function of the nucleon could be measured cleanly and systematically. Relevant experience developed in conjunction with the Fermilab Polarized Beam program is also presented. 8 refs., 2 tabs

  20. Unlocking the Full Potential of Extragalactic Lyα through Its Polarization Properties

    Science.gov (United States)

    Eide, Marius B.; Gronke, Max; Dijkstra, Mark; Hayes, Matthew

    2018-04-01

    Lyα is a powerful astrophysical probe. Not only is it ubiquitous at high redshifts, it is also a resonant line, making Lyα photons scatter. This scattering process depends on the physical conditions of the gas through which Lyα propagates, and these conditions are imprinted on observables such as the Lyα spectrum and its surface brightness profile. In this work, we focus on a less-used observable capable of probing any scattering process: polarization. We implement the density matrix formalism of polarization into the Monte Carlo radiative transfer code tlac. This allows us to treat it as a quantum mechanical process where single photons develop and lose polarization from scatterings in arbitrary gas geometries. We explore static and expanding ellipsoids, biconical outflows, and clumpy multiphase media. We find that photons become increasingly polarized as they scatter and diffuse into the wings of the line profiles, making scattered Lyα polarized in general. The degree and orientation of Lyα polarization depends on the kinematics and distribution of the scattering H I gas. We find that it generally probes spatial or velocity space asymmetries and aligns itself tangentially to the emission source. We show that the mentioned observables, when studied separately, can leave similar signatures for different source models. We conclude by revealing how a joint analysis of the Lyα spectra, surface brightness profiles, and polarization can break these degeneracies and help us extract unique physical information on galaxies and their environments from their strongest, most prominent emission line.

  1. Molecular description of eye defects in the zebrafish Pax6b mutant, sunrise, reveals a Pax6b-dependent genetic network in the developing anterior chamber.

    Directory of Open Access Journals (Sweden)

    Masanari Takamiya

    Full Text Available The cornea is a central component of the camera eye of vertebrates and even slight corneal disturbances severely affect vision. The transcription factor PAX6 is required for normal eye development, namely the proper separation of the lens from the developing cornea and the formation of the iris and anterior chamber. Human PAX6 mutations are associated with severe ocular disorders such as aniridia, Peters anomaly and chronic limbal stem cell insufficiency. To develop the zebrafish as a model for corneal disease, we first performed transcriptome and in situ expression analysis to identify marker genes to characterise the cornea in normal and pathological conditions. We show that, at 7 days post fertilisation (dpf, the zebrafish cornea expresses the majority of marker genes (67/84 tested genes found also expressed in the cornea of juvenile and adult stages. We also characterised homozygous pax6b mutants. Mutant embryos have a thick cornea, iris hypoplasia, a shallow anterior chamber and a small lens. Ultrastructure analysis revealed a disrupted corneal endothelium. pax6b mutants show loss of corneal epithelial gene expression including regulatory genes (sox3, tfap2a, foxc1a and pitx2. In contrast, several genes (pitx2, ctnnb2, dcn and fabp7a were ectopically expressed in the malformed corneal endothelium. Lack of pax6b function leads to severe disturbance of the corneal gene regulatory programme.

  2. Regulation of per and cry genes reveals a central role for the D-box enhancer in light-dependent gene expression.

    Directory of Open Access Journals (Sweden)

    Philipp Mracek

    Full Text Available Light serves as a key environmental signal for synchronizing the circadian clock with the day night cycle. The zebrafish represents an attractive model for exploring how light influences the vertebrate clock mechanism. Direct illumination of most fish tissues and cell lines induces expression of a broad range of genes including DNA repair, stress response and key clock genes. We have previously identified D- and E-box elements within the promoter of the zebrafish per2 gene that together direct light-induced gene expression. However, is the combined regulation by E- and D-boxes a general feature for all light-induced gene expression? We have tackled this question by examining the regulation of additional light-inducible genes. Our results demonstrate that with the exception of per2, all other genes tested are not induced by light upon blocking of de novo protein synthesis. We reveal that a single D-box serves as the principal light responsive element within the cry1a promoter. Furthermore, upon inhibition of protein synthesis D-box mediated gene expression is abolished while the E-box confers light driven activation as observed in the per2 gene. Given the existence of different photoreceptors in fish cells, our results implicate the D-box enhancer as a general convergence point for light driven signaling.

  3. Crystal Structure of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated Csn2 Protein Revealed Ca[superscript 2+]-dependent Double-stranded DNA Binding Activity

    Energy Technology Data Exchange (ETDEWEB)

    Nam, Ki Hyun; Kurinov, Igor; Ke, Ailong (Cornell); (NWU)

    2012-05-22

    Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated protein genes (cas genes) are widespread in bacteria and archaea. They form a line of RNA-based immunity to eradicate invading bacteriophages and malicious plasmids. A key molecular event during this process is the acquisition of new spacers into the CRISPR loci to guide the selective degradation of the matching foreign genetic elements. Csn2 is a Nmeni subtype-specific cas gene required for new spacer acquisition. Here we characterize the Enterococcus faecalis Csn2 protein as a double-stranded (ds-) DNA-binding protein and report its 2.7 {angstrom} tetrameric ring structure. The inner circle of the Csn2 tetrameric ring is {approx}26 {angstrom} wide and populated with conserved lysine residues poised for nonspecific interactions with ds-DNA. Each Csn2 protomer contains an {alpha}/{beta} domain and an {alpha}-helical domain; significant hinge motion was observed between these two domains. Ca{sup 2+} was located at strategic positions in the oligomerization interface. We further showed that removal of Ca{sup 2+} ions altered the oligomerization state of Csn2, which in turn severely decreased its affinity for ds-DNA. In summary, our results provided the first insight into the function of the Csn2 protein in CRISPR adaptation by revealing that it is a ds-DNA-binding protein functioning at the quaternary structure level and regulated by Ca{sup 2+} ions.

  4. Crystal structure of clustered regularly interspaced short palindromic repeats (CRISPR)-associated Csn2 protein revealed Ca2+-dependent double-stranded DNA binding activity.

    Science.gov (United States)

    Nam, Ki Hyun; Kurinov, Igor; Ke, Ailong

    2011-09-02

    Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated protein genes (cas genes) are widespread in bacteria and archaea. They form a line of RNA-based immunity to eradicate invading bacteriophages and malicious plasmids. A key molecular event during this process is the acquisition of new spacers into the CRISPR loci to guide the selective degradation of the matching foreign genetic elements. Csn2 is a Nmeni subtype-specific cas gene required for new spacer acquisition. Here we characterize the Enterococcus faecalis Csn2 protein as a double-stranded (ds-) DNA-binding protein and report its 2.7 Å tetrameric ring structure. The inner circle of the Csn2 tetrameric ring is ∼26 Å wide and populated with conserved lysine residues poised for nonspecific interactions with ds-DNA. Each Csn2 protomer contains an α/β domain and an α-helical domain; significant hinge motion was observed between these two domains. Ca(2+) was located at strategic positions in the oligomerization interface. We further showed that removal of Ca(2+) ions altered the oligomerization state of Csn2, which in turn severely decreased its affinity for ds-DNA. In summary, our results provided the first insight into the function of the Csn2 protein in CRISPR adaptation by revealing that it is a ds-DNA-binding protein functioning at the quaternary structure level and regulated by Ca(2+) ions.

  5. Temperature dependent polarization reversal mechanism in 0.94(Bi1/2Na1/2) TiO3-0.06Ba(Zr0.02Ti0.98)O3 relaxor ceramics

    DEFF Research Database (Denmark)

    Glaum, Julia; Simons, Hugh; Hudspeth, Jessica

    2015-01-01

    The temperature at which the electric field induced long-range ordered ferroelectric state undergoes transition into the short-range ordered relaxor state, TF-R, is commonly defined by the onset of strong dispersion of the dielectric permittivity. However, this combined macroscopic property and s...... associated with different polarization reversal processes. Such diagrams are useful tools for identifying the best operational temperature regimes for a given composition in actuator applications....... and structural investigation of the polarization reversal process in the prototypical lead-free relaxor 0.94(Bi1/2Na1/2)TiO3-0.06Ba(Zr0.02Ti0.98)O3 reveals that an applied electric field can trigger depolarization and onset of relaxor-like behavior well below TF-R. The polarization reversal process can....... These results are concomitant with a continuous ferroelectric to relaxortransition occurring over a broad temperature range, during which mixed behavior is observed. The nature of polarization reversal can be illustrated in electric-field-temperature (E-T) diagrams showing the electric field amplitudes...

  6. Mg2+-Dependent High Mechanical Anisotropy of Three-Way-Junction pRNA as Revealed by Single-Molecule Force Spectroscopy.

    Science.gov (United States)

    Sun, Yang; Di, Weishuai; Li, Yiran; Huang, Wenmao; Wang, Xin; Qin, Meng; Wang, Wei; Cao, Yi

    2017-08-01

    Mechanical anisotropy is ubiquitous in biological tissues but is hard to reproduce in synthetic biomaterials. Developing molecular building blocks with anisotropic mechanical response is the key towards engineering anisotropic biomaterials. The three-way-junction (3WJ) pRNA, derived from ϕ29 DNA packaging motor, shows strong mechanical anisotropy upon Mg 2+ binding. In the absence of Mg 2+ , 3WJ-pRNA is mechanically weak without noticeable mechanical anisotropy. In the presence of Mg 2+ , the unfolding forces can differ by more than 4-fold along different pulling directions, ranging from about 47 pN to about 219 pN. Mechanical anisotropy of 3WJ-pRNA stems from pulling direction dependent cooperativity for the rupture of two Mg 2+ binding sites, which is a novel mechanism for the mechanical anisotropy of biomacromolecules. It is anticipated that 3WJ-pRNA can be used as a key element for the construction of biomaterials with controllable mechanical anisotropy. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Structure of thrombospondin type 3 repeats in bacterial outer membrane protein A reveals its intra-repeat disulfide bond-dependent calcium-binding capability

    Energy Technology Data Exchange (ETDEWEB)

    Dai, Shuyan; Sun, Cancan; Tan, Kemin; Ye, Sheng; Zhang, Rongguang

    2017-09-01

    Eukaryotic thrombospondin type 3 repeat (TT3R) is an efficient calcium ion (Ca2+) binding motif only found in mammalian thrombospondin family. TT3R has also been found in prokaryotic cellulase Cel5G, which was thought to forfeit the Ca2+-binding capability due to the formation of intra-repeat disulfide bonds, instead of the inter-repeat ones possessed by eukaryotic TT3Rs. In this study, we have identified an enormous number of prokaryotic TT3R-containing proteins belonging to several different protein families, including outer membrane protein A (OmpA), an important structural protein connecting the outer membrane and the periplasmic peptidoglycan layer in gram-negative bacteria. Here, we report the crystal structure of the periplasmic region of OmpA from Capnocytophaga gingivalis, which contains a linker region comprising five consecutive TT3Rs. The structure of OmpA-TT3R exhibits a well-ordered architecture organized around two tightly-coordinated Ca2+ and confirms the presence of abnormal intra-repeat disulfide bonds. Further mutagenesis studies showed that the Ca2+-binding capability of OmpA-TT3R is indeed dependent on the proper formation of intra-repeat disulfide bonds, which help to fix a conserved glycine residue at its proper position for Ca2+ coordination. Additionally, despite lacking inter repeat disulfide bonds, the interfaces between adjacent OmpA-TT3Rs are enhanced by both hydrophobic and conserved aromatic-proline interactions.

  8. Response of heat shock protein genes of the oriental fruit moth under diapause and thermal stress reveals multiple patterns dependent on the nature of stress exposure.

    Science.gov (United States)

    Zhang, Bo; Peng, Yu; Zheng, Jincheng; Liang, Lina; Hoffmann, Ary A; Ma, Chun-Sen

    2016-07-01

    Heat shock protein gene (Hsp) families are thought to be important in thermal adaptation, but their expression patterns under various thermal stresses have still been poorly characterized outside of model systems. We have therefore characterized Hsp genes and their stress responses in the oriental fruit moth (OFM), Grapholita molesta, a widespread global orchard pest, and compared patterns of expression in this species to that of other insects. Genes from four Hsp families showed variable expression levels among tissues and developmental stages. Members of the Hsp40, 70, and 90 families were highly expressed under short exposures to heat and cold. Expression of Hsp40, 70, and Hsc70 family members increased in OFM undergoing diapause, while Hsp90 was downregulated. We found that there was strong sequence conservation of members of large Hsp families (Hsp40, Hsp60, Hsp70, Hsc70) across taxa, but this was not always matched by conservation of expression patterns. When the large Hsps as well as small Hsps from OFM were compared under acute and ramping heat stress, two groups of sHsps expression patterns were apparent, depending on whether expression increased or decreased immediately after stress exposure. These results highlight potential differences in conservation of function as opposed to sequence in this gene family and also point to Hsp genes potentially useful as bioindicators of diapause and thermal stress in OFM.

  9. A forward-genetic screen and dynamic analysis of lambda phage host-dependencies reveals an extensive interaction network and a new anti-viral strategy.

    Directory of Open Access Journals (Sweden)

    Nathaniel D Maynard

    2010-07-01

    Full Text Available Latently infecting viruses are an important class of virus that plays a key role in viral evolution and human health. Here we report a genome-scale forward-genetics screen for host-dependencies of the latently-infecting bacteriophage lambda. This screen identified 57 Escherichia coli (E. coli genes--over half of which have not been previously associated with infection--that when knocked out inhibited lambda phage's ability to replicate. Our results demonstrate a highly integrated network between lambda and its host, in striking contrast to the results from a similar screen using the lytic-only infecting T7 virus. We then measured the growth of E. coli under normal and infected conditions, using wild-type and knockout strains deficient in one of the identified host genes, and found that genes from the same pathway often exhibited similar growth dynamics. This observation, combined with further computational and experimental analysis, led us to identify a previously unannotated gene, yneJ, as a novel regulator of lamB gene expression. A surprising result of this work was the identification of two highly conserved pathways involved in tRNA thiolation-one pathway is required for efficient lambda replication, while the other has anti-viral properties inhibiting lambda replication. Based on our data, it appears that 2-thiouridine modification of tRNAGlu, tRNAGln, and tRNALys is particularly important for the efficient production of infectious lambda phage particles.

  10. Time-dependent flux from pulsed neutrons revealed by superconducting Nb current-biased kinetic inductance detector with 10B converter operated at 4 K

    International Nuclear Information System (INIS)

    Miyajima, Shigeyuki; Narukami, Yoshito; Shishido, Hiroaki; Yoshioka, Naohito; Ishida, Takekazu; Fujimaki, Akira; Hidaka, Mutsuo; Oikawa, Kenichi; Harada, Masahide; Oku, Takayuki; Arai, Masatoshi

    2015-01-01

    We have demonstrated a new superconducting detector for a neutron based on Nb superconductor meanderline with a 10 B conversion layer. We use a current-biased kinetic inductance detector (CB-KID), which is composed of a meanderline, for detection of a neutron with high spatial resolution and fast response. The thickness of Nb meanderlines is 40 nm and widths are 3 μm, 1 μm, and 0.6 μm. The CB-KIDs are fabricated at the center of the Si chip of the size 22 mm × 22 mm and the total area of CB-KIDs covers 8 mm × 8 mm. The chip was cooled to a temperature lower than 4 K below the transition temperature of Nb using a Gifford-McMahon (GM) cryocooler. The Nb CB-KIDs with a 10 B conversion layer output the voltage by irradiating pulsed neutrons at the material life science experimental facility (MLF) of Japan Proton Accelerator Research Complex (J-PARC) center. The response time of CB-KIDs is about a few tens ns. We have also obtained the time dependence of neutron flux generated from pulsed neutrons using a CB-KID. Experimental results were in good agreement with the simulated results. (author)

  11. Mechanisms of interannual variations in the western boundary currents along the Madagascar coast as revealed by the extended Time-Dependent Island Rule

    Science.gov (United States)

    Yamagami, Y.; Tozuka, T.

    2016-12-01

    The South Equatorial Current in the South Indian Ocean bifurcates at the east coast of Madagascar into the Northeast and Southeast Madagascar Currents. The dynamical mechanisms of interannual variations in the western boundary currents along Madagascar are examined using the "Time-Dependent Island Rule (TDIR)" for the first time. Since Rossby waves radiated from the Australian coast and the Indonesian Throghflow are known to play a role in oceanic variability over the southern Indian Ocean, the original TDIR is extended to incorporate these effects. Also, inertial effects are included for a more complete discussion. Using this modified TDIR, interannual variability of western boundary currents along Madagascar is shown to be predominantly a response to the meridional transport anomaly in the interior, which is a result of westward propagating Rossby waves induced by wind stress curl anomalies mainly in 60°E-90°E. On the other hand, the interannual variability is not much influenced by inertial effects and the Indonesian Throughflow. Although the damping of Rossby waves has an impact on the amplitude of the interannual variation, it does not alter the above mechanism qualitatively.

  12. Culture-dependent and culture-independent analyses reveal no prokaryotic community shifts or recovery of Serratia marcescens in Acropora palmata with white pox disease.

    Science.gov (United States)

    Lesser, Michael P; Jarett, Jessica K

    2014-06-01

    Recently, the etiological agent of white pox (WP) disease, also known as acroporid serratiosis, in the endangered coral Acropora palmata is the enteric bacterium Serratia marcescens with the source being localized sewage release onto coastal coral reef communities. Here, we show that both culture-dependent and culture-independent approaches could not recover this bacterium from samples of tissue and mucus from A. palmata colonies affected by WP disease in the Bahamas, or seawater collected adjacent to A. palmata colonies. Additionally, a metagenetic 16S rRNA pyrosequencing study shows no significant difference in the bacterial communities of coral tissues with and without WP lesions. As recent studies have shown for other coral diseases, S. marcescens cannot be identified in all cases of WP disease in several geographically separated populations of A. palmata with the same set of signs. As a result, its identification as the etiological agent of WP disease, and cause of a reverse zoonosis, cannot be broadly supported. However, the prevalence of WP disease associated with S. marcescens does appear to be associated with proximity to population centers, and research efforts should be broadened to examine this association, and to identify other causes of this syndrome. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  13. Functional and structural studies of the disulfide isomerase DsbC from the plant pathogen Xylella fastidiosa reveals a redox-dependent oligomeric modulation in vitro.

    Science.gov (United States)

    Santos, Clelton A; Toledo, Marcelo A S; Trivella, Daniela B B; Beloti, Lilian L; Schneider, Dilaine R S; Saraiva, Antonio M; Crucello, Aline; Azzoni, Adriano R; Souza, Alessandra A; Aparicio, Ricardo; Souza, Anete P

    2012-10-01

    Xylella fastidiosa is a Gram-negative bacterium that grows as a biofilm inside the xylem vessels of susceptible plants and causes several economically relevant crop diseases. In the present study, we report the functional and low-resolution structural characterization of the X. fastidiosa disulfide isomerase DsbC (XfDsbC). DsbC is part of the disulfide bond reduction/isomerization pathway in the bacterial periplasm and plays an important role in oxidative protein folding. In the present study, we demonstrate the presence of XfDsbC during different stages of X. fastidiosa biofilm development. XfDsbC was not detected during X. fastidiosa planktonic growth; however, after administering a sublethal copper shock, we observed an overexpression of XfDsbC that also occurred during planktonic growth. These results suggest that X. fastidiosa can use XfDsbC in vivo under oxidative stress conditions similar to those induced by copper. In addition, using dynamic light scattering and small-angle X-ray scattering, we observed that the oligomeric state of XfDsbC in vitro may be dependent on the redox environment. Under reducing conditions, XfDsbC is present as a dimer, whereas a putative tetrameric form was observed under nonreducing conditions. Taken together, our findings demonstrate the overexpression of XfDsbC during biofilm formation and provide the first structural model of a bacterial disulfide isomerase in solution. © 2012 The Authors Journal compilation © 2012 FEBS.

  14. Rosa26-GFP direct repeat (RaDR-GFP mice reveal tissue- and age-dependence of homologous recombination in mammals in vivo.

    Directory of Open Access Journals (Sweden)

    Michelle R Sukup-Jackson

    2014-06-01

    Full Text Available Homologous recombination (HR is critical for the repair of double strand breaks and broken replication forks. Although HR is mostly error free, inherent or environmental conditions that either suppress or induce HR cause genomic instability. Despite its importance in carcinogenesis, due to limitations in our ability to detect HR in vivo, little is known about HR in mammalian tissues. Here, we describe a mouse model in which a direct repeat HR substrate is targeted to the ubiquitously expressed Rosa26 locus. In the Rosa26 Direct Repeat-GFP (RaDR-GFP mice, HR between two truncated EGFP expression cassettes can yield a fluorescent signal. In-house image analysis software provides a rapid method for quantifying recombination events within intact tissues, and the frequency of recombinant cells can be evaluated by flow cytometry. A comparison among 11 tissues shows that the frequency of recombinant cells varies by more than two orders of magnitude among tissues, wherein HR in the brain is the lowest. Additionally, de novo recombination events accumulate with age in the colon, showing that this mouse model can be used to study the impact of chronic exposures on genomic stability. Exposure to N-methyl-N-nitrosourea, an alkylating agent similar to the cancer chemotherapeutic temozolomide, shows that the colon, liver and pancreas are susceptible to DNA damage-induced HR. Finally, histological analysis of the underlying cell types reveals that pancreatic acinar cells and liver hepatocytes undergo HR and also that HR can be specifically detected in colonic somatic stem cells. Taken together, the RaDR-GFP mouse model provides new understanding of how tissue and age impact susceptibility to HR, and enables future studies of genetic, environmental and physiological factors that modulate HR in mammals.

  15. Chromosome painting reveals asynaptic full alignment of homologs and HIM-8-dependent remodeling of X chromosome territories during Caenorhabditis elegans meiosis.

    Directory of Open Access Journals (Sweden)

    Kentaro Nabeshima

    2011-08-01

    Full Text Available During early meiotic prophase, a nucleus-wide reorganization leads to sorting of chromosomes into homologous pairs and to establishing associations between homologous chromosomes along their entire lengths. Here, we investigate global features of chromosome organization during this process, using a chromosome painting method in whole-mount Caenorhabditis elegans gonads that enables visualization of whole chromosomes along their entire lengths in the context of preserved 3D nuclear architecture. First, we show that neither spatial proximity of premeiotic chromosome territories nor chromosome-specific timing is a major factor driving homolog pairing. Second, we show that synaptonemal complex-independent associations can support full lengthwise juxtaposition of homologous chromosomes. Third, we reveal a prominent elongation of chromosome territories during meiotic prophase that initiates prior to homolog association and alignment. Mutant analysis indicates that chromosome movement mediated by association of chromosome pairing centers (PCs with mobile patches of the nuclear envelope (NE-spanning SUN-1/ZYG-12 protein complexes is not the primary driver of territory elongation. Moreover, we identify new roles for the X chromosome PC (X-PC and X-PC binding protein HIM-8 in promoting elongation of X chromosome territories, separable from their role(s in mediating local stabilization of pairing and association of X chromosomes with mobile SUN-1/ZYG-12 patches. Further, we present evidence that HIM-8 functions both at and outside of PCs to mediate chromosome territory elongation. These and other data support a model in which synapsis-independent elongation of chromosome territories, driven by PC binding proteins, enables lengthwise juxtaposition of chromosomes, thereby facilitating assessment of their suitability as potential pairing partners.

  16. DNA microarray analyses reveal a post-irradiation differential time-dependent gene expression profile in yeast cells exposed to X-rays and γ-rays

    International Nuclear Information System (INIS)

    Kimura, Shinzo; Ishidou, Emi; Kurita, Sakiko; Suzuki, Yoshiteru; Shibato, Junko; Rakwal, Randeep; Iwahashi, Hitoshi

    2006-01-01

    Ionizing radiation (IR) is the most enigmatic of genotoxic stress inducers in our environment that has been around from the eons of time. IR is generally considered harmful, and has been the subject of numerous studies, mostly looking at the DNA damaging effects in cells and the repair mechanisms therein. Moreover, few studies have focused on large-scale identification of cellular responses to IR, and to this end, we describe here an initial study on the transcriptional responses of the unicellular genome model, yeast (Saccharomyces cerevisiae strain S288C), by cDNA microarray. The effect of two different IR, X-rays, and gamma (γ)-rays, was investigated by irradiating the yeast cells cultured in YPD medium with 50 Gy doses of X- and γ-rays, followed by resuspension of the cells in YPD for time-course experiments. The samples were collected for microarray analysis at 20, 40, and 80 min after irradiation. Microarray analysis revealed a time-course transcriptional profile of changed gene expressions. Up-regulated genes belonged to the functional categories mainly related to cell cycle and DNA processing, cell rescue defense and virulence, protein and cell fate, and metabolism (X- and γ-rays). Similarly, for X- and γ-rays, the down-regulated genes belonged to mostly transcription and protein synthesis, cell cycle and DNA processing, control of cellular organization, cell fate, and C-compound and carbohydrate metabolism categories, respectively. This study provides for the first time a snapshot of the genome-wide mRNA expression profiles in X- and γ-ray post-irradiated yeast cells and comparatively interprets/discusses the changed gene functional categories as effects of these two radiations vis-a-vis their energy levels

  17. A live-cell, high-content imaging survey of 206 endogenous factors across five stress conditions reveals context-dependent survival effects in mouse primary beta cells.

    Science.gov (United States)

    Yang, Yu Hsuan Carol; Wills, Quin F; Johnson, James D

    2015-06-01

    Beta cell death is a hallmark of diabetes. It is not known whether specific cellular stresses associated with type 1 or type 2 diabetes require specific factors to protect pancreatic beta cells. No systematic comparison of endogenous soluble factors in the context of multiple pro-apoptotic conditions has been published. Primary mouse islet cells were cultured in conditions mimicking five type 1 or type 2 diabetes-related stresses: basal 5 mmol/l glucose, cytokine cocktail (25 ng/ml TNF-α, 10 ng/ml IL-1β, 10 ng/ml IFN-γ), 1 μmol/l thapsigargin, 1.5 mmol/l palmitate and 20 mmol/l glucose (all in the absence of serum). We surveyed the effects of a library of 206 endogenous factors (selected based on islet expression of their receptors) on islet cell survival through multi-parameter, live-cell imaging. Our survey pointed to survival factors exhibiting generalised protective effects across conditions meant to model different types of diabetes and stages of the diseases. For example, our survey and follow-up experiments suggested that OLFM1 is a novel protective factor for mouse and human beta cells across multiple conditions. Most strikingly, we also found specific protective survival factors for each model stress condition. For example, semaphorin4A (SEMA4A) was toxic to islet cells in the serum-free baseline and serum-free 20 mmol/l glucose conditions, but protective in the context of lipotoxicity. Rank product testing supported the consistency of our observations. Collectively, our survey reveals previously unidentified islet cell survival factors and suggest their potential utility in individualised medicine.

  18. DNA microarray analyses reveal a post-irradiation differential time-dependent gene expression profile in yeast cells exposed to X-rays and gamma-rays.

    Science.gov (United States)

    Kimura, Shinzo; Ishidou, Emi; Kurita, Sakiko; Suzuki, Yoshiteru; Shibato, Junko; Rakwal, Randeep; Iwahashi, Hitoshi

    2006-07-21

    Ionizing radiation (IR) is the most enigmatic of genotoxic stress inducers in our environment that has been around from the eons of time. IR is generally considered harmful, and has been the subject of numerous studies, mostly looking at the DNA damaging effects in cells and the repair mechanisms therein. Moreover, few studies have focused on large-scale identification of cellular responses to IR, and to this end, we describe here an initial study on the transcriptional responses of the unicellular genome model, yeast (Saccharomyces cerevisiae strain S288C), by cDNA microarray. The effect of two different IR, X-rays, and gamma (gamma)-rays, was investigated by irradiating the yeast cells cultured in YPD medium with 50 Gy doses of X- and gamma-rays, followed by resuspension of the cells in YPD for time-course experiments. The samples were collected for microarray analysis at 20, 40, and 80 min after irradiation. Microarray analysis revealed a time-course transcriptional profile of changed gene expressions. Up-regulated genes belonged to the functional categories mainly related to cell cycle and DNA processing, cell rescue defense and virulence, protein and cell fate, and metabolism (X- and gamma-rays). Similarly, for X- and gamma-rays, the down-regulated genes belonged to mostly transcription and protein synthesis, cell cycle and DNA processing, control of cellular organization, cell fate, and C-compound and carbohydrate metabolism categories, respectively. This study provides for the first time a snapshot of the genome-wide mRNA expression profiles in X- and gamma-ray post-irradiated yeast cells and comparatively interprets/discusses the changed gene functional categories as effects of these two radiations vis-à-vis their energy levels.

  19. Combined lipidomic and proteomic analysis of isolated human islets exposed to palmitate reveals time-dependent changes in insulin secretion and lipid metabolism.

    Science.gov (United States)

    Roomp, Kirsten; Kristinsson, Hjalti; Schvartz, Domitille; Ubhayasekera, Kumari; Sargsyan, Ernest; Manukyan, Levon; Chowdhury, Azazul; Manell, Hannes; Satagopam, Venkata; Groebe, Karlfried; Schneider, Reinhard; Bergquist, Jonas; Sanchez, Jean-Charles; Bergsten, Peter

    2017-01-01

    Studies on the pathophysiology of type 2 diabetes mellitus (T2DM) have linked the accumulation of lipid metabolites to the development of beta-cell dysfunction and impaired insulin secretion. In most in vitro models of T2DM, rodent islets or beta-cell lines are used and typically focus is on specific cellular pathways or organs. Our aim was to, firstly, develop a combined lipidomics and proteomics approach for lipotoxicity in isolated human islets and, secondly, investigate if the approach could delineate novel and/ or confirm reported mechanisms of lipotoxicity. To this end isolated human pancreatic islets, exposed to chronically elevated palmitate concentrations for 0, 2 and 7 days, were functionally characterized and their levels of multiple targeted lipid and untargeted protein species determined. Glucose-stimulated insulin secretion from the islets increased on day 2 and decreased on day 7. At day 7 islet insulin content decreased and the proinsulin to insulin content ratio doubled. Amounts of cholesterol, stearic acid, C16 dihydroceramide and C24:1 sphingomyelin, obtained from the lipidomic screen, increased time-dependently in the palmitate-exposed islets. The proteomic screen identified matching changes in proteins involved in lipid biosynthesis indicating up-regulated cholesterol and lipid biosynthesis in the islets. Furthermore, proteins associated with immature secretory granules were decreased when palmitate exposure time was increased despite their high affinity for cholesterol. Proteins associated with mature secretory granules remained unchanged. Pathway analysis based on the protein and lipid expression profiles implicated autocrine effects of insulin in lipotoxicity. Taken together the study demonstrates that combining different omics approaches has potential in mapping of multiple simultaneous cellular events. However, it also shows that challenges exist for effectively combining lipidomics and proteomics in primary cells. Our findings provide

  20. Bacteria abundance and diversity of different life stages of Plutella xylostella (Lepidoptera: Plutellidae), revealed by bacteria culture-dependent and PCR-DGGE methods.

    Science.gov (United States)

    Lin, Xiao-Li; Pan, Qin-Jian; Tian, Hong-Gang; Douglas, Angela E; Liu, Tong-Xian

    2015-03-01

    Microbial abundance and diversity of different life stages (fourth instar larvae, pupae and adults) of the diamondback moth, Plutella xylostella L., collected from field and reared in laboratory, were investigated using bacteria culture-dependent method and PCR-DGGE analysis based on the sequence of bacteria 16S rRNA V3 region gene. A large quantity of bacteria was found in all life stages of P. xylostella. Field population had higher quantity of bacteria than laboratory population, and larval gut had higher quantity than pupae and adults. Culturable bacteria differed in different life stages of P. xylostella. Twenty-five different bacterial strains were identified in total, among them 20 strains were presented in larval gut, only 8 strains in pupae and 14 strains in adults were detected. Firmicutes bacteria, Bacillus sp., were the most dominant species in every life stage. 15 distinct bands were obtained from DGGE electrophoresis gel. The sequences blasted in GenBank database showed these bacteria belonged to six different genera. Phylogenetic analysis showed the sequences of the bacteria belonged to the Actinobacteri, Proteobacteria and Firmicutes. Serratia sp. in Proteobacteria was the most abundant species in larval gut. In pupae, unculturable bacteria were the most dominant species, and unculturable bacteria and Serratia sp. were the most dominant species in adults. Our study suggested that a combination of molecular and traditional culturing methods can be effectively used to analyze and to determine the diversity of gut microflora. These known bacteria may play important roles in development of P. xylostella. © 2013 Institute of Zoology, Chinese Academy of Sciences.

  1. Stochastic losses of fire-dependent endemic herbs revealed by a 65-year chronosequence of dispersal-limited woody plant encroachment.

    Science.gov (United States)

    Brewer, John Stephen

    2017-06-01

    The factors responsible for maintaining diverse groundcover plant communities of high conservation value in frequently burned wet pine savannas are poorly understood. While most management involves manipulating extrinsic factors important in maintaining species diversity (e.g., fire regimes), most ecological theory (e.g., niche theory and neutral theory) examines how traits exhibited by the species promote species coexistence. Furthermore, although many ecologists focus on processes that maintain local species diversity, conservation biologists have argued that other indices (e.g., phylogenetic diversity) are better for evaluating assemblages in terms of their conservation value. I used a null model that employed beta-diversity calculations based on Raup-Crick distances to test for deterministic herbaceous species losses associated with a 65-year chronosequence of woody species encroachment within each of three localities. I quantified conservation value of assemblages by measuring taxonomic distinctness, endemism, and floristic quality of plots with and without woody encroachment. Reductions in herb species richness per plot attributable to woody encroachment were largely stochastic, as indicated by a lack of change in the mean or variance in beta-diversity caused by woody encroachment in the savannas studied here. Taxonomic distinctness, endemism, and floristic quality (when summed across all species) were all greater in areas that had not experienced woody encroachment. However, when corrected for local species richness, only average endemism and floristic quality of assemblages inclusive of herbs and woody plants were greater in areas that had not experienced woody encroachment, due to the more restricted ranges and habitat requirements of herbs. Results suggest that frequent fires maintain diverse assemblages of fire-dependent herb species endemic to the region. The stochastic loss of plant species, irrespective of their taxonomic distinctness, to woody

  2. Systems Biology Reveals Cigarette Smoke-Induced Concentration-Dependent Direct and Indirect Mechanisms That Promote Monocyte-Endothelial Cell Adhesion.

    Science.gov (United States)

    Poussin, Carine; Laurent, Alexandra; Peitsch, Manuel C; Hoeng, Julia; De Leon, Hector

    2015-10-01

    Cigarette smoke (CS) affects the adhesion of monocytes to endothelial cells, a critical step in atherogenesis. Using an in vitro adhesion assay together with innovative computational systems biology approaches to analyze omics data, our study aimed at investigating CS-induced mechanisms by which monocyte-endothelial cell adhesion is promoted. Primary human coronary artery endothelial cells (HCAECs) were treated for 4 h with (1) conditioned media of human monocytic Mono Mac-6 (MM6) cells preincubated with low or high concentrations of aqueous CS extract (sbPBS) from reference cigarette 3R4F for 2 h (indirect treatment, I), (2) unconditioned media similarly prepared without MM6 cells (direct treatment, D), or (3) freshly generated sbPBS (fresh direct treatment, FD). sbPBS promoted MM6 cells-HCAECs adhesion following I and FD, but not D. In I, the effect was mediated at a low concentration through activation of vascular inflammation processes promoted in HCAECs by a paracrine effect of the soluble mediators secreted by sbPBS-treated MM6 cells. Tumor necrosis factor α (TNFα), a major inducer, was actually shed by unstable CS compound-activated TNFα-converting enzyme. In FD, the effect was triggered at a high concentration that also induced some toxicity. This effect was mediated through an yet unknown mechanism associated with a stress damage response promoted in HCAECs by unstable CS compounds present in freshly generated sbPBS, which had decayed in D unconditioned media. Aqueous CS extract directly and indirectly promotes monocytic cell-endothelial cell adhesion in vitro via distinct concentration-dependent mechanisms. © The Author 2015. Published by Oxford University Press on behalf of the Society of Toxicology. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  3. Combined lipidomic and proteomic analysis of isolated human islets exposed to palmitate reveals time-dependent changes in insulin secretion and lipid metabolism.

    Directory of Open Access Journals (Sweden)

    Kirsten Roomp

    Full Text Available Studies on the pathophysiology of type 2 diabetes mellitus (T2DM have linked the accumulation of lipid metabolites to the development of beta-cell dysfunction and impaired insulin secretion. In most in vitro models of T2DM, rodent islets or beta-cell lines are used and typically focus is on specific cellular pathways or organs. Our aim was to, firstly, develop a combined lipidomics and proteomics approach for lipotoxicity in isolated human islets and, secondly, investigate if the approach could delineate novel and/ or confirm reported mechanisms of lipotoxicity. To this end isolated human pancreatic islets, exposed to chronically elevated palmitate concentrations for 0, 2 and 7 days, were functionally characterized and their levels of multiple targeted lipid and untargeted protein species determined. Glucose-stimulated insulin secretion from the islets increased on day 2 and decreased on day 7. At day 7 islet insulin content decreased and the proinsulin to insulin content ratio doubled. Amounts of cholesterol, stearic acid, C16 dihydroceramide and C24:1 sphingomyelin, obtained from the lipidomic screen, increased time-dependently in the palmitate-exposed islets. The proteomic screen identified matching changes in proteins involved in lipid biosynthesis indicating up-regulated cholesterol and lipid biosynthesis in the islets. Furthermore, proteins associated with immature secretory granules were decreased when palmitate exposure time was increased despite their high affinity for cholesterol. Proteins associated with mature secretory granules remained unchanged. Pathway analysis based on the protein and lipid expression profiles implicated autocrine effects of insulin in lipotoxicity. Taken together the study demonstrates that combining different omics approaches has potential in mapping of multiple simultaneous cellular events. However, it also shows that challenges exist for effectively combining lipidomics and proteomics in primary cells. Our

  4. Crystal complexes of a predicted S-adenosylmethionine-dependent methyltransferase reveal a typical AdoMet binding domain and a substrate recognition domain

    Energy Technology Data Exchange (ETDEWEB)

    Miller, D.J.; Ouellette, N.; Evodokimova, E.; Savchenko, A.; Edwards, A.; Anderson, W.F. (Toronto); (NWU)

    2010-03-08

    S-adenosyl-L-methionine-dependent methyltransferases (MTs) are abundant, and highly conserved across phylogeny. These enzymes use the cofactor AdoMet to methylate a wide variety of molecular targets, thereby modulating important cellular and metabolic activities. Thermotoga maritima protein 0872 (TM0872) belongs to a large sequence family of predicted MTs, ranging phylogenetically from relatively simple bacteria to humans. The genes for many of the bacterial homologs are located within operons involved in cell wall synthesis and cell division. Despite preliminary biochemical studies in E. coli and B. subtilis, the substrate specificity of this group of more than 150 proteins is unknown. As part of the Midwest Center for Structural Genomics initiative (www.mcsg.anl.gov), we have determined the structure of TM0872 in complexes with AdoMet and with S-adenosyl-L-homocysteine (AdoHcy). As predicted, TM0872 has a typical MT domain, and binds endogenous AdoMet, or co-crystallized AdoHcy, in a manner consistent with other known MT structures. In addition, TM0872 has a second domain that is novel among MTs in both its location in the sequence and its structure. The second domain likely acts in substrate recognition and binding, and there is a potential substrate-binding cleft spanning the two domains. This long and narrow cleft is lined with positively charged residues which are located opposite the S{sup +}-CH{sub 3} bond, suggesting that a negatively charged molecule might be targeted for catalysis. However, AdoMet and AdoHcy are both buried, and access to the methyl group would presumably require structural rearrangement. These TM0872 crystal structures offer the first structural glimpses at this phylogenetically conserved sequence family.

  5. Ab initio structural modeling of and experimental validation for Chlamydia trachomatis protein CT296 reveal structural similarity to Fe(II) 2-oxoglutarate-dependent enzymes

    Energy Technology Data Exchange (ETDEWEB)

    Kemege, Kyle E.; Hickey, John M.; Lovell, Scott; Battaile, Kevin P.; Zhang, Yang; Hefty, P. Scott (Michigan); (Kansas); (HWMRI)

    2012-02-13

    Chlamydia trachomatis is a medically important pathogen that encodes a relatively high percentage of proteins with unknown function. The three-dimensional structure of a protein can be very informative regarding the protein's functional characteristics; however, determining protein structures experimentally can be very challenging. Computational methods that model protein structures with sufficient accuracy to facilitate functional studies have had notable successes. To evaluate the accuracy and potential impact of computational protein structure modeling of hypothetical proteins encoded by Chlamydia, a successful computational method termed I-TASSER was utilized to model the three-dimensional structure of a hypothetical protein encoded by open reading frame (ORF) CT296. CT296 has been reported to exhibit functional properties of a divalent cation transcription repressor (DcrA), with similarity to the Escherichia coli iron-responsive transcriptional repressor, Fur. Unexpectedly, the I-TASSER model of CT296 exhibited no structural similarity to any DNA-interacting proteins or motifs. To validate the I-TASSER-generated model, the structure of CT296 was solved experimentally using X-ray crystallography. Impressively, the ab initio I-TASSER-generated model closely matched (2.72-{angstrom} C{alpha} root mean square deviation [RMSD]) the high-resolution (1.8-{angstrom}) crystal structure of CT296. Modeled and experimentally determined structures of CT296 share structural characteristics of non-heme Fe(II) 2-oxoglutarate-dependent enzymes, although key enzymatic residues are not conserved, suggesting a unique biochemical process is likely associated with CT296 function. Additionally, functional analyses did not support prior reports that CT296 has properties shared with divalent cation repressors such as Fur.

  6. A new β-estradiol-inducible vector set that facilitates easy construction and efficient expression of transgenes reveals CBL3-dependent cytoplasm to tonoplast translocation of CIPK5.

    Science.gov (United States)

    Schlücking, Kathrin; Edel, Kai H; Köster, Philipp; Drerup, Maria M; Eckert, Christian; Steinhorst, Leonie; Waadt, Rainer; Batistic, Oliver; Kudla, Jörg

    2013-11-01

    Transient and stable expression of transgenes is central to many investigations in plant biology research. Chemical regulation of expression can circumvent problems of plant lethality caused by constitutive overexpression or allow inducible knock (out/down) approaches. Several chemically inducible or repressible systems have been described and successfully applied. However, cloning and application-specific modification of most available inducible expression systems have been limited and remained complicated due to restricted cloning options. Here we describe a new set of 57 vectors that enable transgene expression in transiently or stably transformed cells. All vectors harbor a synthetically optimized XVE expression cassette, allowing β-estradiol mediated protein expression. Plasmids are equipped with the reporter genes GUS, GFP, mCherry, or with HA and StrepII epitope tags and harbor an optimized multiple cloning site for flexible and simple cloning strategies. Moreover, the vector design allows simple substitution of the driving promoter to achieve tissue-specificity or to modulate expression ranges of inducible transgene expression. We report details of the kinetics and dose-dependence of expression induction in Arabidopsis leaf mesophyll protoplasts, transiently transformed Nicotiana benthamiana leaves, and stably transformed Arabidopsis plants. Using these vectors, we investigated the influence of CBL (Calcineurin B-like) protein expression on the subcellular localization of CIPKs (Calcineurin B-like interacting protein kinases). These analyses uncovered that induced co-expression of CBL3 is fully sufficient for dynamic translocation of CIPK5 from the cytoplasm to the tonoplast. Thus, the vector system presented here facilitates a broad range of research applications.

  7. Bone Abnormalities in Mice with Protein Kinase A (PKA) Defects Reveal a Role of Cyclic AMP Signaling in Bone Stromal Cell-Dependent Tumor Development.

    Science.gov (United States)

    Liu, S; Shapiro, J M; Saloustros, E; Stratakis, C A

    2016-11-01

    Protein kinase A (PKA) is an important enzyme for all eukaryotic cells. PKA phosphorylates other proteins, thus, it is essential for the regulation of many diverse cellular functions, including cytoplasmic trafficking and signaling, organelle structure and mitochondrial oxidation, nuclear gene expression, the cell cycle, and cellular division. The PKA holoenzyme is composed of 2 regulatory and 2 catalytic subunits. Four regulatory (R1α, R1β, R2α, and R2β) and 4 catalytic subunits (Cα, Cβ, Cγ, and Prkx) have been identified, giving rise to mainly PKA-I (when the 2 regulatory subunits are either R1α or R1β), or PKA-II (when the 2 regulatory subunits are either R2α or R2β). Mutations in the PKA subunits can lead to altered total PKA activity or abnormal PKA-I to PKA-II ratio, leading to various abnormalities in both humans and mice. These effects can be tissue-specific. We studied the effect of PKA subunit defects on PKA activity and bone morphology of mice that were single or double heterozygous for null alleles of the various PKA subunit genes. Bone lesions including fibrous dysplasia, myxomas, osteo-sarcomas, -chondromas and -chondrosarcomas were found in these mice. Observational and molecular studies showed that these lesions were derived from bone stromal cells (BSCs). We conclude that haploinsufficiency for different PKA subunit genes affected bone lesion formation, new bone generation, organization, and mineralization in variable ways. This work identified a PKA subunit- and activity-dependent pathway of bone lesion formation from BSCs with important implications for understanding how cyclic AMP affects the skeleton and its tumorigenesis. © Georg Thieme Verlag KG Stuttgart · New York.

  8. Silencing of EEF2K (eukaryotic elongation factor-2 kinase) reveals AMPK-ULK1-dependent autophagy in colon cancer cells.

    Science.gov (United States)

    Xie, Chuan-Ming; Liu, Xiao-Yu; Sham, Kathy W Y; Lai, Josie M Y; Cheng, Christopher H K

    2014-09-01

    EEF2K (eukaryotic elongation factor-2 kinase), also known as Ca (2+)/calmodulin-dependent protein kinase III, functions in downregulating peptide chain elongation through inactivation of EEF2 (eukaryotic translation elongation factor 2). Currently, there is a limited amount of information on the promotion of autophagic survival by EEF2K in breast and glioblastoma cell lines. However, the precise role of EEF2K in carcinogenesis as well as the underlying mechanism involved is still poorly understood. In this study, contrary to the reported autophagy-promoting activity of EEF2K in certain cancer cells, EEF2K is shown to negatively regulate autophagy in human colon cancer cells as indicated by the increase of LC3-II levels, the accumulation of LC3 dots per cell, and the promotion of autophagic flux in EEF2K knockdown cells. EEF2K negatively regulates cell viability, clonogenicity, cell proliferation, and cell size in colon cancer cells. Autophagy induced by EEF2K silencing promotes cell survival and does not potentiate the anticancer efficacy of the AKT inhibitor MK-2206. In addition, autophagy induced by silencing of EEF2K is attributed to induction of protein synthesis and activation of the AMPK-ULK1 pathway, independent of the suppression of MTOR activity and ROS generation. Knockdown of AMPK or ULK1 significantly abrogates EEF2K silencing-induced increase of LC3-II levels, accumulation of LC3 dots per cell as well as cell proliferation in colon cancer cells. In conclusion, silencing of EEF2K promotes autophagic survival via activation of the AMPK-ULK1 pathway in colon cancer cells. This finding suggests that upregulation of EEF2K activity may constitute a novel approach for the treatment of human colon cancer.

  9. Host-dependent differences in resource use associated with Anilocra spp. parasitism in two coral reef fishes, as revealed by stable carbon and nitrogen isotope analyses

    Science.gov (United States)

    Welicky, Rachel; Demopoulos, Amanda W. J.; Sikkel, Paul C.

    2017-01-01

    The role of parasites in trophic ecology is poorly understood in marine ecosystems. Stable isotope analyses (SIA) have been widely used in studies of trophic ecology, but have rarely been applied to study the role of parasites. Considering that some parasites are associated with altered host foraging patterns, SIA can help elucidate whether parasitism influences host trophic interactions. French grunt (Haemulon flavolineatum), an abundant Caribbean coral reef fish, contributes greatly to trophic connectivity. They typically depart the reef at dusk, feed overnight in seagrass beds, and return to the reef at dawn. The large parasitic isopod Anilocra haemuli commonly infects French grunt, and infected fish are less likely to complete their diel migration, and are in poorer condition than uninfected conspecifics. Brown chromis (Chromis multilineata) are diurnally feeding planktivores and infection by Anilocra chromis does not influence host condition. To determine if Anilocra infection influences host diet and foraging locality, we conducted stable carbon and nitrogen isotope analyses on scale, muscle, heart and gill tissues of infected and uninfected French grunt and brown chromis. We determined that all French grunt had δ13C values representative of seagrass habitats, but infected French grunt were significantly enriched in 13C and 15N compared to uninfected conspecifics. This suggests that compared to uninfected conspecifics, infected French grunt forage in seagrass, but on isotopically enriched prey, and/or are in poorer condition, which can elevate δ13C and δ15N values. For brown chromis, infection did not significantly influence any δ13C and δ15N values; hence they all foraged in the same environment and on similar prey. This is the first study to use SIA to examine differences in resource use by Caribbean coral reef fishes associated with parasitism and to evaluate how closely related parasites might have host-dependent effects on host trophic ecology.

  10. [Review] Polarization and Polarimetry

    Science.gov (United States)

    Trippe, Sascha

    2014-02-01

    Polarization is a basic property of light and is fundamentally linked to the internal geometry of a source of radiation. Polarimetry complements photometric, spectroscopic, and imaging analyses of sources of radiation and has made possible multiple astrophysical discoveries. In this article I review (i) the physical basics of polarization: electromagnetic waves, photons, and parameterizations; (ii) astrophysical sources of polarization: scattering, synchrotron radiation, active media, and the Zeeman, Goldreich-Kylafis, and Hanle effects, as well as interactions between polarization and matter (like birefringence, Faraday rotation, or the Chandrasekhar-Fermi effect); (iii) observational methodology: on-sky geometry, influence of atmosphere and instrumental polarization, polarization statistics, and observational techniques for radio, optical, and X/γ wavelengths; and (iv) science cases for astronomical polarimetry: solar and stellar physics, planetary system bodies, interstellar matter, astrobiology, astronomical masers, pulsars, galactic magnetic fields, gamma-ray bursts, active galactic nuclei, and cosmic microwave background radiation.

  11. Polarization feedback laser stabilization

    Science.gov (United States)

    Esherick, P.; Owyoung, A.

    1987-09-28

    A system for locking two Nd:YAG laser oscillators includes an optical path for feeding the output of one laser into the other with different polarizations. Elliptical polarization is incorporated into the optical path so that the change in polarization that occurs when the frequencies coincide may be detected to provide a feedback signal to control one laser relative to the other. 4 figs.

  12. Polarization in Sagittarius A*

    OpenAIRE

    Bower, Geoffrey C.

    2000-01-01

    We summarize the current state of polarization observations of Sagittarius A*, the compact radio source and supermassive black hole candidate in the Galactic Center. These observations are providing new tools for understanding accretion disks, jets and their environments. Linear polarization observations have shown that Sgr A* is unpolarized at frequencies as high as 86 GHz. However, recent single-dish observations indicate that Sgr A* may have strong linear polarization at frequencies higher...

  13. The catalytic mechanism of NADH-dependent reduction of 9,10-phenanthrenequinone by Candida tenuis xylose reductase reveals plasticity in an aldo-keto reductase active site.

    Science.gov (United States)

    Pival, Simone L; Klimacek, Mario; Nidetzky, Bernd

    2009-06-12

    Despite their widely varying physiological functions in carbonyl metabolism, AKR2B5 (Candida tenuis xylose reductase) and many related enzymes of the aldo-keto reductase protein superfamily utilise PQ (9,10-phenanthrenequinone) as a common in vitro substrate for NAD(P)H-dependent reduction. The catalytic roles of the conserved active-site residues (Tyr51, Lys80 and His113) of AKR2B5 in the conversion of the reactive alpha-dicarbonyl moiety of PQ are not well understood. Using wild-type and mutated (Tyr51, Lys80 and His113 individually replaced by alanine) forms of AKR2B5, we have conducted steady-state and transient kinetic studies of the effects of varied pH and deuterium isotopic substitutions in coenzyme and solvent on the enzymatic rates of PQ reduction. Each mutation caused a 10(3)-10(4)-fold decrease in the rate constant for hydride transfer from NADH to PQ, whose value in the wild-type enzyme was determined as approximately 8 x 10(2) s(-1). The data presented support an enzymic mechanism in which a catalytic proton bridge from the protonated side chain of Lys80 (pK=8.6+/-0.1) to the carbonyl group adjacent to the hydride acceptor carbonyl facilitates the chemical reaction step. His113 contributes to positioning of the PQ substrate for catalysis. Contrasting its role as catalytic general acid for conversion of the physiological substrate xylose, Tyr51 controls release of the hydroquinone product. The proposed chemistry of AKR2B5 action involves delivery of both hydrogens required for reduction of the alpha-dicarbonyl substrate to the carbonyl group undergoing (stereoselective) transformation. Hydride transfer from NADH probably precedes the transfer of a proton from Tyr51 whose pK of 7.3+/-0.3 in the NAD+-bound enzyme appears suitable for protonation of a hydroquinone anion (pK=8.8). These results show that the mechanism of AKR2B5 is unusually plastic in the exploitation of the active-site residues, for the catalytic assistance provided to carbonyl group

  14. Interactions within a [ionic liquid + poly(ethylene glycol)] mixture revealed by temperature-dependent synergistic dynamic viscosity and probe-reported microviscosity.

    Science.gov (United States)

    Trivedi, Shruti; Pandey, Siddharth

    2011-06-09

    Mixtures of ionic liquid (IL) with poly(ethylene glycol) (PEG) may afford media with favorable properties. Dynamic viscosities of mixtures of a common and popular IL 1-butyl-3-methylimidazolium hexafluorophosphate ([bmim][PF(6)]) with PEGs of average molecular weight (MW) 200 (PEG200), average MW 400 (PEG400), number-average MW M(n) 570-630 (PEG600), and number-average MW M(n) 950-1050 (PEG1000) over a complete composition range at 10° intervals in the temperature range of 10-90 °C are measured. The temperature dependence of the dynamic viscosity shows ([bmim][PF(6)] + PEG) mixtures to behave as Newtonian fluids and is found to follow Arrhenius-type behavior. In the IL-rich region, excess logarithmic viscosities for the ([bmim][PF(6)] + PEG200) mixture are found to be negative and independent of the temperature. Mixtures of ([bmim][PF(6)] + PEG600) and ([bmim][PF(6)] + PEG1000) show rare and unusual viscosity "synergism" or "hyperviscosity" in the sense that the mixture viscosity is observed to be significantly higher than the viscosity of both the neat components forming the mixture, giving rise to large positive excess logarithmic viscosities. These positive excess logarithmic viscosities decrease with increasing temperature. Formation of extensive H-bonding between the IL and PEG more than compensates for the losses in Coulombic attractive and van der Waals interactions within [bmim][PF(6)] and PEG600/PEG1000, respectively, giving rise to viscosity synergism. This compensation is not enough for ([bmim][PF(6)] + PEG200) and ([bmim][PF(6)] + PEG400) mixtures. The evidence for H-bonding in the mixtures is provided by FTIR absorbance data. The product of the monomer-to-excimer emission intensity ratio and the lifetime of the intramolecular excimer fluorescence of a microfluidity probe, 1,3-bis(1-pyrenyl)propane (BPP), is used as a reflection of the microviscosity of the mixture at different temperatures. The microviscosity shows synergistic effects in all four

  15. Strand specific RNA-sequencing and membrane lipid profiling reveals growth phase-dependent cold stress response mechanisms in Listeria monocytogenes.

    Directory of Open Access Journals (Sweden)

    Patricia Hingston

    Full Text Available The human pathogen Listeria monocytogenes continues to pose a challenge in the food industry, where it is known to contaminate ready-to-eat foods and grow during refrigerated storage. Increased knowledge of the cold-stress response of this pathogen will enhance the ability to control it in the food-supply-chain. This study utilized strand-specific RNA sequencing and whole cell fatty acid (FA profiling to characterize the bacterium's cold stress response. RNA and FAs were extracted from a cold-tolerant strain at five time points between early lag phase and late stationary-phase, both at 4°C and 20°C. Overall, more genes (1.3× were suppressed than induced at 4°C. Late stationary-phase cells exhibited the greatest number (n = 1,431 and magnitude (>1,000-fold of differentially expressed genes (>2-fold, p<0.05 in response to cold. A core set of 22 genes was upregulated at all growth phases, including nine genes required for branched-chain fatty acid (BCFA synthesis, the osmolyte transporter genes opuCBCD, and the internalin A and D genes. Genes suppressed at 4°C were largely associated with cobalamin (B12 biosynthesis or the production/export of cell wall components. Antisense transcription accounted for up to 1.6% of total mapped reads with higher levels (2.5× observed at 4°C than 20°C. The greatest number of upregulated antisense transcripts at 4°C occurred in early lag phase, however, at both temperatures, antisense expression levels were highest in late stationary-phase cells. Cold-induced FA membrane changes included a 15% increase in the proportion of BCFAs and a 15% transient increase in unsaturated FAs between lag and exponential phase. These increases probably reduced the membrane phase transition temperature until optimal levels of BCFAs could be produced. Collectively, this research provides new information regarding cold-induced membrane composition changes in L. monocytogenes, the growth-phase dependency of its cold

  16. Polarization at SLC

    International Nuclear Information System (INIS)

    Swartz, M.L.

    1988-07-01

    The SLAC Linear Collider has been designed to readily accommodate polarized electron beams. Considerable effort has been made to implement a polarized source, a spin rotation system, and a system to monitor the beam polarization. Nearly all major components have been fabricated. At the current time, several source and polarimeter components have been installed. The installation and commissioning of the entire system will take place during available machine shutdown periods as the commissioning of SLC progresses. It is expected that a beam polarization of 45% will be achieved with no loss in luminosity. 13 refs., 15 figs

  17. The HIP 79977 debris disk in polarized light

    Science.gov (United States)

    Engler, N.; Schmid, H. M.; Thalmann, Ch.; Boccaletti, A.; Bazzon, A.; Baruffolo, A.; Beuzit, J. L.; Claudi, R.; Costille, A.; Desidera, S.; Dohlen, K.; Dominik, C.; Feldt, M.; Fusco, T.; Ginski, C.; Gisler, D.; Girard, J. H.; Gratton, R.; Henning, T.; Hubin, N.; Janson, M.; Kasper, M.; Kral, Q.; Langlois, M.; Lagadec, E.; Ménard, F.; Meyer, M. R.; Milli, J.; Mouillet, D.; Olofsson, J.; Pavlov, A.; Pragt, J.; Puget, P.; Quanz, S. P.; Roelfsema, R.; Salasnich, B.; Siebenmorgen, R.; Sissa, E.; Suarez, M.; Szulagyi, J.; Turatto, M.; Udry, S.; Wildi, F.

    2017-11-01

    Context. Debris disks are observed around 10 to 20% of FGK main-sequence stars as infrared excess emission. They are important signposts for the presence of colliding planetesimals and therefore provide important information about the evolution of planetary systems. Direct imaging of such disks reveals their geometric structure and constrains their dust-particle properties. Aims: We present observations of the known edge-on debris disk around HIP 79977 (HD 146897) taken with the ZIMPOL differential polarimeter of the SPHERE instrument. We measure the observed polarization signal and investigate the diagnostic potential of such data with model simulations. Methods: SPHERE-ZIMPOL polarimetric data of the 15 Myr-old F star HIP 79977 (Upper Sco, 123 pc) were taken in the Very Broad Band (VBB) filter (λc = 735 nm, Δλ = 290 nm) with a spatial resolution of about 25 mas. Imaging polarimetry efficiently suppresses the residual speckle noise from the AO system and provides a differential signal with relatively small systematic measuring uncertainties. We measure the polarization flux along and perpendicular to the disk spine of the highly inclined disk for projected separations between 0.2'' (25 AU) and 1.6'' (200 AU). We perform model calculations for the polarized flux of an optically thin debris disk which are used to determine or constrain the disk parameters of HIP 79977. Results: We measure a polarized flux contrast ratio for the disk of (Fpol)disk/F∗ = (5.5 ± 0.9) × 10-4 in the VBB filter. The surface brightness of the polarized flux reaches a maximum of SBmax = 16.2 mag arcsec-2 at a separation of 0.2''-0.5'' along the disk spine with a maximum surface brightness contrast of 7.64 mag arcsec-2. The polarized flux has a minimum near the star 1''. This can be explained by a radial blow-out of small grains. The data are modelled as a circular dust belt with a well defined disk inclination I = 85( ± 1.5)° and a radius between r0 = 60 and 90 AU. The radial

  18. Field theory of polar continua

    International Nuclear Information System (INIS)

    Heinz, C.

    1988-01-01

    A Lagrangian density in the polar space X 1+3+3 depending of the potentials and their derivativs and of the fluxes is introduced. The potentials are then the mechanical and electromagnetic potentials, the potentials of gravity and in the polar space X 1+3+3 the components of affine connection. The fluxes are essentially the tangential motors of the mechanical and electromagnetic world-lines multiplied with the density of mass and electric charge. The Hamilton principle gives, with the in variational calculus usual integrations by part, here done via the theorem of Gauss, the equations of motion and the field equations. The conditions of integrability for these equations are discussed. (author)

  19. Preliminary Analysis of Chinese GF-3 SAR Quad-Polarization Measurements to Extract Winds in Each Polarization

    Directory of Open Access Journals (Sweden)

    Lin Ren

    2017-11-01

    Full Text Available This study analyzed the noise equivalent sigma zero (NESZ and ocean wind sensitivity for Chinese C-band Gaofen-3 (GF-3 quad-polarization synthetic aperture radar (SAR measurements to facilitate further operational wind extraction from GF-3 data. Data from the GF-3 quad-polarization SAR and collocated winds from both NOAA/NCEP Global Forecast System (GFS atmospheric model and National Data Buoy Center (NDBC buoys were used in the analysis. For NESZ, the co-polarization was slightly higher compared to the cross-polarization. Regarding co-polarization and cross-polarization, NESZ was close to RadarSAT-2 and Sentinel-1 A. Wind sensitivity was analyzed by evaluating the dependence on winds in terms of normalized radar cross-sections (NRCS and polarization combinations. The closest geophysical model function (GMF and the polarization ratio (PR model to GF-3 data were determined by comparing data and the model results. The dependence of co-polarized NRCS on wind speed and azimuth angle was consistent with the proposed GMF models. The combination of CMOD5 and CMOD5.N was considered to be the closest GMF in co-polarization. The cross-polarized NRCS exhibited a strong linear relationship with moderate wind speeds higher than 4 m·s−1, but a weak correlation with the azimuth angle. The proposed model was considered as the closest GMF in cross-polarization. For polarization combinations, PR and polarization difference (PD were considered. PR increased only with the incidence angle, whereas PD increased with wind speed and varied with azimuth angle. There were three very close PR models and each can be considered as the closest. Preliminary results indicate that GF-3 quad-polarization data are valid and have the ability to extract winds in each polarization.

  20. Vacuum UV Polarization Spectroscopy of p-Terphenyl.

    Science.gov (United States)

    Nguyen, Duy Duc; Jones, Nykola C; Hoffmann, Søren V; Spanget-Larsen, Jens

    2018-01-11

    p-Terphenyl is used as a component in a variety of optical devices. In this investigation, the electronic transitions of p-terphenyl are investigated by synchrotron radiation linear dichroism (SRLD) spectroscopy in the range 30000-58000 cm -1 (330-170 nm) on molecular samples aligned in stretched polyethylene, thereby extending the region investigated by polarization spectroscopy into the vacuum UV. The resulting partial absorbance curves reveal that the vacuum UV band system with a maximum at 55000 cm -1 (180 nm) is predominantly short axis-polarized. This result is of interest in the optical applications of p-terphenyl, for example as a wavelength shifter. The observed polarization spectra are compared with the results of quantum chemical model calculations. Convoluted versions of the transitions predicted with the semiempirical ZINDO method and with the long-range-corrected time-dependent density functional theory (TD-DFT) procedures TD-CAM-B3LYP, TD-LC-ωPBE, and TD-ωB97XD are in similar qualitative agreement with the observed partial absorbance curves throughout the investigated spectral regions, while TD-B3LYP fails to predict qualitatively the spectrum of p-terphenyl in the region above 40000 cm -1 (250 nm).

  1. DNA-wrapped carbon nanotubes aligned in stretched gelatin films: Polarized resonance Raman and absorption spectroscopy study

    Science.gov (United States)

    Glamazda, A. Yu.; Plokhotnichenko, A. M.; Leontiev, V. S.; Karachevtsev, V. A.

    2017-09-01

    We present the study of DNA-wrapped single-walled carbon nanotubes (SWNTs) embedded in the stretched gelatin film by the polarized resonance Raman spectroscopy and visible-NIR optical absorption. The polarized dependent absorption spectra taken along and normal to the stretching direction demonstrate a comparatively high degree of the alignment of isolated SWNTs in the gelatin matrix. The analysis of Raman spectra of isolated SWNTs in the gelatin stretched films showed that the degree of the alignment of carbon nanotubes along the stretching direction is about 62%. The dependence of the peak position of G+-band in Raman spectra on the polarization angle θ between the polarization of the incident light and the direction of the stretching of films was revealed. This shift is explained by the different polarization dependence of the most intensive A and E1 symmetry modes within the G+-band. The performed studies of embedded DNA-wrapped nanotubes in the gelatin film show the simple method for obtaining the controlled ordered biocompatible nanotubes inside a polymer matrix. It can be used for manufacturing sizable flexible self-transparent films with integrated nanoelectrodes.

  2. RHIC Polarized proton operation

    International Nuclear Information System (INIS)

    Huang, H.; Ahrens, L.; Alekseev, I.G.; Aschenauer, E.; Atoian, G.; Bai, M.; Bazilevsky, A.; Blaskiewicz, M.; Brennan, J.M.; Brown, K.A.; Bruno, D.; Connolly, R.; Dion, A.; D'Ottavio, T.; Drees, K.A.; Fischer, W.; Gardner, C.; Glenn, J.W.; Gu, X.; Harvey, M.; Hayes, T.; Hoff, L.; Hulsart, R.L.; Laster, J.; Liu, C.; Luo, Y.; MacKay, W.W.; Makdisi, Y.; Marr, G.J.; Marusic, A.; Meot, F.; Mernick, K.; Michnoff, R.; Minty, M.; Montag, C.; Morris, J.; Nemesure, S.; Poblaguev, A.; Ptitsyn, V.; Ranjibar, V.; Robert-Demolaize, G.; Roser, T.; Schmidke, B.; Schoefer, V.; Severino, F.; Smirnov, D.; Smith, K.; Steski, D.; Svirida, D.; Tepikian, S.; Trbojevic, D.; Tsoupas, N.; Tuozzolo, J.E.; Wang, G.; Wilinski, M.; Yip, K.; Zaltsman, A.; Zelenski,