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Sample records for smectic-c mesophases revealed

  1. Smectic C chevrons in nanocylinders

    SciTech Connect

    Lefort, R. Morineau, D.; Jean, F.; Noirez, L.; Ndao, M.; Cerclier, C. V.

    2014-11-17

    The structure of an achiral smectic-C liquid crystal confined in nanocylinders with a planar surface anchoring is studied by small angle neutron scattering. We observe an invariant alignment of the nematic director with the pore axis, that promotes an original chevron structure with revolution symmetry.

  2. Molecular Order and Mesophase Investigation of Thiophene-Based Forked Mesogens.

    PubMed

    Reddy, K Rajasekhar; Lobo, Nitin P; Narasimhaswamy, T

    2016-07-14

    Thiophene-based rodlike molecules constructed from a three phenyl ring core and terminal dialkoxy chains recognized as forked mesogens are synthesized, and their mesophase properties as well as the molecular order are investigated. The synthesized forked mesogens would serve as model compounds for tetracatenar or biforked mesogens. On the basis of the position of the thiophene link with the rest of the core, 2-substituted and 3-substituted mesogens are realized in which the length of the terminal alkoxy chains is varied. The mesophase properties are evaluated using a hot-stage polarizing microscope and differential scanning calorimetry. For both homologues, the appearance of either nematic phase alone or in conjunction with smectic C phase is noticed depending on the length of the terminal alkoxy chains. The existence of layer ordering characteristic of the smectic C phase is confirmed for a representative mesogen using variable-temperature powder X-ray diffraction. High-resolution solid-state (13)C NMR measurements of C12 homologues of the two series reveal orientational order parameters of all rings of the core as well as terminal chains in the liquid crystalline phase. For both homologues, because of the asymmetry of ring I, the order parameter value is higher in contrast to ring II, ring III, and the thiophene ring. The chemical shifts and (13)C-(1)H dipolar couplings of OCH2 carbons of the terminal dodecyloxy chains provide contrasting conformations, reflecting the orientational constraints. Furthermore, the investigations also reveal that the mesophase range and the tendency for layer ordering are higher for 3-substituted mesogens compared to 2-substituted homologues. PMID:27294350

  3. Freedericksz transitions in circular toroidal layers of smectic C liquid crystals

    NASA Astrophysics Data System (ADS)

    Kidd, J. E.; Stewart, I. W.; Constanda, C.

    2001-08-01

    The aim of this paper is to consider theoretically a Freedericksz transition for concentric toroidal layers of smectic C liquid crystal arising from a simple geometric setup, thereby extending the results of Atkin & Stewart [Q. Jl Mech. Appl. Math., 47, 1994] who considered spherical layers of smectic C in the usual cone and plate geometry. Application of smectic continuum theory leads, after suitable approximations are made, to a linear governing equilibrium equation which is satisfied by both the trivial solution and a variable solution involving Bessel functions. We are able to determine the critical magnitude cH of the magnetic field H at which this variable solution exists, and a standard energy comparison reveals that the variable solution is expected to be more energetically favourable than the zero solution provided H > cH. Numerical examples of critical thresholds are given, which are comparable to those in the literature for nematics. The paper ends with a discussion section and some indication of possible future work.

  4. Gradual phase transition between the smectic- C and smectic- C{A} phases and the thresholdless antiferroelectricity.

    PubMed

    Song, Jang-Kun; Fukuda, Atsuo; Vij, J K

    2008-10-01

    We have constructed the phase diagrams for a binary-mixture system of antiferroelectric and ferroelectric liquid-crystalline materials in both thick and thin cells. In the phase diagrams the boundary between the smectic- C and smectic- C{A} phases runs almost parallel to the temperature axis below from ca. 70 degrees C down to at least -25 degrees C . The SmC-SmC_{A} phase transition for a thin cell shows a large supercooling, and a gradual transition occurs near the boundary. Moreover, the thin cell shows a continuous evolution from the antiferroelectric to the ferroelectric state by increasing the electric field applied across the cell. The continuous evolution seemingly reflects the phenomenon of thresholdless antiferroelectricity. In order to explain these phenomena and in clarifying the mechanism of the so-called frustration between ferroelectricity and antiferroelectricity, we have measured the interlayer interaction energy by varying the constituent concentrations in the binary-mixture system. The measured interlayer interaction close to the boundary indicates that the gradual phase transition and continuous evolution result from the suppression of the solitary-wave propagation by the effect of surfaces. PMID:18999440

  5. Investigations of nanoscale helical pitch in smectic-C*alpha and smectic-C* phases of a chiral smectic liquid crystal using differential optical reflectivity measurements.

    PubMed

    Panov, V P; McCoy, B K; Liu, Z Q; Vij, J K; Goodby, J W; Huang, C C

    2006-07-01

    Differential optical reflectivity (DOR) was used to study the temperature dependence of the short helical pitch in freestanding films of a liquid crystal compound. The experimentally measured DOR signal was fitted using Berreman's 4 x 4 matrix method to get the pitch value in the smectic-C*alpha (sMC*alpha) phase. The results show continuous evolution of the pitch between the smectic-C*alpha and sMC*alpha phases. In sMC*alpha, the pitch decreases as temperature increases and is found to level off at 16+/-1 smectic layers at the sMC*alpha to smectic-A* transition. PMID:16907105

  6. Molecular models for the smectic A smectic C phase transition in a system of biaxial molecules

    NASA Astrophysics Data System (ADS)

    Gorkunov, Maxim V.; Osipov, Mikhail A.

    2008-07-01

    A molecular theory of the smectic A-smectic C transition in a system of biaxial molecules is developed in the mean-field approximation. The influence of molecular biaxiality on the transition is considered in detail and it is demonstrated how the biaxial order parameters are induced by the tilt. It is shown that the ordering of biaxial molecules of low symmetry in the smectic C phase is generally described by ten independent orientational order parameters, and there exist three different tilt angles which specify the tilt of three ordering tensors. The order parameters are calculated numerically as functions of temperature for two models of biaxial molecules: molecules with two principal axes and molecules with a pair of off-center transverse dipoles. A substantial difference between the three tilt angles is found, which makes impossible a strict definition of a unique director in the smectic C phase. It is also shown that biaxial interactions may lead to an anomalously weak layer contraction in the smectic C phase. Finally, it is demonstrated that the smectic A-smectic C phase transition may be directly driven by biaxial intermolecular interactions. In this case, the tilt of long molecular axes is not a primary order parameter, and its temperature dependence is very different from convention.

  7. Amphiphilic Liquid Crystal Exhibiting the Smectic A to Smectic C Phase Transition without Layer Contraction

    NASA Astrophysics Data System (ADS)

    Ishida, Norihiro; Takanishi, Yoichi; Yamamoto, Jun; Yoshizawa, Atsushi

    2011-02-01

    We prepared an amphiphilic liquid crystal composed of a semiperfluorinated alkyl chain and a 2,3-difluoro-1,4-diphenylbenzene core, and investigated its physical properties using polarized optical microscopy, differential scanning calorimetry, and X-ray diffraction analysis. The compound was found to exhibit the smectic A to smectic C phase transition without layer contraction. The compound doped with a ferroelectric liquid crystal exhibited a fast electro-optical switching with a response time of 10 µs in the chiral smectic A phase in spite of the absence of a chiral smectic C phase. The phase transition behavior is interpreted using the de Vries cone model.

  8. Diffuse cone behavior and microscopic structure of the de Vries smectic-A and smectic-C phases

    NASA Astrophysics Data System (ADS)

    Yoon, HyunGuen; Agra-Kooijman, Dena M.; Ayub, Khurshid; Lemieux, Robert P.; Kumar, Satyendra

    2011-10-01

    Direct synchrotron x-ray scattering measurements of the orientational order parameter, S, corresponding to the siloxane and hydrocarbon parts of the molecule, smectic layer spacing, and director tilt angle with respect to the smectic-C (SmC) layer normal in the de Vries smectics-A (SmA) and SmC phases of two organosiloxane mesogens are reported. The results reveal that (i) the SmC (tilt) order parameter exponent β = 0.26 +/- 0.01 for 2nd order SmA-SmC transition in excellent agreement with the tricritical behavior, (ii) the siloxane and hydrocarbon parts of the molecules are segregated and oriented parallel to the director with different degree of orientational order, and (iii) thermal evolution of the effective molecular length is different in the two phases contrary to the conventional wisdom.

  9. Layer modulated smectic-C phase in liquid crystals with a terminal hydroxyl group

    NASA Astrophysics Data System (ADS)

    Kimoto, Yasuhiro; Nishizawa, Ayumi; Takanishi, Yoichi; Yoshizawa, Atsushi; Yamamoto, Jun

    2014-04-01

    We investigated local layer structures of the three smectic-C phases (SmC, SmC', and SmC″) in a liquid crystal with the terminal hydroxyl group using high resolution and microbeam x-ray diffraction. It is found that SmC is the conventional SmC1 phase and SmC″ is the bilayer SmC2 phase. The SmC' phase forms an in-plane modulation structure, so that this phase is the smectic-C antiphase. From the Fourier transform infrared spectroscopy, it is suggested that the intermolecular hydrogen bonding is important to induce the SmC' and SmC″ phases.

  10. Solubilization of gabapentin into HII mesophases.

    PubMed

    Achrai, Ben; Libster, Dima; Aserin, Abraham; Garti, Nissim

    2011-02-10

    In the present work, we report on the solubilization of gabapentin (GBP) into lyotropic hexagonal mesophases composed of monoolein, tricaprylin, and water. It was demonstrated that the hexagonal structure remained intact up to 2 wt % gabapentin, whereas the lamellar phase coexisted with the hexagonal one in the concentration range of 3-4 wt % of the drug. At gabapentin content of 5-6 wt %, only lamellar phases containing defects such as dislocations and multilamellar vesicles were detected. Incorporation of GBP decreased the lattice parameter of the H(II) mesophase from 56.6 to 50.6 Å, while the structural dimensions of the lamellar phase were not affected. ATR-FTIR analysis suggested enhanced hydrogen bonding between the protonated amine of GBP and the O-H groups of the GMO and the water surrounding in the inner hydrophilic interface region. This led to intercalation of the drug into the water-lipid interface. At higher GBP loads of 4-6 wt %, thermal analysis revealed disordering within the lipid packing, apparently induced by the spatially altered interface area. Rheological measurements correlated the macroscopic features of the systems with alterations on the molecular level and allowed distinguishing between closely related mesophases due to their different rheological characteristics. In vitro transdermal delivery studies showed that the examined mesophases enabled a sustained release of GBP compared to its aqueous solution. Sustained release was more pronounced in the case of the hexagonal mesophase, compared to the lamellar one. PMID:21182317

  11. (13)C NMR Studies, Molecular Order, and Mesophase Properties of Thiophene Mesogens.

    PubMed

    Veeraprakash, B; Lobo, Nitin P; Narasimhaswamy, T

    2015-12-01

    Three-ring mesogens with a core comprising thiophene linked to one phenyl ring directly and to the other via flexible ester are synthesized with terminal alkoxy chains to probe the mesophase properties and find the molecular order. The phenyl thiophene link in the core offers a comparison of the mesophase features with the molecular shape of the mesogen. The synthesized mesogens display enantiotropic polymesomorphism and accordingly nematic, smectic A, smectic C and smectic B mesophases are perceived depending upon the terminal chain length. For some of the homologues, monotropic higher order smectic phases such as smectic F and crystal E are also witnessed. The existence of polymesomorphism are originally observed by HOPM and DSC and further confirmed by powder X-ray diffraction studies. For the C8 homologue, high resolution solid state (13)C NMR spectroscopy is employed to find the molecular structure in the liquid crystalline phase and using the 2D SLF technique, the (13)C-(1)H dipolar couplings are extracted to calculate the order parameter. By comparing the ratio of local order of thiophene as well as phenyl rings, we establish the bent-core shape of the mesogen. Importantly, for assigning the carbon chemical shifts of the core unit of aligned C8 mesogen, the (13)C NMR measured in mesophase of the synthetic intermediate is employed. Thus, the proposed approach addresses the key step in the spectral assignment of target mesogens with the use of (13)C NMR data of mesomorphic intermediate. PMID:26551439

  12. Multistability in the mixtures of smectic-C^{*} materials with compensated twisting power.

    PubMed

    Emelyanenko, A V; Pozhidaev, E P

    2016-04-01

    The effect of multistability in the mixtures of smectic-C^{*} materials with compensated twisting power, i.e., the existence of a large number of almost equiprobable states in the same mixture under the same conditions, is analyzed in the framework of elastic continuum theory. A simple molecular model is also considered. It is shown that multistability can follow from the bulk properties of the smectic-C^{*} materials with compensated twisting power, but with high spontaneous polarization. Multistability leads to the formation of ferroelectric domains, in which the director oscillates in space. The length and amplitude of this oscillation is tunable smoothly by an electric field. Theoretical results for the domain length agree completely with the experimental data. A suggestion is made as to why each domain structure is remembered without the energy consumption, when the electric field is abruptly switched off. The structural dependence on material parameters, such as the spontaneous polarization, the elastic constant, and the equilibrium wave number, is predicted. PMID:27176364

  13. Smectic-C tilt under shear in smectic-A elastomers.

    PubMed

    Stenull, Olaf; Lubensky, T C; Adams, J M; Warner, Mark

    2008-08-01

    Stenull and Lubensky [Phys. Rev. E 76, 011706 (2007)] have argued that shear strain and tilt of the director relative to the layer normal are coupled in smectic elastomers and that the imposition of one necessarily leads to the development of the other. This means, in particular, that a smectic-A elastomer subjected to a simple shear will develop smectic-C-like tilt of the director. Recently, Kramer and Finkelmann [e-print arXiv:0708.2024; Phys. Rev. E 78, 021704 (2008)], performed shear experiments on smectic-A elastomers using two different shear geometries. One of the experiments, which implements simple shear, produces clear evidence for the development of smectic-C-like tilt. Here, we generalize a model for smectic elastomers introduced by Adams and Warner [Phys. Rev. E 71, 021708 (2005)] and use it to study the magnitude of SmC-like tilt under shear for the two geometries investigated by Kramer and Finkelmann. Using reasonable estimates of model parameters, we estimate the tilt angle for both geometries, and we compare our estimates to the experimental results. The other shear geometry is problematic since it introduces additional in-plane compressions in a sheetlike sample, thus inducing instabilities that we discuss. PMID:18850850

  14. Multistability in the mixtures of smectic-C* materials with compensated twisting power

    NASA Astrophysics Data System (ADS)

    Emelyanenko, A. V.; Pozhidaev, E. P.

    2016-04-01

    The effect of multistability in the mixtures of smectic-C* materials with compensated twisting power, i.e., the existence of a large number of almost equiprobable states in the same mixture under the same conditions, is analyzed in the framework of elastic continuum theory. A simple molecular model is also considered. It is shown that multistability can follow from the bulk properties of the smectic-C* materials with compensated twisting power, but with high spontaneous polarization. Multistability leads to the formation of ferroelectric domains, in which the director oscillates in space. The length and amplitude of this oscillation is tunable smoothly by an electric field. Theoretical results for the domain length agree completely with the experimental data. A suggestion is made as to why each domain structure is remembered without the energy consumption, when the electric field is abruptly switched off. The structural dependence on material parameters, such as the spontaneous polarization, the elastic constant, and the equilibrium wave number, is predicted.

  15. Orientational relaxation in free-standing smectic C film driven by rotating circular frame

    NASA Astrophysics Data System (ADS)

    Zakharov, A. V.; Vakulenko, A. A.

    2015-09-01

    The pecularities in the c ˆ -director reorientation in free-standing smectic C film without of defects and stretched between two circular frames, the rest outer and rotating inner, have been investigated theoretically based on the hydrodynamic theory including the c ˆ -director motion and with accounting for backflow. Since the orientation of the c ˆ -director is fixed at the rims of the smectic film, the shear flow induced by rotating frame winds up of the c ˆ -director field. It is found that the higher shearing flow produces the greater twisting rotation of the c ˆ -director around the normal to the smectic film directed in the opposite sense with respect to the direction of the angular velocity. Calculations also show that the relaxation dynamics of the c ˆ -director field depends crucially on the curvature of the inner rotating frame.

  16. Effect of cell surfaces on the stability of chiral smectic-C phases.

    PubMed

    Manna, U; Song, Jang-Kun; Power, G; Vij, J K

    2008-08-01

    The effect of surfaces on the stability of smectic-C* (SmC*) variant phases is investigated. The results obtained using dielectric spectroscopy by varying the cell thickness show that the temperature ranges of SmCalpha*, SmCA*(1/2) , and SmCA*(1/3) phases decrease with decreasing cell thickness, and the SmCA*(1/3) phase is more stable than the SmCA*(1/2) phase. The relative stability of any phase is found to be due to its large polar anchoring strength and low free energy compared to other phases in a cell. Experimental results are found to agree with the theory. PMID:18850856

  17. Smectic-A*-smectic-C* transition in a ferroelectric liquid crystal without smectic layer shrinkage.

    PubMed

    Giesselmann, F; Zugenmaier, P; Dierking, I; Lagerwall, S T; Stebler, B; Kaspar, M; Hamplová, V; Glogarová, M

    1999-07-01

    The smectic layer spacing of a nonfluorinated ferroelectric liquid crystal (FLC) compound with almost no shrinkage and only minor tendency to form zigzag defects was characterized by small angle x-ray diffraction. The material lacks a nematic phase. The smectic-A*-smectic-C* phase transition was studied by measuring the thermal and electric field response of the optical tilt and the electric polarization. These properties are described very well by a Landau expansion even without introduction of a higher-order Theta(6) term. This result suggests a pure second-order phase transition far from tricriticality and differs considerably from the typical behavior of the A*-C* transition in most FLC materials. PMID:11969798

  18. Pretransitional effects near the smectic-A-smectic-C* phase transition of hydrophilic and hydrophobic aerosil networks dispersed in ferroelectric liquid crystals

    SciTech Connect

    Cordoyiannis, George; Kralj, Samo; Nounesis, George; Kutnjak, Zdravko; Zumer, Slobodan

    2007-02-15

    A detailed x-ray scattering and high-resolution ac calorimetric study has been carried out near the smectic-A to chiral smectic-C phase transition of liquid-crystal compounds 4-(2-methyl butyl) phenyl 4-n-octylbiphenyl-4-carboxylate (CE8) and p-(n-decyloxy) benzylidene-p-amino-(2-methylbutyl) cinnamate (DOBAMBC) confined in hydrophilic and hydrophobic aerosil nanoparticle networks. The character of the transition, which is mean field near a tricritical point in bulk, is changed dramatically with an increase of aerosil-induced disorder. X-ray measurements revealed pretransitional behavior and compression of the smectic layers, phenomena that are strongly pronounced in high aerosil concentrations. A theoretical model that takes into account the interplay of relevant mechanisms is proposed to explain the observed phenomena. The effect of chirality on the interaction of liquid crystals with aerosils is discussed.

  19. Pretransitional effects near the smectic- A -smectic- C* phase transition of hydrophilic and hydrophobic aerosil networks dispersed in ferroelectric liquid crystals

    NASA Astrophysics Data System (ADS)

    Cordoyiannis, George; Kralj, Samo; Nounesis, George; Kutnjak, Zdravko; Žumer, Slobodan

    2007-02-01

    A detailed x-ray scattering and high-resolution ac calorimetric study has been carried out near the smectic- A to chiral smectic- C phase transition of liquid-crystal compounds 4-(2-methyl butyl) phenyl 4- n -octylbiphenyl-4-carboxylate (CE8) and p -( n -decyloxy) benzylidene- p -amino-(2-methylbutyl) cinnamate (DOBAMBC) confined in hydrophilic and hydrophobic aerosil nanoparticle networks. The character of the transition, which is mean field near a tricritical point in bulk, is changed dramatically with an increase of aerosil-induced disorder. X-ray measurements revealed pretransitional behavior and compression of the smectic layers, phenomena that are strongly pronounced in high aerosil concentrations. A theoretical model that takes into account the interplay of relevant mechanisms is proposed to explain the observed phenomena. The effect of chirality on the interaction of liquid crystals with aerosils is discussed.

  20. Smectic C liquid crystal growth through surface orientation by ZnxCd1-xSe thin films

    NASA Astrophysics Data System (ADS)

    Katranchev, B.; Petrov, M.; Bineva, I.; Levi, Z.; Mineva, M.

    2012-12-01

    A smectic C liquid crystal (LC) texture, consisting of distinct local single crystals (DLSCs) was grown using predefined orientation of ternary nanocrystalline thin films of ZnxCd1-xSe. The surface morphology and orientation features of the ZnxCd1-xSe films were investigated by AFM measurements and micro-texture polarization analysis. The ZnxCd1-xSe surface causes a substantial enlargement of the smectic C DLSCs and induction of a surface bistable state. The specific character of the morphology of this coating leads to the decrease of the corresponding anchoring energy. Two new chiral states, not typical for this LC were indicated. The physical mechanism providing these new effects is presented.

  1. Polarity sensitive electric responses in a twisted smectic-C liquid crystal.

    PubMed

    Krishnamurthy, K S

    2013-12-01

    The observation of two polarity-sensitive electrical responses found in the low-frequency (<1 Hz) regime of a square wave field is reported for an achiral rodlike smectic-C liquid crystal with negative dielectric and conductivity anisotropies and in the 90°-twisted configuration. The first involves a transient director modulation appearing at each polarity reversal and vanishing under steady field conditions. The instability is polarity sensitive, with the maximum distortion localized near the negative electrode instead of the sample midplane. This is inferred from the wave-vector orientation alternating in the two halves of the driving cycle between the alignment directions at the two substrates. Various electro-optic characteristics of this temporal phenomenon are also described. Following a similar observation in nematic liquid crystals, we associate the transient periodic order with the Carr-Helfrich mechanism assisted by quadrupolar flexoelectric polarization obtaining under electric field gradients. The second polarity-sensitive effect manifests in the relative shift of the periodic Fréedericksz pattern upon field reversal. The shift, which is linear in field for low fields, tends to saturate for large fields. It is interpreted as due to flexoelectric polarization associated primarily with the c director twist about the layer normal. A model involving a periodic wedgelike band, which has the twist localized within it and is flanked by two uniformly and transversely aligned regions, accounts for the flexoelectric shift of the optical pattern. PMID:24483464

  2. Polarity sensitive electric responses in a twisted smectic-C liquid crystal

    NASA Astrophysics Data System (ADS)

    Krishnamurthy, K. S.

    2013-12-01

    The observation of two polarity-sensitive electrical responses found in the low-frequency (<1 Hz) regime of a square wave field is reported for an achiral rodlike smectic-C liquid crystal with negative dielectric and conductivity anisotropies and in the 90°-twisted configuration. The first involves a transient director modulation appearing at each polarity reversal and vanishing under steady field conditions. The instability is polarity sensitive, with the maximum distortion localized near the negative electrode instead of the sample midplane. This is inferred from the wave-vector orientation alternating in the two halves of the driving cycle between the alignment directions at the two substrates. Various electro-optic characteristics of this temporal phenomenon are also described. Following a similar observation in nematic liquid crystals, we associate the transient periodic order with the Carr-Helfrich mechanism assisted by quadrupolar flexoelectric polarization obtaining under electric field gradients. The second polarity-sensitive effect manifests in the relative shift of the periodic Fréedericksz pattern upon field reversal. The shift, which is linear in field for low fields, tends to saturate for large fields. It is interpreted as due to flexoelectric polarization associated primarily with the c director twist about the layer normal. A model involving a periodic wedgelike band, which has the twist localized within it and is flanked by two uniformly and transversely aligned regions, accounts for the flexoelectric shift of the optical pattern.

  3. Polymer stabilization of the smectic C-alpha* liquid crystal phase—Over tenfold thermal stabilization by confining networks of photo-polymerized reactive mesogens

    SciTech Connect

    Labeeb, A.; Gleeson, H. F.; Hegmann, T.

    2015-12-07

    The smectic C*-alpha (SmC{sub α}*) phase is one of the sub-phases of ferroelectric liquid crystals that has drawn much interest due to its electro-optical properties and ultrafast switching. Generally observed above the ferroelectric SmC* phase in temperature, the SmC{sub α}* commonly shows only very narrow phase temperature range of a few degree Celsius. To broaden the SmC{sub α}* phase, polymer stabilization was investigated for thermal phase stabilization. Two different reactive monomers were tested in three mixtures, and all three broadened the temperature range of the SmC{sub α}* phase from 3 °C to 39 °C. The current reversal method was used to determine the phase existence versus temperature. Moreover, the texture and network structure was studied by polarized optical microscopy and scanning electron microscopy, with the latter revealing the confinement of the smectic layer structure within the porous polymer network.

  4. Crystalline mesophases: Structure, mobility, and pharmaceutical properties.

    PubMed

    Shalaev, Evgenyi; Wu, Ke; Shamblin, Sheri; Krzyzaniak, Joseph F; Descamps, Marc

    2016-05-01

    Crystalline mesophases, which are commonly classified according to their translational, orientational, and conformational order as liquid crystals, plastic crystals, and conformationally disordered crystals, represent a common state of condensed matter. As an intermediate state between crystalline and amorphous materials, crystalline mesophases resemble amorphous materials in relation to their molecular mobility, with the glass transition being their common property, and at the same time possessing a certain degree of translational periodicity (with the exception of nematic phase), with corresponding narrow peaks in X-ray diffraction patterns. For example, plastic crystals, which can be formed both by near-spherical molecules and molecules of lower symmetry, such as planar or chain molecules, can have both extremely sharp X-ray diffraction lines and exhibit glass transition. Fundamentals of structural arrangements in mesophases are compared with several types of disorder in crystalline materials, as well as with short-range ordering in amorphous solids. Main features of the molecular mobility in crystalline mesophases are found to be generally similar to amorphous materials, although some important differences do exist, depending on a particular type of mobility modes involved in relaxation processes. In several case studies reviewed, chemical stability appears to follow the extent of disorder, with the stability of crystalline mesophase found to be intermediate between amorphous (least stable) and crystalline (most stable) materials. Finally, detection of crystalline mesophases during manufacturing of two different types of dosage forms is discussed. PMID:27067607

  5. Mesophases in nearly 2D room-temperature ionic liquids.

    PubMed

    Manini, N; Cesaratto, M; Del Pópolo, M G; Ballone, P

    2009-11-26

    Computer simulations of (i) a [C(12)mim][Tf(2)N] film of nanometric thickness squeezed at kbar pressure by a piecewise parabolic confining potential reveal a mesoscopic in-plane density and composition modulation reminiscent of mesophases seen in 3D samples of the same room-temperature ionic liquid (RTIL). Near 2D confinement, enforced by a high normal load, as well as relatively long aliphatic chains are strictly required for the mesophase formation, as confirmed by computations for two related systems made of (ii) the same [C(12)mim][Tf(2)N] adsorbed at a neutral solid surface and (iii) a shorter-chain RTIL ([C(4)mim][Tf(2)N]) trapped in the potential well of part i. No in-plane modulation is seen for ii and iii. In case ii, the optimal arrangement of charge and neutral tails is achieved by layering parallel to the surface, while, in case iii, weaker dispersion and packing interactions are unable to bring aliphatic tails together into mesoscopic islands, against overwhelming entropy and Coulomb forces. The onset of in-plane mesophases could greatly affect the properties of long-chain RTILs used as lubricants. PMID:19886615

  6. Mesophase behavior and rheology of polyhedral particles

    NASA Astrophysics Data System (ADS)

    Agarwal, Umang; Escobedo, Fernando

    2011-03-01

    Translational and orientational excluded volume fields can guide assembly of particles with anisotropic shape to diverse morphologies. A roadmap elucidating correlations between phase behavior and particle shape may help devising efficient strategies for self-assembly of desired nanocrystal superlattices. To explore these complex correlations we performed detailed Monte Carlo simulations of six convex multi-faceted shapes belonging to the diverse class of space-filling polyhedrons. Simulations predict formation of various novel liquid-crystalline and plastic-crystalline phases at intermediate volume fractions. By correlating these findings with particle anisotropy and order of rotational symmetry, simple guidelines for predicting phase behavior of polyhedral particles are proposed. Moreover, detailed analysis of the structures of mesophases reveals importance of dynamical order in defining these phases and preliminary information about kinetics of these transitions is also obtained. Finally, to elucidate the effect of particle shape anisotropy on rheology, preliminary results will be reported from non equilibrium molecular dynamics simulations of the isotropic and cubatic(LC) phase of cuboidal particles. This work was supported by a Department of Energy Basic Energy Science Grant ER46517.

  7. Crystallizing Membrane Proteins Using Lipidic Mesophases

    PubMed Central

    Caffrey, Martin; Cherezov, Vadim

    2009-01-01

    A detailed protocol for crystallizing membrane proteins that makes use of lipidic mesophases is described. This has variously been referred to as the lipid cubic phase or in meso method. The method has been shown to be quite general in that it has been used to solve X-ray crystallographic structures of prokaryotic and eukaryotic proteins, proteins that are monomeric, homo- and hetero-multimeric, chromophore-containing and chromophore-free, and α-helical and β-barrel proteins. Its most recent successes are the human engineered β2-adrenergic and adenosine A2A G protein-coupled receptors. Protocols are provided for preparing and characterizing the lipidic mesophase, for reconstituting the protein into the monoolein-based mesophase, for functional assay of the protein in the mesophase, and for setting up crystallizations in manual mode. Methods for harvesting micro-crystals are also described. The time required to prepare the protein-loaded mesophase and to set up a crystallization plate manually is about one hour. PMID:19390528

  8. Induced Mesophase in Mixtures of Photopolymerizable Hyperbranched Polyester and Liquid Crystal Mesogen

    NASA Astrophysics Data System (ADS)

    Kim, Namil; Kyu, Thein; Nosaka, Mami; Kudo, Hiroto; Nishikubo, Tadatomi

    2008-03-01

    Phase behavior of a mixture of eutectic liquid crystals (E7) and hyperbranched polyester (HBPEAc-COOH) has been investigated using polarized optical microscopy and differential scanning calorimetry. The observed phase diagram is an upper azeotrope, exhibiting the coexistence of nematic + isotropic phase in the vicinity of 90˜110^oC above the clearing temperature of neat E7 (60^oC). With decreasing temperature a focal-conic fan shaped texture develops in the composition range of 70˜90 wt% of E7, suggestive of induced smectic Sm-A phase in the mixture containing no known smectic phase in their neat forms. Wide angle x-ray diffraction (WAXD) technique revealed the existence of higher order mesophase(s). The phenomenon of induced mesophase in the hyperbranched polyester/E7 system will be discussed.

  9. Critical behavior at the isotropic to nematic, nematic to smectic-A and smectic-A to smectic-C phase transitions in a pyrimidine liquid crystal compound

    NASA Astrophysics Data System (ADS)

    Chakraborty, Anish; Chakraborty, Susanta; Kumar Das, Malay

    2015-12-01

    High-resolution optical birefringence (∆n) measurement of a pyrimidine liquid crystal compound having nematic, smectic-A and smectic-C phases are reported. The high-resolution ∆n data are rather successful in assessing the critical anomaly at different phase transitions in the investigated compound with a reasonably good accuracy. The critical exponent β, describing the limiting behavior of the nematic order parameter close to the isotropic-nematic (I-N) phase transition, is found to be in good agreement with the tricritical hypothesis. The critical behavior at the nematic-smectic-A (N-Sm-A) and the smectic-A-smectic-C (Sm-A-Sm-C) phase transitions has been explored with the aid of a differential quotient extracted from the ∆n values. The yielded effective critical exponent α‧ is appeared to be nearly tricritical in nature for the N-Sm-A phase transition. For the Sm-A-Sm-C phase transition, α‧ exhibits a weak dependence on the fit range and assumes tricritical value for large temperature range considered, which again is found to be diminished slightly with reduction in the temperature range. Related critical amplitude quotient and corrections-to-scaling quotient are found to display deviations from the theoretical models. Such behavior signals the appearance of a non-Landau character for the orthogonal to tilted smectic phase transition in the investigated compound.

  10. Molecular Dynamics in a Liquid Crystal with Reentrant Mesophases

    NASA Astrophysics Data System (ADS)

    Sebastião, P. J.; Ribeiro, A. C.; Nguyen, H. T.; Noack, F.

    1995-11-01

    It is well known that liquid crystalline compounds with a cyano terminal group can present peculiar polymorphisms in particular different types of smectic A mesophases and a reentrant behaviour for both nematic and smectic A mesophases. In this work we study by proton NMR relaxation the influence of these features on the molecular dynamics of the compound 4-cyanobenzoate-4'-octylbenzoyloxyphenyl (DB8CN Sym) in its nematic (N), partial bilayer smectic A (SAd), reentrant nematic (Nre) and reentrant smectic A (SA1) mesophases. Standard and fast field-cycling techniques were used for our spin-lattice relaxation's study over a broad frequency range of 6 decades (200 Hz up to 300 MHz). It was found that the molecular dynamics in the nematic mesophases is rather different from the molecular dynamics in the smectic A mesophases. However, the reentrant aspect present in both nematic and smectic A states is not associated to a major difference on the molecular dynamics of the nematic and reentrant nematic or smectic and reentrant smectic A mesophases. Order director fluctuations and rotations/reorientations are the most important relaxation mechanisms in the nematic mesophases in the lower and higher frequency limits, respectively, while self-diffusion has a very small contribution to the overall relaxation. As for the smectic A mesophases, self-diffusion and rotations/reorientations are the predominant relaxation mechanisms for frequencies above 20 kHz. The collective motions, which for these mesophases have to be associated with layer undulations with the frequency law T_1sim ν, are only important to the spin-lattice relaxation on the low part of the frequency spectrum (ν<10 kHz). The inclusion in the relaxation study of a contribution from the cross-relaxation between protons and nitrogen nuclei improves the quality of the 1/T_1 data fits in both kinds of mesophases. The combined study of the molecular dynamics in the N, SAd, Nre and SA1 mesophases of DB8CN Sym reveals

  11. Hydrophilic nanoparticles stabilising mesophase curvature at low concentration but disrupting mesophase order at higher concentrations.

    PubMed

    Beddoes, Charlotte M; Berge, Johanna; Bartenstein, Julia E; Lange, Kathrin; Smith, Andrew J; Heenan, Richard K; Briscoe, Wuge H

    2016-07-13

    Using high pressure small angle X-ray scattering (HP-SAXS), we have studied monoolein (MO) mesophases at 18 wt% hydration in the presence of 10 nm silica nanoparticles (NPs) at NP-lipid number ratios (ν) of 1 × 10(-6), 1 × 10(-5) and 1 × 10(-4) over the pressure range 1-2700 bar and temperature range 20-60 °C. In the absence of the silica NPs, the pressure-temperature (p-T) phase diagram of monoolein exhibited inverse bicontinuous cubic gyroid (Q), lamellar alpha (Lα), and lamellar crystalline (Lc) phases. The addition of the NPs significantly altered the p-T phase diagram, changing the pressure (p) and the temperature (T) at which the transitions between these mesophases occurred. In particular, a strong NP concentration effect on the mesophase behaviour was observed. At low NP concentration, the p-T region pervaded by the Q phase and the Lα-Q mixture increased, and we attribute this behaviour to the NPs forming clusters at the mesophase domain boundaries, encouraging transition to the mesophase with a higher curvature. At high NP concentrations, the Q phase was no longer observed in the p-T phase diagram. Instead, it was dominated by the lamellar (L) phases until the transition to a fluid isotropic (FI) phase at 60 °C at low pressure. We speculate that NPs formed aggregates with a "chain of pearls" structure at the mesophase domain boundaries, hindering transitions to the mesophases with higher curvatures. These observations were supported by small angle neutron scattering (SANS) and scanning electron microscopy (SEM). Our results have implications to nanocomposite materials and nanoparticle cellular entry where the interactions between NPs and organised lipid structures are an important consideration. PMID:27340807

  12. Crystallizing Transmembrane Peptides in Lipidic Mesophases

    SciTech Connect

    Höfer, Nicole; Aragão, David; Caffrey, Martin

    2011-09-28

    Structure determination of membrane proteins by crystallographic means has been facilitated by crystallization in lipidic mesophases. It has been suggested, however, that this so-called in meso method, as originally implemented, would not apply to small protein targets having {le}4 transmembrane crossings. In our study, the hypothesis that the inherent flexibility of the mesophase would enable crystallogenesis of small proteins was tested using a transmembrane pentadecapeptide, linear gramicidin, which produced structure-grade crystals. This result suggests that the in meso method should be considered as a viable means for high-resolution structure determination of integral membrane peptides, many of which are predicted to be coded for in the human genome.

  13. Operating characteristics of pixelated gray-scale optically addressed spatial light modulators incorporating the twisted smectic-C* liquid crystal effect

    NASA Astrophysics Data System (ADS)

    Yim, Louis W.; Davey, Anthony B.; Travis, Adrian R.

    1998-08-01

    An optically addressed spatial light modulator using the twisted smectic-C* liquid crystal effect in the light- modulating layer and an intrinsic hydrogenated amorphous silicon in the photosensitive layer is fabricated. The device incorporates a layer of pixelated aluminum mirrors, sandwiched between photosensitive and modulating layers, to increase the reflectivity of the modulated output read beam. The device is capable of achieving an intrinsic gray-scale optical output. A spatial resolution of 27 lp/mm (i.e., 54 lines/mm) at 50% modulation depth driving at 2.0 kHz and a maximum frame rate of 2.5 kHz at 80% modulation depth for which a frame cycle includes erase, write, and read operations have been demonstrated. Other operating characteristics, i.e., the sensitivity and contrast ratio, are reported.

  14. Experimental study of high-temperature smectic- C_{FI2}{ *} phase in chiral smectic liquid crystals that exhibit phase-sequence reversal.

    PubMed

    Sandhya, K L; Song, J K; Panarin, Yu P; Vij, J K; Kumar, S

    2008-05-01

    We report the results of an experimental study of a recently observed phase sequence reversal of smectic-C_{FI2}{ *} [ SmC;{ *}(q_{T}=1/2); a four layer antiferroelectric] phase appearing in the temperature range above the smectic-C{ *} (SmC;{ *}) phase from the results of optical birefringence, spontaneous polarization, selective reflection, conoscopy, and dielectric spectroscopy. The SmC_{FI2}{ *} phase is observed in an antiferroelectric liquid crystalline compound, 10OHF, in a temperature range above that of SmC{ *} phase and is found to be thermodynamically monotropic, i.e., it appears only upon cooling from SmC_{alpha}{ *} phase. This is also unstable as if it is once transformed to SmC{ *} by the application of the bias, it does not return to its original state unless the sample is heated and cooled again in the absence of the bias. Nevertheless this phase is stabilized by the addition of a chiral smectic compound 9OTBBB1M7 (abbreviated as C9), having a wide temperature range of the SmC_{FI2}{ *} phase. The temperature range of the low temperature SmC{ *} decreases with increase in the concentration of C9 and for a concentration of 55 wt. %, SmC{ *} disappears and the transition takes place directly from SmC_{FI2}{ *} to the crystalline phase on cooling. The existence of such a high-temperature SmC_{FI2}{ *} phase is also supported by a phenomenological model. PMID:18643087

  15. Tailoring the properties of polymers via formation of a mesophase

    NASA Astrophysics Data System (ADS)

    Di Girolamo, Rocco; Auriemma, Finizia; De Rosa, Claudio; Malafronte, Anna

    2015-12-01

    The combination of the control of the concentration of stereodefects in isotactic polypropylene using metallocene catalysts and the crystallization via the mesophase is a strategy to tailor the mechanical properties. Stiff materials, flexible materials, and thermoplastic elastomers can be produced depending only on the concentration of rr stereodefects. We show that in the case of isotactic polypropylene (iPP) the material properties can be finely tuned at molecular level via formation of a solid mesophase, characterized by an intermediate degree of order between amorphous and crystalline state. The effect of different degree of stereoregularity on the mesophase formation, thermal stability, morphology, is analyzed at different length scales, using different technique including wide angle X-ray scattering, atomic and optical microscopy. Different morphologies are observed depending on the stereoregularity and conditions of crystallization. In contrast to the lamellar morphology of crystals normally obtained from the melt, the solid mesophase show a nodular morphology.

  16. Tailoring the properties of polymers via formation of a mesophase

    SciTech Connect

    Di Girolamo, Rocco Auriemma, Finizia; De Rosa, Claudio; Malafronte, Anna

    2015-12-17

    The combination of the control of the concentration of stereodefects in isotactic polypropylene using metallocene catalysts and the crystallization via the mesophase is a strategy to tailor the mechanical properties. Stiff materials, flexible materials, and thermoplastic elastomers can be produced depending only on the concentration of rr stereodefects. We show that in the case of isotactic polypropylene (iPP) the material properties can be finely tuned at molecular level via formation of a solid mesophase, characterized by an intermediate degree of order between amorphous and crystalline state. The effect of different degree of stereoregularity on the mesophase formation, thermal stability, morphology, is analyzed at different length scales, using different technique including wide angle X-ray scattering, atomic and optical microscopy. Different morphologies are observed depending on the stereoregularity and conditions of crystallization. In contrast to the lamellar morphology of crystals normally obtained from the melt, the solid mesophase show a nodular morphology.

  17. Kinetics and mechanism of the interconversion of inverse bicontinuous cubic mesophases

    SciTech Connect

    Squires, Adam M.; Templer, R.H.; Seddon, J.M.; Woenkhaus, J.; Winter, R.; Narayanan, T.; Finet, S.

    2005-07-01

    This paper describes time-resolved x-ray diffraction data monitoring the transformation of one inverse bicontinuous cubic mesophase into another, in a hydrated lipid system. The first section of the paper describes a mechanism for the transformation that conserves the topology of the bilayer, based on the work of Charvolin and Sadoc, Fogden and Hyde, and Benedicto and O'Brien in this area. We show a pictorial representation of this mechanism, in terms of both the water channels and the lipid bilayer. The second section describes the experimental results obtained. The system under investigation was 2:1 lauric acid: dilauroylphosphatidylcholine at a hydration of 50% water by weight. A pressure-jump was used to induce a phase transition from the gyroid (Q{sub II}{sup G}) to the diamond (Q{sub II}{sup D}) bicontinuous cubic mesophase, which was monitored by time-resolved x-ray diffraction. The lattice parameter of both mesophases was found to decrease slightly throughout the transformation, but at the stage where the Q{sub II}{sup D} phase first appeared, the ratio of lattice parameters of the two phases was found to be approximately constant for all pressure-jump experiments. The value is consistent with a topology-preserving mechanism. However, the polydomain nature of our sample prevents us from confirming that the specific pathway is that described in the first section of the paper. Our data also reveal signals from two different intermediate structures, one of which we have identified as the inverse hexagonal (H{sub II}) mesophase. We suggest that it plays a role in the transfer of water during the transformation. The rate of the phase transition was found to increase with both temperature and pressure-jump amplitude, and its time scale varied from the order of seconds to minutes, depending on the conditions employed.

  18. Kinetics and mechanism of the interconversion of inverse bicontinuous cubic mesophases

    NASA Astrophysics Data System (ADS)

    Squires, Adam M.; Templer, R. H.; Seddon, J. M.; Woenkhaus, J.; Winter, R.; Narayanan, T.; Finet, S.

    2005-07-01

    This paper describes time-resolved x-ray diffraction data monitoring the transformation of one inverse bicontinuous cubic mesophase into another, in a hydrated lipid system. The first section of the paper describes a mechanism for the transformation that conserves the topology of the bilayer, based on the work of Charvolin and Sadoc, Fogden and Hyde, and Benedicto and O’Brien in this area. We show a pictorial representation of this mechanism, in terms of both the water channels and the lipid bilayer. The second section describes the experimental results obtained. The system under investigation was 2:1 lauric acid: dilauroylphosphatidylcholine at a hydration of 50% water by weight. A pressure-jump was used to induce a phase transition from the gyroid (QIIG) to the diamond (QIID) bicontinuous cubic mesophase, which was monitored by time-resolved x-ray diffraction. The lattice parameter of both mesophases was found to decrease slightly throughout the transformation, but at the stage where the QIID phase first appeared, the ratio of lattice parameters of the two phases was found to be approximately constant for all pressure-jump experiments. The value is consistent with a topology-preserving mechanism. However, the polydomain nature of our sample prevents us from confirming that the specific pathway is that described in the first section of the paper. Our data also reveal signals from two different intermediate structures, one of which we have identified as the inverse hexagonal (HII) mesophase. We suggest that it plays a role in the transfer of water during the transformation. The rate of the phase transition was found to increase with both temperature and pressure-jump amplitude, and its time scale varied from the order of seconds to minutes, depending on the conditions employed.

  19. Salt and mesophase formation in aqueous suspensions of lauric acid.

    PubMed

    Smith, S W; Anderson, B D

    1993-10-01

    The solubility and solution behavior of lauric acid (LA) and its 1:1 acid soap (potassium hydrogen dilaurate) were investigated at 32 degrees C over a pH range of 2.5-8.5 and at varying KCl concentrations to examine the self-association of this long-chain carboxylic acid under these conditions. LA's solubility in water exhibited the classical pH dependence of a monocarboxylic acid with no evidence of self-association. In 0.1 M KCl between pH 6.3 and pH 7.3, filtered samples were turbid, suggesting the presence of high molecular weight aggregates (mesophase), which could be removed by ultrafiltration. The apparent LA solubility vs pH profile in ultrafiltered samples was consistent with a solid phase consisting of either the free acid (pH < 6.5) or potassium hydrogen dilaurate (pH > 6.5), again with no evidence of self-association to form low molecular weight species (dimers, etc.). Quasi-elastic light scattering (QLS) studies and mannitol trapping experiments indicated that vesicles were present in samples containing mesophase. The mesophase composition was characterized and a mass-action law for mesophase formation was developed to describe the apparent LA solubility versus pH in the mesophase region in terms of three parameters. The index of cooperativity, theta, indicated that the mesophase consists of approximately 25 molecules of LA with an acid:anion ratio, rho, of 1.7. The standard free energy of mesophase formation per mole of monomer was determined to be -6.3 kcal/mol. The aggregate size determined thermodynamically is several orders of magnitude less than that of the mesophase particle size determined by QLS measurements, suggesting that the LA monomer concentration in equilibrium with mesophase may be governed by a small unit domain of the vesicle. These observations may have a bearing on the thermodynamics of self-assembly of lipid bilayer membranes. PMID:8272419

  20. Nucleation and growth of mesophase in thermolysis of petroleum pitches

    SciTech Connect

    Gusev, M.A.; Amerik, Y.B.; Anisimov, M.A.; Grishin, A.P.

    1986-01-01

    This paper aims at determining the induction period and the rate of formation of the mesophase in thermolysis of pitches from residues differing in origin. In the thermolysis of isotropic petroleum residues that are mainly of secondary origin, an anistropic phase is formed, the so-called mesophase, similar in strucure to liquid crystals. IR spectroscopic data indicate a considerable content of aromatic hydrocarbons in the pitches. These results also indicate the predominance of aromatic hydrocarbons in the pitches. The formation of an anisotropic phase in the thermolysis of petroleum pitches is explained by the presence of ''blanks'' in these pitches--planar polyaromatic hydrocarbon fragments with a paraffinic-napthenic framework.

  1. Unit cell structure of water-filled monoolein in inverted hexagonal mesophase in the presence of incorporated tricaprylin and entrapped lysozyme.

    PubMed

    Kolev, Vesselin; Ivanova, Anela; Madjarova, Galia; Aserin, Abraham; Garti, Nissim

    2016-03-01

    Molecular dynamics (MD) was employed by means of a specific simulation protocol to investigate the equilibrium structure at 25 °C of the hexagonal inverted (HII) mesophase composed from water, 1-monoolein (GMO), and tricaprylin, with or without entrapped lysozyme. Based on robust and fast MD simulations, the study provides a comprehensive analysis and visualization of the local structure of HII mesophase containing admixtures. The most important physical insight is the possibility to observe the strong self-recovery capacity of the GMO layer, which allows the HII mesophase tubes to reorganize and host lysozyme molecules with a size bigger than the diameter of the water channel. This is a direct message to the experimenters that the HII mesophase has the potential to host molecules larger than the diameter of the water channel. Collective character of the interlipid interactions is outlined, which is not affected by the presence of the cargo and may be the reason for the efficient GMO reorganization. Another important result is the possible explanation of the role of triacylglycerols on the low-temperature stabilization of the HII mesophase. The analysis shows that despite the low amount of tricaprylin, its molecules prevent the extreme inclination of the lipid tails and thus optimize the alignment capacity of the lipid tails layer. The study also reveals that the packing frustration does not depend on the temperature and the presence of admixtures. Hence, it might be numerically defined as a universal invariant parameter of a stable HII mesophase composed of a certain lipid. PMID:26424533

  2. Columnar mesophases of hexabenzocoronene derivatives. II. Charge carrier mobility.

    PubMed

    Kirkpatrick, James; Marcon, Valentina; Kremer, Kurt; Nelson, Jenny; Andrienko, Denis

    2008-09-01

    Combining atomistic molecular dynamic simulations, Marcus-Hush theory description of charge transport rates, and master equation description of charge dynamics, we correlate the temperature-driven change of the mesophase structure with the change of charge carrier mobilities in columnar phases of hexabenzocoronene derivatives. The time dependence of fluctuations in transfer integrals shows that static disorder is predominant in determining charge transport characteristics. Both site energies and transfer integrals are distributed because of disorder in the molecular arrangement. It is shown that the contributions to the site energies from polarization and electrostatic effects are of opposite sign for positive charges. We look at three mesophases of hexabenzocoronene: herringbone, discotic, and columnar disordered. All results are compared to time resolved microwave conductivity data and show excellent agreement with no fitting parameters. PMID:19044876

  3. Crystallizing Membrane Proteins in Lipidic Mesophases. A Host Lipid Screen

    SciTech Connect

    Li, Dianfan; Lee, Jean; Caffrey, Martin

    2011-11-30

    The default lipid for the bulk of the crystallogenesis studies performed to date using the cubic mesophase method is monoolein. There is no good reason, however, why this 18-carbon, cis-monounsaturated monoacylglycerol should be the preferred lipid for all target membrane proteins. The latter come from an array of biomembrane types with varying properties that include hydrophobic thickness, intrinsic curvature, lateral pressure profile, lipid and protein makeup, and compositional asymmetry. Thus, it seems reasonable that screening for crystallizability based on the identity of the lipid creating the hosting mesophase would be worthwhile. For this, monoacylglycerols with differing acyl chain characteristics, such as length and olefinic bond position, must be available. A lipid synthesis and purification program is in place in the author's laboratory to serve this need. In the current study with the outer membrane sugar transporter, OprB, we demonstrate the utility of host lipid screening as a means for generating diffraction-quality crystals. Host lipid screening is likely to prove a generally useful strategy for mesophase-based crystallization of membrane proteins.

  4. Low viscosity reversed hexagonal mesophases induced by hydrophilic additives.

    PubMed

    Amar-Yuli, Idit; Wachtel, Ellen; Shalev, Deborah E; Aserin, Abraham; Garti, Nissim

    2008-04-01

    This study reports on the formation of a low viscosity H(II) mesophase at room temperature upon addition of Transcutol (diethylene glycol mono ethyl ether) or ethanol to the ternary mixture of GMO (glycerol monooleate)/TAG (tricaprylin)/water. The microstructure and bulk properties were characterized in comparison with those of the low viscosity HII mesophase formed in the ternary GMO/TAG/water mixture at elevated temperatures (35-40 degrees C). We characterized the role of Transcutol or ethanol as inducers of disorder and surfactant mobility. The techniques used were rheology, differential scanning calorimetry (DSC), wide- and small-angle X-ray scattering (WAXS and SAXS, respectively), NMR (self-diffusion and (2)H NMR), and Fourier transform infrared (FTIR) spectroscopies. The incorporation of either Transcutol or ethanol induced the formation of less ordered HII mesophases with smaller domain sizes and lattice parameters at room temperature (up to 30 degrees C), similar to those found for the GMO/TAG/water mixture at more elevated temperatures (35-40 degrees C). On the basis of our measurements, we suggest that Transcutol or ethanol causes dehydration of the GMO headgroups and enhances the mobility of the GMO chains. As a result, these two small molecules, which compete for water with the GMO polar headgroups, may increase the curvature of the cylindrical micelles and also perhaps reduce their length. This results in the formation of fluid H(II) structures at room temperature (up to 30 degrees C). It is possible that these phases are a prelude to the H(II)-L(2) transformation, which takes place above 35 degrees C. PMID:18324809

  5. Large-amplitude motion in polymer crystals and mesophases

    SciTech Connect

    Wunderlich, B. |

    1994-12-31

    Large-amplitude motion of macromolecules involves mainly rotation about bonds (conformational motion). In the liquid phases, the large- amplitude motion is coupled with disorder and accounts for the flow and viscoelastic behavior. Perfectly ordered crystals, in contrast, permit only little large-amplitude motion. The mesophases are intermediate in order and mobility. In crystals, large-amplitude motion leads initially to gauche defects and kinks (conformational defects), and ultimately may produce conformationally disordered crystals (conis crystals). Molecular dynamics simulations of crystals with up to 30,000 atoms have been carried out and show the mechanism of defect formation, permit the study of the distribution of defects, and the visualization of hexagonal crystals. Distinction between main-chain liquid-crystalline macromolecules and condis crystals, the two mesophases of polymers, can be done on basis of analysis of phase separation (partial crystallinity), present in condis crystals and not in liquid crystals. Solid state NMR is the tool of choice for detecting mobile and rigid phases. In highly drawn fibers one can find four different states of order and mobility. Besides the (defect) crystalline phase and the isotropic amorphous phase, an intermediate oriented phase and a rigid amorphous phase exists.

  6. Tunable Nanoparticulate Scaffolds from Self assembly in Surfactant Mesophase

    NASA Astrophysics Data System (ADS)

    Sharma, K. P.; Guruswamy, K.; Mondain-Monval, O.; Aswal, V. K.

    2010-03-01

    We examine the organization of silica nanoparticles in non-ionic surfactant, C12E9/water, H1 phase. We show, using SAXS, TEM , Freeze Fracture and Microscopy, that particles with sizes smaller than the mesophase characteristic size, a, template the mesophase; particles with size ˜ a, partition into a dispersed phase and into strand-like aggregates. Particles of size > a phase separate to form particulate strands organized into a scaffold. The particulate network forms by expulsion of particles from growing H1 phase domains; particles are concentrated in the isotropic phase and jam at domain boundaries. Changing the cooling rate into the H1 phase changes the nucleation of domains -- hence providing a route to tune the network mesh size. When the surfactant is heated to the micellar phase, the particles redisperse readily. SANS confirms that C12E9 forms a bilayer on the silica particles, preventing their irreversible aggregation. PEI coated particles (with size >a) also phase separate to form networks. The network of such coated particles can be crosslinked to obtain a free standing nanoparticulate scaffold.

  7. HIV-TAT enhances the transdermal delivery of NSAID drugs from liquid crystalline mesophases.

    PubMed

    Cohen-Avrahami, Marganit; Shames, Alexander I; Ottaviani, M Francesca; Aserin, Abraham; Garti, Nissim

    2014-06-12

    Sodium diclofenac (Na-DFC) and celecoxib (CLXB) are common nonsteroidal anti-inflammatory (NSAID) drugs which suffer from poor bioavailability and severe side effects when consumed orally, and their transdermal delivery might present important advantages. In this study, the drugs were solubilized in cubic and lamellar mesophases as transdermal delivery vehicles, and a cell-penetrating peptide, HIV-TAT (TAT), was examined as a skin penetration enhancer. SD-NMR, ATR-FTIR, and EPR measurements revealed that, in the cubic mesophase (which is rich in water content), TAT populates the aqueous cores and binds water, while in the dense lamellar system (with the lower water content) TAT is bound also to the glycerol monooleate (GMO) and increases the microviscosity and the order degree. TAT secondary structure in the cubic system was found to be a random coil while once it was embedded in the closely packed lamellar system it transforms to a more ordered compact state of β-turns arranged around the GMO headgroups. TAT remarkably increased the diffusion of Na-DFC and CLXB from the cubic systems by 6- and 9-fold enhancement, respectively. TAT effect on drug diffusion from the lamellar systems was limited to an increase of 1.3- and 1.7-fold, respectively. The dense packing and strong binding in the lamellar phase led to slow diffusion rates and slower drug release in controlled pattern. These effects of the chemical composition and vehicle geometry on drug diffusion are demonstrated with the impacts of TAT which can be specifically utilized for controlling skin delivery of drugs as required. PMID:24798650

  8. Thermoreversible hydroferrogels with tunable mechanical properties utilizing block copolymer mesophases as template.

    PubMed

    Krekhova, Marina; Lang, Tobias; Richter, Reinhard; Schmalz, Holger

    2010-12-21

    Thermoreversible hydroferrogels (FGs) have been prepared via gelation of aqueous maghemite ferrofluids (FFs) using the triblock copolymer Pluronic P123 as gelator. In the investigated concentration range of 28-42 wt % P123, long-term stable homogeneous FGs can be prepared from FFs with a maximum maghemite content of 14 wt %. For higher FF concentrations up to 29 wt %, however, homogeneous FGs were formed only for gelator contents up to ca. 33 wt %. A combination of rheology and μ-DSC was applied as an alternative method to construct the P123 phase diagram, without the need for visual methods or scattering techniques. Using this procedure, we could show that maghemite nanoparticles can be effectively templated by the cubic and hexagonal P123 mesophases in a concentration range of 33-38 wt % P123 and FF concentrations up to 14 wt %, respectively. Most importantly, the phase behavior and the corresponding phase-transition temperatures of P123 were not significantly altered. As a result, the FGs show a reversible temperature-triggered transition from a cubic hard gel to a hexagonal gel, which is linked with a softening of the gel. Furthermore, this concept can be applied to template cobalt ferrite nanoparticle effectively, too. Magnetization experiments revealed that the superparamagnetic behavior of the maghemite nanoparticles, which show a Néel type relaxation, is not altered in the corresponding FGs. In contrast, FGs based on blocked cobalt ferrite nanoparticles show a hysteretic behavior, which indicates a strong mechanical coupling between the P123 mesophase and the magnetic nanoparticles. PMID:21090823

  9. Lysozyme entrapped within reverse hexagonal mesophases: physical properties and structural behavior.

    PubMed

    Mishraki, Tehila; Libster, Dima; Aserin, Abraham; Garti, Nissim

    2010-01-01

    A model protein (lysozyme) was incorporated into monoolein-based reverse hexagonal (H(II)) mesophase and its structure effects were characterized by small angle X-ray scattering, ATR-FTIR spectroscopy, and rheological measurements. Modifications in molecular organization of the H(II) mesophases as well as the conformational stability of lysozyme (LSZ) as a function of pH and denaturating agent (urea) were clarified. Up to 3 wt.% LSZ can be solubilized into the H(II). The vibration FTIR analysis revealed that LSZ interacted with OH groups of glycerol monooleate (GMO) in the outer interface region, resulting in strong hydrogen bonding between the surfactant and its environment. Simultaneously, the decrease in the hydrogen-bonded carbonyl population of GMO was monitored, indicating dehydration of the monoolein carbonyls. These molecular interactions yielded a minor decrease in the lattice parameter of the systems, as detected by small angle X-ray scattering. Furthermore, LSZ was crystallized within the medium of the hexagonal structures in a single crystal form. The alpha-helix conformation of lysozyme was stabilized at high pH conditions, demonstrating greater helical structure content, compared to D(2)O solution. Moreover, the hexagonal phase decreased the unfavorable alpha-->beta transition in lysozyme, thereby increasing the stability of the protein under chemical denaturation. The rheological behavior of the hexagonal structures varied with the incorporation of LSZ, reflected in stronger elastic properties and pronounced solid-like response of the systems. The hydrogen bonding enhancement in the interface region of the structures was most likely responsible for these phenomena. The results of this study provided valuable information on the use of hexagonal systems as a carrier for incorporation and stabilization of proteins for various applications. PMID:19748240

  10. Controlling enzymatic activity and kinetics in swollen mesophases by physical nano-confinement

    NASA Astrophysics Data System (ADS)

    Sun, Wenjie; Vallooran, Jijo J.; Zabara, Alexandru; Mezzenga, Raffaele

    2014-05-01

    Bicontinuous lipid cubic mesophases are widely investigated as hosting matrices for functional enzymes to build biosensors and bio-devices due to their unique structural characteristics. However, the enzymatic activity within standard mesophases (in-meso) is severely hindered by the relatively small diameter of the mesophase aqueous channels, which provide only limited space for enzymes, and restrict them into a highly confined environment. We show that the enzymatic activity of a model enzyme, horseradish peroxidase (HRP), can be accurately controlled by relaxing its confinement within the cubic phases' water channels, when the aqueous channel diameters are systematically swollen with varying amount of hydration-enhancing sugar ester. The in-meso activity and kinetics of HRP are then systematically investigated by UV-vis spectroscopy, as a function of the size of the aqueous mesophase channels. The enzymatic activity of HRP increases with the swelling of the water channels. In swollen mesophases with water channel diameter larger than the HRP size, the enzymatic activity is more than double that measured in standard mesophases, approaching again the enzymatic activity of free HRP in bulk water. We also show that the physically-entrapped enzymes in the mesophases exhibit a restricted-diffusion-induced initial lag period and report the first observation of in-meso enzymatic kinetics significantly deviating from the normal Michaelis-Menten behaviour observed in free solutions, with deviations vanishing when enzyme confinement is released by swelling the mesophase.Bicontinuous lipid cubic mesophases are widely investigated as hosting matrices for functional enzymes to build biosensors and bio-devices due to their unique structural characteristics. However, the enzymatic activity within standard mesophases (in-meso) is severely hindered by the relatively small diameter of the mesophase aqueous channels, which provide only limited space for enzymes, and restrict them

  11. Influence of the counteranion on the ability of 1-dodecyl-3-methyltriazolium ionic liquids to form mesophases

    SciTech Connect

    Stappert, Kathrin; Ünal, Derya; Spielberg, Eike T.; Mudring, Anja -Verena

    2014-11-25

    The influence of the counteranion on the ability of the mesogenic cation 1-methyl-3-dodecyl-triazolium to form mesophases is explored. To that avail, salts of the cation with anions of different size, shape, and hydrogen bonding capability such as Cl, Br, I, I3, PF6, and Tf2N [bis(trifluorosulfonyl)amide] were synthesized and characterized. The crystal structures of the bromide, the iodide, and the triiodide reveal that the cations form bilayers with cations oriented in opposite directions featuring interdigitated alkyl tails. Within the layers, the cations are separated by anions. The rod-shaped triiodide anion forces the triazolium cation to align with it in this crystal structure but due to its space requirement reduces the alkyl chain interdigitation which prevents the formation of a mesophase. Rather the compound transforms directly from a crystalline solid to an (ionic) liquid like the analogous bis(trifluorosulfonyl)amide. In contrast, the simple halides and the hexafluorophosphate form liquid crystalline phases. As a result, their clearing points shift with increasing anion radius to lower temperatures.

  12. Influence of the counteranion on the ability of 1-dodecyl-3-methyltriazolium ionic liquids to form mesophases

    DOE PAGESBeta

    Stappert, Kathrin; Ünal, Derya; Spielberg, Eike T.; Mudring, Anja -Verena

    2014-11-25

    The influence of the counteranion on the ability of the mesogenic cation 1-methyl-3-dodecyl-triazolium to form mesophases is explored. To that avail, salts of the cation with anions of different size, shape, and hydrogen bonding capability such as Cl–, Br–, I–, I3–, PF6–, and Tf2N– [bis(trifluorosulfonyl)amide] were synthesized and characterized. The crystal structures of the bromide, the iodide, and the triiodide reveal that the cations form bilayers with cations oriented in opposite directions featuring interdigitated alkyl tails. Within the layers, the cations are separated by anions. The rod-shaped triiodide anion forces the triazolium cation to align with it in this crystalmore » structure but due to its space requirement reduces the alkyl chain interdigitation which prevents the formation of a mesophase. Rather the compound transforms directly from a crystalline solid to an (ionic) liquid like the analogous bis(trifluorosulfonyl)amide. In contrast, the simple halides and the hexafluorophosphate form liquid crystalline phases. As a result, their clearing points shift with increasing anion radius to lower temperatures.« less

  13. Mesophases in polyethylene, polypropylene, and poly(1-butene)

    SciTech Connect

    Androsch, Rene J; Di Lorenzo, Maria; Schick, Christoph; Wunderlich, Bernhard {nmn}

    2010-01-01

    This paper contains new views about the amorphous and partially ordered phases of the three polymers listed in the title. The discussion is based on information on structure, thermodynamic stability, and large-amplitude molecular motion. Polyethylene is the basic backbone of all alkene polymers, and the other two are the first members of the vinyl polymers which have stereospecifically placed alkyl side chains. Their multiphase structures consist of metastable crystals, mesophases, and surrounding rigid and mobile amorphous fractions. All these phases have sizes ranging from micrometer dimensions down to nanometers. Besides the phase structures, information about the molecular coupling between the phases must be considered. Depending on temperature, the polymer phases can vary from solid (rigid) to liquid (mobile). New knowledge is also gained by cross-comparison of the title polymers. The experimental information was gained from (a) various forms of slow, fast, and temperature-modulated thermal analysis to identify equilibrium and non-equilibrium states, (b) measurement of structure and morphology at various length scales, and (c) tracing of the large-amplitude molecular motion, the kinetics of order/disorder changes, and the liquid/solid transitions (glass transitions). It is shown that much more needs to be known about the various phases and their coupling to characterize a given polymer and to fine-tune its properties for a given application.

  14. Mesophase stabilization in ionic liquid crystals through pairing equally shaped mesogenic cations and anions

    DOE PAGESBeta

    Stappert, Kathrin; Lipinski, Gregor; Kopiec, Gabriel; Spielberg, Eike T.; Mudring, Anja -Verena

    2015-07-23

    The synthesis and properties of a set of novel ionic liquid crystals with congruently shaped cations and anions are reported to check whether pairing mesogenic cations with mesogenic anions leads to a stabilization of a liquid crystalline phase. To that avail 1-alkyl-3-methyl-triazolium cations with an alkyl chain length of 10, 12, and 14 carbon atoms have been combined with p-alkyloxy-benzenesulfonate anions with different alkyl chain lengths (n = 10, 12, and 14). The corresponding triazolium iodides have been synthesized as reference compounds where the cation and anion have strong size and shape mismatch. The mesomorphic behavior of all compounds ismore » studied by differential scanning calorimetry and polarizing optical microscopy. All compounds except 1-methyl-3-decyltriazolium iodide, which qualifies as an ionic liquid, are thermotropic ionic liquid crystals. All other compounds adopt smectic A phases. As a result, a comparison of the thermal phase behavior of the 1-methyl-3-decyltriazolium bromides to the corresponding p-alkoxy-benzensulfonates reveals that definitely the mesophase is stabilized by pairing the rod-shaped 1-alkyl-3-methyltriazolium cation with a rod-like anion of similar size.« less

  15. Mesophase stabilization in ionic liquid crystals through pairing equally shaped mesogenic cations and anions

    SciTech Connect

    Stappert, Kathrin; Lipinski, Gregor; Kopiec, Gabriel; Spielberg, Eike T.; Mudring, Anja -Verena

    2015-07-23

    The synthesis and properties of a set of novel ionic liquid crystals with congruently shaped cations and anions are reported to check whether pairing mesogenic cations with mesogenic anions leads to a stabilization of a liquid crystalline phase. To that avail 1-alkyl-3-methyl-triazolium cations with an alkyl chain length of 10, 12, and 14 carbon atoms have been combined with p-alkyloxy-benzenesulfonate anions with different alkyl chain lengths (n = 10, 12, and 14). The corresponding triazolium iodides have been synthesized as reference compounds where the cation and anion have strong size and shape mismatch. The mesomorphic behavior of all compounds is studied by differential scanning calorimetry and polarizing optical microscopy. All compounds except 1-methyl-3-decyltriazolium iodide, which qualifies as an ionic liquid, are thermotropic ionic liquid crystals. All other compounds adopt smectic A phases. As a result, a comparison of the thermal phase behavior of the 1-methyl-3-decyltriazolium bromides to the corresponding p-alkoxy-benzensulfonates reveals that definitely the mesophase is stabilized by pairing the rod-shaped 1-alkyl-3-methyltriazolium cation with a rod-like anion of similar size.

  16. An X-ray transparent microfluidic platform for screening of the phase behavior of lipidic mesophases

    PubMed Central

    Khvostichenko, Daria S.; Kondrashkina, Elena; Perry, Sarah L.; Pawate, Ashtamurthy S.; Brister, Keith

    2013-01-01

    Lipidic mesophases are a class of highly ordered soft materials that form when certain lipids are mixed with water. Understanding the relationship between the composition and the microstructure of mesophases is necessary for fundamental studies of self-assembly in amphiphilic systems and for applications, such as crystallization of membrane proteins. However, the laborious formulation protocol for highly viscous mesophases and the large amounts of material required for sample formulation are significant obstacles in such studies. Here we report a microfluidic platform that facilitates investigations of the phase behavior of mesophases by reducing sample consumption, and automating and parallelizing sample formulation. The mesophases were formulated on-chip using less than 40 nL of material per sample and their microstructure was analyzed in situ using small-angle X-ray scattering (SAXS). The 220 μm-thick X-ray compatible platform was comprised of thin polydimethylsiloxane (PDMS) layers sandwiched between cyclic olefin copolymer (COC) sheets. Uniform mesophases were prepared using an active on-chip mixing strategy coupled with periodic cooling of the sample to reduce the viscosity. We validated the platform by preparing and analyzing mesophases of lipid monoolein (MO) mixed with aqueous solutions of different concentrations of β-octylglucoside (βOG), a detergent frequently used in membrane protein crystallization. Four samples were prepared in parallel on chip, by first metering and automatically diluting βOG to obtain detergent solutions of different concentration, then metering MO, and finally mixing by actuation of pneumatic valves. Integration of detergent dilution and subsequent mixing significantly reduced the number of manual steps needed for sample preparation. Three different types of mesophases typical for monoolein were successfully identified in SAXS data from on-chip samples. Microstructural parameters of identical samples formulated in different

  17. Spectroscopic characterizations of a mixed surfactant mesophase and its application in materials synthesis

    NASA Astrophysics Data System (ADS)

    Liu, Limin

    A viscous lyotropic crystalline mesophase containing bis (2-ethylhexyl) sodium sulfosuccinate (AOT), alpha-phosphatidylcholine (lecithin), with comparable volume fractions of isooctane and water was characterized by Fourier-transform 31P and 1H nuclear magnetic resonance (NMR) spectroscopy. Shear alignment on the reverse hexagonal mesophase was reflected through both 31P NMR and 1H NMR spectra. A complicated 31P spectrum was observed as a result of superposition of chemical shifts according to the distribution of crystalline domains prior to shear. The initially disordered samples with polydomain structures became macroscopically aligned after Couette shear and the alignment retained for a long period of time. 31P NMR chemical shift anisotropy characteristics were used to elucidate orientation of the hexagonal phase. Interestingly, 1H NMR of the water, methyl and methylene groups exhibited spectral changes upon shear alignment closely corresponding with that of 31P NMR spectra. A reverse hexagonal to lamellar phase transition was manifested as an expanding of the expressed 31P NMR chemical shift anisotropy and an apparent reversal of the powder pattern with increasing water content and/or temperature. Correspondingly, 1H NMR spectra also experienced a spectral pattern transition as the water content or temperature was increased. These observations complement the findings of mesophase alignment obtained using small angle neutron scattering (SANS) and imply that 31P and 1H NMR spectroscopy can be used as probes to define microstructure and monitor orientation changes in this binary surfactant system. This is especially beneficial if these mesophases are used as templates for materials synthesis. The mesophase retains its alignment for extended periods allowing materials synthesis to be decoupled from the application of shear. Highly aligned string-like silica nanostructures were obtained through templated synthesis in the columnar hexagonal structure of the viscous

  18. Dynamics of edge dislocations in a sheared lamellar mesophase

    NASA Astrophysics Data System (ADS)

    Kumaran, V.

    2013-10-01

    The dynamics and interactions of edge dislocations in a nearly aligned sheared lamellar mesophase is analysed to provide insights into the relationship between disorder and rheology. First, the mesoscale permeation and momentum equations for the displacement field in the presence of external forces are derived from the model H equations for the concentration and momentum field. The secondary flow generated due to the mean shear around an isolated defect is calculated, and the excess viscosity due to the presence of the defect is determined from the excess energy dissipation due to the secondary flow. The excess viscosity for an isolated defect is found to increase with system size in the cross-stream direction as L3/2 for an isolated defect, though this divergence is cut-off due to interactions in a defect suspension. As the defects are sheared past each other due to the mean flow, the Peach-Koehler force due to elastic interaction between pairs of defects is found to cause no net displacement relative to each other as they approach from large separation to the distance of closest approach. The equivalent force due to viscous interactions is found to increase the separation for defects of opposite sign, and decrease the separation for defects of same sign. During defect interactions, we find that there is no buckling instability due to dilation of layers for systems of realistic size. However, there is another mechanism, which is the velocity difference generated across a slightly deformed bilayer due to the mean shear, which could result in the creation of new defects.

  19. Broadening of mesophase temperature range induced by doping calamitic mesogen with banana-shaped mesogen

    NASA Astrophysics Data System (ADS)

    Cvetinov, Miroslav; Stojanović, Maja; Obadović, Dušanka; Vajda, Aniko; Fodor-Csorba, Katalin; Eber, Nandor

    2016-03-01

    We have investigated three binary mixtures composed of selected banana-shaped dopant in low concentrations and calamitic mesogen in high. Banana-shaped dopant forms a B7 phase, while the calamitic mesogen exhibit nematic and smectic SmA and SmC phases. The occurring mesophases have been identified by their optical textures. At dopant concentrations of 2.2 and 3.1 mol%, there is evident broadening of nematic and smectic SmA temperature ranges in respect to the pure calamitic compound. Yet, the mixture with dopant concentration of 7 mol% exhibits narrower temperature ranges of mesophases. Increasing dopant concentration caused lowering of all phase transitions temperatures (TI-N, TN-SmA, TSmA-SmC) in all investigated mixtures. Therefore, mixing classic calamitic compounds with novel banana-shaped compound in low concentrations is viable way to attain useful mesophase range for application in industry.

  20. Molecular Basis of Mesophase Ordering in a Thiophene-Based Copolymer

    SciTech Connect

    DeLongchamp,D.; Kline, R.; Jung, Y.; Lin, E.; Fischer, D.; Gundlach, D.; Cotts, S.; Moad, A.; Richter, L.; et al

    2008-01-01

    The carrier mobility of poly(2,5-bis(3-alkylthiophen-2-yl)thieno[3,2-b]thiophene) semiconductors can be substantially enhanced after heating through a thermotropic mesophase transition, which causes a significant improvement in thin film structural order. By directly measuring film structure throughout a heating and cooling cycle, we identify the molecular origin of this mesophase transition as the melting of interdigitated linear alkane side chains, in this case quaterdecyl. The morphology and phase behavior throughout the thermal cycle are controlled by the changing conformation of the side chains. Surprisingly, the melting of the side chains allows increases in the backbone order, p-p stacking, and carrier mobility. Upon cooling, the side chains recrystallize to preserve the excellent mesophase order and enhanced electrical performance.

  1. H(II) mesophase and peptide cell-penetrating enhancers for improved transdermal delivery of sodium diclofenac.

    PubMed

    Cohen-Avrahami, Marganit; Aserin, Abraham; Garti, Nissim

    2010-06-01

    This study develops a novel transdermal delivery vehicle for the enhanced delivery of sodium diclofenac (Na-DFC). The system utilizes the advantages of reversed hexagonal lyotropic liquid crystals (H(II)LC), combined with a peptide cell penetration enhancer (CPE), creating together an adaptable system that provides versatile options in the field of transdermal delivery. This enhancer peptide is based on a family of amphipatic peptides that exhibit improved membrane permeability. Franz permeation cell experiments revealed that the peptide enhancer (RALA) improved Na-DFC skin penetration of the liquid crystal 2.2-fold. We studied the structural effects of RALA solubilization on the H(II) mesophase. RALA acts as a chaotropic agent, interfering in the structure of the water, and causes a measurable swelling of the aqueous cylinders by 5A. Small angle X-ray scattering (SAXS) and attenuated total reflectance-Fourier transform infrared (ATR-FTIR) measurements reveal enhanced hydration of the glycerol monooleate (GMO) headgroups and a 6.5% increase in the fraction of non-freezable water resulting from RALA incorporation. RALA caused a gradual increase in the GMO effective headgroup area due to the hydration, leading eventually to a transform of the hexagonal structure towards a lamellar one. Circular dichroism and ATR-FTIR measurements showed a conservation of the peptide structure when incorporated into the H(II) mesophase. The combined H(II)LC-CPE systems can serve as high potential vehicles for a variety of drugs, as they can easily be modified by varying the composition and temperature, according to the required dose and delivery features. PMID:20189781

  2. The effect of dendrimer generations on the structure of Q(G) LLC mesophase and drug release.

    PubMed

    Bitan-Cherbakovsky, Liron; Aserin, Abraham; Garti, Nissim

    2014-10-01

    In this paper the cosolubilization of 2nd, 3rd, and 4th generations of polypropyleneimine (PPI: PPI-G2, -G3, and -G4) dendrimers with sodium diclofenac (Na-DFC) into reverse gyroid cubic (Q(G)) liquid crystals is reported. Structural properties and interactions of PPI dendrimers with and without the drug were studied using small-angle X-ray scattering, attenuated total reflected Fourier transform infrared (ATR-FTIR) spectroscopy, and differential scanning calorimetry (DSC) measurements. Incorporation of PPI-G2 (without Na-DFC) into Q(G) mesophase led to a decrease of 78Å in the lattice parameter. Solubilization of higher PPI generations, G3 and G4, led to increases in the lattice parameter to 57Å and 64Å, respectively. At 25wt%, each of the dendrimers caused a phase transition Q(G)→reverse hexagonal (HII). According to ATR-FTIR and DSC, the large lattice parameter values of G3 and G4 (relative to G2) embedment were assigned to their interactions with the carboxyl groups of GMO at the interface in comparison to the strong interaction of PPI-G2 with the water. Cosolubilization of Na-DFC with PPI-G2 revealed enlargement of the lattice parameter (of the new HII mesophase), while in the case of G3 and G4 systems no significant influence was seen with Na-DFC. The release of Na-DFC from Q(G) and HII systems was followed by UV-vis spectroscopy and revealed generation-dependence on drug release. As dendrimer generation increased, the cumulative drug release decreased. PMID:25016542

  3. X-ray characterization of mesophases of human telomeric G-quadruplexes and other DNA analogues

    DOE PAGESBeta

    Yasar, Selcuk; Schimelman, Jacob B.; Aksoyoglu, M. Alphan; Steinmetz, Nicole F.; French, Roger H.; Parsegian, V. Adrian; Podgornik, Rudolf

    2016-06-02

    We report that observed in the folds of guanine-rich oligonucleotides, non-canonical G-quadruplex structures are based on G-quartets formed by hydrogen bonding and cation-coordination of guanosines. In dilute 5'-guanosine monophosphate (GMP) solutions, G-quartets form by the self-assembly of four GMP nucleotides. We use x-ray diffraction to characterize the columnar liquid-crystalline mesophases in concentrated solutions of various model G-quadruplexes. We then probe the transitions between mesophases by varying the PEG solution osmotic pressure, thus mimicking in vivo molecular crowding conditions. Using the GMP-quadruplex, built by the stacking of G-quartets with no covalent linking between them, as the baseline, we report the liquid-crystallinemore » phase behaviors of two other related G-quadruplexes: (i) the intramolecular parallel-stranded G-quadruplex formed by the 22-mer four-repeat human telomeric sequence AG3 (TTAG3)3 and (ii) the intermolecular parallel-stranded G-quadruplex formed by the TG(4)T oligonucleotides. Finally, we compare the mesophases of the G-quadruplexes, under PEG-induced crowding conditions, with the corresponding mesophases of the canonical duplex and triplex DNA analogues.« less

  4. X-ray characterization of mesophases of human telomeric G-quadruplexes and other DNA analogues.

    PubMed

    Yasar, Selcuk; Schimelman, Jacob B; Aksoyoglu, M Alphan; Steinmetz, Nicole F; French, Roger H; Parsegian, V Adrian; Podgornik, Rudolf

    2016-01-01

    Observed in the folds of guanine-rich oligonucleotides, non-canonical G-quadruplex structures are based on G-quartets formed by hydrogen bonding and cation-coordination of guanosines. In dilute 5'-guanosine monophosphate (GMP) solutions, G-quartets form by the self-assembly of four GMP nucleotides. We use x-ray diffraction to characterize the columnar liquid-crystalline mesophases in concentrated solutions of various model G-quadruplexes. We then probe the transitions between mesophases by varying the PEG solution osmotic pressure, thus mimicking in vivo molecular crowding conditions. Using the GMP-quadruplex, built by the stacking of G-quartets with no covalent linking between them, as the baseline, we report the liquid-crystalline phase behaviors of two other related G-quadruplexes: (i) the intramolecular parallel-stranded G-quadruplex formed by the 22-mer four-repeat human telomeric sequence AG3(TTAG3)3 and (ii) the intermolecular parallel-stranded G-quadruplex formed by the TG4T oligonucleotides. Finally, we compare the mesophases of the G-quadruplexes, under PEG-induced crowding conditions, with the corresponding mesophases of the canonical duplex and triplex DNA analogues. PMID:27249961

  5. X-ray characterization of mesophases of human telomeric G-quadruplexes and other DNA analogues

    PubMed Central

    Yasar, Selcuk; Schimelman, Jacob B.; Aksoyoglu, M. Alphan; Steinmetz, Nicole F.; French, Roger H.; Parsegian, V. Adrian; Podgornik, Rudolf

    2016-01-01

    Observed in the folds of guanine-rich oligonucleotides, non-canonical G-quadruplex structures are based on G-quartets formed by hydrogen bonding and cation-coordination of guanosines. In dilute 5′-guanosine monophosphate (GMP) solutions, G-quartets form by the self-assembly of four GMP nucleotides. We use x-ray diffraction to characterize the columnar liquid-crystalline mesophases in concentrated solutions of various model G-quadruplexes. We then probe the transitions between mesophases by varying the PEG solution osmotic pressure, thus mimicking in vivo molecular crowding conditions. Using the GMP-quadruplex, built by the stacking of G-quartets with no covalent linking between them, as the baseline, we report the liquid-crystalline phase behaviors of two other related G-quadruplexes: (i) the intramolecular parallel-stranded G-quadruplex formed by the 22-mer four-repeat human telomeric sequence AG3(TTAG3)3 and (ii) the intermolecular parallel-stranded G-quadruplex formed by the TG4T oligonucleotides. Finally, we compare the mesophases of the G-quadruplexes, under PEG-induced crowding conditions, with the corresponding mesophases of the canonical duplex and triplex DNA analogues. PMID:27249961

  6. X-ray characterization of mesophases of human telomeric G-quadruplexes and other DNA analogues

    NASA Astrophysics Data System (ADS)

    Yasar, Selcuk; Schimelman, Jacob B.; Aksoyoglu, M. Alphan; Steinmetz, Nicole F.; French, Roger H.; Parsegian, V. Adrian; Podgornik, Rudolf

    2016-06-01

    Observed in the folds of guanine-rich oligonucleotides, non-canonical G-quadruplex structures are based on G-quartets formed by hydrogen bonding and cation-coordination of guanosines. In dilute 5‧-guanosine monophosphate (GMP) solutions, G-quartets form by the self-assembly of four GMP nucleotides. We use x-ray diffraction to characterize the columnar liquid-crystalline mesophases in concentrated solutions of various model G-quadruplexes. We then probe the transitions between mesophases by varying the PEG solution osmotic pressure, thus mimicking in vivo molecular crowding conditions. Using the GMP-quadruplex, built by the stacking of G-quartets with no covalent linking between them, as the baseline, we report the liquid-crystalline phase behaviors of two other related G-quadruplexes: (i) the intramolecular parallel-stranded G-quadruplex formed by the 22-mer four-repeat human telomeric sequence AG3(TTAG3)3 and (ii) the intermolecular parallel-stranded G-quadruplex formed by the TG4T oligonucleotides. Finally, we compare the mesophases of the G-quadruplexes, under PEG-induced crowding conditions, with the corresponding mesophases of the canonical duplex and triplex DNA analogues.

  7. Changes in the microstructure and characteristics of carbon/carbon composites with mesophase mesocarbon microbeads added during graphitization

    SciTech Connect

    Hu, H.L.; Ko, T.H.; Ku, W.S.

    2005-12-05

    Carbon/carbon (C/C) composites were prepared from oxidative PAN fiber felts, a resol-type phenolic resin, and mesophase pitch derived from coal tar. In this study, the effects on mesocarbon microbeads (MCMBs), flexural strength, flexural moduli, electric conductivity, and thermal conductivity of C/C composites with a mesophase content ranging from 0 to 30 wt % were examined during pyrolysis. The results show that the C/C composite with the addition of 10-30 wt % mesophase had a higher density, greater stacking size, and higher preferred orientation than the C/C composites without any mesophase during heat treatment. These composites also exhibited an improvement in flexural strength from 19.7 to 30.3%. The flexural moduli of these composites with mesophase added increased by 15.1 to 31.3% compared to that with no mesophase added. These composites also showed improved electric conductivity, from 15.1 to 43.7%, and thermal conductivity, from 12 to 31.3%.

  8. Polynuclear Silver(I) Triazole Complexes: Ion Conduction and Nanowire Formation in the Mesophase.

    PubMed

    Su, Padi Y S; Hsu, S J; Tseng, Jing C W; Hsu, Hsiu-Fu; Wang, Wen-Jwu; Lin, Ivan J B

    2016-01-01

    Examples of polynuclear metallomesogens are few. Herein,1,2,4-triazole ligands were used to prepare mono- and polynuclear silver(I) triazole metallomesogens. Besides showing an SmA phase in the mesophase, two interesting properties were observed. First, higher ion conductivity is always found for the polynuclear complexes than for the mononuclear complexes with the same anion, an observation contrary to the knowledge that migration of a monomeric cation should be faster than that of a polymeric cation. Second, thermolysis of the polynuclear silver(I) triazole complexes in the assembled mesophase yielded Ag nanowires, in an excellent demonstration of the assembled nature of the polynuclear silver(I) ions in the thermolysis process. PMID:26602494

  9. Mesophase formation in a system of top-shaped hard molecules: Density functional theory and Monte Carlo simulation

    NASA Astrophysics Data System (ADS)

    de las Heras, Daniel; Varga, Szabolcs; Vesely, Franz J.

    2011-06-01

    We present the phase diagram of a system of mesogenic top-shaped molecules based on the Parsons-Lee density functional theory and Monte Carlo simulation. The molecules are modeled as a hard spherocylinder with a hard sphere embedded in its center. The stability of five different phases is studied, namely, isotropic, nematic, smectic A, smectic C, and columnar phases. The positionally ordered phases are investigated only for the case of parallel alignment. It is found that the central spherical unit destabilizes the nematic with respect to the isotropic phase, while increasing the length of the cylinder has the opposite effect. Also, the central hard sphere has a strong destabilizing effect on the smectic A phase, due the inefficient packing of the molecules into layers. For large hard sphere units the smectic A phase is completely replaced by a smectic C structure. The columnar phase is first stabilized with increasing diameter of the central unit, but for very large hard sphere units it becomes less stable again. The density functional results are in good agreement with the simulations.

  10. A macroscopic H+ and Cl- ions pump via reconstitution of EcClC membrane proteins in lipidic cubic mesophases.

    PubMed

    Speziale, Chiara; Salvati Manni, Livia; Manatschal, Cristina; Landau, Ehud M; Mezzenga, Raffaele

    2016-07-01

    Functional reconstitution of membrane proteins within lipid bilayers is crucial for understanding their biological function in living cells. While this strategy has been extensively used with liposomes, reconstitution of membrane proteins in lipidic cubic mesophases presents significant challenges related to the structural complexity of the lipid bilayer, organized on saddle-like minimal surfaces. Although reconstitution of membrane proteins in lipidic cubic mesophases plays a prominent role in membrane protein crystallization, nanotechnology, controlled drug delivery, and pathology of diseased cells, little is known about the molecular mechanism of protein reconstitution and about how transport properties of the doped mesophase mirror the original molecular gating features of the reconstituted membrane proteins. In this work we design a general strategy to demonstrate correct functional reconstitution of active and selective membrane protein transporters in lipidic mesophases, exemplified by the bacterial ClC exchanger from Escherichia coli (EcClC) as a model ion transporter. We show that its correct reconstitution in the lipidic matrix can be used to generate macroscopic proton and chloride pumps capable of selectively transporting charges over the length scale of centimeters. By further exploiting the coupled chloride/proton exchange of this membrane protein and by combining parallel or antiparallel chloride and proton gradients, we show that the doped mesophase can operate as a charge separation device relying only on the reconstituted EcClC protein and an external bias potential. These results may thus also pave the way to possible applications in supercapacitors, ion batteries, and molecular pumps. PMID:27313210

  11. Controlling anisotropic drug diffusion in lipid-Fe3O4 nanoparticle hybrid mesophases by magnetic alignment.

    PubMed

    Vallooran, Jijo J; Negrini, Renata; Mezzenga, Raffaele

    2013-01-29

    We present a new strategy to control the anisotropic diffusion of hydrophilic drugs in lyotropic liquid crystals via the dispersion of magnetic nanoparticles in the mesophase, followed by reorientation of the mesophase domains via an external magnetic field. We select a lipid reverse hexagonal phase doped with magnetic iron oxide nanoparticles and glucose and caffeine as model hybrid mesophase and hydrophilic drugs, respectively. Upon cooling through the disorder-order phase transition of the hexagonal phase and under exposure to an external moderate magnetic field (1.1 T), both the nanoparticles and the hexagonal domains align with their columnar axes along the field direction. As a result, the water nanochannels of the inverted hexagonal domains also align parallel to the field direction, leading to a drug diffusion coefficient parallel to the field direction much larger than what was measured perpendicularly: in the case of glucose, for example, this difference in diffusion coefficients approaches 1 order of magnitude. Drug diffusion of the unaligned reverse hexagonal phase, which consists of randomly distributed domains, shows values in between the parallel and transversal diffusion values. This study shows that modifying the overall alignment of anisotropic mesophases via moderate external fields is a valuable means to control the corresponding transport tensor of the mesophase and demonstrates that the orientation of the domains plays an important role in the diffusion process of foreign hydrophilic molecules. PMID:23302008

  12. Development of Mesophasic Microreservoir-Based Transdermal Drug Delivery System of Propranolol

    PubMed Central

    Omray, L. K.; Kohli, S.; Khopade, A. J.; Patil, S.; Gajbhiye, Asmita; Agrawal, G. P.

    2008-01-01

    The mesophasic microreservoir comprises lyotrophic liquid crystals. The liquid crystals were prepared of Brij-35, cetosteryl alcohol and propranolol and evaluated for parameters viz. anisotropy, size and size distribution and drug entrapment efficiency. Subsequent to this liquid crystals based transdermal drug delivery system (TDS) was prepared by incorporating liquid crystals in previously prepared matrix based transdermal patch and evaluated for stability studies like temperature, humidity and aging. The system was also studied for tensile strength, moisture content, water vapor transmission, drug content, anisotropy and In vitro drug release studies. PMID:21394252

  13. A Monte Carlo study of the mesophases formed by polar bent-shaped molecules.

    PubMed

    Orlandi, Silvia; Berardi, Roberto; Steltzer, Joachim; Zannoni, Claudio

    2006-03-28

    Liquid crystal phases formed by bent-shaped (or "banana") molecules are currently of great interest. Here we investigate by Monte Carlo computer simulations the phases formed by rigid banana molecules modeled combining three Gay-Berne sites and containing either one central or two lateral and transversal dipoles. We show that changing the dipole position and orientation has a profound effect on the mesophase stability and molecular organization. In particular, we find a uniaxial nematic phase only for off-center dipolar models and tilted phases only for the one with terminal dipoles. PMID:16599725

  14. A Monte Carlo study of the mesophases formed by polar bent-shaped molecules

    NASA Astrophysics Data System (ADS)

    Orlandi, Silvia; Berardi, Roberto; Steltzer, Joachim; Zannoni, Claudio

    2006-03-01

    Liquid crystal phases formed by bent-shaped (or "banana") molecules are currently of great interest. Here we investigate by Monte Carlo computer simulations the phases formed by rigid banana molecules modeled combining three Gay-Berne sites and containing either one central or two lateral and transversal dipoles. We show that changing the dipole position and orientation has a profound effect on the mesophase stability and molecular organization. In particular, we find a uniaxial nematic phase only for off-center dipolar models and tilted phases only for the one with terminal dipoles.

  15. Membrane Protein Structure Determination Using Crystallography and Lipidic Mesophases - Recent Advances and Successes

    PubMed Central

    Caffrey, Martin; Li, Dianfan; Dukkipati, Abhiram

    2012-01-01

    The crystal structure of the β2-adrenergic receptor in complex with an agonist and its cognate G protein has just recently been solved. It is now possible to explore in molecular detail the means by which this paradigmatic transmembrane receptor binds agonist, communicates the impulse or signalling event across the membrane and sets in motion a series of G protein-directed intracellular responses. The structure was determined using crystals of the ternary complex grown in a rationally designed lipidic mesophase by the so-called in meso method. The method is proving to be particularly useful in the G protein-coupled receptor field where the structures of thirteen distinct receptor types have been solved in the past five years. In addition to receptors, the method has proven useful with a wide variety of integral membrane protein classes that include bacterial and eukaryotic rhodopsins, a light harvesting complex II (LHII), photosynthetic reaction centers, cytochrome oxidases, β-barrels, an exchanger, and an integral membrane peptide. This attests to the versatility and range of the method and supports the view that the in meso method should be included in the arsenal of the serious membrane structural biologist. For this to happen however, the reluctance in adopting it attributable, in part, to the anticipated difficulties associated with handling the sticky, viscous cubic mesophase in which crystals grow must be overcome. Harvesting and collecting diffraction data with the mesophase-grown crystals is also viewed with some trepidation. It is acknowledged that there are challenges associated with the method. Over the years, we have endeavored to establish how the method works at a molecular level and to make it user-friendly. To these ends, tools for handling the mesophase in the pico- to nano-liter volume range have been developed for highly efficient crystallization screening in manual and robotic modes. Methods have been implemented for evaluating the functional

  16. Symmetry Breaking of In-Plane Order in Confined Copolymer Mesophases

    NASA Astrophysics Data System (ADS)

    Stein, G. E.; Cochran, E. W.; Katsov, K.; Fredrickson, G. H.; Kramer, E. J.; Li, X.; Wang, J.

    2007-04-01

    Packing of spherical-domain block copolymer mesophases confined to a thin film is investigated as a function of the number of layers n. We find an abrupt transition from hexagonal to orthorhombic in-plane ordering of domains when n is increased from 4 to 5. As n increases further (up to 23 in this study), the symmetry of the orthorhombic phase asymptotically approaches that of the body-centered cubic (110) plane. These results are interpreted in terms of the energetics of competing packings in the bulk and at the film interfaces. Detailed structural and thermodynamic properties are obtained with self-consistent field theory.

  17. Three dielectric constants and orientation order parameters in nematic mesophases

    NASA Astrophysics Data System (ADS)

    Yoon, Hyung Guen; Jeong, Seung Yeon; Kumar, Satyendra; Park, Min Sang; Park, Jung Ok; Srinivasarao, M.; Shin, Sung Tae

    2011-03-01

    Temperature dependence of the three components ɛ1 , ɛ2 , and ɛ3 of dielectric constant and orientation order parameters in the nematic phase of mesogens with rod, banana, and zero-order dendritic shape were measured using the in-plane and vertical switching geometries, and micro-Raman technique. Results on the well-known uniaxial (Nu) nematogens, E7 and 5CB, revealed two components ɛ1 = ~ɛ| | and ɛ2 = ~ɛ3 = ~ɛ⊥ , as expected. The three dielectric constants were different for two azo substituted (A131 and A103) and an oxadiazole based (ODBP-Ph-C12) bent core mesogens, and a Ge core tetrapode. In some cases, two of the components became the same indicating a loss of biaxiality at temperatures coinciding with the previously reported Nu to biaxial nematic transition. This interpretation is substantiated by micro-Raman measurements of the uniaxial and biaxial nematic order parameters. Supported by the US Department of Energy, Basic Energy Sciences grant ER46572 and by Samsung Electronics Corporation.

  18. On the use of mesophase pitch for the preparation of hierarchical porous carbon monoliths by nanocasting

    NASA Astrophysics Data System (ADS)

    Adelhelm, Philipp; Cabrera, Karin; Smarsly, Bernd M.

    2012-02-01

    A detailed study is given on the synthesis of a hierarchical porous carbon, possessing both meso- and macropores, using a mesophase pitch (MP) as the carbon precursor. This carbon material is prepared by the nanocasting approach involving the replication of a porous silica monolith (hard templating). While this carbon material has already been tested in energy storage applications, various detailed aspects of its formation and structure are addressed in this study. Scanning electron microscopy (SEM), Hg porosimetry and N2 physisorption are used to characterize the morphology and porosity of the carbon replica. A novel approach for the detailed analysis of wide-angle x-ray scattering (WAXS) from non-graphitic carbons is applied to quantitatively compare the graphene microstructures of carbons prepared using MP and furfuryl alcohol (FA). This WAXS analysis underlines the importance of the carbon precursor in the synthesis of templated porous carbon materials via the nanocasting route. Our study demonstrates that a mesophase pitch is a superior precursor whenever a high-purity, low-micropore-content and well-developed graphene structure is desired.

  19. Modulation of physical properties of reverse hexagonal mesophases: a dielectric spectroscopy study.

    PubMed

    Mishraki, Tehila; Ben Ishai, Paul; Babukh, Dmitry; Aserin, Abraham; Feldman, Yuri; Garti, Nissim

    2013-04-15

    The structural, dynamic, and kinetic aspects of the HII systems based on glycerol monooleate (GMO), phosphatidylcholine (PC), triacylglycerol (TAG), and water were investigated by dielectric spectroscopy in a frequency range of 10(-2)-10(6) Hz, and a temperature range of 290-320 K. Three distinct processes as well as a temperature-activated dc conductivity were detected and examined. These were assigned to the reorientation of the GMO polar heads, the tangential movement of counterions at the interface, the transport of TAGs through the lipids tails, and the ion mobility within the water cylinders. Upon addition of PC, the critical temperature (T0) of the dehydration of the GMO headgroups increased. The optimal concentration found for structural stabilization of the HII mesophase was 10 wt% PC, since it imparted the strongest bonding at the interfacial layer and increased the association between the lipid tails. Within the HII cluster, TAG percolated and shifted between the hexagonal rods themselves. The present study demonstrated the benefit of controlling the critical temperature of the HII mesophase partial dehydration and softening, as well as the percolation of TAGs. These factors influence the diffusion mode of embedded drugs in the physiological temperature range. PMID:23415506

  20. The effect of cation structure on the mesophase architecture of self-assembled and polymerized imidazolium-based ionic liquids.

    SciTech Connect

    Batra, D.; Seifert, S.; Firestone, M. A.; Materials Science Division

    2007-01-01

    The binary phase behavior of a series of imidazolium-based ionic liquids (ILs) has been investigated. In particular, the effect of two structural modifications of the imidazolium cation, alkyl chain length, and the introduction of a polymerizable acryloyl group at the alkyl chain terminus, has been studied using small angle X-ray scattering. Upon increasing water content, the non-polymerizable IL, 1-decyl-3-methylimidazolium chloride, adopts mesophase structures of predominately two-dimensional (2D) hexagonal symmetry, including structures intermediate in character between lamellae and 2D hexagonal micelles. Introduction of a photopolymerizable acryloyl functional group to form 1-(10-(acryloyloxy)decyl)-3-methylimidazolium chloride produces a rod-coil IL cation that yields self-assembled mesophases in which the formation of tetragonal morphologies is favored. Covalent linking of the IL cations by UV-induced polymerization converts the lyotropic mesophase into three-dimensional biocontinuous chemical gels. Reducing the alkyl chain length, as in the polymerizable IL cation 1-(8-(acryloyloxy)octyl)-3-methylimidazolium chloride, severely reduces the self-assembled mesophase order, and triggers the formation of only weakly ordered one-dimensional lamellar structures.

  1. The curvature elastic-energy function of the lipid-water cubic mesophase

    NASA Astrophysics Data System (ADS)

    Chung, Hesson; Caffrey, Martin

    1994-03-01

    CELL and lipid membranes are able to bend, as manifested during membrane fusion and the formation of non-lamellar lyotropic mesopbases in water. But there is an energy cost to bending of lipid layers, called the curvature elastic energy. Although the functional form of this energy is known1, a complete quantitative knowledge of the curvature elastic energy, which is central to predicting the relative stability of the large number of phases that lipid membranes can adopt, has been lacking. Here we use X-ray synchrotron diffraction measurements of the variation of lattice parameter with pressure and temperature for the periodic Ia3d (Q230) cubic phase of hydrated monoolein to calculate the complete curvature elastic-energy function for the lipid cubic mesophase. This allows us to predict the stabilities of different cubic and lamellar phases for this system as a function of composition.

  2. Liquid-crystalline octopus dendrimers: block molecules with unusual mesophase morphologies.

    PubMed

    Gehringer, Lionel; Bourgogne, Cyril; Guillon, Daniel; Donnio, Bertrand

    2004-03-31

    The synthesis and the mesomorphic properties of several new main-chain liquid-crystalline dendrimers, thereafter designated as octopus dendrimers in accordance with their eight sidearms, are reported. In these dendritic systems, the arborescence is ensured by anisotropic segments, acting as branching cells with a double multiplicity, which are incorporated at every node of the dendritic architecture. In such a way, these compounds radically differ from the classical end-functionalized liquid-crystalline dendrimers, the most commonly reported systems. Following our previous report on purely homolithic systems, that is, the building blocks constituting the dendritic matrix are all identical, several heterolithic systems made of different anisotropic blocks have been prepared. The dendritic branches and corresponding dendrimers were synthesized using a modular construction. Polarized optical microscopy and X-ray diffraction studies showed that all of these new octopus dendrimers exhibit either smectic-like or columnar phases with novel morphologies, the nature of the mesophases depending on the number of terminal chains attached to the peripheral groups. The mesomorphism of these heterolithic dendrimers is discussed in terms of their intrinsic architecture and compared to the analogous homolithic octopus systems. Models for the molecular organizations within both the smectic and the columnar phases are proposed on the basis of small Bragg angle X-ray diffraction studies and are supported by molecular modelizations. Moreover, this study showed that the mesophase stability is very sensitive to the nature and to the mutual arrangement (the spatial location) of the mesogenic segments within the dendritic matrix, illustrating the intimate relationships existing between the mesomorphic properties and the molecular architecture of these dendrimers. PMID:15038740

  3. Experimental study and modeling of swelling and bubble growth in carbon nanofiber filled mesophase pitch during carbonization

    NASA Astrophysics Data System (ADS)

    Calebrese, Christopher

    Graphite and all carbon bipolar plates show corrosion resistance in fuel cells and provide good electrical conductivity. These materials typically need to be individually machined, a time consuming and costly process. Mesophase pitch is used to manufacture carbon fibers and carbon-carbon composites. This material provides a good starting point for the production of a moldable, all carbon bipolar plate. However, processing of mesophase pitch to produce all carbon materials requires a time intensive oxidation step to prevent swelling during carbonization. In this work, carbon nanofibers were used to reduce swelling in mesophase pitch. It was found that the increase in viscosity with the addition of carbon nanofibers was responsible for the reduction in swelling. The influence of the filler became apparent above the percolation threshold. At loadings below the percolation threshold, the swelling of the mesophase pitch was not reduced after carbonization. The swelling of the mesophase pitch at a given carbon nanofiber loading was also dependent on the length of the carbon nanofibers. Longer carbon nanofibers led to greater increases in the viscosity of the melt and thus led to greater reduction in swelling. The final carbon product was evaluated for use as a low temperature fuel cell bipolar plate material. Constraining the mesophase pitch during carbonization led to a final product with strength and electrical conductivity comparable to current composite bipolar plate materials. The addition of micron size chopped glass fibers with a softening point near 850°C and carbon nanofibers led to a final product with air permeability less than that of graphite. A spherically symmetric, single bubble growth model was also developed. The model included temperature dependence, liquid to bubble mass transfer and reactions in the system. Results from simulations showed that that the increase in viscosity due to the addition of carbon nanofibers slows the growth of bubbles, but

  4. Evaporation-Induced Self-Assembly of Hybrid Bridged Silsesquioxane Film and Particulate Mesophases with Integral Organic Functionality

    SciTech Connect

    LU,YUNFENG; FAN,HONGYOU; DOKE,NILESH; LOY,DOUGLAS A.; ASSINK,ROGER A.; LAVAN,DAVID A.; BRINKER,C. JEFFREY

    2000-06-12

    Since the discovery of surfactant-templated silica mesophases, the development of organic modification schemes to impart functionality to the pore surfaces has received much attention. Most recently, using the general class of compounds referred to as bridged silsesquioxanes (RO){sub 3}Si-R{prime}-Si(OR){sub 3} (Scheme 1), three research groups have reported the formation of a new class of poly(bridgedsilsesquioxane) mesophases BSQMs with integral organic functionality. In contrast to previous hybrid mesophases where organic ligands or molecules are situated on pore surfaces, this class of materials necessarily incorporates the organic constituents into the framework as molecularly dispersed bridging ligands. Although it is anticipated that this new mesostructural organization should result in synergistic properties derived from the molecular scale mixing of the inorganic and organic components, few properties of BSQMs have been measured. In addition samples prepared to date have been in the form of granular precipitates, precluding their use in applications like membranes, fluidics, and low k dielectric films needed for all foreseeable future generations of microelectronics.

  5. Crystalline-like molecularly ordered mesoporous aluminosilicates derived from aluminosilica-surfactant mesophases via benign template removal.

    PubMed

    Xia, Yongde; Mokaya, Robert

    2006-05-11

    We report the preparation of mesoporous aluminosilicate materials that exhibit molecular-scale ordering in their pore wall framework. The materials were derived from mesoporous aluminosilica-surfactant mesophases via benign template removal methods, which allowed the retention of molecular ordering in surfactant-free materials. The molecularly ordered aluminosilica-surfactant mesophases were obtained from hydrothermal crystallization of cetyltrimethylammonium hydroxide/Al,Si/H2O systems at 135 degrees C for 12 days. Benign template removal via H2O2-mediated oxidation of the surfactant at room temperature was found to be the most effective method in generating surfactant-free materials with molecular ordering, high textural properties (depending on Al content), and high acidity. The Al in the resulting aluminosilicates was entirely incorporated in framework (tetrahedrally coordinated) sites. Template extraction in acidified ethanol also generated molecularly ordered materials but compromised the Al content and acidity. Template removal via conventional calcination generated porous materials with high textural properties but which exhibited only limited molecular ordering and had relatively low acidity and significant amounts of nonframework Al. This work demonstrates that molecular ordering in mesoporous silicate-surfactant mesophases is due to crystallographic ordering within inorganic frameworks rather than the arrangement/packing of surfactant molecules. PMID:16671724

  6. Membrane Protein Crystallization in Lipidic Mesophases. Hosting Lipid Effects on the Crystallization and Structure of a Transmembrane Peptide

    SciTech Connect

    Hfer, Nicole; Aragao, David; Lyons, Joseph A.; Caffrey, Martin

    2011-09-28

    Gramicidin is an apolar pentadecapeptide antibiotic consisting of alternating d- and l-amino acids. It functions, in part, by creating pores in membranes of susceptible cells rendering them leaky to monovalent cations. The peptide should be able to traverse the host membrane either as a double-stranded, intertwined double helix (DSDH) or as a head-to-head single-stranded helix (HHSH). Current structure models are based on macromolecular X-ray crystallography (MX) and nuclear magnetic resonance (NMR). However, the HHSH form has only been observed by NMR. The shape and size of the different gramicidin conformations differ. We speculated therefore that reconstituting it into a lipidic mesophase with bilayers of different microstructures would preferentially stabilize one form over the other. By using such mesophases for in meso crystallogenesis, the expectation was that at least one would generate crystals of gramicidin in the HHSH form for structure determination by MX. This was tested using commercial and in-house synthesized lipids that support in meso crystallogenesis. Lipid acyl chain lengths were varied from 14 to 18 carbons to provide mesophases with a range of bilayer thicknesses. Unexpectedly, all lipids produced high-quality, structure-grade crystals with gramicidin only in the DSDH conformation.

  7. Unit cell structure of water-filled monoolein into inverted hexagonal (H(II)) mesophase modeled by molecular dynamics.

    PubMed

    Kolev, Vesselin L; Ivanova, Anela N; Madjarova, Galia K; Aserin, Abraham; Garti, Nissim

    2014-05-22

    The study investigates the unit cell structure of inverted hexagonal (H(II)) mesophase composed of monoolein (1-monoolein, GMO) and water using atomistic molecular dynamics methods without imposing any restraints on lipid and water molecules. Statistically meaningful and very contrast images of the radial mass density distribution, scrutinizing also the separate components water, monoolein, the polar headgroups of the lipids, the double bond, and the termini of the hydrocarbon chain (the tail), are obtained. The lipid/water interface structure is analyzed based on the obtained water density distribution, on the estimated number of hydrogen bonds per monoolein headgroup, and on the headgroup-water radial distribution functions. The headgroup mass density distribution demonstrates hexagonal shape of the monoolein/water interface that is well-defined at higher water/monoolein ratios. Water interacts with the headgroups by forming a three-layer diffusive mass density distribution, and each layer's shape is close to hexagonal, which is an indication of long-range structural interactions. It is found that the monoolein headgroups form a constant number of hydrogen bonds leaving an excessive amount of water molecules outside the first lipid coordination sphere. Furthermore, the quantity of water at the monoolein/water interface increases steadily upon extension of the unit cell, so the interface should have a very dynamic structure. Investigation of the hydrocarbon residues reveals high compression and well-expressed structuring of the tails. The tails form a very compressed and constrained structure of defined layers across the unit cell with properties corresponding to a more densely packed nonpolar liquid (oil). Due to the hexagonal shape the 2D packing frustration is constant and does not depend on the water content. All reported structural features are based on averaging of the atomic coordinates over the time-length of the simulation trajectories. That kind of

  8. Surfactant removal and silica condensation during the photochemical calcination of thin film silica mesophases.

    PubMed

    Dattelbaum, Andrew M; Amweg, Meri L; Ruiz, Julia D; Ecke, Laurel E; Shreve, Andrew P; Parikh, Atul N

    2005-08-01

    The evolution of photochemical surfactant removal and silica condensation from organically templated thin film silica nanocomposites with mesoscopic ordering has been probed using a combined application of Fourier transform infrared (FT-IR) spectroscopy and single wavelength ellipsometry. Thin films of silica nanocomposites were prepared by a previously reported evaporation-induced self-assembly process. Specifically, oxidized silicon and gold substrates were withdrawn at 25 mm/min from a subcritical micelle concentration solution containing an ethylene oxide surfactant as a structure-directing agent and tetraethyl orthosilicate as a silica precursor. Real-time grazing incidence difference FT-IR spectra of the nanocomposite films on gold taken during exposure to short-wavelength ultraviolet light (184-257 nm) show that surfactant removal and silica condensation occur gradually and concomitantly. Surfactant removal and silica reconstructions were found to be nearly complete after 90 min of exposure. Further, a transient feature was observed in the FT-IR spectra around 1713 cm(-1) during the UV exposure process and was assigned to a carbonyl (C=O) stretching mode absorption, reflecting the transient formation of a partially oxidized surfactant intermediate. From these data we propose a stepwise model for surfactant removal from the nanocomposite films. Ellipsometrically determined index of refraction values collected as a function of UV exposure are also shown to support such a stepwise mechanism of surfactant removal from the ordered nanocomposite silica thin film mesophases studied here. PMID:16852834

  9. Molecular dynamics approach to water structure of H(II) mesophase of monoolein.

    PubMed

    Kolev, Vesselin; Ivanova, Anela; Madjarova, Galia; Aserin, Abraham; Garti, Nissim

    2012-02-21

    The goal of the present work is to study theoretically the structure of water inside the water cylinder of the inverse hexagonal mesophase (H(II)) of glyceryl monooleate (monoolein, GMO), using the method of molecular dynamics. To simplify the computational model, a fixed structure of the GMO tube is maintained. The non-standard cylindrical geometry of the system required the development and application of a novel method for obtaining the starting distribution of water molecules. A predictor-corrector schema is employed for generation of the initial density of water. Molecular dynamics calculations are performed at constant volume and temperature (NVT ensemble) with 1D periodic boundary conditions applied. During the simulations the lipid structure is kept fixed, while the dynamics of water is unrestrained. Distribution of hydrogen bonds and density as well as radial distribution of water molecules across the water cylinder show the presence of water structure deep in the cylinder (about 6 Å below the GMO heads). The obtained results may help understanding the role of water structure in the processes of insertion of external molecules inside the GMO∕water system. The present work has a semi-quantitative character and it should be considered as the initial stage of more comprehensive future theoretical studies. PMID:22360250

  10. Molecular dynamics approach to water structure of HII mesophase of monoolein

    NASA Astrophysics Data System (ADS)

    Kolev, Vesselin; Ivanova, Anela; Madjarova, Galia; Aserin, Abraham; Garti, Nissim

    2012-02-01

    The goal of the present work is to study theoretically the structure of water inside the water cylinder of the inverse hexagonal mesophase (HII) of glyceryl monooleate (monoolein, GMO), using the method of molecular dynamics. To simplify the computational model, a fixed structure of the GMO tube is maintained. The non-standard cylindrical geometry of the system required the development and application of a novel method for obtaining the starting distribution of water molecules. A predictor-corrector schema is employed for generation of the initial density of water. Molecular dynamics calculations are performed at constant volume and temperature (NVT ensemble) with 1D periodic boundary conditions applied. During the simulations the lipid structure is kept fixed, while the dynamics of water is unrestrained. Distribution of hydrogen bonds and density as well as radial distribution of water molecules across the water cylinder show the presence of water structure deep in the cylinder (about 6 Å below the GMO heads). The obtained results may help understanding the role of water structure in the processes of insertion of external molecules inside the GMO/water system. The present work has a semi-quantitative character and it should be considered as the initial stage of more comprehensive future theoretical studies.

  11. Ferrielectricity in smectic-C* dechiralization-line lattices

    NASA Astrophysics Data System (ADS)

    Mettout, B.; Logbo, H. Pasco; Gagou, Y.; Vasseur, H.; Gisse, P.

    2016-04-01

    Recent experiments probing a new ferroelectric liquid crystal (CLF08) confined in cells with planar alignment have shown dielectric and optic anomalies suggesting the onset of ferrielectric ordering within the surface lattice of dechiralization lines. We present a phenomenological theory describing the corresponding phase transition sequence Sm A →Sm C*→Ferri . Phase diagrams and thermodynamic, dielectric, and optic properties are worked out and compared with experiments. The anomalies are related to the predicted tristability of the experimental cells under applied electric field. The order parameters of Landau theory are reinterpreted in terms of line positions, allowing description of the entrance and exit line behavior, and yielding the prediction and identification of new limit phases within a nonconventional Landau approach.

  12. Structural modeling of carbonaceous mesophase amphotropic mixtures under uniaxial extensional flow.

    PubMed

    Golmohammadi, Mojdeh; Rey, Alejandro D

    2010-07-21

    The extended Maier-Saupe model for binary mixtures of model carbonaceous mesophases (uniaxial discotic nematogens) under externally imposed flow, formulated in previous studies [M. Golmohammadi and A. D. Rey, Liquid Crystals 36, 75 (2009); M. Golmohammadi and A. D. Rey, Entropy 10, 183 (2008)], is used to characterize the effect of uniaxial extensional flow and concentration on phase behavior and structure of these mesogenic blends. The generic thermorheological phase diagram of the single-phase binary mixture, given in terms of temperature (T) and Deborah (De) number, shows the existence of four T-De transition lines that define regions that correspond to the following quadrupolar tensor order parameter structures: (i) oblate (perpendicular, parallel), (ii) prolate (perpendicular, parallel), (iii) scalene O(perpendicular, parallel), and (iv) scalene P(perpendicular, parallel), where the symbols (perpendicular, parallel) indicate alignment of the tensor order ellipsoid with respect to the extension axis. It is found that with increasing T the dominant component of the mixture exhibits weak deviations from the well-known pure species response to uniaxial extensional flow (uniaxial perpendicular nematic-->biaxial nematic-->uniaxial parallel paranematic). In contrast, the slaved component shows a strong deviation from the pure species response. This deviation is dictated by the asymmetric viscoelastic coupling effects emanating from the dominant component. Changes in conformation (oblate <==> prolate) and orientation (perpendicular <==> parallel) are effected through changes in pairs of eigenvalues of the quadrupolar tensor order parameter. The complexity of the structural sensitivity to temperature and extensional flow is a reflection of the dual lyotropic/thermotropic nature (amphotropic nature) of the mixture and their cooperation/competition. The analysis demonstrates that the simple structures (biaxial nematic and uniaxial paranematic) observed in pure discotic

  13. Phase states and thermomorphologic, thermotropic, and magnetomorphologic properties of lyotropic mesophases: Sodium lauryl sulphate-water-1-decanol liquid-crystalline system

    NASA Astrophysics Data System (ADS)

    Özden, Pınar; Nesrullajev, Arif; Oktik, Şener

    2010-12-01

    Phase states in sodium lauryl sulphate-water-1-decanol lyotropic liquid-crystalline system have been investigated for different temperature ranges. The dependence of triangle phase diagram types, phase boundaries, and sequence of lyotropic mesophases vs temperature has been found. The thermomorphologic, thermotropic, and magnetomorphologic properties of hexagonal E, lamellar D, nematic-calamitic NC , nematic-discotic ND , and biaxial nematic Nbx mesophases have been studied in detail. Dynamics of transformations of magnetically induced textures has been investigated. Peculiarities of typical and magnetically induced textures have been investigated in detail. Triangle phase diagrams of sodium lauryl sulphate-water-1-decanol lyotropic liquid-crystalline system for different temperatures and typical and magnetically induced textures of E, D, NC , ND , and Nbx mesophases are presented.

  14. John H. Dillon Medal Lecture: Magnetic Field Directed Self-Assembly of Block Copolymers and Surfactant Mesophases

    NASA Astrophysics Data System (ADS)

    Osuji, Chinedum

    2015-03-01

    Molecular self-assembly of block copolymers and small molecule surfactants gives rise to a rich phase behavior as a function of temperature, composition, and other variables. We consider the directed self-assembly of such soft mesophases using magnetic fields, principally through the use of in situ x-ray scattering studies. Field alignment is predicated on a sufficiently large product of magnetic anisotropy and grain size to produce magnetostatic interactions which are substantive relative to thermal forces. We examine the role of field strength on the phase behavior and alignment dynamics of a series of soft mesophases, outlining the possibility to readily create highly ordered functional materials over macroscopic length scales. We show that magnetic fields as large as 10 T have little discernable impact on the stability of block copolymer systems considered, with shifts in order-disorder transition temperatures of roughly 5 mK or smaller. Consequently, directed self-assembly in these systems proceeds by nucleation of randomly aligned grains which thereafter rotate into registry with the field. We highlight the tradeoff between decreasing mobility and increasing anisotropic field interaction that dictates alignment kinetics while transiting from a high temperature disordered state to an ordered system at lower temperatures. NSF support through DMR-0847534 is gratefully acknowledged.

  15. Characterization of Lipid-Templated Silica and Hybrid Thin Film Mesophases by Grazing Incidence Small-Angle X-ray Scattering

    PubMed Central

    Dunphy, Darren R.; Alam, Todd M.; Tate, Michael P.; Hillhouse, Hugh W.; Smarsly, Bernd; Collord, Andrew D.; Carnes, Eric; Baca, Helen K.; Köhn, Ralf; Sprung, Michael; Wang, Jin; Brinker, C. Jeffrey

    2009-01-01

    The nanostructure of silica and hybrid thin film mesophases templated by phospholipids via an evaporation-induced self-assembly (EISA) process was investigated by grazing-incidence small-angle X-ray scattering (GISAXS). Diacyl phosphatidylcholines with two tails of 6 or 8 carbons were found to template 2D hexagonal mesophases, with the removal of lipid from these lipid/silica films by thermal or UV/O3 processing resulting in a complete collapse of the pore volume. Monoacyl phosphatidylcholines with single tails of 10–14 carbons formed 3D micellular mesophases; the lipid was found to be extractable from these 3D materials, yielding a porous material. In contrast to pure lipid/silica thin film mesophases, films formed from the hybrid bridged silsesquioxane precursor bis(triethoxysilyl)ethane exhibited greater stability toward (both diacyl and monoacyl) lipid removal. Ellipsometric, FTIR, and NMR studies show that the presence of phospholipid suppresses siloxane network formation, while actually promoting condensation reactions in the hybrid material. 1D X-ray scattering and FTIR data were found to be consistent with strong interactions between lipid headgroups and the silica framework. PMID:19496546

  16. Design of Light-Triggered Lyotropic Liquid Crystal Mesophases and Their Application as Molecular Switches in "On Demand" Release.

    PubMed

    Aleandri, Simone; Speziale, Chiara; Mezzenga, Raffaele; Landau, Ehud M

    2015-06-30

    Here, we present the design and assembly of a new light-responsive functional lyotropic liquid crystal system using host-guest lipidic mesophases (LMPs). Light as an external stimulus has many advantages in comparison to other stimuli: it is milder than acids or bases, and variation of intensity and duration can provide a high level of pharmacological control. The LMPs are composed of monoolein (MO) and oleic acid (OA) as host lipids and a small amount of a judiciously synthesized lipid bearing an azobenzene photoactive unit as a guest. While preserving the structure and stability of the host lipidic aggregates, the guest lipids render them specific functionalities. Single-step and sequential light-triggered release and retention of the embedded dye molecules are demonstrated, thereby achieving exquisite temporal, spatial, and dosage control of the release, opening up the possibility of using such lipidic biomaterials as effective matrices in therapy, when a continuous release of active drugs might be toxic. PMID:26039728

  17. Analytical contribution of NAD 2D-NMR spectroscopy in polypeptide mesophases to the investigation of triglycerides.

    PubMed

    Lesot, Philippe; Serhan, Zeinab; Aroulanda, Christie; Billault, Isabelle

    2012-12-01

    In this work, we report and discuss on the use and limitations of the natural abundance deuterium two-dimensional NMR spectroscopy in polypeptide chiral and achiral aligning media in the studies of homogenous triglycerides at 14.1 T. As illustrative examples, two triglycerides with short and long alkyl chains were investigated: the 1,3-di(butanoyloxy)propan-2-yl butanoate or tributyrin (TB) and the 1,3-di(tetradecanoyloxy)propan-2-yl tetradecanoate or trimyristin (TM). If both flexible compounds are theoretically of C(s) symmetry on average, according to the Altmann's definition (Proc. Roy. Soc., 1967, A298, 184.), the analysis of spectral data in terms of enantiotopic and diastereotopic discriminations shows noticeable differences related to their orientational ordering behavior inside the mesophases. Although from NMR analysis viewpoint, TB behaves as a C(s) symmetry molecule as expected, the NMR results obtained for TM suggest a behavior that could be formally predicted for a C(3v) symmetry molecule on average. This conclusion was nicely supported by the comparison with the tri-n-propylorthoformate, a real C(3v) symmetry solute on average on the NMR timescale. This difference of effective orientational behavior could originate from the difference of size and shape between lateral and central alkyl chains of the solute molecule. PMID:23280656

  18. A Plug-Based Microfluidic System for Dispensing Lipidic Cubic Phase (LCP) Material Validated by Crystallizing Membrane Proteins in Lipidic Mesophases

    PubMed Central

    Li, Liang; Fu, Qiang; Kors, Christopher A.; Stewart, Lance; Nollert, Peter; Laible, Philip D.; Ismagilov, Rustem F.

    2009-01-01

    This paper presents a plug-based microfluidic system to dispense nanoliter-volume plugs of Lipidic Cubic Phase (LCP) material and subsequently merge the LCP plugs with aqueous plugs. This system was validated by crystallizing membrane proteins in lipidic mesophases, including LCP. This system allows for accurate dispensing of LCP material in nanoliter volumes, prevents inadvertent phase transitions that may occur due to dehydration by enclosing LCP in plugs, and is compatible with the traditional method of forming LCP material using a membrane protein sample, as shown by the successful crystallization of bacteriorhodopsin from Halobacterium salinarum. Conditions for the formation of LCP plugs were characterized and presented in a phase diagram. This system was also implemented using two different methods of introducing the membrane protein: 1) the traditional method of generating the LCP material using a membrane protein sample and 2) Post LCP-formation Incorporation (PLI), which involves making LCP material without protein, adding the membrane protein sample externally to the LCP material, and allowing the protein to diffuse into the LCP material or into other lipidic mesophases that may result from phase transitions. Crystals of bacterial photosynthetic reaction centers from Rhodobacter sphaeroides and Blastochloris viridis were obtained using PLI. The plug-based, LCP-assisted microfluidic system, combined with the PLI method for introducing membrane protein into LCP, should be useful for minimizing consumption of samples and broadening the screening of parameter space in membrane protein crystallization. PMID:20473353

  19. Facile synthesis of mesophase pitch/exfoliated graphite nanoplatelets nanocomposite and its application as anode materials for lithium-ion batteries

    SciTech Connect

    Yang Yishuang; Wang Chengyang; Chen Mingming; Shi Zhiqiang; Zheng Jiaming

    2010-09-15

    Mesophase pitch (MP)/exfoliated graphite nanoplatelets (GNPs) nanocomposite has been prepared by an efficient method with an initiation of graphite intercalation compounds (GIC). X-ray diffraction, optical microscopy, high-resolution transmission electron microscopy and scanning electron microscopy analysis techniques are used to characterize the samples. It is observed that GIC has exfoliated completely into GNPs during the formation of MP/GNPs nanocomposite and the GNPs are distributed uniformly in MP matrix, which represent a conductive path for a movement of electrons throughout the composites. Electrochemical tests demonstrate that the carbonized MP/GNPs nanocomposite displays higher capacity and better cycle performance in comparison with the pure carbonized MP. It is concluded that such a large improvement of electrochemical performance within the nanocomposite may in general be related to the enhanced electronic conductivity, which is achieved by good dispersion of GNPs within MP matrix and formation of a 3D network of GNPs. - Graphical abstract: Uniform mesophase pitch/exfoliated graphite nanoplatelets nanocomposite has been efficiently fabricated with an initiation of graphite intercalation compounds. The as-prepared composite electrode exhibited high electrochemical performance for Li-ion batteries.

  20. Exploring the in meso crystallization mechanism by characterizing the lipid mesophase microenvironment during the growth of single transmembrane α-helical peptide crystals.

    PubMed

    van 't Hag, Leonie; Knoblich, Konstantin; Seabrook, Shane A; Kirby, Nigel M; Mudie, Stephen T; Lau, Deborah; Li, Xu; Gras, Sally L; Mulet, Xavier; Call, Matthew E; Call, Melissa J; Drummond, Calum J; Conn, Charlotte E

    2016-07-28

    The proposed mechanism for in meso crystallization of transmembrane proteins suggests that a protein or peptide is initially uniformly dispersed in the lipid self-assembly cubic phase but that crystals grow from a local lamellar phase, which acts as a conduit between the crystal and the bulk cubic phase. However, there is very limited experimental evidence for this theory. We have developed protocols to investigate the lipid mesophase microenvironment during crystal growth using standard procedures readily available in crystallography laboratories. This technique was used to characterize the microenvironment during crystal growth of the DAP12-TM peptide using synchrotron small angle X-ray scattering (SAXS) with a micro-sized X-ray beam. Crystal growth was found to occur from the gyroid cubic mesophase. For one in four crystals, a highly oriented local lamellar phase was observed, providing supporting evidence for the proposed mechanism for in meso crystallization. A new observation of this study was that we can differentiate diffraction peaks from crystals grown in meso, from peaks originating from the surrounding lipid matrix, potentially opening up the possibility of high-throughput SAXS analysis of in meso grown crystals.This article is part of the themed issue 'Soft interfacial materials: from fundamentals to formulation'. PMID:27298442

  1. Light sensitive achiral polar polymeric composites

    NASA Astrophysics Data System (ADS)

    González-Henríquez, C. M.; Soto-Bustamante, E. A.; Vergara-Toloza, R. O.; Haase, W.

    2011-07-01

    The occurrence of antiferroelectric phenomenon in achiral composites composed of azo-benzene containing liquid crystals was observed. Some of the composites evidenced typical antiferroelectric polarization hysteresis loop in the mesophase, showing bilayer smectic C 2 mesophases with some interdigitation grade at the layer interface in a broad temperature range. Surprisingly composites of similar structure developed pyroelectricity but not switchable states. This new class of antiferroelectric materials is also capable of producing E-Z photoisomerization making them good candidates for energy harvesting.

  2. Strong Acid-Nonionic Surfactant Lyotropic Liquid-Crystalline Mesophases as Media for the Synthesis of Carbon Quantum Dots and Highly Proton Conducting Mesostructured Silica Thin Films and Monoliths.

    PubMed

    Olutaş, Elif B; Balcı, Fadime M; Dag, Ömer

    2015-09-22

    Lyotropic liquid-crystalline (LLC) materials are important in designing porous materials, and acids are as important in chemical synthesis. Combining these two important concepts will be highly beneficial to chemistry and material science. In this work, we show that a strong acid can be used as a solvent for the assembly of nonionic surfactants into various mesophases. Sulfuric acid (SA), 10-lauryl ether (C12E10), and a small amount of water form bicontinuous cubic (V1), 2D-hexagonal (H1), and micelle cubic (I1) mesophases with increasing SA/C12E10 mole ratio. A mixture of SA and C12E10 is fluidic but transforms to a highly ordered LLC mesophase by absorbing ambient water. The LLC mesophase displays high proton conductivity (1.5 to 19.0 mS/cm at room temperature) that increases with an increasing SA content up to 11 SA/C12E10 mole ratio, where the absorbed water is constant with respect to the SA amount but gradually increases from a 2.3 to 4.3 H2O/C12E10 mole ratio with increasing SA/C12E10 from 2 to 11, respectively. The mixture of SA and C12E10 slowly undergoes carbonization to produce carbon quantum dots (c-dots). The carbonization process can be controlled by simply controlling the water content of the media, and it can be almost halted by leaving the samples under ambient conditions, where the mixture slowly absorbs water to form photoluminescent c-dot-embedded mesophases. Over time the c-dots grow in size and increase in number, and the photoluminescence frequency gradually shifts to a lower frequency. The SA/C12E10 mesophase can also be used as a template to produce highly proton conducting mesostructured silica films and monoliths, as high as 19.3 mS/cm under ambient conditions. Aging the silica samples enhances the conductivity that can be even larger than for the LLC mesophase with the same amount of SA. The presence of silica has a positive effect on the proton conductivity of SA/C12E10 systems. PMID:26332603

  3. The structures of the crystalline phase and columnar mesophase of rhodium (II) heptanoate and of its binary mixture with copper (II) heptanoate probed by EXAFS

    NASA Astrophysics Data System (ADS)

    Inb-Elhaj, M.; Guillon, D.; Skoulios, A.; Maldivi, P.; Giroud-Godquin, A. M.; Marchon, J.-C.

    1992-12-01

    EXAFS was used to investigate the local structure of the polar spines of rhodium (II) soaps in the columnar liquid crystalline state. It was also used to ascertain the degree of blending of the cores in binary mixtures of rhodium (II) and copper (II) soaps. For the pure rhodium soaps, the columns are shown to result from the stacking of binuclear metal-metal bonded dirhodium tetracarboxylate units bonded to one another by apical ligation of the metal atom of each complex with one of the oxygen atoms of the adjacent molecule. Mixtures of rhodium (II) and copper (II) soaps give a hexagonal columnar mesophase in which pure rhodium and pure copper columns are randomly distributed.

  4. Thermotropic ionic liquid crystals. II. 1H and 23Na NMR study of the smectic mesophase of molten sodium n-butyrate and sodium isovalerate

    NASA Astrophysics Data System (ADS)

    Bonekamp, J. E.; Eguchi, T.; Plesko, S.; Jonas, J.

    1983-08-01

    The 1H and 23Na NMR studies of smectic ionic mesophases of molten sodium n-butyrate and sodium isovalerate are reported over the temperature range of the stability of the liquid crystalline phases. The 1H spin-lattice relaxation times T1 at ν0=9.2, 24.3, and 60 MHz for the anions of both the systems are interpreted in terms of diffusion intermolecular relaxation mechanism. The predicted anion diffusion coefficients are in agreement with those measured directly by spin-echo technique and indicate that the anion diffuses rapidly. In contrast to the T1 relaxation mechanism the results obtained for the proton relaxation times in the rotating coordinate frame T1ρ indicate that the order-fluctuation relaxation mechanism determines the frequency dispersion of T1ρ. The analysis of the T1ρ data provides an approximate measure of the order parameter S as a function of temperature. Fourier transform spectra of the 23Na transitions show that the electric field gradient (EFG) at the Na+ ion is nonaveraged and of such a strength as to produce a second order quadrupole effect in the spectra of the central transition. From the first-order splitting, the quadrupole coupling constant (QCC) is obtained as a function of temperature. The gradual temperature change of QCC demonstrates that only a single liquid crystalline phase exists over the temperature interval of the stability of the smectic mesophase. Using approximate analysis the correlation time τc for the EFG fluctuation is obtained from the 23Na T1 data for the melts of both sodium n-butyrate and sodium isovalerate.

  5. Effect of enantiomeric excess on the smectic-C* phases under electric field

    NASA Astrophysics Data System (ADS)

    Chemingui, M.; Soltani, T.; Marcerou, J. P.; Othman, T.

    2016-03-01

    A series of enantiomeric mixtures of 4-(1-methylheptyloxycarbonyl) phenol 4'-octyloxybiphenyl-4-carbonate (MHPOBC) is reported to understand the structures and stability conditions of emerging liquid crystal phases. The mesomorphic properties are studied by microscopic observation, electro-optic and dielectric measurements. The electric field-concentration (E-x) phase diagram for each phase at constant temperature is constructed. The complete electric field-temperature (E-T) phase diagrams for several enantiomeric mixtures of the antiferroelectric MHPOBC are established. These phase diagrams show the influence of optical purity on the phase stability and the unwinding threshold.

  6. Effect of Pyridine on the Mesophase of Teraryl Liquid Crystals: A New Series of Nematic Liquid Crystals Named 2-(4-Alkoxybiphen-4′-yl)-5-methylpyridines

    PubMed Central

    Chia, Win-Long; Huang, Yu-Sin

    2016-01-01

    A new series of teraryl 2-(4-alkoxybiphen-4′-yl)-5-methylpyridines (nO-PPPyMe, n = 3–8) nematic liquid crystal compounds, bearing a biphenylene core and a picoline terminus, were synthesized using a short two-step reaction, and overall yields between 34% and 38% were obtained. Spectral analysis results were in accordance with the expected structures. The thermotropic behavior of the teraryl liquid crystal compounds was investigated through polarized optical microscopy and differential scanning calorimetry. All compounds exhibited a solely enantiotropic nematic phase at the medium–high temperature range of 162.4–234.2 °C. Furthermore, the results for the nO-PPPyMe series were analyzed relative to three other compound series, mO-PPPyCN (m = 2–8), iO-PPQMe (i = 3–8) and xO-PPyPMe (x = 1–10). Consequently, the effect of pyridine on the mesophase of teraryl liquid crystals was demonstrated. PMID:26959017

  7. Effect of Pyridine on the Mesophase of Teraryl Liquid Crystals: A New Series of Nematic Liquid Crystals Named 2-(4-Alkoxybiphen-4'-yl)-5-methylpyridines.

    PubMed

    Chia, Win-Long; Huang, Yu-Sin

    2016-01-01

    A new series of teraryl 2-(4-alkoxybiphen-4'-yl)-5-methylpyridines (nO-PPPyMe, n = 3-8) nematic liquid crystal compounds, bearing a biphenylene core and a picoline terminus, were synthesized using a short two-step reaction, and overall yields between 34% and 38% were obtained. Spectral analysis results were in accordance with the expected structures. The thermotropic behavior of the teraryl liquid crystal compounds was investigated through polarized optical microscopy and differential scanning calorimetry. All compounds exhibited a solely enantiotropic nematic phase at the medium-high temperature range of 162.4-234.2 °C. Furthermore, the results for the nO-PPPyMe series were analyzed relative to three other compound series, mO-PPPyCN (m = 2-8), iO-PPQMe (i = 3-8) and xO-PPyPMe (x = 1-10). Consequently, the effect of pyridine on the mesophase of teraryl liquid crystals was demonstrated. PMID:26959017

  8. Structural effects of insulin-loading into HII mesophases monitored by electron paramagnetic resonance (EPR), small angle X-ray spectroscopy (SAXS), and attenuated total reflection Fourier transform spectroscopy (ATR-FTIR).

    PubMed

    Mishraki, Tehila; Ottaviani, Maria Francesca; Shames, Alexander I; Aserin, Abraham; Garti, Nissim

    2011-06-30

    Insulin entrapment within a monoolein-based reverse hexagonal (H(II)) mesophase was investigated under temperature-dependent conditions at acidic (pH 3) and basic (pH 8) conditions. Studying the structure of the host H(II) system and the interactions of insulin under temperature-dependent conditions has great impact on the enhancement of its thermal stabilization and controlled release for the purposes of transdermal delivery. Small angle X-ray spectroscopy (SAXS) measurements show that pH variation and/or insulin entrapment preserve the hexagonal structure and do not influence the lattice parameter. Attenuated total reflection Fourier transform spectroscopy (ATR-FTIR) spectra indicate that, although insulin interacts with hydroxyl groups of GMO in the interface region, it is not affected by pH variations. Hence different microenvironments within the H(II) mesophase were monitored by a computer-aided electron paramagnetic resonance (EPR) analysis using 5-doxylstearic acid (5-DSA) as a pH-dependent probe. The microviscosity, micropolarity, order of systems, and distribution of the probes in different microenvironments were influenced by three factors: temperature, pH, and insulin solubilization. When the temperature is increased, microviscosity and order parameters decreased at both pH 3 and 8, presenting different decrease trends. It was found that, at pH 3, the protein perturbs the lipid structure while "pushing aside" the un-ionized 5-DSA probe to fit into the narrow water cylinders. At the interface region (pH 8), the probe was distributed in two differently structured environments that significantly modifies by increasing temperature. Insulin loading within the H(II) mesophase decreased the order and microviscosity of both the microenvironments and increased their micropolarity. Finally, the EPR analysis also provides information about the unfolding/denaturation of insulin within the channel at high temperatures. PMID:21591776

  9. Anomalous behavior in the crossover between the negative and positive biaxial nematic mesophases in a lyotropic liquid crystal.

    PubMed

    Akpinar, Erol; Reis, Dennys; Figueiredo Neto, Antonio M

    2014-05-19

    A novel quaternary lyotropic liquid-crystalline mixture of dodecyltrimethylammonium bromide (DDTMABr)/sodium bromide/1-dodecanol/water, presenting the biaxial nematic phase (NB ) in addition to two uniaxial discotic (ND) and calamitic (NC) nematic ones, was synthesized. The partial phase diagram of this new mixture was constructed as a function of the DDTMABr molar-fraction concentration. The phase transitions from uniaxial to biaxial nematic phases were studied by means of the temperature dependence of the optical birefringence. In a particular region of the phase diagram, anomalous behavior was observed in the crossover from N-B to N+b: the contrast of the conoscopic fringes, which allows the birefringence measurements, almost vanishes, and the sample loses its alignment. This behavior, which was not observed before in lyotropics, was interpreted as a decrease in the mean diamagnetic susceptibility anisotropy (Δχ) of the sample, which was related to the shape anisotropy of the micelles. Small-angle X-ray scattering measurements were performed to evaluate the micellar shape anisotropy; these revealed that this mixture presented a smaller shape anisotropy than those of other lyotropic micellar systems presenting the NB phase. PMID:24692308

  10. Revealing Rembrandt

    PubMed Central

    Parker, Andrew J.

    2014-01-01

    The power and significance of artwork in shaping human cognition is self-evident. The starting point for our empirical investigations is the view that the task of neuroscience is to integrate itself with other forms of knowledge, rather than to seek to supplant them. In our recent work, we examined a particular aspect of the appreciation of artwork using present-day functional magnetic resonance imaging (fMRI). Our results emphasized the continuity between viewing artwork and other human cognitive activities. We also showed that appreciation of a particular aspect of artwork, namely authenticity, depends upon the co-ordinated activity between the brain regions involved in multiple decision making and those responsible for processing visual information. The findings about brain function probably have no specific consequences for understanding how people respond to the art of Rembrandt in comparison with their response to other artworks. However, the use of images of Rembrandt's portraits, his most intimate and personal works, clearly had a significant impact upon our viewers, even though they have been spatially confined to the interior of an MRI scanner at the time of viewing. Neuroscientific studies of humans viewing artwork have the capacity to reveal the diversity of human cognitive responses that may be induced by external advice or context as people view artwork in a variety of frameworks and settings. PMID:24795552

  11. Revealing Mercury

    NASA Astrophysics Data System (ADS)

    Prockter, L. M.; Solomon, S. C.; Head, J. W.; Watters, T. R.; Murchie, S. L.; Robinson, M. S.; Chapman, C. R.; McNutt, R. L.

    2009-04-01

    The MErcury Surface, Space ENvironment, GEochemistry, and Ranging (MESSENGER) spacecraft, developed under NASA's Discovery Program, launched in August 2004. En route to insertion into orbit about Mercury in 2011, MESSENGER flies by Mercury three times. The first and second of these encounters were accomplished in January and October of 2008. These flybys viewed portions of Mercury's surface that were not observed by Mariner 10 during its reconnaissance of somewhat less than half of the planet in 1974-1975. All MESSENGER instruments operated during each flyby and returned a wealth of new data. Many of the new observations were focused on the planet's geology, including monochrome imaging at resolutions as high as 100 m/pixel, multispectral imaging in 11 filters at resolutions as high as 500 m/pixel, laser altimetry tracks extending over several thousands of kilometers, and high-resolution spectral measurements of several types of terrain. Here we present an overview of the first inferences on the global geology of Mercury from the MESSENGER observations. Whereas evidence for volcanism was equivocal from Mariner 10 data, the new MESSENGER images and altimetry provide compelling evidence that volcanism was widespread and protracted on Mercury. Color imaging reveals three common spectral units on the surface: a higher-reflectance, relatively red material occurring as a distinct class of smooth plains, typically with distinct embayment relationships interpreted to indicate volcanic emplacement; a lower-reflectance, relatively blue material typically excavated by impact craters and therefore inferred to be more common at depth; and a spectrally intermediate terrain that constitutes much of the uppermost crust. Three more minor spectral units are also seen: fresh crater ejecta, reddish material associated with rimless depressions interpreted to be volcanic centers, and high-reflectance deposits seen in some crater floors. Preliminary measurements of crater size

  12. Mesomorphic properties of chiral three-arm liquid crystals containing 1,2,4-butanetriol as core

    NASA Astrophysics Data System (ADS)

    Tian, Mei; Wu, Shuang-jie; Tian, Xiao-Wei; Yao, Dan-Shu; Li, Chong-Liang; Hu, Jian-She; Zhang, Bao-Yan

    2016-03-01

    A series of symmetric and asymmetric three-arm liquid crystals (TALCs) of which the molecular structure with a central core of 1, 2, 4-butanetriol attached by three rod-like mesogenic moieties have successfully been synthesized. The rod-like mesogenic side arms are 4‧-(4-(trifluoromethyl) benzoyloxy) biphenyl-4-carboxylic acid (TFBA) and 4‧-(4-(allyloxy) benzoyloxy) biphenyl-4-carboxylic acid (AOBA), respectively. BTA0 and BTA3 are symmetric TALCs with three TFBA or three AOBA as LC side arms, respectively. BTA1 is an asymmetric TALC with one AOBA and two TFBA as side arms. BTA2 is an asymmetric TALC with two AOBA and one TFBA as side arms. The chemical structures and LC properties of the LC side arms and TALCs were characterised by FTIR, 1H NMR, elemental analysis, DSC, TG, POM and X-ray diffractometer. TFBA displayed smectic B (SmB) phase, AOBA exhibited nematic (N) phase. The TALCs all displayed chiral mesophase properties. BTA0 displayed chiral smectic C (SmC∗) mesophase. BTA1, BTA2 and BTA3 exhibited cholesteric (ch) mesophase. In addition, a chiral smectic A (SmA∗) mesophase was observed for BTA1. The results indicated that the 1, 2, 4-butanetriol is vital in inducing chiral mesophase of the TALCs. The side arms also played an important role in the mesophase type and mesogenic region. The TALCs displayed cholesteric mesophase when nematic LC side arm AOBA was introduced into the chiral core. The mesogenic region of the TALCs increased with the content of the wide-mesophase-region LC side arm AOBA introduced into the TALCs increasing. The melting temperature and the clear temperature of the TALCs were lower than those of the LC side arms (TFBA and AOBA). The mesophase regions of the TALCs were wider than those of the LC side arms.

  13. Spontaneous sense inversion in helical mesophases

    NASA Astrophysics Data System (ADS)

    Wensink, H. H.

    2014-08-01

    We investigate the pitch sensitivity of chiral nematic phases of helicoidal patchy cylinders as a generic model for chiral (bio-)polymers and helix-shaped colloidal rods. The behaviour of the macroscopic helical pitch is studied from microscopic principles by invoking a simple density functional theory generalised to accommodate weakly twisted director fields. Upon changing the degree of alignment along the local helicoidal director we find that chiral nematic phases exhibit a sudden sense inversion whereby the helical symmetry changes from left- to right-handed and vice versa. Since the local alignment is governed by thermodynamic variables such as density, temperature or the amplitude of an external directional field, such pitch sense inversions can be expected in systems of helical mesogens of both thermotropic and lyotropic origin. We show that the spontaneous change of helical symmetry is a direct consequence of an antagonistic effective torque between helical particles with a certain prescribed internal helicity. The results may help opening up new routes towards precise control of the helical handedness of chiral assemblies by a judicious choice of external control parameters.

  14. Shear alignment of lamellar mesophase systems

    NASA Astrophysics Data System (ADS)

    Jaju, S. J.; Kumaran, V.

    2015-11-01

    Mixtures of oil, water and surfactants form different microphases. Some of these phases, e.g. lamellar, hexagonal phases, lead to complex rheological behaviour at macroscale due to inherent anisotropy and irregularities in the microstructures. We present a comprehensive simulation study to examine the structure-rheology relationship in lamellar phase flow. At mesoscale, Reynolds number (Re), Schmidt number (Sc), Ericksen number (Er), extent of segregation between hydrophilic and hydrophobic components (r), ratio of viscosity of the two components (Δμ /μ0), and system size to layer width ratio (L / λ) complete the lamellar phase description. We have used lattice Boltzmann simulations to study a two dimensional lamellar phase system of moderate size. The domains and grain boundaries seen at low Sc are replaced by isolated edge dislocations at high Sc. The alignment mechanism does not change with changes in layer bending moduli (Er), viscosity contrast or r. Increasing segregation, increases disorder; this however does not lead to higher resistance to flow. At high Er, the shear tries homogenise the concentration field and disrupt layer formation. We see significantly higher peak viscosity at low Er at high viscosity contrast and due to defect pinning. The authors would like to thank the Department of Science and Technology, Government of India for financial support, and Supercomputer Education and Research Centre at Indian Institute of Science for the computational resources.

  15. Solubilization of nutraceuticals into reverse hexagonal mesophases.

    PubMed

    Amar-Yuli, Idit; Aserin, Abraham; Garti, Nissim

    2008-08-21

    The solubilization of four bioactive molecules with different polarities, in three reverse hexagonal (HII) systems has been investigated. The three HII systems were a typical reverse hexagonal composed of glycerol monooleate (GMO)/tricaprylin/water and two fluid hexagonal systems containing either 2.75 wt % Transcutol or ethanol as a fourth component. The phase behavior of the liquid crystalline phases in the presence of ascorbic acid, ascorbyl palmitate, D-alpha-tocopherol and D-alpha-tocopherol acetate were determined by small-angle X-ray scattering (SAXS) and optical microscopy. Differential scanning calorimetry (DSC) and Fourier-transform infrared (FT-IR) techniques were utilized to follow modifications in the thermal behavior and in the vibrations of different functional groups upon solubilizing the bioactive molecules. The nature of each guest molecule (in both geometry and polarity) together with the different HII structures (typical and fluids) determined the corresponding phase behavior, swelling or structural transformations and its location in the HII structures. Ascorbic acid was found to act as a chaotropic guest molecule, localized in the water-rich core and at the interface. The AP was also a chaotropic guest molecule with its head located in the vicinity of the GMO headgroup while its tail embedded close to the surfactant tail. D-alpha-tocopherol and D-alpha-tocopherol acetate were incorporated between the GMO tails; however, the D-alpha-tocopherol was located closer to the interface. Once Transcutol or ethanol was present and upon guest molecule incorporation, partial migration was detected. PMID:18665631

  16. Revealing the potential of Didodecyldimethylammonium bromide as efficient scaffold for fabrication of nano liquid crystalline structures.

    PubMed

    Kanwar, Rohini; Kaur, Gurpreet; Mehta, S K

    2016-03-01

    To exploit the potential of Didodecyldimethylammonium bromide (D12DAB) as a core lipidic constituent, an attempt was made to fabricate and optimize cationic nanostructured lipid carriers (cNLCs) using a cost-effective microemulsification methodology. Designed composition was optimized by studying the effect of different microemulsion components on D12DAB cNLCs characteristics. ​Spherical shaped D12DAB cNLCs were obtained with an average size of ∼160nm and zeta potential of +30.2mV. Differential Scanning Calorimetry (DSC) depicted the presence of thermotropic character, whereas polarized optical microscopy confirmed the mesophase like behavior of D12DAB based cNLCs. In addition, hemolysis analysis revealed that the toxicity was concentration dependent as LC50 was reached at a concentration of 50μg/mL of cNLCs. This class of cNLCs is expected to become a potent candidate for a broad spectrum of medicaments as carriers, targeting for pharmaceutical and medicinal purposes, due to the combination of a hard lipid with a soft lipid, where the liquid crystalline structure of the lipid co-exists. PMID:26896840

  17. How Are Preferences Revealed?

    PubMed Central

    Beshears, John; Choi, James J.; Laibson, David; Madrian, Brigitte C.

    2009-01-01

    Revealed preferences are tastes that rationalize an economic agent’s observed actions. Normative preferences represent the agent’s actual interests. It sometimes makes sense to assume that revealed preferences are identical to normative preferences. But there are many cases where this assumption is violated. We identify five factors that increase the likelihood of a disparity between revealed preferences and normative preferences: passive choice, complexity, limited personal experience, third-party marketing, and intertemporal choice. We then discuss six approaches that jointly contribute to the identification of normative preferences: structural estimation, active decisions, asymptotic choice, aggregated revealed preferences, reported preferences, and informed preferences. Each of these approaches uses consumer behavior to infer some property of normative preferences without equating revealed and normative preferences. We illustrate these issues with evidence from savings and investment outcomes. PMID:24761048

  18. US weapons secrets revealed

    SciTech Connect

    Norris, R.S.; Arkin, W.M.

    1993-03-01

    Extraordinary details have only recently been revealed about the struggle over the control of early U.S. nuclear weapons and their initial deployments abroad. The information comes from a newly declassified top secret report, part of a larger study, The History of the Strategic Arms Competition, 1945-1972, commissioned by Defense Secretary James R. Schlisinger in summer 1974.

  19. Revealing power in truth

    PubMed Central

    Lee, Kelley

    2015-01-01

    Jeremy Shiffman’s editorial appropriately calls on making all forms of power more apparent and accountable, notably productive power derived from expertise and claims to moral authority. This commentary argues that relationships based on productive power can be especially difficult to reveal in global health policy because of embedded notions about the nature of power and politics. Yet, it is essential to recognize that global health is shot through with power relationships, that they can take many forms, and that their explicit acknowledgement should be part of, rather than factored out of, any reform of global health governance. PMID:25844390

  20. The Universe Revealed

    NASA Astrophysics Data System (ADS)

    Spence, Pam

    1998-10-01

    The Universe is a bewildering place to the uninitiated. The concepts and theories that govern space seem complex and often contradictory. The Universe Revealed provides the keys to unlocking the wonders of the cosmos. Elegantly written and lavishly illustrated, it begins with the Sun and stretches through our solar system into deepest space. Lucid prose, written by many of the people who have shaped our current thinking on space, and spectacular photographs make the physics of the Universe accessible and provide a solid background for understanding the most recent astronomical discoveries. Covering the most intriguing features of the cosmos, the topics discussed range from the Earth and global warming to cosmic collisions and the size of the Universe. Major sections examine the Solar System, stars, galaxies, cosmology, and the observational techniques used by astronomers, both amateur and professional. The Universe Revealed represents the collaboration of internationally renowned experts in astronomy and cosmology, with contributions from authors including David Malin, F. Duccio Macchetto, Iain Nicholson, Neil Bone, Ian Ridpath, Seth Shostak, Mike Lancaster, Steve Miller, Ken Croswell, Geoff McNamara, and Steven Young. This extraordinary blend of astronomy, astrophysics, and cosmology, will appeal to amateur and armchair astronomers alike.

  1. Gusev's Rim Revealed

    NASA Technical Reports Server (NTRS)

    2004-01-01

    NASA's Mars Exploration Rover Spirit took this panoramic camera image on sol 91 (April 5, 2004). Spirit is looking to the southeast, and through the martian haze has captured the rim of Gusev Crater approximately 80 kilometers (49.7 miles) away on the horizon.

    The right side of this image reveals the portion of the crater edge that descends into the mouth of Ma'adim Vallis, a channel that opens into Gusev Crater. Spirit is currently traveling toward the informally named 'Columbia Hills,' which lie to the left of the region pictured here.

    This image is similar to a panoramic camera image taken on sol 68, but Gusev's ridge is more visible here because the atmospheric dust caused by winter dust storms has settled. Scientists expect to get even clearer images than this one in upcoming sols.

    This image has been modified to make the crater rim more visible.

  2. Titan Casts Revealing Shadow

    NASA Astrophysics Data System (ADS)

    2004-05-01

    A rare celestial event was captured by NASA's Chandra X-ray Observatory as Titan -- Saturn's largest moon and the only moon in the Solar System with a thick atmosphere -- crossed in front of the X-ray bright Crab Nebula. The X-ray shadow cast by Titan allowed astronomers to make the first X-ray measurement of the extent of its atmosphere. On January 5, 2003, Titan transited the Crab Nebula, the remnant of a supernova explosion that was observed to occur in the year 1054. Although Saturn and Titan pass within a few degrees of the Crab Nebula every 30 years, they rarely pass directly in front of it. "This may have been the first transit of the Crab Nebula by Titan since the birth of the Crab Nebula," said Koji Mori of Pennsylvania State University in University Park, and lead author on an Astrophysical Journal paper describing these results. "The next similar conjunction will take place in the year 2267, so this was truly a once in a lifetime event." Animation of Titan's Shadow on Crab Nebula Animation of Titan's Shadow on Crab Nebula Chandra's observation revealed that the diameter of the X-ray shadow cast by Titan was larger than the diameter of its solid surface. The difference in diameters gives a measurement of about 550 miles (880 kilometers) for the height of the X-ray absorbing region of Titan's atmosphere. The extent of the upper atmosphere is consistent with, or slightly (10-15%) larger, than that implied by Voyager I observations made at radio, infrared, and ultraviolet wavelengths in 1980. "Saturn was about 5% closer to the Sun in 2003, so increased solar heating of Titan may account for some of this atmospheric expansion," said Hiroshi Tsunemi of Osaka University in Japan, one of the coauthors on the paper. The X-ray brightness and extent of the Crab Nebula made it possible to study the tiny X-ray shadow cast by Titan during its transit. By using Chandra to precisely track Titan's position, astronomers were able to measure a shadow one arcsecond in

  3. Revealing the Beast Within

    NASA Astrophysics Data System (ADS)

    2003-07-01

    Deeply Embedded Massive Stellar Clusters Discovered in Milky Way Powerhouse Summary Peering into a giant molecular cloud in the Milky Way galaxy - known as W49 - astronomers from the European Southern Observatory (ESO) have discovered a whole new population of very massive newborn stars . This research is being presented today at the International Astronomical Union's 25th General Assembly held in Sydney, Australia, by ESO-scientist João Alves. With the help of infrared images obtained during a period of excellent observing conditions with the ESO 3.5-m New Technology Telescope (NTT) at the La Silla Observatory (Chile), the astronomers looked deep into this molecular cloud and discovered four massive stellar clusters, with hot and energetic stars as massive as 120 solar masses. The exceedingly strong radiation from the stars in the largest of these clusters is "powering" a 20 light-year diameter region of mostly ionized hydrogen gas (a "giant HII region"). W49 is one of the most energetic regions of star formation in the Milky Way. With the present discovery, the true sources of the enormous energy have now been revealed for the first time, finally bringing to an end some decades of astronomical speculations and hypotheses. PR Photo 21a/03 : Colour Composite of W49A (NTT+SOFI). PR Photo 21b/03 : Radio and Near-Infrared Composite of W49A Giant molecular clouds Stars form predominantly inside Giant Molecular Clouds which populate our Galaxy, the Milky Way. One of the most prominent of these is W49 , which has a mass of a million solar masses. It is located some 37,000 light-years away and is the most luminous star-forming region known in our home galaxy: its luminosity is several million times the luminosity of our Sun. A smaller region within this cloud is denoted W49A - this is one of the strongest radio-emitting areas known in the Galaxy . Massive stars are excessive in all ways. Compared to their smaller and ligther brethren, they form at an Olympic speed and

  4. Novel ferroelectric liquid crystals consisting glassy liquid crystal as chiral dopants

    NASA Astrophysics Data System (ADS)

    Chen, Huang-Ming Philip; Tsai, Yun-Yen; Lin, Chi-Wen; Shieh, Han-Ping David

    2006-08-01

    A series of ferroelectric liquid crystals consisting new glassy liquid crystals (GLCs) as chiral dopants were prepared and evaluated for their potentials in fast switching ability less than 1 ms. The properties of pure ferroelectric glassy liquid crystals (FGLCs) and mixtures were reported in this paper. In particular, the novel FGLC possessing wide chiral smectic C mesophase over 100 °C is able to suppress smectic A phase of host. The mixture containing 2.0 % GLC-1 performs greater alignment ability and higher contrast ratio than R2301 (Clariant, Japan) in a 2 μm pre-made cell (EHC, Japan). These results indicate that novel FLC mixtures consisting glassy liquid crystals present a promising liquid crystal materials for fast switching field sequential color displays.

  5. Electrocardiograph abnormalities revealed during laparoscopy

    PubMed Central

    Nijjer, Sukhjinder; Dubrey, Simon William

    2010-01-01

    This brief case presents a well patient in whom an electrocardiograph abnormality consistent with an accessory pathway was found during a routine procedure. We present the electrocardiographs, explain the underlying condition, and consider why the abnormality was revealed in this manner. PMID:22419949

  6. Ischemic Colitis Revealing Polyarteritis Nodosa

    PubMed Central

    Hamzaoui, Amira; Litaiem, Noureddine; Smiti Khanfir, M.; Ayadi, Sofiene; Nfoussi, Haifa; Houman, M. H.

    2013-01-01

    Ischemic colitis is one of the most common intestinal ischemic injuries. It results from impaired perfusion of blood to the bowel and is rarely caused by vasculitis. We report a case of ischemic colitis revealing polyarteritis nodosa (PAN) in a 55-year-old man. Histological examination of the resected colon led to the diagnosis of PAN. PMID:24382967

  7. Confinement-Induced Orientational Order in a Ferroelectric Liquid Crystal Containing Dispersed Aerosils

    NASA Astrophysics Data System (ADS)

    Cordoyiannis, George; Nounesis, George; Bobnar, Vid; Kralj, Samo; Kutnjak, Zdravko

    2005-01-01

    The study of the smectic-A to chiral smectic-C* phase transition of the liquid crystal S-(+)-[4-(2'-methyl butyl) phenyl 4'-n-octylbiphenyl-4-carboxylate] (CE8) containing dispersed hydrophilic aerosils reveals novel properties, important to understanding quenched disorder and confinement in ferroelectric liquid crystals. Smectic layer compression leads to a distribution of transition temperatures inducing smearing of the macroscopic data across the transition. A pronounced confinement-induced pretransitional tilted order is observed.

  8. Urticarial vasculitis reveals unsuspected thyroiditis.

    PubMed

    Ferreira, Olga; Mota, Alberto; Baudrier, Teresa; Azevedo, Filomena

    2012-01-01

    A 38-year-old woman presented with erythematous, violaceous plaques with a serpiginous and unusual appearance located on the left shoulder, left thigh, and right buttock, evolving for 5 days, which eventually became generalized. A skin biopsy revealed leukocytoclastic vasculitis and a diagnosis of urticarial vasculitis was made. The complete blood count, biochemistry, complement levels, and other immunological test results were unremarkable. However, antithyroid antibody titers were increased. Despite having normal thyroid function tests and an absence of specific symptoms, the patient underwent a thyroid ultrasound, which revealed features of thyroiditis, and was subsequently referred to an endocrinologist. Several diseases can be associated with urticarial vasculitis, namely infections and autoimmune connective-tissue disorders such as systemic lupus erythematosus and Sjögren syndrome. Thyroiditis is an uncommon association. PMID:23000939

  9. Plan competitions reveal entrepreneurial talent

    SciTech Connect

    Madison, Alison L.

    2011-05-15

    Monthly economic diversity column for Tri-City Herald business section. Excerpt below: There’s something to be said for gaining valuable real-world experience in a structured, nurturing environment. Take for instance learning to scuba dive in the comfort of my resort pool rather than immediately hanging out with sharks while I figure out little things like oxygen tanks and avoiding underwater panic attacks. Likewise, graduate students are getting some excellent, supportive real-world training through university business plan competitions. These competitions are places where smart minds, new technologies, months of preparation and coaching, and some healthy pre-presentation jitters collide to reveal not only solid new business ideas, but also some promising entrepreneurial talent. In fact, professionals from around our region descend upon college campuses every spring to judge these events, which help to bridge the gap between academics and the real technology and business-driven economy.

  10. Revealing ontological commitments by magic.

    PubMed

    Griffiths, Thomas L

    2015-03-01

    Considering the appeal of different magical transformations exposes some systematic asymmetries. For example, it is more interesting to transform a vase into a rose than a rose into a vase. An experiment in which people judged how interesting they found different magic tricks showed that these asymmetries reflect the direction a transformation moves in an ontological hierarchy: transformations in the direction of animacy and intelligence are favored over the opposite. A second and third experiment demonstrated that judgments of the plausibility of machines that perform the same transformations do not show the same asymmetries, but judgments of the interestingness of such machines do. A formal argument relates this sense of interestingness to evidence for an alternative to our current physical theory, with magic tricks being a particularly pure source of such evidence. These results suggest that people's intuitions about magic tricks can reveal the ontological commitments that underlie human cognition. PMID:25490128

  11. CMB source apportionment during REVEAL

    SciTech Connect

    Lowenthal, D.H.; Gertler, A.W.; Wittorff, D.; Sakiyama, S.

    1997-01-01

    Source contributions to PM{sub 2.5} aerosol measured at Chilliwack and Pitt Meadows in the Lower Fraser Valley, B.C., Canada, during the REVEAL study, were estimated using chemical mass balance (CMB) receptor modeling. ON average, motor vehicles accounted for 34 and 43% of PM{sub 2.5} at Chilliwack and Pitt Meadows, respectively. Secondary sulfate and secondary nitrate were the next most significant PM{sub 2.5} components, accounting for 25 and 27%, respectively, at Chilliwack, and 27 and 12%, respectively, at Pitt Meadows. Geological material accounted for 3 and 5% of PM{sub 2.5} at Chilliwack and Pitt Meadows, respectively. A significant contribution of wood smoke was estimated for both sites: 8% at Chilliwack and 9% at Pitt Meadows.

  12. Archimedes: Accelerator Reveals Ancient Text

    SciTech Connect

    Bergmann, Uwe

    2004-02-24

    Archimedes (287-212 BC), who is famous for shouting 'Eureka' (I found it) is considered one of the most brilliant thinkers of all times. The 10th-century parchment document known as the 'Archimedes Palimpsest' is the unique source for two of the great Greek's treatises. Some of the writings, hidden under gold forgeries, have recently been revealed at the Stanford Synchrotron Radiation Laboratory at SLAC. An intense x-ray beam produced in a particle accelerator causes the iron in original ink, which has been partly erased and covered, to send out a fluorescence glow. A detector records the signal and a digital image showing the ancient writings is produced. Please join us in this fascinating journey of a 1,000-year-old parchment from its origin in the Mediterranean city of Constantinople to a particle accelerator in Menlo Park.

  13. Erosion and what it Reveals

    NASA Technical Reports Server (NTRS)

    2003-01-01

    [figure removed for brevity, see original site]

    Released 20 November 2003

    This image is located near the boundary between Syrtis Major and Isidis Planitia. The top of the image shows rough material that has eroded away from the lower portion of the image, revealing an underlying surface that has many small craters. It also reveals an ancient flow lobe that is barely discernable, crossing the southern part of the image (this flow lobe is much easier to see as a smooth region in the context image).

    Image information: VIS instrument. Latitude 16.4, Longitude 77.9 East (282.1 West). 19 meter/pixel resolution.

    Note: this THEMIS visual image has not been radiometrically nor geometrically calibrated for this preliminary release. An empirical correction has been performed to remove instrumental effects. A linear shift has been applied in the cross-track and down-track direction to approximate spacecraft and planetary motion. Fully calibrated and geometrically projected images will be released through the Planetary Data System in accordance with Project policies at a later time.

    NASA's Jet Propulsion Laboratory manages the 2001 Mars Odyssey mission for NASA's Office of Space Science, Washington, D.C. The Thermal Emission Imaging System (THEMIS) was developed by Arizona State University, Tempe, in collaboration with Raytheon Santa Barbara Remote Sensing. The THEMIS investigation is led by Dr. Philip Christensen at Arizona State University. Lockheed Martin Astronautics, Denver, is the prime contractor for the Odyssey project, and developed and built the orbiter. Mission operations are conducted jointly from Lockheed Martin and from JPL, a division of the California Institute of Technology in Pasadena.

  14. Dunes reveal Titan's recent history

    NASA Astrophysics Data System (ADS)

    Savage, Christopher J.; Radebaugh, Jani

    2010-04-01

    Large fields of linear dunes are abundant on Titan, covering nearly 20% of the surface. They are among the youngest features and represent interactions between near-surface winds and sediment. This interaction may vary from area to area creating unique populations of eolian features identified by dune field parameters such as crest-to-crest spacing, dune width and orientation. These parameters respond to changes in near-surface conditions over periods of time ranging from minutes to many thousands of years depending on dune size and the duration of the changes. While pattern analysis of dune field parameters on Earth and, in this study, Titan reveals much about current climatic conditions, such as wind regimes and wetter vs. drier areas, many inferences about past conditions can also be made. Initial pattern analysis of linear dunes on Titan reveals a single population of linear dunes representing a large percentage of all observed dunes. This single population is the result of two leading possibilities: Either there has been only one long period of dune building, leading to very old cores that have been built upon over long periods of time, perhaps punctuated with few or many intervals of non-deposition; or the current conditions of dune building have persisted long enough to completely erase any evidence of previous conditions. We have not yet worked through all the input parameters to adjust Earth's time scales to Titan's, and thus it is not yet possible to give a precise age for Titan's dunes. However, if these large linear dunes are similar to Earth's large linear dunes, they may represent at least several thousand years of dune building.

  15. Synthesis, mesomorphic properties and X-ray diffraction studies on 7-alkyloxy-3-(4-alkyloxyphenyl-4H-1-benzopyran-4-one: Crystal structure of 7-hexyloxy-3-(4-hexyloxyphenyl)-4H-1-benzopyran-4-one

    NASA Astrophysics Data System (ADS)

    Yeap, Guan-Yeow; Yam, Wan-Sinn; Dobrzyscky, Lucasz; Gorecka, Ewa; Takeuchi, Daisuke; Boey, Peng-Lim; Mahmood, Wan Ahmad Kamil; Ito, Masato M.

    2009-11-01

    Eight new compounds, 7-alkyloxy-3-(4-alkyloxyphenyl)-4H-1-benzopyran-4-one incorporating isoflavone core and identical terminal side chains, OR (where R = C nH 2n+1 with n ranging from 4 to 18 in even parity) have been synthesized and isolated. The thermal stability in relation to the phase behaviour and respective enthalpy values of these compounds were analyzed using differential scanning calorimetry. The texture of the preferred molecular orientation at different temperatures was observed under polarized light wherein all compounds exhibited nematic (N), smectic A (SmA) and smectic C (SmC) phases. The difference in mesogenicity of these compounds was also investigated from the viewpoints of conformation and polarity of the side chains which contributed remarkably towards the change in the intermolecular interaction within the mesophase. X-ray diffraction technique was employed to investigate the molecular packing associated with the intermolecular interaction as well as the correlation between the thermal behaviour of these compounds with their anisotropy properties within a mesophase. The molecular structure of compound 7-hexyloxy-3-(4-hexyloxyphenyl)-4H-1-benzopyran-4-one in crystal phase was confirmed by single-crystal X-ray diffraction.

  16. APEX reveals glowing stellar nurseries

    NASA Astrophysics Data System (ADS)

    2008-11-01

    Illustrating the power of submillimetre-wavelength astronomy, an APEX image reveals how an expanding bubble of ionised gas about ten light-years across is causing the surrounding material to collapse into dense clumps that are the birthplaces of new stars. Submillimetre light is the key to revealing some of the coldest material in the Universe, such as these cold, dense clouds. Glowing Stellar Nurseries ESO PR Photo 40/08 Glowing Stellar Nurseries The region, called RCW120, is about 4200 light years from Earth, towards the constellation of Scorpius. A hot, massive star in its centre is emitting huge amounts of ultraviolet radiation, which ionises the surrounding gas, stripping the electrons from hydrogen atoms and producing the characteristic red glow of so-called H-alpha emission. As this ionised region expands into space, the associated shock wave sweeps up a layer of the surrounding cold interstellar gas and cosmic dust. This layer becomes unstable and collapses under its own gravity into dense clumps, forming cold, dense clouds of hydrogen where new stars are born. However, as the clouds are still very cold, with temperatures of around -250˚ Celsius, their faint heat glow can only be seen at submillimetre wavelengths. Submillimetre light is therefore vital in studying the earliest stages of the birth and life of stars. The submillimetre-wavelength data were taken with the LABOCA camera on the 12-m Atacama Pathfinder Experiment (APEX) telescope, located on the 5000 m high plateau of Chajnantor in the Chilean Atacama desert. Thanks to LABOCA's high sensitivity, astronomers were able to detect clumps of cold gas four times fainter than previously possible. Since the brightness of the clumps is a measure of their mass, this also means that astronomers can now study the formation of less massive stars than they could before. The plateau of Chajnantor is also where ESO, together with international partners, is building a next generation submillimetre telescope, ALMA

  17. Hubble Images Reveal Jupiter's Auroras

    NASA Technical Reports Server (NTRS)

    1996-01-01

    These images, taken by the Hubble Space Telescope, reveal changes in Jupiter's auroral emissions and how small auroral spots just outside the emission rings are linked to the planet's volcanic moon, Io. The images represent the most sensitive and sharply-detailed views ever taken of Jovian auroras.

    The top panel pinpoints the effects of emissions from Io, which is about the size of Earth's moon. The black-and-white image on the left, taken in visible light, shows how Io and Jupiter are linked by an invisible electrical current of charged particles called a 'flux tube.' The particles - ejected from Io (the bright spot on Jupiter's right) by volcanic eruptions - flow along Jupiter's magnetic field lines, which thread through Io, to the planet's north and south magnetic poles. This image also shows the belts of clouds surrounding Jupiter as well as the Great Red Spot.

    The black-and-white image on the right, taken in ultraviolet light about 15 minutes later, shows Jupiter's auroral emissions at the north and south poles. Just outside these emissions are the auroral spots. Called 'footprints,' the spots are created when the particles in Io's 'flux tube' reach Jupiter's upper atmosphere and interact with hydrogen gas, making it fluoresce. In this image, Io is not observable because it is faint in the ultraviolet.

    The two ultraviolet images at the bottom of the picture show how the auroral emissions change in brightness and structure as Jupiter rotates. These false-color images also reveal how the magnetic field is offset from Jupiter's spin axis by 10 to 15 degrees. In the right image, the north auroral emission is rising over the left limb; the south auroral oval is beginning to set. The image on the left, obtained on a different date, shows a full view of the north aurora, with a strong emission inside the main auroral oval.

    The images were taken by the telescope's Wide Field and Planetary Camera 2 between May 1994 and September 1995.

    This image and

  18. Plant transcriptomes reveal hidden guests.

    PubMed

    Zhu, Jiao; Wang, Guirong; Pelosi, Paolo

    2016-06-01

    With the wide adoption of transcriptome sequencing an ever increasing amount of information is becoming available, together with spurious data originating from contamination. We show that sometimes errors and inaccuracy can turn beneficial, revealing insect and arthropod pests when analysing plant transcriptomes. We have found a large number of soluble olfactory proteins, odorant-binding proteins (OBPs) and chemosensory proteins (CSPs), in plant databases, likely due to contamination by guest insects. In fact, both classes of proteins are only expressed in insects, with few CSPs also present in other arthropods. In addition, we found many sequences of the Niemann-Pick (Npc2) family, proteins dedicated to cholesterol transport in vertebrates and hypothesised to be involved in chemical communication in insects, but absent in plants. In several cases we were able to trace down members of the three classes of proteins to the insect or arthopod species responsible for contamination. Our work suggests that genes found in plants and recognised as contaminants can be turned into useful information to investigate plant-insect relationships or to identify new sequences from insects species not yet investigated. PMID:27130825

  19. Revealing ionic motion molecular solids

    NASA Astrophysics Data System (ADS)

    Thurzo, I.; Zahn, D. R. T.

    2006-01-01

    Thin films of mixed valence semiconductor copper-tetracyano-quinodimethane (Cu-TCNQ) and small molecule tris(8-hydroxyquinolinato)aluminum (Alq3) were investigated by current-voltage (I-V) and admittance (C-V,G-V) techniques in single-layer configuration with different combinations of electrodes. The predicted hysteresis of I-V curves and nearly constant loss (NCL) could be observed for both materials. When cycling devices between negative and positive biases, slowly decaying ionic transient currents interfere with steady-state currents and point to unidirectional motions of the ionic species with subsequent redox reaction at one of the electrodes. Plotting the frequency f dependence of the equivalent parallel capacitance at zero bias as log10 C(0) versus log10(f), the dielectric behavior of Cu-TCNQ and Alq3 complies with the effective-medium model for NCL in ionic conductors [J. R. Macdonald J. Appl. Phys. 94, 558 (2003)]. It also holds for a similar plot of the equivalent parallel zero-bias conductance G(0). The nature of the revealed mobile ions is discussed with emphasis on their sources.

  20. Reveal for Salmonella test system.

    PubMed

    Bird, C B; Miller, R L; Miller, B M

    1999-01-01

    The Reveal for Salmonella (RSS) test system is a presumptive qualitative test that detects the presence of Salmonella organisms in foods within 21 h total testing time, allowing the user to release negative products 24 h earlier than when using other rapid test kits. Foods are enriched with a proprietary resuscitation medium called Revive and then selectively enriched with either Selenite Cystine or Rappaport-Vassiliadis selective media. The enriched culture is used to inoculate the RSS detection device, which initiates a lateral flow through a reagent zone containing anti-Salmonella antibodies conjugated to colloidal gold particles that capture antigens present in the culture. The antigen-antibody complex migrates farther and is captured by an additional anti-Salmonella antibody, causing the colloidal gold to precipitate and form a visual line, indicating a positive result. A procedural control line also will form regardless of the presence of Salmonella organisms to indicate the test is working properly. Existing AOAC Official Methods for Salmonella organisms require a 48 h enrichment before testing. Hence, a food product has to be held before release, adding extra cost to the company and the consumer. The RSS test system was evaluated by quantitative spiking studies. Although AOAC encourages inclusion of naturally contaminated foods, almost all microbiological AOAC validation studies have been performed with artificially contaminated foods for absolute control over the study. The RSS test system is designed to test many food types for Salmonella organisms and has a limit of detection of 5-10 colony-forming units (cfu)/25 g with a false-negative rate of < 1% and a false-positive rate of < 5.0%. It showed an 81% overall agreement with the traditional procedure of the U.S. Department of Agriculture's Food Safety Inspection Service. PMID:10367381

  1. Focus groups reveal consumer ambivalence.

    PubMed

    1983-01-01

    According to qualitative research, Salvadoreans are ambivalent about the use of contraceptives. Since complete responsibility for management of the CSM project was accepted by the Association Demografica Salvadorena (ADS), the agency which operates the contraceptive social marketing project in El Salvador, in November 1980, the need for decisions in such areas as product price increases, introduction of new condom brands, promotion of the vaginal foaming tablet, and assessment of product sales performance had arisen. The ICSMP funded market research, completed during 1983, was intended to provide the data on which such decisions by ADS could be based. The qualitative research involved 8 focus groups, comprised of men and women, aged 18-45, contraceptive users and nonusers, from the middle and lower socioeconomic strata of the city of San Salvador and other suburban areas. In each group a moderator led discussion of family planning and probed respondents for specific attitudes, knowledge, and behavior regarding the use of contraceptives. To assess attitudes at a more emotional level, moderators asked respondents to "draw" their ideas on certain issues. A marked discrepancy was revealed between respondents' intellectual responses to the issues raised in group discussion, as opposed to their feelings expressed in the drawings. Intellectually, participants responded very positively to family planning practice, but when they were asked to draw their perceptions, ambivalent feelings emerged. Drawings of both the user and the nonuser convey primarily negative aspects for either choice. The user is tense and moody toward her children; the nonuser loses her attractiveness and "dies." Figures also show drawings of some of the attitudes of single and married male participants. 1 drawing shows an incomplete and a complete circle, symbolizing a sterilized man (incomplete) and a nonsterilized man (complete). Another picture depicts a chained man who has lost his freedom

  2. REVEAL: Software Documentation and Platform Migration

    NASA Technical Reports Server (NTRS)

    Wilson, Michael A.; Veibell, Victoir T.; Freudinger, Lawrence C.

    2008-01-01

    The Research Environment for Vehicle Embedded Analysis on Linux (REVEAL) is reconfigurable data acquisition software designed for network-distributed test and measurement applications. In development since 2001, it has been successfully demonstrated in support of a number of actual missions within NASA s Suborbital Science Program. Improvements to software configuration control were needed to properly support both an ongoing transition to operational status and continued evolution of REVEAL capabilities. For this reason the project described in this report targets REVEAL software source documentation and deployment of the software on a small set of hardware platforms different from what is currently used in the baseline system implementation. This report specifically describes the actions taken over a ten week period by two undergraduate student interns and serves as a final report for that internship. The topics discussed include: the documentation of REVEAL source code; the migration of REVEAL to other platforms; and an end-to-end field test that successfully validates the efforts.

  3. Revealing advantage in a quantum network

    NASA Astrophysics Data System (ADS)

    Mukherjee, Kaushiki; Paul, Biswajit; Sarkar, Debasis

    2016-07-01

    The assumption of source independence was used to reveal nonlocal (apart from standard Bell-CHSH scenario) nature of correlations generated in entanglement swapping experiments. In this work, we have discussed the various utilities of this assumption to reveal nonlocality (via generation of nonbilocal correlations) and thereby exploiting quantumness under lesser requirements compared to some standard means of doing the same. We have also provided with a set of sufficient criteria, imposed on the states (produced by the sources) under which source independence can reveal nonbilocal nature of correlations in a quantum network.

  4. Hiding personal information reveals the worst

    PubMed Central

    John, Leslie K.; Barasz, Kate; Norton, Michael I.

    2016-01-01

    Seven experiments explore people’s decisions to share or withhold personal information, and the wisdom of such decisions. When people choose not to reveal information—to be “hiders”—they are judged negatively by others (experiment 1). These negative judgments emerge when hiding is volitional (experiments 2A and 2B) and are driven by decreases in trustworthiness engendered by decisions to hide (experiments 3A and 3B). Moreover, hiders do not intuit these negative consequences: given the choice to withhold or reveal unsavory information, people often choose to withhold, but observers rate those who reveal even questionable behavior more positively (experiments 4A and 4B). The negative impact of hiding holds whether opting not to disclose unflattering (drug use, poor grades, and sexually transmitted diseases) or flattering (blood donations) information, and across decisions ranging from whom to date to whom to hire. When faced with decisions about disclosure, decision-makers should be aware not just of the risk of revealing, but of what hiding reveals. PMID:26755591

  5. REVEAL: Software Documentation and Platform Migration

    NASA Technical Reports Server (NTRS)

    Wilson, Michael A.; Veibell, Victoir T.

    2011-01-01

    The Research Environment for Vehicle Embedded Analysis on Linux (REVEAL) is reconfigurable data acquisition software designed for network-distributed test and measurement applications. In development since 2001, it has been successfully demonstrated in support of a number of actual missions within NASA's Suborbital Science Program. Improvements to software configuration control were needed to properly support both an ongoing transition to operational status and continued evolution of REVEAL capabilities. For this reason the project described in this report targets REVEAL software source documentation and deployment of the software on a small set of hardware platforms different from what is currently used in the baseline system implementation. This presentation specifically describes the actions taken over a ten week period by two undergraduate student interns and serves as an overview of the content of the final report for that internship.

  6. Omics strategies for revealing Yersinia pestis virulence

    PubMed Central

    Yang, Ruifu; Du, Zongmin; Han, Yanping; Zhou, Lei; Song, Yajun; Zhou, Dongsheng; Cui, Yujun

    2012-01-01

    Omics has remarkably changed the way we investigate and understand life. Omics differs from traditional hypothesis-driven research because it is a discovery-driven approach. Mass datasets produced from omics-based studies require experts from different fields to reveal the salient features behind these data. In this review, we summarize omics-driven studies to reveal the virulence features of Yersinia pestis through genomics, trascriptomics, proteomics, interactomics, etc. These studies serve as foundations for further hypothesis-driven research and help us gain insight into Y. pestis pathogenesis. PMID:23248778

  7. Revealing a Child's Pathology: Physicians' Experiences

    ERIC Educational Resources Information Center

    Scelles, Regine; Aubert-Godard, Anne; Gargiulo, Marcela; Avant, Monique; Gortais, Jean

    2010-01-01

    In this study, 12 physicians and 12 care-givers were interviewed using semi-structured interviews. We explored physicians' experiences when they revealed a diagnosis. We also tried to understand which family members the physician was thinking of, with whom they identified themselves, and their first choice of the person to whom they prefer to…

  8. [Factor VII deficiency revealed by intracranial hemorrhage].

    PubMed

    Sfaihi Ben Mansour, L; Thabet, A; Aloulou, H; Turki, H; Chabchoub, I; Mhiri, F; Mnif, Z; Ben Ali, H; Kammoun, T; Hachicha, M

    2009-07-01

    Constitutional factor VII deficiency is a hereditary disease with recessive autosomic transmission. Its incidence is estimated to be 1/1,000,000 in the general population. We report a case of severe factor VII deficiency in infancy revealed by an intracranial hemorrhage in a 2-month-old infant. We describe the clinical, biological and therapeutic characteristics of this disease. PMID:19409767

  9. Eye Movements Reveal Dynamics of Task Control

    ERIC Educational Resources Information Center

    Mayr, Ulrich; Kuhns, David; Rieter, Miranda

    2013-01-01

    With the goal to determine the cognitive architecture that underlies flexible changes of control settings, we assessed within-trial and across-trial dynamics of attentional selection by tracking of eye movements in the context of a cued task-switching paradigm. Within-trial dynamics revealed a switch-induced, discrete delay in onset of…

  10. PULMONARY ARTERY ACCELERATED FLOW REVEALING HODGKIN'S LYMPHOMA.

    PubMed

    Ibrahim, Tony; Chehab, Ghassan; Saliba, Zakhia; Smayra, Tarek; Baz, Maria; Abdo, Lynn; Haddad, Fady; Abdel-Massih, Tony

    2016-01-01

    We present a case in which transthoracic echocardiography was the first diagnostic tool to suspect mediastinal Hodgkin's lymphoma by revealing a change in the hemodynamic of left pulmonary artery flow, and it was used as a follow-up method for monitoring treatment efficacy by demonstrating a normalization of pulmonary artery hemodynamics. PMID:27169170

  11. The cattle genome reveals its secrets

    PubMed Central

    Burt, David W

    2009-01-01

    The domesticated cow is the latest farm animal to have its genome sequenced and deciphered. The members of the Bovine Genome Consortium have published a series of papers on the assembly and what the sequence reveals so far about the biology of this ruminant and the consequences of its domestication. PMID:19439025

  12. [Skin metastases revealing a bronchial adenocarcinoma].

    PubMed

    Zemmez, Youssef; Zegmout, Adil; Hamama, Jalal; Bouhamidi, Ahmed; El Amraoui, Mohammed; El Azhari, Jaouad; Boui, Mohamed

    2016-01-01

    We report the case of bronchial carcinoma revealed by metastatic skin nodules on the scalp. This fairly common mode of discovery is often associated with poor prognosis. This study aims to underline the importance of directing the search for a primary lung cancer in cases of secondary skin involvement. PMID:27583066

  13. Septic sacroiliitis revealing an infectious endocarditis

    PubMed Central

    Mahfoudhi, Madiha; Hariz, Anis; Turki, Sami; Kheder, Adel

    2014-01-01

    We report the case of a 43-year-old man admitted for right hip ache and fever. Physical examination revealed a fever, an ache at the manipulation of the sacroiliac joint and a limitation of abduction and external rotation of the right hip. There was no murmur in cardiac auscultation. No anomaly was found at the conventional radiographs of the sacroiliac joint, while the pelvic MRI confirmed a right sacroiliitis. A sacroiliac puncture with a study of synovial fluid demonstrated the presence of Streptococcus viridans. The blood culture revealed the same germ. Transthoracic and transoesophageal echocardiography confirmed infectious endocarditis with vegetation in the mitral valve. He received penicillin G and gentamicin relayed by pristinamycin because of an allergy to penicillin G with a total duration of treatment of 40 days. His symptoms and the laboratory and radiological tests abnormalities resolved totally with no recurrence. PMID:25123569

  14. Orbital tumor revealing a systemic sarcoidosis.

    PubMed

    Hannanachi Sassi, Samia; Dhouib, Rim; Kanchal, Fatma; Doghri, Raoudha; Boujelbene, Nadia; Bouguila, Hedi; Mrad, Karima

    2015-01-01

    Ocular involvement is seen in approximately 25% of patients with sarcoidosis. Uveitis is the most common ocular manifestation, but sarcoidosis may involve any part of the eye. Orbital manifestations of sarcoidosis are uncommon with few series in the literature. A 65-year-old woman presented with redness of the right eye and painless, unilateral eyelid swelling. Orbital scanning revealed mass infiltrating the soft tissue of the inferior right orbital quadrant. Biopsy results showed nodular, noncaseating granulomas consistent with sarcoidosis. The complete systemic workup revealed systemic manifestations of sarcoidosis at the time of examination with hilar and mediastinal lymphadenopathies noted on CT scan. The orbital surgical treatment was followed by systemic prednisone therapy with good response. Although rare, orbital sarcoidosis must be considered in the evaluation of orbital tumors in elderly patients. A search for systemic findings should be undertaken and appropriate therapy should be instituted. PMID:25796029

  15. Mediastinal Mature Teratoma Revealed by Empyema.

    PubMed

    Raoufi, Mohammed; Herrak, Laila; Benali, Anas; Achaachi, Leila; El Ftouh, Mustapha; Bellarbi, Salma; Tilfine, Charaf; Taouarsa, Firdaous

    2016-01-01

    Teratomas are germ cell tumors, manifested with a great variety of clinical features; the most common extragonadal site is the anterior mediastinum. In this case, we report the patient with a large mature mediastinal teratoma with several components of ectodermal and endothermal epithelium. A 24-year-old female patient presented with history of persistent chest pain and progressively aggravating dyspnea for the previous 3 months. A chest X-ray showed a large opacity of the entire left hemithorax. Transcutaneous needle aspiration revealed a purulent fluid. The tube thoracostomy was introduced and the effusion was evacuated. Some weeks later, patient was seen in emergency for persistent cough and lateral chest pain. CT scan revealed a mass of the left hemithorax. The mass showed heterogeneous density, without compressing mediastinum great vessels and left hilar structures. Lipase value was elevated in needle aspiration. The patient underwent a total resection of the mediastinum mass via a left posterolateral thoracotomy. Microscopy revealed a mature teratoma with cystic structures. The patient subsequently made a full recovery. This case provide benign mediastinal teratoma with total atelectasis of left lung and elevated lipase value in needle transcutaneous aspiration; this event is explained by pancreatic component in the cystic tumor. Total removal of the tumor is adequate treatment for this type of teratoma and the prognosis is excellent. PMID:27144046

  16. Mediastinal Mature Teratoma Revealed by Empyema

    PubMed Central

    Raoufi, Mohammed; Herrak, Laila; Benali, Anas; Achaachi, Leila; El Ftouh, Mustapha; Bellarbi, Salma; Tilfine, Charaf; Taouarsa, Firdaous

    2016-01-01

    Teratomas are germ cell tumors, manifested with a great variety of clinical features; the most common extragonadal site is the anterior mediastinum. In this case, we report the patient with a large mature mediastinal teratoma with several components of ectodermal and endothermal epithelium. A 24-year-old female patient presented with history of persistent chest pain and progressively aggravating dyspnea for the previous 3 months. A chest X-ray showed a large opacity of the entire left hemithorax. Transcutaneous needle aspiration revealed a purulent fluid. The tube thoracostomy was introduced and the effusion was evacuated. Some weeks later, patient was seen in emergency for persistent cough and lateral chest pain. CT scan revealed a mass of the left hemithorax. The mass showed heterogeneous density, without compressing mediastinum great vessels and left hilar structures. Lipase value was elevated in needle aspiration. The patient underwent a total resection of the mediastinum mass via a left posterolateral thoracotomy. Microscopy revealed a mature teratoma with cystic structures. The patient subsequently made a full recovery. This case provide benign mediastinal teratoma with total atelectasis of left lung and elevated lipase value in needle transcutaneous aspiration; this event is explained by pancreatic component in the cystic tumor. Total removal of the tumor is adequate treatment for this type of teratoma and the prognosis is excellent. PMID:27144046

  17. Effects of graphene on electro-optic switching and spontaneous polarization of a ferroelectric liquid crystal

    SciTech Connect

    Basu, Rajratan

    2014-09-15

    A small quantity of graphene flakes was doped in a ferroelectric liquid crystal (FLC), and the field-induced ferroelectric electro-optic switching was found to be significantly faster in the FLC + graphene hybrid than that of the pure FLC. Further studies revealed that the suspended graphene flakes enhanced the FLC's spontaneous polarization by improving smectic-C ordering resulting from the π–π electron stacking, and reduced rotation viscosity by trapping some of the free ions of the FLC media. These effects coherently impacted the FLC-switching phenomenon, enabling the FLC molecules to switch faster on reversing an external electric field.

  18. Middle atmosphere composition revealed by satellite observations

    NASA Technical Reports Server (NTRS)

    Russell, J. M., III; Solomon, S.; Mccormick, M. P.; Miller, A. J.; Barnett, J. J.; Jones, R. L.; Rusch, D. W.

    1986-01-01

    A series of plots that describe the state of the stratosphere and to some degree, the mesosphere as revealed by satellite observations are shown. The pertinent instrument features, spatial and temporal coverage, and details of accuracy and precision for the experiments providing the data were described. The main features of zonal mean cross sections and polar stereographic projections were noted and intercomparisons were discussed where a parameter was measured by more than one experiment. The main purpose was to collect the available data in one place and provide enough inforamation on limitations or cautions about the data so that they could be used in model comparisons and science studies.

  19. Trench Reveals Two Faces of Soils

    NASA Technical Reports Server (NTRS)

    2004-01-01

    This approximate true-color image mosaic from the panoramic camera on the Mars Exploration Rover Opportunity shows a trench dug by the rover in the vicinity of the 'Anatolia' region. Two imprints from the rover's Mossbauer spectrometer instrument were left in the exposed soils. Detailed comparisons between soils exposed at the surface and those found at depth reveal that surface soils have higher levels of hematite while subsurface soils show fine particles derived from basalt. The trench is approximately 11 centimeters deep. This image was taken on sol 81 with the panoramic camera's 430-, 530- and 750-nanometer filters.

  20. Reveal quantum correlation in complementary bases

    PubMed Central

    Wu, Shengjun; Ma, Zhihao; Chen, Zhihua; Yu, Sixia

    2014-01-01

    An essential feature of genuine quantum correlation is the simultaneous existence of correlation in complementary bases. We reveal this feature of quantum correlation by defining measures based on invariance under a basis change. For a bipartite quantum state, the classical correlation is the maximal correlation present in a certain optimum basis, while the quantum correlation is characterized as a series of residual correlations in the mutually unbiased bases. Compared with other approaches to quantify quantum correlation, our approach gives information-theoretical measures that directly reflect the essential feature of quantum correlation. PMID:24503595

  1. Cerebral venous thrombosis revealing an ulcerative colitis

    PubMed Central

    Taous, Abdellah; Berri, Maha Aït; Lamsiah, Taoufik; Zainoun, Brahim; Ziadi, Tarik; Rouimi, Abdelhadi

    2016-01-01

    Cerebral venous thrombosis (CVT) has been reported as an uncommon and devastating complication of ulcerative colitis (UC), with an annual incidence varying between 0,5 to 6,7%. It is suspected to be a consequence of the hypercoagulable state occurring during disease relapse. We report a case of 22-year-old female patient presenting with CVT revealing an UC. Our case raises the awareness among health professionals about the inflammatory bowel diseases (IBD) as a rare etiology of CVT, and signifies the importance of considering antithrombotic prophylaxis in all hospitalised IBD patients, especially those with active disease. PMID:27279947

  2. Infections Revealing Complement Deficiency in Adults

    PubMed Central

    Audemard-Verger, A.; Descloux, E.; Ponard, D.; Deroux, A.; Fantin, B.; Fieschi, C.; John, M.; Bouldouyre, A.; Karkowsi, L.; Moulis, G.; Auvinet, H.; Valla, F.; Lechiche, C.; Davido, B.; Martinot, M.; Biron, C.; Lucht, F.; Asseray, N.; Froissart, A.; Buzelé, R.; Perlat, A.; Boutboul, D.; Fremeaux-Bacchi, V.; Isnard, S.; Bienvenu, B.

    2016-01-01

    Abstract Complement system is a part of innate immunity, its main function is to protect human from bacterial infection. As genetic disorders, complement deficiencies are often diagnosed in pediatric population. However, complement deficiencies can also be revealed in adults but have been poorly investigated. Herein, we describe a case series of infections revealing complement deficiency in adults to study clinical spectrum and management of complement deficiencies. A nationwide retrospective study was conducted in French university and general hospitals in departments of internal medicine, infectious diseases enrolling patients older than 15 years old who had presented at least one infection leading to a complement deficiency diagnosis. Forty-one patients included between 2002 and 2015 in 19 different departments were enrolled in this study. The male-to-female ratio was 1.3 and the mean age at diagnosis was 28 ± 14 (15–67) years. The main clinical feature was Neisseria meningitidis meningitis 75% (n = 31/41) often involving rare serotype: Y (n = 9) and W 135 (n = 7). The main complement deficiency observed was the common final pathway deficiency 83% (n = 34/41). Half of the cohort displayed severe sepsis or septic shock at diagnosis (n = 22/41) but no patient died. No patient had family history of complement deficiency. The mean follow-up was 1.15 ± 1.95 (0.1–10) years. Half of the patients had already suffered from at least one infection before diagnosis of complement deficiency: meningitis (n = 13), pneumonia (n = 4), fulminans purpura (n = 1), or recurrent otitis (n = 1). Near one-third (n = 10/39) had received prophylactic antibiotics (cotrimoxazole or penicillin) after diagnosis of complement deficiency. The vaccination coverage rate, at the end of the follow-up, for N meningitidis, Streptococcus pneumonia, and Haemophilius influenzae were, respectively, 90% (n = 33/37), 47% (n = 17/36), and 35

  3. What Eye Movements Reveal about Deaf Readers

    PubMed Central

    Bélanger, Nathalie N.; Rayner, Keith

    2014-01-01

    Levels of illiteracy in the deaf populations around the world have been extremely high for decades and much higher than the illiteracy levels found in the general population. Research has mostly focused on deaf readers’ difficulties rather than on their strengths, which can then inform reading education. Deaf readers are a unique population. They process language and the world surrounding them mostly via the visual channel and this greatly affects how they read or might learn to read. The study of eye movements in reading provides highly sophisticated information about how words and sentences are processed and our research with deaf readers reveals the importance of their uniqueness. PMID:26594098

  4. Apocalypto: revealing lost text with XMT

    NASA Astrophysics Data System (ADS)

    Mills, David; Davis, Graham R.; Lai, Yu-kun; Rosin, Paul

    2014-09-01

    "Can brute-force high-contrast tomography techniques and image processing techniques retrieve textual content from damaged heritage materials?" The Dental Institute at Queen Mary University of London (QMUL) is the leading centre for very high contrast X-Ray Microtomography imaging. The Apocalypto Project is our collaboration with the heritage community and experts in Computer Vision systems in the Computer Science Department at Cardiff University. This collaboration has developed techniques and a workflow that allows us to reveal textual content from moisture-damaged parchment rolls. This article will also present some initial results from burned and heat shrunken parchment rolls, an insect damaged Mamluk cap and a birch bark roll.

  5. Saturn's secrets revealed - A special report

    NASA Astrophysics Data System (ADS)

    Sutton, C.

    1980-11-01

    Scientific results of the encounter of Voyager 1 with Saturn are reported. Instruments on the Voyager spacecraft, which was launched on September 5, 1977 and flew within 124,200 km of the Saturn cloud tops on November 12, 1980, revealed the presence of several hundred rings within the six visible from earth, as well as eccentric rings, braiding and clumps within the narrow F ring, and spoke-like structures in the B ring. During its flight beneath the ring plane, Voyager 1 also discovered that the rings extend toward the visible surface of the cloud tops, and are composed of ice chunks or silicate with an icy coating about a meter in diameter. Observations of Titan revealed the satellite to have a dense atmosphere, composed primarily of molecular nitrogen, with as many as three layers of haze above the cloud tops. Three additional moons of Saturn were discovered apparently focusing ring particles, and the moon Janus, discovered from earth in 1966, was shown to be actually two moons. Close approaches to other Saturn satellites show Mimas, Tethys, Dione and Rhea to be heavily cratered, icy bodies, some with features indicating they had been struck by objects almost large enough to shatter them. Surface features on Saturn, which is covered by a deep layer of haze, and the details of the Saturn magnetosphere have also been observed.

  6. Exertional rhabdomyolysis and exercise intolerance revealing dystrophinopathies.

    PubMed

    Figarella-Branger, D; Baeta Machado, A M; Putzu, G A; Malzac, P; Voelckel, M A; Pellissier, J F

    1997-07-01

    Exercise intolerance associated with myalgias, muscle cramps or myoglobinuria may be associated with a dystrophinopathy. A search for abnormal dystrophin expression (using immunohistochemistry, immunoblot and DNA analysis) was carried out in a series of 15 patients. They were selected because they presented exercise intolerance, negative biochemical tests (lipid, glycogen and mitochondrial metabolism) and abnormal immunohistochemistry with at least one anti-dystrophin antibody (anti-Dys 1, rod domain; anti-Dys 2, C terminus; anti-Dys 3, N terminus). Lack of anti-Dys 1 immunoreactivity was seen in three patients and abnormal immunoreactivity with all three anti-dystrophin antibodies in two. Immunoblot confirmed the dystrophinopathy in these five patients only, and multiplex polymerase chain reaction DNA analysis revealed a deletion in the dystrophin gene in two of these patients, affecting the proximal part of the rod domain in one and the distal part of this domain in the other. The clinical, biological and histopathological features of the five patients reported here, together with the previous cases reported in the literature, are described and reveal that exercise intolerance associated with dystrophinopathy displays characteristic clinical, biological and immunohistochemical features and defines a new dystrophinopathy phenotype. The absence of staining in the rod domain provides a secure diagnosis of this syndrome. Dystrophinopathy is one etiology of idiopathic myoglobinuria, requiring genetic counseling. PMID:9224530

  7. Mammalian phylogeny reveals recent diversification rate shifts.

    PubMed

    Stadler, Tanja

    2011-04-12

    Phylogenetic trees of present-day species allow investigation of the rate of evolution that led to the present-day diversity. A recent analysis of the mammalian phylogeny challenged the view of explosive mammalian evolution after the Cretaceous-Tertiary (K/T) boundary (65 Mya). However, due to lack of appropriate methods, the diversification (speciation minus extinction) rates in the more recent past of mammalian evolution could not be determined. In this paper, I provide a method that reveals that the tempo of mammalian evolution did not change until ∼ 33 Mya. This constant period was followed by a peak of diversification rates between 33 and 30 Mya. Thereafter, diversification rates remained high and constant until 8.55 Mya. Diversification rates declined significantly at 8.55 and 3.35 Mya. Investigation of mammalian subgroups (marsupials, placentals, and the six largest placental subgroups) reveals that the diversification rate peak at 33-30 Mya is mainly driven by rodents, cetartiodactyla, and marsupials. The recent diversification rate decrease is significant for all analyzed subgroups but eulipotyphla, cetartiodactyla, and primates. My likelihood approach is not limited to mammalian evolution. It provides a robust framework to infer diversification rate changes and mass extinction events in phylogenies, reconstructed from, e.g., present-day species or virus data. In particular, the method is very robust toward noise and uncertainty in the phylogeny and can account for incomplete taxon sampling. PMID:21444816

  8. Interior Evolution of Ceres Revealed by Dawn

    NASA Astrophysics Data System (ADS)

    Raymond, Carol A.; Park, Ryan S.; Konopliv, Alex S.; Bland, Michael T.; Marchi, Simone; Castillo-Rogez, Julie C.; McCord, Thomas B.; Jaumann, Ralf; Russell, Christopher T.; Prettyman, Thomas H.

    2015-11-01

    Dawn's exploration of Ceres has revealed its geophysical characteristics, informing the processes that have shaped it. Dawn has determined the average diameter of Ceres to be 940 km, smaller than the previously estimated 975 km [1]. This implies a density of 2160 kg/m3, indicating that Ceres is less differentiated than predicted [2]. The low-degree gravity field is consistent with the body being in hydrostatic equilibrium and the magnitude of J2 implies some central condensation. Ceres' entire surface is cratered, implying the lack of a thick (10's of km) water ice layer at the surface. Variability in Ceres' crater morphology indicates that the near-surface layer has variable strength and rheology, likely due to heterogeneity in the near-surface mixture of rock, ice and salt. The lack of a number of expected large impact basins on Ceres can be interpreted to be the result of viscous relaxation, resurfacing or a combination of both. These data provide insights into Ceres' thermal evolution and mechanical properties, which appear to be unique to this warm, icy body.[1] Thomas, P. C., et al., Differentiation of the asteroid Ceres as revealed by its shape, Nature, 437, 224-226, 2005; [2] McCord et al., Ceres: Its Origin, Evolution and Structure and Dawn's Potential Contribution, Space Sci Rev DOI 10.1007/s11214-010-9729-9, 2011.

  9. Semantic priming revealed by mouse movement trajectories.

    PubMed

    Xiao, Kunchen; Yamauchi, Takashi

    2014-07-01

    Congruency effects are taken as evidence that semantic information can be processed automatically. However, these effects are often weak, and the straightforward association between primes and targets can exaggerate congruency effects. To address these problems, a mouse movement method is applied to scrutinize congruency effects. In one experiment, participants judged whether two numbers were the same ("3\\3") or different ("3\\5"), preceded by briefly presented pictures with either positive or negative connotations. Participants indicated their responses by clicking a "Same" or "Different" button on the computer screen, while their cursor trajectories were recorded for each trial. The trajectory data revealed greater deviation to unselected buttons in incongruent trials (e.g., "3\\5" preceded by a green traffic light picture). This effect was influenced by the type of responses but not by prime durations. We suggest that the mouse movement method can complement the reaction time to study masked semantic priming. PMID:24797040

  10. Neutron Imaging Reveals Internal Plant Hydraulic Dynamics

    SciTech Connect

    Warren, Jeffrey; Bilheux, Hassina Z; Kang, Misun; Voisin, Sophie; Cheng, Chu-Lin; Horita, Jusuke; Perfect, Edmund

    2013-01-01

    Many terrestrial ecosystem processes are constrained by water availability and transport within the soil. Knowledge of plant water fluxes is thus critical for assessing mechanistic processes linked to biogeochemical cycles, yet resolution of root structure and xylem water transport dynamics has been a particularly daunting task for the ecologist. Through neutron imaging, we demonstrate the ability to non-invasively monitor individual root functionality and water fluxes within Zea mays L. (maize) and Panicum virgatum L. (switchgrass) seedlings growing in a sandy medium. Root structure and growth were readily imaged by neutron radiography and neutron computed tomography. Seedlings were irrigated with water or deuterium oxide and imaged through time as a growth lamp was cycled on to alter leaf demand for water. Sub-millimeter scale resolution reveals timing and magnitudes of root water uptake, redistribution within the roots, and root-shoot hydraulic linkages, relationships not well characterized by other techniques.

  11. Open chromatin reveals the functional maize genome

    PubMed Central

    Rodgers-Melnick, Eli; Vera, Daniel L.; Bass, Hank W.

    2016-01-01

    Cellular processes mediated through nuclear DNA must contend with chromatin. Chromatin structural assays can efficiently integrate information across diverse regulatory elements, revealing the functional noncoding genome. In this study, we use a differential nuclease sensitivity assay based on micrococcal nuclease (MNase) digestion to discover open chromatin regions in the maize genome. We find that maize MNase-hypersensitive (MNase HS) regions localize around active genes and within recombination hotspots, focusing biased gene conversion at their flanks. Although MNase HS regions map to less than 1% of the genome, they consistently explain a remarkably large amount (∼40%) of heritable phenotypic variance in diverse complex traits. MNase HS regions are therefore on par with coding sequences as annotations that demarcate the functional parts of the maize genome. These results imply that less than 3% of the maize genome (coding and MNase HS regions) may give rise to the overwhelming majority of phenotypic variation, greatly narrowing the scope of the functional genome. PMID:27185945

  12. Social patterns revealed through random matrix theory

    NASA Astrophysics Data System (ADS)

    Sarkar, Camellia; Jalan, Sarika

    2014-11-01

    Despite the tremendous advancements in the field of network theory, very few studies have taken weights in the interactions into consideration that emerge naturally in all real-world systems. Using random matrix analysis of a weighted social network, we demonstrate the profound impact of weights in interactions on emerging structural properties. The analysis reveals that randomness existing in particular time frame affects the decisions of individuals rendering them more freedom of choice in situations of financial security. While the structural organization of networks remains the same throughout all datasets, random matrix theory provides insight into the interaction pattern of individuals of the society in situations of crisis. It has also been contemplated that individual accountability in terms of weighted interactions remains as a key to success unless segregation of tasks comes into play.

  13. Open chromatin reveals the functional maize genome.

    PubMed

    Rodgers-Melnick, Eli; Vera, Daniel L; Bass, Hank W; Buckler, Edward S

    2016-05-31

    Cellular processes mediated through nuclear DNA must contend with chromatin. Chromatin structural assays can efficiently integrate information across diverse regulatory elements, revealing the functional noncoding genome. In this study, we use a differential nuclease sensitivity assay based on micrococcal nuclease (MNase) digestion to discover open chromatin regions in the maize genome. We find that maize MNase-hypersensitive (MNase HS) regions localize around active genes and within recombination hotspots, focusing biased gene conversion at their flanks. Although MNase HS regions map to less than 1% of the genome, they consistently explain a remarkably large amount (∼40%) of heritable phenotypic variance in diverse complex traits. MNase HS regions are therefore on par with coding sequences as annotations that demarcate the functional parts of the maize genome. These results imply that less than 3% of the maize genome (coding and MNase HS regions) may give rise to the overwhelming majority of phenotypic variation, greatly narrowing the scope of the functional genome. PMID:27185945

  14. Revealing effective classifiers through network comparison

    NASA Astrophysics Data System (ADS)

    Gallos, Lazaros K.; Fefferman, Nina H.

    2014-11-01

    The ability to compare complex systems can provide new insight into the fundamental nature of the processes captured, in ways that are otherwise inaccessible to observation. Here, we introduce the n-tangle method to directly compare two networks for structural similarity, based on the distribution of edge density in network subgraphs. We demonstrate that this method can efficiently introduce comparative analysis into network science and opens the road for many new applications. For example, we show how the construction of a “phylogenetic tree” across animal taxa according to their social structure can reveal commonalities in the behavioral ecology of the populations, or how students create similar networks according to the University size. Our method can be expanded to study many additional properties, such as network classification, changes during time evolution, convergence of growth models, and detection of structural changes during damage.

  15. Metabolomics reveals metabolic biomarkers of Crohn's disease

    SciTech Connect

    Jansson, J.K.; Willing, B.; Lucio, M.; Fekete, A.; Dicksved, J.; Halfvarson, J.; Tysk, C.; Schmitt-Kopplin, P.

    2009-06-01

    The causes and etiology of Crohn's disease (CD) are currently unknown although both host genetics and environmental factors play a role. Here we used non-targeted metabolic profiling to determine the contribution of metabolites produced by the gut microbiota towards disease status of the host. Ion Cyclotron Resonance Fourier Transform Mass Spectrometry (ICR-FT/MS) was used to discern the masses of thousands of metabolites in fecal samples collected from 17 identical twin pairs, including healthy individuals and those with CD. Pathways with differentiating metabolites included those involved in the metabolism and or synthesis of amino acids, fatty acids, bile acids and arachidonic acid. Several metabolites were positively or negatively correlated to the disease phenotype and to specific microbes previously characterized in the same samples. Our data reveal novel differentiating metabolites for CD that may provide diagnostic biomarkers and/or monitoring tools as well as insight into potential targets for disease therapy and prevention.

  16. Chain networking revealed by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Zheng, Yexin; Tsige, Mesfin; Wang, Shi-Qing

    Based on Kremer-Grest model for entangled polymer melts, we demonstrate how the response of a polymer glass depends critically on the chain length. After quenching two melts of very different chain lengths (350 beads per chain and 30 beads per chain) into deeply glassy states, we subject them to uniaxial extension. Our MD simulations show that the glass of long chains undergoes stable necking after yielding whereas the system of short chains is unable to neck and breaks up after strain localization. During ductile extension of the polymer glass made of long chain significant chain tension builds up in the load-bearing strands (LBSs). Further analysis is expected to reveal evidence of activation of the primary structure during post-yield extension. These results lend support to the recent molecular model 1 and are the simulations to demonstrate the role of chain networking. This work is supported, in part, by a NSF Grant (DMR-EAGER-1444859)

  17. Licking Microstructure Reveals Rapid Attenuation of Neophobia

    PubMed Central

    Monk, Kevin J.; Rubin, Benjamin D.

    2014-01-01

    Many animals hesitate when initially consuming a novel food and increase their consumption of that food between the first and second sessions of access—a process termed attenuation of neophobia (AN). AN has received attention as a model of learning and memory; it has been suggested that plasticity resulting from an association of the novel tastant with “safe outcome” results in a change in the neural response to the tastant during the second session, such that consumption increases. Most studies have reported that AN emerges only an hour or more after the end of the first exposure to the tastant, consistent with what is known of learning-related plasticity. But these studies have typically measured consumption, rather than real-time behavior, and thus the possibility exists that a more rapidly developing AN remains to be discovered. Here, we tested this possibility, examining both consumption and individual lick times in a novel variant of a brief-access task (BAT). When quantified in terms of consumption, data from the BAT accorded well with the results of a classic one-bottle task—both revealed neophobia/AN specific to higher concentrations (for instance, 28mM) of saccharin. An analysis of licking microstructure, however, additionally revealed a real-time correlate of neophobia—an explicit tendency, similarly specific for 28-mM saccharin, to cut short the initial bout of licks in a single trial (compared with water). This relative hesitancy (i.e., the shortness of the first lick bout to 28-mM saccharin compared with water) that constitutes neophobia not only disappeared between sessions but also gradually declined in magnitude across session 1. These data demonstrate that the BAT accurately measures AN, and that aspects of AN—and the processes underlying familiarization—begin within minutes of the very first taste. PMID:24363269

  18. Ceres Revealed in a Grain of Salt

    NASA Technical Reports Server (NTRS)

    Zolensky, M. E.; Bodnar, R. J.; Fries, M.; Chan, Q. H.-S.; Kebukawa, Y.; Mikouchi, T.; Hagiya, K.; Komatsu, M.; Ohsumi, K.; Steele, A.

    2016-01-01

    Introduction: Zag and Monahans (1998) are H chondrite regolith breccias containing 4.5 giga-year-old halite crystals which contain abundant inclusions of aqueous fluids, solids and organics. These all originated on a cryo-volcanically-active C class asteroid, probably 1 Ceres; the halite was transported to the regolith of the H chondrite parent asteroid, potentially 6 Hebe. Detailed analysis of these solids will thus potentially reveal the mineralogy of Ceres. Mineralogy of solids in the Monahans Halite Solid grains are present in the halites, which were entrained within the mother brines during eruption, including material from the interior and surface of the erupting body. The solids include abundant, widely variable organics that could not have been significantly heated (which would have resulted in the loss of fluids from the halite). Our analyses by Raman microprobe, SEM/EDX, synchrotron X-ray diffraction, UPLC-FD/QToF-MS, C-XANES and TEM reveal that these trapped grains include macromolecular carbon (MMC) similar in structure to CV3 chondrite matrix carbon, aliphatic carbon compounds, olivine (Fo99-59), high- and low-Ca pyroxene, feldspars, phyllosilicates, magnetite, sulfides, metal, lepidocrocite, carbonates, diamond, apatite and zeolites. Conclusions: The halite in Monahans and Zag derive from a water and carbon-rich object that was cryo-volcanically active in the early solar system, probably Ceres. The Dawn spacecraft found that Ceres includes C chondrite materials. Our samples include both protolith and aqueously-altered samples of the body, permitting understanding of alteration conditions. Whatever the halite parent body, it was rich in a wide variety of organics and warm, liquid water at the solar system's dawn.

  19. Quantifying the transport properties of lipid mesophases by theoretical modelling of diffusion experiments.

    PubMed

    Antognini, Luca M; Assenza, Salvatore; Speziale, Chiara; Mezzenga, Raffaele

    2016-08-28

    Lyotropic Liquid Crystals (LLCs) are a class of lipid-based membranes with a strong potential for drug-delivery employment. The characterization and control of their transport properties is a central issue in this regard, and has recently prompted a notable volume of research on the topic. A promising experimental approach is provided by the so-called diffusion setup, where the drug molecules diffuse from a feeding chamber filled with water to a receiving one passing through a LLC. In the present work we provide a theoretical framework for the proper description of this setup, and validate it by means of targeted experiments. Due to the inhomogeneity of the system, a rich palette of different diffusion dynamics emerges from the interplay of the different time- and lengthscales thereby present. Our work paves the way to the employment of diffusion experiments to quantitatively characterize the transport properties of LLCs, and provides the basic tools for device diffusion setups with controlled kinetic properties. PMID:27586942

  20. X-ray diffraction studies on mesophases of cetyl- and dodecyltrimethylammoniumbromide in liquid ammonia.

    PubMed

    Bzik, Stefan; Jansen, Martin

    2003-02-01

    We have studied solutions of the surfactants cetyltrimethylammoniumbromide (CTAB) and dodecyltrimethylammoniumbromide (DTAB) in liquid ammonia with respect to the formation of lyotropic phases. For this purpose, a set-up for performing X-ray scattering experiments at temperatures up to 120 degrees C on samples containing liquid ammonia has been developed. Both systems form hexagonal and monoclinic lyotropic phases above the dissolving temperature of the surfactant, thus representing the first examples for lyotropic phases in liquid ammonia, and for monoclinic phases in nonaqueous solvents. The phase diagrams of CTAB/liquid NH(3) and DTAB/liquid NH(3) show similarities to their respective aqueous systems. However, the regions of existence of monoclinic phases are much larger in the ammonia system, while the cubic phases, as observed in the water based systems, do not seem to exist. The liquid-crystalline phases found provide potentiality for preparing mesoporous, nitride-based solids. PMID:12569452

  1. A Liquid Crystalline Oligomer Exhibiting Nematic and Twist-Bend Nematic Mesophases.

    PubMed

    Mandle, Richard J; Goodby, John W

    2016-04-01

    The twist-bend nematic phase (NTB ) has been described as the structural link between the untilted uniaxial nematic phase (N) and the helical chiral nematic phase (N*). The NTB phase exhibits phenomena of fundamental importance to science, that is, 1) the spontaneous formation of a helical pitch on the nanometer scale in a fluid and 2) the spontaneous breaking of mirror symmetry, leading to the emergence of chiral domains in an achiral system. In this Communication, we present a study on T49 [bis(4-(9-(4-((4-cyanobenzoyl)oxy)phenyl)nonyl)phenyl) 4,4'-(nonane-1,9-diyl)dibenzoate], a liquid-crystalline oligomer exhibiting the twist-bend nematic phase, which has a molecular length that is of comparable dimensions to the sub-10 nm pitch determined for CB9CB, and provide new insights into the differentiation between the nano- and macro-science for self-assembling supermolecular systems. PMID:26777310

  2. Nonequilibrium effects in self-assembled mesophase materials: unexpected supercooling effects for cubosomes and hexosomes.

    PubMed

    Dong, Yao-Da; Tilley, Adam J; Larson, Ian; Lawrence, M Jayne; Amenitsch, Heinz; Rappolt, Michael; Hanley, Tracey; Boyd, Ben J

    2010-06-01

    Polar lipids often exhibit equilibrium liquid crystalline structures in excess water, such as the bicontinuous cubic phases (Q(II)) at low temperatures and inverse hexagonal phase (H(II)) at higher temperatures. In this study, the equilibrium and nonequilibrium phase behavior of glyceryl monooleate (GMO) and phytantriol (PHYT) systems in excess water were investigated using both continuous heating and cooling cycles, and rapid temperature changes. Evolution of the phase structure was followed using small-angle X-ray scattering (SAXS). During cooling, not only was supercooling of the liquid crystalline systems by up to 25 degrees C observed, but evidence for nonequilibrium phase structures (not present on heating; such as the gyroid cubic phase only present at low water content in equilibrium) was also apparent. The nonequilibrium phases were surprisingly stable, with return to equilibrium structure for dispersed submicrometer sized particle systems taking more than 13 h in some cases. Inhibition of phase nucleation was the key to greater supercooling effects observed for the dispersed particles compared to the bulk systems. These findings highlight the need for continued study into the nonequilibrium phase structures for these types of systems, as this may influence performance in applications such as drug delivery. PMID:20364857

  3. Volume and porosity thermal regulation in lipid mesophases by coupling mobile ligands to soft membranes

    NASA Astrophysics Data System (ADS)

    Parolini, Lucia; Mognetti, Bortolo M.; Kotar, Jurij; Eiser, Erika; Cicuta, Pietro; di Michele, Lorenzo

    2015-01-01

    Short DNA linkers are increasingly being exploited for driving-specific self-assembly of Brownian objects. DNA-functionalized colloids can assemble into ordered or amorphous materials with tailored morphology. Recently, the same approach has been applied to compliant units, including emulsion droplets and lipid vesicles. The liquid structure of these substrates introduces new degrees of freedom: the tethers can diffuse and rearrange, radically changing the physics of the interactions. Unlike droplets, vesicles are extremely deformable and DNA-mediated adhesion causes significant shape adjustments. We investigate experimentally the thermal response of pairs and networks of DNA-tethered liposomes and observe two intriguing and possibly useful collective properties: negative thermal expansion and tuneable porosity of the liposome networks. A model providing a thorough understanding of this unexpected phenomenon is developed, explaining the emergent properties out of the interplay between the temperature-dependent deformability of the vesicles and the DNA-mediated adhesive forces.

  4. Some aspects of the orientational order distribution of flexible chains in a diblock mesophase

    SciTech Connect

    Lorthioir, Cédric Randriamahefa, Solo

    2013-12-14

    The segmental motions of flexible chains in the lamellar structure of a strongly segregated poly(styrene)-poly(dimethylsiloxane) (PS-PDMS) diblock were investigated over a time scale of a few tens of microseconds. {sup 2}H NMR experiments were performed on the PDMS block, selectively perdeuterated. Transverse relaxation measurements show that the main part of the PDMS repeat units display anisotropic reorientational motions within the diblock lamellae and such a segmental ordering essentially results from interchain steric repulsions. {sup 2}H double quantum-based experiments evidenced a non-uniform local stretching of PDMS chains and enabled the underlying distribution of the orientational order parameter to be determined quantitatively. Besides, a fraction of the PDMS chain segments, about 14%, were found to display isotropic – or nearly isotropic – reorientations, which could be assigned to repeat units located within a thin sublayer (about 1–2 nm) at the lamellae midplane, but also deeper in the lamellae, close to folded parts of the chains. These experimental results were confronted to theoretical descriptions of opposing polymer brushes and, in particular, to the strong-stretching theory (SST) including the entropic contribution of free chain ends.

  5. Interaction of some laser radiations with the lauric acid in mesophase

    NASA Astrophysics Data System (ADS)

    Dumitru, Mihaela A.; Honciuc, Maria; Popescu, Ion M.

    1994-07-01

    In `optoelectronic devices' area, a new domain occurred: organic and biological optoelectronics. Since 1988 our researches axed on this exciting theme and several works materialize the results we obtained. In this paper, we used the lauric acid, a fatty acid, which can be found, for example, under an esterified form, in the cocobutter.

  6. Stabilization of the Columnar Mesophase of Perylenediimide by Racemic Triple Tails.

    PubMed

    Pereira de Oliveira Santos, Deise M; Belarmino Cabral, Marilia G; Bentaleb, Ahmed; Cristiano, Rodrigo; Gallardo, Hugo; Durola, Fabien; Bock, Harald

    2016-05-23

    Whereas perylene tetracarboxdiimides derived from amino-n-alkanes if at all only show monotropic (thermodynamically unstable) mesogenic self-assembly, the hexagonal columnar liquid crystalline state can be stabilized over a broad temperature range with doubly branched, doubly racemic alkyl residues. An improved tendency to homeotropic surface orientation is observed, and the orientation of the liquid crystalline domains is maintained upon cycling through the crystalline state at room temperature. PMID:27145525

  7. Neutron Imaging Reveals Internal Plant Hydraulic Dynamics

    NASA Astrophysics Data System (ADS)

    Warren, J.; Bilheux, H.; Kang, M.; Voisin, S.; Cheng, C.; Horita, J.; Perfect, E.

    2011-12-01

    In situ quantification of soil-plant water fluxes have not been fully successful due to a lack of non-destructive techniques capable of revealing roots or water fluxes at relevant spatial scales. Neutron imaging is a unique non-invasive tool that can assess sub-millimeter scale material properties and transport in situ, and which has been successfully applied to characterize soil and plant water status. Here, we have applied neutron radiography and tomography to quantify water transport through individual maize roots in response to internal plant demand. Zea mays seedlings were grown for 10 days in Flint silica sand within 2.6 cm diameter Al chambers. Using a reactor-based neutron source at Oak Ridge National Laboratory (HFIR), water fluxes were tracked through the maize soil-root systems by collecting consecutive neutron radiographs over a 12 h period following irrigation with D2O. D has a much lower neutron attenuation than H, thus D2O displacement of existing H2O within the plant vascular system, or influx of D2O into previously dry tissue or soil is readily tracked by changes in image intensity through time. Plant water release and uptake was regulated by periodically cycling on a high-intensity grow light. From each maize replicate, selected regions of interest (ROI) were delineated around individual roots, root free soil, stem and leaf segments. Changes in ROI were tracked through time to reveal patterns of water flux. The hydration of root and stem tissue cycled in response to illumination; root water content often increased during darkness, then decreased with illumination as water was transported from the root into the stem. Relative root-shoot hydration through time illustrates the balance between demand, storage capacity and uptake, which varies depending on root characteristics and its localized soil environment. The dynamic transport of water between soil, individual roots, stems and leaves was readily visualized and quantified illustrating the value

  8. Revealing the Hot Side of Epsilon Aurigae

    NASA Astrophysics Data System (ADS)

    Hoard, Donald; Stencel, Robert; Howell, Steve

    2012-12-01

    We request a small investment of 24 minutes of Spitzer time, to obtain four IRAC observations of epsilon Aurigae. A naked eye object located near Capella, epsilon Aurigae is the eclipsing binary star with the longest known orbital period, showing a single long duration (~2 yr) eclipse every 27.1 yr. For much of the last 200 years, the nature of the eclipsing object defied explanation. We recently demonstrated that epsilon Aurigae consists of a high luminosity F0 post-AGB star in orbit with a B5 V star surrounded by a solar system sized (~8 AU diameter) disk of cool, dust-dominated material. The eclipse of epsilon Aurigae is a rare event; moreover, it is a unique astrophysical opportunity, since the backlighting of the disk by the high luminosity eclipsed star reveals details that cannot be detected in similar dusty disks around single stars. The current eclipse started in August 2009 and ended in July 2011; we are now in the post-eclipse phase, when the irradiation-heated side of the disk will begin rotating into view. The goals for these observations include: (1) extend our ongoing IRAC monitoring campaign covering the current eclipse to post-eclipse visits; (2) provide a consistent, well-calibrated space-based set of IR photometry for comparison with ongoing ground-based work; and (3) use the composite results to constrain the thermal profile of the disk. A key expectation of these particular observations is to reveal the irradiation-heated portion of the disk, which will be visible on its trailing side following eclipse. Observations of this side of the disk will be crucial to test and constrain new models of disk structure. As part of our overall monitoring campaign with Spitzer, Hubble, Herschel, and numerous ground-based facilities, these proposed observations will make an important contribution to the understanding of stellar evolution in binary stars, including mass transfer and evolution studies, along with new insights into astrophysical disks and post

  9. Niche engineering reveals complementary resource use.

    PubMed

    Gable, Jacob T; Crowder, David W; Northfield, Tobin D; Steffan, Shawn A; Snyder, William E

    2012-09-01

    Greater resource use by diverse communities might result from species occupying complementary niches. Demonstrating niche complementarity among species is challenging, however, due to the difficulty in relating differences between species in particular traits to their use of complementary resources. Here, we overcame this obstacle by exploiting plastic foraging behavior in a community of predatory insects common on Brassica oleracea plants in Washington, USA. These predators complemented one another by partitioning foraging space, with some species foraging primarily along leaf edges and others at leaf centers. We hypothesized that emergent biodiversity effects would occur when predators partitioned foraging space on leaves, but not when spatial complementarity was dampened. Indeed, on intact leaves, edge- and center-foraging predators combined to kill more prey than any single predator species could by itself. These emergent diversity effects, however, disappeared on plants damaged by the caterpillar Plutella xylostella. Caterpillar chew-holes brought edge habitats to the center of leaves, so that all predator species could attack aphids anywhere on plants. With spatial niche differences diminished, there were no benefits of predator diversity; the most voracious single predator species killed the most aphids. Thus, caterpillar herbivory determined whether multi-predator-species effects reflected complementarity or species' individual impacts. Our study provides direct evidence for a causative relationship between niche differentiation and increased resource consumption by diverse communities, as revealed by ecological engineers that homogenize the foraging environment. PMID:23094370

  10. VISTA Reveals the Secret of the Unicorn

    NASA Astrophysics Data System (ADS)

    2010-10-01

    A new infrared image from ESO's VISTA survey telescope reveals an extraordinary landscape of glowing tendrils of gas, dark clouds and young stars within the constellation of Monoceros (the Unicorn). This star-forming region, known as Monoceros R2, is embedded within a huge dark cloud. The region is almost completely obscured by interstellar dust when viewed in visible light, but is spectacular in the infrared. An active stellar nursery lies hidden inside a massive dark cloud rich in molecules and dust in the constellation of Monoceros. Although it appears close in the sky to the more familiar Orion Nebula it is actually almost twice as far from Earth, at a distance of about 2700 light-years. In visible light a grouping of massive hot stars creates a beautiful collection of reflection nebulae where the bluish starlight is scattered from parts of the dark, foggy outer layers of the molecular cloud. However, most of the new-born massive stars remain hidden as the thick interstellar dust strongly absorbs their ultraviolet and visible light. In this gorgeous infrared image taken from ESO's Paranal Observatory in northern Chile, the Visible and Infrared Survey Telescope for Astronomy (VISTA [1], eso0949) penetrates the dark curtain of cosmic dust and reveals in astonishing detail the folds, loops and filaments sculpted from the dusty interstellar matter by intense particle winds and the radiation emitted by hot young stars. "When I first saw this image I just said 'Wow!' I was amazed to see all the dust streamers so clearly around the Monoceros R2 cluster, as well as the jets from highly embedded young stellar objects. There is such a great wealth of exciting detail revealed in these VISTA images," says Jim Emerson, of Queen Mary, University of London and leader of the VISTA consortium. With its huge field of view, large mirror and sensitive camera, VISTA is ideal for obtaining deep, high quality infrared images of large areas of the sky, such as the Monoceros R2 region

  11. Overnight lexical consolidation revealed by speech segmentation.

    PubMed

    Dumay, Nicolas; Gareth Gaskell, M

    2012-04-01

    Two experiments explored the consolidation of spoken words, and assessed whether post-sleep novel competitor effects truly reflect engagement of these novel words in competition for lexical segmentation. Two types of competitor relationships were contrasted: the onset-aligned case (such as "frenzylk"), where the novel word is a close variant of the existing word: they start at the same time point and overlap on most of their segments; and the fully embedding case (such as "lirmucktoze"), where the existing word corresponds to a smaller embedded portion of its novel competitor and is thus less noticeable. Experiment 1 (pause detection) revealed a similar performance for both cases, with no competitor effect immediately after exposure, but significant inhibition after 24 h and seven days. Experiment 2 (word spotting) produced exactly the same pattern; however, as is the case with existing word carriers (cf. McQueen, Norris, & Cutler, 1994), the inhibition was much stronger for fully embedded than for onset-aligned targets (e.g., "lirmuckt" vs. "frenzyl"). Meanwhile, explicit measures of learning, i.e., free recall and recognition, improved over time. These results cannot be explained by either consolidation of episodic traces or acquisition of new phonological/dialectal variants. We argue instead that they reflect a general trait of vocabulary learning and consolidation. PMID:22261419

  12. Revealing Invisible Photonic Inscriptions: Images from Strain.

    PubMed

    Ding, Tao; Cao, Guoshuai; Schäfer, Christian G; Zhao, Qibin; Gallei, Markus; Smoukov, Stoyan K; Baumberg, Jeremy J

    2015-06-24

    Photonic structural materials have received intensive interest and have been strongly developed over the past few years for image displays, sensing, and anticounterfeit materials. Their "smartness" arises from their color responsivity to changes of environment, strain, or external fields. Here, we introduce a novel invisible photonic system that reveals encrypted images or characters by simply stretching, or immersing in solvents. This type of intriguing photonic material is composed of regularly arranged core-shell particles that are selectively cross-linked by UV irradiation, giving different strain response compared to un-cross-linked regions. The images reversibly appear and disappear when cycling the strain and releasing it. The unique advantages of this soft polymer opal system compared with other types of photonic gels are that it can be produced in roll to roll quantities, can be vigorously deformed to achieve strong color changes, and has no solvent evaporation issues because it is a photonic rubber system. We demonstrate potential applications together with a fabrication procedure which is straightforward and scalable, vital for user take-up. Our work deepens understanding of this rubbery photonic system based on core-shell nanospheres. PMID:26039279

  13. Chimaeric sounds reveal dichotomies in auditory perception

    NASA Astrophysics Data System (ADS)

    Smith, Zachary M.; Delgutte, Bertrand; Oxenham, Andrew J.

    2002-03-01

    By Fourier's theorem, signals can be decomposed into a sum of sinusoids of different frequencies. This is especially relevant for hearing, because the inner ear performs a form of mechanical Fourier transform by mapping frequencies along the length of the cochlear partition. An alternative signal decomposition, originated by Hilbert, is to factor a signal into the product of a slowly varying envelope and a rapidly varying fine time structure. Neurons in the auditory brainstem sensitive to these features have been found in mammalian physiological studies. To investigate the relative perceptual importance of envelope and fine structure, we synthesized stimuli that we call `auditory chimaeras', which have the envelope of one sound and the fine structure of another. Here we show that the envelope is most important for speech reception, and the fine structure is most important for pitch perception and sound localization. When the two features are in conflict, the sound of speech is heard at a location determined by the fine structure, but the words are identified according to the envelope. This finding reveals a possible acoustic basis for the hypothesized `what' and `where' pathways in the auditory cortex.

  14. Bone structure as revealed by microtomography

    NASA Astrophysics Data System (ADS)

    Hildebrand, Tor; Laib, Andres; Ulrich, Dieter; Kohlbrenner, Adrian; Ruegsegger, Peter

    1997-10-01

    The appearance of cancellous bone architecture is different for various skeletal sites and various disease states. In the iliac crest it is more plate-like, whereas in the spine rods dominate. During aging and disease plates are perforated and connecting rods are dissolved. There is a continuous shift from one structural type to the other. So traditional histomorphometric procedures, which are based on a fixed model type, will lead to questionable results. 3D microtomography allows to assess model independent structural parameters so that trabecular thickness, for example, can be determined directly. Not only mean thicknesses are available but also thickness histograms which are helpful to identify pathological states. Other features such as trabecular separation, degree of anisotropy and structural type index can be extracted from the 3D images and allow to characterize cancellous bone and its changes due to aging, disease and treatment. To fully exploit the significance of bone structure on bone strength large scale finite element (FE) analyses are performed. Hence microtomography, performed with a sufficiently fine isotropic spatial resolution, reveals information on the structural features of cancellous bone which were not available so far and which will, hopefully, lead to a better understanding of the pathogenesis of bone diseases and subsequently to improved treatment regimes.

  15. Biosignatures as revealed by spectropolarimetry of Earthshine.

    PubMed

    Sterzik, Michael F; Bagnulo, Stefano; Palle, Enric

    2012-03-01

    Low-resolution intensity spectra of Earth's atmosphere obtained from space reveal strong signatures of life ('biosignatures'), such as molecular oxygen and methane with abundances far from chemical equilibrium, as well as the presence of a 'red edge' (a sharp increase of albedo for wavelengths longer than 700 nm) caused by surface vegetation. Light passing through the atmosphere is strongly linearly polarized by scattering (from air molecules, aerosols and cloud particles) and by reflection (from oceans and land). Spectropolarimetric observations of local patches of Earth's sky light from the ground contain signatures of oxygen, ozone and water, and are used to characterize the properties of clouds and aerosols. When applied to exoplanets, ground-based spectropolarimetry can better constrain properties of atmospheres and surfaces than can standard intensity spectroscopy. Here we report disk-integrated linear polarization spectra of Earthshine, which is sunlight that has been first reflected by Earth and then reflected back to Earth by the Moon. The observations allow us to determine the fractional contribution of clouds and ocean surface, and are sensitive to visible areas of vegetation as small as 10 per cent. They represent a benchmark for the diagnostics of the atmospheric composition, mean cloud height and surfaces of exoplanets. PMID:22382980

  16. Revealing the values behind convenience food consumption.

    PubMed

    Botonaki, Anna; Mattas, Konstadinos

    2010-12-01

    The increasing importance of convenience in consumer food choices has attracted researchers' interest. In the effort to understand how convenience affects consumers' food preferences, values are believed to play an important role. The present study attempts to examine the way personal values suggested by Schwartz (1992) are associated with behaviour and attitudes regarding convenience food. A number of constructs describing food related attitudes and behaviours were developed and their relationship with personal values was analyzed following the methodology proposed by Brunsø, Scholderer, and Grunert (2004). Data were collected through a questionnaire survey from a random sample of consumers in Thessaloniki city, Greece. The results reveal that convenience food consumption and convenience orientation in the food domain are mainly connected with values that motivate people to seek new experiences, act independently and enhance their own personal interests, while are in conflict with values of conservation and self-transcendence. The opposite holds for other food related attitudes and behaviours like involvement with cooking and variety in diet. The findings seem to be of particular interest not only for marketers of food products, but also for food policy makers. PMID:20875475

  17. Dynamic Environmental Photosynthetic Imaging Reveals Emergent Phenotypes.

    PubMed

    Cruz, Jeffrey A; Savage, Linda J; Zegarac, Robert; Hall, Christopher C; Satoh-Cruz, Mio; Davis, Geoffry A; Kovac, William Kent; Chen, Jin; Kramer, David M

    2016-06-22

    Understanding and improving the productivity and robustness of plant photosynthesis requires high-throughput phenotyping under environmental conditions that are relevant to the field. Here we demonstrate the dynamic environmental photosynthesis imager (DEPI), an experimental platform for integrated, continuous, and high-throughput measurements of photosynthetic parameters during plant growth under reproducible yet dynamic environmental conditions. Using parallel imagers obviates the need to move plants or sensors, reducing artifacts and allowing simultaneous measurement on large numbers of plants. As a result, DEPI can reveal phenotypes that are not evident under standard laboratory conditions but emerge under progressively more dynamic illumination. We show examples in mutants of Arabidopsis of such "emergent phenotypes" that are highly transient and heterogeneous, appearing in different leaves under different conditions and depending in complex ways on both environmental conditions and plant developmental age. These emergent phenotypes appear to be caused by a range of phenomena, suggesting that such previously unseen processes are critical for plant responses to dynamic environments. PMID:27336966

  18. VISTA Reveals the Secret of the Unicorn

    NASA Astrophysics Data System (ADS)

    2010-10-01

    A new infrared image from ESO's VISTA survey telescope reveals an extraordinary landscape of glowing tendrils of gas, dark clouds and young stars within the constellation of Monoceros (the Unicorn). This star-forming region, known as Monoceros R2, is embedded within a huge dark cloud. The region is almost completely obscured by interstellar dust when viewed in visible light, but is spectacular in the infrared. An active stellar nursery lies hidden inside a massive dark cloud rich in molecules and dust in the constellation of Monoceros. Although it appears close in the sky to the more familiar Orion Nebula it is actually almost twice as far from Earth, at a distance of about 2700 light-years. In visible light a grouping of massive hot stars creates a beautiful collection of reflection nebulae where the bluish starlight is scattered from parts of the dark, foggy outer layers of the molecular cloud. However, most of the new-born massive stars remain hidden as the thick interstellar dust strongly absorbs their ultraviolet and visible light. In this gorgeous infrared image taken from ESO's Paranal Observatory in northern Chile, the Visible and Infrared Survey Telescope for Astronomy (VISTA [1], eso0949) penetrates the dark curtain of cosmic dust and reveals in astonishing detail the folds, loops and filaments sculpted from the dusty interstellar matter by intense particle winds and the radiation emitted by hot young stars. "When I first saw this image I just said 'Wow!' I was amazed to see all the dust streamers so clearly around the Monoceros R2 cluster, as well as the jets from highly embedded young stellar objects. There is such a great wealth of exciting detail revealed in these VISTA images," says Jim Emerson, of Queen Mary, University of London and leader of the VISTA consortium. With its huge field of view, large mirror and sensitive camera, VISTA is ideal for obtaining deep, high quality infrared images of large areas of the sky, such as the Monoceros R2 region

  19. Chandra Reveals Remains of Giant Eruption

    NASA Technical Reports Server (NTRS)

    2002-01-01

    This is a photo taken by NASA's Chandra X-ray Observatory that reveals the remains of an explosion in the form of two enormous arcs of multimillion-degree gas in the galaxy Centaurus A that appear to be part of a ring 25,000 light years in diameter. The size and location of the ring suggest that it could have been an explosion that occurred about 10 million years ago. A composite image made with radio (red and green), optical (yellow-orange), and X-ray data (blue) presents a sturning tableau of a turbulent galaxy. A broad band of dust and cold gas is bisected at an angle by opposing jets of high-energy particles blasting away from the supermassive black hole in the nucleus. Lying in a plane perpendicular to the jets are the two large arcs of x-ray emitting multi-million degree gas. This discovery can help astronomers better understand the cause and effect of violent outbursts from the vicinity of supermassive black holes of active galaxies. The Chandra program is managed by the Marshall Space Flight Center in Huntsville, Alabama.

  20. Sequence tagging reveals unexpected modifications in toxicoproteomics

    PubMed Central

    Dasari, Surendra; Chambers, Matthew C.; Codreanu, Simona G.; Liebler, Daniel C.; Collins, Ben C.; Pennington, Stephen R.; Gallagher, William M.; Tabb, David L.

    2010-01-01

    Toxicoproteomic samples are rich in posttranslational modifications (PTMs) of proteins. Identifying these modifications via standard database searching can incur significant performance penalties. Here we describe the latest developments in TagRecon, an algorithm that leverages inferred sequence tags to identify modified peptides in toxicoproteomic data sets. TagRecon identifies known modifications more effectively than the MyriMatch database search engine. TagRecon outperformed state of the art software in recognizing unanticipated modifications from LTQ, Orbitrap, and QTOF data sets. We developed user-friendly software for detecting persistent mass shifts from samples. We follow a three-step strategy for detecting unanticipated PTMs in samples. First, we identify the proteins present in the sample with a standard database search. Next, identified proteins are interrogated for unexpected PTMs with a sequence tag-based search. Finally, additional evidence is gathered for the detected mass shifts with a refinement search. Application of this technology on toxicoproteomic data sets revealed unintended cross-reactions between proteins and sample processing reagents. Twenty five proteins in rat liver showed signs of oxidative stress when exposed to potentially toxic drugs. These results demonstrate the value of mining toxicoproteomic data sets for modifications. PMID:21214251

  1. Revealing Invisible Photonic Inscriptions: Images from Strain

    PubMed Central

    2015-01-01

    Photonic structural materials have received intensive interest and have been strongly developed over the past few years for image displays, sensing, and anticounterfeit materials. Their “smartness” arises from their color responsivity to changes of environment, strain, or external fields. Here, we introduce a novel invisible photonic system that reveals encrypted images or characters by simply stretching, or immersing in solvents. This type of intriguing photonic material is composed of regularly arranged core–shell particles that are selectively cross-linked by UV irradiation, giving different strain response compared to un-cross-linked regions. The images reversibly appear and disappear when cycling the strain and releasing it. The unique advantages of this soft polymer opal system compared with other types of photonic gels are that it can be produced in roll to roll quantities, can be vigorously deformed to achieve strong color changes, and has no solvent evaporation issues because it is a photonic rubber system. We demonstrate potential applications together with a fabrication procedure which is straightforward and scalable, vital for user take-up. Our work deepens understanding of this rubbery photonic system based on core–shell nanospheres. PMID:26039279

  2. [The life of human hair follicle revealed].

    PubMed

    Bernard, Bruno A

    2006-02-01

    The human hair follicle is a unique appendage which results from epithelio-mesenchymal interactions initiated around the 3rd month of development. This appendage has a very complex structure, with a dermal compartment and an epithelial compartment. The dermal compartment comprises the connective tissue sheath and the dermal papilla, both of which are irrigated by microvessels. The epithelial compartment is made of highly replicating matrix cells giving rise to three concentrical domains, namely the outer root sheath, the inner root sheath and the hair shaft. The pigmentation unit, responsible for hair color, is made of fully active melanocytes located on top of the dermal papilla. Altogether a hair follicle contains more than 20 different cell types, engaged in different differentiation pathways and/or interacting with each other. This complex appendage has a unique behavior in mammals since, after a hair production phase, it involutes in place before entering a resting phase after which it renews itself under a cyclical but stochastic way, out of a double reservoir of pluripotent stem cells able to also regenerate epidermis. For yet unknown reasons, this well ordered process can be disturbed, provoking alopecia. The pigmentation unit also renews itself under a cyclical way, out of a melanocyte progenitor reservoir which progressively declines with time, provoking the hair whitening process. Finally, the shape of the hair shaft is programmed from the bulb. What makes this appendage unique and fascinating is its high degree of autonomy, its incredibly complex though stable structure, the number of different cell types interacting under an equilibrated way and its potential of regeneration. It represents a true paradigm of tissue homeostasis, exemplifying in a small living cylinder all the fundamental laws of cell-cell and tissue interactions. This life is revealed in this short synthesis. PMID:16457752

  3. World population profile reveals bleak data.

    PubMed

    1998-06-01

    This article presents selected demographic and HIV/AIDS indicators for 1998 and projections for 2010 for selected African countries. The statistics are provided by the US Bureau of the Census. The Census HIV/AIDS database is one of the best in the world. Findings reveal that Africa is the worst affected by AIDS. Eight countries are particularly affected: Zimbabwe, Namibia, Botswana, Swaziland, Zambia, Kenya, Malawi, and South Africa. In 1998, life expectancy declined by 25.7 years. Population growth is expected to decline from 2.5% to 1.1% due to the impact of AIDS mortality. HIV continues to spread in African countries and its spread and impact is not recorded in present data. With AIDS, life expectancy is likely to decline in Zimbabwe from 39.2 to 38.8 years during 1998-2010; without AIDS, it is expected to rise from 64.9 to 69.5 years during the same time period. Only in Zambia is there a slight increase in life expectancy with AIDS. The overwhelming poor life prospects for Africans are reflected in this article, which can provide statistics only for 21 of 53 African countries. The absence of data may mean low HIV prevalence, lack of data, or the beginning of the HIV epidemic. The UNDP provides a Human Poverty Index with indicators for deprivation in knowledge, deprivation in living standards, and longevity. African countries are likely to shift to the bottom of this index due to the impact of AIDS. PMID:12294386

  4. NASA's Hyperwall Revealing the Big Picture

    NASA Technical Reports Server (NTRS)

    Sellers, Piers

    2011-01-01

    NASA:s hyperwall is a sophisticated visualization tool used to display large datasets. The hyperwall, or video wall, is capable of displaying multiple high-definition data visualizations and/or images simultaneously across an arrangement of screens. Functioning as a key component at many NASA exhibits, the hyperwall is used to help explain phenomena, ideas, or examples of world change. The traveling version of the hyperwall is typically comprised of nine 42-50" flat-screen monitors arranged in a 3x3 array (as depicted below). However, it is not limited to monitor size or number; screen sizes can be as large as 52" and the arrangement of screens can include more than nine monitors. Generally, NASA satellite and model data are used to highlight particular themes in atmospheric, land, and ocean science. Many of the existing hyperwall stories reveal change across space and time, while others display large-scale still-images accompanied by descriptive, story-telling captions. Hyperwall content on a variety of Earth Science topics already exists and is made available to the public at: eospso.gsfc.nasa.gov/hyperwall. Keynote and PowerPoint presentations as well as Summary of Story files are available for download on each existing topic. New hyperwall content and accompanying files will continue being developed to promote scientific literacy across a diverse group of audience members. NASA invites the use of content accessible through this website but requests the user to acknowledge any and all data sources referenced in the content being used.

  5. Saturn Probe: Revealing Solar System Origins

    NASA Astrophysics Data System (ADS)

    Spilker, T. R.

    2015-12-01

    Comparative studies of the gas giant and ice giant planets are needed to reliably discriminate among competing theories of the origin and evolution of giant planets and the solar system, but we lack critical measurements. A Saturn atmospheric entry probe mission would fill a vital part of that gap, allowing comparative studies of Jupiter and Saturn, providing the basis for later comparisons with the ice giants Uranus and Neptune, and informing studies of extrasolar planetary systems now being characterized. The Galileo Probe mission provided the first in situ studies of Jupiter's atmosphere. Similar measurements at Saturn, Uranus and Neptune would provide an important comparative planetology context for the Galileo results. Cassini's "Proximal Orbits" in 2017 will reveal Saturn's internal structure to complement the Juno mission's similar measurements at Jupiter. A Saturn entry probe, complementing the Galileo Probe investigations at Jupiter, would complete a solid basis for improved understanding of both Jupiter and Saturn, an important stepping stone to understanding Uranus and Neptune and solar system formation and evolution. The 2012 Decadal Survey ("DS") added Saturn Probe science objectives to NASA's New Frontiers Program: highest-priority Tier 1 objectives any New Frontiers implementation must achieve, and Tier 2, high priority but lower than Tier 1. A DS mission concept study using extremely conservative assumptions concluded that a Saturn Probe project could fit within New Frontiers resource constraints, giving a PI confidence that they could pursue some Tier 2 objectives, customizing for the proper balance of science return, science team composition, procured or contributed instruments, etc. Contributed instruments could significantly enhance the payload and the science team for greater science return. They also provide international collaboration opportunities, with science benefits well demonstrated by missions such as Cassini-Huygens and Rosetta.

  6. Configuration effects of H-bonded sites and rigid core lengths on h-bonded banana-shaped liquid crystalline supramolecules consisting of symmetric trimers and asymmetric heterodimers.

    PubMed

    Wang, Ling-Yung; Chiang, I-Hung; Yang, Po-Jen; Li, Wan-Sheung; Chao, I-To; Lin, Hong-Cheu

    2009-11-01

    Several series of novel banana-shaped H-bonded symmetric trimers (with two H-bonds) and asymmetric heterodimers (with one H-bond) were self-assembled by appropriate molar ratios of proton donors (H-donors) and acceptors (H-acceptors). The influences of H-bonded linking positions and aromatic ring numbers (4-8 aromatic rings in the rigid cores) as well as the chain lengths (n, m = 12 or 16, respectively, in the flexible parts) on the mesomorphism and the switching behavior of the bent-core supramolecules were evaluated and theoretically analyzed. Except for the supramolecular structures with longer rigid cores or shorter flexible chains possessing the rectangular columnar (Col(r) or B1) phase, the SmC(A)P(A) phase was revealed in most supramolecular asymmetric heterodimers and switched to the SmC(S)P(F) phase by applying electric fields. The polar smectic C phase was dominated for those with H-bonded sites apart from the core center. Interestingly, the SmA and nematic phases were observed in H-bonded asymmetric dimers with H-bonded sites close to the core center, which theoretically proved that the polar smectic C phase was disfavored due to an unfavorable bend angle (smaller than the lower limit of 110 degrees ) in the lowest-energy H-bonded conformer. Compared with the fully covalently bonded analogue, lower transition temperatures and lower threshold voltages were developed in the H-bonded asymmetric dimers with the polar smectic C phase. On the basis of the theoretical calculations of molecular modeling, the existence of polar switching behavior in the polar smectic C phase of asymmetric heterodimers was proven to be associated with their configurations with higher dipole moments and suitable bend angles. Furthermore, the lack of polar switching behavior in supramolecular symmetric trimers, which exhibited the regular SmC phase with weak electrical stabilities, was related to their configurations with smaller dipole moments and confirmed by theoretical

  7. Microradiometers Reveal Ocean Health, Climate Change

    NASA Technical Reports Server (NTRS)

    2013-01-01

    When NASA researcher Stanford Hooker is in the field, he pays close attention to color. For Hooker, being in the field means being at sea. On one such research trip to the frigid waters of the Arctic, with a Coast Guard icebreaker looming nearby and the snow-crusted ice shelf a few feet away, Hooker leaned over the edge of his small boat and lowered a tethered device into the bright turquoise water, a new product devised by a NASA partner and enabled by a promising technology for oceanographers and atmospheric scientists alike. Color is a function of light. Pure water is clear, but the variation in color observed during a visit to the beach or a flight along a coastline depends on the water s depth and the constituents in it, how far down the light penetrates and how it is absorbed and scattered by dissolved and suspended material. Hooker cares about ocean color because of what it can reveal about the health of the ocean, and in turn, the health of our planet. "The main thing we are interested in is the productivity of the water," Hooker says. The seawater contains phytoplankton, microscopic plants, which are the food base for the ocean s ecosystems. Changes in the water s properties, whether due to natural seasonal effects or human influence, can lead to problems for delicate ecosystems such as coral reefs. Ocean color can inform researchers about the quantities and distribution of phytoplankton and other materials, providing clues as to how the world ocean is changing. NASA s Coastal Zone Color Scanner, launched in 1978, was the first ocean color instrument flown on a spacecraft. Since then, the Agency s ocean color research capabilities have become increasingly sophisticated with the launch of the SeaWiFS instrument in 1997 and the twin MODIS instruments carried into orbit on NASA s Terra (1999) and Aqua (2002) satellites. The technology provides sweeping, global information on ocean color on a scale unattainable by any other means. One issue that arises from

  8. Passive seismology reveals biannual calving periodicity

    NASA Astrophysics Data System (ADS)

    Bartholomaus, T. C.; Larsen, C. F.; West, M. E.; Oneel, S.

    2013-12-01

    Iceberg calving is a large and variable component of the total mass loss from marine-terminating glaciers worldwide. However, the processes that control the size and variability of calving fluxes are poorly understood. Even more basic descriptions of iceberg calving, such as its seasonality, are uncertain. Here, we present nearly two years of automatically-estimated calving fluxes at Yahtse Glacier, a tidewater glacier whose terminus flows at ~7 km/yr towards the Gulf of Alaska. At the terminus, ice losses to calving and submarine melt total approximately 1.5 km^3/yr. In order to identify temporal variability in this mean rate, we develop a statistical model of calving size based on characteristics of calving-generated icequakes. These characteristics include 4 amplitude-based variables and 5 variables related to the shape of the icequake envelope. We build our model by combining automatically-detected icequakes (O'Neel et al., 2007) located at the terminus of Yahtse Glacier (Jones et al., 2013) with a training set of 1400 icequakes produced by visually-observed calving events (Bartholomaus et al., 2012). In each of the models tested (regression trees, multinomial logistic regression and multiple linear regession), icequake duration emerges as the single best predictor of iceberg size, consistent with past studies (Qamar, 1988; O'Neel et al., 2007). Additional predictors, such as the mean icequake amplitude and the kurtosis of the icequake envelope improve the predictive capability of the model and reduce the mean squared error to well-within the error of the in-person classification. Once validated, we apply our model to ~ 400,000 icequakes produced by calving events at Yahtse Glacier between June 2009 and September 2011. These results reveal fluctuations in calving rate at a range of timescales, including twice per year. We suggest that the roughly 50%, biannual variation in calving rate is the result of the trade-off between two competing processes at the

  9. Frantic activity revealed in dusty stellar factories

    NASA Astrophysics Data System (ADS)

    2009-01-01

    Thanks to the Very Large Telescope's acute and powerful near-infrared eye, astronomers have uncovered a host of new young, massive and dusty stellar nurseries in nearby galaxy NGC 253. The centre of this galaxy appears to harbour a twin of our own Milky Way's supermassive black hole. ESO PR Photo 02a/09 The Spiral Galaxy NGC 253 Astronomers from the Instituto de Astrofísica de Canarias (Spain) used NACO, a sharp-eyed adaptive optics instrument on ESO's Very Large Telescope (VLT), to study the fine detail in NGC 253, one of the brightest and dustiest spiral galaxies in the sky. Adaptive Optics (AO) corrects for the blurring effect introduced by the Earth's atmosphere. This turbulence causes the stars to twinkle in a way that delights poets, but frustrates astronomers, since it smears out the images. With AO in action the telescope can produce images that are as sharp as is theoretically possible, as if the telescope were in space. NACO revealed features in the galaxy that were only 11 light-years across. "Our observations provide us with so much spatially resolved detail that we can, for the first time, compare them with the finest radio maps for this galaxy -- maps that have existed for more than a decade," says Juan Antonio Fernández-Ontiveros, the lead author of the paper reporting the results [1]. Astronomers identified 37 distinct bright regions, a threefold increase on previous results, packed into a tiny region at the core of the galaxy, comprising just one percent of the galaxy's total size. The astronomers combined their NACO images with data from another VLT instrument, VISIR, as well as with images from the NASA/ESA Hubble Space Telescope and radio observations made by the Very Large Array and the Very Large Baseline Interferometer. Combining these observations, taken in different wavelength regimes, provided a clue to the nature of these regions. "We now think that these are probably very active nurseries that contain many stars bursting from their

  10. Shocking Detail of Superstar's Activity Revealed

    NASA Astrophysics Data System (ADS)

    1999-10-01

    NASA's Chandra X-ray Observatory has imaged Eta Carinae and revealed a hot inner core around this mysterious superstar. The new X-ray observation shows three distinct structures: an outer, horseshoe shaped ring about two light years in diameter, a hot inner core about 3 light months in diameter, and a hot central source less than a light month in diameter which may contain the superstar. All three structures are thought to represent shock waves produced by matter rushing away from the superstar at supersonic speeds. The temperature of the shock-heated gas ranges from 60 million degrees Celsius in the central regions to 3 million degrees Celsius on the outer structure. An earlier image of Eta Carinae by the Hubble Space Telescope revealed two spectacular bubbles of gas expanding in opposite directions away from a central bright region at speeds in excess of a million miles per hour. The inner region visible in the Chandra image has never been resolved before, and appears to be associated with a central disk of high velocity gas rushing out at much higher speeds perpendicular to the bipolar optical nebula. "It is not what I expected," said Dr. Fred Seward of the Harvard-Smithsonian Center for Astrophysics. "I expected to see a strong point source with a little diffuse emission cloud around it. Instead, we see just the opposite- a bright cloud of diffuse emission, and much less radiation from the center." "The Chandra image contains some puzzles for existing ideas of how a star can produce such hot and intense X-rays," agreed Prof. Kris Davidson of the University of Minnesota. "In the most popular theory, X-rays are made by colliding gas streams from two stars so close together that they'd look like a point source to us. But what happens to gas streams that escape to farther distances? The extended hot stuff in the middle of the new image gives demanding new conditions for any theory to meet." Eta Carinae is one of the most enigmatic and intriguing objects in our

  11. Chandra Data Reveal Rapidly Whirling Black Holes

    NASA Astrophysics Data System (ADS)

    2008-01-01

    A new study using results from NASA's Chandra X-ray Observatory provides one of the best pieces of evidence yet that many supermassive black holes are spinning extremely rapidly. The whirling of these giant black holes drives powerful jets that pump huge amounts of energy into their environment and affects galaxy growth. A team of scientists compared leading theories of jets produced by rotating supermassive black holes with Chandra data. A sampling of nine giant galaxies that exhibit large disturbances in their gaseous atmospheres showed that the central black holes in these galaxies must be spinning at near their maximum rates. People Who Read This Also Read... NASA’s Swift Satellite Catches First Supernova in The Act of Exploding Black Holes Have Simple Feeding Habits Jet Power and Black Hole Assortment Revealed in New Chandra Image Erratic Black Hole Regulates Itself "We think these monster black holes are spinning close to the limit set by Einstein's theory of relativity, which means that they can drag material around them at close to the speed of light," said Rodrigo Nemmen, a visiting graduate student at Penn State University, and lead author of a paper on the new results presented at American Astronomical Society in Austin, Texas. The research reinforces other, less direct methods previously used which have indicated that some stellar and supermassive black holes are spinning rapidly. According to Einstein's theory, a rapidly spinning black hole makes space itself rotate. This effect, coupled with gas spiraling toward the black hole, can produce a rotating, tightly wound vertical tower of magnetic field that flings a large fraction of the inflowing gas away from the vicinity of the black hole in an energetic, high-speed jet. Computer simulations by other authors have suggested that black holes may acquire their rapid spins when galaxies merge, and through the accretion of gas from their surroundings. "Extremely fast spin might be very common for large

  12. 21 CFR 1.21 - Failure to reveal material facts.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 1 2014-04-01 2014-04-01 false Failure to reveal material facts. 1.21 Section 1... GENERAL ENFORCEMENT REGULATIONS General Labeling Requirements § 1.21 Failure to reveal material facts. (a... to reveal facts that are: (1) Material in light of other representations made or suggested...

  13. 21 CFR 1.21 - Failure to reveal material facts.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 1 2010-04-01 2010-04-01 false Failure to reveal material facts. 1.21 Section 1... GENERAL ENFORCEMENT REGULATIONS General Labeling Requirements § 1.21 Failure to reveal material facts. (a) Labeling of a food, drug, device, or cosmetic shall be deemed to be misleading if it fails to reveal...

  14. 21 CFR 1.21 - Failure to reveal material facts.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 1 2011-04-01 2011-04-01 false Failure to reveal material facts. 1.21 Section 1... GENERAL ENFORCEMENT REGULATIONS General Labeling Requirements § 1.21 Failure to reveal material facts. (a) Labeling of a food, drug, device, or cosmetic shall be deemed to be misleading if it fails to reveal...

  15. The lower atmosphere of Pluto revealed

    NASA Astrophysics Data System (ADS)

    2009-03-01

    ), attached to ESO's Very Large Telescope, have now revealed that the atmosphere as a whole, not just the upper atmosphere, has a mean temperature of minus 180 degrees Celsius, and so it is indeed "much hotter" than the surface. In contrast to the Earth's atmosphere [2], most, if not all, of Pluto's atmosphere is thus undergoing a temperature inversion: the temperature is higher, the higher in the atmosphere you look. The change is about 3 to 15 degrees per kilometre. On Earth, under normal circumstances, the temperature decreases through the atmosphere by about 6 degrees per kilometre. "It is fascinating to think that with CRIRES we are able to precisely measure traces of a gas in an atmosphere 100 000 times more tenuous than the Earth's, on an object five times smaller than our planet and located at the edge of the Solar System," says co-author Hans-Ulrich Käufl. "The combination of CRIRES and the VLT is almost like having an advanced atmospheric research satellite orbiting Pluto." The reason why Pluto's surface is so cold is linked to the existence of Pluto's atmosphere, and is due to the sublimation of the surface ice; much like sweat cools the body as it evaporates from the surface of the skin, this sublimation has a cooling effect on the surface of Pluto. In this respect, Pluto shares some properties with comets, whose coma and tails arise from sublimating ice as they approach the Sun. The CRIRES observations also indicate that methane is the second most common gas in Pluto's atmosphere, representing half a percent of the molecules. "We were able to show that these quantities of methane play a crucial role in the heating processes in the atmosphere and can explain the elevated atmospheric temperature," says Lellouch. Two different models can explain the properties of Pluto's atmosphere. In the first, the astronomers assume that Pluto's surface is covered with a thin layer of methane, which will inhibit the sublimation of the nitrogen frost. The second scenario invokes

  16. Dramatic Outburst Reveals Nearest Black Hole

    NASA Astrophysics Data System (ADS)

    2000-01-01

    Sgr. The radio observations revealed the presence of a jet escaping from the system at mind-boggling speeds. Only three other galactic X-ray stellar systems have been found to eject material at such speeds. They have been dubbed "microquasars" because, on a smaller scale, they resemble quasars, which lie at the hearts of distant galaxies and also spew out high-velocity jets of particles. In galaxy-core quasars, the black holes are millions of times more massive than the Sun; in the more nearby microquasars the black holes are roughly three to twenty times more massive than the Sun. The extremely high velocity of the jets suggests that their origin lies close to the event horizon of a black hole. Microquasar activity is thought to arise when the black hole in the binary system draws material away from its companion star. The material surrounding the black hole forms a rapidly spinning disk called an accretion disk. This disk is heated by friction to millions of degrees, causing it to emit X-rays. As spiralling gas moves into the gravity well of the black hole, it moves faster and faster. Magnetic fields in the disk are believed to expel the charged subatomic particles at speeds close to that of light. As the charged particles interact with the magnetic fields, they emit radio waves. If some of the material escapes by being magnetically expelled into space, the matter may continue moving at the tremendous speed it had attained near the black hole. After their ejection, the jets of particles expand and cool, fading from astronomers' view. V4641 Sgr excites astronomers because it is close and because it acted so differently from other microquasars. In other microquasars, outbursts have dimmed more slowly over weeks or months rather than hours. "There's something fundamentally different about this one; it's more extreme than any other example," Hjellming said. "And because this system happens to be so close to us, `it is very likely that there are more objects like V4641

  17. Effect of Enantiomeric Excess on the Phase Behavior of Antiferroelectric Liquid Crystals

    SciTech Connect

    L Pan; B McCoy; S Wang; Z Liu; S Wang; R Pindak; C Huang

    2011-12-31

    Null transmission ellipsometry and resonant x-ray diffraction are employed to study the effect of enantiomeric excess (EE) on the phase behavior of antiferroelectric liquid crystal 10OTBBB1M7. Phase sequence, layer spacing, and pitch of the helical structures of the smectic-C*{sub {alpha}} and smectic-C* phases are studied as a function of temperature and EE. Upon reducing EE, a liquid-gas-type critical point of the smectic-C*{sub {alpha}} to smectic-C* transition is observed, as well as the disappearance of the smectic-C*{sub d4} and the smectic-C*{sub d3} phases. Results are analyzed in a mean-field model.

  18. What Facial Appearance Reveals Over Time: When Perceived Expressions in Neutral Faces Reveal Stable Emotion Dispositions

    PubMed Central

    Adams, Reginald B.; Garrido, Carlos O.; Albohn, Daniel N.; Hess, Ursula; Kleck, Robert E.

    2016-01-01

    It might seem a reasonable assumption that when we are not actively using our faces to express ourselves (i.e., when we display nonexpressive, or neutral faces), those around us will not be able to read our emotions. Herein, using a variety of expression-related ratings, we examined whether age-related changes in the face can accurately reveal one’s innermost affective dispositions. In each study, we found that expressive ratings of neutral facial displays predicted self-reported positive/negative dispositional affect, but only for elderly women, and only for positive affect. These findings meaningfully replicate and extend earlier work examining age-related emotion cues in the face of elderly women (Malatesta et al., 1987a). We discuss these findings in light of evidence that women are expected to, and do, smile more than men, and that the quality of their smiles predicts their life satisfaction. Although ratings of old male faces did not significantly predict self-reported affective dispositions, the trend was similar to that found for old female faces. A plausible explanation for this gender difference is that in the process of attenuating emotional expressions over their lifetimes, old men reveal less evidence of their total emotional experiences in their faces than do old women. PMID:27445944

  19. What Facial Appearance Reveals Over Time: When Perceived Expressions in Neutral Faces Reveal Stable Emotion Dispositions.

    PubMed

    Adams, Reginald B; Garrido, Carlos O; Albohn, Daniel N; Hess, Ursula; Kleck, Robert E

    2016-01-01

    It might seem a reasonable assumption that when we are not actively using our faces to express ourselves (i.e., when we display nonexpressive, or neutral faces), those around us will not be able to read our emotions. Herein, using a variety of expression-related ratings, we examined whether age-related changes in the face can accurately reveal one's innermost affective dispositions. In each study, we found that expressive ratings of neutral facial displays predicted self-reported positive/negative dispositional affect, but only for elderly women, and only for positive affect. These findings meaningfully replicate and extend earlier work examining age-related emotion cues in the face of elderly women (Malatesta et al., 1987a). We discuss these findings in light of evidence that women are expected to, and do, smile more than men, and that the quality of their smiles predicts their life satisfaction. Although ratings of old male faces did not significantly predict self-reported affective dispositions, the trend was similar to that found for old female faces. A plausible explanation for this gender difference is that in the process of attenuating emotional expressions over their lifetimes, old men reveal less evidence of their total emotional experiences in their faces than do old women. PMID:27445944

  20. Stated and revealed inequality aversion in three subject pools

    PubMed Central

    Beranek, Benjamin; Cubitt, Robin; Gächter, Simon

    2016-01-01

    This paper reports data from three subject pools (n=717 subjects) using techniques based on those of Loewenstein, et al. (1989) and Blanco, et al. (2011) to obtain parameters, respectively, of stated and revealed inequality aversion. We provide a replication opportunity for those papers, with two innovations: (i) a design which allows stated and revealed preferences to be compared at the individual level; (ii) assessment of robustness of findings across subjects from a UK university, a Turkish university and Amazon Mechanical Turk. Our findings on stated aversion to inequality are qualitatively similar to those of Loewenstein, et al. in each of our subject pools, whereas there are notable differences between some of our findings on revealed preference and those of Blanco, et al. We find that revealed advantageous inequality aversion is often stronger than revealed dis-advantageous inequality aversion. In most subject pools, we find some (weak) correlation between corresponding parameters of stated and revealed inequality aversion. PMID:27069847

  1. Bent core liquid crystal elastomers

    SciTech Connect

    Verduzco, R.; DiMasi, E.; Luchette, P.; Ho Hong, S.; Harden, J.; Palffy-Muhoray, P.; Kilbey II, S.M.; Sprunt, S.; Gleeson, G.T. Jakli, A.

    2010-07-28

    Liquid crystal (LC) elastomers with bent-core side-groups incorporate the properties of bent-core liquid crystals in a flexible and self-supporting polymer network. Bent-core liquid crystal elastomers (BCEs) with uniform alignment were prepared by attaching a reactive bent-core LC to poly(hydrogenmethylsiloxane) and crosslinking with a divinyl crosslinker. Phase behavior studies indicate a nematic phase over a wide temperature range that approaches room temperature, and thermoelastic measurements show that these BCEs can reversibly change their length by more than a factor of two upon heating and cooling. Small-angle X-ray scattering studies reveal multiple, broad low-angle peaks consistent with short-range smectic C order of the bent-core side groups. A comparison of these patterns with predictions of a Landau model for short-range smectic C order shows that the length scale for smectic ordering in BCEs is similar to that seen in pure bent-core LCs. The combination of rubber elasticity and smectic ordering of the bent-core side groups suggests that BCEs may be promising materials for sensing, actuating, and other advanced applications.

  2. Resonant X-Ray Diffraction Study of an Unusually Large Phase Coexistance in Smectic Liquid-Crystal Films

    SciTech Connect

    Pan L.; Pindak R.; Barois, P.; Liu, Z.Q.; McCoy, B.K. & Hyang, C.C.

    2012-01-19

    The recent discovery of the new smectic-C{sub d6}* (SmC{sub d6}*) phase [S. Wang et al. Phys. Rev. Lett. 104 027801 (2010)] also revealed the existence of a noisy region in the temperature window between the SmC{sub d6}* phase and the smectic-C{sub d4}* (SmC{sub d4}*) phase. Characterized by multiple resonant peaks spanning a wide region in Q{sub Z}, the corresponding structure of this temperature window has been a mystery. In this Letter, through a careful resonant x-ray diffraction study and simulations of the diffraction spectra, we show that this region is in fact an unusually large coexistence region of the SmC{sub d6}* phase and the SmC{sub d4}* phase. The structure of the noisy region is found to be a heterogeneous mixture of local SmC{sub d6}* and SmC{sub d4}* orders on the sub-{micro}m scale.

  3. 21 CFR 1.21 - Failure to reveal material facts.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 1 2013-04-01 2013-04-01 false Failure to reveal material facts. 1.21 Section 1.21 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL... to reveal facts that are: (1) Material in light of other representations made or suggested...

  4. 14. DETAIL VIEW, FLUTED PILASTER AND PANELLED REVEAL IN DOORWAY ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    14. DETAIL VIEW, FLUTED PILASTER AND PANELLED REVEAL IN DOORWAY BETWEEN VESTIBULE AND STAIRHALL (NOTE WOOD GRAINING), WITH SCALE - Bowieville, 522 Church Road South, Leeland, Prince George's County, MD

  5. General view of the archaeological site showing excavation and revealing ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    General view of the archaeological site showing excavation and revealing the steps leading down into the eighteenth-century burial vault - Harry Buck House, North of Main Street (14800 Governor Oden Bowie Drive), Upper Marlboro, Prince George's County, MD

  6. [An original revealing mode of sarcoidosis: Sweet's syndrome].

    PubMed

    Bricha, Myriem; Sqalli, Fatimazzahra; Hammi, Sanae; Bourkadi, Jamal Eddine

    2016-01-01

    Sweet's syndrome is a neutrophilic dermatosis which usually presents as an idiopathic disorder. The combination of Sweet's syndrome and sarcoidosis is rare. We report the clinical case of a Sweet's syndrome revealing sarcoidosis. PMID:27279949

  7. Everett Weinreb, Photographer, April 1989 FOUNDATION DETAIL REVEALED AS RESULT ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Everett Weinreb, Photographer, April 1989 FOUNDATION DETAIL REVEALED AS RESULT OF HOUSE DEMOLITION - Irvine Ranch Agricultural Headquarters, Boyd Tenant House, Southeast of Intersection of San Diego & Santa Ana Freeways, Irvine, Orange County, CA

  8. Direct sequencing of the human microbiome readily reveals community differences

    PubMed Central

    2010-01-01

    Culture-independent studies of human microbiota by direct genomic sequencing reveal quite distinct differences among communities, indicating that improved sequencing capacity can be most wisely utilized to study more samples, rather than more sequences per sample. PMID:20441597

  9. Revealing ecological networks using Bayesian network inference algorithms.

    PubMed

    Milns, Isobel; Beale, Colin M; Smith, V Anne

    2010-07-01

    Understanding functional relationships within ecological networks can help reveal keys to ecosystem stability or fragility. Revealing these relationships is complicated by the difficulties of isolating variables or performing experimental manipulations within a natural ecosystem, and thus inferences are often made by matching models to observational data. Such models, however, require assumptions-or detailed measurements-of parameters such as birth and death rate, encounter frequency, territorial exclusion, and predation success. Here, we evaluate the use of a Bayesian network inference algorithm, which can reveal ecological networks based upon species and habitat abundance alone. We test the algorithm's performance and applicability on observational data of avian communities and habitat in the Peak District National Park, United Kingdom. The resulting networks correctly reveal known relationships among habitat types and known interspecific relationships. In addition, the networks produced novel insights into ecosystem structure and identified key species with high connectivity. Thus, Bayesian networks show potential for becoming a valuable tool in ecosystem analysis. PMID:20715607

  10. Revealing the molecular signatures of host-pathogen interactions

    PubMed Central

    2011-01-01

    Advances in sequencing technology and genome-wide association studies are now revealing the complex interactions between hosts and pathogen through genomic variation signatures, which arise from evolutionary co-existence. PMID:22011345

  11. Genome-Wide Scan Reveals Mutation Associated with Melanoma

    MedlinePlus

    ... 1999 Spotlight on Research 2012 July 2012 (historical) Genome-Wide Scan Reveals Mutation Associated with Melanoma A ... out to see if a technology called whole genome sequencing would help them find other genetic risk ...

  12. Revealing of HII-regions in Galaxies with Panoramic Spectroscopy

    NASA Astrophysics Data System (ADS)

    Hakopian, S. A.; Balayan, S. K.

    2016-06-01

    Observations intended to investigation and revealing of nodes of processes of nuclear and starforming activity in galaxies were performed via panoramic spectroscopy. Data obtained on Mrk 1050 revealed evidence of starforming activity also outside the central engine of high surface brightness. Two small HII-regions, being likely a part of the chain, are located in the part of the spiral branch coming from the nucleus part.

  13. On the correlation between the structure of lyotropic carriers and the delivery profiles of two common NSAIDs.

    PubMed

    Cohen-Avrahami, Marganit; Shames, Alexander I; Ottaviani, M Francesca; Aserin, Abraham; Garti, Nissim

    2014-10-01

    Two non-steroidal anti-inflammatory drugs (NSAIDs), sodium diclofenac (Na-DFC) and celecoxib (CLXB) were solubilized within cubic and lamellar mesophases as carriers for transdermal drug delivery. SD-NMR, SAXS, ATR-FTIR, and EPR measurements were performed to examine the systems' characteristics and the interactions between the drugs and their hosting mesophases. The amphiphilic drug Na-DFC was found to incorporate at the interfaces of the cubic and lamellar mesophases and thus to act as a cosurfactant and a "structure stabilizer". It increased the order degree and the interactions between the GMO molecules and led the systems toward denser packing. CLXB exhibits an opposite effect on the mesophases. Its solubilization within both systems is accompanied with significant channel swelling and decrease in the order degree. The hydrophobic, rigid and bulky CLXB behaves as a "structure breaker", incorporated between the GMO tails, disturbing the mesophase packing and enhancing the repulsion at the tails region, limiting their close binding. Release experiments from Franz cells revealed that Na-DFC release is dependent on the quantity of water within the hosting mesophase as the water-rich formulation exhibits 1.5-fold enhancement in the release of the drug, compared to the lamellar phase. In contrast, CLXB release was not influenced by the water quantity, hinting that the release mechanisms of the drugs are different while Na-DFC diffuses from the water channels to the external phase, CLXB diffusion occurs through the continuous lipophilic region. The difference in the solubilization sites and interactions of each drug with the mesophases affect their release profiles and determine the preferred formulations for each drug's delivery vehicle. PMID:25048360

  14. Camelid genomes reveal evolution and adaptation to desert environments.

    PubMed

    Wu, Huiguang; Guang, Xuanmin; Al-Fageeh, Mohamed B; Cao, Junwei; Pan, Shengkai; Zhou, Huanmin; Zhang, Li; Abutarboush, Mohammed H; Xing, Yanping; Xie, Zhiyuan; Alshanqeeti, Ali S; Zhang, Yanru; Yao, Qiulin; Al-Shomrani, Badr M; Zhang, Dong; Li, Jiang; Manee, Manee M; Yang, Zili; Yang, Linfeng; Liu, Yiyi; Zhang, Jilin; Altammami, Musaad A; Wang, Shenyuan; Yu, Lili; Zhang, Wenbin; Liu, Sanyang; Ba, La; Liu, Chunxia; Yang, Xukui; Meng, Fanhua; Wang, Shaowei; Li, Lu; Li, Erli; Li, Xueqiong; Wu, Kaifeng; Zhang, Shu; Wang, Junyi; Yin, Ye; Yang, Huanming; Al-Swailem, Abdulaziz M; Wang, Jun

    2014-01-01

    Bactrian camel (Camelus bactrianus), dromedary (Camelus dromedarius) and alpaca (Vicugna pacos) are economically important livestock. Although the Bactrian camel and dromedary are large, typically arid-desert-adapted mammals, alpacas are adapted to plateaus. Here we present high-quality genome sequences of these three species. Our analysis reveals the demographic history of these species since the Tortonian Stage of the Miocene and uncovers a striking correlation between large fluctuations in population size and geological time boundaries. Comparative genomic analysis reveals complex features related to desert adaptations, including fat and water metabolism, stress responses to heat, aridity, intense ultraviolet radiation and choking dust. Transcriptomic analysis of Bactrian camels further reveals unique osmoregulation, osmoprotection and compensatory mechanisms for water reservation underpinned by high blood glucose levels. We hypothesize that these physiological mechanisms represent kidney evolutionary adaptations to the desert environment. This study advances our understanding of camelid evolution and the adaptation of camels to arid-desert environments. PMID:25333821

  15. [Ovarian torsion revealing an ovarian cavernous hemangioma in a child].

    PubMed

    M'pemba Loufoua-Lemay, A-B; Peko, J-F; Mbongo, J-A; Mokoko, J-C; Nzingoula, S

    2003-11-01

    The authors report one case of cavernous hemangioma of the left ovary, which was revealed by ovarian torsion. Such benign tumors of the blood vessels are rare in ovaries during childhood. This hemangioma was observed in a 13-year-old patient, who presented with abdominal and pelvic pain and vomiting. The pelvic mass was noted and sonography revealed a cystic tumor. An annexectomia was realized. Histology showed narcotized ovary cells, with an increased number of vascular channels composed of thin walled vessels, whose wall consisted of an endothelium. This aspect evoked a cavernous hemangioma of the ovary. PMID:14613693

  16. Perspective view. Fivestory reinforced concrete factory building reveals the structural ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Perspective view. Five-story reinforced concrete factory building reveals the structural frame on the exterior of the facade. Twelve bay facade facing onto Clay Avenue (north facade) has first floor openings bricked up. Mix of typical factory windows and glass block windows fill the majority of the openings on the rest of building - Russell Industrial Center, 1600 Clay Avenue, Detroit, MI

  17. Experimentally implementable criteria revealing substructures of genuine multipartite entanglement

    SciTech Connect

    Huber, Marcus; Schimpf, Hans; Gabriel, Andreas; Spengler, Christoph; Bruss, Dagmar; Hiesmayr, Beatrix C.

    2011-02-15

    We present a general framework that reveals substructures of genuine multipartite entanglement. Via simple inequalities it is possible to discriminate different sets of multipartite qubit states. These inequalities are beneficial regarding experimental examinations as only local measurements are required. Furthermore, the number of observables scales favorably with system size. In exemplary cases we demonstrate the noise resistance and discuss implementations.

  18. In Reporting Lobbying Expenses, Some Institutions Do Not Reveal All.

    ERIC Educational Resources Information Center

    Lederman, Douglas

    1998-01-01

    On a federal tax form, only 75 of 475 colleges and universities surveyed reported that they had spent money on lobbying, defined as direct contacts with legislators or executive-branch officials about specific bills. Guidelines concerning reporting are unclear and confusing, and some institutions reveal as little as possible. Data on 78…

  19. Adaptation to High Ethanol Reveals Complex Evolutionary Pathways.

    PubMed

    Voordeckers, Karin; Kominek, Jacek; Das, Anupam; Espinosa-Cantú, Adriana; De Maeyer, Dries; Arslan, Ahmed; Van Pee, Michiel; van der Zande, Elisa; Meert, Wim; Yang, Yudi; Zhu, Bo; Marchal, Kathleen; DeLuna, Alexander; Van Noort, Vera; Jelier, Rob; Verstrepen, Kevin J

    2015-11-01

    Tolerance to high levels of ethanol is an ecologically and industrially relevant phenotype of microbes, but the molecular mechanisms underlying this complex trait remain largely unknown. Here, we use long-term experimental evolution of isogenic yeast populations of different initial ploidy to study adaptation to increasing levels of ethanol. Whole-genome sequencing of more than 30 evolved populations and over 100 adapted clones isolated throughout this two-year evolution experiment revealed how a complex interplay of de novo single nucleotide mutations, copy number variation, ploidy changes, mutator phenotypes, and clonal interference led to a significant increase in ethanol tolerance. Although the specific mutations differ between different evolved lineages, application of a novel computational pipeline, PheNetic, revealed that many mutations target functional modules involved in stress response, cell cycle regulation, DNA repair and respiration. Measuring the fitness effects of selected mutations introduced in non-evolved ethanol-sensitive cells revealed several adaptive mutations that had previously not been implicated in ethanol tolerance, including mutations in PRT1, VPS70 and MEX67. Interestingly, variation in VPS70 was recently identified as a QTL for ethanol tolerance in an industrial bio-ethanol strain. Taken together, our results show how, in contrast to adaptation to some other stresses, adaptation to a continuous complex and severe stress involves interplay of different evolutionary mechanisms. In addition, our study reveals functional modules involved in ethanol resistance and identifies several mutations that could help to improve the ethanol tolerance of industrial yeasts. PMID:26545090

  20. The Basics of How to Reveal Epilepsy--Part Two

    ERIC Educational Resources Information Center

    Mittan, Robert J.

    2009-01-01

    In the April 2009 edition of "Exceptional Parent," Part One of this series explored why, for their own emotional well-being, it is so important for parents to tell others about their or their child's epilepsy. This month's installment will discuss the basics of how to reveal epilepsy to others, including some additional advantages one receives in…

  1. Carbohydrate active enzymes revealed in Coptotermes formosanus transcriptome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A normalized cDNA library of Coptotermes formosanus was constructed using mixed RNA isolated from workers, soldiers, nymphs and alates of both sexes. Sequencing of this library generated 131,637 EST and 25,939 unigenes were assembled. Carbohydrate active enzymes (CAZymes) revealed in this library we...

  2. [Ulcerated duodenitis revealing Henoch-Schönlein purpura].

    PubMed

    Marting, A; Defrance, P; Wain, E; Van Severen, M; Deflandre, J

    2015-01-01

    Inflammation and duodenal ulcers can meet many etiologies. We report the case of a young adult with an ulcerated duodenitis revealing Henoch-Schönlein purpura. The abdominal symptoms preceded the emergence of the classical cutaneous signs of the disease. PMID:26376566

  3. Adaptation to High Ethanol Reveals Complex Evolutionary Pathways

    PubMed Central

    Das, Anupam; Espinosa-Cantú, Adriana; De Maeyer, Dries; Arslan, Ahmed; Van Pee, Michiel; van der Zande, Elisa; Meert, Wim; Yang, Yudi; Zhu, Bo; Marchal, Kathleen; DeLuna, Alexander; Van Noort, Vera; Jelier, Rob; Verstrepen, Kevin J.

    2015-01-01

    Tolerance to high levels of ethanol is an ecologically and industrially relevant phenotype of microbes, but the molecular mechanisms underlying this complex trait remain largely unknown. Here, we use long-term experimental evolution of isogenic yeast populations of different initial ploidy to study adaptation to increasing levels of ethanol. Whole-genome sequencing of more than 30 evolved populations and over 100 adapted clones isolated throughout this two-year evolution experiment revealed how a complex interplay of de novo single nucleotide mutations, copy number variation, ploidy changes, mutator phenotypes, and clonal interference led to a significant increase in ethanol tolerance. Although the specific mutations differ between different evolved lineages, application of a novel computational pipeline, PheNetic, revealed that many mutations target functional modules involved in stress response, cell cycle regulation, DNA repair and respiration. Measuring the fitness effects of selected mutations introduced in non-evolved ethanol-sensitive cells revealed several adaptive mutations that had previously not been implicated in ethanol tolerance, including mutations in PRT1, VPS70 and MEX67. Interestingly, variation in VPS70 was recently identified as a QTL for ethanol tolerance in an industrial bio-ethanol strain. Taken together, our results show how, in contrast to adaptation to some other stresses, adaptation to a continuous complex and severe stress involves interplay of different evolutionary mechanisms. In addition, our study reveals functional modules involved in ethanol resistance and identifies several mutations that could help to improve the ethanol tolerance of industrial yeasts. PMID:26545090

  4. When Values and Behaviors Conflict: Immigrant BSW Students' Experiences Revealed

    ERIC Educational Resources Information Center

    Calderwood, Kimberly; Harper, Kim; Ball, Kellie; Liang, David

    2009-01-01

    This qualitative study reveals the discomfort seven immigrant bachelor of social work students reported experiencing when the behaviors expected of them as Canadian social workers conflicted with their fundamental family values. Behaviorally, participants had assimilated to Canadian and to social work cultures; however, the values they held from…

  5. Detail of south granite pier revealing riveted truss ends and ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Detail of south granite pier revealing riveted truss ends and iron footing plates on top of granite cap stones. View north - New York, New Haven & Hartford Railroad, Fort Point Channel Rolling Lift Bridge, Spanning Fort Point Channel, Boston, Suffolk County, MA

  6. Chemical milling solution reveals stress corrosion cracks in titanium alloy

    NASA Technical Reports Server (NTRS)

    Braski, D. N.

    1967-01-01

    Solution of hydrogen flouride, hydrogen peroxide, and water reveals hot salt stress corrosion cracks in various titanium alloys. After the surface is rinsed in water, dried, and swabbed with the solution, it can be observed by the naked eye or at low magnification.

  7. 24. Demolitin of Pier G reveals the center bays at ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    24. Demolitin of Pier G reveals the center bays at the track well in transverse section. Note structural system of first, second, and third floors, as well as the monitor roof. - Lehigh Valley Railroad, Pier G, Jersey City, Hudson County, NJ

  8. Revealing Evidence of Spin in Galactic Black Holes

    NASA Astrophysics Data System (ADS)

    Miller, J. M.; Fabian, A. C.; Reynolds, C. S.; Nowak, M.; Wijnands, R.; Homan, J.; Belloni, T.; van der Klis, M.; Lewin, W. H. G.

    2002-12-01

    Our observations of Galactic black holes with Chandra and XMM-Newton have recently revealed broad, skewed Fe K-alpha emission lines similar to those seen in some AGN. If such lines are produced near the inner edge of the accretion disk, they can serve as an excellent spin diagnostic. Our analysis of the XMM-Newton spectrum of XTE J1650-500 reveals a strong, skewed Fe K-alpha emission line that requires near-maximal spin; with RXTE, we have discovered a 250 Hz QPO in this source which may also be produced near to the black hole. Although many Galactic black holes have been studied extensively, it is extremely rare that spectroscopic and timing studies both reveal features plausibly associated with the inner accretion disk. We will present the results of our XMM-Newton, Chandra, and RXTE observations of XTE J1650-500, as well as the results of our Chandra observations of Cygnus X-1 and preliminary results from our observations of GX 339-4 with XMM-Newton. We will discuss these results within the context of the relativistic Fe K lines reported by our group and others, and comment on the prospects for revealing evidence of spin in future observations. (JMM acknowledges support from the NSF through the Astronomy and Astrophysics Fellowship program.)

  9. Nilaja Sun's "No Child"...: Revealing Teaching and Learning through Theater

    ERIC Educational Resources Information Center

    Hetland, Lois

    2009-01-01

    This article presents an analysis of Nilaja Sun's one-woman play, "No Child" . . ., that applies the Studio Habits of Mind framework to reveal essential features of great teaching artistry and great teaching. The play conveys much about twenty-first century schools and the policies that control them; about respect, equity, justice, and the lack of…

  10. Natural Disasters that Reveal Cracks in Our Social Foundation

    ERIC Educational Resources Information Center

    Langer, Nieli

    2004-01-01

    The recent deaths of more than 13,000 French elderly in the European heat wave of 2003 revealed cracks in the social foundation of urban communities, here and abroad. The breakdown occurred in community services, neighborhood networks, and governmental agencies that were responsible for warning of impending dangers to at-risk elderly. This paper…

  11. Mesophase structure and behaviour in bulk and restricted geometry of a dimeric compound exhibiting a nematic-nematic transition.

    PubMed

    Sebastián, N; Tamba, M G; Stannarius, R; de la Fuente, M R; Salamonczyk, M; Cukrov, G; Gleeson, J; Sprunt, S; Jákli, A; Welch, C; Ahmed, Z; Mehl, G H; Eremin, A

    2016-07-28

    We present structural studies of a dimeric compound composed of a central heptyl spacer linking two mesogens consisting of terphenyl units at which two adjacent fluoro groups are attached to each central ring. The terminal rings are linked to pentyl chains as terminal groups. The material exhibits a nematic-nematic transition and a low temperature modulated phase. The higher temperature nematic phase was found to exhibit an anomaly of the bend elastic constant similar to that of the dimers with N-Ntb phase sequence, and the physical properties of the low-temperature nematic phase are similar to those of the known Ntb materials. The structure of the low-temperature modulated smectic/columnar phase is described together with its ability to form freely suspended films and fibres. The relation of the modulated structure to the fibre formation and to the appearance of the labyrinthine instability in freely-suspended films is discussed. PMID:27375037

  12. Designing the topology of ion nano-channels in the mesophases of amphiphilic wedge-shaped molecules.

    PubMed

    Grafskaia, K N; Rueda, J J Hernandz; Zhu, X; Nekipelov, V M; Anokhin, D V; Moeller, M; Ivanov, D A

    2015-11-11

    The wedge-shaped amphiphiles bearing sulfonate groups at the tip of the wedge are prone to form ion nano-channels upon exposure to a humid atmosphere. During swelling, water molecules preferentially accumulate in polar regions of the system resulting in the formation of a lyotropic phase. In this work, the details of the structure formation processes occurring upon swelling in water vapour, including determination of the size and topology of the ion nano-channels, are explored. The electron density profiles across the channel are obtained from the fits of the X-ray scattering data with two- and three-phase structural models the applicability of which is critically analysed. The results show that the ion channel size correlates not only with water uptake but also with the molecular architecture such as the structure of the rigid molecular fragment bearing a polar group. These findings can help optimising the ion transport for development of ion-selective membranes. PMID:26523454

  13. Thermal optical non-linearity of nematic mesophase enhanced by gold nanoparticles - an experimental and numerical investigation.

    PubMed

    Kurochkin, O; Murugesan, Y K; Bennett, T P; D'Alessandro, G; Reznikov, Y; Tang, B J; Mehl, G H; Kaczmarek, M

    2016-04-20

    In this work the mechanisms leading to the enhancement of optical nonlinearity of nematic liquid crystalline material through localized heating by doping the liquid crystals (LCs) with gold nanoparticles (GNPs) are investigated. We present some experimental and theoretical results on the effect of voltage and nanoparticle concentration on the nonlinear response of GNP-LC suspensions. The optical nonlinearity of these systems is characterized by diffraction measurements and the second order nonlinear refractive index, n2, is used to compare systems with different configurations and operating conditions. A theoretical model based on heat diffusion that takes into account the intensity and finite size of the incident beam, the nanoparticle concentration dependent absorbance of GNP doped LC systems and the presence of bounding substrates is developed and validated. We use the model to discuss the possibilities of further enhancing the optical nonlinearity. PMID:27063912

  14. Molecular and crystal structures of p-heptyloxyphenyl p-hexyloxybenzoate and p-butyloxyphenyl p-heptyloxybenzoate: Mesophase design

    SciTech Connect

    Kuz'mina, L. G. Gunina, M. A.; Churakov, A. V.; Pestov, S. M.

    2013-03-15

    Two aromatic esters with the formulas C{sub 6}H{sub 13}-O-C{sub 6}H{sub 4}-C(O)O-C{sub 6}H{sub 4}-O-C{sub 7}H{sub 15} (1) and C{sub 7}H{sub 15}-O-C{sub 6}H{sub 4}-C(O)O-C{sub 6}H{sub 4}-O-C{sub 4}H{sub 9} (2) belonging to nematic liquid-crystal compounds were studied by X-ray diffraction. Compound 1 crystallizes in two modifications: monoclinic (1-m) and triclinic (1-tr). The crystal packing of 1 and 2 is built from alternating loosely packed aliphatic regions and closely packed aromatic regions. In crystal structures 1-m and 2, the aromatic regions are linked into chains by hydrogen bonds with the participation of the carbonyl oxygen atom of the ester group and the C-H fragment of the benzene ring, but these hydrogen bonds in 1-m are much weaker than in 2. In 1-m there are {pi}-stacking interactions between the molecules, resulting in the formation of centrosymmetric dimers with an interplanar distance of 3.45 A. In 1-tr, the aromatic fragments form a herringbone packing motif favorable for a two-dimensional network of directional C-H...{pi}-system interactions.

  15. Direct visualization reveals kinetics of meiotic chromosome synapsis

    SciTech Connect

    Rog, Ofer; Dernburg, Abby  F.

    2015-03-17

    The synaptonemal complex (SC) is a conserved protein complex that stabilizes interactions along homologous chromosomes (homologs) during meiosis. The SC regulates genetic exchanges between homologs, thereby enabling reductional division and the production of haploid gametes. Here, we directly observe SC assembly (synapsis) by optimizing methods for long-term fluorescence recording in C. elegans. We report that synapsis initiates independently on each chromosome pair at or near pairing centers—specialized regions required for homolog associations. Once initiated, the SC extends rapidly and mostly irreversibly to chromosome ends. Quantitation of SC initiation frequencies and extension rates reveals that initiation is a rate-limiting step in homolog interactions. Eliminating the dynein-driven chromosome movements that accompany synapsis severely retards SC extension, revealing a new role for these conserved motions. This work provides the first opportunity to directly observe and quantify key aspects of meiotic chromosome interactions and will enable future in vivo analysis of germline processes.

  16. Ascites and other incidental findings revealing undiagnosed systemic rheumatoid arthritis.

    PubMed

    Szeto, Matthew Chak Hin; Disney, Benjamin; Perkins, Philip; Wood, Gordon

    2015-01-01

    We describe a case of a 43-year-old man presenting to the gastroenterology outpatient department with exudative ascites. Mediastinal lymphadenopathy, pericardial effusion and pleural effusion were detected on further imaging. Further clinical examination revealed subcutaneous nodules on the left arm, which were confirmed to be rheumatoid nodules on histology. Inflammatory markers were elevated with positive serology for rheumatoid factor and anticyclic citrullinated protein antibody. Our investigations excluded tuberculosis, pancreatitis and malignancy in the patient. Following review by a rheumatologist, a diagnosis of systemic rheumatoid arthritis (RA) was made. Pleuritis and pericarditis are well recognised as extra-articular manifestation of RA. Ascites, however, is rarely recognised as a manifestation of RA. Our literature search revealed two other cases of ascites due to RA disease activity, and both patients had long-standing known RA. This case adds to the discussion on whether ascites and peritonitis should be classified as extra-articular manifestations of RA. PMID:26055583

  17. Stable Chromosome Condensation Revealed by Chromosome Conformation Capture.

    PubMed

    Eagen, Kyle P; Hartl, Tom A; Kornberg, Roger D

    2015-11-01

    Chemical cross-linking and DNA sequencing have revealed regions of intra-chromosomal interaction, referred to as topologically associating domains (TADs), interspersed with regions of little or no interaction, in interphase nuclei. We find that TADs and the regions between them correspond with the bands and interbands of polytene chromosomes of Drosophila. We further establish the conservation of TADs between polytene and diploid cells of Drosophila. From direct measurements on light micrographs of polytene chromosomes, we then deduce the states of chromatin folding in the diploid cell nucleus. Two states of folding, fully extended fibers containing regulatory regions and promoters, and fibers condensed up to 10-fold containing coding regions of active genes, constitute the euchromatin of the nuclear interior. Chromatin fibers condensed up to 30-fold, containing coding regions of inactive genes, represent the heterochromatin of the nuclear periphery. A convergence of molecular analysis with direct observation thus reveals the architecture of interphase chromosomes. PMID:26544940

  18. Benign Cystic Peritoneal Mesothelioma Revealed by Small Bowel Obstruction.

    PubMed

    Bray Madoué, Kaimba; Boniface, Moifo; Annick Laure, Edzimbi; Pierre, Herve

    2016-01-01

    Benign cystic peritoneal mesothelioma is a rare tumor which frequently occurs in women of reproductive age. Abdominal pain associated with pelvic or abdominal mass is the common clinical presentation. We report the case of a 22-year-old woman with a pathological proved benign cystic mesothelioma of the peritoneum revealed by a small bowel obstruction and a painful left-sided pelvic mass with signs of psoitis. Contrast enhanced abdominal CT-scan demonstrated a large pelvic cystic mass with mass effect on rectosigmoid and pelvic organs. The patient underwent surgical removal of the tumor. Pathological examination revealed the diagnosis of benign cystic mesothelioma of the peritoneum. The outcome was excellent with a 12-month recoil. PMID:27066288

  19. Albemarle–Pamlico Sounds revealed and stated preference data

    PubMed Central

    Whitehead, John C.

    2015-01-01

    In this article we describe the contingent valuation and behavior methods scenario developed in the 1995 Albemarle–Pamlico Sounds Survey. The survey elicits revealed and stated preference recreation behavior data which are used to estimate the value of water quality improvements [4,8]. The survey elicits willingness to pay data which are used to conduct a split-sample scope test [7]. The data are used to jointly estimate revealed and stated preference recreation and willingness to pay data [2,6]. The data has been, and can continue to be, used to investigate econometric specification [3], bid design and other nonmarket valuation issues. The data have been used as illustrations and examples in three books that develop nonmarket valuation methods [1,5,9]. Data are supplied with this article. PMID:26217724

  20. [Deep dorsal penile vein thrombosis revealing Behcet's disease].

    PubMed

    Beddouche, Ali; Ouaziz, Hicham; Zougaghi, Sinane; Alaoui, Abdelilah; Dergamoun, Hamza; El Sayegh, Hachem; Iken, Ali; Benslimane, Lounis; Nouini, Yassine

    2016-01-01

    Deep dorsal penile vein thrombosis (DDPVT)is a rare and little known urologic emergency. It requires an early etiological and symptomatic approach to preserve erectile function and prevent recurrences. This study reports a case of dorsal penile vein thrombosis revealed by spontaneous priapism that didn't resolve adequately and confirmed by penile Doppler ultrasound. After management of priapism and DDPVT, the etiological investigation revealed Behcet's disease whose diagnosis was based on the association of a major criteria, such as oral aphthous ulcers with 3 minor criteria such as: genital aphthous ulcers, ocular involvement, and a positive skin pathergy test within 24h. The patient underwent etiological treatment with good clinical evolution and preservation of erectile function. PMID:27583081

  1. Benign Cystic Peritoneal Mesothelioma Revealed by Small Bowel Obstruction

    PubMed Central

    Bray Madoué, Kaimba; Boniface, Moifo; Annick Laure, Edzimbi; Pierre, Herve

    2016-01-01

    Benign cystic peritoneal mesothelioma is a rare tumor which frequently occurs in women of reproductive age. Abdominal pain associated with pelvic or abdominal mass is the common clinical presentation. We report the case of a 22-year-old woman with a pathological proved benign cystic mesothelioma of the peritoneum revealed by a small bowel obstruction and a painful left-sided pelvic mass with signs of psoitis. Contrast enhanced abdominal CT-scan demonstrated a large pelvic cystic mass with mass effect on rectosigmoid and pelvic organs. The patient underwent surgical removal of the tumor. Pathological examination revealed the diagnosis of benign cystic mesothelioma of the peritoneum. The outcome was excellent with a 12-month recoil. PMID:27066288

  2. [Massive bilateral subconjunctival hemorrhage revealing acute lymphoblastic leukemia].

    PubMed

    Taamallah-Malek, I; Chebbi, A; Bouladi, M; Nacef, L; Bouguila, H; Ayed, S

    2013-03-01

    We report the case of 20-year-old patient who presented in emergency with bilateral massive, spontaneous subconjunctival hemorrhage. Clinical findings suggested a blood dyscrasia, which was confirmed by blood cell count. The patient was urgently referred to hematology where the diagnosis of acute lymphoblastic leukemia was made. This case highlights the importance of working up any unusual subconjunctival hemorrhage, as it may reveal, in certain cases, a severe life-threatening disease. PMID:23122838

  3. Molecular Markers Reveal Exclusively Clonal Reproduction in Trichophyton rubrum

    PubMed Central

    Gräser, Y.; Kühnisch, J.; Presber, W.

    1999-01-01

    Genotypic variability among 96 Trichophyton rubrum strains which displayed different colony morphologies and were collected from four continents was investigated. Twelve markers representing 57 loci were analyzed by PCR fingerprinting, amplified fragment length polymorphism, and random amplified monomorphic DNA markers. Interestingly, none of the methods used revealed any DNA polymorphism, indicating a strictly clonal mode of reproduction and a strong adaptation to human skin. PMID:10523582

  4. Transient light-induced intracellular oxidation revealed by redox biosensor

    SciTech Connect

    Kolossov, Vladimir L.; Beaudoin, Jessica N.; Hanafin, William P.; DiLiberto, Stephen J.; Kenis, Paul J.A.; Rex Gaskins, H.

    2013-10-04

    Highlights: •Time-resolved live cell imaging revealed light-induced oxidation. •Only the roGFP probe fused with glutaredoxin reveals photooxidation. •The transient oxidation is rapidly reduced by the cytosolic antioxidant system. •Intracellular photooxidation is media-dependent. •Oxidation is triggered exclusively by exposure to short wavelength excitation. -- Abstract: We have implemented a ratiometric, genetically encoded redox-sensitive green fluorescent protein fused to human glutaredoxin (Grx1-roGFP2) to monitor real time intracellular glutathione redox potentials of mammalian cells. This probe enabled detection of media-dependent oxidation of the cytosol triggered by short wavelength excitation. The transient nature of light-induced oxidation was revealed by time-lapse live cell imaging when time intervals of less than 30 s were implemented. In contrast, transient ROS generation was not observed with the parental roGFP2 probe without Grx1, which exhibits slower thiol-disulfide exchange. These data demonstrate that the enhanced sensitivity of the Grx1-roGFP2 fusion protein enables the detection of short-lived ROS in living cells. The superior sensitivity of Grx1-roGFP2, however, also enhances responsiveness to environmental cues introducing a greater likelihood of false positive results during image acquisition.

  5. Using metabarcoding to reveal and quantify plant-pollinator interactions.

    PubMed

    Pornon, André; Escaravage, Nathalie; Burrus, Monique; Holota, Hélène; Khimoun, Aurélie; Mariette, Jérome; Pellizzari, Charlène; Iribar, Amaia; Etienne, Roselyne; Taberlet, Pierre; Vidal, Marie; Winterton, Peter; Zinger, Lucie; Andalo, Christophe

    2016-01-01

    Given the ongoing decline of both pollinators and plants, it is crucial to implement effective methods to describe complex pollination networks across time and space in a comprehensive and high-throughput way. Here we tested if metabarcoding may circumvent the limits of conventional methodologies in detecting and quantifying plant-pollinator interactions. Metabarcoding experiments on pollen DNA mixtures described a positive relationship between the amounts of DNA from focal species and the number of trnL and ITS1 sequences yielded. The study of pollen loads of insects captured in plant communities revealed that as compared to the observation of visits, metabarcoding revealed 2.5 times more plant species involved in plant-pollinator interactions. We further observed a tight positive relationship between the pollen-carrying capacities of insect taxa and the number of trnL and ITS1 sequences. The number of visits received per plant species also positively correlated to the number of their ITS1 and trnL sequences in insect pollen loads. By revealing interactions hard to observe otherwise, metabarcoding significantly enlarges the spatiotemporal observation window of pollination interactions. By providing new qualitative and quantitative information, metabarcoding holds great promise for investigating diverse facets of interactions and will provide a new perception of pollination networks as a whole. PMID:27255732

  6. Using metabarcoding to reveal and quantify plant-pollinator interactions

    PubMed Central

    Pornon, André; Escaravage, Nathalie; Burrus, Monique; Holota, Hélène; Khimoun, Aurélie; Mariette, Jérome; Pellizzari, Charlène; Iribar, Amaia; Etienne, Roselyne; Taberlet, Pierre; Vidal, Marie; Winterton, Peter; Zinger, Lucie; Andalo, Christophe

    2016-01-01

    Given the ongoing decline of both pollinators and plants, it is crucial to implement effective methods to describe complex pollination networks across time and space in a comprehensive and high-throughput way. Here we tested if metabarcoding may circumvent the limits of conventional methodologies in detecting and quantifying plant-pollinator interactions. Metabarcoding experiments on pollen DNA mixtures described a positive relationship between the amounts of DNA from focal species and the number of trnL and ITS1 sequences yielded. The study of pollen loads of insects captured in plant communities revealed that as compared to the observation of visits, metabarcoding revealed 2.5 times more plant species involved in plant-pollinator interactions. We further observed a tight positive relationship between the pollen-carrying capacities of insect taxa and the number of trnL and ITS1 sequences. The number of visits received per plant species also positively correlated to the number of their ITS1 and trnL sequences in insect pollen loads. By revealing interactions hard to observe otherwise, metabarcoding significantly enlarges the spatiotemporal observation window of pollination interactions. By providing new qualitative and quantitative information, metabarcoding holds great promise for investigating diverse facets of interactions and will provide a new perception of pollination networks as a whole. PMID:27255732

  7. Transcriptome Reveals Cathepsin K in Periodontal Ligament Differentiation.

    PubMed

    Yamada, S; Ozaki, N; Tsushima, K; Yamaba, S; Fujihara, C; Awata, T; Sakashita, H; Kajikawa, T; Kitagaki, J; Yamashita, M; Yanagita, M; Murakami, S

    2016-08-01

    Periodontal ligaments (PDLs) play an important role in remodeling the alveolar bond and cementum. Characterization of the periodontal tissue transcriptome remains incomplete, and an improved understanding of PDL features could aid in developing new regenerative therapies. Here, we aimed to generate and analyze a large human PDL transcriptome. We obtained PDLs from orthodontic treatment patients, isolated the RNA, and used a vector-capping method to make a complementary DNA library from >20,000 clones. Our results revealed that 58% of the sequences were full length. Furthermore, our analysis showed that genes expressed at the highest frequencies included those for collagen type I, collagen type III, and proteases. We also found 5 genes whose expressions have not been previously reported in human PDL. To access which of the highly expressed genes might be important for PDL cell differentiation, we used real-time polymerase chain reaction to measure their expression in differentiating cells. Among the genes tested, the cysteine protease cathepsin K had the highest upregulation, so we measured its relative expression in several tissues, as well as in osteoclasts, which are known to express high levels of cathepsin K. Our results revealed that PDL cells express cathepsin K at similar levels as osteoclasts, which are both expressed at higher levels than those of the other tissues tested. We also measured cathepsin K protein expression and enzyme activity during cell differentiation and found that both increased during this process. Immunocytochemistry experiments revealed that cathepsin K localizes to the interior of lysosomes. Last, we examined the effect of inhibiting cathepsin K during cell differentiation and found that cathepsin K inhibition stimulated calcified nodule formation and increased the levels of collagen type I and osteocalcin gene expression. Based on these results, cathepsin K seems to regulate collagen fiber accumulation during human PDL cell

  8. Genes but Not Genomes Reveal Bacterial Domestication of Lactococcus Lactis

    PubMed Central

    Passerini, Delphine; Beltramo, Charlotte; Coddeville, Michele; Quentin, Yves; Ritzenthaler, Paul

    2010-01-01

    Background The population structure and diversity of Lactococcus lactis subsp. lactis, a major industrial bacterium involved in milk fermentation, was determined at both gene and genome level. Seventy-six lactococcal isolates of various origins were studied by different genotyping methods and thirty-six strains displaying unique macrorestriction fingerprints were analyzed by a new multilocus sequence typing (MLST) scheme. This gene-based analysis was compared to genomic characteristics determined by pulsed-field gel electrophoresis (PFGE). Methodology/Principal Findings The MLST analysis revealed that L. lactis subsp. lactis is essentially clonal with infrequent intra- and intergenic recombination; also, despite its taxonomical classification as a subspecies, it displays a genetic diversity as substantial as that within several other bacterial species. Genome-based analysis revealed a genome size variability of 20%, a value typical of bacteria inhabiting different ecological niches, and that suggests a large pan-genome for this subspecies. However, the genomic characteristics (macrorestriction pattern, genome or chromosome size, plasmid content) did not correlate to the MLST-based phylogeny, with strains from the same sequence type (ST) differing by up to 230 kb in genome size. Conclusion/Significance The gene-based phylogeny was not fully consistent with the traditional classification into dairy and non-dairy strains but supported a new classification based on ecological separation between “environmental” strains, the main contributors to the genetic diversity within the subspecies, and “domesticated” strains, subject to recent genetic bottlenecks. Comparison between gene- and genome-based analyses revealed little relationship between core and dispensable genome phylogenies, indicating that clonal diversification and phenotypic variability of the “domesticated” strains essentially arose through substantial genomic flux within the dispensable genome

  9. Interior Evolution of Ceres and Vesta Revealed by Dawn

    NASA Astrophysics Data System (ADS)

    Raymond, C. A.; Russell, C. T.; Bland, M. T.; Castillo, J. C.; De Sanctis, M. C.; Ermakov, A.; Jaumann, R.; Konopliv, A. S.; Marchi, S.; McCord, T. B.; McSween, H. Y., Jr.; Nathues, A.; Park, R. S.; Prettyman, T. H.; Toplis, M. J.; Zuber, M. T.

    2015-12-01

    Dawn's exploration of Vesta and Ceres has revealed their geophysical characteristics, informing the processes that shaped the bodies. Dawn has determined the average diameter of Ceres to be 940 km, smaller than the previously estimated 975 km [1]. This implies a density of 2160 kg/m3, indicating that Ceres is less differentiated than predicted [2]. Ceres' entire surface is cratered, implying the lack of a thick (10's of km) water ice layer at the surface. Variability in Ceres' crater morphology indicates that the near-surface layer has variable strength and rheology, likely due to heterogeneity in the near-surface mixture of rock, ice and salt. These observations may indicate that Ceres lost a significant amount of an original surface ice layer due to impact erosion. The lack of large impact basins on Ceres can be interpreted to be the result of viscous relaxation. These data provide insights into Ceres' thermal evolution and mechanical properties, which appear to be unique to this warm, icy body. In contrast to Ceres, Vesta formed very early and hot, resulting in a fully differentiated body. Dawn's exploration revealed geophysical and geochemical evidence for an iron-rich core and basaltic crust. However, unlike the pre-Dawn paradigm of Vesta's evolution, Dawn found that the crust and mantle of Vesta are less distinct than predicted by classical differentiation models. [1] Thomas, P. C., et al., Differentiation of the asteroid Ceres as revealed by its shape, Nature, 437, 224-226, 2005; [2] McCord et al., Ceres: Its Origin, Evolution and Structure and Dawn's Potential Contribution, Space Sci Rev
DOI 10.1007/s11214-010-9729-9, 2011.

  10. How the ``Blues'' reveals the intimacy of music and physics

    NASA Astrophysics Data System (ADS)

    Gibson, J. Murray

    2013-03-01

    Little do most people know when they hear blues piano - and you'll hear some live in this talk - that physics permeates the style, as it does all of music. Why should you care? By deconstructing blues piano the intimacy of physics, mathematics and music will be revealed in its glory.[1] The exercise says something about how the brains of the music composer and of the listener must be intimately linked to the physical principles of acoustics. And it provides a great vehicle to explain physical phenomena to non-scientists - everything from quantum mechanics to protein structure.

  11. Revealing and Characterizing Dark Excitons through Coherent Multidimensional Spectroscopy.

    PubMed

    Tollerud, Jonathan O; Cundiff, Steven T; Davis, Jeffrey A

    2016-08-26

    Dark excitons are of fundamental importance in a broad range of contexts but are difficult to study using conventional optical spectroscopy due to their weak interaction with light. We show how coherent multidimensional spectroscopy can reveal and characterize dark states. Using this approach, we identify parity-forbidden and spatially indirect excitons in InGaAs/GaAs quantum wells and determine details regarding lifetimes, homogeneous and inhomogeneous linewidths, broadening mechanisms, and coupling strengths. The observations of coherent coupling between these states and bright excitons hint at a role for a multistep process by which excitons in the barrier can relax into the quantum wells. PMID:27610881

  12. Tributaries of West Antarctic Ice Streams Revealed by RADARSAT Interferometry.

    PubMed

    Joughin; Gray; Bindschadler; Price; Morse; Hulbe; Mattar; Werner

    1999-10-01

    Interferometric RADARSAT data are used to map ice motion in the source areas of four West Antarctic ice streams. The data reveal that tributaries, coincident with subglacial valleys, provide a spatially extensive transition between slow inland flow and rapid ice stream flow and that adjacent ice streams draw from shared source regions. Two tributaries flow into the stagnant ice stream C, creating an extensive region that is thickening at an average rate of 0.49 meters per year. This is one of the largest rates of thickening ever reported in Antarctica. PMID:10514370

  13. Population dynamics of flaviviruses revealed by molecular phylogenies.

    PubMed Central

    Zanotto, P M; Gould, E A; Gao, G F; Harvey, P H; Holmes, E C

    1996-01-01

    The phylogeny of 123 complete envelope gene sequences was reconstructed in order to understand the evolution of tick- and mosquito-borne flaviviruses. An analysis of phylogenetic tree structure reveals a continual and asymmetric branching process in the tick-borne flaviviruses, compared with an explosive radiation in the last 200 years in viruses transmitted by mosquitoes. The distinction between these two viral groups probably reflects differences in modes of dispersal, propagation, and changes in the size of host populations. The most serious implication of this work is that growing human populations are being exposed to an expanding range of increasingly diverse viral strains. PMID:8570593

  14. Data mining of VDJ genes reveals interesting clues.

    PubMed

    Joshi, Rajani R; Gupta, Vinay K

    2006-01-01

    Hypervariability of the complementary determining regions in characteristic structure of Immunoglobulins and the distinct, cell-specific expressions of the genes coding for this important class of proteins pose intriguing problems in experimental and computational/informatics research requiring a special approach different from those for the other proteins. We present here an Average Linkage Hierarchical Clustering of the Homosapien VDJ genes and the Immunoglobulin polypeptides generated by them using special kind of data structures and correlation matrices in place of the microarray data. The results reveal interesting clues on the heterogeneity of exon - intron locations in these gene-families and its possible role in hypervariability of the Immunoglobulins. PMID:16842114

  15. Revealed distributional preferences: Individuals vs. teams☆☆☆

    PubMed Central

    Balafoutas, Loukas; Kerschbamer, Rudolf; Kocher, Martin; Sutter, Matthias

    2014-01-01

    We compare experimentally the revealed distributional preferences of individuals and teams in allocation tasks. We find that teams are significantly more benevolent than individuals in the domain of disadvantageous inequality while the benevolence in the domain of advantageous inequality is similar across decision makers. A consequence for the frequency of preference types is that while a substantial fraction of individuals is classified as inequality averse, this type disappears completely in teams. Spiteful types are markedly more frequent among individuals than among teams. On the other hand, by far more teams than individuals are classified as efficiency lovers. PMID:25843995

  16. [Neonatal adrenal hemorrhage revealed by jaundice: a case report].

    PubMed

    Oulmaati, A; Hays, S; Mory-Thomas, N; Bretones, P; Bensaid, M; Jordan, I; Bonfils, M; Godbert, I; Picaud, J-C

    2012-04-01

    The clinical presentation of adrenal hemorrhage varies, depending on the extent of hemorrhage as well as the amount of adrenal cortex involved by the hemorrhage. We report here a case of neonatal adrenal hemorrhage revealed by late onset of neonatal jaundice. This adrenal hemorrhage most probably resulted from shoulder dystocia. The aim of this work was to focus on the fact that jaundice can be caused by adrenal hemorrhage and to emphasize the crucial importance of abdominal ultrasound in cases of persistent jaundice. PMID:22424898

  17. Indentation Tests Reveal Geometry-Regulated Stiffening of Nanotube Junctions.

    PubMed

    Ozden, Sehmus; Yang, Yang; Tiwary, Chandra Sekhar; Bhowmick, Sanjit; Asif, Syed; Penev, Evgeni S; Yakobson, Boris I; Ajayan, Pulickel M

    2016-01-13

    Here we report a unique method to locally determine the mechanical response of individual covalent junctions between carbon nanotubes (CNTs), in various configurations such as "X", "Y", and "Λ"-like. The setup is based on in situ indentation using a picoindenter integrated within a scanning electron microscope. This allows for precise mapping between junction geometry and mechanical behavior and uncovers geometry-regulated junction stiffening. Molecular dynamics simulations reveal that the dominant contribution to the nanoindentation response is due to the CNT walls stretching at the junction. Targeted synthesis of desired junction geometries can therefore provide a "structural alphabet" for construction of macroscopic CNT networks with tunable mechanical response. PMID:26618517

  18. Nonclassical light revealed by the joint statistics of simultaneous measurements.

    PubMed

    Luis, Alfredo

    2016-04-15

    Nonclassicality cannot be a single-observable property, since the statistics of any quantum observable is compatible with classical physics. We develop a general procedure to reveal nonclassical behavior of light states from the joint statistics arising in the practical measurement of multiple observables. Beside embracing previous approaches, this protocol can disclose nonclassical features for standard examples of classical-like behavior, such as SU(2) and Glauber coherent states. When combined with other criteria, this would imply that every light state is nonclassical. PMID:27082346

  19. Anticipatory eye fixations reveal tool knowledge for tool interaction.

    PubMed

    Belardinelli, Anna; Barabas, Marissa; Himmelbach, Marc; Butz, Martin V

    2016-08-01

    Action-oriented eye-tracking studies have shown that eye fixations reveal much about current behavioral intentions. The eyes typically fixate those positions of a tool or an object where the fingers will be placed next, or those positions in a scene, where obstacles need to be avoided to successfully reach or transport a tool or object. Here, we asked to what extent eye fixations can also reveal active cognitive inference processes, which are expected to integrate bottom-up visual information with internal knowledge for planning suitable object interactions task-dependently. In accordance to the available literature, we expected that task-relevant knowledge will include sensorimotor, semantic, and mechanical aspects. To investigate if and in which way this internal knowledge influences eye fixation behavior while planning an object interaction, we presented pictures of familiar and unfamiliar tools and instructed participants to either pantomime 'lifting' or 'using' the respective tool. When confronted with unfamiliar tools, participants fixated the tool's effector part closer and longer in comparison with familiar tools. This difference was particularly prominent during 'using' trials when compared with 'lifting' trials. We suggest that this difference indicates that the brain actively extracts mechanical information about the unknown tool in order to infer its appropriate usage. Moreover, the successive fixations over a trial indicate that a dynamic, task-oriented, active cognitive process unfolds, which integrates available tool knowledge with visually gathered information to plan and determine the currently intended tool interaction. PMID:27068808

  20. Aberrant Activity in Degenerated Retinas Revealed by Electrical Imaging

    PubMed Central

    Zeck, Günther

    2016-01-01

    In this review, I present and discuss the current understanding of aberrant electrical activity found in the ganglion cell layer (GCL) of rod-degenerated (rd) mouse retinas. The reported electrophysiological properties revealed by electrical imaging using high-density microelectrode arrays can be subdivided between spiking activity originating from retinal ganglion cells (RGCs) and local field potentials (LFPs) reflecting strong trans-membrane currents within the GCL. RGCs in rd retinas show increased and rhythmic spiking compared to age-matched wild-type retinas. Fundamental spiking frequencies range from 5 to 15 Hz in various mouse models. The rhythmic RGC spiking is driven by a presynaptic network comprising AII amacrine and bipolar cells. In the healthy retina this rhythm-generating circuit is inhibited by photoreceptor input. A unique physiological feature of rd retinas is rhythmic LFP manifested as spatially-restricted low-frequency (5–15 Hz) voltage changes. Their spatiotemporal characterization revealed propagation and correlation with RGC spiking. LFPs rely on gap-junctional coupling and are shaped by glycinergic and by GABAergic transmission. The aberrant RGC spiking and LFPs provide a simple readout of the functionality of the remaining retinal circuitry which can be used in the development of improved vision restoration strategies. PMID:26903810

  1. Blue whale earplug reveals lifetime contaminant exposure and hormone profiles

    PubMed Central

    Trumble, Stephen J.; Robinson, Eleanor M.; Berman-Kowalewski, Michelle; Potter, Charles W.; Usenko, Sascha

    2013-01-01

    Lifetime contaminant and hormonal profiles have been reconstructed for an individual male blue whale (Balaenoptera musculus, Linnaeus 1758) using the earplug as a natural aging matrix that is also capable of archiving and preserving lipophilic compounds. These unprecedented lifetime profiles (i.e., birth to death) were reconstructed with a 6-mo resolution for a wide range of analytes including cortisol (stress hormone), testosterone (developmental hormone), organic contaminants (e.g., pesticides and flame retardants), and mercury. Cortisol lifetime profiles revealed a doubling of cortisol levels over baseline. Testosterone profiles suggest this male blue whale reached sexual maturity at approximately 10 y of age, which corresponds well with and improves on previous estimates. Early periods of the reconstructed contaminant profiles for pesticides (such as dichlorodiphenyltrichloroethanes and chlordanes), polychlorinated biphenyls, and polybrominated diphenyl ethers demonstrate significant maternal transfer occurred at 0–12 mo. The total lifetime organic contaminant burden measured between the earplug (sum of contaminants in laminae layers) and blubber samples from the same organism were similar. Total mercury profiles revealed reduced maternal transfer and two distinct pulse events compared with organic contaminants. The use of a whale earplug to reconstruct lifetime chemical profiles will allow for a more comprehensive examination of stress, development, and contaminant exposure, as well as improve the assessment of contaminant use/emission, environmental noise, ship traffic, and climate change on these important marine sentinels. PMID:24043814

  2. Ancient DNA sequence revealed by error-correcting codes.

    PubMed

    Brandão, Marcelo M; Spoladore, Larissa; Faria, Luzinete C B; Rocha, Andréa S L; Silva-Filho, Marcio C; Palazzo, Reginaldo

    2015-01-01

    A previously described DNA sequence generator algorithm (DNA-SGA) using error-correcting codes has been employed as a computational tool to address the evolutionary pathway of the genetic code. The code-generated sequence alignment demonstrated that a residue mutation revealed by the code can be found in the same position in sequences of distantly related taxa. Furthermore, the code-generated sequences do not promote amino acid changes in the deviant genomes through codon reassignment. A Bayesian evolutionary analysis of both code-generated and homologous sequences of the Arabidopsis thaliana malate dehydrogenase gene indicates an approximately 1 MYA divergence time from the MDH code-generated sequence node to its paralogous sequences. The DNA-SGA helps to determine the plesiomorphic state of DNA sequences because a single nucleotide alteration often occurs in distantly related taxa and can be found in the alternative codon patterns of noncanonical genetic codes. As a consequence, the algorithm may reveal an earlier stage of the evolution of the standard code. PMID:26159228

  3. Direct visualization reveals kinetics of meiotic chromosome synapsis

    DOE PAGESBeta

    Rog, Ofer; Dernburg, Abby  F.

    2015-03-17

    The synaptonemal complex (SC) is a conserved protein complex that stabilizes interactions along homologous chromosomes (homologs) during meiosis. The SC regulates genetic exchanges between homologs, thereby enabling reductional division and the production of haploid gametes. Here, we directly observe SC assembly (synapsis) by optimizing methods for long-term fluorescence recording in C. elegans. We report that synapsis initiates independently on each chromosome pair at or near pairing centers—specialized regions required for homolog associations. Once initiated, the SC extends rapidly and mostly irreversibly to chromosome ends. Quantitation of SC initiation frequencies and extension rates reveals that initiation is a rate-limiting step inmore » homolog interactions. Eliminating the dynein-driven chromosome movements that accompany synapsis severely retards SC extension, revealing a new role for these conserved motions. This work provides the first opportunity to directly observe and quantify key aspects of meiotic chromosome interactions and will enable future in vivo analysis of germline processes.« less

  4. Nanoscience of single polymer chains revealed by nanofishing.

    PubMed

    Nakajima, Ken; Nishi, Toshio

    2006-01-01

    The invention of atomic force microscopy (AFM) enabled us to study the statistical properties of single polymer chains by a method called "nanofishing," which stretches a single polymer chain adsorbed on a substrate with its one end by picking it at the other end. A force-extension curve obtained for a single polystyrene chain in a Theta solvent (cyclohexane) shows good agreement with a worm-like chain model and, therefore, gives microscopic information about entropic elasticity. Furthermore, the nanofishing technique can be used for dynamic viscoelastic measurement of single polymer chains. An AFM cantilever is mechanically oscillated at its resonant frequency during the stretching process. This technique enables the estimation of quantitative and simultaneous elongation-dependent changes of stiffness and viscosity of a single chain with the use of a phenomenological model. In this study, the effect of solvent on viscosity in low extension regions reveals that the viscosity is attributed to monomer-solvent friction. Thus, static and dynamic nanofishing techniques are shown to give powerful experimental proofs for several basic questions in polymer physics. The techniques are expected to reveal hidden properties of polymer chains or polymer solutions by any types of macroscopic measurements in the future. PMID:17099889

  5. Genome Sequencing Reveals a Phage in Helicobacter pylori

    PubMed Central

    Lehours, Philippe; Vale, Filipa F.; Bjursell, Magnus K.; Melefors, Ojar; Advani, Reza; Glavas, Steve; Guegueniat, Julia; Gontier, Etienne; Lacomme, Sabrina; Alves Matos, António; Menard, Armelle; Mégraud, Francis; Engstrand, Lars; Andersson, Anders F.

    2011-01-01

    ABSTRACT Helicobacter pylori chronically infects the gastric mucosa in more than half of the human population; in a subset of this population, its presence is associated with development of severe disease, such as gastric cancer. Genomic analysis of several strains has revealed an extensive H. pylori pan-genome, likely to grow as more genomes are sampled. Here we describe the draft genome sequence (63 contigs; 26× mean coverage) of H. pylori strain B45, isolated from a patient with gastric mucosa-associated lymphoid tissue (MALT) lymphoma. The major finding was a 24.6-kb prophage integrated in the bacterial genome. The prophage shares most of its genes (22/27) with prophage region II of Helicobacter acinonychis strain Sheeba. After UV treatment of liquid cultures, circular DNA carrying the prophage integrase gene could be detected, and intracellular tailed phage-like particles were observed in H. pylori cells by transmission electron microscopy, indicating that phage production can be induced from the prophage. PCR amplification and sequencing of the integrase gene from 341 H. pylori strains from different geographic regions revealed a high prevalence of the prophage (21.4%). Phylogenetic reconstruction showed four distinct clusters in the integrase gene, three of which tended to be specific for geographic regions. Our study implies that phages may play important roles in the ecology and evolution of H. pylori. PMID:22086490

  6. Diffusion Tensor Imaging Reveals Evolution of Primate Brain Architectures

    PubMed Central

    Zhang, Degang; Guo, Lei; Zhu, Dajiang; Li, Kaiming; Li, Longchuan; Chen, Hanbo; Zhao, Qun; Hu, Xiaoping; Liu, Tianming

    2013-01-01

    Evolution of the brain has been an inherently interesting problem for centuries. Recent studies have indicated that neuroimaging is a powerful technique for studying brain evolution. In particular, a variety of reports have demonstrated that consistent white matter fiber connection patterns derived from diffusion tensor imaging (DTI) tractography reveal common brain architecture and are predictive of brain functions. In this paper, based on our recently discovered 358 Dense Individualized and Common Connectivity-based Cortical Landmarks (DICCCOL) defined by consistent fiber connection patterns in DTI datasets of human brains, we derived 65 DICCCOLs that are common in macaque monkey, chimpanzee and human brains and 175 DICCCOLs that exhibit significant discrepancies amongst these three primate species. Qualitative and quantitative evaluations not only demonstrated the consistencies of anatomical locations and structural fiber connection patterns of these 65 common DICCCOLs across three primates, suggesting an evolutionarily-preserved common brain architecture, but also revealed regional patterns of evolutionarily-induced complexity and variability of those 175 discrepant DICCCOLs across the three species. PMID:23135357

  7. Computational Assembly of Polymorphic Amyloid Fibrils Reveals Stable Aggregates

    PubMed Central

    Smaoui, Mohamed Raef; Poitevin, Frédéric; Delarue, Marc; Koehl, Patrice; Orland, Henri; Waldispühl, Jérôme

    2013-01-01

    Amyloid proteins aggregate into polymorphic fibrils that damage tissues of the brain, nerves, and heart. Experimental and computational studies have examined the structural basis and the nucleation of short fibrils, but the ability to predict and precisely quantify the stability of larger aggregates has remained elusive. We established a complete classification of fibril shapes and developed a tool called CreateFibril to build such complex, polymorphic, modular structures automatically. We applied stability landscapes, a technique we developed to reveal reliable fibril structural parameters, to assess fibril stability. CreateFibril constructed HET-s, Aβ, and amylin fibrils up to 17 nm in length, and utilized a novel dipolar solvent model that captured the effect of dipole-dipole interactions between water and very large molecular systems to assess their aqueous stability. Our results validate experimental data for HET-s and Aβ, and suggest novel (to our knowledge) findings for amylin. In particular, we predicted the correct structural parameters (rotation angles, packing distances, hydrogen bond lengths, and helical pitches) for the one and three predominant HET-s protofilaments. We reveal and structurally characterize all known Aβ polymorphic fibrils, including structures recently classified as wrapped fibrils. Finally, we elucidate the predominant amylin fibrils and assert that native amylin is more stable than its amyloid form. CreateFibril and a database of all stable polymorphic fibril models we tested, along with their structural energy landscapes, are available at http://amyloid.cs.mcgill.ca. PMID:23442919

  8. Pneumoretroperitoneum and Pneumomediastinum Revealing a Left Colon Perforation

    PubMed Central

    Montori, Giulia; Di Giovanni, Giacomo; Mzoughi, Zeineb; Angot, Cedric; Al Samman, Sophie; Solaini, Leonardo; Cheynel, Nicolas

    2015-01-01

    Left colon perforation usually occurs in complicated diverticulitis or cancer. The most frequent signs are intraperitoneal abscess or peritonitis. In cases of retroperitoneal colonic perforation, diagnosis may be difficult. A 59-year-old woman presented with left thigh pain and with abdominal discomfort associated with mild dyspnea. Computed tomography scan showed air bubbles and purulent collection in the retroperitoneum, with subcutaneous emphysema extending from the left thigh to the neck. Computed tomography scan also revealed portal vein gas and thrombosis with multiple liver abscesses. An emergency laparotomy revealed a perforation of the proximal left colon. No masses were found. A left colectomy was performed. The retroperitoneum was drained and washed extensively. A negative pressure wound therapy was applied. A second-look laparotomy was performed 48 hours later. The retroperitoneum was drained and an end colostomy was performed. Intensive Care Unit postoperative stay was 9 days, and the patient was discharged on the 32nd postoperative day. Pneumoretroperitoneum and pneumomediastinum are rare signs of colonic retroperitoneal perforation. The diagnosis may be delayed, especially in the absence of peritoneal irritation. Clinical, laboratory, and especially radiologic parameters might be useful. Surgical treatment must be prompt to improve prognosis. PMID:26414818

  9. Previously Unrecognized Large Lunar Impact Basins Revealed by Topographic Data

    NASA Technical Reports Server (NTRS)

    Frey, Herbert V.

    2008-01-01

    The discovery of a large population of apparently buried impact craters on Mars, revealed as Quasi- Circular Depressions (QCDs) in Mars Orbiting Laser Altimeter (MOLA) data [1,2,3] and as Circular Thin Areas (CTAs) [4] in crustal thickness model data [5] leads to the obvious question: are there unrecognized impact features on the Moon and other bodies in the solar system? Early analysis of Clementine topography revealed several large impact basins not previously known [6,7], so the answer certainly is "Yes." How large a population of previously undetected impact basins, their size frequency distribution, and how much these added craters and basins will change ideas about the early cratering history and Late Heavy Bombardment on the Moon remains to be determined. Lunar Orbiter Laser Altimeter (LOLA) data [8] will be able to address these issues. As a prelude, we searched the state-of-the-art global topographic grid for the Moon, the Unified Lunar Control Net (ULCN) [9] for evidence of large impact features not previously recognized by photogeologic mapping, as summarized by Wilhelms [lo].

  10. Environmental and genetic perturbations reveal different networks of metabolic regulation

    PubMed Central

    Greenberg, Anthony J; Hackett, Sean R; Harshman, Lawrence G; Clark, Andrew G

    2011-01-01

    Progress in systems biology depends on accurate descriptions of biological networks. Connections in a regulatory network are identified as correlations of gene expression across a set of environmental or genetic perturbations. To use this information to predict system behavior, we must test how the nature of perturbations affects topologies of networks they reveal. To probe this question, we focused on metabolism of Drosophila melanogaster. Our source of perturbations is a set of crosses among 92 wild-derived lines from five populations, replicated in a manner permitting separate assessment of the effects of genetic variation and environmental fluctuation. We directly assayed activities of enzymes and levels of metabolites. Using a multivariate Bayesian model, we estimated covariance among metabolic parameters and built fine-grained probabilistic models of network topology. The environmental and genetic co-regulation networks are substantially the same among five populations. However, genetic and environmental perturbations reveal qualitative differences in metabolic regulation, suggesting that environmental shifts, such as diet modifications, produce different systemic effects than genetic changes, even if the primary targets are the same. PMID:22186737

  11. Circulating protein synthesis rates reveal skeletal muscle proteome dynamics.

    PubMed

    Shankaran, Mahalakshmi; King, Chelsea L; Angel, Thomas E; Holmes, William E; Li, Kelvin W; Colangelo, Marc; Price, John C; Turner, Scott M; Bell, Christopher; Hamilton, Karyn L; Miller, Benjamin F; Hellerstein, Marc K

    2016-01-01

    Here, we have described and validated a strategy for monitoring skeletal muscle protein synthesis rates in rodents and humans over days or weeks from blood samples. We based this approach on label incorporation into proteins that are synthesized specifically in skeletal muscle and escape into the circulation. Heavy water labeling combined with sensitive tandem mass spectrometric analysis allowed integrated synthesis rates of proteins in muscle tissue across the proteome to be measured over several weeks. Fractional synthesis rate (FSR) of plasma creatine kinase M-type (CK-M) and carbonic anhydrase 3 (CA-3) in the blood, more than 90% of which is derived from skeletal muscle, correlated closely with FSR of CK-M, CA-3, and other proteins of various ontologies in skeletal muscle tissue in both rodents and humans. Protein synthesis rates across the muscle proteome generally changed in a coordinate manner in response to a sprint interval exercise training regimen in humans and to denervation or clenbuterol treatment in rodents. FSR of plasma CK-M and CA-3 revealed changes and interindividual differences in muscle tissue proteome dynamics. In human subjects, sprint interval training primarily stimulated synthesis of structural and glycolytic proteins. Together, our results indicate that this approach provides a virtual biopsy, sensitively revealing individualized changes in proteome-wide synthesis rates in skeletal muscle without a muscle biopsy. Accordingly, this approach has potential applications for the diagnosis, management, and treatment of muscle disorders. PMID:26657858

  12. Circulating protein synthesis rates reveal skeletal muscle proteome dynamics

    PubMed Central

    Shankaran, Mahalakshmi; King, Chelsea L.; Angel, Thomas E.; Holmes, William E.; Li, Kelvin W.; Colangelo, Marc; Price, John C.; Turner, Scott M.; Bell, Christopher; Hamilton, Karyn L.; Miller, Benjamin F.; Hellerstein, Marc K.

    2015-01-01

    Here, we have described and validated a strategy for monitoring skeletal muscle protein synthesis rates in rodents and humans over days or weeks from blood samples. We based this approach on label incorporation into proteins that are synthesized specifically in skeletal muscle and escape into the circulation. Heavy water labeling combined with sensitive tandem mass spectrometric analysis allowed integrated synthesis rates of proteins in muscle tissue across the proteome to be measured over several weeks. Fractional synthesis rate (FSR) of plasma creatine kinase M-type (CK-M) and carbonic anhydrase 3 (CA-3) in the blood, more than 90% of which is derived from skeletal muscle, correlated closely with FSR of CK-M, CA-3, and other proteins of various ontologies in skeletal muscle tissue in both rodents and humans. Protein synthesis rates across the muscle proteome generally changed in a coordinate manner in response to a sprint interval exercise training regimen in humans and to denervation or clenbuterol treatment in rodents. FSR of plasma CK-M and CA-3 revealed changes and interindividual differences in muscle tissue proteome dynamics. In human subjects, sprint interval training primarily stimulated synthesis of structural and glycolytic proteins. Together, our results indicate that this approach provides a virtual biopsy, sensitively revealing individualized changes in proteome-wide synthesis rates in skeletal muscle without a muscle biopsy. Accordingly, this approach has potential applications for the diagnosis, management, and treatment of muscle disorders. PMID:26657858

  13. Revealing quantum correlation by negativity of the Wigner function

    NASA Astrophysics Data System (ADS)

    Taghiabadi, Razieh; Akhtarshenas, Seyed Javad; Sarbishaei, Mohsen

    2016-05-01

    We analyze two two-mode continuous variable separable states with the same marginal states. We adopt the definition of classicality in the form of well-defined positive Wigner function describing the state and find that although the states possess positive local Wigner functions, they exhibit negative Wigner functions for the global states. Using the negativity of Wigner function as an indicator of nonclassicality, we show that despite these states possess different negativities of the Wigner function, they do not reveal this difference as phase space nonclassicalities such as negativity of the Mandel Q parameter or quadrature squeezing. We then concentrate on quantum correlation of these states and show that quantum discord and local quantum uncertainty, as two well-defined measures of quantum correlation, manifest the difference between negativity of the Wigner functions. The non-Gaussianity of these states is also examined and show that the difference in behavior of their non-Gaussianity is the same as the difference between negativity of their Wigner functions. We also investigate the influence of correlation rank criterion and find that when the states can be produced locally from classical states, the Wigner functions cannot reveal their quantum correlations.

  14. Blue whale earplug reveals lifetime contaminant exposure and hormone profiles.

    PubMed

    Trumble, Stephen J; Robinson, Eleanor M; Berman-Kowalewski, Michelle; Potter, Charles W; Usenko, Sascha

    2013-10-15

    Lifetime contaminant and hormonal profiles have been reconstructed for an individual male blue whale (Balaenoptera musculus, Linnaeus 1758) using the earplug as a natural aging matrix that is also capable of archiving and preserving lipophilic compounds. These unprecedented lifetime profiles (i.e., birth to death) were reconstructed with a 6-mo resolution for a wide range of analytes including cortisol (stress hormone), testosterone (developmental hormone), organic contaminants (e.g., pesticides and flame retardants), and mercury. Cortisol lifetime profiles revealed a doubling of cortisol levels over baseline. Testosterone profiles suggest this male blue whale reached sexual maturity at approximately 10 y of age, which corresponds well with and improves on previous estimates. Early periods of the reconstructed contaminant profiles for pesticides (such as dichlorodiphenyltrichloroethanes and chlordanes), polychlorinated biphenyls, and polybrominated diphenyl ethers demonstrate significant maternal transfer occurred at 0-12 mo. The total lifetime organic contaminant burden measured between the earplug (sum of contaminants in laminae layers) and blubber samples from the same organism were similar. Total mercury profiles revealed reduced maternal transfer and two distinct pulse events compared with organic contaminants. The use of a whale earplug to reconstruct lifetime chemical profiles will allow for a more comprehensive examination of stress, development, and contaminant exposure, as well as improve the assessment of contaminant use/emission, environmental noise, ship traffic, and climate change on these important marine sentinels. PMID:24043814

  15. Functionalities of expressed messenger RNAs revealed from mutant phenotypes.

    PubMed

    Liao, Ben-Yang; Weng, Meng-Pin

    2016-07-01

    Total messenger RNAs mRNAs that are produced from a given gene under a certain set of conditions include both functional and nonfunctional transcripts. The high prevalence of nonfunctional mRNAs that have been detected in cells has raised questions regarding the functional implications of mRNA expression patterns and divergences. Phenotypes that result from the mutagenesis of protein-coding genes have provided the most straightforward descriptions of gene functions, and such data obtained from model organisms have facilitated investigations of the functionalities of expressed mRNAs. Mutant phenotype data from mouse tissues have revealed various attributes of functional mRNAs, including tissue-specificity, strength of expression, and evolutionary conservation. In addition, the role that mRNA expression evolution plays in driving morphological evolution has been revealed from studies designed to exploit morphological and physiological phenotypes of mouse mutants. Investigations into yeast essential genes (defined by an absence of colony growth after gene deletion) have further described gene regulatory strategies that reduce protein expression noise by mediating the rates of transcription and translation. In addition to the functional significance of expressed mRNAs as described in the abovementioned findings, the functionalities of other type of RNAs (i.e., noncoding RNAs) remain to be characterized with systematic mutations and phenotyping of the DNA regions that encode these RNA molecules. WIREs RNA 2016, 7:416-427. doi: 10.1002/wrna.1329 For further resources related to this article, please visit the WIREs website. PMID:26748449

  16. Ancient DNA sequence revealed by error-correcting codes

    PubMed Central

    Brandão, Marcelo M.; Spoladore, Larissa; Faria, Luzinete C. B.; Rocha, Andréa S. L.; Silva-Filho, Marcio C.; Palazzo, Reginaldo

    2015-01-01

    A previously described DNA sequence generator algorithm (DNA-SGA) using error-correcting codes has been employed as a computational tool to address the evolutionary pathway of the genetic code. The code-generated sequence alignment demonstrated that a residue mutation revealed by the code can be found in the same position in sequences of distantly related taxa. Furthermore, the code-generated sequences do not promote amino acid changes in the deviant genomes through codon reassignment. A Bayesian evolutionary analysis of both code-generated and homologous sequences of the Arabidopsis thaliana malate dehydrogenase gene indicates an approximately 1 MYA divergence time from the MDH code-generated sequence node to its paralogous sequences. The DNA-SGA helps to determine the plesiomorphic state of DNA sequences because a single nucleotide alteration often occurs in distantly related taxa and can be found in the alternative codon patterns of noncanonical genetic codes. As a consequence, the algorithm may reveal an earlier stage of the evolution of the standard code. PMID:26159228

  17. Memory activation reveals abnormal EEG in preclinical Huntington's disease.

    PubMed

    van der Hiele, Karin; Jurgens, Caroline K; Vein, Alla A; Reijntjes, Robert H A M; Witjes-Ané, Marie-Noëlle W; Roos, Raymund A C; van Dijk, Gert; Middelkoop, Huub A M

    2007-04-15

    The EEG is potentially useful as a marker of early Huntington's disease (HD). In dementia, the EEG during a memory activation challenge showed abnormalities where the resting EEG did not. We investigated whether memory activation also reveals EEG abnormalities in preclinical HD. Sixteen mutation carriers for HD and 13 nonmutation carriers underwent neurological, neuropsychological, MRI and EEG investigations. The EEG was registered during a rest condition, i.e. eyes closed, and a working memory task. In each condition we determined absolute power in the theta (4-8 Hz) and alpha (8-13 Hz) bands and subsequently calculated relative alpha power. The EEG during eyes closed did not differ between groups. The EEG during memory activation showed less relative alpha power in mutation carriers as compared to nonmutation carriers, even though memory performance was similar [F (1,27) = 10.87; P = 0.003]. Absolute powers also showed less alpha power [F (1,27) = 7.02; P = 0.013] but similar theta power. No correlations were found between absolute and relative alpha power on the one hand and neuropsychological scores, motor scores or number of CAG repeats on the other. In conclusion, memory activation reveals functional brain changes in Huntington's disease before clinical signs become overt. PMID:17266047

  18. Piriform Spider Silk Sequences Reveal Unique Repetitive Elements

    PubMed Central

    Perry, David J.; Bittencourt, Daniela; Siltberg-Liberles, Jessica; Rech, Elibio L.; Lewis, Randolph V.

    2010-01-01

    Orb-weaving spider silk fibers are assembled from very large, highly repetitive proteins. The repeated segments contain, in turn, short, simple repetitive amino acid motifs that account for the physical and mechanical properties of the assembled fiber. Of the six orb-weaver silk fibroins, the piriform silk that makes the attachment discs, which lashes the joints of the web and attaches dragline silk to surfaces has not been previously characterized. Piriform silk protein cDNAs were isolated from phage libraries of three species, A. trifasciata, N. clavipes, and N. cruentata. The deduced amino acid sequences from these genes revealed two new repetitive motifs: an alternating proline motif where every other amino acid is proline, and a glutamine-rich motif of 6 to 8 amino acids. Similar to other spider silk proteins, the repeated segments are large (>200 amino acids) and highly homogenized within a species. There is also substantial sequence similarity across the genes from the three species with particular conservation of the repetitive motifs. Northern blot analysis revealed that the messenger RNA is larger than 11kb and is expressed exclusively in the piriform glands of the spider. Phylogenetic analysis of the C-terminal regions of the new proteins with published spidroins robustly shows that the pirifom sequences form an ortholog group. PMID:20954740

  19. Membrane protein properties revealed through data-rich electrostatics calculations

    PubMed Central

    Guerriero, Christopher J.; Brodsky, Jeffrey L.; Grabe, Michael

    2015-01-01

    SUMMARY The electrostatic properties of membrane proteins often reveal many of their key biophysical characteristics, such as ion channel selectivity and the stability of charged membrane-spanning segments. The Poisson-Boltzmann (PB) equation is the gold standard for calculating protein electrostatics, and the software APBSmem enables the solution of the PB equation in the presence of a membrane. Here, we describe significant advances to APBSmem including: full automation of system setup, per-residue energy decomposition, incorporation of PDB2PQR, calculation of membrane induced pKa shifts, calculation of non-polar energies, and command-line scripting for large scale calculations. We highlight these new features with calculations carried out on a number of membrane proteins, including the recently solved structure of the ion channel TRPV1 and a large survey of 1,614 membrane proteins of known structure. This survey provides a comprehensive list of residues with large electrostatic penalties for being embedded in the membrane potentially revealing interesting functional information. PMID:26118532

  20. The Microbiome of Brazilian Mangrove Sediments as Revealed by Metagenomics

    PubMed Central

    Andreote, Fernando Dini; Jiménez, Diego Javier; Chaves, Diego; Dias, Armando Cavalcante Franco; Luvizotto, Danice Mazzer; Dini-Andreote, Francisco; Fasanella, Cristiane Cipola; Lopez, Maryeimy Varon; Baena, Sandra; Taketani, Rodrigo Gouvêa; de Melo, Itamar Soares

    2012-01-01

    Here we embark in a deep metagenomic survey that revealed the taxonomic and potential metabolic pathways aspects of mangrove sediment microbiology. The extraction of DNA from sediment samples and the direct application of pyrosequencing resulted in approximately 215 Mb of data from four distinct mangrove areas (BrMgv01 to 04) in Brazil. The taxonomic approaches applied revealed the dominance of Deltaproteobacteria and Gammaproteobacteria in the samples. Paired statistical analysis showed higher proportions of specific taxonomic groups in each dataset. The metabolic reconstruction indicated the possible occurrence of processes modulated by the prevailing conditions found in mangrove sediments. In terms of carbon cycling, the sequences indicated the prevalence of genes involved in the metabolism of methane, formaldehyde, and carbon dioxide. With respect to the nitrogen cycle, evidence for sequences associated with dissimilatory reduction of nitrate, nitrogen immobilization, and denitrification was detected. Sequences related to the production of adenylsulfate, sulfite, and H2S were relevant to the sulphur cycle. These data indicate that the microbial core involved in methane, nitrogen, and sulphur metabolism consists mainly of Burkholderiaceae, Planctomycetaceae, Rhodobacteraceae, and Desulfobacteraceae. Comparison of our data to datasets from soil and sea samples resulted in the allotment of the mangrove sediments between those samples. The results of this study add valuable data about the composition of microbial communities in mangroves and also shed light on possible transformations promoted by microbial organisms in mangrove sediments. PMID:22737213

  1. A complex North Atlantic permanent pycnocline revealed by Argo data

    NASA Astrophysics Data System (ADS)

    Feucher, Charlène; Maze, Guillaume; Mercier, Herlé

    2015-04-01

    In the North Atlantic subtropical gyre, the oceanic vertical structure of density is characterized by a region of rapid increase with depth. This layer is called the permanent pycnocline. The pycnocline is the transition layer between light, low-latitude, surface water masses which are ventilated every winter when penetrated locally by the mixed layer and dense, deeper water masses whose properties are set in the high latitudes. Assessing the structure and variability of the permanent pycnocline is of a major interest in the understanding of the climate system because the pycnocline embeds the warm water sphere and most of the wind-forced horizontal circulation. We characterized the large scale structure of the permanent pycnocline with in-situ data from the Argo array. We developed a new method to objectively characterize its properties (depth, thickness, temperature, salinity, density, potential vorticity). Results reveal a surprisingly complex structure with inhomogeneous properties. In the Gulf Stream recirculation region the pycnocline is deep, thick, the maximum of stratification is found in the middle on the layer and follow an isopycnal surface. But away from this textbook regional description, the pycnocline is characterized by vertical asymmetries and gradients in thermohaline properties. T/S distribution along the permanent pycnocline depth reveals a diversity of water masses. We will present the mean observed structure and properties of the permanent pycnocline and relate them to physical processes that constraint them.

  2. NeuCode Proteomics Reveals Bap1 Regulation of Metabolism.

    PubMed

    Baughman, Joshua M; Rose, Christopher M; Kolumam, Ganesh; Webster, Joshua D; Wilkerson, Emily M; Merrill, Anna E; Rhoads, Timothy W; Noubade, Rajkumar; Katavolos, Paula; Lesch, Justin; Stapleton, Donald S; Rabaglia, Mary E; Schueler, Kathy L; Asuncion, Raymond; Domeyer, Melanie; Zavala-Solorio, Jose; Reich, Michael; DeVoss, Jason; Keller, Mark P; Attie, Alan D; Hebert, Alexander S; Westphall, Michael S; Coon, Joshua J; Kirkpatrick, Donald S; Dey, Anwesha

    2016-07-12

    We introduce neutron-encoded (NeuCode) amino acid labeling of mice as a strategy for multiplexed proteomic analysis in vivo. Using NeuCode, we characterize an inducible knockout mouse model of Bap1, a tumor suppressor and deubiquitinase whose in vivo roles outside of cancer are not well established. NeuCode proteomics revealed altered metabolic pathways following Bap1 deletion, including profound elevation of cholesterol biosynthetic machinery coincident with reduced expression of gluconeogenic and lipid homeostasis proteins in liver. Bap1 loss increased pancreatitis biomarkers and reduced expression of mitochondrial proteins. These alterations accompany a metabolic remodeling with hypoglycemia, hypercholesterolemia, hepatic lipid loss, and acinar cell degeneration. Liver-specific Bap1 null mice present with fully penetrant perinatal lethality, severe hypoglycemia, and hepatic lipid deficiency. This work reveals Bap1 as a metabolic regulator in liver and pancreas, and it establishes NeuCode as a reliable proteomic method for deciphering in vivo biology. PMID:27373151

  3. Revealing short-period normal modes of the atmosphere

    NASA Astrophysics Data System (ADS)

    Shved, G. M.; Ermolenko, S. I.; Hoffmann, P.

    2015-09-01

    Barometer and seismometer measurements at Collm, Germany (51.3° N, 13.0° E) for all of 2002 are used to search for atmospheric normal modes (ANMs) in the frequency range 50-310 µHz. The measurements are spectrally analyzed using a 5-day window sliding along the 1-year series with a 1-day step. The subsequent analysis follows two procedures: (a) revealing features in the frequency distribution of the number of statistically significant spectral peaks in histograms built on the basis of these spectra and (b) calculating the multiplication spectra for the raw spectra. The two procedures yield the same result for the two instruments, i.e., reveal a periodicity in the clustering of atmospheric modes on the frequency axis with a period of ˜6 µHz. The fact that this period is close to 7 μHz, which is predicted by the crude theory of gravity—inertia ANMs [3] for their frequency distribution, suggests that ANMs are generated down to as small a period as ˜1 h.

  4. A systems biology approach reveals common metastatic pathways in osteosarcoma

    PubMed Central

    2012-01-01

    Background Osteosarcoma (OS) is the most common malignant bone tumor in children and adolescents. The survival rate of patients with metastatic disease remains very dismal. Nevertheless, metastasis is a complex process and a single-level analysis is not likely to identify its key biological determinants. In this study, we used a systems biology approach to identify common metastatic pathways that are jointly supported by both mRNA and protein expression data in two distinct human metastatic OS models. Results mRNA expression microarray and N-linked glycoproteomic analyses were performed on two commonly used isogenic pairs of human metastatic OS cell lines, namely HOS/143B and SaOS-2/LM7. Pathway analysis of the differentially regulated genes and glycoproteins separately revealed pathways associated to metastasis including cell cycle regulation, immune response, and epithelial-to-mesenchymal-transition. However, no common significant pathway was found at both genomic and proteomic levels between the two metastatic models, suggesting a very different biological nature of the cell lines. To address this issue, we used a topological significance analysis based on a “shortest-path” algorithm to identify topological nodes, which uncovered additional biological information with respect to the genomic and glycoproteomic profiles but remained hidden from the direct analyses. Pathway analysis of the significant topological nodes revealed a striking concordance between the models and identified significant common pathways, including “Cytoskeleton remodeling/TGF/WNT”, “Cytoskeleton remodeling/Cytoskeleton remodeling”, and “Cell adhesion/Chemokines and adhesion”. Of these, the “Cytoskeleton remodeling/TGF/WNT” was the top ranked common pathway from the topological analysis of the genomic and proteomic profiles in the two metastatic models. The up-regulation of proteins in the “Cytoskeleton remodeling/TGF/WNT” pathway in the SaOS-2/LM7 and HOS/143B models

  5. Endoperoxides Revealed as Origin of the Toxicity of Graphene Oxide.

    PubMed

    Pieper, Hanna; Chercheja, Serghei; Eigler, Siegfried; Halbig, Christian E; Filipovic, Milos R; Mokhir, Andriy

    2016-01-01

    Potential biomedicinal applications of graphene oxide (GO), for example, as a carrier of biomolecules or a reagent for photothermal therapy and biosensing, are limited by its cytotoxicity and mutagenicity. It is believed that these properties are at least partially caused by GO-induced oxidative stress in cells. However, it is not known which chemical fragments of GO are responsible for this unfavorable effect. We generated four GOs containing variable redox-active groups on the surface, including Mn(2+), C-centered radicals, and endoperoxides (EPs). A comparison of the abilities of these materials to generate reactive oxygen species in human cervical cancer cells revealed that EPs play a crucial role in GO-induced oxidative stress. These data could be applied to the rational design of biocompatible nontoxic GOs for biomedical applications. PMID:26549205

  6. Treated-skin temperature regularities revealed by IR thermography

    NASA Astrophysics Data System (ADS)

    Vainer, Boris G.

    2001-03-01

    Experimental results disclosing temperature change of human skin affected by various unnatural factors are presented in detail. Thermograms are obtained with the IR thermograph containing high performance InAs CID FPA-based photosensitive unit. Using logarithmic scale of time, evolution of skin temperature after moistening, spirit sponging, and olive oil lubrication is investigated. A comparative analysis of the resulting effects of treatments including alpha-hydroxy acid, cosmetic regenerating cream, spirit, and water, is made. Quantitative distinctions between skin regions characterized by ordinary, and depleted blood supply, including areas located directly above surface main vessels, are revealed. Strongly logarithmic time- dependence of a skin temperature is discovered when the skin is cooled down after its preliminary heating with a hot wax. Non-monotonic change of a local temperature during electrically active procedure is described. Low level light therapy equipment is also applied. A special role of the temperature of nose is discussed.

  7. Topological structure dynamics revealing collective evolution in active nematics

    PubMed Central

    Shi, Xia-qing; Ma, Yu-qiang

    2013-01-01

    Topological defects frequently emerge in active matter like bacterial colonies, cytoskeleton extracts on substrates, self-propelled granular or colloidal layers and so on, but their dynamical properties and the relations to large-scale organization and fluctuations in these active systems are seldom touched. Here we reveal, through a simple model for active nematics using self-driven hard elliptic rods, that the excitation, annihilation and transportation of topological defects differ markedly from those in non-active media. These dynamical processes exhibit strong irreversibility in active nematics in the absence of detailed balance. Moreover, topological defects are the key factors in organizing large-scale dynamic structures and collective flows, resulting in multi-spatial temporal effects. These findings allow us to control the self-organization of active matter through topological structures. PMID:24346733

  8. Structural characterization of human heparanase reveals insights into substrate recognition

    PubMed Central

    Wu, Liang; Viola, Cristina M.; Brzozowski, Andrzej M.; Davies, Gideon J.

    2016-01-01

    Heparan Sulfate (HS) is a glycosaminoglycan (GAG) which forms a key component of the extracellular matrix (ECM). Breakdown of HS is carried out by heparanase (HPSE), an endo-β-glucuronidase of the glycoside hydrolase (GH)79 family. Overexpression of HPSE is strongly linked to cancer metastases - reflecting breakdown of extracellular HS and release of stored growth factors. Here we present crystal structures of human HPSE at 1.6-1.9 Å resolution reveal how an endo-acting binding cleft is exposed by proteolytic activation of latent proHPSE. Oligosaccharide complexes map the substrate-binding and sulfate recognition motifs. These data shed light on the structure and interactions for a key enzyme involved in ECM maintenance, and provide a starting point for design of HPSE inhibitors as biochemical tools and anti-cancer therapeutics. PMID:26575439

  9. Locations of marine animals revealed by carbon isotopes.

    PubMed

    MacKenzie, Kirsteen M; Palmer, Martin R; Moore, Andy; Ibbotson, Anton T; Beaumont, William R C; Poulter, David J S; Trueman, Clive N

    2011-01-01

    Knowing the distribution of marine animals is central to understanding climatic and other environmental influences on population ecology. This information has proven difficult to gain through capture-based methods biased by capture location. Here we show that marine location can be inferred from animal tissues. As the carbon isotope composition of animal tissues varies with sea surface temperature, marine location can be identified by matching time series of carbon isotopes measured in tissues to sea surface temperature records. Applying this technique to populations of Atlantic salmon (Salmo salar L.) produces isotopically-derived maps of oceanic feeding grounds, consistent with the current understanding of salmon migrations, that additionally reveal geographic segregation in feeding grounds between individual philopatric populations and age-classes. Carbon isotope ratios can be used to identify the location of open ocean feeding grounds for any pelagic animals for which tissue archives and matching records of sea surface temperature are available. PMID:22355540

  10. Color preferences revealed by statistical color rendition metric

    NASA Astrophysics Data System (ADS)

    Liu, Anqing; Tuzikas, ArÅ«nas; Žukauskas, ArtÅ«ras; Vaicekauskas, Rimantas; Vitta, Pranciškus; Shur, Michael

    2013-09-01

    The color rendition engine based on the statistical metric allows us to uniquely quantify the characteristics of color quality of illumination and assess the color rendition preferences. We now report on using the color rendition engine for revealing individual and cultural differences in color quality preferences of 205 American and Chinese subjects. Our study demonstrated that the majority of individuals preferred the color blend with the same statistical figures of merit on the average but with a much larger spread of blends for Americans. For both groups, the color rendition preferences depended on the object being illuminated. This was demonstrated by illuminating a set of common colored objects and three different paintings. We conclude that the color quality of lighting can be optimized and enhanced using the feedback to change the spectral power distribution of the illuminating source depending on the object being illuminated and on the preferences of an individual observer and a cultural group.

  11. Proteomic profiling reveals insights into Triticeae stigma development and function.

    PubMed

    Nazemof, Nazila; Couroux, Philippe; Rampitsch, Christof; Xing, Tim; Robert, Laurian S

    2014-11-01

    To our knowledge, this study represents the first high-throughput characterization of a stigma proteome in the Triticeae. A total of 2184 triticale mature stigma proteins were identified using three different gel-based approaches combined with mass spectrometry. The great majority of these proteins are described in a Triticeae stigma for the first time. These results revealed many proteins likely to play important roles in stigma development and pollen-stigma interactions, as well as protection against biotic and abiotic stresses. Quantitative comparison of the triticale stigma transcriptome and proteome showed poor correlation, highlighting the importance of having both types of analysis. This work makes a significant contribution towards the elucidation of the Triticeae stigma proteome and provides novel insights into its role in stigma development and function. PMID:25170101

  12. Insights revealed by rodent models of sugar binge eating.

    PubMed

    Murray, Susan M; Tulloch, Alastair J; Chen, Eunice Y; Avena, Nicole M

    2015-12-01

    Binge eating is seen across the spectrum of eating disorder diagnoses as well as among individuals who do not meet diagnostic criteria. Analyses of the specific types of foods that are frequently binged upon reveal that sugar-rich items feature prominently in binge-type meals, making the effects of binge consumption of sugar an important focus of study. One avenue to do this involves the use of animal models. Foundational and recent studies of animal models of sugar bingeing, both outlined here, lend insight into the various neurotransmitters and neuropeptides that may participate in or be altered by this behavior. Further, several preclinical studies incorporating sugar bingeing paradigms have explored the utility of pharmacological agents that target such neural systems for reducing sugar bingeing in an effort to enhance clinical treatment. Indeed, the translational implications of findings generated using animal models of sugar bingeing are considered here, along with potential avenues for further study. PMID:26510689

  13. Pupillometry reveals reduced unconscious emotional reactivity in autism.

    PubMed

    Nuske, Heather J; Vivanti, Giacomo; Hudry, Kristelle; Dissanayake, Cheryl

    2014-09-01

    Recent theoretical conceptualisations have suggested that emotion processing impairments in autism stem from disruption to the sub-cortical, rapid emotion-processing system. We argue that a clear way to ascertain whether this system is affected in autism is by measuring unconscious emotional reactivity. Using backwards masking, we presented fearful expressions non-consciously (subliminally) as well as consciously (supraliminally), and measured pupillary responses as an index of emotional reactivity in 19 children with autism and 19 typically developing children, aged 2-5 years. The pupillary responses of the children with autism revealed reduced unconscious emotional reactivity, with no group differences on consciously presented emotion. Together, these results indicate a hyporesponsiveness to non-consciously presented emotion suggesting a fundamental difference in emotion processing in autism, which requires consciousness and more time. PMID:25017502

  14. Dramatic changes in electronic structure revealed by fractionally charged nuclei

    SciTech Connect

    Cohen, Aron J.; Mori-Sánchez, Paula

    2014-01-28

    Discontinuous changes in the electronic structure upon infinitesimal changes to the Hamiltonian are demonstrated. These are revealed in one and two electron molecular systems by full configuration interaction (FCI) calculations when the realm of the nuclear charge is extended to be fractional. FCI electron densities in these systems show dramatic changes in real space and illustrate the transfer, hopping, and removal of electrons. This is due to the particle nature of electrons seen in stretched systems and is a manifestation of an energy derivative discontinuity at constant number of electrons. Dramatic errors of density functional theory densities are seen in real space as this physics is missing from currently used approximations. The movements of electrons in these simple systems encapsulate those in real physical processes, from chemical reactions to electron transport and pose a great challenge for the development of new electronic structure methods.

  15. Physical Principles of Skeletal Minerals Revealed with Spectromicroscopy

    ScienceCinema

    Gilbert, Pupa [U of Wisconsin-Madison, Wisconsin, United States

    2010-01-08

    Skeletal elements of marine and terrestrial organisms have the most fascinating nano-to-macro-structures, attracting the attention of physicists, biologists, chemists, and materials scientists. Using X-PEEM spectromicroscopy we revealed some of the fundamental mechanisms leading to the formation of these biominerals. Specifically, we addressed the following questions and provided the answers: 1Q) How do teeth, bones, and echinoderm and mollusk shells acquire their unusual, curved and complex morphology, if they are composed of single crystals? 1A) Via amorphous precursor phases; 2Q) How does crystallinity propagate through the amorophous precursor phases in sea urchin spicules and teeth? 2A) By secondary nucleation, following random walk patterns; 3Q) How does iridescent mother-of-pearl become ordered? 3A) Gradually, through a kinetic mechanisms in which fastest growing single-crystals win the competition for space, thus end up being approximately co-oriented.

  16. Ternary structure reveals mechanism of a membrane diacylglycerol kinase

    SciTech Connect

    Li, Dianfan; Stansfeld, Phillip J.; Sansom, Mark S. P.; Keogh, Aaron; Vogeley, Lutz; Howe, Nicole; Lyons, Joseph A.; Aragao, David; Fromme, Petra; Fromme, Raimund; Basu, Shibom; Grotjohann, Ingo; Kupitz, Christopher; Rendek, Kimberley; Weierstall, Uwe; Zatsepin, Nadia A.; Cherezov, Vadim; Liu, Wei; Bandaru, Sateesh; English, Niall J.; Gati, Cornelius; Barty, Anton; Yefanov, Oleksandr; Chapman, Henry N.; Diederichs, Kay; Messerschmidt, Marc; Boutet, Sébastien; Williams, Garth J.; Marvin Seibert, M.; Caffrey, Martin

    2015-12-17

    Diacylglycerol kinase catalyses the ATP-dependent conversion of diacylglycerol to phosphatidic acid in the plasma membrane of Escherichia coli. The small size of this integral membrane trimer, which has 121 residues per subunit, means that available protein must be used economically to craft three catalytic and substrate-binding sites centred about the membrane/cytosol interface. How nature has accomplished this extraordinary feat is revealed here in a crystal structure of the kinase captured as a ternary complex with bound lipid substrate and an ATP analogue. Residues, identified as essential for activity by mutagenesis, decorate the active site and are rationalized by the ternary structure. The γ-phosphate of the ATP analogue is positioned for direct transfer to the primary hydroxyl of the lipid whose acyl chain is in the membrane. A catalytic mechanism for this unique enzyme is proposed. As a result, the active site architecture shows clear evidence of having arisen by convergent evolution.

  17. Divergence of multimodular polyketide synthases revealed by a didomain structure.

    PubMed

    Zheng, Jianting; Gay, Darren C; Demeler, Borries; White, Mark A; Keatinge-Clay, Adrian T

    2012-07-01

    The enoylreductase (ER) is the final common enzyme from modular polyketide synthases (PKSs) to be structurally characterized. The 3.0 Å-resolution structure of the didomain comprising the ketoreductase (KR) and ER from the second module of the spinosyn PKS reveals that ER shares an ∼600-Å(2) interface with KR distinct from that of the related mammalian fatty acid synthase (FAS). In contrast to the ER domains of the mammalian FAS, the ER domains of the second module of the spinosyn PKS do not make contact across the two-fold axis of the synthase. This monomeric organization may have been necessary in the evolution of multimodular PKSs to enable acyl carrier proteins to access each of their cognate enzymes. The isolated ER domain showed activity toward a substrate analog, enabling us to determine the contributions of its active site residues. PMID:22634636

  18. Divergence of multimodular polyketide synthases revealed by a didomain structure

    PubMed Central

    Zheng, Jianting; Gay, Darren C.; Demeler, Borries; White, Mark A.; Keatinge-Clay, Adrian T.

    2012-01-01

    The enoylreductase (ER) is the final common enzyme from modular polyketide synthases (PKSs) to be structurally characterized. The 3.0 Å resolution structure of the didomain comprised of the ketoreductase (KR) and ER from the second module of the spinosyn PKS reveals that ER shares an ~600 Å2 interface with KR distinct from that of the related mammalian fatty acid synthase (FAS). In contrast to the ER domains of the mammalian FAS, the ER domains of the second module of the spinosyn PKS do not make contact across the twofold axis of the synthase. This monomeric organization may have been necessary in the evolution of multimodular PKSs to enable acyl carrier proteins (ACPs) to access each of their cognate enzymes. The isolated ER domain showed activity towards a substrate analog, enabling the contributions of its active site residues to be determined. PMID:22634636

  19. Structure of plant photosystem I revealed by theoretical modeling.

    PubMed

    Jolley, Craig; Ben-Shem, Adam; Nelson, Nathan; Fromme, Petra

    2005-09-30

    Photosystem (PS) I is a large membrane protein complex vital for oxygenic photosynthesis, one of the most important biological processes on the planet. We present an "atomic" model of higher plant PSI, based on theoretical modeling using the recent 4.4 angstroms x-ray crystal structure of PSI from pea. Because of the lack of information on the amino acid side chains in the x-ray structural model and the high cofactor content in this system, novel modeling techniques were developed. Our model reveals some important structural features of plant PSI that were not visible in the crystal structure, and our model sheds light on the evolutionary relationship between plant and cyanobacterial PSI. PMID:15955818

  20. Synthetic protein interactions reveal a functional map of the cell

    PubMed Central

    Berry, Lisa K; Ólafsson, Guðjón; Ledesma-Fernández, Elena; Thorpe, Peter H

    2016-01-01

    To understand the function of eukaryotic cells, it is critical to understand the role of protein-protein interactions and protein localization. Currently, we do not know the importance of global protein localization nor do we understand to what extent the cell is permissive for new protein associations – a key requirement for the evolution of new protein functions. To answer this question, we fused every protein in the yeast Saccharomyces cerevisiae with a partner from each of the major cellular compartments and quantitatively assessed the effects upon growth. This analysis reveals that cells have a remarkable and unanticipated tolerance for forced protein associations, even if these associations lead to a proportion of the protein moving compartments within the cell. Furthermore, the interactions that do perturb growth provide a functional map of spatial protein regulation, identifying key regulatory complexes for the normal homeostasis of eukaryotic cells. DOI: http://dx.doi.org/10.7554/eLife.13053.001 PMID:27098839

  1. Anisotropic MRI contrast reveals enhanced ionic transport in plastic crystals.

    PubMed

    Romanenko, Konstantin; Jin, Liyu; Madsen, Louis A; Pringle, Jennifer M; O'Dell, Luke A; Forsyth, Maria

    2014-11-01

    Organic ionic plastic crystals (OIPCs) are attractive as solid-state electrolytes for electrochemical devices such as lithium-ion batteries and solar and fuel cells. OIPCs offer high ionic conductivity, nonflammability, and versatility of molecular design. Nevertheless, intrinsic ion transport behavior of OIPCs is not fully understood, and their measured properties depend heavily on thermal history. Solid-state magnetic resonance imaging experiments reveal a striking image contrast anisotropy sensitive to the orientation of grain boundaries in polycrystalline OIPCs. Probing triethyl(methyl)phosphonium bis(fluorosulfonyl)imide (P1222FSI) samples with different thermal history demonstrates vast variations in microcrystallite alignment. Upon slow cooling from the melt, microcrystallites exhibit a preferred orientation throughout the entire sample, leading to an order of magnitude increase in conductivity as probed using impedance spectroscopy. This investigation describes both a new conceptual window and a new characterization method for understanding polycrystalline domain structure and transport in plastic crystals and other solid-state conductors. PMID:25312993

  2. Mathematical Analysis of Biomolecular Network Reveals Connections Between Diseases

    NASA Astrophysics Data System (ADS)

    Wang, Guanyu

    2012-02-01

    Connections between cancer and metabolic diseases may consist in the complex network of interactions among a common set of biomolecules. By applying singularity and bifurcation analysis, the phenotypes constrained by the AKT signaling pathway are identified and mapped onto the parameter space, which include cancer and certain metabolic diseases. By considering physiologic properties (sensitivity, robustness and adaptivity) the AKT pathway must possess in order to efficiently sense growth factors and nutrients, the region of normal responses is located. The analysis illuminates the parameter space and reveals system-level mechanisms in regulating biological functions (cell growth, survival, proliferation and metabolism) and how their deregulation may lead to the development of diseases. The analytical expressions summarize the synergistic interactions among many molecules, which provides valuable insights into therapeutic interventions.

  3. Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes

    PubMed Central

    Chen, Rui; Mias, George I.; Li-Pook-Than, Jennifer; Jiang, Lihua; Lam, Hugo Y. K.; Chen, Rong; Miriami, Elana; Karczewski, Konrad J.; Hariharan, Manoj; Dewey, Frederick E.; Cheng, Yong; Clark, Michael J.; Im, Hogune; Habegger, Lukas; Balasubramanian, Suganthi; O'Huallachain, Maeve; Dudley, Joel T.; Hillenmeyer, Sara; Haraksingh, Rajini; Sharon, Donald; Euskirchen, Ghia; Lacroute, Phil; Bettinger, Keith; Boyle, Alan P.; Kasowski, Maya; Grubert, Fabian; Seki, Scott; Garcia, Marco; Whirl-Carrillo, Michelle; Gallardo, Mercedes; Blasco, Maria A.; Greenberg, Peter L.; Snyder, Phyllis; Klein, Teri E.; Altman, Russ B.; Butte, Atul; Ashley, Euan A.; Nadeau, Kari C.; Gerstein, Mark; Tang, Hua; Snyder, Michael

    2012-01-01

    SUMMARY Personalized medicine is expected to benefit from combining genomic information with regular monitoring of physiological states by multiple high-throughput methods. Here we present an integrative Personal Omics Profile (iPOP), an analysis that combines genomic, transcriptomic, proteomic, metabolomic, and autoantibody profiles from a single individual over a 14-month period. Our iPOP analysis revealed various medical risks, including Type II diabetes. It also uncovered extensive, dynamic changes in diverse molecular components and biological pathways across healthy and diseased conditions. Extremely high coverage genomic and transcriptomic data, which provide the basis of our iPOP, discovered extensive heteroallelic changes during healthy and diseased states and an unexpected RNA editing mechanism. This study demonstrates that longitudinal iPOP can be used to interpret healthy and disease states by connecting genomic information with additional dynamic omics activity. PMID:22424236

  4. Geophysical imaging reveals topographic stress control of bedrock weathering.

    PubMed

    St Clair, J; Moon, S; Holbrook, W S; Perron, J T; Riebe, C S; Martel, S J; Carr, B; Harman, C; Singha, K; Richter, D deB

    2015-10-30

    Bedrock fracture systems facilitate weathering, allowing fresh mineral surfaces to interact with corrosive waters and biota from Earth's surface, while simultaneously promoting drainage of chemically equilibrated fluids. We show that topographic perturbations to regional stress fields explain bedrock fracture distributions, as revealed by seismic velocity and electrical resistivity surveys from three landscapes. The base of the fracture-rich zone mirrors surface topography where the ratio of horizontal compressive tectonic stresses to near-surface gravitational stresses is relatively large, and it parallels the surface topography where the ratio is relatively small. Three-dimensional stress calculations predict these results, suggesting that tectonic stresses interact with topography to influence bedrock disaggregation, groundwater flow, chemical weathering, and the depth of the "critical zone" in which many biogeochemical processes occur. PMID:26516279

  5. Hybridization Reveals the Evolving Genomic Architecture of Speciation

    PubMed Central

    Kronforst, Marcus R.; Hansen, Matthew E.B.; Crawford, Nicholas G.; Gallant, Jason R.; Zhang, Wei; Kulathinal, Rob J.; Kapan, Durrell D.; Mullen, Sean P.

    2014-01-01

    SUMMARY The rate at which genomes diverge during speciation is unknown, as are the physical dynamics of the process. Here, we compare full genome sequences of 32 butterflies, representing five species from a hybridizing Heliconius butterfly community, to examine genome-wide patterns of introgression and infer how divergence evolves during the speciation process. Our analyses reveal that initial divergence is restricted to a small fraction of the genome, largely clustered around known wing-patterning genes. Over time, divergence evolves rapidly, due primarily to the origin of new divergent regions. Furthermore, divergent genomic regions display signatures of both selection and adaptive introgression, demonstrating the link between microevolutionary processes acting within species and the origin of species across macroevolutionary timescales. Our results provide a uniquely comprehensive portrait of the evolving species boundary due to the role that hybridization plays in reducing the background accumulation of divergence at neutral sites. PMID:24183670

  6. Oscillatory Enzyme Dynamics Revealed by Two-Dimensional Infrared Spectroscopy.

    PubMed

    Pagano, Philip; Guo, Qi; Kohen, Amnon; Cheatum, Christopher M

    2016-07-01

    Enzymes move on a variety of length and time scales. While much is known about large structural fluctuations that impact binding of the substrates and release of products, little is known about faster motions of enzymes and how these motions may influence enzyme-catalyzed reactions. This Letter reports frequency fluctuations of the azide anion bound to the active site of formate dehydrogenase measured via 2D IR spectroscopy. These measurements reveal an underdamped oscillatory component to the frequency-frequency correlation function when the azide is bound to the NAD(+) ternary complex. This oscillation disappears when the reduced cofactor is added, indicating that the oscillating contributions most likely come from the charged nicotinamide ring. These oscillatory motions may be relevant to donor-acceptor distance sampling of the catalyzed hydride transfer and therefore may give future insights into the dynamic behavior involved in enzyme catalysis. PMID:27305279

  7. Macrophage characteristics of stem cells revealed by transcriptome profiling

    SciTech Connect

    Charriere, Guillaume M.; Cousin, Beatrice; Arnaud, Emmanuelle; Saillan-Barreau, Corinne; Andre, Mireille; Massoudi, Ali; Dani, Christian; Penicaud, Luc; Casteilla, Louis . E-mail: casteil@toulouse.inserm.fr

    2006-10-15

    We previously showed that the phenotypes of adipocyte progenitors and macrophages were close. Using functional analyses and microarray technology, we first tested whether this intriguing relationship was specific to adipocyte progenitors or could be shared with other progenitors. Measurements of phagocytic activity and gene profiling analysis of different progenitor cells revealed that the latter hypothesis should be retained. These results encouraged us to pursue and to confirm our analysis with a gold-standard stem cell population, embryonic stem cells or ESC. The transcriptomic profiles of ESC and macrophages were clustered together, unlike differentiated ESC. In addition, undifferentiated ESC displayed higher phagocytic activity than other progenitors, and they could phagocytoze apoptotic bodies. These data suggest that progenitors and stem cells share some characteristics of macrophages. This opens new perspectives on understanding stem cell phenotype and functionalities such as a putative role of stem cells in tissue remodeling by discarding dead cells but also their immunomodulation or fusion properties.

  8. Inheritance Patterns in Citation Networks Reveal Scientific Memes

    NASA Astrophysics Data System (ADS)

    Kuhn, Tobias; Perc, Matjaž; Helbing, Dirk

    2014-10-01

    Memes are the cultural equivalent of genes that spread across human culture by means of imitation. What makes a meme and what distinguishes it from other forms of information, however, is still poorly understood. Our analysis of memes in the scientific literature reveals that they are governed by a surprisingly simple relationship between frequency of occurrence and the degree to which they propagate along the citation graph. We propose a simple formalization of this pattern and validate it with data from close to 50 million publication records from the Web of Science, PubMed Central, and the American Physical Society. Evaluations relying on human annotators, citation network randomizations, and comparisons with several alternative approaches confirm that our formula is accurate and effective, without a dependence on linguistic or ontological knowledge and without the application of arbitrary thresholds or filters.

  9. Central tolerance to self revealed by the autoimmune regulator.

    PubMed

    Chan, Alice Y; Anderson, Mark S

    2015-11-01

    The autoimmune regulator (Aire) was initially identified as the gene causing multiorgan system autoimmunity in humans, and deletion of this gene in mice also resulted in organ-specific autoimmunity. Aire regulates the expression of tissue-specific antigens (TSAs) in medullary thymic epithelial cells (mTECs), which play a critical role in the negative selection of autoreactive T cells and the generation of regulatory T cells. More recently, the role of Aire in the development of mTECs has helped elucidate its ability to present the spectrum of TSAs needed to prevent autoimmunity. Molecular characterization of the functional domains of Aire has revealed multiple binding partners that assist Aire's function in altering gene transcription and chromatin remodeling. These recent advances have further highlighted the importance of Aire in central tolerance. PMID:26579596

  10. [Hodgkin disease revealed by a nephrotic syndrome: A case report].

    PubMed

    Cheptou, M; Pichault, V; Campagni, R; Vodoff, M-V; Fischbach, M; Paillard, C

    2015-12-01

    Pediatric nephrotic syndrome (NS) is most often idiopathic or primary but in rare cases, it can be secondary to neoplasia. We report on a case of steroid-resistant NS revealing as a paraneoplastic syndrome of Hodgkin disease (HD) in a 12-year-old boy. The onset of the NS can be earlier, later, or simultaneous to the HD. Treatment of the lymphoma allows the disappearance of the NS. In the case we observed, the diagnosis of HD was delayed because HD presented with an isolated, hilar adenopathy in the absence of retroperitoneal or peripheral locations. In children aged 10 years or more presenting with NS, steroid-resistant or otherwise, a possible paraneoplastic origin such as Hodgkin lymphoma should always be taken into consideration and eventually eliminated. PMID:26598043

  11. Biosensor reveals multiple sources for mitochondrial NAD⁺.

    PubMed

    Cambronne, Xiaolu A; Stewart, Melissa L; Kim, DongHo; Jones-Brunette, Amber M; Morgan, Rory K; Farrens, David L; Cohen, Michael S; Goodman, Richard H

    2016-06-17

    Nicotinamide adenine dinucleotide (NAD(+)) is an essential substrate for sirtuins and poly(adenosine diphosphate-ribose) polymerases (PARPs), which are NAD(+)-consuming enzymes localized in the nucleus, cytosol, and mitochondria. Fluctuations in NAD(+) concentrations within these subcellular compartments are thought to regulate the activity of NAD(+)-consuming enzymes; however, the challenge in measuring compartmentalized NAD(+) in cells has precluded direct evidence for this type of regulation. We describe the development of a genetically encoded fluorescent biosensor for directly monitoring free NAD(+) concentrations in subcellular compartments. We found that the concentrations of free NAD(+) in the nucleus, cytoplasm, and mitochondria approximate the Michaelis constants for sirtuins and PARPs in their respective compartments. Systematic depletion of enzymes that catalyze the final step of NAD(+) biosynthesis revealed cell-specific mechanisms for maintaining mitochondrial NAD(+) concentrations. PMID:27313049

  12. Quasisoft X-ray Sources: their physical natures revealed

    NASA Astrophysics Data System (ADS)

    Di Stefano, Rosanne; Primini, Francis A.; Guo, Jincheng; Liu, Jifeng

    2016-04-01

    Quasisoft X-ray sources (QSSs) have been the Mona Lisa of X-ray sources. They have remained enigmatic, even though we have known of their existence and basic properties for more than a decade. QSSs have X-ray luminosities greater than 10^{36} erg/s, but emit few or no photons above 2 keV. They were discovered in external galaxies during searches for softer sources, supersoft X-ray sources (SSSs). Every external galaxy contains QSSs, but it has been challenging to find any in the Milky Way and the Magellanic Clouds. Recent work, however, reveals that a significant fraction of QSSs may be black holes. We review what is known about QSSs to date, because this obscure class of objects may at last to be ready for "prime time'', capable of identifying BHs in a wide range of Galactic environments.

  13. Comparative genomics reveals insights into avian genome evolution and adaptation

    PubMed Central

    Zhang, Guojie; Li, Cai; Li, Qiye; Li, Bo; Larkin, Denis M.; Lee, Chul; Storz, Jay F.; Antunes, Agostinho; Greenwold, Matthew J.; Meredith, Robert W.; Ödeen, Anders; Cui, Jie; Zhou, Qi; Xu, Luohao; Pan, Hailin; Wang, Zongji; Jin, Lijun; Zhang, Pei; Hu, Haofu; Yang, Wei; Hu, Jiang; Xiao, Jin; Yang, Zhikai; Liu, Yang; Xie, Qiaolin; Yu, Hao; Lian, Jinmin; Wen, Ping; Zhang, Fang; Li, Hui; Zeng, Yongli; Xiong, Zijun; Liu, Shiping; Zhou, Long; Huang, Zhiyong; An, Na; Wang, Jie; Zheng, Qiumei; Xiong, Yingqi; Wang, Guangbiao; Wang, Bo; Wang, Jingjing; Fan, Yu; da Fonseca, Rute R.; Alfaro-Núñez, Alonzo; Schubert, Mikkel; Orlando, Ludovic; Mourier, Tobias; Howard, Jason T.; Ganapathy, Ganeshkumar; Pfenning, Andreas; Whitney, Osceola; Rivas, Miriam V.; Hara, Erina; Smith, Julia; Farré, Marta; Narayan, Jitendra; Slavov, Gancho; Romanov, Michael N; Borges, Rui; Machado, João Paulo; Khan, Imran; Springer, Mark S.; Gatesy, John; Hoffmann, Federico G.; Opazo, Juan C.; Håstad, Olle; Sawyer, Roger H.; Kim, Heebal; Kim, Kyu-Won; Kim, Hyeon Jeong; Cho, Seoae; Li, Ning; Huang, Yinhua; Bruford, Michael W.; Zhan, Xiangjiang; Dixon, Andrew; Bertelsen, Mads F.; Derryberry, Elizabeth; Warren, Wesley; Wilson, Richard K; Li, Shengbin; Ray, David A.; Green, Richard E.; O’Brien, Stephen J.; Griffin, Darren; Johnson, Warren E.; Haussler, David; Ryder, Oliver A.; Willerslev, Eske; Graves, Gary R.; Alström, Per; Fjeldså, Jon; Mindell, David P.; Edwards, Scott V.; Braun, Edward L.; Rahbek, Carsten; Burt, David W.; Houde, Peter; Zhang, Yong; Yang, Huanming; Wang, Jian; Jarvis, Erich D.; Gilbert, M. Thomas P.; Wang, Jun

    2015-01-01

    Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits. PMID:25504712

  14. Structural characterization of human heparanase reveals insights into substrate recognition.

    PubMed

    Wu, Liang; Viola, Cristina M; Brzozowski, Andrzej M; Davies, Gideon J

    2015-12-01

    Heparan sulfate (HS) is a glycosaminoglycan that forms a key component of the extracellular matrix (ECM). Breakdown of HS is carried out by heparanase (HPSE), an endo-β-glucuronidase of the glycoside hydrolase 79 (GH79) family. Overexpression of HPSE results in breakdown of extracellular HS and release of stored growth factors and hence is strongly linked to cancer metastasis. Here we present crystal structures of human HPSE at 1.6-Å to 1.9-Å resolution that reveal how an endo-acting binding cleft is exposed by proteolytic activation of latent proHPSE. We used oligosaccharide complexes to map the substrate-binding and sulfate-recognition motifs. These data shed light on the structure and interactions of a key enzyme involved in ECM maintenance and provide a starting point for the design of HPSE inhibitors for use as biochemical tools and anticancer therapeutics. PMID:26575439

  15. Spring-Block Model Reveals Region-Like Structures

    PubMed Central

    Máté, Gabriell; Néda, Zoltán; Benedek, József

    2011-01-01

    A mechanical spring-block model is used for realizing an objective space partition of settlements from a geographic territory in region-like structures. The method is based on the relaxation-dynamics of the spring-block system and reveals in a hierarchical manner region-like entities at different spatial scales. It takes into account in an elegant manner both the spatiality of the elements and the connectivity relations among them. Spatiality is taken into account by using the geographic coordinates of the settlements, and by detecting the neighbors with the help of a Delaunay triangulation. Connectivity between neighboring settlements are quantified using a Pearson-like correlation for the relative variation of a relevant socio-economic parameter (population size, GDP, tax payed per inhabitant, etc.). The method is implemented in an interactive JAVA application and it is applied with success for an artificially generated society and for the case of USA, Hungary and Transylvania. PMID:21346819

  16. Silk protein aggregation kinetics revealed by Rheo-IR.

    PubMed

    Boulet-Audet, Maxime; Terry, Ann E; Vollrath, Fritz; Holland, Chris

    2014-02-01

    The remarkable mechanical properties of silk fibres stem from a multi-scale hierarchical structure created when an aqueous protein "melt" is converted to an insoluble solid via flow. To directly relate a silk protein's structure and function in response to flow, we present the first application of a Rheo-IR platform, which couples cone and plate rheology with attenuated total reflectance infrared spectroscopy. This technique provides a new window into silk processing by linking shear thinning to an increase in molecular alignment, with shear thickening affecting changes in the silk protein's secondary structure. Additionally, compared to other static characterization methods for silk, Rheo-IR proved particularly useful at revealing the intrinsic difference between natural (native) and reconstituted silk feedstocks. Hence Rheo-IR offers important novel insights into natural silk processing. This has intrinsic academic merit, but it might also be useful when designing reconstituted silk analogues alongside other polymeric systems, whether natural or synthetic. PMID:24200713

  17. MNase titration reveals differences between nucleosome occupancy and chromatin accessibility

    PubMed Central

    Mieczkowski, Jakub; Cook, April; Bowman, Sarah K.; Mueller, Britta; Alver, Burak H.; Kundu, Sharmistha; Deaton, Aimee M.; Urban, Jennifer A.; Larschan, Erica; Park, Peter J.; Kingston, Robert E.; Tolstorukov, Michael Y.

    2016-01-01

    Chromatin accessibility plays a fundamental role in gene regulation. Nucleosome placement, usually measured by quantifying protection of DNA from enzymatic digestion, can regulate accessibility. We introduce a metric that uses micrococcal nuclease (MNase) digestion in a novel manner to measure chromatin accessibility by combining information from several digests of increasing depths. This metric, MACC (MNase accessibility), quantifies the inherent heterogeneity of nucleosome accessibility in which some nucleosomes are seen preferentially at high MNase and some at low MNase. MACC interrogates each genomic locus, measuring both nucleosome location and accessibility in the same assay. MACC can be performed either with or without a histone immunoprecipitation step, and thereby compares histone and non-histone protection. We find that changes in accessibility at enhancers, promoters and other regulatory regions do not correlate with changes in nucleosome occupancy. Moreover, high nucleosome occupancy does not necessarily preclude high accessibility, which reveals novel principles of chromatin regulation. PMID:27151365

  18. Stochastic heart-rate model can reveal pathologic cardiac dynamics

    NASA Astrophysics Data System (ADS)

    Kuusela, Tom

    2004-03-01

    A simple one-dimensional Langevin-type stochastic difference equation can simulate the heart-rate fluctuations in a time scale from minutes to hours. The model consists of a deterministic nonlinear part and a stochastic part typical of Gaussian noise, and both parts can be directly determined from measured heart-rate data. Data from healthy subjects typically exhibit the deterministic part with two or more stable fixed points. Studies of 15 congestive heart-failure subjects reveal that the deterministic part of pathologic heart dynamics has no clear stable fixed points. Direct simulations of the stochastic model for normal and pathologic cases can produce statistical parameters similar to those of real subjects. Results directly indicate that pathologic situations simplify the heart-rate control system.

  19. Phosphoproteome Integration Reveals Patient-Specific Networks in Prostate Cancer.

    PubMed

    Drake, Justin M; Paull, Evan O; Graham, Nicholas A; Lee, John K; Smith, Bryan A; Titz, Bjoern; Stoyanova, Tanya; Faltermeier, Claire M; Uzunangelov, Vladislav; Carlin, Daniel E; Fleming, Daniel Teo; Wong, Christopher K; Newton, Yulia; Sudha, Sud; Vashisht, Ajay A; Huang, Jiaoti; Wohlschlegel, James A; Graeber, Thomas G; Witte, Owen N; Stuart, Joshua M

    2016-08-11

    We used clinical tissue from lethal metastatic castration-resistant prostate cancer (CRPC) patients obtained at rapid autopsy to evaluate diverse genomic, transcriptomic, and phosphoproteomic datasets for pathway analysis. Using Tied Diffusion through Interacting Events (TieDIE), we integrated differentially expressed master transcriptional regulators, functionally mutated genes, and differentially activated kinases in CRPC tissues to synthesize a robust signaling network consisting of druggable kinase pathways. Using MSigDB hallmark gene sets, six major signaling pathways with phosphorylation of several key residues were significantly enriched in CRPC tumors after incorporation of phosphoproteomic data. Individual autopsy profiles developed using these hallmarks revealed clinically relevant pathway information potentially suitable for patient stratification and targeted therapies in late stage prostate cancer. Here, we describe phosphorylation-based cancer hallmarks using integrated personalized signatures (pCHIPS) that shed light on the diversity of activated signaling pathways in metastatic CRPC while providing an integrative, pathway-based reference for drug prioritization in individual patients. PMID:27499020

  20. Ternary structure reveals mechanism of a membrane diacylglycerol kinase

    PubMed Central

    Li, Dianfan; Stansfeld, Phillip J.; Sansom, Mark S. P.; Keogh, Aaron; Vogeley, Lutz; Howe, Nicole; Lyons, Joseph A.; Aragao, David; Fromme, Petra; Fromme, Raimund; Basu, Shibom; Grotjohann, Ingo; Kupitz, Christopher; Rendek, Kimberley; Weierstall, Uwe; Zatsepin, Nadia A.; Cherezov, Vadim; Liu, Wei; Bandaru, Sateesh; English, Niall J.; Gati, Cornelius; Barty, Anton; Yefanov, Oleksandr; Chapman, Henry N.; Diederichs, Kay; Messerschmidt, Marc; Boutet, Sébastien; Williams, Garth J.; Marvin Seibert, M.; Caffrey, Martin

    2015-01-01

    Diacylglycerol kinase catalyses the ATP-dependent conversion of diacylglycerol to phosphatidic acid in the plasma membrane of Escherichia coli. The small size of this integral membrane trimer, which has 121 residues per subunit, means that available protein must be used economically to craft three catalytic and substrate-binding sites centred about the membrane/cytosol interface. How nature has accomplished this extraordinary feat is revealed here in a crystal structure of the kinase captured as a ternary complex with bound lipid substrate and an ATP analogue. Residues, identified as essential for activity by mutagenesis, decorate the active site and are rationalized by the ternary structure. The γ-phosphate of the ATP analogue is positioned for direct transfer to the primary hydroxyl of the lipid whose acyl chain is in the membrane. A catalytic mechanism for this unique enzyme is proposed. The active site architecture shows clear evidence of having arisen by convergent evolution. PMID:26673816

  1. Microstructure of subretinal drusenoid deposits revealed by adaptive optics imaging.

    PubMed

    Meadway, Alexander; Wang, Xiaolin; Curcio, Christine A; Zhang, Yuhua

    2014-03-01

    Subretinal drusenoid deposits (SDD), a recently recognized lesion associated with progression of age-related macular degeneration, were imaged with adaptive optics scanning laser ophthalmoscopy (AO-SLO) and optical coherence tomography (AO-OCT). AO-SLO revealed a distinct en face structure of stage 3 SDD, showing a hyporeflective annulus surrounded reflective core packed with hyperreflective dots bearing a superficial similarity to the photoreceptors in the unaffected retina. However, AO-OCT suggested that the speckled appearance over the SDD rendered by AO-SLO was the lesion material itself, rather than photoreceptors. AO-OCT assists proper interpretation and understanding of the SDD structure and the lesions' impact on surrounding photoreceptors produced by AO-SLO and vice versa. PMID:24688808

  2. Surprise maximization reveals the community structure of complex networks

    NASA Astrophysics Data System (ADS)

    Aldecoa, Rodrigo; Marín, Ignacio

    2013-01-01

    How to determine the community structure of complex networks is an open question. It is critical to establish the best strategies for community detection in networks of unknown structure. Here, using standard synthetic benchmarks, we show that none of the algorithms hitherto developed for community structure characterization perform optimally. Significantly, evaluating the results according to their modularity, the most popular measure of the quality of a partition, systematically provides mistaken solutions. However, a novel quality function, called Surprise, can be used to elucidate which is the optimal division into communities. Consequently, we show that the best strategy to find the community structure of all the networks examined involves choosing among the solutions provided by multiple algorithms the one with the highest Surprise value. We conclude that Surprise maximization precisely reveals the community structure of complex networks.

  3. Surprise maximization reveals the community structure of complex networks.

    PubMed

    Aldecoa, Rodrigo; Marín, Ignacio

    2013-01-01

    How to determine the community structure of complex networks is an open question. It is critical to establish the best strategies for community detection in networks of unknown structure. Here, using standard synthetic benchmarks, we show that none of the algorithms hitherto developed for community structure characterization perform optimally. Significantly, evaluating the results according to their modularity, the most popular measure of the quality of a partition, systematically provides mistaken solutions. However, a novel quality function, called Surprise, can be used to elucidate which is the optimal division into communities. Consequently, we show that the best strategy to find the community structure of all the networks examined involves choosing among the solutions provided by multiple algorithms the one with the highest Surprise value. We conclude that Surprise maximization precisely reveals the community structure of complex networks. PMID:23320141

  4. Early MAVEN Deep Dip campaign reveals thermosphere and ionosphere variability.

    PubMed

    Bougher, S; Jakosky, B; Halekas, J; Grebowsky, J; Luhmann, J; Mahaffy, P; Connerney, J; Eparvier, F; Ergun, R; Larson, D; McFadden, J; Mitchell, D; Schneider, N; Zurek, R; Mazelle, C; Andersson, L; Andrews, D; Baird, D; Baker, D N; Bell, J M; Benna, M; Brain, D; Chaffin, M; Chamberlin, P; Chaufray, J-Y; Clarke, J; Collinson, G; Combi, M; Crary, F; Cravens, T; Crismani, M; Curry, S; Curtis, D; Deighan, J; Delory, G; Dewey, R; DiBraccio, G; Dong, C; Dong, Y; Dunn, P; Elrod, M; England, S; Eriksson, A; Espley, J; Evans, S; Fang, X; Fillingim, M; Fortier, K; Fowler, C M; Fox, J; Gröller, H; Guzewich, S; Hara, T; Harada, Y; Holsclaw, G; Jain, S K; Jolitz, R; Leblanc, F; Lee, C O; Lee, Y; Lefevre, F; Lillis, R; Livi, R; Lo, D; Ma, Y; Mayyasi, M; McClintock, W; McEnulty, T; Modolo, R; Montmessin, F; Morooka, M; Nagy, A; Olsen, K; Peterson, W; Rahmati, A; Ruhunusiri, S; Russell, C T; Sakai, S; Sauvaud, J-A; Seki, K; Steckiewicz, M; Stevens, M; Stewart, A I F; Stiepen, A; Stone, S; Tenishev, V; Thiemann, E; Tolson, R; Toublanc, D; Vogt, M; Weber, T; Withers, P; Woods, T; Yelle, R

    2015-11-01

    The Mars Atmosphere and Volatile Evolution (MAVEN) mission, during the second of its Deep Dip campaigns, made comprehensive measurements of martian thermosphere and ionosphere composition, structure, and variability at altitudes down to ~130 kilometers in the subsolar region. This altitude range contains the diffusively separated upper atmosphere just above the well-mixed atmosphere, the layer of peak extreme ultraviolet heating and primary reservoir for atmospheric escape. In situ measurements of the upper atmosphere reveal previously unmeasured populations of neutral and charged particles, the homopause altitude at approximately 130 kilometers, and an unexpected level of variability both on an orbit-to-orbit basis and within individual orbits. These observations help constrain volatile escape processes controlled by thermosphere and ionosphere structure and variability. PMID:26542579

  5. Ternary structure reveals mechanism of a membrane diacylglycerol kinase

    NASA Astrophysics Data System (ADS)

    Li, Dianfan; Stansfeld, Phillip J.; Sansom, Mark S. P.; Keogh, Aaron; Vogeley, Lutz; Howe, Nicole; Lyons, Joseph A.; Aragao, David; Fromme, Petra; Fromme, Raimund; Basu, Shibom; Grotjohann, Ingo; Kupitz, Christopher; Rendek, Kimberley; Weierstall, Uwe; Zatsepin, Nadia A.; Cherezov, Vadim; Liu, Wei; Bandaru, Sateesh; English, Niall J.; Gati, Cornelius; Barty, Anton; Yefanov, Oleksandr; Chapman, Henry N.; Diederichs, Kay; Messerschmidt, Marc; Boutet, Sébastien; Williams, Garth J.; Marvin Seibert, M.; Caffrey, Martin

    2015-12-01

    Diacylglycerol kinase catalyses the ATP-dependent conversion of diacylglycerol to phosphatidic acid in the plasma membrane of Escherichia coli. The small size of this integral membrane trimer, which has 121 residues per subunit, means that available protein must be used economically to craft three catalytic and substrate-binding sites centred about the membrane/cytosol interface. How nature has accomplished this extraordinary feat is revealed here in a crystal structure of the kinase captured as a ternary complex with bound lipid substrate and an ATP analogue. Residues, identified as essential for activity by mutagenesis, decorate the active site and are rationalized by the ternary structure. The γ-phosphate of the ATP analogue is positioned for direct transfer to the primary hydroxyl of the lipid whose acyl chain is in the membrane. A catalytic mechanism for this unique enzyme is proposed. The active site architecture shows clear evidence of having arisen by convergent evolution.

  6. Early MAVEN Deep Dip campaign reveals thermosphere and ionosphere variability

    NASA Astrophysics Data System (ADS)

    Bougher, S.; Jakosky, B.; Halekas, J.; Grebowsky, J.; Luhmann, J.; Mahaffy, P.; Connerney, J.; Eparvier, F.; Ergun, R.; Larson, D.; McFadden, J.; Mitchell, D.; Schneider, N.; Zurek, R.; Mazelle, C.; Andersson, L.; Andrews, D.; Baird, D.; Baker, D. N.; Bell, J. M.; Benna, M.; Brain, D.; Chaffin, M.; Chamberlin, P.; Chaufray, J.-Y.; Clarke, J.; Collinson, G.; Combi, M.; Crary, F.; Cravens, T.; Crismani, M.; Curry, S.; Curtis, D.; Deighan, J.; Delory, G.; Dewey, R.; DiBraccio, G.; Dong, C.; Dong, Y.; Dunn, P.; Elrod, M.; England, S.; Eriksson, A.; Espley, J.; Evans, S.; Fang, X.; Fillingim, M.; Fortier, K.; Fowler, C. M.; Fox, J.; Gröller, H.; Guzewich, S.; Hara, T.; Harada, Y.; Holsclaw, G.; Jain, S. K.; Jolitz, R.; Leblanc, F.; Lee, C. O.; Lee, Y.; Lefevre, F.; Lillis, R.; Livi, R.; Lo, D.; Ma, Y.; Mayyasi, M.; McClintock, W.; McEnulty, T.; Modolo, R.; Montmessin, F.; Morooka, M.; Nagy, A.; Olsen, K.; Peterson, W.; Rahmati, A.; Ruhunusiri, S.; Russell, C. T.; Sakai, S.; Sauvaud, J.-A.; Seki, K.; Steckiewicz, M.; Stevens, M.; Stewart, A. I. F.; Stiepen, A.; Stone, S.; Tenishev, V.; Thiemann, E.; Tolson, R.; Toublanc, D.; Vogt, M.; Weber, T.; Withers, P.; Woods, T.; Yelle, R.

    2015-11-01

    The Mars Atmosphere and Volatile Evolution (MAVEN) mission, during the second of its Deep Dip campaigns, made comprehensive measurements of martian thermosphere and ionosphere composition, structure, and variability at altitudes down to ~130 kilometers in the subsolar region. This altitude range contains the diffusively separated upper atmosphere just above the well-mixed atmosphere, the layer of peak extreme ultraviolet heating and primary reservoir for atmospheric escape. In situ measurements of the upper atmosphere reveal previously unmeasured populations of neutral and charged particles, the homopause altitude at approximately 130 kilometers, and an unexpected level of variability both on an orbit-to-orbit basis and within individual orbits. These observations help constrain volatile escape processes controlled by thermosphere and ionosphere structure and variability.

  7. Silicon-wafer-surface damage revealed by surface photovoltage measurements

    NASA Astrophysics Data System (ADS)

    Goodman, Alvin M.

    1982-11-01

    Anomalous results of surface photovoltage (SPV) measurements on Si wafers are shown to be associated with a damaged region beneath the illuminated surface of the wafer being measured. The anomaly is a concave-upward curvature of the I0(α-1) plot with an r2 value, derived from linear regression analysis, less than the normally observed minimum value (˜0.98). Removal of the damaged region by an appropriate etching procedure allows subsequent SPV measurements whose results are substantially free of the previously observed anomaly. The qualitative character of the anomaly can be reproduced by a simple theoretical model in which only one effect of the damage is considered; this effect is a diminished quantum efficiency for hole-electron pair generation by photon absorption in the damaged region. The results suggest the use of SPV measurements as a test procedure for revealing the presence of surface damage in Si wafers.

  8. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

    PubMed Central

    Ma, Li-Jun; van der Does, H. Charlotte; Borkovich, Katherine A.; Coleman, Jeffrey J.; Daboussi, Marie-Josée; Di Pietro, Antonio; Dufresne, Marie; Freitag, Michael; Grabherr, Manfred; Henrissat, Bernard; Houterman, Petra M.; Kang, Seogchan; Shim, Won-Bo; Woloshuk, Charles; Xie, Xiaohui; Xu, Jin-Rong; Antoniw, John; Baker, Scott E.; Bluhm, Burton H.; Breakspear, Andrew; Brown, Daren W.; Butchko, Robert A. E.; Chapman, Sinead; Coulson, Richard; Coutinho, Pedro M.; Danchin, Etienne G. J.; Diener, Andrew; Gale, Liane R.; Gardiner, Donald M.; Goff, Stephen; Hammond-Kosack, Kim E.; Hilburn, Karen; Hua-Van, Aurélie; Jonkers, Wilfried; Kazan, Kemal; Kodira, Chinnappa D.; Koehrsen, Michael; Kumar, Lokesh; Lee, Yong-Hwan; Li, Liande; Manners, John M.; Miranda-Saavedra, Diego; Mukherjee, Mala; Park, Gyungsoon; Park, Jongsun; Park, Sook-Young; Proctor, Robert H.; Regev, Aviv; Ruiz-Roldan, M. Carmen; Sain, Divya; Sakthikumar, Sharadha; Sykes, Sean; Schwartz, David C.; Turgeon, B. Gillian; Wapinski, Ilan; Yoder, Olen; Young, Sarah; Zeng, Qiandong; Zhou, Shiguo; Galagan, James; Cuomo, Christina A.; Kistler, H. Corby; Rep, Martijn

    2011-01-01

    Fusarium species are among the most important phytopathogenic and toxigenic fungi. To understand the molecular underpinnings of pathogenicity in the genus Fusarium, we compared the genomes of three phenotypically diverse species: Fusarium graminearum, Fusarium verticillioides and Fusarium oxysporum f. sp. lycopersici. Our analysis revealed lineage-specific (LS) genomic regions in F. oxysporum that include four entire chromosomes and account for more than one-quarter of the genome. LS regions are rich in transposons and genes with distinct evolutionary profiles but related to pathogenicity, indicative of horizontal acquisition. Experimentally, we demonstrate the transfer of two LS chromosomes between strains of F. oxysporum, converting a non-pathogenic strain into a pathogen. Transfer of LS chromosomes between otherwise genetically isolated strains explains the polyphyletic origin of host specificity and the emergence of new pathogenic lineages in F. oxysporum. These findings put the evolution of fungal pathogenicity into a new perspective. PMID:20237561

  9. Physical Principles of Skeletal Minerals Revealed with Spectromicroscopy

    SciTech Connect

    Gilbert, Pupa

    2009-08-05

    Skeletal elements of marine and terrestrial organisms have the most fascinating nano-to-macro-structures, attracting the attention of physicists, biologists, chemists, and materials scientists. Using X-PEEM spectromicroscopy we revealed some of the fundamental mechanisms leading to the formation of these biominerals. Specifically, we addressed the following questions and provided the answers: 1Q) How do teeth, bones, and echinoderm and mollusk shells acquire their unusual, curved and complex morphology, if they are composed of single crystals? 1A) Via amorphous precursor phases; 2Q) How does crystallinity propagate through the amorophous precursor phases in sea urchin spicules and teeth? 2A) By secondary nucleation, following random walk patterns; 3Q) How does iridescent mother-of-pearl become ordered? 3A) Gradually, through a kinetic mechanisms in which fastest growing single-crystals win the competition for space, thus end up being approximately co-oriented.

  10. Internal structure of sponge glass fiber revealed by ptychographic nanotomography.

    PubMed

    Birkbak, Mie E; Guizar-Sicairos, Manuel; Holler, Mirko; Birkedal, Henrik

    2016-04-01

    Sponge glass spicules have solicited great interest due to their mechanical and optical properties. Herein we use ptychographic nanotomography to obtain detailed insights into the internal structure of an anchor spicule from the Venus flower basket. The obtained dataset has 90nm resolution in 3D and provides quantitative determination of the electron density. The data reveal significant variations in electron density across the spicule. The central organic filament is found to be slightly but significantly displaced from the spicule central axis. Analysis of the electron density affords an estimate of a protein volume fraction in the organic filament of about 70%. In the highly mineralized part of the spicule, the electron density is seen to display circular symmetry and be neigh independent of position along the spicule long axis. Variations in the electron density beyond those included in current models of spicule mechanics are observed. PMID:26853498

  11. ID-Check: Online Concealed Information Test Reveals True Identity.

    PubMed

    Verschuere, Bruno; Kleinberg, Bennett

    2016-01-01

    The Internet has already changed people's lives considerably and is likely to drastically change forensic research. We developed a web-based test to reveal concealed autobiographical information. Initial studies identified a number of conditions that affect diagnostic efficiency. By combining these moderators, this study investigated the full potential of the online ID-check. Participants (n = 101) tried to hide their identity and claimed a false identity in a reaction time-based Concealed Information Test. Half of the participants were presented with personal details (e.g., first name, last name, birthday), whereas the others only saw irrelevant details. Results showed that participants' true identity could be detected with high accuracy (AUC = 0.98; overall accuracy: 86-94%). Online memory detection can reliably and validly detect whether someone is hiding their true identity. This suggests that online memory detection might become a valuable tool for forensic applications. PMID:26390033

  12. Karyotype revealed 47, xxy chromosome (Klinefelter syndrome): a case report.

    PubMed

    Jha, Chandra Bhushan; Dhungel, Shaligram; Rai, Dilip

    2007-09-01

    The Klinefelter syndrome is most common chromosomal cause of male infertility. However, the many cases of the syndrome remain undiagnosed due to variations in clinical presentation. A patient attended to surgical OPD with complaints of loss of secondary sexual characteristics and infertility. Physical examination revealed tall stature, thin built, small testes size, and absence of beard and pubic hairs. Karyotype and biochemical tests were performed to detect chromosomal abnormality as well hormonal level to confirm the diagnosis of androgen deficiency syndrome. Chromosomal complement confirmed the case of Klinefelter syndrome (47, XXY) causing androgen deficiency. Timely detection of Klinefelter syndrome is important to formulate further treatment modalities for the benefit of the patient. PMID:18092444

  13. Spanning tree separation reveals community structure in networks

    NASA Astrophysics Data System (ADS)

    Kim, Jongkwang; Wilhelm, Thomas

    2013-03-01

    We present a simple, intuitive, and effective approach for network clustering. It is based on basic concepts of linear algebra such as efficient calculation of spanning trees, and can be implemented in a few lines of code. We introduce the node separation measure spanning tree separation (STS) and the corresponding graph distance measure spanning tree vector similarity distance (STVSD). We demonstrate that the STS is a link salience measure able to identify the backbone of networks. The STVSD is used to reveal the hierarchical community structure of networks. We show that it, together with the clustering quality measure partition density, is on a par with the best graph or network clustering methods known, in terms of both quality and efficiency. In perspective, we note that our approach could also handle weighted and directed networks and could be used for identification of overlapping communities.

  14. Ultrafast cooling reveals microsecond-scale biomolecular dynamics.

    PubMed

    Polinkovsky, Mark E; Gambin, Yann; Banerjee, Priya R; Erickstad, Michael J; Groisman, Alex; Deniz, Ashok A

    2014-01-01

    The temperature-jump technique, in which the sample is rapidly heated by a powerful laser pulse, has been widely used to probe the fast dynamics of folding of proteins and nucleic acids. However, the existing temperature-jump setups tend to involve sophisticated and expensive instrumentation, while providing only modest temperature changes of ~10-15 °C, and the temperature changes are only rapid for heating, but not cooling. Here we present a setup comprising a thermally conductive sapphire substrate with light-absorptive nano-coating, a microfluidic device and a rapidly switched moderate-power infrared laser with the laser beam focused on the nano-coating, enabling heating and cooling of aqueous solutions by ~50 °C on a 1-μs time scale. The setup is used to probe folding and unfolding dynamics of DNA hairpins after direct and inverse temperature jumps, revealing low-pass filter behaviour during periodic temperature variations. PMID:25517430

  15. Integrative Acoustic Mapping Reveals Hudson RIver Sediment Processes an Habitats

    NASA Astrophysics Data System (ADS)

    Nitsche, F. O.; Bell, R.; Carbotte, S. M.; Ryan, W. B. F.; Slagle, A.; Chillrud, S.; Kenna, T.; Flood, R.; Ferrini, V.; Cerrato, R.; McHugh, C.; Strayer, D.

    2005-06-01

    Rivers and estuaries around the world are the focus of human settlements and activities. Needs for clean water, ecosystem preservation, commercial navigation, industrial development, and recreational access compete for the use of estuaries, and management of these resources requires a detailed understanding of estuarine morphology and sediment dynamics. This article presents an overview of the first estuary-wide study of a heavily used estuary, the Hudson River, based on high-resolution acoustic mapping of the river bottom. The integration of three high-resolution acoustic methods with extensive sampling reveals an unexpected complexity of bottom features and allows detailed classification of the benthic environment in terms of riverbed morphology, sediment type, and sedimentary processes.

  16. Graph analysis of cortical networks reveals complex anatomical communication substrate

    NASA Astrophysics Data System (ADS)

    Zamora-López, Gorka; Zhou, Changsong; Kurths, Jürgen

    2009-03-01

    Sensory information entering the nervous system follows independent paths of processing such that specific features are individually detected. However, sensory perception, awareness, and cognition emerge from the combination of information. Here we have analyzed the corticocortical network of the cat, looking for the anatomical substrate which permits the simultaneous segregation and integration of information in the brain. We find that cortical communications are mainly governed by three topological factors of the underlying network: (i) a large density of connections, (ii) segregation of cortical areas into clusters, and (iii) the presence of highly connected hubs aiding the multisensory processing and integration. Statistical analysis of the shortest paths reveals that, while information is highly accessible to all cortical areas, the complexity of cortical information processing may arise from the rich and intricate alternative paths in which areas can influence each other.

  17. Early allelic selection in maize as revealed by ancient DNA.

    PubMed

    Jaenicke-Després, Viviane; Buckler, Ed S; Smith, Bruce D; Gilbert, M Thomas P; Cooper, Alan; Doebley, John; Pääbo, Svante

    2003-11-14

    Maize was domesticated from teosinte, a wild grass, by approximately 6300 years ago in Mexico. After initial domestication, early farmers continued to select for advantageous morphological and biochemical traits in this important crop. However, the timing and sequence of character selection are, thus far, known only for morphological features discernible in corn cobs. We have analyzed three genes involved in the control of plant architecture, storage protein synthesis, and starch production from archaeological maize samples from Mexico and the southwestern United States. The results reveal that the alleles typical of contemporary maize were present in Mexican maize by 4400 years ago. However, as recently as 2000 years ago, allelic selection at one of the genes may not yet have been complete. PMID:14615538

  18. Comparative genomics reveals insights into avian genome evolution and adaptation.

    PubMed

    Zhang, Guojie; Li, Cai; Li, Qiye; Li, Bo; Larkin, Denis M; Lee, Chul; Storz, Jay F; Antunes, Agostinho; Greenwold, Matthew J; Meredith, Robert W; Ödeen, Anders; Cui, Jie; Zhou, Qi; Xu, Luohao; Pan, Hailin; Wang, Zongji; Jin, Lijun; Zhang, Pei; Hu, Haofu; Yang, Wei; Hu, Jiang; Xiao, Jin; Yang, Zhikai; Liu, Yang; Xie, Qiaolin; Yu, Hao; Lian, Jinmin; Wen, Ping; Zhang, Fang; Li, Hui; Zeng, Yongli; Xiong, Zijun; Liu, Shiping; Zhou, Long; Huang, Zhiyong; An, Na; Wang, Jie; Zheng, Qiumei; Xiong, Yingqi; Wang, Guangbiao; Wang, Bo; Wang, Jingjing; Fan, Yu; da Fonseca, Rute R; Alfaro-Núñez, Alonzo; Schubert, Mikkel; Orlando, Ludovic; Mourier, Tobias; Howard, Jason T; Ganapathy, Ganeshkumar; Pfenning, Andreas; Whitney, Osceola; Rivas, Miriam V; Hara, Erina; Smith, Julia; Farré, Marta; Narayan, Jitendra; Slavov, Gancho; Romanov, Michael N; Borges, Rui; Machado, João Paulo; Khan, Imran; Springer, Mark S; Gatesy, John; Hoffmann, Federico G; Opazo, Juan C; Håstad, Olle; Sawyer, Roger H; Kim, Heebal; Kim, Kyu-Won; Kim, Hyeon Jeong; Cho, Seoae; Li, Ning; Huang, Yinhua; Bruford, Michael W; Zhan, Xiangjiang; Dixon, Andrew; Bertelsen, Mads F; Derryberry, Elizabeth; Warren, Wesley; Wilson, Richard K; Li, Shengbin; Ray, David A; Green, Richard E; O'Brien, Stephen J; Griffin, Darren; Johnson, Warren E; Haussler, David; Ryder, Oliver A; Willerslev, Eske; Graves, Gary R; Alström, Per; Fjeldså, Jon; Mindell, David P; Edwards, Scott V; Braun, Edward L; Rahbek, Carsten; Burt, David W; Houde, Peter; Zhang, Yong; Yang, Huanming; Wang, Jian; Jarvis, Erich D; Gilbert, M Thomas P; Wang, Jun

    2014-12-12

    Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits. PMID:25504712

  19. Spring-block model reveals region-like structures.

    PubMed

    Máté, Gabriell; Néda, Zoltán; Benedek, József

    2011-01-01

    A mechanical spring-block model is used for realizing an objective space partition of settlements from a geographic territory in region-like structures. The method is based on the relaxation-dynamics of the spring-block system and reveals in a hierarchical manner region-like entities at different spatial scales. It takes into account in an elegant manner both the spatiality of the elements and the connectivity relations among them. Spatiality is taken into account by using the geographic coordinates of the settlements, and by detecting the neighbors with the help of a Delaunay triangulation. Connectivity between neighboring settlements are quantified using a Pearson-like correlation for the relative variation of a relevant socio-economic parameter (population size, GDP, tax payed per inhabitant, etc.). The method is implemented in an interactive JAVA application and it is applied with success for an artificially generated society and for the case of USA, Hungary and Transylvania. PMID:21346819

  20. Revealing the superior perceptibility of words in Arabic.

    PubMed

    Jordan, Timothy R; Paterson, Kevin B; Almabruk, Abubaker A A

    2010-01-01

    When alphabetic stimuli are presented very briefly, people perceive real words better than nonwords. It is generally accepted that this word superiority effect reflects the efficiency of visual word perception. However, much of what is known about this effect comes from research conducted in languages using the Latin alphabet (eg English, French, Italian), and little is known about whether alphabetic languages with visual properties fundamentally different from Latinate languages also produce word superiority effects. We report an experiment in which stimuli (words, illegal nonwords, and pseudowords) were presented in Arabic, which is a cursive script, read from right to left. The findings revealed advantages for words over pseudowords and illegal nonwords, and for pseudowords over illegal nonwords, indicating that the superiority effects reported for Latinate languages are also observed in Arabic. Implications of these findings for understanding the processes involved in word recognition are discussed. PMID:20465177

  1. Multicentric Castleman's Disease in a Child Revealed by Chronic Diarrhea

    PubMed Central

    Benmiloud, Sarra; Chaouki, Sana; Atmani, Samir; Hida, Moustapha

    2015-01-01

    Multicentric Castleman's disease is a rare benign and unexplained lymphoproliferative disorder that is extremely uncommon in children. It presents with fever, systemic symptoms, generalized lymphadenopathy, and laboratory markers of inflammation. Its treatment is not standardized and its prognosis is poor. We report a novel case of multicentric Castleman's disease in a 13-year-old girl who had presented with chronic diarrhea as the only initial presenting symptom. The diagnosis of celiac or inflammatory bowel diseases was suspected, but two and a half years later, the diagnosis of multicentric Castleman's disease was brought following the appearance of abdominal mass whose biopsy revealed Castleman's disease in the plasma cell form. The outcome was favorable after treatment by corticosteroid, chemotherapy, and surgery. The occurrence of diarrhea as the initial symptom of multicentric Castleman's disease without lymph node involvement is very rare. This case report underlines the diagnostic difficulties and the long interval between onset and diagnosis when diarrhea occurs first. PMID:25737793

  2. MNase titration reveals differences between nucleosome occupancy and chromatin accessibility.

    PubMed

    Mieczkowski, Jakub; Cook, April; Bowman, Sarah K; Mueller, Britta; Alver, Burak H; Kundu, Sharmistha; Deaton, Aimee M; Urban, Jennifer A; Larschan, Erica; Park, Peter J; Kingston, Robert E; Tolstorukov, Michael Y

    2016-01-01

    Chromatin accessibility plays a fundamental role in gene regulation. Nucleosome placement, usually measured by quantifying protection of DNA from enzymatic digestion, can regulate accessibility. We introduce a metric that uses micrococcal nuclease (MNase) digestion in a novel manner to measure chromatin accessibility by combining information from several digests of increasing depths. This metric, MACC (MNase accessibility), quantifies the inherent heterogeneity of nucleosome accessibility in which some nucleosomes are seen preferentially at high MNase and some at low MNase. MACC interrogates each genomic locus, measuring both nucleosome location and accessibility in the same assay. MACC can be performed either with or without a histone immunoprecipitation step, and thereby compares histone and non-histone protection. We find that changes in accessibility at enhancers, promoters and other regulatory regions do not correlate with changes in nucleosome occupancy. Moreover, high nucleosome occupancy does not necessarily preclude high accessibility, which reveals novel principles of chromatin regulation. PMID:27151365

  3. Deciphering CAPTCHAs: what a Turing test reveals about human cognition.

    PubMed

    Hannagan, Thomas; Ktori, Maria; Chanceaux, Myriam; Grainger, Jonathan

    2012-01-01

    Turning Turing's logic on its head, we used widespread letter-based Turing Tests found on the internet (CAPTCHAs) to shed light on human cognition. We examined the basis of the human ability to solve CAPTCHAs, where machines fail. We asked whether this is due to our use of slow-acting inferential processes that would not be available to machines, or whether fast-acting automatic orthographic processing in humans has superior robustness to shape variations. A masked priming lexical decision experiment revealed efficient processing of CAPTCHA words in conditions that rule out the use of slow inferential processing. This shows that the human superiority in solving CAPTCHAs builds on a high degree of invariance to location and continuous transforms, which is achieved during the very early stages of visual word recognition in skilled readers. PMID:22396750

  4. A tylosin ketoreductase reveals how chirality is determined in polyketides.

    PubMed

    Keatinge-Clay, Adrian T

    2007-08-01

    Because it controls the majority of polyketide stereocenters, the ketoreductase (KR) is a central target in engineering polyketide synthases (PKSs). To elucidate the mechanisms of stereocontrol, the structure of KR from the first module of the tylosin PKS was determined. A comparison with a recently solved erythromycin KR that operates on the same substrate explains why their products have opposite alpha-substituent chiralities. The structure reveals how polyketides are guided into the active site by key residues in different KR types. There are four types of reductase-competent KRs, each capable of fixing a unique combination of alpha-substituent and beta-hydroxyl group chiralities, as well as two types of reductase-incompetent KRs that control alpha-substituent chirality alone. A protocol to assign how a module will enforce substituent chirality based on its sequence is presented. PMID:17719489

  5. Mediated amperometry reveals different modes of yeast responses to sugars.

    PubMed

    Garjonyte, Rasa; Melvydas, Vytautas; Malinauskas, Albertas

    2016-02-01

    Menadione-mediated amperometry at carbon paste electrodes modified with various yeasts (Saccharomyces cerevisiae, Candida pulcherrima, Pichia guilliermondii and Debaryomyces hansenii) was employed to monitor redox activity inside the yeast cells induced by glucose, fructose, sucrose, maltose or galactose. Continuous measurements revealed distinct modes (transient or gradually increasing) of the current development during the first 2 to 3 min after subjection to glucose, fructose and sucrose at electrodes containing S. cerevisiae and non-Saccharomyces strains. Different modes (increasing or decreasing) of the current development after yeast subjection to galactose at electrodes with S. cerevisiae or D. hansenii and at electrodes with C. pulcherrima and P. guilliermondii suggested different mechanisms of galactose assimilation. PMID:26523505

  6. The genome of Tetranychus urticae reveals herbivorous pest adaptations

    PubMed Central

    Grbić, Miodrag; Van Leeuwen, Thomas; Clark, Richard M.; Rombauts, Stephane; Rouzé, Pierre; Grbić, Vojislava; Osborne, Edward J.; Dermauw, Wannes; Ngoc, Phuong Cao Thi; Ortego, Félix; Hernández-Crespo, Pedro; Diaz, Isabel; Martinez, Manuel; Navajas, Maria; Sucena, Élio; Magalhães, Sara; Nagy, Lisa; Pace, Ryan M.; Djuranović, Sergej; Smagghe, Guy; Iga, Masatoshi; Christiaens, Olivier; Veenstra, Jan A.; Ewer, John; Villalobos, Rodrigo Mancilla; Hutter, Jeffrey L.; Hudson, Stephen D.; Velez, Marisela; Yi, Soojin V.; Zeng, Jia; Pires-daSilva, Andre; Roch, Fernando; Cazaux, Marc; Navarro, Marie; Zhurov, Vladimir; Acevedo, Gustavo; Bjelica, Anica; Fawcett, Jeffrey A.; Bonnet, Eric; Martens, Cindy; Baele, Guy; Wissler, Lothar; Sanchez-Rodriguez, Aminael; Tirry, Luc; Blais, Catherine; Demeestere, Kristof; Henz, Stefan R.; Gregory, T. Ryan; Mathieu, Johannes; Verdon, Lou; Farinelli, Laurent; Schmutz, Jeremy; Lindquist, Erika; Feyereisen, René; Van de Peer, Yves

    2016-01-01

    The spider mite Tetranychus urticae is a cosmopolitan agricultural pest with an extensive host plant range and an extreme record of pesticide resistance. Here we present the completely sequenced and annotated spider mite genome, representing the first complete chelicerate genome. At 90 megabases T. urticae has the smallest sequenced arthropod genome. Compared with other arthropods, the spider mite genome shows unique changes in the hormonal environment and organization of the Hox complex, and also reveals evolutionary innovation of silk production. We find strong signatures of polyphagy and detoxification in gene families associated with feeding on different hosts and in new gene families acquired by lateral gene transfer. Deep transcriptome analysis of mites feeding on different plants shows how this pest responds to a changing host environment. The T. urticae genome thus offers new insights into arthropod evolution and plant–herbivore interactions, and provides unique opportunities for developing novel plant protection strategies. PMID:22113690

  7. Proteomic profiling reveals insights into Triticeae stigma development and function

    PubMed Central

    Nazemof, Nazila; Couroux, Philippe; Rampitsch, Christof; Xing, Tim; Robert, Laurian S.

    2014-01-01

    To our knowledge, this study represents the first high-throughput characterization of a stigma proteome in the Triticeae. A total of 2184 triticale mature stigma proteins were identified using three different gel-based approaches combined with mass spectrometry. The great majority of these proteins are described in a Triticeae stigma for the first time. These results revealed many proteins likely to play important roles in stigma development and pollen–stigma interactions, as well as protection against biotic and abiotic stresses. Quantitative comparison of the triticale stigma transcriptome and proteome showed poor correlation, highlighting the importance of having both types of analysis. This work makes a significant contribution towards the elucidation of the Triticeae stigma proteome and provides novel insights into its role in stigma development and function. PMID:25170101

  8. T-cadherin structures reveal a novel adhesive binding mechanism

    SciTech Connect

    Ciatto, Carlo; Bahna, Fabiana; Zampieri, Niccolò; VanSteenhouse, Harper C.; Katsamba, Phini S; Ahlsen, Goran; Harrison, Oliver J.; Brasch, Julia; Jin, Xiangshu; Posy, Shoshana; Vendome, Jeremie; Ranscht, Barbara; Jessell, Thomas M.; Honig, Barry; Shapiro, Lawrence

    2010-03-30

    Vertebrate genomes encode 19 classical cadherins and about 100 nonclassical cadherins. Adhesion by classical cadherins depends on binding interactions in their N-terminal EC1 domains, which swap N-terminal {beta}-strands between partner molecules from apposing cells. However, strand-swapping sequence signatures are absent from nonclassical cadherins, raising the question of how these proteins function in adhesion. Here, we show that T-cadherin, a glycosylphosphatidylinositol (GPI)-anchored cadherin, forms dimers through an alternative nonswapped interface near the EC1-EC2 calcium-binding sites. Mutations within this interface ablate the adhesive capacity of T-cadherin. These nonadhesive T-cadherin mutants also lose the ability to regulate neurite outgrowth from T-cadherin-expressing neurons. Our findings reveal the likely molecular architecture of the T-cadherin homophilic interface and its requirement for axon outgrowth regulation. The adhesive binding mode used by T-cadherin may also be used by other nonclassical cadherins

  9. Ethiopian population dermatoglyphic study reveals linguistic stratification of diversity.

    PubMed

    Yohannes, Seile; Bekele, Endashaw

    2015-01-01

    The manifestation of ethnic, blood type, & gender-wise population variations regarding Dermatoglyphic manifestations are of interest to assess intra-group diversity and differentiation. The present study reports on the analysis of qualitaive and quantitative finger Dermatoglyphic traits of 382 individuals cross-sectionally sampled from an administrative region of Ethiopia, consisting of five ethnic cohorts from the Afro-Asiatic & Nilo-Saharan affiliations. These Dermatoglyphic parameters were then applied in the assessment of diversity & differentiation, including Heterozygosity, Fixation, Panmixia, Wahlund's variance, Nei's measure of genetic diversity, and thumb & finger pattern genotypes, which were inturn used in homology inferences as summarized by a Neighbour-Joining tree constructed from Nei's standard genetic distance. Results revealed significant correlation between Dermatoglyphics & population parameters that were further found to be in concordance with the historical accounts of the ethnic groups. Such inductions as the ancient north-eastern presence and subsequent admixure events of the Oromos (PII= 15.01), the high diversity of the Amharas (H= 0.1978, F= 0.6453, and P= 0.4144), and the Nilo-Saharan origin of the Berta group (PII= 10.66) are evidences to this. The study has further tested the possibility of applying Dermatoglyphics in population genetic & anthropologic research, highlighting on the prospect of developing a method to trace back population origins & ancient movement patterns. Additionally, linguistic clustering was deemed significant for the Ethiopian population, coinciding with recent genome wide studies that have ascertained that linguistic clustering as to being more crucial than the geographical patterning in the Ethiopian context. Finally, Dermatoglyphic markers have been proven to be endowed with a strong potential as non-invasive preliminary tools applicable prior to genetic studies to analyze ethnically sub-divided populations and

  10. Subfield profitability analysis reveals an economic case for cropland diversification

    NASA Astrophysics Data System (ADS)

    Brandes, E.; McNunn, G. S.; Schulte, L. A.; Bonner, I. J.; Muth, D. J.; Babcock, B. A.; Sharma, B.; Heaton, E. A.

    2016-01-01

    Public agencies and private enterprises increasingly desire to achieve ecosystem service outcomes in agricultural systems, but are limited by perceived conflicts between economic and ecosystem service goals and a lack of tools enabling effective operational management. Here we use Iowa—an agriculturally homogeneous state representative of the Maize Belt—to demonstrate an economic rationale for cropland diversification at the subfield scale. We used a novel computational framework that integrates disparate but publicly available data to map ˜3.3 million unique potential management polygons (9.3 Mha) and reveal subfield opportunities to increase overall field profitability. We analyzed subfield profitability for maize/soybean fields during 2010-2013—four of the most profitable years in recent history—and projected results for 2015. While cropland operating at a loss of US 250 ha-1 or more was negligible between 2010 and 2013 at 18 000-190 000 ha (<2% of row-crop land), the extent of highly unprofitable land increased to 2.5 Mha, or 27% of row-crop land, in the 2015 projection. Aggregation of these areas to the township level revealed ‘hotspots’ for potential management change in Western, Central, and Northeast Iowa. In these least profitable areas, incorporating conservation management that breaks even (e.g., planting low-input perennials), into low-yielding portions of fields could increase overall cropland profitability by 80%. This approach is applicable to the broader region and differs substantially from the status quo of ‘top-down’ land management for conservation by harnessing private interest to align profitability with the production of ecosystem services.

  11. Architecture of cognitive flexibility revealed by lesion mapping

    PubMed Central

    Barbey, Aron K.; Colom, Roberto; Grafman, Jordan

    2013-01-01

    Neuroscience has made remarkable progress in understanding the architecture of human intelligence, identifying a distributed network of brain structures that support goal-directed, intelligent behavior. However, the neural foundations of cognitive flexibility and adaptive aspects of intellectual function remain to be well characterized. Here, we report a human lesion study (n = 149) that investigates the neural bases of key competencies of cognitive flexibility (i.e., mental flexibility and the fluent generation of new ideas) and systematically examine their contributions to a broad spectrum of cognitive and social processes, including psychometric intelligence (Wechsler Adult Intelligence Scale), emotional intelligence (Mayer, Salovey, Caruso Emotional Intelligence Test), and personality (Neuroticism–Extraversion–Openness Personality Inventory). Latent variable modeling was applied to obtain error-free indices of each factor, followed by voxel-based lesion-symptom mapping to elucidate their neural substrates. Regression analyses revealed that latent scores for psychometric intelligence reliably predict latent scores for cognitive flexibility (adjusted R2 = 0.94). Lesion mapping results further indicated that these convergent processes depend on a shared network of frontal, temporal, and parietal regions, including white matter association tracts, which bind these areas into an integrated system. A targeted analysis of the unique variance explained by cognitive flexibility further revealed selective damage within the right superior temporal gyrus, a region known to support insight and the recognition of novel semantic relations. The observed findings motivate an integrative framework for understanding the neural foundations of adaptive behavior, suggesting that core elements of cognitive flexibility emerge from a distributed network of brain regions that support specific competencies for human intelligence. PMID:23721727

  12. Running over rough terrain reveals limb control for intrinsic stability

    PubMed Central

    Daley, Monica A.; Biewener, Andrew A.

    2006-01-01

    Legged animals routinely negotiate rough, unpredictable terrain with agility and stability that outmatches any human-built machine. Yet, we know surprisingly little about how animals accomplish this. Current knowledge is largely limited to studies of steady movement. These studies have revealed fundamental mechanisms used by terrestrial animals for steady locomotion. However, it is unclear whether these models provide an appropriate framework for the neuromuscular and mechanical strategies used to achieve dynamic stability over rough terrain. Perturbation experiments shed light on this issue, revealing the interplay between mechanics and neuromuscular control. We measured limb mechanics of helmeted guinea fowl (Numida meleagris) running over an unexpected drop in terrain, comparing their response to predictions of the mass–spring running model. Adjustment of limb contact angle explains 80% of the variation in stance-phase limb loading following the perturbation. Surprisingly, although limb stiffness varies dramatically, it does not influence the response. This result agrees with a mass–spring model, although it differs from previous findings on humans running over surfaces of varying compliance. However, guinea fowl sometimes deviate from mass–spring dynamics through posture-dependent work performance of the limb, leading to substantial energy absorption following the perturbation. This posture-dependent actuation allows the animal to absorb energy and maintain desired velocity on a sudden substrate drop. Thus, posture-dependent work performance of the limb provides inherent velocity control over rough terrain. These findings highlight how simple mechanical models extend to unsteady conditions, providing fundamental insights into neuromuscular control of movement and the design of dynamically stable legged robots and prosthetic devices. PMID:17032779

  13. Architecture of cognitive flexibility revealed by lesion mapping.

    PubMed

    Barbey, Aron K; Colom, Roberto; Grafman, Jordan

    2013-11-15

    Neuroscience has made remarkable progress in understanding the architecture of human intelligence, identifying a distributed network of brain structures that support goal-directed, intelligent behavior. However, the neural foundations of cognitive flexibility and adaptive aspects of intellectual function remain to be well characterized. Here, we report a human lesion study (n=149) that investigates the neural bases of key competencies of cognitive flexibility (i.e., mental flexibility and the fluent generation of new ideas) and systematically examine their contributions to a broad spectrum of cognitive and social processes, including psychometric intelligence (Wechsler Adult Intelligence Scale), emotional intelligence (Mayer, Salovey, Caruso Emotional Intelligence Test), and personality (Neuroticism-Extraversion-Openness Personality Inventory). Latent variable modeling was applied to obtain error-free indices of each factor, followed by voxel-based lesion-symptom mapping to elucidate their neural substrates. Regression analyses revealed that latent scores for psychometric intelligence reliably predict latent scores for cognitive flexibility (adjusted R(2)=0.94). Lesion mapping results further indicated that these convergent processes depend on a shared network of frontal, temporal, and parietal regions, including white matter association tracts, which bind these areas into an integrated system. A targeted analysis of the unique variance explained by cognitive flexibility further revealed selective damage within the right superior temporal gyrus, a region known to support insight and the recognition of novel semantic relations. The observed findings motivate an integrative framework for understanding the neural foundations of adaptive behavior, suggesting that core elements of cognitive flexibility emerge from a distributed network of brain regions that support specific competencies for human intelligence. PMID:23721727

  14. Sand Dunes And Large Rocks Revealed By Camera 1

    NASA Technical Reports Server (NTRS)

    1976-01-01

    Sand dunes and large rocks are revealed in this panorama picture of Mars, the first photograph taken by Viking l's Camera 1 on July 23. The horizon is approximately 3 kilometers (2 miles) away. The left and right thirds of this picture are the same areas that were photographed on July 20 (Sol O) by Camera 2 and provide stereo coverage. The middle third reveals a part of the Martian surface not seen on the July 20 panorama. The late afternoon sun is high in the sky over the left side of the picture. The support struts of the S-band high-gain antenna extend to the top of the picture. The American flags are located on the two RTG (Radioisotope Thermoelectric Generator) wind screens. In the middle third of the picture, the rocky surface is covered by thick deposits of wind-blown material, forming numerous dunes. At the center of the picture on the horizon are two low hills which may be part of the rim of a distant crater. Two very large rocks are visible in the middleground; the nearer one is 3 meters (10 feet) in diameter and is 8 meters (25 feet) from the spacecraft. A cloud layer is visible halfway between the horizon and the top of the picture. The meteorology boom is located right of center. Behind it, the 'White Mesa' is visible, which could be seen on the far left side of the Sol O Camera 2 panorama. In the near ground are numerous rocks about 10 cm (4 inches) across, with horseshoe-shaped scour marks on their upwind side and wind tails in their lee. The fine-grained material in front of them contains small pits formed by impact of material kicked out by the Lander spacecraft's rocket engines.

  15. Next Generation Sequencing Reveals the Hidden Diversity of Zooplankton Assemblages

    PubMed Central

    Harmer, Rachel A.; Somerfield, Paul J.; Atkinson, Angus

    2013-01-01

    Background Zooplankton play an important role in our oceans, in biogeochemical cycling and providing a food source for commercially important fish larvae. However, difficulties in correctly identifying zooplankton hinder our understanding of their roles in marine ecosystem functioning, and can prevent detection of long term changes in their community structure. The advent of massively parallel next generation sequencing technology allows DNA sequence data to be recovered directly from whole community samples. Here we assess the ability of such sequencing to quantify richness and diversity of a mixed zooplankton assemblage from a productive time series site in the Western English Channel. Methodology/Principle Findings Plankton net hauls (200 µm) were taken at the Western Channel Observatory station L4 in September 2010 and January 2011. These samples were analysed by microscopy and metagenetic analysis of the 18S nuclear small subunit ribosomal RNA gene using the 454 pyrosequencing platform. Following quality control a total of 419,041 sequences were obtained for all samples. The sequences clustered into 205 operational taxonomic units using a 97% similarity cut-off. Allocation of taxonomy by comparison with the National Centre for Biotechnology Information database identified 135 OTUs to species level, 11 to genus level and 1 to order, <2.5% of sequences were classified as unknowns. By comparison a skilled microscopic analyst was able to routinely enumerate only 58 taxonomic groups. Conclusions Metagenetics reveals a previously hidden taxonomic richness, especially for Copepoda and hard-to-identify meroplankton such as Bivalvia, Gastropoda and Polychaeta. It also reveals rare species and parasites. We conclude that Next Generation Sequencing of 18S amplicons is a powerful tool for elucidating the true diversity and species richness of zooplankton communities. While this approach allows for broad diversity assessments of plankton it may become increasingly

  16. Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

    PubMed Central

    Math, M.; Tarpey, Patrick; Varela, Ignacio; Phillimore, Benjamin; Begum, Sharmin; McDonald, Neil Q.; Butler, Adam; Jones, David; Raine, Keiran; Latimer, Calli; Santos, Claudio R.; Nohadani, Mahrokh; Eklund, Aron C.; Spencer-Dene, Bradley; Clark, Graham; Pickering, Lisa; Stamp, Gordon; Gore, Martin; Szallasi, Zoltan; Downward, Julian; Futreal, P. Andrew

    2016-01-01

    Background Intratumor heterogeneity may foster tumor evolution and adaptation and hinder personalized-medicine strategies that depend on results from single tumor-biopsy samples. Methods To examine intratumor heterogeneity, we performed exome sequencing, chromosome aberration analysis, and ploidy profiling on multiple spatially separated samples obtained from primary renal carcinomas and associated metastatic sites. We characterized the consequences of intratumor heterogeneity using immunohistochemical analysis, mutation functional analysis, and profiling of messenger RNA expression. Results Phylogenetic reconstruction revealed branched evolutionary tumor growth, with 63 to 69% of all somatic mutations not detectable across every tumor region. Intratumor heterogeneity was observed for a mutation within an autoinhibitory domain of the mammalian target of rapamycin (mTOR) kinase, correlating with S6 and 4EBP phosphorylation in vivo and constitutive activation of mTOR kinase activity in vitro. Mutational intratumor heterogeneity was seen for multiple tumor-suppressor genes converging on loss of function; SETD2, PTEN, and KDM5C underwent multiple distinct and spatially separated inactivating mutations within a single tumor, suggesting convergent phenotypic evolution. Gene-expression signatures of good and poor prognosis were detected in different regions of the same tumor. Allelic composition and ploidy profiling analysis revealed extensive intratumor heterogeneity, with 26 of 30 tumor samples from four tumors harboring divergent allelic-imbalance profiles and with ploidy heterogeneity in two of four tumors. Conclusions Intratumor heterogeneity can lead to underestimation of the tumor genomics landscape portrayed from single tumor-biopsy samples and may present major challenges to personalized-medicine and biomarker development. Intratumor heterogeneity, associated with heterogeneous protein function, may foster tumor adaptation and therapeutic failure through

  17. Four not six: Revealing culturally common facial expressions of emotion.

    PubMed

    Jack, Rachael E; Sun, Wei; Delis, Ioannis; Garrod, Oliver G B; Schyns, Philippe G

    2016-06-01

    As a highly social species, humans generate complex facial expressions to communicate a diverse range of emotions. Since Darwin's work, identifying among these complex patterns which are common across cultures and which are culture-specific has remained a central question in psychology, anthropology, philosophy, and more recently machine vision and social robotics. Classic approaches to addressing this question typically tested the cross-cultural recognition of theoretically motivated facial expressions representing 6 emotions, and reported universality. Yet, variable recognition accuracy across cultures suggests a narrower cross-cultural communication supported by sets of simpler expressive patterns embedded in more complex facial expressions. We explore this hypothesis by modeling the facial expressions of over 60 emotions across 2 cultures, and segregating out the latent expressive patterns. Using a multidisciplinary approach, we first map the conceptual organization of a broad spectrum of emotion words by building semantic networks in 2 cultures. For each emotion word in each culture, we then model and validate its corresponding dynamic facial expression, producing over 60 culturally valid facial expression models. We then apply to the pooled models a multivariate data reduction technique, revealing 4 latent and culturally common facial expression patterns that each communicates specific combinations of valence, arousal, and dominance. We then reveal the face movements that accentuate each latent expressive pattern to create complex facial expressions. Our data questions the widely held view that 6 facial expression patterns are universal, instead suggesting 4 latent expressive patterns with direct implications for emotion communication, social psychology, cognitive neuroscience, and social robotics. (PsycINFO Database Record PMID:27077757

  18. Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth

    PubMed Central

    Cuomo, Christina A.; Desjardins, Christopher A.; Bakowski, Malina A.; Goldberg, Jonathan; Ma, Amy T.; Becnel, James J.; Didier, Elizabeth S.; Fan, Lin; Heiman, David I.; Levin, Joshua Z.; Young, Sarah; Zeng, Qiandong; Troemel, Emily R.

    2012-01-01

    Microsporidia comprise a large phylum of obligate intracellular eukaryotes that are fungal-related parasites responsible for widespread disease, and here we address questions about microsporidia biology and evolution. We sequenced three microsporidian genomes from two species, Nematocida parisii and Nematocida sp1, which are natural pathogens of Caenorhabditis nematodes and provide model systems for studying microsporidian pathogenesis. We performed deep sequencing of transcripts from a time course of N. parisii infection. Examination of pathogen gene expression revealed compact transcripts and a dramatic takeover of host cells by Nematocida. We also performed phylogenomic analyses of Nematocida and other microsporidian genomes to refine microsporidian phylogeny and identify evolutionary events of gene loss, acquisition, and modification. In particular, we found that all microsporidia lost the tumor-suppressor gene retinoblastoma, which we speculate could accelerate the parasite cell cycle and increase the mutation rate. We also found that microsporidia acquired transporters that could import nucleosides to fuel rapid growth. In addition, microsporidian hexokinases gained secretion signal sequences, and in a functional assay these were sufficient to export proteins out of the cell; thus hexokinase may be targeted into the host cell to reprogram it toward biosynthesis. Similar molecular changes appear during formation of cancer cells and may be evolutionary strategies adopted independently by microsporidia to proliferate rapidly within host cells. Finally, analysis of genome polymorphisms revealed evidence for a sexual cycle that may provide genetic diversity to alleviate problems caused by clonal growth. Together these events may explain the emergence and success of these diverse intracellular parasites. PMID:22813931

  19. Comparison on extreme pathways reveals nature of different biological processes

    PubMed Central

    2014-01-01

    Background Constraint-based reconstruction and analysis (COBRA) is used for modeling genome-scale metabolic networks (MNs). In a COBRA model, extreme pathways (ExPas) are the edges of its conical solution space, which is formed by all viable steady-state flux distributions. ExPa analysis has been successfully applied to MNs to reveal their phenotypic capabilities and properties. Recently, the COBRA framework has been extended to transcriptional regulatory networks (TRNs) and transcriptional and translational networks (TTNs), so efforts are needed to determine whether ExPa analysis is also effective on these two types of networks. Results In this paper, the ExPas resulting from the COBRA models of E.coli's MN, TRN and TTN were horizontally compared from 5 aspects: (1) Total number and the ratio of their amount to reaction amount; (2) Length distribution; (3) Reaction participation; (4) Correlated reaction sets (CoSets); (5) interconnectivity degree. Significant discrepancies in above properties were observed during the comparison, which reveals the biological natures of different biological processes. Besides, by demonstrating the application of ExPa analysis on E.coli, we provide a practical guidance of an improved approach to compute ExPas on COBRA models of TRNs. Conclusions ExPas of E.coli's MN, TRN and TTN have different properties, which are strongly connected with various biological natures of biochemical networks, such as topological structure, specificity and redundancy. Our study shows that ExPas are biologically meaningful on the newborn models and suggests the effectiveness of ExPa analysis on them. PMID:24565046

  20. [Munchhausen syndrome by proxy revealed by falsely toxic methotrexate levels].

    PubMed

    Charfi, Rim; Trabelsi, Sameh; Salouage, Issam; Gaïes, Emna; Jebabli, Nadia; Lakhal, Mohamed; Klouz, Anis

    2012-01-01

    Methotrexate is an antifolate drug used intravenously at high-dose in acute lymphocytic leukemia (ALL). Therapeutic drug monitoring is required to identify patients at risk of developing toxicity and to control folinic acid rescue. We report a case of Münchausen syndrome by proxy revealed by high and persistent falsely toxic methotrexate plasmatic levels. A 12 year-old child was treated with chemotherapy including methotrexate every 70 days for an ALL. The last methotrexate plasmatic level was 0.15 μmol/L at the 72th hour of the infusion. Then, he was treated by oral rout low-dose methotrexate. Ten days after methotrexate infusion, the patient consulted for asthenia, vomiting and presented a mucositis. Methotrexate plasmatic level was 2323 μmol/L. Renal function was normal. All drugs' intake was stopped. Folinic acid rescue was instituted. Even though there was no clinical sign of toxicity, therapeutic drug monitoring showed persistent high methotrexate plasmatic levels. Investigations eliminated measurement errors and pharmacokinetic problems. A deliberate methotrexate addition in each child blood sample brought by the mother was highly suspected. We confirmed this hypothesis by measuring methotrexate plasmatic levels in three samples: one brought by the mother, the second brought by the child's doctor and the last collected in our laboratory. Methotrexate plasmatic levels were respectively over 10,000 μmol/L (first sample) and lower than 0.02 μmol/L (the two others). The diagnosis of Munchausen's syndrome by proxy revealed by falsely toxic methotrexate plasmatic levels was made and the mother was addressed to the psychiatric department. PMID:22484536

  1. Antibody protection reveals extended epitopes on the human TSH receptor.

    PubMed

    Latif, Rauf; Teixeira, Avelino; Michalek, Krzysztof; Ali, M Rejwan; Schlesinger, Max; Baliram, Ramkumarie; Morshed, Syed A; Davies, Terry F

    2012-01-01

    Stimulating, and some blocking, antibodies to the TSH receptor (TSHR) have conformation-dependent epitopes reported to involve primarily the leucine rich repeat region of the ectodomain (LRD). However, successful crystallization of TSHR residues 22-260 has omitted important extracellular non-LRD residues including the hinge region which connects the TSHR ectodomain to the transmembrane domain and which is involved in ligand induced signal transduction. The aim of the present study, therefore, was to determine if TSHR antibodies (TSHR-Abs) have non-LRD binding sites outside the LRD. To obtain this information we employed the method of epitope protection in which we first protected TSHR residues 1-412 with intact TSHR antibodies and then enzymatically digested the unprotected residues. Those peptides remaining were subsequently delineated by mass spectrometry. Fourteen out of 23 of the reported stimulating monoclonal TSHR-Ab crystal contact residues were protected by this technique which may reflect the higher binding energies of certain residues detected in this approach. Comparing the protected epitopes of two stimulating TSHR-Abs we found both similarities and differences but both antibodies also contacted the hinge region and the amino terminus of the TSHR following the signal peptide and encompassing cysteine box 1 which has previously been shown to be important for TSH binding and activation. A monoclonal blocking TSHR antibody revealed a similar pattern of binding regions but the residues that it contacted on the LRD were again distinct. These data demonstrated that conformationally dependent TSHR-Abs had epitopes not confined to the LRDs but also incorporated epitopes not revealed in the available crystal structure. Furthermore, the data also indicated that in addition to overlapping contact regions within the LRD, there are unique epitope patterns for each of the antibodies which may contribute to their functional heterogeneity. PMID:22957097

  2. Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth.

    PubMed

    Cuomo, Christina A; Desjardins, Christopher A; Bakowski, Malina A; Goldberg, Jonathan; Ma, Amy T; Becnel, James J; Didier, Elizabeth S; Fan, Lin; Heiman, David I; Levin, Joshua Z; Young, Sarah; Zeng, Qiandong; Troemel, Emily R

    2012-12-01

    Microsporidia comprise a large phylum of obligate intracellular eukaryotes that are fungal-related parasites responsible for widespread disease, and here we address questions about microsporidia biology and evolution. We sequenced three microsporidian genomes from two species, Nematocida parisii and Nematocida sp1, which are natural pathogens of Caenorhabditis nematodes and provide model systems for studying microsporidian pathogenesis. We performed deep sequencing of transcripts from a time course of N. parisii infection. Examination of pathogen gene expression revealed compact transcripts and a dramatic takeover of host cells by Nematocida. We also performed phylogenomic analyses of Nematocida and other microsporidian genomes to refine microsporidian phylogeny and identify evolutionary events of gene loss, acquisition, and modification. In particular, we found that all microsporidia lost the tumor-suppressor gene retinoblastoma, which we speculate could accelerate the parasite cell cycle and increase the mutation rate. We also found that microsporidia acquired transporters that could import nucleosides to fuel rapid growth. In addition, microsporidian hexokinases gained secretion signal sequences, and in a functional assay these were sufficient to export proteins out of the cell; thus hexokinase may be targeted into the host cell to reprogram it toward biosynthesis. Similar molecular changes appear during formation of cancer cells and may be evolutionary strategies adopted independently by microsporidia to proliferate rapidly within host cells. Finally, analysis of genome polymorphisms revealed evidence for a sexual cycle that may provide genetic diversity to alleviate problems caused by clonal growth. Together these events may explain the emergence and success of these diverse intracellular parasites. PMID:22813931

  3. Micro-spectroscopic mapping: revealing internal structures of zircon crystals

    NASA Astrophysics Data System (ADS)

    Nasdala, L.; Reiners, P. W.; Hanchar, J. M.

    2003-04-01

    Natural zircon crystals typically deviate from perfect crystallinity and ideal chemical composition. If non-ideality features are not homogeneously distributed within a crystal but show a heterogeneity pattern, this is referred to as its "internal structure". Internal structures of zircon are mostly first caused by the heterogeneous incorporation of trace elements during crystal growth. Over time, these primary patterns may become more complex after being overprinted by radioactive self-irradiation and heterogeneous alteration or recrystallization. Internal structures may provide valuable information about the origin and post-growth history of zircon crystals. Further, they need to be recognized for sound microprobe dating, for instance to avoid biased results when straddling zones of different age. Revealing internal structures has thus become an important tool in zircon research. It is mostly done by means of backscattered electrons or cathodoluminescence imaging. These two techniques are advantageous over optical microscopy in the cross-polarized mode as the volume resolution is better and simple polished mounts instead of doubly-sided sections are needed. A disadvantage, however, is that the impact of electron beam during analysis causes local structural changes. Quantitative studies of the real structure of zircon samples, such as determination of the degree of the radiation damage, is therefore tainted with potential uncertainty when being done after electron probe analysis. As an alternative, we present images of internal zircon structures generated through visible laser excitation and mapping of the Raman and photoluminescence light. Due to the time-consuming mapping procedure, such images will perhaps not be routinely used. For detailed studies, however, they may provide most valuable information. Photoluminescence maps provide, for instance, information on both the distribution of rare earth elements (band integrals) and the short-range order (band

  4. HUBBLE REVEALS THE HEART OF THE WHIRLPOOL GALAXY

    NASA Technical Reports Server (NTRS)

    2002-01-01

    New images from NASA's Hubble Space Telescope are helping researchers view in unprecedented detail the spiral arms and dust clouds of a nearby galaxy, which are the birth sites of massive and luminous stars. The Whirlpool galaxy, M51, has been one of the most photogenic galaxies in amateur and professional astronomy. Easily photographed and viewed by smaller telescopes, this celestial beauty is studied extensively in a range of wavelengths by large ground- and space-based observatories. This Hubble composite image shows visible starlight as well as light from the emission of glowing hydrogen, which is associated with the most luminous young stars in the spiral arms. M51, also known as NGC 5194, is having a close encounter with a nearby companion galaxy, NGC 5195, just off the upper edge of this image. The companion's gravitational pull is triggering star formation in the main galaxy, as seen in brilliant detail by numerous, luminous clusters of young and energetic stars. The bright clusters are highlighted in red by their associated emission from glowing hydrogen gas. This Wide Field Planetary Camera 2 image enables a research group, led by Nick Scoville (Caltech), to clearly define the structure of both the cold dust clouds and the hot hydrogen and link individual clusters to their parent dust clouds. Team members include M. Polletta (U. Geneva); S. Ewald and S. Stolovy (Caltech); R. Thompson and M. Rieke (U. of Arizona). Intricate structure is also seen for the first time in the dust clouds. Along the spiral arms, dust 'spurs' are seen branching out almost perpendicular to the main spiral arms. The regularity and large number of these features suggests to astronomers that previous models of 'two-arm' spiral galaxies may need to be revisited. The new images also reveal a dust disk in the nucleus, which may provide fuel for a nuclear black hole. The team is also studying this galaxy at near-infrared wavelengths with the NICMOS instrument onboard Hubble. At these

  5. Episodic Sexual Transmission of HIV Revealed by Molecular Phylodynamics

    PubMed Central

    Rambaut, Andrew; Pozniak, Anton; Leigh Brown, Andrew J.

    2008-01-01

    Background The structure of sexual contact networks plays a key role in the epidemiology of sexually transmitted infections, and their reconstruction from interview data has provided valuable insights into the spread of infection. For HIV, the long period of infectivity has made the interpretation of contact networks more difficult, and major discrepancies have been observed between the contact network and the transmission network revealed by viral phylogenetics. The high rate of HIV evolution in principle allows for detailed reconstruction of links between virus from different individuals, but often sampling has been too sparse to describe the structure of the transmission network. The aim of this study was to analyze a high-density sample of an HIV-infected population using recently developed techniques in phylogenetics to infer the short-term dynamics of the epidemic among men who have sex with men (MSM). Methods and Findings Sequences of the protease and reverse transcriptase coding regions from 2,126 patients, predominantly MSM, from London were compared: 402 of these showed a close match to at least one other subtype B sequence. Nine large clusters were identified on the basis of genetic distance; all were confirmed by Bayesian Monte Carlo Markov chain (MCMC) phylogenetic analysis. Overall, 25% of individuals with a close match with one sequence are linked to 10 or more others. Dated phylogenies of the clusters using a relaxed clock indicated that 65% of the transmissions within clusters took place between 1995 and 2000, and 25% occurred within 6 mo after infection. The likelihood that not all members of the clusters have been identified renders the latter observation conservative. Conclusions Reconstruction of the HIV transmission network using a dated phylogeny approach has revealed the HIV epidemic among MSM in London to have been episodic, with evidence of multiple clusters of transmissions dating to the late 1990s, a period when HIV prevalence is known

  6. Cold exposure reveals two populations of microtubules in pulmonary endothelia.

    PubMed

    Ochoa, Cristhiaan D; Stevens, Troy; Balczon, Ron

    2011-01-01

    Microtubules are composed of α-tubulin and β-tubulin dimers. Microtubules yield tubulin dimers when exposed to cold, which reassemble spontaneously to form microtubule fibers at 37°C. However, mammalian neurons, glial cells, and fibroblasts have cold-stable microtubules. While studying the microtubule toxicity mechanisms of the exotoxin Y from Pseudomonas aeruginosa in pulmonary microvascular endothelial cells, we observed that some endothelial microtubules were very difficult to disassemble in the cold. As a consequence, we designed studies to test the hypothesis that microvascular endothelium has a population of cold-stable microtubules. Pulmonary microvascular endothelial cells and HeLa cells (control) were grown under regular cell culture conditions, followed by exposure to an ice-cold water bath and a microtubule extraction protocol. Polymerized microtubules were detected by immunofluorescence confocal microscopy and Western blot analyses. After cold exposure, immunofluorescence revealed that the majority of HeLa cell microtubules disassembled, whereas a smaller population of endothelial cell microtubules disassembled. Immunoblot analyses showed that microvascular endothelial cells express the microtubule cold-stabilizing protein N-STOP (neuronal stable tubule-only polypeptides), and that N-STOP binds to endothelial microtubules after cold exposure, but not if microtubules are disassembled with nocodazole before cold exposure. Hence, pulmonary endothelia have a population of cold-stable microtubules. PMID:20971804

  7. Revealing biological information using data structuring and automated learning.

    PubMed

    Mohorianu, Irina; Moulton, Vincent

    2010-11-01

    The intermediary steps between a biological hypothesis, concretized in the input data, and meaningful results, validated using biological experiments, commonly employ bioinformatics tools. Starting with storage of the data and ending with a statistical analysis of the significance of the results, every step in a bioinformatics analysis has been intensively studied and the resulting methods and models patented. This review summarizes the bioinformatics patents that have been developed mainly for the study of genes, and points out the universal applicability of bioinformatics methods to other related studies such as RNA interference. More specifically, we overview the steps undertaken in the majority of bioinformatics analyses, highlighting, for each, various approaches that have been developed to reveal details from different perspectives. First we consider data warehousing, the first task that has to be performed efficiently, optimizing the structure of the database, in order to facilitate both the subsequent steps and the retrieval of information. Next, we review data mining, which occupies the central part of most bioinformatics analyses, presenting patents concerning differential expression, unsupervised and supervised learning. Last, we discuss how networks of interactions of genes or other players in the cell may be created, which help draw biological conclusions and have been described in several patents. PMID:21288193

  8. Cytoplasmic Dynamics Reveals Two Modes of Nucleoid-Dependent Mobility

    PubMed Central

    Stylianidou, Stella; Kuwada, Nathan J.; Wiggins, Paul A.

    2014-01-01

    It has been proposed that forces resulting from the physical exclusion of macromolecules from the bacterial nucleoid play a central role in organizing the bacterial cell, yet this proposal has not been quantitatively tested. To investigate this hypothesis, we mapped the generic motion of large protein complexes in the bacterial cytoplasm through quantitative analysis of thousands of complete cell-cycle trajectories of fluorescently tagged ectopic MS2-mRNA complexes. We find the motion of these complexes in the cytoplasm is strongly dependent on their spatial position along the long axis of the cell, and that their dynamics are consistent with a quantitative model that requires only nucleoid exclusion and membrane confinement. This analysis also reveals that the nucleoid increases the mobility of MS2-mRNA complexes, resulting in a fourfold increase in diffusion coefficients between regions of the lowest and highest nucleoid density. These data provide strong quantitative support for two modes of nucleoid action: the widely accepted mechanism of nucleoid exclusion in organizing the cell and a newly proposed mode, in which the nucleoid facilitates rapid motion throughout the cytoplasm. PMID:25468347

  9. Recombination patterns reveal information about centromere location on linkage maps.

    PubMed

    Limborg, Morten T; McKinney, Garrett J; Seeb, Lisa W; Seeb, James E

    2016-05-01

    Linkage mapping is often used to identify genes associated with phenotypic traits and for aiding genome assemblies. Still, many emerging maps do not locate centromeres - an essential component of the genomic landscape. Here, we demonstrate that for genomes with strong chiasma interference, approximate centromere placement is possible by phasing the same data used to generate linkage maps. Assuming one obligate crossover per chromosome arm, information about centromere location can be revealed by tracking the accumulated recombination frequency along linkage groups, similar to half-tetrad analyses. We validate the method on a linkage map for sockeye salmon (Oncorhynchus nerka) with known centromeric regions. Further tests suggest that the method will work well in other salmonids and other eukaryotes. However, the method performed weakly when applied to a male linkage map (rainbow trout; O. mykiss) characterized by low and unevenly distributed recombination - a general feature of male meiosis in many species. Further, a high frequency of double crossovers along chromosome arms in barley reduced resolution for locating centromeric regions on most linkage groups. Despite these limitations, our method should work well for high-density maps in species with strong recombination interference and will enrich many existing and future mapping resources. PMID:26561199

  10. Initiation process of a thrust fault revealed by analog experiments

    NASA Astrophysics Data System (ADS)

    Yamada, Yasuhiro; Dotare, Tatsuya; Adam, Juergen; Hori, Takane; Sakaguchi, Hide

    2016-04-01

    We conducted 2D (cross-sectional) analog experiments with dry sand using a high resolution digital image correlation (DIC) technique to reveal initiation process of a thrust fault in detail, and identified a number of "weak shear bands" and minor uplift prior to the thrust initiation. The observations suggest that the process can be divided into three stages. Stage 1: characterized by a series of abrupt and short-lived weak shear bands at the location where the thrust will be generated later. Before initiation of the fault, the area to be the hanging wall starts to uplift. Stage 2: defined by the generation of the new thrust and its active displacement. The location of the new thrust seems to be constrained by its associated back-thrust, produced at the foot of the surface slope (by the previous thrust). The activity of the previous thrust turns to zero once the new thrust is generated, but the timing of these two events is not the same. Stage 3: characterized by a constant displacement along the (new) thrust. Similar minor shear bands can be seen in the toe area of the Nankai accretionary prism, SW Japan and we can correlate the along-strike variations in seismic profiles to the model results that show the characteristic features in each thrust development stage.

  11. Cassava root membrane proteome reveals activities during storage root maturation.

    PubMed

    Naconsie, Maliwan; Lertpanyasampatha, Manassawe; Viboonjun, Unchera; Netrphan, Supatcharee; Kuwano, Masayoshi; Ogasawara, Naotake; Narangajavana, Jarunya

    2016-01-01

    Cassava (Manihot esculenta Crantz) is one of the most important crops of Thailand. Its storage roots are used as food, feed, starch production, and be the important source for biofuel and biodegradable plastic production. Despite the importance of cassava storage roots, little is known about the mechanisms involved in their formation. This present study has focused on comparison of the expression profiles of cassava root proteome at various developmental stages using two-dimensional gel electrophoresis and LC-MS/MS. Based on an anatomical study using Toluidine Blue, the secondary growth was confirmed to be essential during the development of cassava storage root. To investigate biochemical processes occurring during storage root maturation, soluble and membrane proteins were isolated from storage roots harvested from 3-, 6-, 9-, and 12-month-old cassava plants. The proteins with differential expression pattern were analysed and identified to be associated with 8 functional groups: protein folding and degradation, energy, metabolism, secondary metabolism, stress response, transport facilitation, cytoskeleton, and unclassified function. The expression profiling of membrane proteins revealed the proteins involved in protein folding and degradation, energy, and cell structure were highly expressed during early stages of development. Integration of these data along with the information available in genome and transcriptome databases is critical to expand knowledge obtained solely from the field of proteomics. Possible role of identified proteins were discussed in relation with the activities during storage root maturation in cassava. PMID:26547558

  12. Quantification of the stapedial reflex reveals delayed responses in autism.

    PubMed

    Lukose, Richard; Brown, Kevin; Barber, Carol M; Kulesza, Randy Joseph

    2013-10-01

    Autism is a developmental disorder characterized, in part, by sensory abnormalities. It is well established that most if not all patients with autism have problems with auditory processing, ranging from deafness to hyperacusis, and physiological testing of auditory function (i.e. auditory brain stem responses) implicates brain stem dysfunction in autism. Additionally, previous research from this lab has revealed significantly fewer auditory brain stem neurons in autistic subjects as young as 2 years of age. These observations have led us to hypothesize that objective, noninvasive measures of auditory function can be used as an early screening tool to identify neonates with an elevated risk of carrying a diagnosis of autism. Here, we provide a detailed quantitative investigation of the acoustic stapedial reflex (ASR), a three- or four-neuron brain stem circuit, in young autistic subjects and normal developing controls. Indeed, we find significantly lower thresholds, responses occurring at significantly longer latency and right-left asymmetry in autistic subjects. The results from this investigation support deficits in auditory function as a cardinal feature of autism and suggest that individuals with autism can be identified by their ASR responses. PMID:23825093

  13. Revealing Bell's nonlocality for unstable systems in high energy physics

    NASA Astrophysics Data System (ADS)

    Hiesmayr, Beatrix C.; Di Domenico, Antonio; Curceanu, Catalina; Gabriel, Andreas; Huber, Marcus; Larsson, Jan-Åke; Moskal, Pawel

    2012-01-01

    Entanglement and its consequences—in particular the violation of Bell inequalities, which defies our concepts of realism and locality—have been proven to play key roles in Nature by many experiments for various quantum systems. Entanglement can also be found in systems not consisting of ordinary matter and light, i.e. in massive meson-antimeson systems. Bell inequalities have been discussed for these systems, but up to date no direct experimental test to conclusively exclude local realism was found. This mainly stems from the fact that one only has access to a restricted class of observables and that these systems are also decaying. In this Letter we put forward a Bell inequality for unstable systems which can be tested at accelerator facilities with current technology. Herewith, the long awaited proof that such systems at different energy scales can reveal the sophisticated " dynamical" nonlocal feature of Nature in a direct experiment gets feasible. Moreover, the role of entanglement and mathcal{CP} violation, an asymmetry between matter and antimatter, is explored, a special feature offered only by these meson-antimeson systems.

  14. Geometric morphometric analysis reveals sexual dimorphism in the distal femur.

    PubMed

    Cavaignac, Etienne; Savall, Frederic; Faruch, Marie; Reina, Nicolas; Chiron, Philippe; Telmon, Norbert

    2016-02-01

    An individual's sex can be determined by the shape of their distal femur. The goal of this study was to show that differences in distal femur shape related to sexual dimorphism could be identified, visualized, and quantified using 3D geometric morphometric analysis. Geometric morphometric analysis was carried out on CT scans of the distal femur of 256 subjects living in the south of France. Ten landmarks were defined on 3D reconstructions of the distal femur. Both traditional metric and geometric morphometric analyses were carried out on these bone reconstructions; these analyses identified trends in bone shape in sex-based subgroups. Sex-related differences in shape were statistically significant. The subject's sex was correctly assigned in 77.3% of cases using geometric morphometric analysis. This study has shown that geometric morphometric analysis of the distal femur is feasible and has revealed sexual dimorphism differences in this bone segment. This reliable, accurate method could be used for virtual autopsy and be used to perform diachronic and interethnic comparisons. Moreover, this study provides updated morphometric data for a modern population in the south of France. PMID:26743712

  15. Seismic Tremor Reveals Subglacial Discharge at Tidewater Glaciers

    NASA Astrophysics Data System (ADS)

    Bartholomaus, T. C.; Larsen, C. F.; O'Neel, S.; West, M. E.; Amundson, J. M.; Walter, J. I.; Catania, G. A.; Stearns, L. A.; Walker, R. T.; Sutherland, D.; Shroyer, E.; Nash, J. D.

    2014-12-01

    Subglacial discharge from the termini of tidewater glaciers drives submarine terminus melting, influences fjord circulation, erodes and redeposits subglacial sediment, and is a central component of proglacial marine ecosystems. The timing and variability of subglacial discharge can also exert a strong influence on the upstream flow of tidewater glaciers through hydrology-mediated changes in basal motion. However, a lack of observations of subglacial discharge at the ice-ocean interface hinders progress in understanding these processes and contributes to some of the largest uncertainties in sea level rise projections. Here we demonstrate that passive seismic observations collected adjacent to glaciers can meet this observational need. At tidewater and lake-terminating glaciers in Alaska and Greenland, we observe hourly to seasonal variations in low-amplitude, background seismic noise, termed glacio-hydraulic tremor. Variations in tremor amplitude correlate with discharge during the drainage of a glacially-dammed lake and reveal increases in discharge efficiency over the course of the melt season. Recordings of glacio-hydraulic tremor across a range of settings suggest widespread utility for our method. Reliable prediction of future sea level rise requires observations of subglacial discharge that elicit physical insight and can validate models. Our findings provide a platform for new understanding of ice-ocean interactions and related oceanographic, geologic, and ecological disciplines.

  16. Identification of disulfide bond isomerase substrates reveals bacterial virulence factors

    PubMed Central

    Ren, Guoping; Champion, Matthew M.; Huntley, Jason F.

    2014-01-01

    Summary Bacterial pathogens are exposed to toxic molecules inside the host and require efficient systems to form and maintain correct disulfide bonds for protein stability and function. The intracellular pathogen Francisella tularensis encodes a disulfide bond formation protein ortholog, DsbA, which previously was reported to be required for infection of macrophages and mice. However, the molecular mechanisms by which F. tularensis DsbA contributes to virulence are unknown. Here, we demonstrate that F. tularensis DsbA is a bifunctional protein that oxidizes and, more importantly, isomerizes complex disulfide connectivity in substrates. A single amino acid in the conserved cis-proline loop of the DsbA thioredoxin domain was shown to modulate both isomerase activity and F. tularensis virulence. Trapping experiments in F. tularensis identified over 50 F. tularensis DsbA substrates, including outer membrane proteins, virulence factors, and many hypothetical proteins. Six of these hypothetical proteins were randomly selected and deleted, revealing two novel proteins, FTL_1548 and FTL_1709, which are required for F. tularensis virulence. We propose that the extreme virulence of F. tularensis is partially due to the bifunctional nature of DsbA, that many of the newly-identified substrates are required for virulence, and that the development of future DsbA inhibitors could have broad anti-bacterial implications. PMID:25257164

  17. Historical Reconstruction Reveals Recovery in Hawaiian Coral Reefs

    PubMed Central

    Kittinger, John N.; Pandolfi, John M.; Blodgett, Jonathan H.; Hunt, Terry L.; Jiang, Hong; Maly, Kepā; McClenachan, Loren E.; Schultz, Jennifer K.; Wilcox, Bruce A.

    2011-01-01

    Coral reef ecosystems are declining worldwide, yet regional differences in the trajectories, timing and extent of degradation highlight the need for in-depth regional case studies to understand the factors that contribute to either ecosystem sustainability or decline. We reconstructed social-ecological interactions in Hawaiian coral reef environments over 700 years using detailed datasets on ecological conditions, proximate anthropogenic stressor regimes and social change. Here we report previously undetected recovery periods in Hawaiian coral reefs, including a historical recovery in the MHI (∼AD 1400–1820) and an ongoing recovery in the NWHI (∼AD 1950–2009+). These recovery periods appear to be attributed to a complex set of changes in underlying social systems, which served to release reefs from direct anthropogenic stressor regimes. Recovery at the ecosystem level is associated with reductions in stressors over long time periods (decades+) and large spatial scales (>103 km2). Our results challenge conventional assumptions and reported findings that human impacts to ecosystems are cumulative and lead only to long-term trajectories of environmental decline. In contrast, recovery periods reveal that human societies have interacted sustainably with coral reef environments over long time periods, and that degraded ecosystems may still retain the adaptive capacity and resilience to recover from human impacts. PMID:21991311

  18. Geometric Mechanics Reveals Optimal Complex Terrestrial Undulation Patterns

    NASA Astrophysics Data System (ADS)

    Gong, Chaohui; Astley, Henry; Schiebel, Perrin; Dai, Jin; Travers, Matthew; Goldman, Daniel; Choset, Howie; CMU Team; GT Team

    Geometric mechanics offers useful tools for intuitively analyzing biological and robotic locomotion. However, utility of these tools were previously restricted to systems that have only two internal degrees of freedom and in uniform media. We show kinematics of complex locomotors that make intermittent contacts with substrates can be approximated as a linear combination of two shape bases, and can be represented using two variables. Therefore, the tools of geometric mechanics can be used to analyze motions of locomotors with many degrees of freedom. To demonstrate the proposed technique, we present studies on two different types of snake gaits which utilize combinations of waves in the horizontal and vertical planes: sidewinding (in the sidewinder rattlesnake C. cerastes) and lateral undulation (in the desert specialist snake C. occipitalis). C. cerastes moves by generating posteriorly traveling body waves in the horizontal and vertical directions, with a relative phase offset equal to +/-π/2 while C. occipitalismaintains a π/2 offset of a frequency doubled vertical wave. Geometric analysis reveals these coordination patterns enable optimal movement in the two different styles of undulatory terrestrial locomotion. More broadly, these examples demonstrate the utility of geometric mechanics in analyzing realistic biological and robotic locomotion.

  19. Phenotypic Expression in Wheat Revealed Using FT-IR Microspectroscopy

    SciTech Connect

    Brewer, L.; Wetzel, D

    2009-01-01

    Wheat selected for cultivation through the centuries has a glume that is 'soft' instead of 'tough' as naturally occurring. In production, this is desirable because it enables mechanical threshing with efficient separation of kernel from the head of each stalk without damaging the kernel. FT-IR microspectroscopy provides chemically based, objective assessment of genetic expression by measuring the extent of genetic expression. In the Microbeam Molecular Spectroscopy Laboratory, Manhattan, KS, an imaging FT-IR microspectrometer with a detector array focused on the image plane was used to obtain spectral data from dissected glume specimens of nine tough and eleven soft wheat cultivars in a rectangular mapping pattern. With cellulose as the substrate, the extent of lignification is measurable from the ratio of the lignin (1508 cm{sup -1}) baseline adjusted band area to the representative cellulosic (1370 cm{sup -1}) band area. A distinction between soft and tough glumes is obtained in numerical terms. Using a band ratio minimizes variation due to thickness differences. While analyzing mapped sections of glume, care is taken to avoid tabulation of spectral data from vascular bundles. Inclusion of these data would to avoid tabulation of spectral data from vascular bundles. Inclusion of these data would bias the analysis toward the composition of highly lignified vascular bundles. Spatially resolved focal plane array FT-IR microspectroscopy reveals the extent of glume lignification that is coincident with the toughness trait. This enables breeders to rank the degree of lignin expression and discriminate between soft and tough breeding results.

  20. Planarian Phototactic Assay Reveals Differential Behavioral Responses Based on Wavelength

    PubMed Central

    Paskin, Taylor R.; Jellies, John; Bacher, Jessica; Beane, Wendy S.

    2014-01-01

    Planarians are free-living aquatic flatworms that possess a well-documented photophobic response to light. With a true central nervous system and simple cerebral eyes (ocelli), planarians are an emerging model for regenerative eye research. However, comparatively little is known about the physiology of their photoreception or how their behavior is affected by various wavelengths. Most phototactic studies have examined planarian behavior using white light. Here, we describe a novel planarian behavioral assay to test responses to small ranges of visible wavelengths (red, blue, green), as well as ultraviolet (UV) and infrared (IR) which have not previously been examined. Our data show that planarians display behavioral responses across a range of wavelengths. These responses occur in a hierarchy, with the shortest wavelengths (UV) causing the most intense photophobic responses while longer wavelengths produce no effect (red) or an apparent attraction (IR). In addition, our data reveals that planarian photophobia is comprised of both a general photophobic response (that drives planarians to escape the light source regardless of wavelength) and wavelength-specific responses that encompass specific behavioral reactions to individual wavelengths. Our results serve to improve the understanding of planarian phototaxis and suggest that behavioral studies performed with white light mask a complex behavioral interaction with the environment. PMID:25493551

  1. Super-resolution Microscopy Reveals Compartmentalization of Peroxisomal Membrane Proteins.

    PubMed

    Galiani, Silvia; Waithe, Dominic; Reglinski, Katharina; Cruz-Zaragoza, Luis Daniel; Garcia, Esther; Clausen, Mathias P; Schliebs, Wolfgang; Erdmann, Ralf; Eggeling, Christian

    2016-08-12

    Membrane-associated events during peroxisomal protein import processes play an essential role in peroxisome functionality. Many details of these processes are not known due to missing spatial resolution of technologies capable of investigating peroxisomes directly in the cell. Here, we present the use of super-resolution optical stimulated emission depletion microscopy to investigate with sub-60-nm resolution the heterogeneous spatial organization of the peroxisomal proteins PEX5, PEX14, and PEX11 around actively importing peroxisomes, showing distinct differences between these peroxins. Moreover, imported protein sterol carrier protein 2 (SCP2) occupies only a subregion of larger peroxisomes, highlighting the heterogeneous distribution of proteins even within the peroxisome. Finally, our data reveal subpopulations of peroxisomes showing only weak colocalization between PEX14 and PEX5 or PEX11 but at the same time a clear compartmentalized organization. This compartmentalization, which was less evident in cases of strong colocalization, indicates dynamic protein reorganization linked to changes occurring in the peroxisomes. Through the use of multicolor stimulated emission depletion microscopy, we have been able to characterize peroxisomes and their constituents to a yet unseen level of detail while maintaining a highly statistical approach, paving the way for equally complex biological studies in the future. PMID:27311714

  2. Revealing the structure of the world airline network

    PubMed Central

    Verma, T.; Araújo, N. A. M.; Herrmann, H. J.

    2014-01-01

    Resilience of most critical infrastructures against failure of elements that appear insignificant is usually taken for granted. The World Airline Network (WAN) is an infrastructure that reduces the geographical gap between societies, both small and large, and brings forth economic gains. With the extensive use of a publicly maintained data set that contains information about airports and alternative connections between these airports, we empirically reveal that the WAN is a redundant and resilient network for long distance air travel, but otherwise breaks down completely due to removal of short and apparently insignificant connections. These short range connections with moderate number of passengers and alternate flights are the connections that keep remote parts of the world accessible. It is surprising, insofar as there exists a highly resilient and strongly connected core consisting of a small fraction of airports (around 2.3%) together with an extremely fragile star-like periphery. Yet, in spite of their relevance, more than 90% of the world airports are still interconnected upon removal of this core. With standard and unconventional removal measures we compare both empirical and topological perceptions for the fragmentation of the world. We identify how the WAN is organized into different classes of clusters based on the physical proximity of airports and analyze the consequence of this fragmentation. PMID:25005934

  3. Revealing catastrophic failure of leaf networks under stress.

    PubMed

    Brodribb, Timothy J; Bienaimé, Diane; Marmottant, Philippe

    2016-04-26

    The intricate patterns of veins that adorn the leaves of land plants are among the most important networks in biology. Water flows in these leaf irrigation networks under tension and is vulnerable to embolism-forming cavitations, which cut off water supply, ultimately causing leaf death. Understanding the ways in which plants structure their vein supply network to protect against embolism-induced failure has enormous ecological and evolutionary implications, but until now there has been no way of observing dynamic failure in natural leaf networks. Here we use a new optical method that allows the initiation and spread of embolism bubbles in the leaf network to be visualized. Examining embolism-induced failure of architecturally diverse leaf networks, we found that conservative rules described the progression of hydraulic failure within veins. The most fundamental rule was that within an individual venation network, susceptibility to embolism always increased proportionally with the size of veins, and initial nucleation always occurred in the largest vein. Beyond this general framework, considerable diversity in the pattern of network failure was found between species, related to differences in vein network topology. The highest-risk network was found in a fern species, where single events caused massive disruption to leaf water supply, whereas safer networks in angiosperm leaves contained veins with composite properties, allowing a staged failure of water supply. These results reveal how the size structure of leaf venation is a critical determinant of the spread of embolism damage to leaves during drought. PMID:27071104

  4. The Mass Donor of Scorpius X-1 Revealed

    NASA Astrophysics Data System (ADS)

    Steeghs, D.; Casares, J.

    2002-03-01

    We present the first detection of the mass donor star in the prototype X-ray binary Scorpius X-1. Phase-resolved spectroscopy revealed narrow emission line components from the irradiated secondary star. Radial velocity fits to the Bowen blend emission are used to establish an absolute orbital ephemeris and derive an accurate value for the systemic velocity, γ=-113.8+/-0.6 km s-1. Emission from the irradiated front side of the secondary leads to solid limits to the radial velocity of the mass donor of 87<~K2<~148 km s-1. In conjunction with an upper limit to the velocity of the primary K1<=53 km s-1, we derive a firm limit on the mass ratio of Sco X-1 of q<~0.61. A likely set of system parameters satisfying the various constraints as well as the recent inclination estimate by Fomalont, Geldzahler, & Bradshaw (2001) is K1=40 km s-1, K2=133 km s-1, q=0.30 corresponding to component masses of M1=1.4Msolar and M2=0.42Msolar for an orbital inclination of 38°.

  5. Pyrosequencing Reveals Fungal Communities in the Rhizosphere of Xinjiang Jujube

    PubMed Central

    Wang, Xiao-Hui; Li, Jian-Gui; Qin, Wei; Xiao, Cheng-Ze; Zhao, Xu; Jiang, Hong-Xia; Sui, Jun-Kang; Sa, Rong-Bo; Wang, Wei-Yan; Liu, Xun-Li

    2015-01-01

    Fungi are important soil components as both decomposers and plant symbionts and play a major role in ecological and biogeochemical processes. However, little is known about the richness and structure of fungal communities. DNA sequencing technologies allow for the direct estimation of microbial community diversity, avoiding culture-based biases. We therefore used 454 pyrosequencing to investigate the fungal communities in the rhizosphere of Xinjiang jujube. We obtained no less than 40,488 internal transcribed spacer (ITS) rDNA reads, the number of each sample was 6943, 6647, 6584, 6550, 6860, and 6904, and we used bioinformatics and multivariate statistics to analyze the results. The index of diversity showed greater richness in the rhizosphere fungal community of a 3-year-old jujube than in that of an 8-year-old jujube. Most operational taxonomic units belonged to Ascomycota, and taxonomic analyses identified Hypocreales as the dominant fungal order. Our results demonstrated that the fungal orders are present in different proportions in different sampling areas. Redundancy analysis (RDA) revealed a significant correlation between soil properties and the abundance of fungal phyla. Our results indicated lower fungal diversity in the rhizosphere of Xinjiang jujube than that reported in other studies, and we hope our findings provide a reference for future research. PMID:25685820

  6. Small molecules reveal an alternative mechanism of Bax activation

    PubMed Central

    Brahmbhatt, Hetal; Uehling, David; Al-awar, Rima; Leber, Brian; Andrews, David

    2016-01-01

    The pro-apoptotic protein Bax commits a cell to death by permeabilizing the mitochondrial outer membrane (MOM). To obtain small-molecule probes for elucidating the molecular mechanism(s) of Bax activation, we screened for compounds that induced Bax-mediated liposome permeabilization. We identified five structurally different small molecules that promoted both Bax targeting to and oligomerization at membranes. All five compounds initiated Bax oligomerization in the absence of membranes by a mechanism unlike Bax activation by Bcl-2 homology 3 domain (BH3) proteins. Some of the compounds induced Bax/Bak-dependent apoptosis in cells. Activation of Bax by the most active compound was poorly inhibited by the anti-apoptotic protein Bcl-XL and requires a cysteine residue at position 126 of Bax that is not required for activation by BH3 proteins. Our results reveal a novel pathway for Bax activation independent of pro-apoptotic BH3 proteins that may have important implications for the regulation of Bax activity in cells. PMID:26916338

  7. Comparative Genomic Indexing Reveals the Phylogenomics of Escherichia coli Pathogens

    PubMed Central

    Anjum, Muna F.; Lucchini, Sacha; Thompson, Arthur; Hinton, Jay C. D.; Woodward, Martin J.

    2003-01-01

    The Escherichia coli O26 serogroup includes important food-borne pathogens associated with human and animal diarrheal disease. Current typing methods have revealed great genetic heterogeneity within the O26 group; the data are often inconsistent and focus only on verotoxin (VT)-positive O26 isolates. To improve current understanding of diversity within this serogroup, the genomic relatedness of VT-positive and -negative O26 strains was assessed by comparative genomic indexing. Our results clearly demonstrate that irrespective of virulence characteristics and pathotype designation, the O26 strains show greater genomic similarity to each other than to any other strain included in this study. Our data suggest that enteropathogenic and VT-expressing E. coli O26 strains represent the same clonal lineage and that VT-expressing E. coli O26 strains have gained additional virulence characteristics. Using this approach, we established the core genes which are central to the E. coli species and identified regions of variation from the E. coli K-12 chromosomal backbone. PMID:12874348

  8. Single-cell chromatin accessibility reveals principles of regulatory variation.

    PubMed

    Buenrostro, Jason D; Wu, Beijing; Litzenburger, Ulrike M; Ruff, Dave; Gonzales, Michael L; Snyder, Michael P; Chang, Howard Y; Greenleaf, William J

    2015-07-23

    Cell-to-cell variation is a universal feature of life that affects a wide range of biological phenomena, from developmental plasticity to tumour heterogeneity. Although recent advances have improved our ability to document cellular phenotypic variation, the fundamental mechanisms that generate variability from identical DNA sequences remain elusive. Here we reveal the landscape and principles of mammalian DNA regulatory variation by developing a robust method for mapping the accessible genome of individual cells by assay for transposase-accessible chromatin using sequencing (ATAC-seq) integrated into a programmable microfluidics platform. Single-cell ATAC-seq (scATAC-seq) maps from hundreds of single cells in aggregate closely resemble accessibility profiles from tens of millions of cells and provide insights into cell-to-cell variation. Accessibility variance is systematically associated with specific trans-factors and cis-elements, and we discover combinations of trans-factors associated with either induction or suppression of cell-to-cell variability. We further identify sets of trans-factors associated with cell-type-specific accessibility variance across eight cell types. Targeted perturbations of cell cycle or transcription factor signalling evoke stimulus-specific changes in this observed variability. The pattern of accessibility variation in cis across the genome recapitulates chromosome compartments de novo, linking single-cell accessibility variation to three-dimensional genome organization. Single-cell analysis of DNA accessibility provides new insight into cellular variation of the 'regulome'. PMID:26083756

  9. Crystallographic and spectroscopic snapshots reveal a dehydrogenase in action

    SciTech Connect

    Huo, Lu; Davis, Ian; Liu, Fange; Andi, Babak; Esaki, Shingo; Iwaki, Hiroaki; Hasegawa, Yoshie; Orville, Allen M.; Liu, Aimin

    2015-01-07

    Aldehydes are ubiquitous intermediates in metabolic pathways and their innate reactivity can often make them quite unstable. There are several aldehydic intermediates in the metabolic pathway for tryptophan degradation that can decay into neuroactive compounds that have been associated with numerous neurological diseases. An enzyme of this pathway, 2-aminomuconate-6-semialdehyde dehydrogenase, is responsible for ‘disarming’ the final aldehydic intermediate. Here we show the crystal structures of a bacterial analogue enzyme in five catalytically relevant forms: resting state, one binary and two ternary complexes, and a covalent, thioacyl intermediate. We also report the crystal structures of a tetrahedral, thiohemiacetal intermediate, a thioacyl intermediate and an NAD+-bound complex from an active site mutant. These covalent intermediates are characterized by single-crystal and solution-state electronic absorption spectroscopy. The crystal structures reveal that the substrate undergoes an E/Z isomerization at the enzyme active site before an sp3-to-sp2 transition during enzyme-mediated oxidation.

  10. Mitochondrial Genome Sequences Effectively Reveal the Phylogeny of Hylobates Gibbons

    PubMed Central

    Chan, Yi-Chiao; Roos, Christian; Inoue-Murayama, Miho; Inoue, Eiji; Shih, Chih-Chin; Pei, Kurtis Jai-Chyi; Vigilant, Linda

    2010-01-01

    Background Uniquely among hominoids, gibbons exist as multiple geographically contiguous taxa exhibiting distinctive behavioral, morphological, and karyotypic characteristics. However, our understanding of the evolutionary relationships of the various gibbons, especially among Hylobates species, is still limited because previous studies used limited taxon sampling or short mitochondrial DNA (mtDNA) sequences. Here we use mtDNA genome sequences to reconstruct gibbon phylogenetic relationships and reveal the pattern and timing of divergence events in gibbon evolutionary history. Methodology/Principal Findings We sequenced the mitochondrial genomes of 51 individuals representing 11 species belonging to three genera (Hylobates, Nomascus and Symphalangus) using the high-throughput 454 sequencing system with the parallel tagged sequencing approach. Three phylogenetic analyses (maximum likelihood, Bayesian analysis and neighbor-joining) depicted the gibbon phylogenetic relationships congruently and with strong support values. Most notably, we recover a well-supported phylogeny of the Hylobates gibbons. The estimation of divergence times using Bayesian analysis with relaxed clock model suggests a much more rapid speciation process in Hylobates than in Nomascus. Conclusions/Significance Use of more than 15 kb sequences of the mitochondrial genome provided more informative and robust data than previous studies of short mitochondrial segments (e.g., control region or cytochrome b) as shown by the reliable reconstruction of divergence patterns among Hylobates gibbons. Moreover, molecular dating of the mitogenomic divergence times implied that biogeographic change during the last five million years may be a factor promoting the speciation of Sundaland animals, including Hylobates species. PMID:21203450

  11. Crystallographic and spectroscopic snapshots reveal a dehydrogenase in action

    DOE PAGESBeta

    Huo, Lu; Davis, Ian; Liu, Fange; Andi, Babak; Esaki, Shingo; Iwaki, Hiroaki; Hasegawa, Yoshie; Orville, Allen M.; Liu, Aimin

    2015-01-07

    Aldehydes are ubiquitous intermediates in metabolic pathways and their innate reactivity can often make them quite unstable. There are several aldehydic intermediates in the metabolic pathway for tryptophan degradation that can decay into neuroactive compounds that have been associated with numerous neurological diseases. An enzyme of this pathway, 2-aminomuconate-6-semialdehyde dehydrogenase, is responsible for ‘disarming’ the final aldehydic intermediate. Here we show the crystal structures of a bacterial analogue enzyme in five catalytically relevant forms: resting state, one binary and two ternary complexes, and a covalent, thioacyl intermediate. We also report the crystal structures of a tetrahedral, thiohemiacetal intermediate, a thioacylmore » intermediate and an NAD+-bound complex from an active site mutant. These covalent intermediates are characterized by single-crystal and solution-state electronic absorption spectroscopy. The crystal structures reveal that the substrate undergoes an E/Z isomerization at the enzyme active site before an sp3-to-sp2 transition during enzyme-mediated oxidation.« less

  12. [Meningococcal Septicemia Revealing Multiple Myeloma: A Case Report].

    PubMed

    Arakawa, Risturo; Mori, Nobuaki; Kagawa, Narito; Higuchi, Akiko; Tanaka, Masashi; Aoki, Yasuko; Seki, Shiko; Suzuki, Ryo

    2016-05-01

    Meningococcal infection is among the most devastating diseases. It is rarely seen in Japan. However, several environmental and host factors have been associated with increased risks of Neisseria meningitidis infection. We present a case of invasive N. meningitidis infection that revealed the presence of multiple myeloma. A 55-year-old Japanese man was admitted with fever and altered consciousness. He was sent to the intensive care unit for septic shock and disseminated intravascular coagulation. In addition to standard septic shock and multiple organ failure treatment, polymyxin-B immobilized column direct hemoperfusion was performed. His blood culture was positive for N. meningitidis. The patient gradually improved and was discharged on day 35. We evaluated the risk factors for the development of meningococcal infection. A laboratory examination showed that the patient was negative for human immunodeficiency virus antibody and had a normal total complement function. However, his serum immunoglobulin G level was high, and serum and urine protein electrophoresis detected a monoclonal gammopathy. A bone marrow examination led to the diagnosis of multiple myeloma. Because N. meningitidis bacteria spreads between individuals in close contact through the exchange of oral secretions, droplet precautions and antimicrobial chemoprophylaxis (ciprofloxacin, 500 mg) were implemented to prevent the spread of the meningococcal infection. Sporadic meningococcal infection warrants an evaluation for immunodeficiency and the prevention of secondary infection. PMID:27529971

  13. Revealing Amphiphilic Nanodornains of Anti-Biofouling Polymer Coatings

    SciTech Connect

    Amadei, CA; Yang, R; Chiesa, M; Gleason, KK; Santos, S

    2014-04-09

    Undesired bacterial adhesion and biofilm formation on wetted surfaces leads to significant economic and environmental costs in various industries. Amphiphilic coatings with molecular hydrophilic and hydrophobic patches can mitigate such biofouling effectively in an environmentally friendly manner. The coatings are synthesized by copolymerizing (Hydroxyethyl)methacrylate and perfluorodecylacrylate via initiated chemical vapor deposition (iCVD). In previous studies, the size of the patches was estimated to be similar to 1.4-1.75 nm by fitting protein adsorption data to a theoretical model. However, no direct observations of the molecular heterogeneity exist and therefore the origin of the fouling resistance of amphiphilic coatings remains unclear. Here, the amphiphilic nature is investigated by amplitude modulation atomic force microscopy (AM-AFM). High-resolution images obtained by penetrating and oscillating the AFM tip under the naturally present water layer with sub-nanometer amplitudes reveal, for the first time, the existence of amphiphilic nanodomains (1-2 nm(2)). Compositional heterogeneity at the nanoscale is further corroborated by a statistical analysis on the data obtained with dynamic AM-AFM force spectroscopy. Variations in the long range attractive forces, responsible for water affinity, are also identified. These nanoscopic results on the polymers wettability are also confirmed by contact angle measurements (i.e., static and dynamic). The unprecedented ability to visualize the amphiphilic nanodomains as well as sub-nanometer crystalline structures provides strong evidence for the existence of previously postulated nanostructures, and sheds light on the underlying antifouling mechanism of amphiphilic chemistry.

  14. Scurvy revealed by difficulty walking: three cases in young children.

    PubMed

    Kitcharoensakkul, Maleewan; Schulz, Christa G; Kassel, Rachel; Khanna, Geetika; Liang, Shannon; Ngwube, Alexander; Baszis, Kevin W; Hunstad, David A; White, Andrew J

    2014-06-01

    Scurvy is rare in developed countries but is known to cause lower-extremity pain and refusal to ambulate in children. Since the discovery of the link between scurvy and dietary deficiency of ascorbic acid, there has been a substantial decrease in its prevalence and recognition. Here we describe 3 cases of scurvy in young children presenting with difficulty walking. Only 1 of 3 patients had gingival lesions at the initial presentation. Two cases underwent an extensive evaluation for hematologic and rheumatologic diseases before the diagnosis of scurvy was made. Dietary histories eventually revealed that all 3 patients had sharply limited intake of fruits and vegetables secondary to oral aversion, and 1 patient had autism. Radiographic changes of long bones were observed in all patients. Interestingly, all patients had concomitant vitamin D deficiency. After replacement with vitamin C, all patients recovered and started to walk again with improved leg pain. These clinical manifestations and radiologic findings highlight the importance for rheumatologists to have a higher index of suspicion for scurvy in nonambulatory children. PMID:24847751

  15. Distributed neural system for emotional intelligence revealed by lesion mapping

    PubMed Central

    Colom, Roberto; Grafman, Jordan

    2014-01-01

    Cognitive neuroscience has made considerable progress in understanding the neural architecture of human intelligence, identifying a broadly distributed network of frontal and parietal regions that support goal-directed, intelligent behavior. However, the contributions of this network to social and emotional aspects of intellectual function remain to be well characterized. Here we investigated the neural basis of emotional intelligence in 152 patients with focal brain injuries using voxel-based lesion-symptom mapping. Latent variable modeling was applied to obtain measures of emotional intelligence, general intelligence and personality from the Mayer, Salovey, Caruso Emotional Intelligence Test (MSCEIT), the Wechsler Adult Intelligence Scale and the Neuroticism-Extroversion-Openness Inventory, respectively. Regression analyses revealed that latent scores for measures of general intelligence and personality reliably predicted latent scores for emotional intelligence. Lesion mapping results further indicated that these convergent processes depend on a shared network of frontal, temporal and parietal brain regions. The results support an integrative framework for understanding the architecture of executive, social and emotional processes and make specific recommendations for the interpretation and application of the MSCEIT to the study of emotional intelligence in health and disease. PMID:23171618

  16. Microscopic study reveals the singular origins of growth

    NASA Astrophysics Data System (ADS)

    Yaari, G.; Nowak, A.; Rakocy, K.; Solomon, S.

    2008-04-01

    Anderson [Science 177, 293 (1972)] proposed the concept of complexity in order to describe the emergence and growth of macroscopic collective patterns out of the simple interactions of many microscopic agents. In the physical sciences this paradigm was implemented systematically and confirmed repeatedly by successful confrontation with reality. In the social sciences however, the possibilities to stage experiments to validate it are limited. During the 90's a series of dramatic political and economic events have provided the opportunity to do so. We exploit the resulting empirical evidence to validate a simple agent based alternative to the classical logistic dynamics. The post-liberalization empirical data from Poland confirm the theoretical prediction that the dynamics is dominated by singular rare events which insure the resilience and adaptability of the system. We have shown that growth is led by few singular “growth centers" (Fig. 1), that initially developed at a tremendous rate (Fig. 3), followed by a diffusion process to the rest of the country and leading to a positive growth rate uniform across the counties. In addition to the interdisciplinary unifying potential of our generic formal approach, the present work reveals the strong causal ties between the “softer" social conditions and their “hard" economic consequences.

  17. Genetic investigation within Lactococcus garvieae revealed two genomic lineages.

    PubMed

    Ferrario, Chiara; Ricci, Giovanni; Borgo, Francesca; Rollando, Alessandro; Fortina, Maria Grazia

    2012-07-01

    The diversity of a collection of 49 Lactococcus garvieae strains, including isolates of dairy, fish, meat, vegetable and cereal origin, was explored using a molecular polyphasic approach comprising PCR-ribotyping, REP and RAPD-PCR analyses and a multilocus restriction typing (MLRT) carried out on six partial genes (atpA, tuf, dltA, als, gapC, and galP). This approach allowed high-resolution cluster analysis in which two major groups were distinguishable: one group included dairy isolates, the other group meat isolates. Unexpectedly, of the 12 strains coming from fish, four grouped with dairy isolates, whereas the others with meat isolates. Likewise, strains isolated from vegetables allocated between the two main groups. These findings revealed high variability within the species at both gene and genome levels. The observed genetic heterogeneity among L. garvieae strains was not entirely coherent with the ecological niche of origin of the strains, but rather supports the idea of an early separation of L. garvieae population into two independent genomic lineages. PMID:22568590

  18. Nicotinamide Riboside Kinase Structures Reveal New Pathways to NAD+

    PubMed Central

    Bogan, Katrina L; Belenky, Peter; Wojcik, Marzena; Seidle, Heather F; Nedyalkova, Lyudmila; Yang, Tianle; Sauve, Anthony A; Park, Hee-Won; Brenner, Charles

    2007-01-01

    The eukaryotic nicotinamide riboside kinase (Nrk) pathway, which is induced in response to nerve damage and promotes replicative life span in yeast, converts nicotinamide riboside to nicotinamide adenine dinucleotide (NAD+) by phosphorylation and adenylylation. Crystal structures of human Nrk1 bound to nucleoside and nucleotide substrates and products revealed an enzyme structurally similar to Rossmann fold metabolite kinases and allowed the identification of active site residues, which were shown to be essential for human Nrk1 and Nrk2 activity in vivo. Although the structures account for the 500-fold discrimination between nicotinamide riboside and pyrimidine nucleosides, no enzyme feature was identified to recognize the distinctive carboxamide group of nicotinamide riboside. Indeed, nicotinic acid riboside is a specific substrate of human Nrk enzymes and is utilized in yeast in a novel biosynthetic pathway that depends on Nrk and NAD+ synthetase. Additionally, nicotinic acid riboside is utilized in vivo by Urh1, Pnp1, and Preiss-Handler salvage. Thus, crystal structures of Nrk1 led to the identification of new pathways to NAD+. PMID:17914902

  19. Network deconstruction reveals network structure in responsive microgels.

    PubMed

    Smith, Michael H; Herman, Emily S; Lyon, L Andrew

    2011-04-14

    Detailed characterization of hydrogel particle erosion revealed critical physicochemical differences between spheres, where network decomposition was informative of network structure. Real-time, in situ monitoring of the triggered erosion of colloidal hydrogels (microgels) was performed via multiangle light scattering. The solution-average molar mass and root-mean-square radii of eroding particles were measured as a function of time for microgels prepared from N-isopropylacrylamide (NIPAm) or N-isopropylmethacrylamide (NIPMAm), copolymerized with a chemically labile cross-linker (1,2-dihydroxylethylene)bisacrylamide (DHEA). Precipitation polymerization was employed to yield particles of comparable dimensions but with distinct topological features. Heterogeneous cross-linker incorporation resulted in a heterogeneous network structure for pNIPAm microgels. During the erosion reaction, mass loss proceeded from the exterior toward the interior of the polymer. In contrast, pNIPMAm microgels had a more homogeneous network structure, which resulted in a more uniform mass loss throughout the particle during erosion. Although both particle types degraded into low molar mass products, pNIPAm microgels were incapable of complete dissolution due to the presence of nondegradable cross-links arising from chain transfer and branching during particle synthesis. The observations described herein provide insight into key design parameters associated with the synthesis of degradable hydrogel particles, which may be of use in various biotechnological applications. PMID:21425815

  20. Can strong correlations be experimentally revealed for Ҡ -mesons?

    NASA Astrophysics Data System (ADS)

    Hiesmayr, Beatrix C.

    2014-11-01

    In 1964 the physicists John St. Bell working at CERN took the 1935-idea of Einstein-Podolsky-Rosen seriously and found that all theories based on local realism have to satisfy a certain inequality, nowadays dubbed Bell's inequality. Experiments with ordinary matter systems or light show violations of Bell's inequality favouring the quantum theory though a loophole free experiment has not yet been performed. This contribution presents an experimentally feasible Bell inequality for systems at higher energy scales, i.e. entangled neutral Ҡ -meson pairs that are typically produced in Φ -mesons decays or proton-antiproton annihilation processes. Strong requirements have to be overcome in order to achieve a conclusive tests, such a proposal was recently published. Surprisingly, this new Bell inequality reveals new features for weakly decaying particles, in particular, a strong sensitivity to the combined charge-conjugation-parity (CP) symmetry. Here-with, a puzzling relation between a symmetry breaking for mesons and Bell's inequality—which is a necessary and sufficient condition for the security of quantum cryptography protocols— is established. This becomes the more important since CP symmetry is related to the cosmological question why the antimatter disappeared after the Big Bang.

  1. Maximal Neighbor Similarity Reveals Real Communities in Networks

    NASA Astrophysics Data System (ADS)

    Žalik, Krista Rizman

    2015-12-01

    An important problem in the analysis of network data is the detection of groups of densely interconnected nodes also called modules or communities. Community structure reveals functions and organizations of networks. Currently used algorithms for community detection in large-scale real-world networks are computationally expensive or require a priori information such as the number or sizes of communities or are not able to give the same resulting partition in multiple runs. In this paper we investigate a simple and fast algorithm that uses the network structure alone and requires neither optimization of pre-defined objective function nor information about number of communities. We propose a bottom up community detection algorithm in which starting from communities consisting of adjacent pairs of nodes and their maximal similar neighbors we find real communities. We show that the overall advantage of the proposed algorithm compared to the other community detection algorithms is its simple nature, low computational cost and its very high accuracy in detection communities of different sizes also in networks with blurred modularity structure consisting of poorly separated communities. All communities identified by the proposed method for facebook network and E-Coli transcriptional regulatory network have strong structural and functional coherence.

  2. From C to Parton Sea: How Supercomputing Reveals Nucleon Structure

    NASA Astrophysics Data System (ADS)

    Lin, Huey-Wen

    2016-03-01

    Studying the structure of nucleons is not only important to understanding the strong interactions of quarks and gluons, but also to improving the precision of new-physics searches. Since a broad class of experiments, including the LHC and dark-matter detection, require interactions with nucleons, the mission to probe femtoscale physics is also essential for disentangling Standard-Model contributions from potential new physics. These SM backgrounds require parton distribution functions (PDFs) as inputs. However, after decades of experiments and theoretical efforts, there still remain many unknowns, especially in the sea flavor structure and transversely polarized structure. In a discrete spacetime, we can make a direct numerical calculation of the implications of QCD using sufficiently large supercomputing resources. A nonperturbative approach from first principles, lattice QCD, provides hope to expand our understanding of nucleon structure, especially in regions that are difficult to observe in experiments. In this work, we present a first direct calculation of the Bjorken-x dependence of the PDFs using Large-Momentum Effective Theory (LaMET) and comment on the surprising result revealed for the nucleon sea-flavor asymmetry. The work of HWL is supported in part by the M. Hildred Blewett Fellowship of the American Physical Society, www.aps.org.

  3. Colored microspheres reveal interarterial microvascular anastomoses in canine myocardium.

    PubMed

    Cicutti, N; Rakusan, K; Downey, H F

    1992-01-01

    While the presence of microvascular intercommunication within an individual myocardial arterial bed is well documented, there is a paucity of data to support the existence of anastomoses emanating from independent arterial beds. Simultaneous in-vivo infusion of two different colored microsphere suspensions into the left anterior descending (LAD) and left circumflex (LCx) coronary arteries identified a specific interface region of canine myocardium that was perfused by both arterial branches. Subsequent microscopic/morphometric analysis of 40 microns serial sections in eight hearts revealed clustering of microspheres in their respective perfusion territories (red microspheres in the LAD region away from the interface, blue microspheres in the LCx field away from the interface), along with a mutually perfused borderzone. In each tissue section, two regions within this zone were identified and their maximum widths measured. One region was defined as the Interface Transition Zone (ITZ) (mean width = 5251 +/- 770 microns; mean +/- SD). This region was formed by an intermingling of microvessels supplied by the parent arteries of the adjacent perfusion territories; it separated tissue containing only one or the other colored microspheres. The second region was defined as the Boundary Watershed Zone (BWZ) (mean zone width = 3151 +/- 611 microns; mean +/- SD). This region was formed by capillaries containing sphere aggregates of both colors; it was located exclusively within the ITZ. In addition, the ITZ and BWZ were significantly wider in subepicardial than in subendocardial regions (p less than 0.001). PMID:1417709

  4. The eyes of Tullimonstrum reveal a vertebrate affinity.

    PubMed

    Clements, Thomas; Dolocan, Andrei; Martin, Peter; Purnell, Mark A; Vinther, Jakob; Gabbott, Sarah E

    2016-04-28

    Tullimonstrum gregarium is an iconic soft-bodied fossil from the Carboniferous Mazon Creek Lagerstätte (Illinois, USA). Despite a large number of specimens and distinct anatomy, various analyses over the past five decades have failed to determine the phylogenetic affinities of the 'Tully monster', and although it has been allied to such disparate phyla as the Mollusca, Annelida or Chordata, it remains enigmatic. The nature and phylogenetic affinities of Tullimonstrum have defied confident systematic placement because none of its preserved anatomy provides unequivocal evidence of homology, without which comparative analysis fails. Here we show that the eyes of Tullimonstrum possess ultrastructural details indicating homology with vertebrate eyes. Anatomical analysis using scanning electron microscopy reveals that the eyes of Tullimonstrum preserve a retina defined by a thick sheet comprising distinct layers of spheroidal and cylindrical melanosomes. Time-of-flight secondary ion mass spectrometry and multivariate statistics provide further evidence that these microbodies are melanosomes. A range of animals have melanin in their eyes, but the possession of melanosomes of two distinct morphologies arranged in layers, forming retinal pigment epithelium, is a synapomorphy of vertebrates. Our analysis indicates that in addition to evidence of colour patterning, ecology and thermoregulation, fossil melanosomes can also carry a phylogenetic signal. Identification in Tullimonstrum of spheroidal and cylindrical melanosomes forming the remains of retinal pigment epithelium indicates that it is a vertebrate; considering its body parts in this new light suggests it was an anatomically unusual member of total group Vertebrata. PMID:27074512

  5. Eukaryote Culturomics of the Gut Reveals New Species

    PubMed Central

    Gouba, Nina; Raoult, Didier; Drancourt, Michel

    2014-01-01

    The repertoire of microeukaryotes in the human gut has been poorly explored, mainly in individuals living in northern hemisphere countries. We further explored this repertoire using PCR-sequencing and culture in seven individuals living in four tropical countries. A total of 41 microeukaryotes including 38 different fungal species and three protists were detected. Four fungal species, Davidiella tassiana, Davidiella sp., Corticiaceae sp., and Penicillium sp., were uniquely detected by culture; 27 fungal species were uniquely detected using PCR-sequencing and Candida albicans, Candida glabrata, Trichosporon asahii, Clavispora lusitaniae, Debaryomyces hansenii, Malassezia restricta, and Malassezia sp. were detected using both molecular and culture methods. Fourteen microeukaryotes were shared by the seven individuals, whereas 27 species were found in only one individual, including 11 species in Amazonia, nine species in Polynesia, five species in India, and two species in Senegal. These data support a worldwide distribution of Malassezia sp., Trichosporon sp., and Candida sp. in the gut mycobiome. Here, 13 fungal species and two protists, Stentor roeseli and Vorticella campanula, were observed for first time in the human gut. This study revealed a previously unsuspected diversity in the repertoire of human gut microeukaryotes, suggesting spots for further exploring this repertoire. PMID:25210972

  6. Beyond Contagion: Reality Mining Reveals Complex Patterns of Social Influence.

    PubMed

    Alshamsi, Aamena; Pianesi, Fabio; Lepri, Bruno; Pentland, Alex; Rahwan, Iyad

    2015-01-01

    Contagion, a concept from epidemiology, has long been used to characterize social influence on people's behavior and affective (emotional) states. While it has revealed many useful insights, it is not clear whether the contagion metaphor is sufficient to fully characterize the complex dynamics of psychological states in a social context. Using wearable sensors that capture daily face-to-face interaction, combined with three daily experience sampling surveys, we collected the most comprehensive data set of personality and emotion dynamics of an entire community of work. From this high-resolution data about actual (rather than self-reported) face-to-face interaction, a complex picture emerges where contagion (that can be seen as adaptation of behavioral responses to the behavior of other people) cannot fully capture the dynamics of transitory states. We found that social influence has two opposing effects on states: adaptation effects that go beyond mere contagion, and complementarity effects whereby individuals' behaviors tend to complement the behaviors of others. Surprisingly, these effects can exhibit completely different directions depending on the stable personality or emotional dispositions (stable traits) of target individuals. Our findings provide a foundation for richer models of social dynamics, and have implications on organizational engineering and workplace well-being. PMID:26313449

  7. Lipidome analysis reveals antifungal polyphenol curcumin affects membrane lipid homeostasis.

    PubMed

    Sharma, Monika; Dhamgaye, Sanjiveeni; Singh, Ashutosh; Prasad, Rajendra

    2012-01-01

    This study shows that antifungal curcumin (CUR), significantly depletes ergosterol levels in Candida albicans. CUR while displaying synergy with fluconazole (FLC) lowers ergosterol. However, CUR alone at its synergistic concentration (lower than MIC50), could not affect ergosterol contents. For deeper insight of CUR effects on lipids, we performed high throughput mass spectroscopy (MS) based lipid profiling of C. albicans cells. The lipidome analysis revealed that there were no major changes in phosphoglycerides (PGLs) composition following CUR treatment of Candida, however, significant differences in molecular species of PGLs were detected. Among major SPLs, CUR treatment resulted in the reduction of ceramide and accumulation of IPCs levels. The lipidome of CUR treated cells confirmed a dramatic drop in the ergosterol levels with a simultaneous accumulation of its biosynthetic precursors. This was further supported by the fact that the mutants defective in ergosterol biosynthesis (ERG2 and ERG11) and those lacking the transcription factor regulating ergosterol biosynthesis, UPC2, were highly susceptible to CUR. Our study first time shows that CUR, for its antifungal activity, targets and down regulates delta 5, 6 desaturase (ERG3) resulting in depletion of ergosterol. This results in parallel accumulation of ergosterol biosynthetic precursors, generation of reactive oxygen species (ROS) and cell death. PMID:22201946

  8. Global Isotope Metabolomics Reveals Adaptive Strategies for Nitrogen Assimilation.

    PubMed

    Kurczy, Michael E; Forsberg, Erica M; Thorgersen, Michael P; Poole, Farris L; Benton, H Paul; Ivanisevic, Julijana; Tran, Minerva L; Wall, Judy D; Elias, Dwayne A; Adams, Michael W W; Siuzdak, Gary

    2016-06-17

    Nitrogen cycling is a microbial metabolic process essential for global ecological/agricultural balance. To investigate the link between the well-established ammonium and the alternative nitrate assimilation metabolic pathways, global isotope metabolomics was employed to examine three nitrate reducing bacteria using (15)NO3 as a nitrogen source. In contrast to a control (Pseudomonas stutzeri RCH2), the results show that two of the isolates from Oak Ridge, Tennessee (Pseudomonas N2A2 and N2E2) utilize nitrate and ammonia for assimilation concurrently with differential labeling observed across multiple classes of metabolites including amino acids and nucleotides. The data reveal that the N2A2 and N2E2 strains conserve nitrogen-containing metabolites, indicating that the nitrate assimilation pathway is a conservation mechanism for the assimilation of nitrogen. Co-utilization of nitrate and ammonia is likely an adaption to manage higher levels of nitrite since the denitrification pathways utilized by the N2A2 and N2E2 strains from the Oak Ridge site are predisposed to the accumulation of the toxic nitrite. The use of global isotope metabolomics allowed for this adaptive strategy to be investigated, which would otherwise not have been possible to decipher. PMID:27045776

  9. Acoustic telemetry reveals cryptic residency of whale sharks

    PubMed Central

    Cagua, E. Fernando; Cochran, Jesse E. M.; Rohner, Christoph A.; Prebble, Clare E. M.; Sinclair-Taylor, Tane H.; Pierce, Simon J.; Berumen, Michael L.

    2015-01-01

    Although whale sharks (Rhincodon typus) have been documented to move thousands of kilometres, they are most frequently observed at a few predictable seasonal aggregation sites. The absence of sharks at the surface during visual surveys has led to the assumption that sharks disperse to places unknown during the long ‘off-seasons’ at most of these locations. Here we compare 2 years of R. typus visual sighting records from Mafia Island in Tanzania to concurrent acoustic telemetry of tagged individuals. Sightings revealed a clear seasonal pattern with a peak between October and February and no sharks observed at other times. By contrast, acoustic telemetry demonstrated year-round residency of R. typus. The sharks use a different habitat in the off-season, swimming deeper and further away from shore, presumably in response to prey distributions. This behavioural change reduces the sharks' visibility, giving the false impression that they have left the area. We demonstrate, for the first time to our knowledge, year-round residency of unprovisioned, individual R. typus at an aggregation site, and highlight the importance of using multiple techniques to study the movement ecology of marine megafauna. PMID:25832816

  10. Structure of the Angiotensin Receptor Revealed by Serial Femtosecond Crystallography

    SciTech Connect

    Zhang, Haitao; Unal, Hamiyet; Gati, Cornelius; Han, Gye Won; Liu, Wei; Zatsepin, Nadia A.; James, Daniel; Wang, Dingjie; Nelson, Garrett; Weierstall, Uwe; Sawaya, Michael R.; Xu, Qingping; Messerschmidt, Marc; Williams, Garth J.; Boutet, Sébastien; Yefanov, Oleksandr M.; White, Thomas A.; Wang, Chong; Ishchenko, Andrii; Tirupula, Kalyan C.; Desnoyer, Russell; Coe, Jesse; Conrad, Chelsie E.; Fromme, Petra; Stevens, Raymond C.; Katritch, Vsevolod; Karnik, Sadashiva S.; Cherezov, Vadim

    2015-05-07

    We report that angiotensin II type 1 receptor (AT1R) is a G protein-coupled receptor that serves as a primary regulator for blood pressure maintenance. Although several anti-hypertensive drugs have been developed as AT1R blockers (ARBs), the structural basis for AT1R ligand-binding and regulation has remained elusive, mostly due to the difficulties of growing high quality crystals for structure determination using synchrotron radiation. By applying the recently developed method of serial femtosecond crystallography at an X-ray free-electron laser, we successfully determined the room-temperature crystal structure of the human AT1R in complex with its selective antagonist ZD7155 at 2.9 Å resolution. The AT1R-ZD7155 complex structure revealed key structural features ofAT1R and critical interactions for ZD7155 binding. Finally, docking simulations of the clinically used ARBs into the AT1R structure further elucidated both the common and distinct binding modes for these anti-hypertensive drugs. Our results thereby provide fundamental insights into AT1R structure-function relationship and structure-based drug design.

  11. Early Neolithic Water Wells Reveal the World's Oldest Wood Architecture

    PubMed Central

    Tegel, Willy; Elburg, Rengert; Hakelberg, Dietrich; Stäuble, Harald; Büntgen, Ulf

    2012-01-01

    The European Neolithization ∼6000−4000 BC represents a pivotal change in human history when farming spread and the mobile style of life of the hunter-foragers was superseded by the agrarian culture. Permanent settlement structures and agricultural production systems required fundamental innovations in technology, subsistence, and resource utilization. Motivation, course, and timing of this transformation, however, remain debatable. Here we present annually resolved and absolutely dated dendroarchaeological information from four wooden water wells of the early Neolithic period that were excavated in Eastern Germany. A total of 151 oak timbers preserved in a waterlogged environment were dated between 5469 and 5098 BC and reveal unexpectedly refined carpentry skills. The recently discovered water wells enable for the first time a detailed insight into the earliest wood architecture and display the technological capabilities of humans ∼7000 years ago. The timbered well constructions made of old oak trees feature an unopened tree-ring archive from which annually resolved and absolutely dated environmental data can be culled. Our results question the principle of continuous evolutionary development in prehistoric technology, and contradict the common belief that metal was necessary for complex timber constructions. Early Neolithic craftsmanship now suggests that the first farmers were also the first carpenters. PMID:23284685

  12. An acoustic microscopy technique reveals hidden morphological defenses in Daphnia.

    PubMed

    Laforsch, Christian; Ngwa, Wilfred; Grill, Wolfgang; Tollrian, Ralph

    2004-11-01

    Inducible defenses are common strategies for coping with the selective force of predation in heterogeneous environments. In recent years the conspicuous and often dramatic morphological plasticity of several waterflea species of the genus Daphnia have been found to be inducible defenses activated by chemical cues released by predators. However, the exact defensive mechanisms remained mysterious. Because even some minute morphological alterations proved to be protective against predatory invertebrates, it has been suggested that the visible morphological changes are only the tip of the iceberg of the entire protective mechanisms. Here we applied a method of ultrasonic microscopy with vector contrast at 1.2 GHz to probe hidden morphological defenses. We found that induction with predator kairomones increases the stability of the carapace in two Daphnia species up to 350%. This morphological plasticity provides a major advantage for the induced morphs during predation because predatory invertebrates need to crush or puncture the carapace of their prey to consume them. Our ultrastructural analyses revealed that the internal architecture of the carapace ensures maximal rigidity with minimal material investment. Our results uncover hidden morphological plasticity and suggest a reconsideration of former classification systems in defended and undefended genotypes in Daphnia and possibly in other prey organisms as well. PMID:15520396

  13. Graphene grain boundary resistivity revealed by scanning tunneling potentiometry

    NASA Astrophysics Data System (ADS)

    Durand, Corentin; Clark, Kendal W.; Zhang, Xiaoguang; Vlassiouk, Ivan V.; Li, An-Ping; Oak Ridge National Lab Team

    2014-03-01

    All large-scale graphene films contain extended topological defects dividing graphene into domains or grains. Here, we study grain boundary (GB) resistivity in CVD graphene on Cu subsequently transferred to a SiO2 substrate. By using a scanning tunneling potentiometry (STP) setup with a cryogenic four-probe STM, the spatial variation of the local electrochemical potential is resolved across individual GBs on a graphene surface in the presence of a current. The 2D distributions of electric field and conductivity were then numerically extracted by solving conduction equations. The derived conductivity of individual grains was compared to that measured with microscopic four-probe STM method to provide a model-independent determination of conductivity map for specific type of defect in graphene. The resistance of a GB is found to change with the width of the disordered transition region between adjacent grains. A quantitative modeling of boundary resistance reveals the increased electron Fermi wave vector within the boundary region, possibly due to boundary induced charge density variation.

  14. In vivo behavior of NTBI revealed by automated quantification system.

    PubMed

    Ito, Satoshi; Ikuta, Katsuya; Kato, Daisuke; Lynda, Addo; Shibusa, Kotoe; Niizeki, Noriyasu; Toki, Yasumichi; Hatayama, Mayumi; Yamamoto, Masayo; Shindo, Motohiro; Iizuka, Naomi; Kohgo, Yutaka; Fujiya, Mikihiro

    2016-08-01

    Non-Tf-bound iron (NTBI), which appears in serum in iron overload, is thought to contribute to organ damage; the monitoring of serum NTBI levels may therefore be clinically useful in iron-overloaded patients. However, NTBI quantification methods remain complex, limiting their use in clinical practice. To overcome the technical difficulties often encountered, we recently developed a novel automated NTBI quantification system capable of measuring large numbers of samples. In the present study, we investigated the in vivo behavior of NTBI in human and animal serum using this newly established automated system. Average NTBI in healthy volunteers was 0.44 ± 0.076 μM (median 0.45 μM, range 0.28-0.66 μM), with no significant difference between sexes. Additionally, serum NTBI rapidly increased after iron loading, followed by a sudden disappearance. NTBI levels also decreased in inflammation. The results indicate that NTBI is a unique marker of iron metabolism, unlike other markers of iron metabolism, such as serum ferritin. Our new automated NTBI quantification method may help to reveal the clinical significance of NTBI and contribute to our understanding of iron overload. PMID:27086349

  15. Covert Waking Brain Activity Reveals Instantaneous Sleep Depth

    PubMed Central

    McKinney, Scott M.; Dang-Vu, Thien Thanh; Buxton, Orfeu M.; Solet, Jo M.; Ellenbogen, Jeffrey M.

    2011-01-01

    The neural correlates of the wake-sleep continuum remain incompletely understood, limiting the development of adaptive drug delivery systems for promoting sleep maintenance. The most useful measure for resolving early positions along this continuum is the alpha oscillation, an 8–13 Hz electroencephalographic rhythm prominent over posterior scalp locations. The brain activation signature of wakefulness, alpha expression discloses immediate levels of alertness and dissipates in concert with fading awareness as sleep begins. This brain activity pattern, however, is largely ignored once sleep begins. Here we show that the intensity of spectral power in the alpha band actually continues to disclose instantaneous responsiveness to noise—a measure of sleep depth—throughout a night of sleep. By systematically challenging sleep with realistic and varied acoustic disruption, we found that sleepers exhibited markedly greater sensitivity to sounds during moments of elevated alpha expression. This result demonstrates that alpha power is not a binary marker of the transition between sleep and wakefulness, but carries rich information about immediate sleep stability. Further, it shows that an empirical and ecologically relevant form of sleep depth is revealed in real-time by EEG spectral content in the alpha band, a measure that affords prediction on the order of minutes. This signal, which transcends the boundaries of classical sleep stages, could potentially be used for real-time feedback to novel, adaptive drug delivery systems for inducing sleep. PMID:21408616

  16. First cranial remains of a gondwanatherian mammal reveal remarkable mosaicism.

    PubMed

    Krause, David W; Hoffmann, Simone; Wible, John R; Kirk, E Christopher; Schultz, Julia A; von Koenigswald, Wighart; Groenke, Joseph R; Rossie, James B; O'Connor, Patrick M; Seiffert, Erik R; Dumont, Elizabeth R; Holloway, Waymon L; Rogers, Raymond R; Rahantarisoa, Lydia J; Kemp, Addison D; Andriamialison, Haingoson

    2014-11-27

    Previously known only from isolated teeth and lower jaw fragments recovered from the Cretaceous and Palaeogene of the Southern Hemisphere, the Gondwanatheria constitute the most poorly known of all major mammaliaform radiations. Here we report the discovery of the first skull material of a gondwanatherian, a complete and well-preserved cranium from Upper Cretaceous strata in Madagascar that we assign to a new genus and species. Phylogenetic analysis strongly supports its placement within Gondwanatheria, which are recognized as monophyletic and closely related to multituberculates, an evolutionarily successful clade of Mesozoic mammals known almost exclusively from the Northern Hemisphere. The new taxon is the largest known mammaliaform from the Mesozoic of Gondwana. Its craniofacial anatomy reveals that it was herbivorous, large-eyed and agile, with well-developed high-frequency hearing and a keen sense of smell. The cranium exhibits a mosaic of primitive and derived features, the disparity of which is extreme and probably reflective of a long evolutionary history in geographic isolation. PMID:25383528

  17. Transcriptome meta-analysis reveals dysregulated pathways in nasopharyngeal carcinoma.

    PubMed

    Tulalamba, Warut; Larbcharoensub, Noppadol; Sirachainan, Ekaphop; Tantiwetrueangdet, Aunchalee; Janvilisri, Tavan

    2015-08-01

    Nasopharyngeal carcinoma (NPC) is a malignant cancer arising from the epithelial surface of the nasopharynx that mostly appears in advanced stages of the disease, leading to a poor prognosis. To date, a number of mRNA profiling investigations on NPC have been reported in order to identify suitable biomarkers for early detection. However, the results may be specific to each study with distinct sample types. In this study, an integrative meta-analysis of NPC transcriptome data was performed to determine dysregulated pathways, potentially leading to identification of molecular markers. Ten independent NPC gene expression profiling microarray datasets, including 135 samples from NPC cell lines, primary cell lines, and tissues were assimilated into a meta-analysis and cross-validation to identify a cohort of genes that were significantly dysregulated in NPC. Bioinformatics analyses of these genes revealed the significant pathways and individual players involving in cellular metabolism, cell cycle regulation, DNA repair, as well as ErbB pathway. Altogether, we propose that dysregulation of these molecular pathways in NPC might play a role in the NPC pathogenesis, providing clues, which could eventually translate into diagnostic and therapeutic approaches. PMID:25724187

  18. Prolonged stimulus exposure reveals prolonged neurobehavioral response patterns.

    PubMed

    Johnson, Brett A; Woo, Cynthia C; Zeng, Yu; Xu, Zhe; Hingco, Edna E; Ong, Joan; Leon, Michael

    2010-05-15

    Although it has been shown repeatedly that minimum response times in sensory systems can be quite short, organisms more often continue to respond to sensory stimuli over considerably longer periods of time. The continuing response to sensory stimulation may be a more realistic assessment of natural sensory responses, so we determined for how long a stimulus would evoke a response in naïve, freely moving animals. Specifically, we determined for how long such rats responded to odorants during continuous passive exposures by monitoring their sniffing with whole-body plethysmography. We found that naïve rats continue to sniff odorants vigorously for up to 3 minutes, much longer than what has been reported for highly trained, highly motivated rats. Patterns of 2-deoxyglucose (2-DG) uptake in the glomerular layer of the rat olfactory bulb also were seen after only 1-5 minutes of odorant exposure, overlapping with the period of increased respiration to odorants. Moreover, these 2-DG uptake patterns closely resembled the patterns that emerge from prolonged odorant exposures, suggesting that activity mapping over prolonged periods can identify areas of activity that are present when rats are still attending and responding to odorant stimuli. Given these findings, it seems important to consider the possibility that prolonged exposure to other sensory stimuli will reveal more realistic neural response patterns. PMID:20232477

  19. Statistical universals reveal the structures and functions of human music

    PubMed Central

    Savage, Patrick E.; Brown, Steven; Sakai, Emi; Currie, Thomas E.

    2015-01-01

    Music has been called “the universal language of mankind.” Although contemporary theories of music evolution often invoke various musical universals, the existence of such universals has been disputed for decades and has never been empirically demonstrated. Here we combine a music-classification scheme with statistical analyses, including phylogenetic comparative methods, to examine a well-sampled global set of 304 music recordings. Our analyses reveal no absolute universals but strong support for many statistical universals that are consistent across all nine geographic regions sampled. These universals include 18 musical features that are common individually as well as a network of 10 features that are commonly associated with one another. They span not only features related to pitch and rhythm that are often cited as putative universals but also rarely cited domains including performance style and social context. These cross-cultural structural regularities of human music may relate to roles in facilitating group coordination and cohesion, as exemplified by the universal tendency to sing, play percussion instruments, and dance to simple, repetitive music in groups. Our findings highlight the need for scientists studying music evolution to expand the range of musical cultures and musical features under consideration. The statistical universals we identified represent important candidates for future investigation. PMID:26124105

  20. Circular RNA profile in gliomas revealed by identification tool UROBORUS

    PubMed Central

    Song, Xiaofeng; Zhang, Naibo; Han, Ping; Moon, Byoung-San; Lai, Rose K.; Wang, Kai; Lu, Wange

    2016-01-01

    Recent evidence suggests that many endogenous circular RNAs (circRNAs) may play roles in biological processes. However, the expression patterns and functions of circRNAs in human diseases are not well understood. Computationally identifying circRNAs from total RNA-seq data is a primary step in studying their expression pattern and biological roles. In this work, we have developed a computational pipeline named UROBORUS to detect circRNAs in total RNA-seq data. By applying UROBORUS to RNA-seq data from 46 gliomas and normal brain samples, we detected thousands of circRNAs supported by at least two read counts, followed by successful experimental validation on 24 circRNAs from the randomly selected 27 circRNAs. UROBORUS is an efficient tool that can detect circRNAs with low expression levels in total RNA-seq without RNase R treatment. The circRNAs expression profiling revealed more than 476 circular RNAs differentially expressed in control brain tissues and gliomas. Together with parental gene expression, we found that circRNA and its parental gene have diversified expression patterns in gliomas and control brain tissues. This study establishes an efficient and sensitive approach for predicting circRNAs using total RNA-seq data. The UROBORUS pipeline can be accessed freely for non-commercial purposes at http://uroborus.openbioinformatics.org/. PMID:26873924

  1. Transcriptome Profiling Reveals TGF-β Signaling Involvement in Epileptogenesis

    PubMed Central

    Cacheaux, Luisa P; Ivens, Sebastian; David, Yaron; Lakhter, Alexander J; Bar-Klein, Guy; Shapira, Michael; Heinemann, Uwe; Friedman, Alon; Kaufer, Daniela

    2010-01-01

    Brain injury may result in the development of epilepsy, one of the most common neurological disorders. We previously demonstrated that albumin is critical in the generation of epilepsy following blood-brain barrier (BBB) compromise. Here we identify TGF-β pathway activation as the underlying mechanism. We demonstrate that direct activation of the TGF-β pathway by TGF-β1 results in epileptiform activity similar to that following exposure to albumin. Co-immunoprecipitation revealed binding of albumin to TGF-β receptor II and Smad2 phosphorylation confirmed downstream activation of this pathway. Transcriptome profiling demonstrated similar expression patterns following BBB breakdown, albumin and TGF-β1 exposure, including modulation of genes associated with the TGF-β pathway, early astrocytic activation, inflammation, and reduced inhibitory transmission. Importantly, TGF-β pathway blockers suppressed most albumin-induced transcriptional changes and prevented the generation of epileptiform activity. Our present data identifies the TGF-β pathway as a novel putative epileptogenic signaling cascade and therapeutic target for the prevention of injury-induced epilepsy. PMID:19605630

  2. Enzyme kinetics: the whole picture reveals hidden meanings.

    PubMed

    Pinto, Maria F; Estevinho, Berta N; Crespo, Rosa; Rocha, Fernando A; Damas, Ana M; Martins, Pedro M

    2015-06-01

    The methodology adopted by Michaelis and Menten in 1913 is still routinely used to characterize the catalytic power and selectivity of enzymes. These kinetic measurements must be performed soon after the purified enzyme is mixed with a large excess of substrate. Other time scales and solution compositions are no less physiologically relevant, but fall outside the range of applicability of the classical formalism. Here we show that the complete picture of an enzyme's mode of function is critically obscured by the limited scope of conventional kinetic analysis, even in the simplest case of a single active site without inhibition. This picture is now unveiled in a mathematically closed form that remains valid over the reaction time for all combinations of enzyme/substrate concentrations and rate constants. Algebraic simplicity is maintained in the new formalism when stationary reaction phases are considered. By achieving this century-old objective, the otherwise hidden role of the reversible binding step is revealed and atypical kinetic profiles are explained. Most singular kinetic behaviors are identified in a critical region of conditions that coincide with typical cell conditions. Because it is not covered by the Michaelis-Menten model, the critical region has been missed until now by low- and high-throughput screenings of new drugs. New possibilities are therefore raised for novel and once-promising inhibitors to therapeutically target enzymes. PMID:25808291

  3. Revealing the Intricate Effect of Collaboration on Innovation

    PubMed Central

    Inoue, Hiroyasu; Liu, Yang-Yu

    2015-01-01

    We studied the Japan and U.S. patent records of several decades to demonstrate the effect of collaboration on innovation. We found that statistically inventor teams slightly outperform solo inventors while company teams perform equally well as solo companies. By tracking the performance record of individual teams, we found that inventor teams’ performance generally degrades with more repeat collaborations. Though company teams’ performance displays strongly bursty behavior, long-term collaboration does not significantly help innovation. To systematically study the effect of repeat collaboration, we defined the repeat collaboration number of a team as the average number of collaborations over all the teammate pairs. We found that mild repeat collaboration improves the performance of Japanese inventor teams and U.S. company teams. Yet, excessive repeat collaboration does not significantly help innovation at both the inventor and company levels in both countries. To control for unobserved heterogeneity, we performed a detailed regression analysis and the results were consistent with our simple observations. The presented results revealed the intricate effect of collaboration on innovation, which may also be observed in other creative projects. PMID:25799138

  4. Nicotinamide riboside kinase structures reveal new pathways to NAD+.

    PubMed

    Tempel, Wolfram; Rabeh, Wael M; Bogan, Katrina L; Belenky, Peter; Wojcik, Marzena; Seidle, Heather F; Nedyalkova, Lyudmila; Yang, Tianle; Sauve, Anthony A; Park, Hee-Won; Brenner, Charles

    2007-10-01

    The eukaryotic nicotinamide riboside kinase (Nrk) pathway, which is induced in response to nerve damage and promotes replicative life span in yeast, converts nicotinamide riboside to nicotinamide adenine dinucleotide (NAD+) by phosphorylation and adenylylation. Crystal structures of human Nrk1 bound to nucleoside and nucleotide substrates and products revealed an enzyme structurally similar to Rossmann fold metabolite kinases and allowed the identification of active site residues, which were shown to be essential for human Nrk1 and Nrk2 activity in vivo. Although the structures account for the 500-fold discrimination between nicotinamide riboside and pyrimidine nucleosides, no enzyme feature was identified to recognize the distinctive carboxamide group of nicotinamide riboside. Indeed, nicotinic acid riboside is a specific substrate of human Nrk enzymes and is utilized in yeast in a novel biosynthetic pathway that depends on Nrk and NAD+ synthetase. Additionally, nicotinic acid riboside is utilized in vivo by Urh1, Pnp1, and Preiss-Handler salvage. Thus, crystal structures of Nrk1 led to the identification of new pathways to NAD+. PMID:17914902

  5. Seabird movement reveals the ecological footprint of fishing vessels.

    PubMed

    Bodey, Thomas W; Jessopp, Mark J; Votier, Stephen C; Gerritsen, Hans D; Cleasby, Ian R; Hamer, Keith C; Patrick, Samantha C; Wakefield, Ewan D; Bearhop, Stuart

    2014-06-01

    Exploitation of the seas is currently unsustainable, with increasing demand for marine resources placing intense pressure on the Earth's largest ecosystem [1]. The scale of anthropogenic effects varies from local to entire ocean basins [1-3]. For example, discards of commercial capture fisheries can have both positive and negative impacts on scavengers at the population and community-level [2-6], although this is driven by individual foraging behaviour [3,7]. Currently, we have little understanding of the scale at which individual animals initiate such behaviours. We use the known interaction between fisheries and a wide-ranging seabird, the Northern gannet Morus bassanus[3], to investigate how fishing vessels affect individual birds' behaviours in near real-time. We document the footprint of fishing vessels' (≥15 m length) influence on foraging decisions (≤11 km), and a potential underlying behavioural mechanism, by revealing how birds respond differently to vessels depending on gear type and activity. Such influences have important implications for fisheries, including the proposed discard ban [8]), and wider marine management. PMID:24892908

  6. Strategy revealing phenotypic differences among synthetic oscillator designs.

    PubMed

    Lomnitz, Jason G; Savageau, Michael A

    2014-09-19

    Considerable progress has been made in identifying and characterizing the component parts of genetic oscillators, which play central roles in all organisms. Nonlinear interaction among components is sufficiently complex that mathematical models are required to elucidate their elusive integrated behavior. Although natural and synthetic oscillators exhibit common architectures, there are numerous differences that are poorly understood. Utilizing synthetic biology to uncover basic principles of simpler circuits is a way to advance understanding of natural circadian clocks and rhythms. Following this strategy, we address the following questions: What are the implications of different architectures and molecular modes of transcriptional control for the phenotypic repertoire of genetic oscillators? Are there designs that are more realizable or robust? We compare synthetic oscillators involving one of three architectures and various combinations of the two modes of transcriptional control using a methodology that provides three innovations: a rigorous definition of phenotype, a procedure for deconstructing complex systems into qualitatively distinct phenotypes, and a graphical representation for illuminating the relationship between genotype, environment, and the qualitatively distinct phenotypes of a system. These methods provide a global perspective on the behavioral repertoire, facilitate comparisons of alternatives, and assist the rational design of synthetic gene circuitry. In particular, the results of their application here reveal distinctive phenotypes for several designs that have been studied experimentally as well as a best design among the alternatives that has yet to be constructed and tested. PMID:25019938

  7. Individual olfactory perception reveals meaningful nonolfactory genetic information

    PubMed Central

    Secundo, Lavi; Snitz, Kobi; Weissler, Kineret; Pinchover, Liron; Shoenfeld, Yehuda; Loewenthal, Ron; Agmon-Levin, Nancy; Frumin, Idan; Bar-Zvi, Dana; Shushan, Sagit; Sobel, Noam

    2015-01-01

    Each person expresses a potentially unique subset of ∼400 different olfactory receptor subtypes. Given that the receptors we express partially determine the odors we smell, it follows that each person may have a unique nose; to capture this, we devised a sensitive test of olfactory perception we termed the “olfactory fingerprint.” Olfactory fingerprints relied on matrices of perceived odorant similarity derived from descriptors applied to the odorants. We initially fingerprinted 89 individuals using 28 odors and 54 descriptors. We found that each person had a unique olfactory fingerprint (P < 10−10), which was odor specific but descriptor independent. We could identify individuals from this pool using randomly selected sets of 7 odors and 11 descriptors alone. Extrapolating from this data, we determined that using 34 odors and 35 descriptors we could individually identify each of the 7 billion people on earth. Olfactory perception, however, fluctuates over time, calling into question our proposed perceptual readout of presumably stable genetic makeup. To test whether fingerprints remain informative despite this temporal fluctuation, building on the linkage between olfactory receptors and HLA, we hypothesized that olfactory perception may relate to HLA. We obtained olfactory fingerprints and HLA typing for 130 individuals, and found that olfactory fingerprint matching using only four odorants was significantly related to HLA matching (P < 10−4), such that olfactory fingerprints can save 32% of HLA tests in a population screen (P < 10−6). In conclusion, a precise measure of olfactory perception reveals meaningful nonolfactory genetic information. PMID:26100865

  8. Osmolyte perturbation reveals conformational equilibria in spin-labeled proteins

    PubMed Central

    López, Carlos J; Fleissner, Mark R; Guo, Zhefeng; Kusnetzow, Ana K; Hubbell, Wayne L

    2009-01-01

    Recent evidence suggests that proteins at equilibrium can exist in a manifold of conformational substates, and that these substates play important roles in protein function. Therefore, there is great interest in identifying regions in proteins that are in conformational exchange. Electron paramagnetic resonance spectra of spin-labeled proteins containing the nitroxide side chain (R1) often consist of two (or more) components that may arise from slow exchange between conformational substates (lifetimes > 100 ns). However, crystal structures of proteins containing R1 have shown that multicomponent spectra can also arise from equilibria between rotamers of the side chain itself. In this report, it is shown that these scenarios can be distinguished by the response of the system to solvent perturbation with stabilizing osmolytes such as sucrose. Thus, site-directed spin labeling (SDSL) emerges as a new tool to explore slow conformational exchange in proteins of arbitrary size, including membrane proteins in a native-like environment. Moreover, equilibrium between substates with even modest differences in conformation is revealed, and the simplicity of the method makes it suitable for facile screening of multiple proteins. Together with previously developed strategies for monitoring picosecond to millisecond backbone dynamics, the results presented here expand the timescale over which SDSL can be used to explore protein flexibility. PMID:19585559

  9. Diagnostic phylogenetics reveals a new Porcine circovirus 2 cluster.

    PubMed

    Davies, Brendan; Wang, Xiong; Dvorak, Cheryl M T; Marthaler, Douglas; Murtaugh, Michael P

    2016-06-01

    Porcine circovirus 2 (PCV2) was prevalent in swine in the United States before PCV2-associated disease (PCVAD) appeared in 2006. Limited nucleotide sequencing of open reading frame 2 (ORF2) encoding capsid, the only structural protein, revealed the presence of two genotypes, PCV2a and PCV2b. Later, PCV2c and mutant PCV2b, or PCV2d, were also described. However, extensive PCV2 ORF2 sequence databases in veterinary diagnostic laboratories have not been analyzed systematically to determine the genetic diversity of field isolates. Here, we interrogated >1100 PCV2 ORF2 nucleotide sequences to assess population diversity and genetic variation. We detected a novel PCV2 genotype that is substantially different, primarily in ORF2, from all known PCV2. Notably, ORF2 contains a unique carboxyl terminal amino acid insertion resulting in a 238 amino acid ORF2. All other PCV2 ORF2 proteins are 233 or 234 aa in length. Phylogenetic analysis indicates that it is more ancient than other PCV2 genotypes. The findings demonstrate the value of analyzing routine diagnostic laboratory sequence databases in population genetic analyses of animal pathogens. PMID:26948261

  10. Crystallographic and spectroscopic snapshots reveal a dehydrogenase in action

    PubMed Central

    Huo, Lu; Davis, Ian; Liu, Fange; Andi, Babak; Esaki, Shingo; Iwaki, Hiroaki; Hasegawa, Yoshie; Orville, Allen M.; Liu, Aimin

    2015-01-01

    Aldehydes are ubiquitous intermediates in metabolic pathways and their innate reactivity can often make them quite unstable. There are several aldehydic intermediates in the metabolic pathway for tryptophan degradation that can decay into neuroactive compounds that have been associated with numerous neurological diseases. An enzyme of this pathway, 2-aminomuconate-6-semialdehyde dehydrogenase, is responsible for ‘disarming’ the final aldehydic intermediate. Here we show the crystal structures of a bacterial analogue enzyme in five catalytically relevant forms: resting state, one binary and two ternary complexes, and a covalent, thioacyl intermediate. We also report the crystal structures of a tetrahedral, thiohemiacetal intermediate, a thioacyl intermediate and an NAD+-bound complex from an active site mutant. These covalent intermediates are characterized by single-crystal and solution-state electronic absorption spectroscopy. The crystal structures reveal that the substrate undergoes an E/Z isomerization at the enzyme active site before an sp3-to-sp2 transition during enzyme-mediated oxidation. PMID:25565451

  11. Deep sequencing reveals 50 novel genes for recessive cognitive disorders.

    PubMed

    Najmabadi, Hossein; Hu, Hao; Garshasbi, Masoud; Zemojtel, Tomasz; Abedini, Seyedeh Sedigheh; Chen, Wei; Hosseini, Masoumeh; Behjati, Farkhondeh; Haas, Stefan; Jamali, Payman; Zecha, Agnes; Mohseni, Marzieh; Püttmann, Lucia; Vahid, Leyla Nouri; Jensen, Corinna; Moheb, Lia Abbasi; Bienek, Melanie; Larti, Farzaneh; Mueller, Ines; Weissmann, Robert; Darvish, Hossein; Wrogemann, Klaus; Hadavi, Valeh; Lipkowitz, Bettina; Esmaeeli-Nieh, Sahar; Wieczorek, Dagmar; Kariminejad, Roxana; Firouzabadi, Saghar Ghasemi; Cohen, Monika; Fattahi, Zohreh; Rost, Imma; Mojahedi, Faezeh; Hertzberg, Christoph; Dehghan, Atefeh; Rajab, Anna; Banavandi, Mohammad Javad Soltani; Hoffer, Julia; Falah, Masoumeh; Musante, Luciana; Kalscheuer, Vera; Ullmann, Reinhard; Kuss, Andreas Walter; Tzschach, Andreas; Kahrizi, Kimia; Ropers, H Hilger

    2011-10-01

    Common diseases are often complex because they are genetically heterogeneous, with many different genetic defects giving rise to clinically indistinguishable phenotypes. This has been amply documented for early-onset cognitive impairment, or intellectual disability, one of the most complex disorders known and a very important health care problem worldwide. More than 90 different gene defects have been identified for X-chromosome-linked intellectual disability alone, but research into the more frequent autosomal forms of intellectual disability is still in its infancy. To expedite the molecular elucidation of autosomal-recessive intellectual disability, we have now performed homozygosity mapping, exon enrichment and next-generation sequencing in 136 consanguineous families with autosomal-recessive intellectual disability from Iran and elsewhere. This study, the largest published so far, has revealed additional mutations in 23 genes previously implicated in intellectual disability or related neurological disorders, as well as single, probably disease-causing variants in 50 novel candidate genes. Proteins encoded by several of these genes interact directly with products of known intellectual disability genes, and many are involved in fundamental cellular processes such as transcription and translation, cell-cycle control, energy metabolism and fatty-acid synthesis, which seem to be pivotal for normal brain development and function. PMID:21937992

  12. Multiple etiologies for Alzheimer disease are revealed by segregation analysis

    SciTech Connect

    Rao, V.S.; Connor-Lacke, L.; Cupplies, L.A.; Growdon, J.H.; Farrer, L.A.; Duijn, C.M. van

    1994-11-01

    We have evaluated several transmission models for Alzheimer disease (AD), using the logistic regressive approach in 401 nuclear families of consecutively ascertained and rigorously diagnosed probands. Models postulating no major gene effect, random environmental transmission, recessive inheritance, and sporadic occurrence were rejected under varied assumptions regarding the associations among sex, age, and major gene susceptibility. Transmission of the disorder was not fully explained by a single Mendelian model for all families. Stratification of families as early- and late-onset by using the median of family mean onset ages showed that, regardless of the model studied, two groups of families fit better than a single group. AD in early-onset families is transmitted as an autosomal dominant trait with full penetrance in both sexes and has a gene frequency of 1.5%. Dominant inheritance also gave the best fit of the data in late-onset families, but this hypothesis was rejected, suggesting the presence of heterogeneity within this subset. Our study also revealed that genetically nonsusceptible males and females develop AD, indicating the presence of phenocopies within early-onset and late-onset groups. Moreover, our results suggest that the higher risk to females is not solely due to their increased longevity. 50 refs., 5 tabs.

  13. Next generation sequencing in synovial sarcoma reveals novel gene mutations.

    PubMed

    Vlenterie, Myrella; Hillebrandt-Roeffen, Melissa H S; Flucke, Uta E; Groenen, Patricia J T A; Tops, Bastiaan B J; Kamping, Eveline J; Pfundt, Rolph; de Bruijn, Diederik R H; Geurts van Kessel, Ad H M; van Krieken, Han J H J M; van der Graaf, Winette T A; Versleijen-Jonkers, Yvonne M H

    2015-10-27

    Over 95% of all synovial sarcomas (SS) share a unique translocation, t(X;18), however, they show heterogeneous clinical behavior. We analyzed multiple SS to reveal additional genetic alterations besides the translocation. Twenty-six SS from 22 patients were sequenced for 409 cancer-related genes using the Comprehensive Cancer Panel (Life Technologies, USA) on an Ion Torrent platform. The detected variants were verified by Sanger sequencing and compared to matched normal DNAs. Copy number variation was assessed in six tumors using the Oncoscan array (Affymetrix, USA). In total, eight somatic mutations were detected in eight samples. These mutations have not been reported previously in SS. Two of these, in KRAS and CCND1, represent known oncogenic mutations in other malignancies. Additional mutations were detected in RNF213, SEPT9, KDR, CSMD3, MLH1 and ERBB4. DNA alterations occurred more often in adult tumors. A distinctive loss of 6q was found in a metastatic lesion progressing under pazopanib, but not in the responding lesion. Our results emphasize t(X;18) as a single initiating event in SS and as the main oncogenic driver. Our results also show the occurrence of additional genetic events, mutations or chromosomal aberrations, occurring more frequently in SS with an onset in adults. PMID:26415226

  14. Ternary structure reveals mechanism of a membrane diacylglycerol kinase

    DOE PAGESBeta

    Li, Dianfan; Stansfeld, Phillip J.; Sansom, Mark S. P.; Keogh, Aaron; Vogeley, Lutz; Howe, Nicole; Lyons, Joseph A.; Aragao, David; Fromme, Petra; Fromme, Raimund; et al

    2015-12-17

    Diacylglycerol kinase catalyses the ATP-dependent conversion of diacylglycerol to phosphatidic acid in the plasma membrane of Escherichia coli. The small size of this integral membrane trimer, which has 121 residues per subunit, means that available protein must be used economically to craft three catalytic and substrate-binding sites centred about the membrane/cytosol interface. How nature has accomplished this extraordinary feat is revealed here in a crystal structure of the kinase captured as a ternary complex with bound lipid substrate and an ATP analogue. Residues, identified as essential for activity by mutagenesis, decorate the active site and are rationalized by the ternarymore » structure. The γ-phosphate of the ATP analogue is positioned for direct transfer to the primary hydroxyl of the lipid whose acyl chain is in the membrane. A catalytic mechanism for this unique enzyme is proposed. As a result, the active site architecture shows clear evidence of having arisen by convergent evolution.« less

  15. Proteomics Analysis Reveals Previously Uncharacterized Virulence Factors in Vibrio proteolyticus

    PubMed Central

    Ray, Ann; Kinch, Lisa N.; de Souza Santos, Marcela; Grishin, Nick V.

    2016-01-01

    ABSTRACT Members of the genus Vibrio include many pathogens of humans and marine animals that share genetic information via horizontal gene transfer. Hence, the Vibrio pan-genome carries the potential to establish new pathogenic strains by sharing virulence determinants, many of which have yet to be characterized. Here, we investigated the virulence properties of Vibrio proteolyticus, a Gram-negative marine bacterium previously identified as part of the Vibrio consortium isolated from diseased corals. We found that V. proteolyticus causes actin cytoskeleton rearrangements followed by cell lysis in HeLa cells in a contact-independent manner. In search of the responsible virulence factor involved, we determined the V. proteolyticus secretome. This proteomics approach revealed various putative virulence factors, including active type VI secretion systems and effectors with virulence toxin domains; however, these type VI secretion systems were not responsible for the observed cytotoxic effects. Further examination of the V. proteolyticus secretome led us to hypothesize and subsequently demonstrate that a secreted hemolysin, belonging to a previously uncharacterized clan of the leukocidin superfamily, was the toxin responsible for the V. proteolyticus-mediated cytotoxicity in both HeLa cells and macrophages. Clearly, there remains an armory of yet-to-be-discovered virulence factors in the Vibrio pan-genome that will undoubtedly provide a wealth of knowledge on how a pathogen can manipulate host cells. PMID:27460800

  16. Super-resolution Microscopy Reveals Compartmentalization of Peroxisomal Membrane Proteins*

    PubMed Central

    Galiani, Silvia; Waithe, Dominic; Reglinski, Katharina; Cruz-Zaragoza, Luis Daniel; Garcia, Esther; Clausen, Mathias P.; Schliebs, Wolfgang; Erdmann, Ralf; Eggeling, Christian

    2016-01-01

    Membrane-associated events during peroxisomal protein import processes play an essential role in peroxisome functionality. Many details of these processes are not known due to missing spatial resolution of technologies capable of investigating peroxisomes directly in the cell. Here, we present the use of super-resolution optical stimulated emission depletion microscopy to investigate with sub-60-nm resolution the heterogeneous spatial organization of the peroxisomal proteins PEX5, PEX14, and PEX11 around actively importing peroxisomes, showing distinct differences between these peroxins. Moreover, imported protein sterol carrier protein 2 (SCP2) occupies only a subregion of larger peroxisomes, highlighting the heterogeneous distribution of proteins even within the peroxisome. Finally, our data reveal subpopulations of peroxisomes showing only weak colocalization between PEX14 and PEX5 or PEX11 but at the same time a clear compartmentalized organization. This compartmentalization, which was less evident in cases of strong colocalization, indicates dynamic protein reorganization linked to changes occurring in the peroxisomes. Through the use of multicolor stimulated emission depletion microscopy, we have been able to characterize peroxisomes and their constituents to a yet unseen level of detail while maintaining a highly statistical approach, paving the way for equally complex biological studies in the future. PMID:27311714

  17. Immunoprofiling of Rice Root Cortex Reveals Two Cortical Subdomains

    PubMed Central

    Henry, Sophia; Divol, Fanchon; Bettembourg, Mathilde; Bureau, Charlotte; Guiderdoni, Emmanuel; Périn, Christophe; Diévart, Anne

    2016-01-01

    The formation and differentiation of aerenchyma, i.e., air-containing cavities that are critical for flooding tolerance, take place exclusively in the cortex. The understanding of development and differentiation of the cortex is thus an important issue; however, studies on this tissue are limited, partly because of the lack of available molecular tools. We screened a commercially available library of cell wall antibodies to identify markers of cortical tissue in rice roots. Out of the 174 antibodies screened, eight were cortex-specific. Our analysis revealed that two types of cortical tissues are present in rice root seedlings. We named these cell layers “inner” and “outer” based on their location relative to the stele. We then used the antibodies to clarify cell identity in lateral roots. Without these markers, previous studies could not distinguish between the cortex and sclerenchyma in small lateral roots. By immunostaining lateral root sections, we showed that the internal ground tissue in small lateral roots has outer cortical identity. PMID:26779208

  18. Phosphoproteomic analysis reveals regulatory mechanisms at the kidney filtration barrier.

    PubMed

    Rinschen, Markus M; Wu, Xiongwu; König, Tim; Pisitkun, Trairak; Hagmann, Henning; Pahmeyer, Caroline; Lamkemeyer, Tobias; Kohli, Priyanka; Schnell, Nicole; Schermer, Bernhard; Dryer, Stuart; Brooks, Bernard R; Beltrao, Pedro; Krueger, Marcus; Brinkkoetter, Paul T; Benzing, Thomas

    2014-07-01

    Diseases of the kidney filtration barrier are a leading cause of ESRD. Most disorders affect the podocytes, polarized cells with a limited capacity for self-renewal that require tightly controlled signaling to maintain their integrity, viability, and function. Here, we provide an atlas of in vivo phosphorylated, glomerulus-expressed proteins, including podocyte-specific gene products, identified in an unbiased tandem mass spectrometry-based approach. We discovered 2449 phosphorylated proteins corresponding to 4079 identified high-confidence phosphorylated residues and performed a systematic bioinformatics analysis of this dataset. We discovered 146 phosphorylation sites on proteins abundantly expressed in podocytes. The prohibitin homology domain of the slit diaphragm protein podocin contained one such site, threonine 234 (T234), located within a phosphorylation motif that is mutated in human genetic forms of proteinuria. The T234 site resides at the interface of podocin dimers. Free energy calculation through molecular dynamic simulations revealed a role for T234 in regulating podocin dimerization. We show that phosphorylation critically regulates formation of high molecular weight complexes and that this may represent a general principle for the assembly of proteins containing prohibitin homology domains. PMID:24511133

  19. Structure of the Angiotensin Receptor Revealed by Serial Femtosecond Crystallography

    DOE PAGESBeta

    Zhang, Haitao; Unal, Hamiyet; Gati, Cornelius; Han, Gye Won; Liu, Wei; Zatsepin, Nadia A.; James, Daniel; Wang, Dingjie; Nelson, Garrett; Weierstall, Uwe; et al

    2015-05-07

    We report that angiotensin II type 1 receptor (AT1R) is a G protein-coupled receptor that serves as a primary regulator for blood pressure maintenance. Although several anti-hypertensive drugs have been developed as AT1R blockers (ARBs), the structural basis for AT1R ligand-binding and regulation has remained elusive, mostly due to the difficulties of growing high quality crystals for structure determination using synchrotron radiation. By applying the recently developed method of serial femtosecond crystallography at an X-ray free-electron laser, we successfully determined the room-temperature crystal structure of the human AT1R in complex with its selective antagonist ZD7155 at 2.9 Å resolution. Themore » AT1R-ZD7155 complex structure revealed key structural features ofAT1R and critical interactions for ZD7155 binding. Finally, docking simulations of the clinically used ARBs into the AT1R structure further elucidated both the common and distinct binding modes for these anti-hypertensive drugs. Our results thereby provide fundamental insights into AT1R structure-function relationship and structure-based drug design.« less

  20. Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs

    SciTech Connect

    Curtis, Bruce A.; Tanifuji, Goro; Burki, Fabien; Gruber, Ansgar; Irimia, Manuuel; Maruyama, Shinichiro; Arias, Maria C.; Ball, Steven G.; Gile, Gillian H.; Hirakawa, Yoshihisa; Hopkins, Julia F.; Kuo, Alan; Rensing, Stefan A.; Schmutz, Jeremy; Symeonidi, Aikaterini; Elias, Marek; Eveleigh, Robert J. M.; Herman, Emily K.; Klute, Mary J.; Nakayama, Takuro; Obornik, Miroslav; Reyes-Prieto, Adrian; Armbrust, E. Virginia; Aves, Stephen J.; Beiko, Robert G.; Coutinho, Pedro; Dacks, Joel B.; Durnford, Dion G.; Fast, Naomi M.; Green, Beverley R.; Grisdale, Cameron J.; Hempel, Franziska; Henrissat, Bernard; Hoppner, Marc P.; Ishida, Ken-Ichiro; Kim, Eunsoo; Koreny, Ludek; Kroth, Peter G.; Liu, Yuan; Malik, Shehre-Banoo; Maier, Uwe G.; McRose, Darcy; Mock, Thomas; Neilson, Jonathan A. D.; Onodera, Naoko T.; Poole, Anthony M.; Pritham, Ellen J.; Richards, Thomas A.; Rocap, Gabrielle; Roy, Scott W.; Sarai, Chihiro; Schaack, Sarah; Shirato, Shu; Slamovits, Claudio H.; Spencer, Davie F.; Suzuki, Shigekatsu; Worden, Alexandra Z.; Zauner, Stefan; Barry, Kerrie; Bell, Callum; Bharti, Arvind K.; Crow, John A.; Grimwood, Jane; Kramer, Robin; Lindquist, Erika; Lucas, Susan; Salamov, Asaf; McFadden, Geoffrey I.; Lane, Christopher E.; Keeling, Patrick J.; Gray, Michael W.; Grigoriev, Igor V.; Archibald, John M.

    2012-08-10

    Cryptophyte and chlorarachniophyte algae are transitional forms in the widespread secondary endosymbiotic acquisition of photosynthesis by engulfment of eukaryotic algae. Unlike most secondary plastid-bearing algae, miniaturized versions of the endosymbiont nuclei (nucleomorphs) persist in cryptophytes and chlorarachniophytes. To determine why, and to address other fundamental questions about eukaryote eukaryote endosymbiosis, we sequenced the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. Both genomes have 21,000 protein genes and are intron rich, and B. natans exhibits unprecedented alternative splicing for a single-celled organism. Phylogenomic analyses and subcellular targeting predictions reveal extensive genetic and biochemical mosaicism, with both host- and endosymbiont-derived genes servicing the mitochondrion, the host cell cytosol, the plastid and the remnant endosymbiont cytosol of both algae. Mitochondrion-to-nucleus gene transfer still occurs in both organisms but plastid-to-nucleus and nucleomorph-to-nucleus transfers do not, which explains why a small residue of essential genes remains locked in each nucleomorph.

  1. Maximal Neighbor Similarity Reveals Real Communities in Networks

    PubMed Central

    Žalik, Krista Rizman

    2015-01-01

    An important problem in the analysis of network data is the detection of groups of densely interconnected nodes also called modules or communities. Community structure reveals functions and organizations of networks. Currently used algorithms for community detection in large-scale real-world networks are computationally expensive or require a priori information such as the number or sizes of communities or are not able to give the same resulting partition in multiple runs. In this paper we investigate a simple and fast algorithm that uses the network structure alone and requires neither optimization of pre-defined objective function nor information about number of communities. We propose a bottom up community detection algorithm in which starting from communities consisting of adjacent pairs of nodes and their maximal similar neighbors we find real communities. We show that the overall advantage of the proposed algorithm compared to the other community detection algorithms is its simple nature, low computational cost and its very high accuracy in detection communities of different sizes also in networks with blurred modularity structure consisting of poorly separated communities. All communities identified by the proposed method for facebook network and E-Coli transcriptional regulatory network have strong structural and functional coherence. PMID:26680448

  2. Effective Connectivity Reveals Strategy Differences in an Expert Calculator

    PubMed Central

    Minati, Ludovico; Sigala, Natasha

    2013-01-01

    Mathematical reasoning is a core component of cognition and the study of experts defines the upper limits of human cognitive abilities, which is why we are fascinated by peak performers, such as chess masters and mental calculators. Here, we investigated the neural bases of calendrical skills, i.e. the ability to rapidly identify the weekday of a particular date, in a gifted mental calculator who does not fall in the autistic spectrum, using functional MRI. Graph-based mapping of effective connectivity, but not univariate analysis, revealed distinct anatomical location of “cortical hubs” supporting the processing of well-practiced close dates and less-practiced remote dates: the former engaged predominantly occipital and medial temporal areas, whereas the latter were associated mainly with prefrontal, orbitofrontal and anterior cingulate connectivity. These results point to the effect of extensive practice on the development of expertise and long term working memory, and demonstrate the role of frontal networks in supporting performance on less practiced calculations, which incur additional processing demands. Through the example of calendrical skills, our results demonstrate that the ability to perform complex calculations is initially supported by extensive attentional and strategic resources, which, as expertise develops, are gradually replaced by access to long term working memory for familiar material. PMID:24086291

  3. Circular RNA profile in gliomas revealed by identification tool UROBORUS.

    PubMed

    Song, Xiaofeng; Zhang, Naibo; Han, Ping; Moon, Byoung-San; Lai, Rose K; Wang, Kai; Lu, Wange

    2016-05-19

    Recent evidence suggests that many endogenous circular RNAs (circRNAs) may play roles in biological processes. However, the expression patterns and functions of circRNAs in human diseases are not well understood. Computationally identifying circRNAs from total RNA-seq data is a primary step in studying their expression pattern and biological roles. In this work, we have developed a computational pipeline named UROBORUS to detect circRNAs in total RNA-seq data. By applying UROBORUS to RNA-seq data from 46 gliomas and normal brain samples, we detected thousands of circRNAs supported by at least two read counts, followed by successful experimental validation on 24 circRNAs from the randomly selected 27 circRNAs. UROBORUS is an efficient tool that can detect circRNAs with low expression levels in total RNA-seq without RNase R treatment. The circRNAs expression profiling revealed more than 476 circular RNAs differentially expressed in control brain tissues and gliomas. Together with parental gene expression, we found that circRNA and its parental gene have diversified expression patterns in gliomas and control brain tissues. This study establishes an efficient and sensitive approach for predicting circRNAs using total RNA-seq data. The UROBORUS pipeline can be accessed freely for non-commercial purposes at http://uroborus.openbioinformatics.org/. PMID:26873924

  4. Multifunctional proteins revealed by overlapping clustering in protein interaction network

    PubMed Central

    Chapple, Charles E.; Guénoche, Alain; Brun, Christine

    2012-01-01

    Motivation: Multifunctional proteins perform several functions. They are expected to interact specifically with distinct sets of partners, simultaneously or not, depending on the function performed. Current graph clustering methods usually allow a protein to belong to only one cluster, therefore impeding a realistic assignment of multifunctional proteins to clusters. Results: Here, we present Overlapping Cluster Generator (OCG), a novel clustering method which decomposes a network into overlapping clusters and which is, therefore, capable of correct assignment of multifunctional proteins. The principle of OCG is to cover the graph with initial overlapping classes that are iteratively fused into a hierarchy according to an extension of Newman's modularity function. By applying OCG to a human protein–protein interaction network, we show that multifunctional proteins are revealed at the intersection of clusters and demonstrate that the method outperforms other existing methods on simulated graphs and PPI networks. Availability: This software can be downloaded from http://tagc.univ-mrs.fr/welcome/spip.php?rubrique197 Contact: brun@tagc.univ-mrs.fr Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22080466

  5. Revealing the structure of the world airline network

    NASA Astrophysics Data System (ADS)

    Verma, T.; Araújo, N. A. M.; Herrmann, H. J.

    2014-07-01

    Resilience of most critical infrastructures against failure of elements that appear insignificant is usually taken for granted. The World Airline Network (WAN) is an infrastructure that reduces the geographical gap between societies, both small and large, and brings forth economic gains. With the extensive use of a publicly maintained data set that contains information about airports and alternative connections between these airports, we empirically reveal that the WAN is a redundant and resilient network for long distance air travel, but otherwise breaks down completely due to removal of short and apparently insignificant connections. These short range connections with moderate number of passengers and alternate flights are the connections that keep remote parts of the world accessible. It is surprising, insofar as there exists a highly resilient and strongly connected core consisting of a small fraction of airports (around 2.3%) together with an extremely fragile star-like periphery. Yet, in spite of their relevance, more than 90% of the world airports are still interconnected upon removal of this core. With standard and unconventional removal measures we compare both empirical and topological perceptions for the fragmentation of the world. We identify how the WAN is organized into different classes of clusters based on the physical proximity of airports and analyze the consequence of this fragmentation.

  6. Transcriptome profiling reveals mosaic genomic origins of modern cultivated barley

    PubMed Central

    Dai, Fei; Chen, Zhong-Hua; Wang, Xiaolei; Li, Zefeng; Jin, Gulei; Wu, Dezhi; Cai, Shengguan; Wang, Ning; Wu, Feibo; Nevo, Eviatar; Zhang, Guoping

    2014-01-01

    The domestication of cultivated barley has been used as a model system for studying the origins and early spread of agrarian culture. Our previous results indicated that the Tibetan Plateau and its vicinity is one of the centers of domestication of cultivated barley. Here we reveal multiple origins of domesticated barley using transcriptome profiling of cultivated and wild-barley genotypes. Approximately 48-Gb of clean transcript sequences in 12 Hordeum spontaneum and 9 Hordeum vulgare accessions were generated. We reported 12,530 de novo assembled transcripts in all of the 21 samples. Population structure analysis showed that Tibetan hulless barley (qingke) might have existed in the early stage of domestication. Based on the large number of unique genomic regions showing the similarity between cultivated and wild-barley groups, we propose that the genomic origin of modern cultivated barley is derived from wild-barley genotypes in the Fertile Crescent (mainly in chromosomes 1H, 2H, and 3H) and Tibet (mainly in chromosomes 4H, 5H, 6H, and 7H). This study indicates that the domestication of barley may have occurred over time in geographically distinct regions. PMID:25197090

  7. Structure of the Angiotensin Receptor Revealed by Serial Femtosecond Crystallography

    PubMed Central

    Zhang, Haitao; Unal, Hamiyet; Gati, Cornelius; Han, Gye Won; Liu, Wei; Zatsepin, Nadia A.; James, Daniel; Wang, Dingjie; Nelson, Garrett; Weierstall, Uwe; Sawaya, Michael R.; Xu, Qingping; Messerschmidt, Marc; Williams, Garth J.; Boutet, Sébastien; Yefanov, Oleksandr M.; White, Thomas A.; Wang, Chong; Ishchenko, Andrii; Tirupula, Kalyan C.; Desnoyer, Russell; Coe, Jesse; Conrad, Chelsie E.; Fromme, Petra; Stevens, Raymond C.; Katritch, Vsevolod; Karnik, Sadashiva S.; Cherezov, Vadim

    2015-01-01

    SUMMARY Angiotensin II type 1 receptor (AT1R) is a G protein-coupled receptor that serves as a primary regulator for blood pressure maintenance. Although several anti-hypertensive drugs have been developed as AT1R blockers (ARBs), the structural basis for AT1R ligand-binding and regulation has remained elusive, mostly due to the difficulties of growing high quality crystals for structure determination using synchrotron radiation. By applying the recently developed method of serial femtosecond crystallography at an X-ray free-electron laser, we successfully determined the room-temperature crystal structure of the human AT1R in complex with its selective antagonist ZD7155 at 2.9 Å resolution. The AT1R-ZD7155 complex structure revealed key structural features of AT1R and critical interactions for ZD7155 binding. Docking simulations of the clinically used ARBs into the AT1R structure further elucidated both the common and distinct binding modes for these anti-hypertensive drugs. Our results thereby provide fundamental insights into AT1R structure-function relationship and structure-based drug design. PMID:25913193

  8. Proteomics Analysis Reveals Novel RASSF2 Interaction Partners.

    PubMed

    Barnoud, Thibaut; Wilkey, Daniel W; Merchant, Michael L; Clark, Jennifer A; Donninger, Howard

    2016-01-01

    RASSF2 is a tumor suppressor that shares homology with other Ras-association domain (RASSF) family members. It is a powerful pro-apoptotic K-Ras effector that is frequently inactivated in many human tumors. The exact mechanism by which RASSF2 functions is not clearly defined, but it likely acts as a scaffolding protein, modulating the activity of other pro-apoptotic effectors, thereby regulating and integrating tumor suppressor pathways. However, only a limited number of RASSF2 interacting partners have been identified to date. We used a proteomics based approach to identify additional RASSF2 interactions, and thereby gain a better insight into the mechanism of action of RASSF2. We identified several proteins, including C1QBP, Vimentin, Protein phosphatase 1G and Ribonuclease inhibitor that function in diverse biological processes, including protein post-translational modifications, epithelial-mesenchymal transition, cell migration and redox homeostasis, which have not previously been reported to interact with RASSF2. We independently validated two of these novel interactions, C1QBP and Vimentin and found that the interaction with C1QBP was enhanced by K-Ras whereas, interestingly, the Vimentin interaction was reduced by K-Ras. Additionally, RASSF2/K-Ras regulated the acetylation of Vimentin. Our data thus reveal novel mechanisms by which RASSF2 may exert its functions, several of which may be Ras-regulated. PMID:26999212

  9. Individual Differences Reveal Correlates of Hidden Hearing Deficits

    PubMed Central

    Masud, Salwa; Mehraei, Golbarg; Verhulst, Sarah; Shinn-Cunningham, Barbara G.

    2015-01-01

    Clinical audiometry has long focused on determining the detection thresholds for pure tones, which depend on intact cochlear mechanics and hair cell function. Yet many listeners with normal hearing thresholds complain of communication difficulties, and the causes for such problems are not well understood. Here, we explore whether normal-hearing listeners exhibit such suprathreshold deficits, affecting the fidelity with which subcortical areas encode the temporal structure of clearly audible sound. Using an array of measures, we evaluated a cohort of young adults with thresholds in the normal range to assess both cochlear mechanical function and temporal coding of suprathreshold sounds. Listeners differed widely in both electrophysiological and behavioral measures of temporal coding fidelity. These measures correlated significantly with each other. Conversely, these differences were unrelated to the modest variation in otoacoustic emissions, cochlear tuning, or the residual differences in hearing threshold present in our cohort. Electroencephalography revealed that listeners with poor subcortical encoding had poor cortical sensitivity to changes in interaural time differences, which are critical for localizing sound sources and analyzing complex scenes. These listeners also performed poorly when asked to direct selective attention to one of two competing speech streams, a task that mimics the challenges of many everyday listening environments. Together with previous animal and computational models, our results suggest that hidden hearing deficits, likely originating at the level of the cochlear nerve, are part of “normal hearing.” PMID:25653371

  10. Phylogenies reveal predictive power of traditional medicine in bioprospecting

    PubMed Central

    Saslis-Lagoudakis, C. Haris; Savolainen, Vincent; Williamson, Elizabeth M.; Forest, Félix; Wagstaff, Steven J.; Baral, Sushim R.; Watson, Mark F.; Pendry, Colin A.; Hawkins, Julie A.

    2012-01-01

    There is controversy about whether traditional medicine can guide drug discovery, and investment in bioprospecting informed by ethnobotanical data has fluctuated. One view is that traditionally used medicinal plants are not necessarily efficacious and there are no robust methods for distinguishing those which are most likely to be bioactive when selecting species for further testing. Here, we reconstruct a genus-level molecular phylogenetic tree representing the 20,000 species found in the floras of three disparate biodiversity hotspots: Nepal, New Zealand, and the Cape of South Africa. Borrowing phylogenetic methods from community ecology, we reveal significant clustering of the 1,500 traditionally used species, and provide a direct measure of the relatedness of the three medicinal floras. We demonstrate shared phylogenetic patterns across the floras: related plants from these regions are used to treat medical conditions in the same therapeutic areas. This finding strongly indicates independent discovery of plant efficacy, an interpretation corroborated by the presence of a significantly greater proportion of known bioactive species in these plant groups than in random samples. We conclude that phylogenetic cross-cultural comparisons can focus screening efforts on a subset of traditionally used plants that are richer in bioactive compounds, and could revitalize the use of traditional knowledge in bioprospecting. PMID:22984175

  11. Transcriptome profiling reveals mosaic genomic origins of modern cultivated barley.

    PubMed

    Dai, Fei; Chen, Zhong-Hua; Wang, Xiaolei; Li, Zefeng; Jin, Gulei; Wu, Dezhi; Cai, Shengguan; Wang, Ning; Wu, Feibo; Nevo, Eviatar; Zhang, Guoping

    2014-09-16

    The domestication of cultivated barley has been used as a model system for studying the origins and early spread of agrarian culture. Our previous results indicated that the Tibetan Plateau and its vicinity is one of the centers of domestication of cultivated barley. Here we reveal multiple origins of domesticated barley using transcriptome profiling of cultivated and wild-barley genotypes. Approximately 48-Gb of clean transcript sequences in 12 Hordeum spontaneum and 9 Hordeum vulgare accessions were generated. We reported 12,530 de novo assembled transcripts in all of the 21 samples. Population structure analysis showed that Tibetan hulless barley (qingke) might have existed in the early stage of domestication. Based on the large number of unique genomic regions showing the similarity between cultivated and wild-barley groups, we propose that the genomic origin of modern cultivated barley is derived from wild-barley genotypes in the Fertile Crescent (mainly in chromosomes 1H, 2H, and 3H) and Tibet (mainly in chromosomes 4H, 5H, 6H, and 7H). This study indicates that the domestication of barley may have occurred over time in geographically distinct regions. PMID:25197090

  12. Parallel Selection Revealed by Population Sequencing in Chicken.

    PubMed

    Qanbari, Saber; Seidel, Michael; Strom, Tim-Mathias; Mayer, Klaus F X; Preisinger, Ruedi; Simianer, Henner

    2015-12-01

    Human-driven selection during domestication and subsequent breed formation has likely left detectable signatures within the genome of modern chicken. The elucidation of these signatures of selection is of interest from the perspective of evolutionary biology, and for identifying genes relevant to domestication and improvement that ultimately may help to further genetically improve this economically important animal. We used whole genome sequence data from 50 hens of commercial white (WL) and brown (BL) egg-laying chicken along with pool sequences of three meat-type chicken to perform a systematic screening of past selection in modern chicken. Evidence of positive selection was investigated in two steps. First, we explored evidence of parallel fixation in regions with overlapping elevated allele frequencies in replicated populations of layers and broilers, suggestive of selection during domestication or preimprovement ages. We confirmed parallel fixation in BCDO2 and TSHR genes and found four candidates including AGTR2, a gene heavily involved in "Ascites" in commercial birds. Next, we explored differentiated loci between layers and broilers suggestive of selection during improvement in chicken. This analysis revealed evidence of parallel differentiation in genes relevant to appearance and production traits exemplified with the candidate gene OPG, implicated in Osteoporosis, a disorder related to overconsumption of calcium in egg-laying hens. Our results illustrate the potential for population genetic techniques to identify genomic regions relevant to the phenotypes of importance to breeders. PMID:26568375

  13. Substrate Channel in Nitrogenase Revealed by a Molecular Dynamics Approach

    SciTech Connect

    Smith, Dayle; Danyal, Karamatullah; Raugei, Simone; Seefeldt, Lance C.

    2014-03-22

    Mo-dependent nitrogenase catalyzes the biological reduction of N2 to 2NH3 at the FeMo-cofactor buried deep inside the MoFe protein. Access of substrates, such as N2, to the active site is likely restricted by the surrounding protein, requiring substrate channels that lead from the surface to the active site. Earlier studies on crystallographic structures of the MoFe protein have suggested three putative substrate channels. Here, we have utilized sub-microsecond atomistic molecular dynamics simulations to allow the nitrogenase MoFe protein to explore its conformational space in an aqueous solution at physiological ionic strength, revealing a putative substrate channel not previously reported. The viability of the proposed channel was tested by examining the free energy of passage of N2 from the surface through the channel to FeMo-cofactor, with discovery of a very low energy barrier. These studies point to a viable substrate channel in nitrogenase that appears during thermal motions of the protein in an aqueous environment that approaches a face of FeMo-cofactor earlier implicated in substrate binding.

  14. Historical reconstruction reveals recovery in Hawaiian coral reefs.

    PubMed

    Kittinger, John N; Pandolfi, John M; Blodgett, Jonathan H; Hunt, Terry L; Jiang, Hong; Maly, Kepā; McClenachan, Loren E; Schultz, Jennifer K; Wilcox, Bruce A

    2011-01-01

    Coral reef ecosystems are declining worldwide, yet regional differences in the trajectories, timing and extent of degradation highlight the need for in-depth regional case studies to understand the factors that contribute to either ecosystem sustainability or decline. We reconstructed social-ecological interactions in Hawaiian coral reef environments over 700 years using detailed datasets on ecological conditions, proximate anthropogenic stressor regimes and social change. Here we report previously undetected recovery periods in Hawaiian coral reefs, including a historical recovery in the MHI (~AD 1400-1820) and an ongoing recovery in the NWHI (~AD 1950-2009+). These recovery periods appear to be attributed to a complex set of changes in underlying social systems, which served to release reefs from direct anthropogenic stressor regimes. Recovery at the ecosystem level is associated with reductions in stressors over long time periods (decades+) and large spatial scales (>10(3) km(2)). Our results challenge conventional assumptions and reported findings that human impacts to ecosystems are cumulative and lead only to long-term trajectories of environmental decline. In contrast, recovery periods reveal that human societies have interacted sustainably with coral reef environments over long time periods, and that degraded ecosystems may still retain the adaptive capacity and resilience to recover from human impacts. PMID:21991311

  15. Archaeopteryx feathers and bone chemistry fully revealed via synchrotron imaging

    PubMed Central

    Bergmann, U.; Morton, R. W.; Manning, P. L.; Sellers, W. I.; Farrar, S.; Huntley, K. G.; Wogelius, R. A.; Larson, P.

    2010-01-01

    Evolution of flight in maniraptoran dinosaurs is marked by the acquisition of distinct avian characters, such as feathers, as seen in Archaeopteryx from the Solnhofen limestone. These rare fossils were pivotal in confirming the dinosauria-avian lineage. One of the key derived avian characters is the possession of feathers, details of which were remarkably preserved in the Lagerstätte environment. These structures were previously simply assumed to be impressions; however, a detailed chemical analysis has, until now, never been completed on any Archaeopteryx specimen. Here we present chemical imaging via synchrotron rapid scanning X-ray fluorescence (SRS-XRF) of the Thermopolis Archaeopteryx, which shows that portions of the feathers are not impressions but are in fact remnant body fossil structures, maintaining elemental compositions that are completely different from the embedding geological matrix. Our results indicate phosphorous and sulfur retention in soft tissue as well as trace metal (Zn and Cu) retention in bone. Other previously unknown chemical details of Archaeopteryx are also revealed in this study including: bone chemistry, taphonomy (fossilization process), and curation artifacts. SRS-XRF represents a major advancement in the study of the life chemistry and fossilization processes of Archaeopteryx and other extinct organisms because it is now practical to image the chemistry of large specimens rapidly at concentration levels of parts per million. This technique has wider application to the archaeological, forensic, and biological sciences, enabling the mapping of “unseen” compounds critical to understanding biological structures, modes of preservation, and environmental context. PMID:20457935

  16. Genetically engineered immunoglobulins reveal structural features controlling segmental flexibility.

    PubMed Central

    Schneider, W P; Wensel, T G; Stryer, L; Oi, V T

    1988-01-01

    We have carried out nanosecond fluorescence polarization studies of genetically engineered immunoglobulins to determine the structural features controlling their segmental flexibility. The proteins studied were hybrids of a relatively rigid isotype (mouse IgG1) and a relatively flexible one (mouse IgG2a). They have identical light chains and heavy chain variable regions and have the same combining sites for epsilon-dansyl-L-lysine, a fluorescent hapten. The fluorescence of the bound dansyl chromophore was excited at 348 nm with subnanosecond laser pulses, and the emission in the nanosecond time range was measured with a single-photon-counting apparatus. The emission anisotropy kinetics of the hybrid antibodies revealed that segmental flexibility is controlled by the heavy chain constant region 1 (CH1) as well as by the hinge. In contrast, the CH2 and CH3 domains did not influence segmental flexibility. The hinge and CH1 domains must be properly matched to allow facile movement of the Fab units. Studies of hybrids of IgG1 and IgG2a within CH1 showed that the loop formed by residues 131-139 is important in controlling segmental flexibility. X-ray crystallographic studies by others of human IgG1 have shown that this loop makes several van der Waals contacts with the hinge. Images PMID:3128789

  17. Interactome Analysis Reveals Ezrin Can Adopt Multiple Conformational States*

    PubMed Central

    Viswanatha, Raghuvir; Wayt, Jessica; Ohouo, Patrice Y.; Smolka, Marcus B.; Bretscher, Anthony

    2013-01-01

    Ezrin, a member of the ezrin-radixin-moesin family (ERM), is an essential regulator of the structure of microvilli on the apical aspect of epithelial cells. Ezrin provides a linkage between membrane-associated proteins and F-actin, oscillating between active/open and inactive/closed states, and is regulated in part by phosphorylation of a C-terminal threonine. In the open state, ezrin can bind a number of ligands, but in the closed state the ligand-binding sites are inaccessible. In vitro analysis has proposed that there may be a third hyperactivated form of ezrin. To gain a better understanding of ezrin, we conducted an unbiased proteomic analysis of ezrin-binding proteins in an epithelial cell line, Jeg-3. We refined our list of interactors by comparing the interactomes using quantitative mass spectrometry between wild-type ezrin, closed ezrin, open ezrin, and hyperactivated ezrin. The analysis reveals several novel interactors confirmed by their localization to microvilli, as well as a significant class of proteins that bind closed ezrin. Taken together, the data indicate that ezrin can exist in three different conformational states, and different ligands “perceive” ezrin conformational states differently. PMID:24151071

  18. Pyrosequencing reveals regional differences in fruit-associated fungal communities.

    PubMed

    Taylor, Michael W; Tsai, Peter; Anfang, Nicole; Ross, Howard A; Goddard, Matthew R

    2014-09-01

    We know relatively little of the distribution of microbial communities generally. Significant work has examined a range of bacterial communities, but the distribution of microbial eukaryotes is less well characterized. Humans have an ancient association with grape vines (Vitis vinifera) and have been making wine since the dawn of civilization, and fungi drive this natural process. While the molecular biology of certain fungi naturally associated with vines and wines is well characterized, complementary investigations into the ecology of fungi associated with fruiting plants is largely lacking. DNA sequencing technologies allow the direct estimation of microbial diversity from a given sample, avoiding culture-based biases. Here, we use deep community pyrosequencing approaches, targeted at the 26S rRNA gene, to examine the richness and composition of fungal communities associated with grapevines and test for geographical community structure among four major regions in New Zealand (NZ). We find over 200 taxa using this approach, which is 10-fold more than previously recovered using culture-based methods. Our analyses allow us to reject the null hypothesis of homogeneity in fungal species richness and community composition across NZ and reveal significant differences between major areas. PMID:24650123

  19. Small molecules reveal an alternative mechanism of Bax activation.

    PubMed

    Brahmbhatt, Hetal; Uehling, David; Al-Awar, Rima; Leber, Brian; Andrews, David

    2016-04-15

    The pro-apoptotic protein Bax commits a cell to death by permeabilizing the mitochondrial outer membrane (MOM). To obtain small-molecule probes for elucidating the molecular mechanism(s) of Bax activation, we screened for compounds that induced Bax-mediated liposome permeabilization. We identified five structurally different small molecules that promoted both Bax targeting to and oligomerization at membranes. All five compounds initiated Bax oligomerization in the absence of membranes by a mechanism unlike Bax activation by Bcl-2 homology 3 domain (BH3) proteins. Some of the compounds induced Bax/Bak-dependent apoptosis in cells. Activation of Bax by the most active compound was poorly inhibited by the anti-apoptotic protein Bcl-XL and requires a cysteine residue at position 126 of Bax that is not required for activation by BH3 proteins. Our results reveal a novel pathway for Bax activation independent of pro-apoptotic BH3 proteins that may have important implications for the regulation of Bax activity in cells. PMID:26916338

  20. Sequential analysis of the numerical Stroop effect reveals response suppression.

    PubMed

    Cohen Kadosh, Roi; Gevers, Wim; Notebaert, Wim

    2011-09-01

    Automatic processing of irrelevant stimulus dimensions has been demonstrated in a variety of tasks. Previous studies have shown that conflict between relevant and irrelevant dimensions can be reduced when a feature of the irrelevant dimension is repeated. The specific level at which the automatic process is suppressed (e.g., perceptual repetition, response repetition), however, is less understood. In the current experiment we used the numerical Stroop paradigm, in which the processing of irrelevant numerical values of 2 digits interferes with the processing of their physical size, to pinpoint the precise level of the suppression. Using a sequential analysis, we dissociated perceptual repetition from response repetition of the relevant and irrelevant dimension. Our analyses of reaction times, error rates, and diffusion modeling revealed that the congruity effect is significantly reduced or even absent when the response sequence of the irrelevant dimension, rather than the numerical value or the physical size, is repeated. These results suggest that automatic activation of the irrelevant dimension is suppressed at the response level. The current results shed light on the level of interaction between numerical magnitude and physical size as well as the effect of variability of responses and stimuli on automatic processing. PMID:21500951

  1. First cranial remains of a gondwanatherian mammal reveal remarkable mosaicism

    NASA Astrophysics Data System (ADS)

    Krause, David W.; Hoffmann, Simone; Wible, John R.; Kirk, E. Christopher; Schultz, Julia A.; von Koenigswald, Wighart; Groenke, Joseph R.; Rossie, James B.; O'Connor, Patrick M.; Seiffert, Erik R.; Dumont, Elizabeth R.; Holloway, Waymon L.; Rogers, Raymond R.; Rahantarisoa, Lydia J.; Kemp, Addison D.; Andriamialison, Haingoson

    2014-11-01

    Previously known only from isolated teeth and lower jaw fragments recovered from the Cretaceous and Palaeogene of the Southern Hemisphere, the Gondwanatheria constitute the most poorly known of all major mammaliaform radiations. Here we report the discovery of the first skull material of a gondwanatherian, a complete and well-preserved cranium from Upper Cretaceous strata in Madagascar that we assign to a new genus and species. Phylogenetic analysis strongly supports its placement within Gondwanatheria, which are recognized as monophyletic and closely related to multituberculates, an evolutionarily successful clade of Mesozoic mammals known almost exclusively from the Northern Hemisphere. The new taxon is the largest known mammaliaform from the Mesozoic of Gondwana. Its craniofacial anatomy reveals that it was herbivorous, large-eyed and agile, with well-developed high-frequency hearing and a keen sense of smell. The cranium exhibits a mosaic of primitive and derived features, the disparity of which is extreme and probably reflective of a long evolutionary history in geographic isolation.

  2. Spatial Congruity Effects Reveal Metaphorical Thinking, not Polarity Correspondence

    PubMed Central

    Dolscheid, Sarah; Casasanto, Daniel

    2015-01-01

    Spatial congruity effects have often been interpreted as evidence for metaphorical thinking, but an alternative account based on polarity correspondence (a.k.a. markedness) has challenged this view. Here we compared metaphor- and polarity-correspondence-based explanations for spatial congruity effects, using musical pitch as a testbed. In one experiment, English speakers classified high- and low-frequency pitches as “high” and “low,” or as “front” and “back,” to determine whether space-pitch congruity effects could be elicited by any marked spatial continuum. Although both pairs of terms describe bipolar spatial continuums, we found congruity effects only for high/low judgments, indicating that markedness is not sufficient to produce space-pitch congruity effects. A second experiment confirmed that there were no space-pitch congruity effects for another pair of terms that have clear markedness (big/small), but which do not denote spatial height. By contrast, this experiment showed congruity effects for words that cued an appropriate vertical spatial schema (tall/short), even though these words are not used conventionally in English to describe pitches, ruling out explanations for the observed pattern of results based on verbal polysemy. Together, results suggest that space-pitch congruity effects reveal metaphorical uses of spatial schemas, not polarity correspondence effects. PMID:26635713

  3. Next generation sequencing in synovial sarcoma reveals novel gene mutations

    PubMed Central

    Vlenterie, Myrella; Hillebrandt-Roeffen, Melissa H.S.; Flucke, Uta E.; Groenen, Patricia J.T.A.; Tops, Bastiaan B.J.; Kamping, Eveline J.; Pfundt, Rolph; de Bruijn, Diederik R.H.; van Kessel, Ad H.M. Geurts; van Krieken, Han J.H.J.M.; van der Graaf, Winette T.A.; Versleijen-Jonkers, Yvonne M.H.

    2015-01-01

    Over 95% of all synovial sarcomas (SS) share a unique translocation, t(X;18), however, they show heterogeneous clinical behavior. We analyzed multiple SS to reveal additional genetic alterations besides the translocation. Twenty-six SS from 22 patients were sequenced for 409 cancer-related genes using the Comprehensive Cancer Panel (Life Technologies, USA) on an Ion Torrent platform. The detected variants were verified by Sanger sequencing and compared to matched normal DNAs. Copy number variation was assessed in six tumors using the Oncoscan array (Affymetrix, USA). In total, eight somatic mutations were detected in eight samples. These mutations have not been reported previously in SS. Two of these, in KRAS and CCND1, represent known oncogenic mutations in other malignancies. Additional mutations were detected in RNF213, SEPT9, KDR, CSMD3, MLH1 and ERBB4. DNA alterations occurred more often in adult tumors. A distinctive loss of 6q was found in a metastatic lesion progressing under pazopanib, but not in the responding lesion. Our results emphasize t(X;18) as a single initiating event in SS and as the main oncogenic driver. Our results also show the occurrence of additional genetic events, mutations or chromosomal aberrations, occurring more frequently in SS with an onset in adults. PMID:26415226

  4. Integrative modelling reveals mechanisms linking productivity and plant species richness

    NASA Astrophysics Data System (ADS)

    Grace, James B.; Anderson, T. Michael; Seabloom, Eric W.; Borer, Elizabeth T.; Adler, Peter B.; Harpole, W. Stanley; Hautier, Yann; Hillebrand, Helmut; Lind, Eric M.; Pärtel, Meelis; Bakker, Jonathan D.; Buckley, Yvonne M.; Crawley, Michael J.; Damschen, Ellen I.; Davies, Kendi F.; Fay, Philip A.; Firn, Jennifer; Gruner, Daniel S.; Hector, Andy; Knops, Johannes M. H.; MacDougall, Andrew S.; Melbourne, Brett A.; Morgan, John W.; Orrock, John L.; Prober, Suzanne M.; Smith, Melinda D.

    2016-01-01

    How ecosystem productivity and species richness are interrelated is one of the most debated subjects in the history of ecology. Decades of intensive study have yet to discern the actual mechanisms behind observed global patterns. Here, by integrating the predictions from multiple theories into a single model and using data from 1,126 grassland plots spanning five continents, we detect the clear signals of numerous underlying mechanisms linking productivity and richness. We find that an integrative model has substantially higher explanatory power than traditional bivariate analyses. In addition, the specific results unveil several surprising findings that conflict with classical models. These include the isolation of a strong and consistent enhancement of productivity by richness, an effect in striking contrast with superficial data patterns. Also revealed is a consistent importance of competition across the full range of productivity values, in direct conflict with some (but not all) proposed models. The promotion of local richness by macroecological gradients in climatic favourability, generally seen as a competing hypothesis, is also found to be important in our analysis. The results demonstrate that an integrative modelling approach leads to a major advance in our ability to discern the underlying processes operating in ecological systems.

  5. Global Population Genetic Structure of Caenorhabditis remanei Reveals Incipient Speciation

    PubMed Central

    Dey, Alivia; Jeon, Yong; Wang, Guo-Xiu; Cutter, Asher D.

    2012-01-01

    Mating system transitions dramatically alter the evolutionary trajectories of genomes that can be revealed by contrasts of species with disparate modes of reproduction. For such transitions in Caenorhabditis nematodes, some major causes of genome variation in selfing species have been discerned. And yet, we have only limited understanding of species-wide population genetic processes for their outcrossing relatives, which represent the reproductive state of the progenitors of selfing species. Multilocus–multipopulation sequence polymorphism data provide a powerful means to uncover the historical demography and evolutionary processes that shape genomes. Here we survey nucleotide polymorphism across the X chromosome for three populations of the outcrossing nematode Caenorhabditis remanei and demonstrate its divergence from a fourth population describing a closely related new species from China, C. sp. 23. We find high genetic variation globally and within each local population sample. Despite geographic barriers and moderate genetic differentiation between Europe and North America, considerable gene flow connects C. remanei populations. We discovered C. sp. 23 while investigating C. remanei, observing strong genetic differentiation characteristic of reproductive isolation that was confirmed by substantial F2 hybrid breakdown in interspecific crosses. That C. sp. 23 represents a distinct biological species provides a cautionary example of how standard practice can fail for mating tests of species identity in this group. This species pair permits full application of divergence population genetic methods to obligately outcrossing species of Caenorhabditis and also presents a new focus for interrogation of the genetics and evolution of speciation with the Caenorhabditis model system. PMID:22649079

  6. Excited states of ribosome translocation revealed through integrative molecular modeling

    PubMed Central

    Whitford, Paul C.; Ahmed, Aqeel; Yu, Yanan; Hennelly, Scott P.; Tama, Florence; Spahn, Christian M. T.; Onuchic, José N.; Sanbonmatsu, Karissa Y.

    2011-01-01

    The dynamic nature of biomolecules leads to significant challenges when characterizing the structural properties associated with function. While X-ray crystallography and imaging techniques (such as cryo-electron microscopy) can reveal the structural details of stable molecular complexes, strategies must be developed to characterize configurations that exhibit only marginal stability (such as intermediates) or configurations that do not correspond to minima on the energy landscape (such as transition-state ensembles). Here, we present a methodology (MDfit) that utilizes molecular dynamics simulations to generate configurations of excited states that are consistent with available biophysical and biochemical measurements. To demonstrate the approach, we present a sequence of configurations that are suggested to be associated with transfer RNA (tRNA) movement through the ribosome (translocation). The models were constructed by combining information from X-ray crystallography, cryo-electron microscopy, and biochemical data. These models provide a structural framework for translocation that may be further investigated experimentally and theoretically to determine the precise energetic character of each configuration and the transition dynamics between them. PMID:22080606

  7. Excited states of ribosome translocation revealed through integrative molecular modeling.

    PubMed

    Whitford, Paul C; Ahmed, Aqeel; Yu, Yanan; Hennelly, Scott P; Tama, Florence; Spahn, Christian M T; Onuchic, José N; Sanbonmatsu, Karissa Y

    2011-11-22

    The dynamic nature of biomolecules leads to significant challenges when characterizing the structural properties associated with function. While X-ray crystallography and imaging techniques (such as cryo-electron microscopy) can reveal the structural details of stable molecular complexes, strategies must be developed to characterize configurations that exhibit only marginal stability (such as intermediates) or configurations that do not correspond to minima on the energy landscape (such as transition-state ensembles). Here, we present a methodology (MDfit) that utilizes molecular dynamics simulations to generate configurations of excited states that are consistent with available biophysical and biochemical measurements. To demonstrate the approach, we present a sequence of configurations that are suggested to be associated with transfer RNA (tRNA) movement through the ribosome (translocation). The models were constructed by combining information from X-ray crystallography, cryo-electron microscopy, and biochemical data. These models provide a structural framework for translocation that may be further investigated experimentally and theoretically to determine the precise energetic character of each configuration and the transition dynamics between them. PMID:22080606

  8. Revealing the wood and the trees: reporting qualitative research.

    PubMed

    Blignault, Ilse; Ritchie, Jan

    2009-08-01

    Qualitative research methodologies, which are oriented to better understanding of the context, meaning and experiences of people's lives, have much to contribute to health promotion. For researchers trained in quantitative methods, writing up qualitative research for a peer-reviewed journal can be a challenge, especially keeping within the prescribed word limits. How well you explain and disseminate your research will influence how others evaluate its quality; this has implications not only for what you write and the terminology you use but for how you structure your article. This paper provides a general guide to presenting qualitative research for publication in a way that has meaning for authors and readers, is acceptable to editors and reviewers, and meets criteria for high standards of qualitative research reporting across the board. We discuss the writing of all sections of an article, placing particular emphasis on how you might best present your findings, illustrating our points with examples drawn from previous issues of this Journal. Overall, we emphasise that reporting qualitative research involves sharing both the process and the findings, that is, revealing both the wood and the trees. PMID:19642963

  9. Key herbivores reveal limited functional redundancy on inshore coral reefs

    NASA Astrophysics Data System (ADS)

    Johansson, C. L.; van de Leemput, I. A.; Depczynski, M.; Hoey, A. S.; Bellwood, D. R.

    2013-12-01

    Marine ecosystems are facing increasing exposure to a range of stressors and declines in critical ecological functions. The likelihood of further loss of functions and resilience is dependent, in part, on the extent of functional redundancy (i.e. the capacity of one species to functionally compensate for the loss of another species) within critical functional groups. We used multiple metrics; species richness, generic richness, abundance and reserve capacity (i.e. the relative number of individuals available to fulfil the function if the numerically dominant species is lost), as indicators to assess the potential functional redundancy of four functional groups of herbivorous fishes (browsers, excavators, grazers and scrapers) in two of the worlds' most intact coral reef ecosystems: the Great Barrier Reef (GBR) and Ningaloo Reef in Western Australia. We found marked variations in potential redundancy among habitats within each reef system and functional groups. Despite negligible fishing of herbivorous fishes, coastal habitats in both reef systems had lower functional redundancy compared to offshore locations for all herbivorous fishes collectively and the four functional groups independently. This pattern was consistent in all four indicators of redundancy. The potential vulnerability of these coastal habitats is highlighted by recent shifts from coral to macroalgal dominance on several coastal reefs of the GBR. Our approach provides a simple yet revealing evaluation of potential functional redundancy. Moreover, it highlights the spatial variation in potential vulnerability and resilience of reef systems.

  10. Integrating Phosphoproteome and Transcriptome Reveals New Determinants of Macrophage Multinucleation*

    PubMed Central

    Rotival, Maxime; Ko, Jeong-Hun; Srivastava, Prashant K.; Kerloc'h, Audrey; Montoya, Alex; Mauro, Claudio; Faull, Peter; Cutillas, Pedro R.; Petretto, Enrico; Behmoaras, Jacques

    2015-01-01

    Macrophage multinucleation (MM) is essential for various biological processes such as osteoclast-mediated bone resorption and multinucleated giant cell-associated inflammatory reactions. Here we study the molecular pathways underlying multinucleation in the rat through an integrative approach combining MS-based quantitative phosphoproteomics (LC-MS/MS) and transcriptome (high-throughput RNA-sequencing) to identify new regulators of MM. We show that a strong metabolic shift toward HIF1-mediated glycolysis occurs at transcriptomic level during MM, together with modifications in phosphorylation of over 50 proteins including several ARF GTPase activators and polyphosphate inositol phosphatases. We use shortest-path analysis to link differential phosphorylation with the transcriptomic reprogramming of macrophages and identify LRRFIP1, SMARCA4, and DNMT1 as novel regulators of MM. We experimentally validate these predictions by showing that knock-down of these latter reduce macrophage multinucleation. These results provide a new framework for the combined analysis of transcriptional and post-translational changes during macrophage multinucleation, prioritizing essential genes, and revealing the sequential events leading to the multinucleation of macrophages. PMID:25532521

  11. Genomic analysis of primordial dwarfism reveals novel disease genes.

    PubMed

    Shaheen, Ranad; Faqeih, Eissa; Ansari, Shinu; Abdel-Salam, Ghada; Al-Hassnan, Zuhair N; Al-Shidi, Tarfa; Alomar, Rana; Sogaty, Sameera; Alkuraya, Fowzan S

    2014-02-01

    Primordial dwarfism (PD) is a disease in which severely impaired fetal growth persists throughout postnatal development and results in stunted adult size. The condition is highly heterogeneous clinically, but the use of certain phenotypic aspects such as head circumference and facial appearance has proven helpful in defining clinical subgroups. In this study, we present the results of clinical and genomic characterization of 16 new patients in whom a broad definition of PD was used (e.g., 3M syndrome was included). We report a novel PD syndrome with distinct facies in two unrelated patients, each with a different homozygous truncating mutation in CRIPT. Our analysis also reveals, in addition to mutations in known PD disease genes, the first instance of biallelic truncating BRCA2 mutation causing PD with normal bone marrow analysis. In addition, we have identified a novel locus for Seckel syndrome based on a consanguineous multiplex family and identified a homozygous truncating mutation in DNA2 as the likely cause. An additional novel PD disease candidate gene XRCC4 was identified by autozygome/exome analysis, and the knockout mouse phenotype is highly compatible with PD. Thus, we add a number of novel genes to the growing list of PD-linked genes, including one which we show to be linked to a novel PD syndrome with a distinct facial appearance. PD is extremely heterogeneous genetically and clinically, and genomic tools are often required to reach a molecular diagnosis. PMID:24389050

  12. Parallel Selection Revealed by Population Sequencing in Chicken

    PubMed Central

    Qanbari, Saber; Seidel, Michael; Strom, Tim-Mathias; Mayer, Klaus F.X.; Preisinger, Ruedi; Simianer, Henner

    2015-01-01

    Human-driven selection during domestication and subsequent breed formation has likely left detectable signatures within the genome of modern chicken. The elucidation of these signatures of selection is of interest from the perspective of evolutionary biology, and for identifying genes relevant to domestication and improvement that ultimately may help to further genetically improve this economically important animal. We used whole genome sequence data from 50 hens of commercial white (WL) and brown (BL) egg-laying chicken along with pool sequences of three meat-type chicken to perform a systematic screening of past selection in modern chicken. Evidence of positive selection was investigated in two steps. First, we explored evidence of parallel fixation in regions with overlapping elevated allele frequencies in replicated populations of layers and broilers, suggestive of selection during domestication or preimprovement ages. We confirmed parallel fixation in BCDO2 and TSHR genes and found four candidates including AGTR2, a gene heavily involved in “Ascites” in commercial birds. Next, we explored differentiated loci between layers and broilers suggestive of selection during improvement in chicken. This analysis revealed evidence of parallel differentiation in genes relevant to appearance and production traits exemplified with the candidate gene OPG, implicated in Osteoporosis, a disorder related to overconsumption of calcium in egg-laying hens. Our results illustrate the potential for population genetic techniques to identify genomic regions relevant to the phenotypes of importance to breeders. PMID:26568375

  13. Revealing hidden regularities with a general approach to fission

    NASA Astrophysics Data System (ADS)

    Schmidt, Karl-Heinz; Jurado, Beatriz

    2015-12-01

    Selected aspects of a general approach to nuclear fission are described with the focus on the possible benefit of meeting the increasing need of nuclear data for the existing and future emerging nuclear applications. The most prominent features of this approach are the evolution of quantum-mechanical wave functions in systems with complex shape, memory effects in the dynamics of stochastic processes, the influence of the Second Law of thermodynamics on the evolution of open systems in terms of statistical mechanics, and the topological properties of a continuous function in multi-dimensional space. It is demonstrated that this approach allows reproducing the measured fission barriers and the observed properties of the fission fragments and prompt neutrons. Our approach is based on sound physical concepts, as demonstrated by the fact that practically all the parameters have a physical meaning, and reveals a high degree of regularity in the fission observables. Therefore, we expect a good predictive power within the region extending from Po isotopes to Sg isotopes where the model parameters have been adjusted. Our approach can be extended to other regions provided that there is enough empirical information available that allows determining appropriate values of the model parameters. Possibilities for combining this general approach with microscopic models are suggested. These are supposed to enhance the predictive power of the general approach and to help improving or adjusting the microscopic models. This could be a way to overcome the present difficulties for producing evaluations with the required accuracy.

  14. Designed protein reveals structural determinants of extreme kinetic stability

    PubMed Central

    Broom, Aron; Ma, S. Martha; Xia, Ke; Rafalia, Hitesh; Trainor, Kyle; Colón, Wilfredo; Gosavi, Shachi; Meiering, Elizabeth M.

    2015-01-01

    The design of stable, functional proteins is difficult. Improved design requires a deeper knowledge of the molecular basis for design outcomes and properties. We previously used a bioinformatics and energy function method to design a symmetric superfold protein composed of repeating structural elements with multivalent carbohydrate-binding function, called ThreeFoil. This and similar methods have produced a notably high yield of stable proteins. Using a battery of experimental and computational analyses we show that despite its small size and lack of disulfide bonds, ThreeFoil has remarkably high kinetic stability and its folding is specifically chaperoned by carbohydrate binding. It is also extremely stable against thermal and chemical denaturation and proteolytic degradation. We demonstrate that the kinetic stability can be predicted and modeled using absolute contact order (ACO) and long-range order (LRO), as well as coarse-grained simulations; the stability arises from a topology that includes many long-range contacts which create a large and highly cooperative energy barrier for unfolding and folding. Extensive data from proteomic screens and other experiments reveal that a high ACO/LRO is a general feature of proteins with strong resistances to denaturation and degradation. These results provide tractable approaches for predicting resistance and designing proteins with sufficient topological complexity and long-range interactions to accommodate destabilizing functional features as well as withstand chemical and proteolytic challenge. PMID:26554002

  15. Dense sampling reveals behavioral oscillations in rapid visual categorization.

    PubMed

    Drewes, Jan; Zhu, Weina; Wutz, Andreas; Melcher, David

    2015-01-01

    Perceptual systems must create discrete objects and events out of a continuous flow of sensory information. Previous studies have demonstrated oscillatory effects in the behavioral outcome of low-level visual tasks, suggesting a cyclic nature of visual processing as the solution. To investigate whether these effects extend to more complex tasks, a stream of "neutral" photographic images (not containing targets) was rapidly presented (20 ms/image). Embedded were one or two presentations of a randomly selected target image (vehicles and animals). Subjects reported the perceived target category. On dual-presentation trials, the ISI varied systematically from 0 to 600 ms. At randomized timing before first target presentation, the screen was flashed with the intent of creating a phase reset in the visual system. Sorting trials by temporal distance between flash and first target presentation revealed strong oscillations in behavioral performance, peaking at 5 Hz. On dual-target trials, longer ISIs led to reduced performance, implying a temporal integration window for object category discrimination. The "animal" trials exhibited a significant oscillatory component around 5 Hz. Our results indicate that oscillatory effects are not mere fringe effects relevant only with simple stimuli, but are resultant from the core mechanisms of visual processing and may well extend into real-life scenarios. PMID:26542183

  16. Ecoinformatics Reveals Effects of Crop Rotational Histories on Cotton Yield

    PubMed Central

    Meisner, Matthew H.; Rosenheim, Jay A.

    2014-01-01

    Crop rotation has been practiced for centuries in an effort to improve agricultural yield. However, the directions, magnitudes, and mechanisms of the yield effects of various crop rotations remain poorly understood in many systems. In order to better understand how crop rotation influences cotton yield, we used hierarchical Bayesian models to analyze a large ecoinformatics database consisting of records of commercial cotton crops grown in California's San Joaquin Valley. We identified several crops that, when grown in a field the year before a cotton crop, were associated with increased or decreased cotton yield. Furthermore, there was a negative association between the effect of the prior year's crop on June densities of the pest Lygus hesperus and the effect of the prior year's crop on cotton yield. This suggested that some crops may enhance L. hesperus densities in the surrounding agricultural landscape, because residual L. hesperus populations from the previous year cannot continuously inhabit a focal field and attack a subsequent cotton crop. In addition, we found that cotton yield declined approximately 2.4% for each additional year in which cotton was grown consecutively in a field prior to the focal cotton crop. Because L. hesperus is quite mobile, the effects of crop rotation on L. hesperus would likely not be revealed by small plot experimentation. These results provide an example of how ecoinformatics datasets, which capture the true spatial scale of commercial agriculture, can be used to enhance agricultural productivity. PMID:24465657

  17. Artemin Crystal Structure Reveals Insights into Heparan Sulfate Binding

    SciTech Connect

    Silvian,L.; Jin, P.; Carmillo, P.; Boriack-Sjodin, P.; Pelletier, C.; Rushe, M.; Gong, B.; Sah, D.; Pepinsky, B.; Rossomando, A.

    2006-01-01

    Artemin (ART) promotes the growth of developing peripheral neurons by signaling through a multicomponent receptor complex comprised of a transmembrane tyrosine kinase receptor (cRET) and a specific glycosylphosphatidylinositol-linked co-receptor (GFR{alpha}3). Glial cell line-derived neurotrophic factor (GDNF) signals through a similar ternary complex but requires heparan sulfate proteoglycans (HSPGs) for full activity. HSPG has not been demonstrated as a requirement for ART signaling. We crystallized ART in the presence of sulfate and solved its structure by isomorphous replacement. The structure reveals ordered sulfate anions bound to arginine residues in the pre-helix and amino-terminal regions that were organized in a triad arrangement characteristic of heparan sulfate. Three residues in the pre-helix were singly or triply substituted with glutamic acid, and the resulting proteins were shown to have reduced heparin-binding affinity that is partly reflected in their ability to activate cRET. This study suggests that ART binds HSPGs and identifies residues that may be involved in HSPG binding.

  18. Metabolomics reveals insect metabolic responses associated with fungal infection.

    PubMed

    Xu, Yong-Jiang; Luo, Feifei; Gao, Qiang; Shang, Yanfang; Wang, Chengshu

    2015-06-01

    The interactions between insects and pathogenic fungi are complex. We employed metabolomic techniques to profile insect metabolic dynamics upon infection by the pathogenic fungus Beauveria bassiana. Silkworm larvae were infected with fungal spores and microscopic observations demonstrated that the exhaustion of insect hemocytes was coupled with fungal propagation in the insect body cavity. Metabolomic analyses revealed that fungal infection could significantly alter insect energy and nutrient metabolisms as well as the immune defense responses, including the upregulation of carbohydrates, amino acids, fatty acids, and lipids, but the downregulation of eicosanoids and amines. The insect antifeedant effect of the fungal infection was evident with the reduced level of maclurin (a component of mulberry leaves) in infected insects but elevated accumulations in control insects. Insecticidal and cytotoxic mycotoxins like oosporein and beauveriolides were also detected in insects at the later stages of infection. Taken together, the metabolomics data suggest that insect immune responses are energy-cost reactions and the strategies of nutrient deprivation, inhibition of host immune responses, and toxin production would be jointly employed by the fungus to kill insects. The data obtained in this study will facilitate future functional studies of genes and pathways associated with insect-fungus interactions. PMID:25895944

  19. Response trajectories reveal conflict phase in image-word mismatch.

    PubMed

    van Vugt, Floris T; Cavanagh, Patrick

    2012-02-01

    In the present study, response trajectories were used in a picture–word conflict task to determine the timing of intermediate processing stages that are relatively inaccessible to response time measures. A marker was placed above or below the word ABOVE or BELOW so that its location was congruent or in conflict with the word's meaning. To report either word location(above or below the marker) or word meaning, participants moved a mouse upward toward the appropriate top left or right answer corner on the display screen.Their response trajectories showed a number of distinctive features: First, at about 200 ms after stimulus onset(the "decision moment"), the trajectory abruptly began to arc toward the appropriate answer corner; second,when the word's meaning and position were in conflict,the trajectory showed an interruption that continued until the conflict was resolved. By varying the SOA of the word and marker onsets, we found that the word meaning and word position became available at approximately 325 ms and 251 ms, respectively, after their onsets, and that the delay to resolve conflicts was about 138 ms. The timing of these response trajectory events was more stable than any extracted from the final response times, demonstrating the power of response trajectories to reveal processing stages that are only poorly resolved, if at all, by response time measures [added]. PMID:22219088

  20. Metabolic phenotyping reveals a lipid mediator response to ionizing radiation.

    PubMed

    Laiakis, Evagelia C; Strassburg, Katrin; Bogumil, Ralf; Lai, Steven; Vreeken, Rob J; Hankemeier, Thomas; Langridge, James; Plumb, Robert S; Fornace, Albert J; Astarita, Giuseppe

    2014-09-01

    Exposure to ionizing radiation has dramatically increased in modern society, raising serious health concerns. The molecular response to ionizing radiation, however, is still not completely understood. Here, we screened mouse serum for metabolic alterations following an acute exposure to γ radiation using a multiplatform mass-spectrometry-based strategy. A global, molecular profiling revealed that mouse serum undergoes a series of significant molecular alterations following radiation exposure. We identified and quantified bioactive metabolites belonging to key biochemical pathways and low-abundance, oxygenated, polyunsaturated fatty acids (PUFAs) in the two groups of animals. Exposure to γ radiation induced a significant increase in the serum levels of ether phosphatidylcholines (PCs) while decreasing the levels of diacyl PCs carrying PUFAs. In exposed mice, levels of pro-inflammatory, oxygenated metabolites of arachidonic acid increased, whereas levels of anti-inflammatory metabolites of omega-3 PUFAs decreased. Our results indicate a specific serum lipidomic biosignature that could be utilized as an indicator of radiation exposure and as novel target for therapeutic intervention. Monitoring such a molecular response to radiation exposure might have implications not only for radiation pathology but also for countermeasures and personalized medicine. PMID:25126707