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Sample records for na isoelectronic sequence

  1. Spectral lines behavior of Be I and Na I isoelectronic sequence in Debye plasma environment

    SciTech Connect

    Chaudhuri, Rajat K.; Chattopadhyay, Sudip; Sinha Mahapatra, Uttam

    2012-08-15

    We report the plasma screening effect on the first ionization potential (IP) and [He]2s{sup 2} ({sup 1}S{sub 0}){yields}[He]2s2p/2s3p allowed ({sup 1}P{sub 1}) and inter-combination transitions ({sup 3}P{sub 1}) in some selected Be-like ions. In addition, we investigate the spectral properties of [Ne]3s ({sup 2}S{sub 1/2}){yields}[Ne]np ({sup 2}P{sub 1/2} and {sup 2}P{sub 3/2} for n = 3, 4) transitions in Ca X and Fe XVI ions (Na I isoelectronic sequence) and [He]3s({sup 2}S{sub 1/2}){yields}[He]np ({sup 2}P{sub 1/2} and {sup 2}P{sub 3/2} for n = 2, 3) transitions in Li, B II, and N IV (Li I isoelectronic sequence) under plasma environment. The state-of-the-art relativistic coupled cluster calculations using the Debye model of plasma for electron-nucleus interaction show that (a) the ionization potential decreases sharply with increasing plasma strength and (b) the gap between the [He]2s{sup 2} ({sup 1}S{sub 0}){yields}[He]2s2p({sup 1,3}P{sub 1}) energy levels increases with increasing plasma potential and nuclear charge. It is found that the [He]2s{sup 2} ({sup 1}S{sub 0}){yields}2s3p ({sup 1,3}P{sub 1}) transition energy decreases uniformly with increasing plasma potential and nuclear charge. In other words, the spectral lines associated with 2s-2p (i.e., {Delta}n=0, where n corresponds to principle quantum number) transitions in Be I isoelectronic sequence exhibit a blue-shift (except for Be I, B II, and the lowest inter-combination line in C III, which exhibit a red-shift), whereas those associated with 2s-3p (i.e., {Delta}n{ne}0) transitions are red-shifted. Similar trend is observed in Li I and Na I isoelectronic sequences, where spectral lines associated with {Delta}n=0 ({Delta}n{ne}0) are blue-shifted (red-shifted). The effect of Coulomb screening on the spectral lines of ions subjected to plasma is also addressed.

  2. Spectral lines behavior of Be I and Na I isoelectronic sequence in Debye plasma environment

    NASA Astrophysics Data System (ADS)

    Chaudhuri, Rajat K.; Chattopadhyay, Sudip; Sinha Mahapatra, Uttam

    2012-08-01

    We report the plasma screening effect on the first ionization potential (IP) and [He]2s2(1S0)→[He]2s2p /2s3p allowed (P11) and inter-combination transitions (P31) in some selected Be-like ions. In addition, we investigate the spectral properties of [Ne]3s (2S1/2)→[Ne]np(2P1/2 and P23/2 for n = 3, 4) transitions in Ca X and Fe XVI ions (Na I isoelectronic sequence) and [He]3s(2S1/2)→[He]np(2P1/2 and P23/2 for n = 2, 3) transitions in Li, B II, and N IV (Li I isoelectronic sequence) under plasma environment. The state-of-the-art relativistic coupled cluster calculations using the Debye model of plasma for electron-nucleus interaction show that (a) the ionization potential decreases sharply with increasing plasma strength and (b) the gap between the [He]2s2(1S0)→[He]2s2p(1,3P1) energy levels increases with increasing plasma potential and nuclear charge. It is found that the [He]2s2 (1S0)→2s3p(1,3P1) transition energy decreases uniformly with increasing plasma potential and nuclear charge. In other words, the spectral lines associated with 2s-2p (i.e., Δn=0, where n corresponds to principle quantum number) transitions in Be I isoelectronic sequence exhibit a blue-shift (except for Be I, B II, and the lowest inter-combination line in C III, which exhibit a red-shift), whereas those associated with 2s-3p (i.e., Δn≠0) transitions are red-shifted. Similar trend is observed in Li I and Na I isoelectronic sequences, where spectral lines associated with Δn=0 (Δn≠0) are blue-shifted (red-shifted). The effect of Coulomb screening on the spectral lines of ions subjected to plasma is also addressed.

  3. Isoelectronic trends of line strength data in the Li and Be isoelectronic sequences

    SciTech Connect

    Trabert, E; Curtis, L J

    2006-03-01

    The decays of the 2p J = 1/2 and J = 3/2 levels of Li-like ions and of the 2s2p {sup 1,3}P{sub 1}{sup 0} levels of Be-like ions can be used as simple-atom test beds for experimental lifetime measurements and for the development of accurate calculations of the transition rates. They have summarized and filtered the experimental data in order to obtain consistent data sets and isoelectronic trends that can be compared to theoretical predictions. The graphical presentation of line strength data enables direct comparison and evaluation of the merit of data along extended isoelectronic sequences. From this, the precision that is necessary in future meaningful experiments can be deduced.

  4. Radioactive transitions in the helium isoelectronic sequence

    NASA Technical Reports Server (NTRS)

    Dalgarno, A.

    1971-01-01

    The principles of the atomic spectrum theory are used to quantitatively analyze radiation transitions in two-electron helium-like atomic systems. Quantum theoretical methods, describing absorption and emission of a single photon in a radiative transition between two stationary states of an atomic system, reproduced the energy level diagram for the low lying states of helium. Reliable values are obtained from accurate variationally determined two-electron nonrelativistic wave functions for radiative transition probabilities of 2 3p states in the helium isoelectric sequence, and for the 2 1s and 2 3s1 states of the helium sequence.

  5. Spectra of the W VIII isoelectronic sequence: III. Re IX

    NASA Astrophysics Data System (ADS)

    Ryabtsev, A. N.; Kononov, E. Ya; Kildiyarova, R. R.; Tchang-Brillet, W.-Ü. L.; Wyart, J.-F.; Champion, N.; Blaess, C.

    2015-09-01

    Rhenium spectra excited in vacuum spark sources of different setups and electric circuits were recorded on two high resolution vacuum spectrographs: a 10 m normal incidence spectrograph with a 3600 l mm-1 grating in the Meudon Observatory and a 3 m grazing incidence spectrograph with a 3600 l mm-1 grating in the Institute of Spectroscopy in Troitsk. A total of 112 lines in the region 146-244 Å were identified as transitions from the interacting excited even configurations 4f125s25p65d + 4f135s25p5(5d + 6s) + 4f145s25p4(5d + 6s) to the low-lying odd configurations 4f135s25p6 and 4f145s25p5. A change of the ground configuration from 4f135s25p6 to 4f145s25p5 in a comparison with the previous spectra of the isoelectronic sequence Hf VI-W VIII was observed. Fine structure splittings and relative positions of the odd terms were established, and 83 levels of the excited even configurations were found.

  6. Relativistic MR-MP energy levels: Low-lying states in the Mg isoelectronic sequence

    NASA Astrophysics Data System (ADS)

    Santana, Juan A.

    2016-09-01

    The relativistic Multi-Reference Møller-Plesset (MR-MP) many-body perturbation theory was applied to calculate the energies of all excited states within the 3s3p, 3p2, 3s3d, 3p3d and 3d2 configurations for every ion of the Mg isoelectronic sequence (Z = 12 - 100). The results are compared with previous calculations and available experimental data. The MR-MP excitation energies agree with experiment typically within 100 ppm over a wide range of Z, particularly for mid- and high-range Z. Experimental data for highly charged ions in this isoelectronic sequence are limited and the complete and accurate dataset presented here is expected to ease the identification process upon measurements.

  7. Ground-state Landé g factors for selected ions along the boron isoelectronic sequence

    NASA Astrophysics Data System (ADS)

    Marques, J. P.; Indelicato, P.; Parente, F.; Sampaio, J. M.; Santos, J. P.

    2016-10-01

    Landé g factors for the fine-structure 1 s22 s22 p 1/2 2P and 3/2 2P levels in the boron isoelectronic sequence for selected Z values have been calculated using the multiconfiguration Dirac-Fock method with both quantum-electrodynamic and electronic correlation corrections included. All-order Breit and vacuum polarization corrections were included in the calculation, with a fully optimized active set wave function. The results are compared with the available theoretical data, showing a very good agreement.

  8. Relativistic oscillator strengths of the rubidium isoelectronic sequence in the vicinity of the d orbital collapse region

    NASA Astrophysics Data System (ADS)

    Migdalek, J.

    2016-09-01

    The influence of valence–core electron local and nonlocal exchange and valence–core electron correlation (core polarization) on oscillator strengths is studied along the Rb isoelectronic sequence in the vicinity of the d orbital collapse region using model potential and Dirac–Fock methods.

  9. S-matrix Calculations of Energy Levels of the Lithium Isoelectronic Sequence

    SciTech Connect

    sapirstein, J; Cheng, K T

    2010-11-02

    A QED approach to the calculation of the spectra of the lithium isoelectronic sequence is implemented. A modified Furry representation based on the Kohn-Sham potential is used to evaluate all one- and two-photon diagrams with the exception of the two-loop Lamb shift. Three-photon diagrams are estimated with Hamiltonian methods. After incorporating recent calculations of the two-loop Lamb shift and recoil corrections a comprehensive tabulation of the 2s, 2p{sub 1/2} and 2p{sub 3/2} energy levels as well as the 2s - 2p{sub 1/2} and 2s - 2p{sub 3/2} transition energies for Z = 10 - 100 is presented.

  10. S-matrix calculations of energy levels of the lithium isoelectronic sequence

    NASA Astrophysics Data System (ADS)

    Sapirstein, J.; Cheng, K. T.

    2012-06-01

    A QED approach to the calculation of the spectra of the lithium isoelectronic sequence is implemented. A modified Furry representation based on the Kohn-Sham potential is used to evaluate all one- and two-photon diagrams with the exception of the two-loop Lamb shift. Three-photon diagrams are estimated with Hamiltonian methods. After incorporating recent calculations of the two-loop Lamb shift and recoil corrections a comprehensive tabulation of the 2s, 2p1/2 and 2p3/2 energy levels as well as the 2s-2p1/2 and 2s-2p3/2 transition energies for Z=10-100 is presented.

  11. S-matrix calculations of energy levels of the lithium isoelectronic sequence

    NASA Astrophysics Data System (ADS)

    Sapirstein, J.; Cheng, K. T.

    2011-01-01

    A QED approach to the calculation of the spectra of the lithium isoelectronic sequence is implemented. A modified Furry representation based on the Kohn-Sham potential is used to evaluate all one- and two-photon diagrams with the exception of the two-loop Lamb shift. Three-photon diagrams are estimated with Hamiltonian methods. After incorporating recent calculations of the two-loop Lamb shift and recoil corrections, a comprehensive tabulation of the 2s, 2p1/2, and 2p3/2 energy levels as well as the 2s-2p1/2 and 2s-2p3/2 transition energies for Z=10-100 is presented.

  12. Dielectronic recombination rate coefficients for the CoI isoelectronic sequence

    NASA Astrophysics Data System (ADS)

    Meng, Fan-Chang; Zhou, Li; Huang, Min; Chen, Chong-Yang; Wang, Yan-Sen; Zou, Ya-Ming

    2009-05-01

    In our recent reports (2007 J. Phys. B: At. Mol. Opt. Phys. 40 4269-86 and 2008 J. Quant. Spectrosc. Radiat. Transfer 109 2000-2008), we performed detailed and large-scale ab initio calculations on the total dielectronic recombination (DR) rate coefficients for Co-like gold and tungsten. Here we extend the calculations for another eight ions (Kr9+, Mo15+, Ag20+, Xe27+, Pr32+, Dy39+, At58+ and U65+) along the CoI isoelectronic sequence in the ground state employing the flexible atomic code. The total DR rates mainly come from complex series 3d84ln'l' and 3p53d94ln'l'. The complex series 3p53d10n'l' and 3d85ln'l' also contribute significantly at low (<0.1EI, EI is the ionization energy of the corresponding Ni-like ions) and high (>1.0EI) electron temperatures, respectively. On the basis of the calculated results, a general analytic formula for the total DR rate coefficients of all the ions along the CoI isoelectronic sequence is constructed. This formula can generally reproduce the calculated DR rate coefficients to within 3% for electron temperatures above 0.1EI. Comparisons of the present results with those obtained from the commonly used Burgess-Merts (BM) semiempirical formula show that the BM formula is not adequate to predict the total DR rate coefficients at relatively low electron temperatures and for low-Z ions. In addition, the total DR rate coefficients from the first excited state are also presented.

  13. Excitation energies, polarizabilities, multipole transition rates, and lifetimes of ions along the francium isoelectronic sequence

    SciTech Connect

    Safronova, U. I.; Johnson, W. R.; Safronova, M. S.

    2007-10-15

    Relativistic many-body perturbation theory is applied to study properties of ions of the francium isoelectronic sequence. Specifically, energies of the 7s, 7p, 6d, and 5f states of Fr-like ions with nuclear charges Z=87-100 are calculated through third order; reduced matrix elements, oscillator strengths, transition rates, and lifetimes are determined for 7s-7p, 7p-6d, and 6d-5f electric-dipole transitions; and 7s-6d, 7s-5f, and 5f{sub 5/2}-5f{sub 7/2} multipole matrix elements are evaluated to obtain the lifetimes of low-lying excited states. Moreover, for the ions Z=87-92 calculations are also carried out using the relativistic all-order single-double method, in which single and double excitations of Dirac-Fock wave functions are included to all orders in perturbation theory. With the aid of the single-double wave functions, we obtain accurate values of energies, transition rates, oscillator strengths, and the lifetimes of these six ions. Ground state scalar polarizabilities in Fr I, Ra II, Ac III, and Th IV are calculated using relativistic third-order and all-order methods. Ground state scalar polarizabilities for other Fr-like ions are calculated using a relativistic second-order method. These calculations provide a theoretical benchmark for comparison with experiment and theory.

  14. VizieR Online Data Catalog: B-like iso-electronic sequence (Liang+, 2012)

    NASA Astrophysics Data System (ADS)

    Liang, G. Y.; Badnell, N. R.; Zhao, G.

    2012-09-01

    We present our calculated data including energy levels, radiative decay rates and effective collision strengths for all the transitions among the 204 fine-structure levels of boron-like iso-electronic sequence, belonging to configurations of 2sx 2py (x+y=3), 2s2 3l, 2s2 4l, 2s 2p 3l, 2s 2p 4l, 2p2 3l The effective collision strengths at 13 temperatures ranging from 2x102(q+1)2 to 2x106(q+1)2^K, where q is the residual charge of ions, i.e. Z-5, have been calculated using the ICFT R-matrix method. The data format adopts ADAS adf04 format, see the file at website http://www.adas.ac.uk/man/appxa-04.pdf Filename format: sequenceauthor(nospace)yearelement(nospace)charge.dat. For example Ne^5+, blikelgy12ne5.dat (2 data files).

  15. Soft x-ray laser gain prediction at high density for the nitrogen isoelectronic sequence

    SciTech Connect

    Klapisch, M. ); Cohen, M.; Goldstein, W.H. ); Feldman, U. . E.O. Hulburt Center for Space Research)

    1991-01-11

    In model calculation, population inversions for 2s{sup 2}2p{sup 2}3s-2s{sup 2}2p{sup 2}3p and for 2s{sup 2}2p{sup 2}d3p-2s{sup 2}2p{sup 2}3d are predicted for ions of the N-like isoelectronic sequence (Kr{sup 29+}, Zr{sup 33+}, Mo{sup 35+}, Pd{sup 39+}, Sn{sup 43+} and Xe{sup 47+}), at electron densities higher than 10{sup 22} cm{sup {minus}3}. Maximum gains of 46 cm{sup {minus}1} for Kr{sup 29+} at 245{angstrom}, and 231 cm{sup {minus}1} at 126{angstrom} for Xe{sup 47+} are obtained. The electron temperature T{sub e} is fixed at half the ionization potential for all ions. A detailed analysis shows that the mechanisms responsible for the population inversion enhancement are collisional de-excitation and radiation trapping. 16 refs., 6 figs.

  16. [Study on the n = 5 complex transitions for ions Nd XIII-Sm XV in Cd I isoelectronic sequence].

    PubMed

    Ding, Kai; Mu, Zhi-Dong; Ye, Shi-Wang

    2011-01-01

    The energy levels of the n = 5 complex configuration 5s2, 5s5p, 5s5d and 5p2 were computed for Cd I isoelectronic sequence ions from I VI to Sm XV by Hartree-Fock with relativistic corrections (HFR) method. By analyzing the variation of difference deltaE between energy levels calculated by HFR method and the experimental values with Z(c) along this isoelectronic sequence, the authors put forward a new fitting formula for generalized-least-square-fit (LSF) calculation. Using this formula and the FORTRAN programme designed by us, the energy levels of configurations mentioned above were calculated. The unknown energy levels of configuration 5s2 , 5s5p, 5s5d and 5p2 for ions from Nd XIII-Sm XV were predicted by extrapolation (or interpolation). Also, the wavelengths and HFR probabilities of transition 5s2-5s5p, 5s5p-5p2 and 5s5p-5s5d were computed. The calculated energy levels and wavelength results are in good agreement with corresponding experimental data reported in the references. PMID:21428048

  17. Hylleraas-configuration-interaction nonrelativistic energies for the {sup 1}S ground states of the beryllium isoelectronic sequence

    SciTech Connect

    Sims, James S.; Hagstrom, Stanley A.

    2014-06-14

    In a previous work, Sims and Hagstrom [“Hylleraas-configuration-interaction study of the 1 {sup 1}S ground state of neutral beryllium,” Phys. Rev. A 83, 032518 (2011)] reported Hylleraas-configuration-interaction (Hy-CI) method variational calculations for the {sup 1}S ground state of neutral beryllium with an estimated accuracy of a tenth of a microhartree. In this work, the calculations have been extended to higher accuracy and, by simple scaling of the orbital exponents, to the entire Be 2 {sup 1}S isoelectronic sequence. The best nonrelativistic energies for Be, B{sup +}, and C{sup ++} obtained are −14.6673 5649 269, −24.3488 8446 36, and −36.5348 5236 25 hartree, respectively. Except for Be, all computed nonrelativistic energies are superior to the known reference energies for these states.

  18. Density sensitive X-ray line ratios in the Be I, B I, and Ne I isoelectronic sequences

    NASA Technical Reports Server (NTRS)

    Feldman, U.; Seely, J. F.; Bhatia, A. K.

    1985-01-01

    The intensities of X-ray transitions in highly charged ions in the Be I, B I, and Ne I isoelectronic sequences have been calculated as functions of electron density. The intensities of the transitions from the 2s(n)2p(m)3p configuration, relative to the intensities from the 2s(n)2p(m)3s and 2s(n)p(m)3d configurations, are strong functions of electron density in high-density plasmas. The density sensitivity occurs at electron densities between 10 to the 16th/cu cm (for Si ions) and 10 to the 22nd/cu cm (for Kr ions). Opacity is unimportant for plasma dimensions that are characteristic of dense laser-produced plasmas. These X-ray line ratios represent a promising new density diagnostic for high-density plasmas.

  19. R-matrix electron-impact excitation data for the Mg-like iso-electronic sequence

    NASA Astrophysics Data System (ADS)

    Fernández-Menchero, L.; Del Zanna, G.; Badnell, N. R.

    2014-12-01

    Aims: Emission lines from ions in the Mg-like iso-electronic sequence can be used as reliable diagnostics of temperature and density of astrophysical and fusion plasmas over a wide range of parameters. Data in the literature are quite lacking, there are no calculations for many of the ions in the sequence. Methods: We have carried-out intermediate coupling frame transformation R-matrix calculations which include a total of 283 fine-structure levels in both the configuration interaction target and close-coupling collision expansions. These arise from the configurations 1s2 2s2 2p6 3 {s,p,d} nl with n = 4,5, and for l = 0-4. Results: We obtain ordinary collision strengths and Maxwell-averaged effective collision strengths for the electron-impact excitation of all the ions of the Mg-like sequence, from Al+ to Zn18 +. We compare our results with those from previous R-matrix and distorted waves calculations, where available, for some benchmark ions. We find good agreement with the results of previous calculations for the transitions n = 3-3. We also find good agreement for the most intense transitions n = 3-4. These transitions are important for populating the upper levels of the main diagnostic lines. These data are made available in the APAP archive via http://www.apap-network.org, CHIANTI via http://www.chiantidatabase.org and open-ADAS via http://open.adas.ac.uk

  20. K-shell photoabsorption and photoionisation of trace elements. I. Isoelectronic sequences with electron number 3 ≤N ≤ 11

    NASA Astrophysics Data System (ADS)

    Palmeri, P.; Quinet, P.; Mendoza, C.; Bautista, M. A.; Witthoeft, M. C.; Kallman, T. R.

    2016-05-01

    Context. With the recent launching of the Hitomi X-ray space observatory, K lines and edges of chemical elements with low cosmic abundances, namely F, Na, P, Cl, K, Sc, Ti, V, Cr, Mn, Co, Cu and Zn, can be resolved and used to determine important properties of supernova remnants, galaxy clusters and accreting black holes and neutron stars. Aims: The second stage of the present ongoing project involves the computation of the accurate photoabsorption and photoionisation cross sections required to interpret the X-ray spectra of such trace elements. Methods: Depending on target complexity and computer tractability, ground-state cross sections are computed either with the close-coupling Breit-Pauli R-matrix method or with the autostructure atomic structure code in the isolated-resonance approximation. The intermediate-coupling scheme is used whenever possible. In order to determine a realistic K-edge behaviour for each species, both radiative and Auger dampings are taken into account, the latter being included in the R-matrix formalism by means of an optical potential. Results: Photoabsorption and total and partial photoionisation cross sections are reported for isoelectronic sequences with electron numbers 3 ≤ N ≤ 11. The Na sequence (N = 11) is used to estimate the contributions from configurations with a 2s hole (i.e. [2s]μ) and those containing 3d orbitals, which will be crucial when considering sequences with N > 11. Conclusions: It is found that the [2s]μ configurations must be included in the target representations of species with N ≥ 11 as they contribute significantly to the monotonic background of the cross section between the L and K edges. Configurations with 3d orbitals are important in rendering an accurate L edge, but they can be practically neglected in the K-edge region.

  1. R-matrix electron-impact excitation data for the Be-like iso-electronic sequence

    NASA Astrophysics Data System (ADS)

    Fernández-Menchero, L.; Del Zanna, G.; Badnell, N. R.

    2014-06-01

    Aims: Emission lines from ions in the Be-like isoelectronic sequence can be used for reliable diagnostics of temperature and density of astrophysical and fusion plasmas over a wide range of temperatures. Surprisingly, interpolated data is all that is available for a number of astrophysically important ions. Methods: We have carried out intermediate coupling frame transformation R-matrix calculations which include a total of 238 fine-structure levels in both the configuration interaction target and close-coupling collision expansions. These arise from the configurations 1s2 2 {s, p} nl with n = 3-7, and l = 0-4 for n ≤ 5 and l = 0-2 for n = 6,7. Results: We obtain ordinary collision strengths and Maxwell-averaged effective collision strengths for the electron-impact excitation of all the ions of the Be-like sequence, from B+ to Zn26+. We compare with previous R-matrix calculations and interpolated values for some benchmark ions. We find good agreement for transitions n = 2-2 with previous R-matrix calculations but some disagreements with interpolated values. We also find good agreement for the most intense transitions n = 2-3 which contribute via cascade to the (n = 2) diagnostic radiating levels. These data are made available in the archives of APAP via http://www.apap-network.org and OPEN-ADAS via http://open.adas.ac.uk

  2. Energies, radiative rates, and Auger widths of the doubly-excited 1s23l3l‧ states of the Be isoelectronic sequence

    NASA Astrophysics Data System (ADS)

    Li, Kaikai; Zhuo, Lin; Gou, Bingcong

    2016-10-01

    Relativistic energies, radiative and Auger rates of the high-lying doubly-excited 1s23l3l‧1,3L states of the Be isoelectronic sequence are studied using the saddle-point variational method with complex rotation. The relativistic and mass polarization corrections are calculated using the first-order perturbation theory. Autoionizing levels and widths above the 1s22s and 1s22p thresholds are considered and their contributions are analysed. The regular change of the radiative and Auger rates along the Be isoelectronic sequence is discussed in this work. The results are compared with the available experimental and other theoretical data in the literature.

  3. Transitions 2s/2/ 2p/k/ - 2s 2p/k+1/ of the F I, O I, and N I isoelectronic sequences. [in laser plasma spectra

    NASA Technical Reports Server (NTRS)

    Doschek, G. A.; Cowan, R. D.; Cohen, L.; Feldman, U.

    1974-01-01

    Transitions of the type 2s/2/ 2p/k/ - 2s 2p/k+1/ have been identified for the elements from titanium through nickel for ions of the fluorine, oxygen, and nitrogen isoelectronic sequences. Wavelengths, visual intensity estimates, and energies are given. The energy differences of levels of the ground configuration are compared with predictions based on semiempirical equations derived by Edlen. Some of the lines of these isoelectronic sequences should be strong lines in solar-flare spectra.

  4. R-matrix electron-impact excitation data for the B-like iso-electronic sequence

    NASA Astrophysics Data System (ADS)

    Liang, G. Y.; Badnell, N. R.; Zhao, G.

    2012-11-01

    We have carried-out parallel intermediate-coupling frame transformation R-matrix calculations for electron-impact excitation amongst the 204 close-coupling levels of the 2sx2py (x + y = 3), 2s2{3,4}l, 2s2p{3,4}l, and 2p23l configurations for all boron-like ions from C+ to Kr31+. We have also included the configuration interaction due to the 2p24l, 2s3l3l' and 2p3s3l configurations. A detailed comparison has been made of the target structure and excitation data for four specific ions (viz., Ne5+, Ar13+, Fe21+ and Kr31+) that span the sequence, so as to assess the accuracy over the entire sequence. Effective collision strengths (Υs) are presented at temperatures ranging from 2 × 102(z + 1)2 K to 2 × 106(z + 1)2 K (where z is the residual charge of the ions, i.e. Z - 5). Detailed comparisons for the (effective) collision strengths (Υs) Ω are made with the results of previous calculations for the four representative ions. Furthermore, we examine the iso-electronic trends of the effective collision strengths as a function of temperature. These data are made available in the archives of APAP via http://www.apap-network.org, OPEN-ADAS via http://open.adas.ac.uk as well as at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/547/A87

  5. R-matrix electron-impact excitation data for the Li-like iso-electronic sequence including Auger and radiation damping

    NASA Astrophysics Data System (ADS)

    Liang, G. Y.; Badnell, N. R.

    2011-04-01

    We present results for the electron-impact excitation of all Li-like ions from Be+ to Kr33+ which we obtained using the radiation- and Auger-damped intermediate-coupling frame transformation R-matrix approach. We have included both valence- and core-electron excitations up to the 1s25l and 1s2l4l' levels, respectively. A detailed comparison of the target structure and collision data has been made for four specific ions (O5+, Ar15+, Fe23+ and Kr33+) spanning the sequence so as to assess the accuracy for the entire sequence. Effective collision strengths (Υs) are presented at temperatures ranging from 2 × 102(z + 1)2 K to 2 × 106(z + 1)2 K (where z is the residual charge of the ions, i.e. Z - 3). Detailed comparisons for the Υs are made with the results of previous calculations for several ions which span the sequence. The radiation and Auger damping effects were explored for core-excitations along the iso-electronic sequence. Furthermore, we examined the iso-electronic trends of effective collision strengths as a function of temperature. These data are made available in the archives of APAP via http://www.apap-network.org, OPEN-ADAS via http://open.adas.ac.uk, as well as anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsweb.u-strasbg.fr/cgi-bin/qcat?J/A+A/528/A69

  6. Isoelectronic co-doping

    DOEpatents

    Mascarenhas, Angelo

    2004-11-09

    Isoelectronic co-doping of semiconductor compounds and alloys with deep acceptors and deep donors is used to decrease bandgap, to increase concentration of the dopant constituents in the resulting alloys, and to increase carrier mobilities lifetimes. Group III-V compounds and alloys, such as GaAs and GaP, are isoelectronically co-doped with, for example, N and Bi, to customize solar cells, thermal voltaic cells, light emitting diodes, photodetectors, and lasers on GaP, InP, GaAs, Ge, and Si substrates. Isoelectronically co-doped Group II-VI compounds and alloys are also included.

  7. The CHIANTI database, a consistency check on the accuracy of the stored cross-section values in He i to O i isoelectronic sequence ions

    NASA Astrophysics Data System (ADS)

    Feldman, U.

    2016-07-01

    CHIANTI is an atomic database with software for calculating emission properties. It is extensively used in deriving the atomic properties of spectra recorded from astrophysical and low density laboratory plasmas. In order to obtain an insight into the accuracy of the CHIANTI calculated level populations, a consistency check was conducted along the He i, Be i, B i, C i, N i, and O i isoelectronic sequences. In the evaluation process, levels of the ground configuration and the first and second excited configurations were considered. These are the levels responsible for most of the spectral lines used when deriving the plasma properties of astrophysical objects. As is documented below, the accuracy of the CHIANTI level population calculations depends on the particular ion, level and on the electron density. Under some conditions the calculations appear quite robust while in others they are not.

  8. Wavelengths and levels of the Na I isoelectronic sequence from K IX through Mn XV

    NASA Technical Reports Server (NTRS)

    Cohen, L.; Behring, W. E.

    1976-01-01

    The seven spectra K IX through Mn XV have been analyzed and the series limits determined. We present the adopted wavelengths and the derived energy levels and term splittings. The highly ionized atoms were produced in a spark source and recorded mainly on a 3 m grazing incidence spectrograph. Many new lines have been identified and many previously given wavelengths have been revised. All wavelengths have been examined for consistency by least-squares-fitting procedures and other tests. These procedures indicated misidentified lines and incorrect wavelengths which we corrected when possible. A discussion of the errors is given.

  9. Laser gain on 3p-3d and 3s-3p transitions and X-ray line ratios for the nitrogen isoelectronic sequence

    NASA Technical Reports Server (NTRS)

    Feldman, U.; Seely, J. F.; Bhatia, A. K.

    1989-01-01

    Results are presented on calculations of the 72 levels belonging to the 2s(2)2p(3), 2s2p(4), 2p(5), 2s(2)2p(2)3s, 2s(2)2p(2)3p, and 2s(2)2p(2)3d configurations of the N I isoelectronic sequence for the ions Ar XII, Ti XVI, Fe XX, Zn XXIV, and Kr XXX, for electron densities up to 10 to the 24th/cu cm. It was found that large population inversions and gain occur between levels in the 2s(2)2p(2)3p configuration and levels in the 2s(2)2p(2)3d configuration that cannot decay to the ground configuration by an electric dipole transition. For increasing electron densities, the intensities of the X-ray transitions from the 2s(2)2p(2)3p configuration to the ground configuration decrease relative to the transitions from the 2s(2)2p(2)3s and 2s(2)2p(2)3d configurations to the ground configuration. The density dependence of these X-ray line ratios is presented.

  10. Contribution of the 4 f -core-excited states in determination of atomic properties in the Promethium Isoelectronic Sequence

    NASA Astrophysics Data System (ADS)

    Beiersdorfer, Peter; Safronova, U. I.; Safronova, A. S.

    2014-05-01

    The atomic properties of Pm-like ions were comprehensively studied using relativistic atomic codes with the main emphasis on W ion. Excitation energies of the 4f14 nl (with nl = 5 s , 6 s , 5 p , 6 p , 5 d , 6 d , and 5 f) states in Pm-like ions with nuclear charge Z ranging from 74 to 100 are evaluated within the framework of relativistic many-body theory (RMBPT). First- and second-order Coulomb energies and first- and second-order Breit corrections to the energies are calculated. The important question of what is the ground state in Pm-like ions was answered. Properties of the 4 f -core-excited states are evaluated using the multiconfiguration relativistic Hebrew University Lawrence Livermore Atomic Code (HULLAC code) and the Hartree-Fock-Relativistic method (COWAN code). Our large scale calculations includes the following set of configurations: 4f14 5 s , 4f14 5 p , 4f13 5s2 , 4f13 5p2 , 4f13 5 s 5 p , 4f12 5s2 5 p , 4f12 5 s 5p2 , and 4f12 5p3 . Excitation energies, transition rates, and lifetimes in Pm-like tungsten are evaluated with additional inclusion of the 4f11 5s2 5p2 , 4f11 5 s 5p3 , 4f10 5s2 5p3 , and 4f10 5 s 5p4 configurations. Wavelengths of the 5 s - 5 p transitions are obtained by the COWAN, HULLAC, and RMBPT codes. This research was sponsored by DOE under the OFES grant DE-FG02-08ER54951 and in part by NNSA Cooperative Agreement DE-NA0001984. Work at Lawrence Livermore National Lab. was performed under the auspices of DOE under Contract DE-AC52-07NA27344.

  11. Calculations with Spectroscopic Accuracy: Energies and Transition Rates in the Nitrogen Isoelectronic Sequence from Ar XII to Zn XXIV

    NASA Astrophysics Data System (ADS)

    Wang, K.; Si, R.; Dang, W.; Jönsson, P.; Guo, X. L.; Li, S.; Chen, Z. B.; Zhang, H.; Long, F. Y.; Liu, H. T.; Li, D. F.; Hutton, R.; Chen, C. Y.; Yan, J.

    2016-03-01

    Combined relativistic configuration interaction and many-body perturbation calculations are performed for the 359 fine-structure levels of the 2s2 2p3, 2 s2p4, 2p5, 2s2 2p2 3l, 2 s2p3 3l, 2p4 3l, and 2s2 2p2 4l configurations in N-like ions from Ar xii to Zn xxiv. Complete and consistent data sets of energies, wavelengths, radiative rates, oscillator strengths, and line strengths for all possible electric dipole, magnetic dipole, electric quadrupole, and magnetic quadrupole transitions among the 359 levels are given for each ion. The present work significantly increases the amount of accurate data for ions in the nitrogen-like sequence, and the accuracy of the energy levels is high enough to enable the identification and interpretation of observed spectra involving the n = 3, 4 levels, for which experimental values are largely scarce. Meanwhile, the results should be of great help for modeling and diagnosing astrophysical and fusion plasmas.

  12. Ionization Potentials for Isoelectronic Series.

    ERIC Educational Resources Information Center

    Agmon, Noam

    1988-01-01

    Presents a quantitative treatment of ionization potentials of isoelectronic atoms. By looking at the single-electron view of calculating the total energy of an atom, trends in the screening and effective quantum number parameters are examined. Approaches the question of determining electron affinities. (CW)

  13. Genome Sequences of Cupriavidus metallidurans Strains NA1, NA4, and NE12, Isolated from Space Equipment.

    PubMed

    Monsieurs, Pieter; Mijnendonckx, Kristel; Provoost, Ann; Venkateswaran, Kasthuri; Ott, C Mark; Leys, Natalie; Van Houdt, Rob

    2014-01-01

    Cupriavidus metallidurans NA1, NA4, and NE12 were isolated from space and spacecraft-associated environments. Here, we report their draft genome sequences with the aim of gaining insight into their potential to adapt to these environments.

  14. Isoelectronic determination of the thermal Casimir force

    NASA Astrophysics Data System (ADS)

    Bimonte, G.; López, D.; Decca, R. S.

    2016-05-01

    Differential force measurements between spheres coated with either nickel or gold and rotating disks with periodic distributions of nickel and gold are reported. The rotating samples are covered by a thin layer of titanium and a layer of gold. While titanium is used for fabrication purposes, the gold layer (nominal thicknesses of 21, 37, 47, and 87 nm) provides an isoelectronic environment, and is used to nullify the electrostatic contribution but allow the passage of long wavelength Casimir photons. A direct comparison between the experimental results and predictions from Drude and plasma models for the electrical permittivity is carried out. In the models, the magnetic permeability of nickel is allowed to change to investigate its effects. Possible sources of errors, both in the experimental and theoretical sides, are taken into account. It is found that a Drude response with magnetic properties of nickel taken into account is unequivocally ruled out. The full analysis of the data indicates that a dielectric plasma response with the magnetic properties of Ni included shows good agreement with the data. Neither a Drude nor a plasma dielectric response provide a satisfactory description if the magnetic properties of nickel are disregarded.

  15. Genome Sequences of Cupriavidus metallidurans Strains NA1, NA4, and NE12, Isolated from Space Equipment

    PubMed Central

    Monsieurs, Pieter; Mijnendonckx, Kristel; Provoost, Ann; Venkateswaran, Kasthuri; Ott, C. Mark; Leys, Natalie

    2014-01-01

    Cupriavidus metallidurans NA1, NA4, and NE12 were isolated from space and spacecraft-associated environments. Here, we report their draft genome sequences with the aim of gaining insight into their potential to adapt to these environments. PMID:25059868

  16. Methods of Calculating Ionization Energies of Multielectron (Five or More) Isoelectronic Atomic Ions

    PubMed Central

    Lang, Peter F.; Smith, Barry C.

    2013-01-01

    We have previously used simple empirical equations to reproduce the literature values of the ionization energies of isoelectronic sequences of up to four electrons which gave very good agreement. We reproduce here a kinetic energy expression with corrections for relativity and Lamb shift effects which give excellent agreement with the literature values. These equations become more complex as the number of electrons in the system increases. Alternative simple quadratic expressions for calculating ionization energies of multielectron ions are discussed. A set of coefficients when substituted into a simple expression produces very good agreement with the literature values. Our work shows that Slater's rules are not appropriate for predicting trends or screening constants. This work provides very strong evidence that ionization energies are not functions of complete squares, and when calculating ionization energies electron transition/relaxation has to be taken into account. We demonstrate clearly that for particular isoelectronic sequences, the ionizing electrons may occupy different orbitals and in such cases more than one set of constants are needed to calculate the ionization energies. PMID:23766674

  17. The Helium Atom and Isoelectronic Ions in Two Dimensions

    ERIC Educational Resources Information Center

    Patil, S. H.

    2008-01-01

    The energy levels of the helium atom and isoelectronic ions in two dimensions are considered. The difficulties encountered in the analytical evaluation of the perturbative and variational expressions for the ground state, promote an interesting factorization of the inter-electronic interaction, leading to simple expressions for the energy. This…

  18. Reduction of magnetic interlayer coupling in barlowite through isoelectronic substitution

    NASA Astrophysics Data System (ADS)

    Guterding, Daniel; Valentí, Roser; Jeschke, Harald O.

    2016-09-01

    Materials with a perfect kagome lattice structure of magnetic ions are intensively sought after, because they may exhibit exotic ground states like a quantum spin liquid phase. Barlowite is a natural mineral that features perfect kagome layers of copper ions. However, in barlowite there are also copper ions between the kagome layers, which mediate strong interkagome couplings and lead to an ordered ground state. Using ab initio density functional theory calculations we investigate whether selective isoelectronic substitution of the interlayer copper ions is feasible. After identifying several promising candidates for substitution we calculate the magnetic exchange couplings based on crystal structures predicted from first-principles calculations. We find that isoelectronic substitution with nonmagnetic ions significantly reduces the interkagome exchange coupling. As a consequence, interlayer-substituted barlowite can be described by a simple two-parameter Heisenberg Hamiltonian, for which a quantum spin liquid ground state has been predicted.

  19. Draft Genome Sequence of Ureolytic Environmental Isolate Staphylococcus sp. NA309

    PubMed Central

    Gaiero, Jonathan R.; Hsiang, Tom; Nicol, Rob W.

    2016-01-01

    We report the 2.7 Mb draft genome sequence of Staphylococcus sp. NA309 isolated from poultry litter. The isolate was a dominant member of the cultivable aerobic bacteria identified to have ureolytic activity, responsible for ammonia generation in poultry litter residue. PMID:27795244

  20. Biexciton emission from single isoelectronic traps formed by nitrogen-nitrogen pairs in GaAs

    SciTech Connect

    Takamiya, Kengo; Fukushima, Toshiyuki; Yagi, Shuhei; Hijikata, Yasuto; Yaguchi, Hiroyuki; Mochizuki, Toshimitsu; Yoshita, Masahiro; Akiyama, Hidefumi; Kuboya, Shigeyuki; Onabe, Kentaro; Katayama, Ryuji

    2013-12-04

    We have studied photoluminescence (PL) from individual isoelectronic traps formed by nitrogen-nitrogen (NN) pairs in GaAs. Sharp emission lines due to exciton and biexciton were observed from individual isoelectronic traps in nitrogen atomic-layer doped (ALD) GaAs. The binding energy of biexciton bound to individual isoelectronic traps was approximately 8 meV. Both the exciton and biexciton luminescence lines show completely random polarization and no fine-structure splitting. These results are desirable to the application to the quantum cryptography used in the field of quantum information technology.

  1. Energy levels of isoelectronic impurities by large scale LDA calculations

    SciTech Connect

    Li, Jingbo; Wang, Lin-Wang

    2002-11-22

    Isoelectronic impurity states are localized states induced by stoichiometric single atom substitution in bulk semiconductor. Photoluminescence spectra indicate deep impurity levels of 0.5 to 0.9eV above the top of valence band for systems like: GaN:As, GaN:P, CdS:Te, ZnS:Te. Previous calculations based on small supercells seemingly confirmed these experimental results. However, the current ab initio calculations based on thousand atom supercells indicate that the impurity levels of the above systems are actually much shallower(0.04 to 0.23 eV), and these impurity levels should be compared with photoluminescence excitation spectra, not photoluminescence spectra.

  2. Expressed sequence tags from a NaCl-treated Suaeda salsa cDNA library.

    PubMed

    Zhang, L; Ma, X L; Zhang, Q; Ma, C L; Wang, P P; Sun, Y F; Zhao, Y X; Zhang, H

    2001-04-18

    Past efforts to improve plant tolerance to osmotic stress have had limited success owing to the genetic complexity of stress responses. The first step towards cataloging and categorizing genetically complex abotic stress responses is the rapid discovery of genes by the large-scale partial sequencing of randomly selected cDNA clones or expressed sequence tags (ESTs). Suaeda salsa, which can survive seawater-level salinity, is a favorite halophytic model for salt tolerant research. We constructed a NaCl-treated cDNA library of Suaeda salsa and sequenced 1048 randomly selected clones, out of which 1016 clones produced readable sequences (773 showed homology to previously identified genes, 227 matched unknown protein coding regions, 16 anomalous sequences or sequences of bacterial origin were excluded from further analysis). By sequence analysis we identified 492 unique clones: 315 showed homology to previously identified genes, 177 matched unknown protein coding regions (101 of which have been found before in other organisms and 76 are completely novel). All our EST data are available on the Internet. We believe that our dbEST and the associated DNA materials will be a useful source to scientists engaging in stress-tolerance study. PMID:11313146

  3. Topological disposition of the sequences -QRKIVE- and -KETYY in native (Na sup + + K sup + )-ATPase

    SciTech Connect

    Bayer, R. )

    1990-03-06

    The dispositions with respect to the plane of the membrane of lysine-905 in the internal sequence -EQRKIVE- and of lysine-1012 in the carboxy-terminal sequence -RRPGGWVEKETYY of the {alpha}-polypeptide of sodium and potassium ion activated adenosinetriphosphatase have been determined. These lysines are found in peptides released from the intact {alpha}-polypeptide by the extracellular protease from Staphylococcus aureus strain V8 and by trypsin, respectively. Synthetic peptides containing terminal sequences of these were used to prepare polyclonal antibodies, which were then used to prepare immunoadsorbents directed against the respective peptides. Sealed, right-side-out membrane vesicles containing native (Na{sup +} + K{sup +})-ATPase were labeled with pyridoxal phosphate and sodium ({sup 3}H)borohydride in the absence or presence of saponin. The labeled {alpha}-polypeptide was isolated from these vesicles and digested with appropriate proteases. The incorporation of radioactivity into the peptides binding to the immunoadsorbent directed against the sequence pyrERXIVE increased 3-fold int the presence of saponin as a result of the increased accessibility of this portion of the protein to the reagent when the vesicles were breached by saponin; hence, this sequence is located on the cytoplasmic face of the membrane. It was inferred that the carboxy-terminal sequence -KETYY is on the extracytoplasmic face since the incorporation of radioactivity into peptides binding to the immunoadsorbent directed against the sequence -ETYY did not change when the vesicles were breached with saponin.

  4. Phonon sidebands of excitons bound to isoelectronic impurities in semiconductors

    SciTech Connect

    Zhang, Y.; Ge, W.; Sturge, M.D. ); Zheng, J.; Wu, B. )

    1993-03-15

    The configuration coordinate (CC) and momentum conservation (MC) models have been widely used to explain the phonon sidebands of impurity spectra in semiconductors. In this paper, the distinction between the CC and MC models is discussed. We conclude that the MC model only applies to shallow Coulombic impurities; in other cases, such as isoelectronic traps, the CC model is more appropriate. We show that the Huang-Rhys parameters for bulk phonon modes coupling to a bound electron or exciton can be calculated from the bound-state wave function in [ital k] space if the phonon-induced intervalley and intravalley electron scattering processes of the pure crystal are known. We study in detail the phonon sidebands of nitrogen-bound excitons in GaP, giving the selection rules for electron-phonon coupling in the CC model, and showing that their strength can be well accounted for by the CC model. The apparently anomalous [ital X]'' peak of the LO-phonon sideband in GaP:N is shown to be associated with intervalley scattering in the conduction band. The MC model, which has been used in an attempt to explain the phonon sidebands of GaP:N in some previous work, is shown to be inapplicable to this case.

  5. Dipolar Quinoidal Acene Analogues as Stable Isoelectronic Structures of Pentacene and Nonacene.

    PubMed

    Shi, Xueliang; Kueh, Weixiang; Zheng, Bin; Huang, Kuo-Wei; Chi, Chunyan

    2015-11-23

    Quinoidal thia-acene analogues, as the respective isoelectronic structures of pentacene and nonacene, were synthesized and an unusual 1,2-sulfur migration was observed during the Friedel-Crafts alkylation reaction. The analogues display a closed-shell quinoidal structure in the ground state with a distinctive dipolar character. In contrast to their acene isoelectronic structures, both compounds are stable because of the existence of more aromatic sextet rings, a dipolar character, and kinetic blocking. They exhibit unique packing in single crystals resulting from balanced dipole-dipole and [C-H⋅⋅⋅π]/[C-H⋅⋅⋅S] interactions. PMID:26447720

  6. Superatom spectroscopy and the electronic state correlation between elements and isoelectronic molecular counterparts.

    PubMed

    Peppernick, Samuel J; Gunaratne, K D Dasitha; Castleman, A W

    2010-01-19

    Detailed in the present investigation are results pertaining to the photoelectron spectroscopy of negatively charged atomic ions and their isoelectronic molecular counterparts. Experiments utilizing the photoelectron imaging technique are performed on the negative ions of the group 10 noble metal block (i.e. Ni-, Pd-, and Pt-) of the periodic table at a photon energy of 2.33 eV (532 nm). The accessible electronic transitions, term energies, and orbital angular momentum components of the bound electronic states in the atom are then compared with photoelectron images collected for isoelectronic early transition metal heterogeneous diatomic molecules, M-X- (M = Ti,Zr,W; X = O or C). A superposition principle connecting the spectroscopy between the atomic and molecular species is observed, wherein the electronic structure of the diatomic is observed to mimic that present in the isoelectronic atom. The molecular ions studied in this work, TiO-, ZrO-, and WC- can then be interpreted as possessing superatomic electronic structures reminiscent of the isoelectronic elements appearing on the periodic table, thereby quantifying the superatom concept.

  7. Application and Analysis of the Isoelectronic Line Ratio Temperature Diagnostic in a Planar Ablating-Plasma Experiment at the National Ignition Facility

    NASA Astrophysics Data System (ADS)

    Epstein, R.; Rosenberg, M. J.; Solodov, A. A.; Myatt, J. F.; Regan, S. P.; Seka, W.; Hohenberger, M.; Barrios, M. A.; Moody, J. D.

    2015-11-01

    The Mn/Co isoelectronic emission-line ratio from a microdot source in planar CH foil targets was measured to infer the electron temperature (Te) in the ablating plasma during two-plasmon-decay experiments at the National Ignition Facility (NIF). We examine the systematic uncertainty in the Te estimate based on the temperature and density sensitivities of the line ratio in conjunction with plausible density constraints, and its contribution to the total Te estimate uncertainty. The potential advantages of alternative microdot elements (e.g., Ti/Cr and Sc/V) are considered. The microdot mass was selected to provide ample line strength while minimizing the effect of self-absorption on the line emission, which is of particular concern, given the narrow linewidths of mid- Z emitters at subcritical electron densities. Atomic line-formation theory and detailed atomic-radiative simulations show that the straight forward interpretation of the isoelectronic ratio solely in terms of its temperature independence remains valid with lines of moderate optical thickness (up to ~ 10) at line center. This material is based upon work supported by the Department of Energy National Nuclear Security Administration under Award Number DE-NA0001944.

  8. Magnetic and Ising quantum phase transitions in a model for isoelectronically tuned iron pnictides

    NASA Astrophysics Data System (ADS)

    Wu, Jianda; Si, Qimiao; Abrahams, Elihu

    2016-03-01

    Considerations of the observed bad-metal behavior in Fe-based superconductors led to an early proposal for quantum criticality induced by isoelectronic P for As doping in iron arsenides, which has since been experimentally confirmed. We study here an effective model for the isoelectronically tuned pnictides using a large-N approach. The model contains antiferromagnetic and Ising-nematic order parameters appropriate for J1-J2 exchange-coupled local moments on an Fe square lattice, and a damping caused by coupling to itinerant electrons. The zero-temperature magnetic and Ising transitions are concurrent and essentially continuous. The order-parameter jumps are very small, and are further reduced by the interplane coupling; consequently, quantum criticality occurs over a wide dynamical range. Our results reconcile recent seemingly contradictory experimental observations concerning the quantum phase transition in the P-doped iron arsenides.

  9. An isoelectronic NO dioxygenase reaction using a nonheme iron(III)-peroxo complex and nitrosonium ion.

    PubMed

    Yokoyama, Atsutoshi; Han, Jung Eun; Karlin, Kenneth D; Nam, Wonwoo

    2014-02-18

    Reaction of a nonheme iron(III)-peroxo complex, [Fe(III)(14-TMC)(O2)](+), with NO(+), a transformation which is essentially isoelectronic with that for nitric oxide dioxygenases [Fe(III)(O2˙(-)) + NO], affords an iron(IV)-oxo complex, [Fe(IV)(14-TMC)(O)](2+), and nitrogen dioxide (NO2), followed by conversion to an iron(III)-nitrato complex, [Fe(III)(14-TMC)(NO3)(F)](+).

  10. Evolutionary History and Phylodynamics of Influenza A and B Neuraminidase (NA) Genes Inferred from Large-Scale Sequence Analyses

    PubMed Central

    Xu, Jianpeng; Davis, C. Todd; Christman, Mary C.; Rivailler, Pierre; Zhong, Haizhen; Donis, Ruben O.; Lu, Guoqing

    2012-01-01

    Background Influenza neuraminidase (NA) is an important surface glycoprotein and plays a vital role in viral replication and drug development. The NA is found in influenza A and B viruses, with nine subtypes classified in influenza A. The complete knowledge of influenza NA evolutionary history and phylodynamics, although critical for the prevention and control of influenza epidemics and pandemics, remains lacking. Methodology/Principal findings Evolutionary and phylogenetic analyses of influenza NA sequences using Maximum Likelihood and Bayesian MCMC methods demonstrated that the divergence of influenza viruses into types A and B occurred earlier than the divergence of influenza A NA subtypes. Twenty-three lineages were identified within influenza A, two lineages were classified within influenza B, and most lineages were specific to host, subtype or geographical location. Interestingly, evolutionary rates vary not only among lineages but also among branches within lineages. The estimated tMRCAs of influenza lineages suggest that the viruses of different lineages emerge several months or even years before their initial detection. The dN/dS ratios ranged from 0.062 to 0.313 for influenza A lineages, and 0.257 to 0.259 for influenza B lineages. Structural analyses revealed that all positively selected sites are at the surface of the NA protein, with a number of sites found to be important for host antibody and drug binding. Conclusions/Significance The divergence into influenza type A and B from a putative ancestral NA was followed by the divergence of type A into nine NA subtypes, of which 23 lineages subsequently diverged. This study provides a better understanding of influenza NA lineages and their evolutionary dynamics, which may facilitate early detection of newly emerging influenza viruses and thus improve influenza surveillance. PMID:22808012

  11. Draft Genome Sequence of Bacillus thuringiensis Serovar Tolworthi Strain Na205-3, an Isolate Toxic for Helicoverpa armigera

    PubMed Central

    Palma, Leopoldo; Muñoz, Delia; Murillo, Jesús

    2014-01-01

    We report here the complete annotated 6,510,053-bp draft genome sequence of Bacillus thuringiensis serovar tolworthi strain Na205-3, which is toxic for Helicoverpa armigera. This strain potentially contains nine insecticidal toxin genes homologous to cry1Aa12, cry1Ab1, cry1Ab8, cry1Ba1, cry1Af1, cry1Ia10, vip1Bb1, vip2Ba2, and vip3Aa6. PMID:24625875

  12. Binding energies of the lithium isoelectronic sequence approaching the critical charge

    NASA Astrophysics Data System (ADS)

    Katriel, Jacob; Puchalski, Mariusz; Pachucki, Krzysztof

    2012-10-01

    The Simon-Zhislin-Hunziker theorem implies that Zc, the critical charge below which the three electron atom is not bound, is at most 2. The vanishing electron affinity of He implies that Zc is not less than 2. Hence, Zc=2. To elucidate the approach to the critical charge, we calculated nonrelativistic binding energies for the third electron in the ground state, 1s22s2S, and in the first and second excited states, 1s22p2P and 1s23s2S, for nuclear charges approaching Zc. At this limit the quantum defects for both 2S states are found to approach unity. This implies that the orbital specifying the outer (ns,n=2,3) electron becomes a very diffuse (n-1)s-type orbital, except within the relatively tiny space occupied by the inner two-electron shell. For the 2P state the quantum defect approaches zero both as Z→∞ and as Z→2. An expression for the s-p splitting at Z→2 is suggested, that improves upon earlier results based on energies computed (or measured) at integer values of Z. Rigorous large Z asymptotic expressions for the quantum defects in the 1s2ns2S states are presented, exhibiting the expected mild dependence on the principal quantum number.

  13. Experimental study of the x-ray transitions in the heliumlike isoelectronic sequence

    SciTech Connect

    Beiersdorfer, P.; Bitter, M.; von Goeler, S.; Hill, K.W.

    1989-05-01

    The wavelengths of the transition 1s2p /sup 1/P/sub 1/ ..-->.. 1s/sup 2/ /sup 1/S/sub 0/ in heliumlike potassium, scandium, titanium, vanadium, chromium, and iron have been measured with an experimental precision of ..delta..lambda/lambda approx. 1/20,000. The data typically agree within error bars with recent theoretical predictions which include quantum electrodynamical corrections. However, the comparison shows that there are systematic differences between data and predictions, which indicate a need to include additional corrections in the calculations. In particular, it is found that the experimental wavelengths are consistently shorter than the calculated values by amounts which depend on the particular theoretical prediction used in the comparison. Measurements of the wavelengths of ..delta..n greater than or equal to 2 x-ray transitions in heliumlike argon, scandium, titanium, vanadium, chromium, and iron are also presented. 42 refs., 8 figs., 2 tabs.

  14. VizieR Online Data Catalog: Sulphur ions iso-electronic sequence (Liang+, 2011)

    NASA Astrophysics Data System (ADS)

    Liang, G. Y.; Badnell, N. R.; Zhao, G.; Zhong, J. Y.; Wang, F. L.

    2011-08-01

    The effective collision strengths at 13 temperatures ranging from 2x102(q+1)2 to 2x106(q+1)2K, where q is the residual charge of ions, have been calculated using the ICFT R-matrix method. The data format adopts ADAS adf04 format, see the file at website http://www.adas.ac.uk/man/appxa-04.pdf Additionally, tables of level energies for S10+ and S11+, along with other predictions are available in this online material. (6 data files).

  15. Third-order many-body perturbation theory calculations for the beryllium and magnesium isoelectronic sequences

    NASA Astrophysics Data System (ADS)

    Ho, H. C.; Johnson, W. R.; Blundell, S. A.; Safronova, M. S.

    2006-08-01

    Third-order relativistic many-body perturbation theory (MBPT) is applied to obtain energies of ions with two valence electrons in the no virtual-pair approximation (NVPA). A total of 302 third-order Goldstone diagrams are organized into 12 one-body and 23 two-body terms. Only third-order two-body terms and diagrams are presented in this paper, owing to the fact that the one-body terms are identical to the previously studied third-order terms in monovalent ions. Dominant classes of diagrams are identified. The model potential is the Dirac-Hartree-Fock potential VN-2 , and B -spline basis functions in a cavity of finite radius are employed in the numerical calculations. The Breit interaction is taken into account through the second order of perturbation theory, and the lowest-order Lamb shift is also evaluated. Sample calculations are performed for berylliumlike ions with Z=4-7 , and for the magnesiumlike ion PIV . The third-order excitation energies are in excellent agreement with measurement with an accuracy at 0.2% level for the cases considered. Comparisons are made with second-order MBPT results, and with other calculations. The third-order energy correction is shown to be significant, improving the previous second-order calculations by an order of magnitude.

  16. Scaling of collisionally pumped 3s-3p lasers in the neon isoelectronic sequence

    NASA Technical Reports Server (NTRS)

    Feldman, U.; Seely, J. F.; Bhatia, A. K.

    1984-01-01

    Atomic-number scaling in the 3p-3s population-inversion and plasma parameters of neonlike ions of Si, Ar, Ti, Fe, Ge, and Kr is investigated theoretically. The population levels are calculated; the Z-scaling relationships are defined; the results are presented in tables and graphs; and the implications for the laser gain are explored. Laser gain in excess of 1/cm are predicted for all ions except Si V, with a peak of 30/cm for Fe XVII at electron density 10 to the 21st/cu cm.

  17. Evaluation of two-photon exchange graphs for the helium isoelectronic sequence

    NASA Astrophysics Data System (ADS)

    Sapirstein, J.

    1989-06-01

    Two-photon exchange graph contributions to the ground state energy of two-electron ions are evaluated in Furry picture QED. The natural separation of correlation effects from negative energy state effects is demonstrated. Some of these latter effects are evaluated both analytically and numerically, and shown to contribute at the level (Zα)3 a.u.

  18. Effect of Isoelectronic Doping at the As Site in Iron-based Superconducting Systems

    NASA Astrophysics Data System (ADS)

    Cao, Guang-Han

    2011-03-01

    FeAs-based superconductivity can be induced with various doping strategies---either electron doping, hole doping or isoelectronic doping. In this talk, we will focus on the unique isoelectronic doping at the As site. By using different dopants such as P [1,2] or Sb, positive or negative chemical pressure can be generated onto the FeAs layers. The positive chemical pressure suppresses/destroys the spin-density-wave (SDW) ordering, and then superconductivity emerges around a quantum critical point. In contrast, the negative pressure tends to recover the suppressed/hidden SDW ordering. The isoelectronic doping also influences the electronic and magnetic state of 4f electrons in the rare-earth atomic layers and 3d electrons of the Fe planes, especially in the case of proximity between 4f and 3d energy levels. This was manifested by the observation of local-moment ferromagnetism of 4f electrons in EuFe 2 (As 1-x Px)2 , CeFeAs 1-x Px O and CeFeAs 1-x Px O0.95 F0.05 systems. Our results demonstrate the intriguing interplay/competition of intersite RKKY coupling among 4f-moments, intrasite Kondo interaction between 4f- and 3d- electrons, and k-space Cooper pairing of 3d electrons. This work was done in collaboration with Zhu-An Xu and Jian-Hui Dai, and was supported by National Basic Research Program of China (Grant Nos. 2007CB925001 and 2010CB923003).

  19. Tuning dissociation using isoelectronically doped graphene and hexagonal boron nitride: Water and other small molecules

    NASA Astrophysics Data System (ADS)

    Al-Hamdani, Yasmine S.; Alfè, Dario; von Lilienfeld, O. Anatole; Michaelides, Angelos

    2016-04-01

    Novel uses for 2-dimensional materials like graphene and hexagonal boron nitride (h-BN) are being frequently discovered especially for membrane and catalysis applications. Still however, a great deal remains to be understood about the interaction of environmentally and industrially relevant molecules such as water with these materials. Taking inspiration from advances in hybridising graphene and h-BN, we explore using density functional theory, the dissociation of water, hydrogen, methane, and methanol on graphene, h-BN, and their isoelectronic doped counterparts: BN doped graphene and C doped h-BN. We find that doped surfaces are considerably more reactive than their pristine counterparts and by comparing the reactivity of several small molecules, we develop a general framework for dissociative adsorption. From this a particularly attractive consequence of isoelectronic doping emerges: substrates can be doped to enhance their reactivity specifically towards either polar or non-polar adsorbates. As such, these substrates are potentially viable candidates for selective catalysts and membranes, with the implication that a range of tuneable materials can be designed.

  20. Tuning dissociation using isoelectronically doped graphene and hexagonal boron nitride: Water and other small molecules.

    PubMed

    Al-Hamdani, Yasmine S; Alfè, Dario; von Lilienfeld, O Anatole; Michaelides, Angelos

    2016-04-21

    Novel uses for 2-dimensional materials like graphene and hexagonal boron nitride (h-BN) are being frequently discovered especially for membrane and catalysis applications. Still however, a great deal remains to be understood about the interaction of environmentally and industrially relevant molecules such as water with these materials. Taking inspiration from advances in hybridising graphene and h-BN, we explore using density functional theory, the dissociation of water, hydrogen, methane, and methanol on graphene, h-BN, and their isoelectronic doped counterparts: BN dopedgraphene and C doped h-BN. We find that dopedsurfaces are considerably more reactive than their pristine counterparts and by comparing the reactivity of several small molecules, we develop a general framework for dissociative adsorption. From this a particularly attractive consequence of isoelectronic doping emerges: substrates can be doped to enhance their reactivity specifically towards either polar or non-polar adsorbates. As such, these substrates are potentially viable candidates for selective catalysts and membranes, with the implication that a range of tuneable materials can be designed. PMID:27389233

  1. The Complete Genome Sequence of Thermococcus onnurineus NA1 Reveals a Mixed Heterotrophic and Carboxydotrophic Metabolism▿ †

    PubMed Central

    Lee, Hyun Sook; Kang, Sung Gyun; Bae, Seung Seob; Lim, Jae Kyu; Cho, Yona; Kim, Yun Jae; Jeon, Jeong Ho; Cha, Sun-Shin; Kwon, Kae Kyoung; Kim, Hyung-Tae; Park, Cheol-Joo; Lee, Hee-Wook; Kim, Seung Il; Chun, Jongsik; Colwell, Rita R.; Kim, Sang-Jin; Lee, Jung-Hyun

    2008-01-01

    Members of the genus Thermococcus, sulfur-reducing hyperthermophilic archaea, are ubiquitously present in various deep-sea hydrothermal vent systems and are considered to play a significant role in the microbial consortia. We present the complete genome sequence and feature analysis of Thermococcus onnurineus NA1 isolated from a deep-sea hydrothermal vent area, which reveal clues to its physiology. Based on results of genomic analysis, T. onnurineus NA1 possesses the metabolic pathways for organotrophic growth on peptides, amino acids, or sugars. More interesting was the discovery that the genome encoded unique proteins that are involved in carboxydotrophy to generate energy by oxidation of CO to CO2, thereby providing a mechanistic basis for growth with CO as a substrate. This lithotrophic feature in combination with carbon fixation via RuBisCO (ribulose 1,5-bisphosphate carboxylase/oxygenase) introduces a new strategy with a complementing energy supply for T. onnurineus NA1 potentially allowing it to cope with nutrient stress in the surrounding of hydrothermal vents, providing the first genomic evidence for the carboxydotrophy in Thermococcus. PMID:18790866

  2. From Saturated BN Compounds to Isoelectronic BN/CC Counterparts: An Insight from Computational Perspective.

    PubMed

    Sagan, Filip; Piękoś, Łukasz; Andrzejak, Marcin; Mitoraj, Mariusz Paweł

    2015-10-19

    In the present study, the inorganic analogues of alkanes as well as their isoelectronic BN/CC counterparts that bridge the gap between organic and inorganic chemistry are comparatively studied on the grounds of static DFT and Car-Parrinello molecular dynamics simulations. The BN/CC butanes CH3 CH2 BH2 NH3 , BH3 CH2 NH2 CH3 , and NH3 CH2 BH2 CH3 were considered and compared with their isoelectronic counterparts NH3 BH2 NH2 BH3 and CH3 CH2 CH2 CH3 . In addition, systematical replacement of the NH2 BH2 fragment by the isoelectronic CH2 CH2 moiety is studied in the molecules H3 N(NH2 BH2 )3-m (CH2 CH2 )m BH3 (for m=0, 1, 2, or 3) and H3 N(NH2 BH2 )2-m (CH2 CH2 )m BH3 (for m=0, 1, or 2). The DFT and Car-Parrinello simulations show that the isosteres of the BN/CC butanes CH3 CH2 BH2 NH3 , BH3 CH2 NH2 CH3 , and NH3 CH2 BH2 CH3 and of larger oligomers of the type (BN)k (CC)l where k≥l are stable compounds. The BN/CC butane H3 NCH2 CH2 BH3 spontaneously produces molecular hydrogen at room temperature. The reaction, prompted by very strong dihydrogen bonding NH⋅⋅⋅HB, undergoes through the neutral, hypervalent, pentacoordinated boron dihydrogen complex RBH2 (H2 ) [R=(CH2 CH2 )n NH2 ]. The calculations suggest that such intermediate and the other BN/CC butanes CH3 CH2 BH2 NH3 , BH3 CH2 NH2 CH3 , and NH3 CH2 BH2 CH3 as well as larger BN/CC oligomers are viable experimentally. A simple recipe for the synthesis of CH3 CH2 BH2 NH3 is proposed. The strength of the dihydrogen bonding appeared to be crucial for the overall stability of the saturated BN/CC derivatives.

  3. Genome sequence of the soil bacterium Saccharomonospora azurea type strain (NA-128T)

    SciTech Connect

    Klenk, Hans-Peter; Held, Brittany; Lucas, Susan; Lapidus, Alla L.; Copeland, A; Hammon, Nancy; Pitluck, Sam; Goodwin, Lynne A.; Han, Cliff; Tapia, Roxanne; Brambilla, Evelyne-Marie; Potter, Gabriele; Land, Miriam L; Ivanova, N; Rohde, Manfred; Goker, Markus; Detter, J. Chris; Kyrpides, Nikos C; Woyke, Tanja

    2012-01-01

    Saccharomonospora azurea Runmao et al. 1987 is a member to the genomically so far poorly characterized genus Saccharomonospora in the family Pseudonocardiaceae. Members of the genus Sacharomonosoras are of interest because they originate from diverse habitats, such as leaf litter, manure, compost, surface of peat, moist and over-heated grain, where they might play a role in the primary degradation of plant material by attacking hemicellulose. They are Gram-negative staining organisms classified among the usually Gram-positive actinomycetes. Next to S. viridis, S. azurea is only the second member in the genus Saccharomonospora for with a completely sequenced type strain genome will be published. Here we describe the features of this organism, together with the complete genome sequence with project status 'permanent draft', and annotation. The 4,763,832 bp long chromosome with its 4,472 protein-coding and 58 RNA genes was sequenced as part of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome Institute (JGI).

  4. Genome sequence of the chemoheterotrophic soil bacterium Saccharomonospora cyanea type strain (NA-134(T))

    SciTech Connect

    Meier-Kolthoff, Jan P.; Lu, Megan; Huntemann, Marcel; Lucas, Susan; Lapidus, Alla L.; Copeland, A; Pitluck, Sam; Goodwin, Lynne A.; Han, Cliff; Tapia, Roxanne; Potter, Gabriele; Land, Miriam L; Ivanova, N; Rohde, Manfred; Goker, Markus; Detter, J. Chris; Woyke, Tanja; Kyrpides, Nikos C; Klenk, Hans-Peter

    2013-01-01

    Saccharomonospora cyanea Runmao et al. 1988 is a member of the genus Saccharomonospora in the family Pseudonocardiaceae that is moderately well characterized at the genome level thus far. Members of the genus Saccharomonospora are of interest because they originate from diverse habitats, such as soil, leaf litter, manure, compost, surface of peat, moist, over-heated grain, and ocean sediment, where they probably play a role in the primary degradation of plant material by attacking hemicellulose. Species of the genus Saccharomonospora are usually Gram-positive, non-acid fast, and are classified among the actinomycetes. S. cyanea is characterized by a dark blue (= cyan blue) aerial mycelium. After S. viridis, S. azurea, and S. marina, S. cyanea is only the fourth member in the genus for which a completely sequenced (non-contiguous finished draft status) type strain genome will be published. Here we describe the features of this organism, together with the draft genome sequence, and annotation. The 5,408,301 bp long chromosome with its 5,139 protein-coding and 57 RNA genes was sequenced as part of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome Institute (JGI).

  5. Genome sequence of the chemoheterotrophic soil bacterium Saccharomonospora cyanea type strain (NA-134T)

    PubMed Central

    Meier-Kolthoff, Jan P.; Lu, Megan; Huntemann, Marcel; Lucas, Susan; Lapidus, Alla; Copeland, Alex; Pitluck, Sam; Goodwin, Lynne A.; Han, Cliff; Tapia, Roxanne; Pötter, Gabriele; Land, Miriam; Ivanova, Natalia; Rohde, Manfred; Göker, Markus; Detter, John C.; Woyke, Tanja; Kyrpides, Nikos C.; Klenk, Hans-Peter

    2013-01-01

    Saccharomonospora cyanea Runmao et al. 1988 is a member of the genus Saccharomonospora in the family Pseudonocardiaceae that is moderately well characterized at the genome level thus far. Members of the genus Saccharomonospora are of interest because they originate from diverse habitats, such as soil, leaf litter, manure, compost, surface of peat, moist, over-heated grain, and ocean sediment, where they probably play a role in the primary degradation of plant material by attacking hemicellulose. Species of the genus Saccharomonospora are usually Gram-positive, non-acid fast, and are classified among the actinomycetes. S. cyanea is characterized by a dark blue (= cyan blue) aerial mycelium. After S. viridis, S. azurea, and S. marina, S. cyanea is only the fourth member in the genus for which a completely sequenced (non-contiguous finished draft status) type strain genome will be published. Here we describe the features of this organism, together with the draft genome sequence, and annotation. The 5,408,301 bp long chromosome with its 5,139 protein-coding and 57 RNA genes was sequenced as part of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome Institute (JGI). PMID:24501643

  6. Antiferromagnetism and hidden order in isoelectronic doping of URu2Si2

    DOE PAGESBeta

    Wilson, Murray N.; Williams, Travis J.; Cai, Yipeng; Hallas, Alannah M.; Medina, Teresa; Munsie, Timothy J.; Cheung, Sky C.; Frandsen, Benjamin A.; Liu, Lian; Uemura, Yasutomo J.; et al

    2016-02-01

    In this paper, we present muon spin rotation (mu SR) and susceptibility measurements on single crystals of isoelectronically doped URu2-xTxSi2 (T = Fe, Os) for doping levels up to 50%. Zero field (ZF) μ SR measurements show long-lived oscillations demonstrating that an antiferromagnetic state exists down to low doping levels for both Os and Fe dopants. The measurements further show an increase in the internal field with doping for both Fe and Os. Comparison of the local moment-hybridization crossover temperature from susceptibility measurements and our magnetic transition temperature shows that changes in hybridization, rather than solely chemical pressure, are importantmore » in driving the evolution of magnetic order with doping.« less

  7. Isoelectronic tungsten doping in monolayer MoSe2 for carrier type modulation

    DOE PAGESBeta

    Li, Xufan; Lin, Ming -Wei; Basile, Leonardo; Hus, Saban M.; Puretzky, Alexander A.; Lee, Jaekwang; Kuo, Yen -Chien; Chang, Lo -Yueh; Wang, Kai; Idrobo, Juan C.; et al

    2016-07-06

    Doping and alloying are effective ways to engineer the band structure and modulate the optoelectronic functionality of monolayer transition metal dichalcogenides (TMDs). In this work, we explore the synthesis and electronic properties of monolayer Mo1-xWxSe2 (0 < x < 0.18) alloys with almost 100% alloying degree. The isoelectronic substitutional doping of tungsten for molybdenum in the monolayer MoSe2 is shown to suppress its intrinsically n-type conduction behavior, with p-type conduction gradually emerging to become dominant with increasing W concentration in the alloys. Atomic resolution Z-contrast electron microscopy show that W is shown to substitute directly for Mo without the introductionmore » of noticeable vacancy or interstitial defects, however with randomly-distributed W-rich regions ~2 nm in diameter. Scanning tunneling microscopy/spectroscopy measurements reveal that these W-rich regions exhibit a local band structure with the valence band maximum (VBM) closer to the Fermi level as compared with the Mo-rich regions in the monolayer Mo1-xWxSe2 crystal. These localized upshifts of the VBM in the local band structure appear responsible for the overall p-type behavior observed for the monolayer Mo1-xWxSe2 crystals. Stacked monolayers of n-type MoSe2 and p-type Mo1-xWxSe2 were demonstrated to form atomically thin, vertically stacked p n homojunctions with gate-tunable characteristics, which appear useful for future optoelectronic applications. Lastly, these results indicate that alloying with isoelectronic dopant atoms appears to be an effective and advantageous alternate strategy to doping or alloying with electron donors or acceptors in two-dimensional TMDs.« less

  8. Encoding and recall of finger sequences in experienced pianists compared with musically naïve controls: a combined behavioral and functional imaging study.

    PubMed

    Pau, S; Jahn, G; Sakreida, K; Domin, M; Lotze, M

    2013-01-01

    Long-term intensive sensorimotor training alters functional representation of the motor and sensory system and might even result in structural changes. However, there is not much knowledge about how previous training impacts learning transfer and functional representation. We tested 14 amateur pianists and 15 musically naïve participants in a short-term finger sequence training procedure, differing considerably from piano playing and measured associated functional representation with functional magnetic resonance imaging. The conditions consisted of encoding a finger sequence indicated by hand symbols ("sequence encoding") and subsequently replaying the sequence from memory, both with and without auditory feedback ("sequence retrieval"). Piano players activated motor areas and the mirror neuron system more strongly than musically naïve participants during encoding. When retrieving the sequence, musically naïve participants showed higher activation in similar brain areas. Thus, retrieval activations of naïve participants were comparable to encoding activations of piano players, who during retrieval performed the sequences more accurately despite lower motor activations. Interestingly, both groups showed primary auditory activation even during sequence retrieval without auditory feedback, supporting previous reports about coactivation of the auditory cortex after learned association with motor performance. When playing with auditory feedback, only pianists lateralized to the left auditory cortex. During encoding activation in left primary somatosensory cortex in the height of the finger representations had a predictive value for increased motor performance later on (error rates). Contrarily, decreased performance was associated with increased visual cortex activation during encoding. Our study extends previous reports about training transfer of motor knowledge resulting in superior training effects in musicians. Performance increase went along with activity in

  9. Sequence conservation in the Ancylostoma secreted protein-2 of Necator americanus (Na-ASP-2) from hookworm infected individuals in Thailand.

    PubMed

    Ungcharoensuk, Charoenchai; Putaporntip, Chaturong; Pattanawong, Urassaya; Jongwutiwes, Somchai

    2012-12-01

    The Ancylostoma secreted protein-2 of Necator americanus (Na-ASP-2) was one of the promising vaccine candidates against the most prevalent human hookworm species as adverse vaccine reaction has compromised further human vaccine trials. To elucidate the gene structure and the extent of sequence diversity, we determined the complete nucleotide sequence of the Na-asp-2 gene of individual larvae from 32 infected subjects living in 3 different endemic areas of Thailand. Sequence analysis revealed that the gene encoding Na-ASP-2 comprised 8 exons. Of 3 nucleotide substitutions in these exons, only one causes an amino acid change from leucine to methionine. A consensus conserved GT and AG at the 5' and the 3' boundaries of each intron was observed akin to those found in other eukaryotic genes. Introns of Na-asp-2 contained 23 nucleotide substitutions and 0-18 indels. The mean number of nucleotide substitutions per site (d) in introns was not significantly different from the mean number of synonymous substitutions per synonymous site (d(S)) in exons whereas d in introns was significantly exceeded d(N) (the mean number of nonsynonymous substitutions per nonsynonymous site) in exons (p<0.05), suggesting that introns and synonymous sites in exons may evolve at a similar rate whereas functional constraints at the amino acid could limit amino acid substitutions in Na-ASP-2. A recombination site was identified in an intron near the 3' portion of the gene. The positions of introns and the intron phases in the Na-asp-2 gene comparing with those in other pathogenesis-related-1 proteins of Loa loa, Onchocerca volvulus, Heterodera glycines, Caenorhabditis elegans and human were relatively conserved, suggesting evolutionary conservation of these genes. Sequence conservation in Na-ASP-2 may not compromise further vaccine design if adverse vaccine effects could be resolved whereas microheterogeneity in introns of this locus may be useful for population genetics analysis of N. americanus

  10. Sequence conservation in the Ancylostoma secreted protein-2 of Necator americanus (Na-ASP-2) from hookworm infected individuals in Thailand.

    PubMed

    Ungcharoensuk, Charoenchai; Putaporntip, Chaturong; Pattanawong, Urassaya; Jongwutiwes, Somchai

    2012-12-01

    The Ancylostoma secreted protein-2 of Necator americanus (Na-ASP-2) was one of the promising vaccine candidates against the most prevalent human hookworm species as adverse vaccine reaction has compromised further human vaccine trials. To elucidate the gene structure and the extent of sequence diversity, we determined the complete nucleotide sequence of the Na-asp-2 gene of individual larvae from 32 infected subjects living in 3 different endemic areas of Thailand. Sequence analysis revealed that the gene encoding Na-ASP-2 comprised 8 exons. Of 3 nucleotide substitutions in these exons, only one causes an amino acid change from leucine to methionine. A consensus conserved GT and AG at the 5' and the 3' boundaries of each intron was observed akin to those found in other eukaryotic genes. Introns of Na-asp-2 contained 23 nucleotide substitutions and 0-18 indels. The mean number of nucleotide substitutions per site (d) in introns was not significantly different from the mean number of synonymous substitutions per synonymous site (d(S)) in exons whereas d in introns was significantly exceeded d(N) (the mean number of nonsynonymous substitutions per nonsynonymous site) in exons (p<0.05), suggesting that introns and synonymous sites in exons may evolve at a similar rate whereas functional constraints at the amino acid could limit amino acid substitutions in Na-ASP-2. A recombination site was identified in an intron near the 3' portion of the gene. The positions of introns and the intron phases in the Na-asp-2 gene comparing with those in other pathogenesis-related-1 proteins of Loa loa, Onchocerca volvulus, Heterodera glycines, Caenorhabditis elegans and human were relatively conserved, suggesting evolutionary conservation of these genes. Sequence conservation in Na-ASP-2 may not compromise further vaccine design if adverse vaccine effects could be resolved whereas microheterogeneity in introns of this locus may be useful for population genetics analysis of N. americanus.

  11. Dynamics of excitons bound to nitrogen isoelectronic centers in GaAs

    NASA Astrophysics Data System (ADS)

    St-Jean, P.; Éthier-Majcher, G.; Francoeur, S.

    2015-03-01

    A detailed analysis of the dynamics of excitons bound to two nitrogen atoms forming an isoelectronic center of C2 v symmetry in GaAs is presented. The temperature dependence of photoluminescence (PL) intensities under both continuous and pulsed excitations reveals (1) overall decay rates significantly slower than that of spontaneous emission, (2) a decay rate anisotropy between states of orthogonal symmetry representations, and (3) a complementary behavior of relative intensities measured from states of identical symmetry representations. A comprehensive model of the exciton fine structure and the exciton dynamics allows the determination of the strength of the exchange and crystal-field interactions, the light- and heavy-hole splitting and composition of exciton states, the exciton capture time, the rates of spontaneous and nonradiative emission, and the rates of interlevel transfers induced by interactions with nuclear spins and by longitudinal acoustic phonons. It is found that the rate of electron spin flips is comparable to that measured in quantum dots but that the near degeneracy of light and heavy holes results in an efficient transfer channel between light- and heavy-hole states of identical symmetry representation.

  12. Stability and electronic structures of isoelectronic impurity complexes in Si: First-principles study

    NASA Astrophysics Data System (ADS)

    Iizuka, Shota; Nakayama, Takashi

    2016-10-01

    The stability and electronic structures of various isoelectronic cation+anion pairs in Si were studied by first-principles calculations. It was shown that the nearest-neighboring substitutional configuration is the most stable structure for most cation+anion pairs, while B+N, Mg+O, and Be+O pairs preferentially occupy a single Si site owing to the small atomic radii of B, N, and O atoms. We found that only Al+N, Ga+N, and In+N pairs produce electron-unoccupied weakly localized states in the band gap of Si, reflecting the large negativity of N atoms. We also showed that single N doping produces N+N pairs and that such pairs induce no electronic states in the band gap of Si. Therefore, the codoping of Al and N atoms is essential to produce an electronic state in the Si band gap and increase the tunneling current in Si tunneling field-effect transistors.

  13. Chemical pressure tuning of URu2 Si2 via isoelectronic substitution of Ru with Fe

    NASA Astrophysics Data System (ADS)

    Janoschek, Marc; Das, Pinaki; Kanchanavatee, Noravee; Helton, Joel S.; Huang, Kevin; Baumbach, Ryan E.; Bauer, Eric D.; Zhao, Yang; Ratcliff, William; White, Ben D.; Maple, M. Brian; Lynn, Jeff W.

    2015-03-01

    We have used specific heat and neutron diffraction measurements on single crystals of URu2-xFexSi2 for Fe concentrations x <= 0.7 to establish that isoelectronic substitution of Ru with Fe acts as ``chemical pressure'' Pch. Neutron diffraction reveals a sharp increase of the uranium magnetic moment at x = 0 . 1 , reminiscent of the ``hidden order'' (HO) to large moment antiferromagnetic (LMAFM) phase transition in URu2Si2. Using the unit cell volume, and the isothermal compressibility κT for URu2Si2, we determine Pch as function of x. The resulting temperature T-chemical pressure Pch phase diagram for URu2-xFexSi2 is in good agreement with the established temperature T-external pressure P phase diagram of URu2Si2. Thus, URu2-xFexSi2 provides a new opportunity to study the close relationship between the HO and LMAFM phases with methods that cannot be used under pressure, and may shed some new light on the on the elusive order parameter of the HO.

  14. Magneto-optical properties and recombination dynamics of isoelectronic bound excitons in ZnO

    SciTech Connect

    Chen, S. L.; Chen, W. M.; Buyanova, I. A.

    2014-02-21

    Magneto-optical and time-resolved photoluminescence (PL) spectroscopies are employed to evaluate electronic structure of a bound exciton (BX) responsible for the 3.364 eV line (labeled as I{sub 1}{sup *}) in bulk ZnO. From time-resolved PL spectroscopy, I{sub 1}{sup *} is concluded to originate from the exciton ground state. Based on performed magneto-PL studies, the g-factors of the involved electron and hole are determined as being g{sub e} = 1.98 and g{sub h}{sup ∥}(g{sub h}{sup ⊥}) = 1.2(1.62), respectively. These values are nearly identical to the reported g-factors for the I{sup *} line in ZnO (Phys. Rev. B 86, 235205 (2012)), which proves that I{sub 1}{sup *} should have a similar origin as I{sup *} and should arise from an exciton bound to an isoelectronic center with a hole-attractive potential.

  15. First-Principles Design of Hydrogen Dissociation Catalysts Based on Isoelectronic Metal Solid Solutions.

    PubMed

    Seo, Dong-Hwa; Shin, Hyeyoung; Kang, Kisuk; Kim, Hyungjun; Han, Sang Soo

    2014-06-01

    We report an innovative route for designing novel functional alloys based on first-principles calculations, which is an isoelectronic solid solution (ISS) of two metal elements to create new characteristics that are not native to the constituent elements. Neither Rh nor Ag exhibits hydrogen storage properties, whereas the Rh50Ag50 ISS exhibits properties similar to Pd; furthermore, Au cannot dissociate H2, and Ir has a higher energy barrier for the H2 dissociation reaction than Pt, whereas the Ir50Au50 ISS can dissociate H2 in a similar way to Pt. In the periodic table, Pd is located between Rh and Ag, and Pt is located between Ir and Au, leading to similar atomic and electronic structures between the pure metals (Pd and Pt) and the ISS alloys (Rh50Ag50 and Ir50Au50). From a practical perspective, the Ir-Au ISS would be more cost-effective to use than pure Pt, and could exhibit catalytic activity equivalent to Pt. Therefore, the Ir50Au50 ISS alloy can be a potential catalyst candidate for the replacement of Pt. PMID:26273859

  16. Different Variants in Reverse Transcriptase Domain Determined by Ultra-deep Sequencing in Treatment-naïve and Treated Indonesian Patients Infected with Hepatitis B Virus.

    PubMed

    Wasityastuti, Widya; Yano, Yoshihiko; Widasari, Dewiyani Indah; Yamani, Laura Navika; Ratnasari, Neneng; Heriyanto, Didik Setyo; Okada, Rina; Tanahashi, Toshihito; Murakami, Yoshiki; Azuma, Takeshi; Hayashi, Yoshitake

    2016-01-01

    A nucleos(t)ide analog (NA) is the common antiviral drug available for directly treating hepatitis B virus (HBV) infection. However, its application has led to the emergence of NA-resistant mutations mostly in a conserved region of the reverse transcriptase domain of HBV polymerase. Harboring NA-resistant mutations decreases drug effectiveness and increases the frequency of end-stage liver disease. The invention of next-generation sequencing that can generate thousands of sequences from viral complex mixtures provides opportunities to detect minor changes and early viral evolution under drug stress. The present study used ultra-deep sequencing to evaluate discrepant quasispecies in the reverse transcriptase domain of HBV including NA-resistant hotspots between seven treatment-naïve Indonesian patients infected with HBV and five at the early phase of treatment. The most common sub-genotype was HBV B3 (83.34%). The substitution rate of variants determined among amino acids with a ratio of ≥ 1% changes was higher among the population in conserved regions (23.19% vs. 4.59%, P = 0.001) and in the inter-reverse transcriptase domain (23.95% vs. 2.94%, P = 0.002) in treatment naïve, than in treated patients. Nine hotspots of antiviral resistance were identified in both groups, and the mean frequency of changes in all patients was < 1%. The known rtM204I mutation was the most frequent in both groups. The lower rate of variants in HBV quasispecies in patients undergoing treatment could be associated with virus elimination and the extinction of sensitive species by NA therapy. The present findings imply that HBV quasispecies dynamically change during treatment. PMID:27492206

  17. R-matrix calculations along sequences: photoionization and electron-impact excitation

    SciTech Connect

    Witthoeft, M. C.

    2009-09-10

    As computer power continues to increase, so does our ability to carry out extensive, non-perturbative calculations of atomic processes. Much work has been done on increasing the target representation of complex systems in step with advances in computational power. However there is also a need for coverage in terms of atomic data used in astrophysical or fusion plasma modeling. In this talk, we discuss recent R-matrix calculations of electron-impact excitation and photoionization over iso-electronic sequences. While automation of R-matrix codes and data analysis are reviewed, the talk is focused on iso-electronic trends observed in the data. Specifically, we show the effect that resonant enhancement and level mixing can have on expected iso-electronic trends.

  18. Optical properties of ZnS1-xSex alloys fabricated by plasma-induced isoelectronic substitution

    NASA Astrophysics Data System (ADS)

    Rujkorakarn, Rong; Nelson, Art J.

    2000-06-01

    Nonequilibrium growth of thin-film ternary ZnS1-xSex semiconductor alloys was accomplished using physical vapor deposition with simultaneous electron cyclotron resonance H2S plasma activation. Substrate temperature, gas flow, and plasma power determine the ZnS1-xSex alloy composition and structure. Integrated optical transmission spectra for the ZnS1-xSex semiconductor alloys as a function of H2S plasma power are presented. Using the α2 vs hν plots for the various ZnS1-xSex films, the optical band gap Eg is extrapolated from each curve. This methodology yields the values of the band gap as a function of stoichiometry. We observe that the plasma induced isoelectronic substitution of S into the ZnSe lattice increases the band gap. This study shows that plasma-induced isoelectronic substitution is technologically feasible and useful for fabricating ternary II-VI alloys under nonequilibrium conditions.

  19. Individual iso-electronic N and Bi centers in GaAs studied by Scanning Tunneling Microscopy

    NASA Astrophysics Data System (ADS)

    Koenraad, Paul; Krammel, Christian; Plantenga, Rianne; Kortan, Victoria; Flatté, Michael; Tilley, Freddy; Roy, Mervin; Maksym, Peter; Kita, Takashi

    Nitrogen and bismuth iso-electronic doping centers in GaAs have received considerable interest in the last few years due to their peculiar behaviour in dilute nitrides and bismides. In these materials effects such as a strong band bowing and the formation of resonant states in respectively the conduction and valence band have been reported. In this contribution we will report our exploration of individual nitrogen and bismuth atoms in the outermost layers of a freshly cleaved (110) GaAs surface by STM. Depending on the tunnel conditions we are able to either visualise the lattice distortion or image the charge distribution of the resonant state. We clearly observe that nitrogen pulls its neighbouring atoms inwards whereas bismuth pushes its neighbouring atoms away. A straightforward geometrical model based on the covalent radii of the dopants and substrate atoms is used to interpret the observed crystal deformation seen in our STM images of nitrogen and bismuth under the appropriate tunnel conditions. At small positive voltages we could observe the charge distribution of the resonant state induced by iso-electronic nitrogen atoms in GaAs. Tight Binding Modelling (TBM) was used to explain the observed strongly anisotropic charge distribution.

  20. Probing Collins conjecture with correlation energies and entanglement entropies for the ground state of the helium isoelectronic sequence

    NASA Astrophysics Data System (ADS)

    Ho, Yew Kam; Lin, Yen-Chang

    2016-05-01

    Correlation energy of a quantum system is defined as the difference between its exact energy Eex, and its Hartree-Fock energy EHF. In a recent related development, entanglement measures can be quantified with von Neumann entropy SvN(ρ) = - Tr(ρlog2 ρ) or linear entropy SL(ρ) = 1 - Tr(ρ2) , where ρ is the one-particle reduced density matrix, and Tr(ρ2) is defined as the purity of state. In the present work we calculate SL and SvN for the ground 1s21 S states in helium-like ions for Z = 2 to 15, using configuration interaction (CI) with B-Spline basis up to about 6000 terms to construct the wave functions, and with which density matrix, linear and von Neumann entropies are calculated. We have found close relationship between the reduced correlation energy, defined as Ecorr = (ECI- EHF) /ECI (with ECI being our calculated energy), and SL or SvN. Our results support Collins conjecture that there is a linear relationship between correlation energy and entanglement entropy, i.e., Ecorr = CS, where C is called Collins constant. Using the calculated ground state energies for Z = 2 to Z = 15, and the entanglement measured with linear entropy SL for such states, C is determined as 0.90716. At the meeting, we will present result for Collins constant determined from von Neumann entropy, and details of our calculations. This work was supported by the MOST in Taiwan.

  1. Theoretical energies for the n = 1 and 2 states of the helium isoelectronic sequence up to Z = 100

    NASA Technical Reports Server (NTRS)

    Drake, G. W.

    1988-01-01

    The unified method described previously for combining high-precision nonrelativistic variational calculations with relativistic and quantum electrodynamic corrections is applied to the 1s2 1S0, 1s2s 1S0, 1s2s 1S0, 1s2s 3S1, 1s2p 1P1, and 1s2p 3P(0.1,2) states of helium-like ions. Detailed tabulations are presented for all ions in the range Z = 2-100 and are compared with a wide range of experimental data up to (Kr-34)+. The results for (U-90)+ significantly alter the recent Lamb shift measurement of Munger and Gould (1986) from 70.4 + or - 8.3 to 71.0 + or - 8.3 eV, in comparison with a revised theoretical value of 74.3 + or - 0.4 eV. The improved agreement is due to the inclusion of higher order two-electron corrections in the present work.

  2. Rapid and accurate taxonomic classification of insect (class Insecta) cytochrome c oxidase subunit 1 (COI) DNA barcode sequences using a naïve Bayesian classifier

    PubMed Central

    Porter, Teresita M; Gibson, Joel F; Shokralla, Shadi; Baird, Donald J; Golding, G Brian; Hajibabaei, Mehrdad

    2014-01-01

    Current methods to identify unknown insect (class Insecta) cytochrome c oxidase (COI barcode) sequences often rely on thresholds of distances that can be difficult to define, sequence similarity cut-offs, or monophyly. Some of the most commonly used metagenomic classification methods do not provide a measure of confidence for the taxonomic assignments they provide. The aim of this study was to use a naïve Bayesian classifier (Wang et al. Applied and Environmental Microbiology, 2007; 73: 5261) to automate taxonomic assignments for large batches of insect COI sequences such as data obtained from high-throughput environmental sequencing. This method provides rank-flexible taxonomic assignments with an associated bootstrap support value, and it is faster than the blast-based methods commonly used in environmental sequence surveys. We have developed and rigorously tested the performance of three different training sets using leave-one-out cross-validation, two field data sets, and targeted testing of Lepidoptera, Diptera and Mantodea sequences obtained from the Barcode of Life Data system. We found that type I error rates, incorrect taxonomic assignments with a high bootstrap support, were already relatively low but could be lowered further by ensuring that all query taxa are actually present in the reference database. Choosing bootstrap support cut-offs according to query length and summarizing taxonomic assignments to more inclusive ranks can also help to reduce error while retaining the maximum number of assignments. Additionally, we highlight gaps in the taxonomic and geographic representation of insects in public sequence databases that will require further work by taxonomists to improve the quality of assignments generated using any method.

  3. Habit learning by naïve macaques is marked by response sharpening of striatal neurons representing the cost and outcome of acquired action sequences

    PubMed Central

    Desrochers, Theresa M.; Amemori, Ken-ichi; Graybiel, Ann M.

    2015-01-01

    SUMMARY Over a century of scientific work has focused on defining the factors motivating behavioral learning. Observations in animals and humans trained on a wide range of tasks support reinforcement learning (RL) algorithms as accounting for the learning. Still unknown, however, are the signals that drive learning in naïve, untrained subjects. Here, we capitalized on a sequential saccade task in which macaque monkeys acquired repetitive scanning sequences without instruction. We found that spike activity in the caudate nucleus after each trial corresponded to an integrated cost-benefit signal that was highly correlated with the degree of naturalistic untutored learning by the monkeys. Across learning, neurons encoding both cost and outcome gradually acquired increasingly sharp phasic trial-end responses that paralleled the development of the habit-like, repetitive saccade sequences. Our findings demonstrate a novel integrated cost-benefit signal by which RL and its neural correlates could drive naturalistic behaviors in freely behaving primates. PMID:26291166

  4. Divergent Coupling of Alcohols and Amines Catalyzed by Isoelectronic Hydride Mn(I) and Fe(II) PNP Pincer Complexes.

    PubMed

    Mastalir, Matthias; Glatz, Mathias; Gorgas, Nikolaus; Stöger, Berthold; Pittenauer, Ernst; Allmaier, Günter; Veiros, Luis F; Kirchner, Karl

    2016-08-22

    Herein, we describe an efficient coupling of alcohols and amines catalyzed by well-defined isoelectronic hydride Mn(I) and Fe(II) complexes, which are stabilized by a PNP ligand based on the 2,6-diaminopyridine scaffold. This reaction is an environmentally benign process implementing inexpensive, earth-abundant non-precious metal catalysts, and is based on the acceptorless alcohol dehydrogenation concept. A range of alcohols and amines including both aromatic and aliphatic substrates were efficiently converted in good to excellent isolated yields. Although in the case of Mn selectively imines were obtained, with Fe-exclusively monoalkylated amines were formed. These reactions proceed under base-free conditions and required the addition of molecular sieves. PMID:27377955

  5. High-Fidelity and Ultrafast Initialization of a Hole Spin Bound to a Te Isoelectronic Center in ZnSe

    NASA Astrophysics Data System (ADS)

    St-Jean, P.; Éthier-Majcher, G.; André, R.; Francoeur, S.

    2016-10-01

    We demonstrate the optical initialization of a hole-spin qubit bound to an isoelectronic center (IC) formed by a pair of Te impurities in ZnSe, an impurity-host system providing high optical homogeneity, large electric dipole moments, and potentially advantageous coherence times. The initialization scheme is based on the spin-preserving tunneling of a resonantly excited donor-bound exciton to a positively charged Te IC, thus forming a positive trion. The radiative decay of the trion within less than 50 ps leaves a heavy hole in a well-defined polarization-controlled spin state. The initialization fidelity exceeds 98.5% for an initialization time of less than 150 ps.

  6. Time-resolved photoluminescence of type-II quantum dots and isoelectronic centers in Zn-Se-Te superlattice structures

    NASA Astrophysics Data System (ADS)

    Cheung, M. C.-K.; Cartwright, A. N.; Sellers, I. R.; McCombe, B. D.; Kuskovsky, I. L.

    2008-01-01

    Spectrally and time-resolved photoluminescence of a ZnTe /ZnSe superlattice reveals a smooth transition of the photoluminescence (PL) lifetime from ˜100ns at 2.35eV to less than a few nanoseconds at 2.8eV. The significant increase of the lifetime in the low energy region is strong evidence to support the formation of type-II quantum dots (QDs), since in these nanostructures the spatial separation of carriers is increased. The shorter lived emission above 2.5eV is attributed to excitons bound to Te isoelectronic centers in the ZnSe matrix. The smooth transition of the PL lifetime confirms that clusters of these Te atoms evolve into type-II ZnTe /ZnSe QDs.

  7. Effect of isoelectronic doping on the honeycomb-lattice iridate A2IrO3

    NASA Astrophysics Data System (ADS)

    Manni, S.; Choi, Sungkyun; Mazin, I. I.; Coldea, R.; Altmeyer, Michaela; Jeschke, Harald O.; Valentí, Roser; Gegenwart, P.

    2014-06-01

    We have investigated, experimentally and theoretically, the series (Na1-xLix)2IrO3. Contrary to what has been believed so far, only for x ≤0.25 does the system form uniform solid solutions where Li preferentially goes to the Ir2Na planes, as observed in our density functional theory calculations and consistent with x-ray diffraction analysis. For larger Li content, as evidenced by powder x-ray diffraction, scanning electron microscopy, and density functional theory calculations, the system shows a miscibility gap and a phase separation into an ordered Na3LiIr2O6 phase with alternating Na3 and LiIr2O6 planes, and a Li-rich phase close to pure Li2IrO3. For x ≤0.25 we observe (1) an increase of c /a with Li doping up to x =0.25, despite the fact that c /a in pure Li2IrO3 is smaller than in Na2IrO3, and (2) a gradual reduction of the antiferromagnetic ordering temperature TN and ordered moment. In view of our results showing clear evidence for phase separation for 0.25≤x≤0.6, more detailed studies are needed to confirm the presence or absence of phase separation at the higher doping x ˜0.7, where a continuum quantum phase transition has been proposed previously.

  8. Cationic terminal gallylene complexes by halide abstraction: coordination chemistry of a valence isoelectronic analogue of CO and N2.

    PubMed

    Coombs, Natalie D; Vidovic, Dragoslav; Day, Joanna K; Thompson, Amber L; Le Pevelen, Delphine D; Stasch, Andreas; Clegg, William; Russo, Luca; Male, Louise; Hursthouse, Michael B; Willock, David J; Aldridge, Simon

    2008-11-26

    While N(2) and CO have played central roles in developing models of electronic structure, and their interactions with transition metals have been widely investigated, the valence isoelectronic diatomic molecules EX (E = group 13 element, X = group 17 element) have yet to be isolated under ambient conditions, either as the "free" molecule or as a ligand in a simple metal complex. As part of a program designed to address this deficiency, together with wider issues of the chemistry of cationic systems [L(n)M(ER)](+) (E = B, Al, Ga; R = aryl, amido, halide), we have targeted complexes of the type [L(n)M(GaX)](+). Halide abstraction is shown to be a viable method for the generation of mononuclear cationic complexes containing gallium donor ligands. The ability to isolate tractable two-coordinate products, however, is strongly dependent on the steric and electronic properties of the metal/ligand fragment. In the case of complexes containing ancillary pi-acceptor ligands such as CO, cationic complexes can only be isolated as base-trapped adducts, even with bulky aryl substituents at gallium. Base-free gallylene species such as [Cp*Fe(CO)(2)(GaMes)](+) can be identified only in the vapor phase by electrospray mass spectrometry experiments. With bis(phosphine) donor sets at the metal, the more favorable steric/electronic environment allows for the isolation of two-coordinate ligand systems, even with halide substituents at gallium. Thus, [Cp*Fe(dppe)(GaI)](+)[BAr(f)(4)](-) (9) can be synthesized and shown crystallographically to feature a terminally bound GaI ligand; 9 represents the first experimental realization of a complex containing a valence isoelectronic group 13/group 17 analogue of CO and N(2). DFT calculations reveal a relatively weakly bound GaI ligand, which is confirmed experimentally by the reaction of 9 with CO to give [Cp*Fe(dppe)(CO)](+)[BAr(f)(4)](-). In the absence of such reagents, 9 is stable for weeks in fluorobenzene solution, presumably reflecting (i

  9. Thermochemical considerations and bond enthalpy ratios involving triatomic 16-valence electron neutrals and ions and some isoelectronically related pentaatomics

    NASA Astrophysics Data System (ADS)

    Deakyne, Carol A.; Norton, Lisa K.; Abele, Ashley M.; Ludden, Alicia K.; Liebman, Joel F.

    2007-11-01

    Following thermochemical studies and the accompanying analysis in the calorimetric literature, in earlier computational and conceptual studies we investigated the systematics of the mean bond enthalpy ratio /Dm°(XY) for 16-valence electron neutral and ionic triatomic species. For neutral species wherein X is a group 14 element and Y is from group 16, the ratio was ca. 0.8 rising to ca. 0.9 for the corresponding anions with X from group 13, and falling to ca. 0.7 for the cations with X from group 15. Good agreement between theory and experiment was found where admittedly the majority of the data for the latter is for the neutral species. In the current study at the G2 computational level (and G3 for selected systems), the related asymmetric valence isoelectronic triatomic species YXZ are discussed and this pattern calculationally preserved. The results are in concurrence with the one experimentally available datum for comparison, namely from the literature measured value for the enthalpy of formation of OCS. Other surprises and systematics are discussed as well for what otherwise might have been superficially considered to be simple species, for these and related pentaatomic species of the type HYXYH.

  10. Energy density functionals from the strong-coupling limit applied to the anions of the He isoelectronic series

    SciTech Connect

    Mirtschink, André; Gori-Giorgi, Paola; Umrigar, C. J.; Morgan, John D.

    2014-05-14

    Anions and radicals are important for many applications including environmental chemistry, semiconductors, and charge transfer, but are poorly described by the available approximate energy density functionals. Here we test an approximate exchange-correlation functional based on the exact strong-coupling limit of the Hohenberg-Kohn functional on the prototypical case of the He isoelectronic series with varying nuclear charge Z < 2, which includes weakly bound negative ions and a quantum phase transition at a critical value of Z, representing a big challenge for density functional theory. We use accurate wavefunction calculations to validate our results, comparing energies and Kohn-Sham potentials, thus also providing useful reference data close to and at the quantum phase transition. We show that our functional is able to bind H{sup −} and to capture in general the physics of loosely bound anions, with a tendency to strongly overbind that can be proven mathematically. We also include corrections based on the uniform electron gas which improve the results.

  11. Theory of hyperfine interactions in potassium and Sc2+sion:Trends in systems isoelectronic with potassium

    NASA Astrophysics Data System (ADS)

    Owusu, Alfred; Yuan, Xing; Panigrahy, S. N.; Dougherty, R. W.; Das, T. P.; Andriessen, J.

    1997-04-01

    A first-principles relativistic many-body investigation of magnetic hyperfine fields has been carried out for the ground states 4 2 S1/2 of the alkali atom K and doubly charged ion Sc2+ completing the investigation over the three members of the isoelectronic series K, Ca+ , and Sc2+ with a single valence electron in the 4s state, since Ca+ had been investigated by us previously. This allows one to study both the nature of agreement with experiment over this series as the charge increases and the trends in the contributions from the major mechanisms responsible for the hyperfine fields in these systems. The calculated magnetic hyperfine fields in tesla for K, Ca+ , and Sc2+ are 56.81, 135.90, and 239.29, respectively. These agree very well with the measured values of 58.02 T for K and 140.30 T for Ca+ . No experimental data are available for the Sc2+ system. The exchange core polarization (ECP) and correlation contributions, as fractions of the valence contribution, are found to decrease rapidly as one goes to systems with higher ionic charges, the decrease being more drastic for correlation effects. The trend of the ratios of ECP and correlation contributions to the valence contribution for both K and Sc2+ were compared with those calculated for the neighboring alkali-metal systems, sodium and rubidium. The physical explanations for the results and the observed trends in the contributions from the different mechanisms are discussed.

  12. How Does the Ionic Liquid Organizational Landscape Change when Nonpolar Cationic Alkyl Groups Are Replaced by Polar Isoelectronic Diethers?

    SciTech Connect

    Kashyap, Hemant K.; Santos, Cherry S.; Daly, Ryan P.; Hettige, Jeevapani J.; Murthy, N. Sanjeeva; Shirota, Hideaki; Edward W. Castner Jr.; Margulis, Claudio J.

    2012-12-21

    The X-ray scattering experiments and molecular dynamics simulations have been performed to investigate the structure of four room temperature ionic liquids (ILs) comprising the bis(trifluoromethylsulfonyl)amide (NTf2) anion paired with the triethyloctylammonium (N2228+) and triethyloctylphosphonium (P2228+) cations and their isoelectronic diether analogs, the (2-ethoxyethoxy)ethyltriethylammonium (N222(2O2O2)+) and (2-ethoxyethoxy)ethyltriethylphosphonium (P222(2O2O2)+) cations. Agreement between simulations and experiments is good and permits a clear interpretation of the important topological differences between these systems. The first sharp diffraction peak (or prepeak) in the structure function S(q) that is present in the case of the liquids containing the alkyl-substituted cations is absent in the case of the diether substituted analogs. Using different theoretical partitioning schemes for the X-ray structure function, we show that the prepeak present in the alkyl-substituted ILs arises from polarity alternations between charged groups and nonpolar alkyl tails. In the case of the diether substituted ILs, we find considerable curling of tails. Anions can be found with high probability in two different environments: close to the cationic nitrogen (phosphorus) and also close to the two ether groups. Moreover, for the two diether systems, anions are found in locations from which they are excluded in the alkyl-substituted systems. This removes the longer range (polar/nonpolar) pattern of alternation that gives rise to the prepeak in alkyl-substituted systems.

  13. Stereo-Selectivity of Human Serum Albumin to Enantiomeric and Isoelectronic Pollutants Dissected by Spectroscopy, Calorimetry and Bioinformatics

    PubMed Central

    Ahmad, Ejaz; Rabbani, Gulam; Zaidi, Nida; Singh, Saurabh; Rehan, Mohd; Khan, Mohd Moin; Rahman, Shah Kamranur; Quadri, Zainuddin; Shadab, Mohd.; Ashraf, Mohd Tashfeen; Subbarao, Naidu; Bhat, Rajiv; Khan, Rizwan Hasan

    2011-01-01

    1–naphthol (1N), 2–naphthol (2N) and 8–quinolinol (8H) are general water pollutants. 1N and 2N are the configurational enantiomers and 8H is isoelectronic to 1N and 2N. These pollutants when ingested are transported in the blood by proteins like human serum albumin (HSA). Binding of these pollutants to HSA has been explored to elucidate the specific selectivity of molecular recognition by this multiligand binding protein. The association constants (Kb) of these pollutants to HSA were moderate (104–105 M−1). The proximity of the ligands to HSA is also revealed by their average binding distance, r, which is estimated to be in the range of 4.39–5.37 nm. The binding free energy (ΔG) in each case remains effectively the same for each site because of enthalpy–entropy compensation (EEC). The difference observed between ΔCpexp and ΔCpcalc are suggested to be caused by binding–induced flexibility changes in the HSA. Efforts are also made to elaborate the differences observed in binding isotherms obtained through multiple approaches of calorimetry, spectroscopy and bioinformatics. We suggest that difference in dissociation constants of pollutants by calorimetry, spectroscopic and computational approaches could correspond to occurrence of different set of populations of pollutants having different molecular characteristics in ground state and excited state. Furthermore, our observation of enhanced binding of pollutants (2N and 8H) in the presence of hemin signifies that ligands like hemin may enhance the storage period of these pollutants in blood that may even facilitate the ill effects of these pollutants. PMID:22073150

  14. Temperature-dependent anisotropic resistivity in electron, hole and isoelectron - doped BaFe2As2 superconductors

    NASA Astrophysics Data System (ADS)

    Tanatar, M. A.

    2012-02-01

    Anisotropic electrical resistivity, ρ(T), was studied in iron-arsenide superconductors, obtained by doping the parent BaFe2As2 compound on three different sites: (1) electron donor transition metal (Co,Ni,Rh,Pd) substitution of Fe [1,2]; (2) hole donor K substitution of Ba [3]; (3) isoelectron P substitution of As. For all three types of dopants a range of T-linear behavior is found at the optimal doping in both the in-plane and the inter-plane ρ(T) above Tc. At some higher temperature this range of T-linear resistivity is capped by a slope-changing anomaly, which, by comparison with NMR, magnetic susceptibility and Hall effect measurements, can be identified with the onset of carrier activation over the pseudogap [1]. The doping-evolution of anisotropic temperature dependent ρ(T) and of the pseudogap are quite different for three types of doping. A three-dimensional T-H phase diagram summarizing our results will be presented. Furthermore, potential correlation of the anisotropic normal state transport and anisotropic superconducting state heat transport will be discussed. [4pt] In collaboration with N. Ni, A. Thaler, S.L.Bud'ko, P.C. Canfield, R. Prozorov, Bing Shen, Hai-Hu Wen, K. Hashimoto, S. Kasahara, T. Terashima, T. Shibauchi and Y. Matsuda. [4pt] [1] M.A.Tanatar et al. PRB 82, 134528 (2010)[0pt] [2] M.A.Tanatar et al. PRB 84, 014519 (2011)[0pt] [3] M.A.Tanatar et al. arXiv:1106.0533

  15. The Z dependence of the total energy, energy components, orbital energy, and MO coefficients for mononuclear, isoelectronic species

    NASA Astrophysics Data System (ADS)

    Murdoch, Joseph R.; Magnoli, Douglas E.

    1982-11-01

    Previous workers have shown that in the limit Z→∞, the total energies, Vne, T, and total orbital energies (E0) of a series of isoelectronic, mononuclear structures are quadratic functions of Z, while Vee is a linear function of Z. In the present paper, a new perturbational treatment is presented which is based on a zero-order solution corresponding to Z=Z0, where Z0 is arbitrary. For first-order corrections to Hartree-Fock wave functions, the same limiting behavior (E,Vne, T, E0≡quadratic functions of Z; Vee≡linear function of Z) is seen as for the high-Z limit (Z→∞). For higher-order corrections, a completely different pattern of behavior emerges. For the ten-electron series (Z=9,18), E and T remain highly quadratic with respect to Z (to within 7 kcal), but Vne, Vee, E 0 exhibit large oscillations (˜60 kcal) around a quadratic function. This behavior is analyzed by applying the virial and Hellmann-Feynman theorems to the total energy, the Hellmann-Feynman theorem to Hartree-Fock orbital energies, and by expressing perturbation expansions for Vne and E in terms of Cheybshev polynomials. The results provide a demonstration of the fact that the total energy and orbital energy may show a different pattern of behavior with respect to substituent effects. The present work has important implications for perturbational treatments, such as Walsh's rules, frontier orbital theory and orbital symmetry correlations, which are based on the behavior of the orbital energy rather than the total energy.

  16. Suppression of a Charge Density Wave in ([SnSe]1.15)1(VSe2)1 Ferecrystals Via Isoelectronic Doping with Ta

    NASA Astrophysics Data System (ADS)

    Westover, Richard D.; Mitchson, Gavin; Hite, Omar K.; Hill, Krista; Johnson, David C.

    2016-10-01

    The charge density wave (CDW) transition in (SnSe)1.15VSe2 ferecrystals was investigated through the systematic addition of isoelectronic Ta dopants. (SnSe)1.15 (V1- x Ta x )Se2 ferecrystals with alloyed V1- x Ta x Se2 layers, where x = 0, 0.04, 0.06, 0.07, and 0.09, were prepared from amorphous precursors using the modulated elemental reactants (MER) method. Structural analysis of the ferecrystals, via x-ray diffraction, shows systematic changes in lattice parameters with increasing Ta content consistent with the formation of alloyed V1- x Ta x Se2 layers. Temperature-dependent electrical resistivity and Hall coefficient measurements of the prepared ferecrystals reveal that both the magnitude and onset temperature of the CDW transition are decreased with the addition of Ta, indicating that the ferecrystal CDW transition, although notably stable to volume defects produced by non-stoichiometric films, is more susceptible to destabilization with the addition of isoelectronic dopants.

  17. 4-Component relativistic calculations of L3 ionization and excitations for the isoelectronic species UO2(2+), OUN(+) and UN2.

    PubMed

    South, Christopher; Shee, Avijit; Mukherjee, Debashis; Wilson, Angela K; Saue, Trond

    2016-08-01

    We present a 4-component relativistic study of uranium 2p3/2 ionization and excitation in the isoelectronic series UO2(2+), OUN(+) and UN2. We calculate ionization energies by ΔSCF at the Hartree-Fock (HF) and Kohn-Sham (KS) level of theory. At the ΔHF level we observe a perfectly linear chemical shift of ionization energies with respect to uranium atomic charges obtained from projection analysis. We have also developed a non-canonical 2nd-order Møller-Plesset code for wave function based correlation studies. We observe the well-known failure of Koopmans' theorem for core ionization due to the dominance of orbital relaxation over electron correlation effects. More unexpectedly, we find that the correlation contribution has the same sign as the relaxation contribution and show that this is due to a strong coupling of relaxation and correlation. We simulate uranium L3 XANES spectra, dominated by 2p3/2 → U6d transitions, by restricted excitation window time-dependent density functional theory (REW-TDDFT) and the complex polarization propagator (CPP) approach and demonstrate that they give identical spectra when the same Lorentz broadening is chosen. We also simulate XANES spectra by the Hartree-Fock based static exchange (STEX) method and show how STEX excitation energies can be reproduced by time-dependent Hartree-Fock calculations within the Tamm-Dancoff approximation. We furthermore show that Koopmans' theorem provide a correct approximation of ionization energies in the linear response regime and use this observation to align REW-TDDFT and CPP spectra with STEX ones. We point out that the STEX method affords the most detailed assignment of spectra since it employs virtual orbitals optimized for the selected core ionization. The calculated XANES spectra reflect the loss of bound virtual orbitals as the molecular charge is reduced along the isoelectronic series. PMID:26878601

  18. Calculations with spectroscopic accuracy: energies, transition rates, and Landé gJ-factors in the carbon isoelectronic sequence from Ar XIII to Zn XXV

    NASA Astrophysics Data System (ADS)

    Ekman, J.; Jönsson, P.; Gustafsson, S.; Hartman, H.; Gaigalas, G.; Godefroid, M. R.; Froese Fischer, C.

    2014-04-01

    Extensive self-consistent multiconfiguration Dirac-Hartree-Fock (MCDHF) calculations and subsequent relativistic configuration interaction calculations are performed for 262 states belonging to the 15 configurations 2s22p2, 2s2p3, 2p4, 2s22p3l, 2s2p23l, 2p33l and 2s22p4l(l = 0,1,2) in selected carbon-like ions from Ar XIII to Zn XXV. Electron correlation effects are accounted for through large configuration state function expansions. Calculated energy levels are compared with existing theoretical calculations and data from the Chianti and NIST databases. In addition, Landé gJ-factors and radiative electric dipole transition rates are given for all ions. The accuracy of the calculations are high enough to facilitate the identification of observed spectral lines. Research supported in part by the Swedish Research council, Swedish Institute and by the IUAP-Belgian State Science Policy (BriX network P7/12).Tables of energy levels and transition rates (Tables 3-22) are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/564/A24

  19. Extended calculations of level and transition properties in the nitrogen isoelectronic sequence: Cr XVIII, Fe XX, Ni XXII, and Zn XXIV

    NASA Astrophysics Data System (ADS)

    Radžiūtė, L.; Ekman, J.; Jönsson, P.; Gaigalas, G.

    2015-10-01

    Extensive multiconfiguration Dirac-Hartree-Fock (MCDHF) calculations and relativistic configuration interaction (RCI) calculations are performed for 272 states of the 2s22p3, 2s2p4, 2p5, 2s22p23l, 2s2p33l, and 2p43l (l = 0,1,2) configurations in the nitrogen-like ions Cr XVIII, Fe XX, Ni XXII, and Zn XXIV. Valence, core-valence, and core-core electron correlation effects are accounted for through large configuration state function expansions. Calculated energy levels are compared with data from other calculations and with experimental data from the NIST database. Landé gJ-factors; hyperfine structures; isotope shifts; and radiative electric dipole (E1), electric quadrupole (E2), and magnetic dipole (M1) transition rates are given for all ions. The accuracy of the calculated energy levels is high enough to facilitate identification of observed spectral lines involving the 2l43l' configurations, for which experimental data are largely missing. Tables 5-21 are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/582/A61

  20. Toxin a from Clostridium difficile binds to rabbit erythrocyte glycolipids with therminal Gal. cap alpha. 1-3Gal. beta. 1-4GlcNaC sequences

    SciTech Connect

    Clark, G.F.; Krivan, H.; Wilkins, T.; Smith, D.F.

    1987-05-01

    Toxin A is one of two clostridial toxins implicated as the causative agent of pseudomembranous colitis in patients undergoing postoperative antibiotic therapy. Evidence that the carbohydrate binding determinant for this toxin is a glycoconjugate(s) with non-reducing Gal..cap alpha..1-3Gal..beta..1-4GlcNAc has recently been reported. Specific agglutination of rabbit erythrocytes by Toxin A is inhibited by bovine thyroglobulin and prevented by pretreatment of cells with ..cap alpha..-galactosidase. Total lipid extracts from rabbit erythrocytes were subjected to thin layer chromatography and the chromatogram overlaid with purified /sup 125/I-labeled Toxin A. Two major and several minor toxin-binding glycolipids were detected following autoradiography. The major toxin-binding glycolipids were identified as pentasaccharide- and decasaccharide-ceramides expressing terminal Gal..cap alpha..1-3Gal..beta..1-4GlcNAc sequences. Treatment of the toxin-binding glycolipids with ..cap alpha..-galactosidase abolished binding. Forsmann glycolipid, globoside, Gal..cap alpha..1-4 Gal..beta..1-4Glc-cer, and Gal..cap alpha..1-3Gal..beta..1-4Glc-cer did not bind the toxin. These observations are consistent with the proposed carbohydrate specificity of the toxin for the non-reducing terminal sequence, Gal..cap alpha..1-3Gal..beta..1-4GlcNAc.

  1. Major differences between the binuclear manganese boronyl carbonyl Mn2(BO)2(CO)9 and its isoelectronic chromium carbonyl analogue Cr2(CO)11.

    PubMed

    Chang, Yu; Li, Qian-Shu; Xie, Yaoming; King, R Bruce

    2013-03-14

    The lowest energy structures of the manganese boronyl carbonyl Mn2(BO)2(CO)9 by more than 8 kcal/mol are found to have a single end-to-end bridging BO group bonding to one manganese atom through its boron atom and to the other manganese atom through its oxygen atom. The long Mn···Mn distances in these structures indicate the lack of direct manganese-manganese bonding as confirmed by essentially zero Wiberg bond indices. These Mn2(BO)2(CO)9 structures are favored thermochemically by more than 25 kcal/mol over dissociation into mononuclear fragments and thus appear to be viable synthetic objectives. This contrasts with the isoelectronic Cr2(CO)11 system, which is predicted to be disfavored relative to the mononuclear fragments Cr(CO)6 + Cr(CO)5. Analogous Mn2(BO)2(CO)9 structures with an end-to-end bridging CO group lie ∼17 kcal/mol in energy above the corresponding structures with end-to-end bridging BO groups. The lowest energy Mn2(BO)2(CO)9 structures without an end-to-end bridging BO group provide unprecedented examples of the coupling of two terminal BO groups to form a terminal dioxodiborene (B2O2) ligand with a B-B distance of ∼1.9 Å. Still higher energy Mn2(BO)2(CO)9 structures include singly bridged and doubly semibridged structures analogous to the previously optimized lowest energy Cr2(CO)11 structures. PMID:23402266

  2. Study of the electronic and magnetic properties as a function of isoelectronic substitution in SmFe(1-x)RuxAsO0.85F0.15.

    PubMed

    Simonelli, L; Al-Zein, A; Moretti Sala, M; Joseph, B; Iadecola, A; Bendele, M; Martinelli, A; Palenzona, A; Putti, M; Monaco, G

    2014-02-12

    We have studied the electronic and magnetic properties of SmFe(1-x)RuxAsO0.85F0.15 (x = 0, 0.05, 0.25, 0.33, 0.5) by high-resolution x-ray absorption and x-ray emission spectroscopy. The local Fe magnetic moment (μ) tends to decrease for a small Ru substitution, but it shows a clear increase with further substitution. It appears that impurity scattering prevails in reducing the μ with small Ru substitution due to an extended Ru d-band. A nanoscale phase separation, that decouples the FeAs layers from the spacer layers, drives the increase of μ at higher Ru substitution. The results provide important information on nanoscale phase separation due to isoelectronic substitution in the active layers of iron-based 1111-superconductors and its effect on the local magnetic properties.

  3. Effect of isoelectronic substitution on phase transition and magnetic properties of Ni{sub 57}Mn{sub 18}Ga{sub 25−x}In{sub x} (0 ≤ x ≤ 8) alloys with Ni excess

    SciTech Connect

    Liu, Jinghua; Wang, Jingmin Zhang, Linfang; Wang, Xiao; Hua, Hui; Jiang, Chengbao

    2015-04-21

    Effect of isoelectronic substitution of In for Ga on the phase transition and magnetic properties was studied in Ni{sub 57}Mn{sub 18}Ga{sub 25−x}In{sub x} (0 ≤ x ≤ 8) alloys. With the increasing In content, the room-temperature phase structure evolved from tetragonal martensite to cubic austenite. The martensitic transformation temperatures were significantly decreased by the substitution of In for Ga, but the austenitic Curie temperature was only slightly decreased. Especially, both thermal and isothermal magnetization measurements revealed that the Curie temperature and saturation magnetization of the martensite were independent on the isoelectronic substitution. The results were discussed by considering the phase structures and the atomic interactions.

  4. The elimination of a hydrogen atom in Na(H2O)n

    NASA Astrophysics Data System (ADS)

    Chan, Ka Wai; Siu, Chi-Kit; Wong, S. Y.; Liu, Zhi-Feng

    2005-09-01

    By a systematic examination on Na(H2O)n, with n =4-7, 9, 10, and 15, we demonstrate that a hydrogen loss reaction can be initiated by a single sodium atom with water molecules. This reaction is similar to the well-known size-dependent intracluster hydrogen loss in Mg+(H2O)n, which is isoelectronic to Na(H2O)n. However, with one less charge on Na(H2O)n than that on Mg+(H2O)n, the hydrogen loss for Na(H2O)n is characterized by a higher barrier and a more flexible solvation shell around the metal ion, although the reaction should be accessible, as the lowest barrier is around 8kcal/mol. Interestingly, the hydroxide ion OH- produced in the process is stabilized by the solvation of H2O molecules and the formation of an ion pair Na+(H2O)4(H2O)n-l-4[OH-(H2O)l]. The activation barrier is reduced as the unpaired electron in Na(H2O)n moves to higher solvation shells with increasing cluster size, and the reaction is not switched off for larger clusters. This is in sharp contrast to the reaction for Mg+(H2O)n, in which the OH- ion is stabilized by direct coordination with Mg2+ and the reaction is switched off for n >17, as the unpaired electron moved to higher solvation shells. Such a contrast illustrates the important link between microsolvation environment and chemical reactivity in solvation clusters.

  5. Dna Sequencing

    DOEpatents

    Tabor, Stanley; Richardson, Charles C.

    1995-04-25

    A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

  6. Intracellular Na+ regulates epithelial Na+ channel maturation.

    PubMed

    Heidrich, Elisa; Carattino, Marcelo D; Hughey, Rebecca P; Pilewski, Joseph M; Kleyman, Thomas R; Myerburg, Mike M

    2015-05-01

    Epithelial Na(+) channel (ENaC) function is regulated by the intracellular Na(+) concentration ([Na(+)]i) through a process known as Na(+) feedback inhibition. Although this process is known to decrease the expression of proteolytically processed active channels on the cell surface, it is unknown how [Na(+)]i alters ENaC cleavage. We show here that [Na(+)]i regulates the posttranslational processing of ENaC subunits during channel biogenesis. At times when [Na(+)]i is low, ENaC subunits develop mature N-glycans and are processed by proteases. Conversely, glycan maturation and sensitivity to proteolysis are reduced when [Na(+)]i is relatively high. Surface channels with immature N-glycans were not processed by endogenous channel activating proteases, nor were they sensitive to cleavage by exogenous trypsin. Biotin chase experiments revealed that the immature surface channels were not converted into mature cleaved channels following a reduction in [Na(+)]i. The hypothesis that [Na(+)]i regulates ENaC maturation within the biosynthetic pathways is further supported by the finding that Brefeldin A prevented the accumulation of processed surface channels following a reduction in [Na(+)]i. Therefore, increased [Na(+)]i interferes with ENaC N-glycan maturation and prevents the channel from entering a state that allows proteolytic processing. PMID:25767115

  7. MSLICE Sequencing

    NASA Technical Reports Server (NTRS)

    Crockett, Thomas M.; Joswig, Joseph C.; Shams, Khawaja S.; Norris, Jeffrey S.; Morris, John R.

    2011-01-01

    MSLICE Sequencing is a graphical tool for writing sequences and integrating them into RML files, as well as for producing SCMF files for uplink. When operated in a testbed environment, it also supports uplinking these SCMF files to the testbed via Chill. This software features a free-form textural sequence editor featuring syntax coloring, automatic content assistance (including command and argument completion proposals), complete with types, value ranges, unites, and descriptions from the command dictionary that appear as they are typed. The sequence editor also has a "field mode" that allows tabbing between arguments and displays type/range/units/description for each argument as it is edited. Color-coded error and warning annotations on problematic tokens are included, as well as indications of problems that are not visible in the current scroll range. "Quick Fix" suggestions are made for resolving problems, and all the features afforded by modern source editors are also included such as copy/cut/paste, undo/redo, and a sophisticated find-and-replace system optionally using regular expressions. The software offers a full XML editor for RML files, which features syntax coloring, content assistance and problem annotations as above. There is a form-based, "detail view" that allows structured editing of command arguments and sequence parameters when preferred. The "project view" shows the user s "workspace" as a tree of "resources" (projects, folders, and files) that can subsequently be opened in editors by double-clicking. Files can be added, deleted, dragged-dropped/copied-pasted between folders or projects, and these operations are undoable and redoable. A "problems view" contains a tabular list of all problems in the current workspace. Double-clicking on any row in the table opens an editor for the appropriate sequence, scrolling to the specific line with the problem, and highlighting the problematic characters. From there, one can invoke "quick fix" as described

  8. Phase transition sequence in Pb-free 0.96(K{sub 0.5}Na{sub 0.5}){sub 0.95}Li{sub 0.05}Nb{sub 0.93} Sb{sub 0.07}O{sub 3}−0.04BaZrO{sub 3} ceramic with large piezoelectric response

    SciTech Connect

    Gao, Jinghui Zhang, Le; Zhang, Ming; Dai, Ye; Hu, Xinghao; Wang, Dong; Zhong, Lisheng; Li, Shengtao; Ren, Shuai; Hao, Yanshuang Fang, Minxia; Ren, Xiaobing

    2015-07-20

    The piezoceramic 0.96(K{sub 0.5}Na{sub 0.5}){sub 0.95}Li{sub 0.05}Nb{sub 0.93}Sb{sub 0.07}O{sub 3}−0.04BaZrO{sub 3} (KNLNS{sub 0.07}-BZ), which shows large piezoelectric response (d{sub 33} ≈ 425 pC/N), has been considered as one of the promising Pb-free substitutions for Pb(Zr,Ti)O{sub 3}. In this paper, we investigate the phase transition sequence for KNLNS{sub 0.07}-BZ by employing the dielectric measurement, mechanical spectroscopy, as well as Raman spectroscopy. Two ferroelectric-ferroelectric transitions have been detected by inspecting anomalies in the spectra, indicating the existence of three ferroelectric phases. Moreover, in-situ X-ray diffraction study has been further performed on KNLNS{sub 0.07}-BZ to identify the crystal structure for each phase. The result reveals that the phase sequence for KNLNS{sub 0.07}-BZ evolves from tetragonal (T) to rhombohedral (R) via an intermediate orthorhombic (O) phase. And the piezoelectric-optimal region for KNLNS{sub 0.07}-BZ locates on a T-O boundary rather than the previously reported T-R boundary. Strong piezoelectricity may stem from the easier polarization rotation on the T-O boundary with reduced polarization anisotropy.

  9. Insertion Sequences

    PubMed Central

    Mahillon, Jacques; Chandler, Michael

    1998-01-01

    Insertion sequences (ISs) constitute an important component of most bacterial genomes. Over 500 individual ISs have been described in the literature to date, and many more are being discovered in the ongoing prokaryotic and eukaryotic genome-sequencing projects. The last 10 years have also seen some striking advances in our understanding of the transposition process itself. Not least of these has been the development of various in vitro transposition systems for both prokaryotic and eukaryotic elements and, for several of these, a detailed understanding of the transposition process at the chemical level. This review presents a general overview of the organization and function of insertion sequences of eubacterial, archaebacterial, and eukaryotic origins with particular emphasis on bacterial elements and on different aspects of the transposition mechanism. It also attempts to provide a framework for classification of these elements by assigning them to various families or groups. A total of 443 members of the collection have been grouped in 17 families based on combinations of the following criteria: (i) similarities in genetic organization (arrangement of open reading frames); (ii) marked identities or similarities in the enzymes which mediate the transposition reactions, the recombinases/transposases (Tpases); (iii) similar features of their ends (terminal IRs); and (iv) fate of the nucleotide sequence of their target sites (generation of a direct target duplication of determined length). A brief description of the mechanism(s) involved in the mobility of individual ISs in each family and of the structure-function relationships of the individual Tpases is included where available. PMID:9729608

  10. The Third Dimension of a More O'Ferrall-Jencks Diagram for Hydrogen Atom Transfer in the Isoelectronic Hydrogen Exchange Reactions of (PhX)(2)H(•) with X = O, NH, and CH(2).

    PubMed

    Cembran, Alessandro; Provorse, Makenzie R; Wang, Changwei; Wu, Wei; Gao, Jiali

    2012-11-13

    A critical element in theoretical characterization of the mechanism of proton-coupled electron transfer (PCET) reactions, including hydrogen atom transfer (HAT), is the formulation of the electron and proton localized diabatic states, based on which a More O'Ferrall-Jencks diagram can be represented to determine the step-wise and concerted nature of the reaction. Although the More O'Ferrall-Jencks diabatic states have often been used empirically to develop theoretical models for PCET reactions, the potential energy surfaces for these states have never been determined directly based on first principles calculations using electronic structure theory. The difficulty is due to a lack of practical method to constrain electron and proton localized diabatic states in wave function or density functional theory calculations. Employing a multistate density functional theory (MSDFT), in which the electron and proton localized diabatic configurations are constructed through block-localization of Kohn-Sham orbitals, we show that distinction between concerted proton-electron transfer (CPET) and HAT, which are not distinguishable experimentally from phenomenological kinetic data, can be made by examining the third dimension of a More O'Ferrall-Jencks diagram that includes both the ground and excited state potential surfaces. In addition, we formulate a pair of effective two-state valence bond models to represent the CPET and HAT mechanisms. We found that the lower energy of the CPET and HAT effective diabatic states at the intersection point can be used as an energetic criterion to distinguish the two mechanisms. In the isoelectronic series of hydrogen exchange reaction in (PhX)(2)H(•), where X = O, NH, and CH(2), there is a continuous transition from a CPET mechanism for the phenoxy radical-phenol pair to a HAT process for benzyl radical and toluene, while the reaction between PhNH(2) and PhNH(•) has a mechanism intermediate of CPET and HAT. The electronically nonadiabatic

  11. The sequence of sequencers: The history of sequencing DNA.

    PubMed

    Heather, James M; Chain, Benjamin

    2016-01-01

    Determining the order of nucleic acid residues in biological samples is an integral component of a wide variety of research applications. Over the last fifty years large numbers of researchers have applied themselves to the production of techniques and technologies to facilitate this feat, sequencing DNA and RNA molecules. This time-scale has witnessed tremendous changes, moving from sequencing short oligonucleotides to millions of bases, from struggling towards the deduction of the coding sequence of a single gene to rapid and widely available whole genome sequencing. This article traverses those years, iterating through the different generations of sequencing technology, highlighting some of the key discoveries, researchers, and sequences along the way.

  12. Preserving sequence annotations across reference sequences

    PubMed Central

    2014-01-01

    Background Matching and comparing sequence annotations of different reference sequences is vital to genomics research, yet many annotation formats do not specify the reference sequence types or versions used. This makes the integration of annotations from different sources difficult and error prone. Results As part of our effort to create linked data for interoperable sequence annotations, we present an RDF data model for sequence annotation using the ontological framework established by the OBO Foundry ontologies and the Basic Formal Ontology (BFO). We defined reference sequences as the common domain of integration for sequence annotations, and identified three semantic relationships between sequence annotations. In doing so, we created the Reference Sequence Annotation to compensate for gaps in the SO and in its mapping to BFO, particularly for annotations that refer to versions of consensus reference sequences. Moreover, we present three integration models for sequence annotations using different reference assemblies. Conclusions We demonstrated a working example of a sequence annotation instance, and how this instance can be linked to other annotations on different reference sequences. Sequence annotations in this format are semantically rich and can be integrated easily with different assemblies. We also identify other challenges of modeling reference sequences with the BFO. PMID:25093075

  13. Theoretical study of isoelectronic molecules: B6H10, 2-CB5H9, 2,3-C2B4H8, 2,3,4-C3B3H7, and 2,3,4,5-C4B2H6.

    PubMed

    Tian, Shan Xi

    2005-07-28

    Isoelectronic molecules regarding B6H10, 2-CB5H9, 2,3-C2B4H8, 2,3,4-C3B3H7, and 2,3,4,5-C4B2H6 are studied by the density functional B3LYP/6-311G(d,p) method and the electron propagator theory in the partial third-order quasiparticale approximation, as well as the extrapolated calculation with the coupled-cluster CCSD(T) theory. The calculated ionization potentials are in good agreement with the experimental data from photoelectron spectroscopy. Valence structures are characterized with natural orbital bond (NBO) theory, exhibiting the multiple three-center two-electron bonds B-H-B, B-B-B, C-B-B, B-C-B, and C-B-C, and chemical bond rearrangements in the cations. PMID:16834005

  14. Shotgun protein sequencing.

    SciTech Connect

    Faulon, Jean-Loup Michel; Heffelfinger, Grant S.

    2009-06-01

    A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

  15. The sequence of sequencers: The history of sequencing DNA

    PubMed Central

    Heather, James M.; Chain, Benjamin

    2016-01-01

    Determining the order of nucleic acid residues in biological samples is an integral component of a wide variety of research applications. Over the last fifty years large numbers of researchers have applied themselves to the production of techniques and technologies to facilitate this feat, sequencing DNA and RNA molecules. This time-scale has witnessed tremendous changes, moving from sequencing short oligonucleotides to millions of bases, from struggling towards the deduction of the coding sequence of a single gene to rapid and widely available whole genome sequencing. This article traverses those years, iterating through the different generations of sequencing technology, highlighting some of the key discoveries, researchers, and sequences along the way. PMID:26554401

  16. Multimodal sequence learning.

    PubMed

    Kemény, Ferenc; Meier, Beat

    2016-02-01

    While sequence learning research models complex phenomena, previous studies have mostly focused on unimodal sequences. The goal of the current experiment is to put implicit sequence learning into a multimodal context: to test whether it can operate across different modalities. We used the Task Sequence Learning paradigm to test whether sequence learning varies across modalities, and whether participants are able to learn multimodal sequences. Our results show that implicit sequence learning is very similar regardless of the source modality. However, the presence of correlated task and response sequences was required for learning to take place. The experiment provides new evidence for implicit sequence learning of abstract conceptual representations. In general, the results suggest that correlated sequences are necessary for implicit sequence learning to occur. Moreover, they show that elements from different modalities can be automatically integrated into one unitary multimodal sequence.

  17. Whole Genome Sequencing

    MedlinePlus

    ... you want to learn. Search form Search Whole Genome Sequencing You are here Home Testing & Services Testing ... the full story, click here . What is whole genome sequencing? Whole genome sequencing is the mapping out ...

  18. Coordinate cytokine regulatory sequences

    DOEpatents

    Frazer, Kelly A.; Rubin, Edward M.; Loots, Gabriela G.

    2005-05-10

    The present invention provides CNS sequences that regulate the cytokine gene expression, expression cassettes and vectors comprising or lacking the CNS sequences, host cells and non-human transgenic animals comprising the CNS sequences or lacking the CNS sequences. The present invention also provides methods for identifying compounds that modulate the functions of CNS sequences as well as methods for diagnosing defects in the CNS sequences of patients.

  19. Science sequence design

    NASA Technical Reports Server (NTRS)

    Koskela, P. E.; Bollman, W. E.; Freeman, J. E.; Helton, M. R.; Reichert, R. J.; Travers, E. S.; Zawacki, S. J.

    1973-01-01

    The activities of the following members of the Navigation Team are recorded: the Science Sequence Design Group, responsible for preparing the final science sequence designs; the Advanced Sequence Planning Group, responsible for sequence planning; and the Science Recommendation Team (SRT) representatives, responsible for conducting the necessary sequence design interfaces with the teams during the mission. The interface task included science support in both advance planning and daily operations. Science sequences designed during the mission are also discussed.

  20. [Effects of NaCl stress on the seedling growth and K(+)- and Na(+) -allocation of four leguminous tree species].

    PubMed

    Mo, Hai-Bo; Yin, Yun-Long; Lu, Zhi-Guo; Wei, Xiu-Jun; Xu, Jian-Hua

    2011-05-01

    Taking the pot-cultured seedlings of four leguminous tree species (Albizia julibrissin, Robinia pseudoacacia, Sophora japonica, and Gleditsia sinensis) as test materials, this paper studied their growth indices, critical salt concentration (C50), and K+ and Na+ allocation under different levels of NaCl stress, aimed to understand the difference of test tree species in salt tolerance. NaCl stress inhibited the seedling growth of the tree species. Under NaCl stress, the dry matter accumulation decreased, while the root/shoot ratio increased, especially for A. julibrissin and G. sinensis. Quadratic regression analysis showed that the C50 of A. julibrissin, R. pseudoacacia, S. japonica, and G. sinensis was 3.0 per thousand, 5.0 per thousand, 4.5 per thousand, and 3.9 per thousand, respectively, i.e., the salt tolerance of the four tree species was in the order of R. pseudoacacia > S. japonica > G. sinensis > A. julibrissin. In the root, stem, and leaf of the four tree species seedlings, the Na+ content increased with the increase of NaCl stress, while the K+ content (except in the root of A. julibrissin) decreased after an initial increase, resulting in a larger difference in the K+/Na+ ratio in the organs. Under the same NaCl stress, the allocation of Na+ in different organs of the four tree species seedlings decreased in the order of root>stem>leaf, while that of K+ differed with tree species and NaCl stress, and leaf was the main storage organ for K+. The K+/Na+ ratio in different organs decreased in the sequence of leaf>stem>root. R. pseudoacacia under NaCl stress accumulated more K+ and less Na+ in stem and leaf, and had higher K+/Na+ ratio in all organs and higher dry mass, being assessed to be more salt-tolerant. In contrast, A. julibrissin under high NaCl stress accumulated more Na+ in stem and leaf, and had a lower K+/Na+ ratio in all organs and lower dry mass, being evaluated to be lesser salt-tolerant. The K+ accumulation in seedling stem and leaf and the Na

  1. Towards environmentally friendly Na-ion batteries: Moisture and water stability of Na2Ti3O7

    NASA Astrophysics Data System (ADS)

    Zarrabeitia, M.; Castillo-Martínez, E.; López Del Amo, J. M.; Eguía-Barrio, A.; Muñoz-Márquez, M. A.; Rojo, T.; Casas-Cabanas, M.

    2016-08-01

    We report here on the moisture and water stability of the promising Na-ion anode material Na2Ti3O7. Spontaneous Na+/H+ exchange is detected by PXRD after air exposure, forming solid solution compounds of the form Na2-xHxTi3O7 (0 < x < 2). By controlled ion exchange in aqueous solution two mixed compositions are prepared and their composition and structure are characterized with a panel of techniques. Both mixed compositions crystallize in C2/m space group like H2Ti3O7, and therefore Na+/H+ exchange is found to involve a structural transition from AA stacking of [TiO6] layers to AB stacking sequence. The electrochemical behaviour of the mixed compositions vs. Na+/Na is studied as well as that of an electrode of pure Na2Ti3O7 prepared in water media. The water-processed electrode is shown to exhibit a superior cycling stability and therefore the results obtained highlight the potential of Na2Ti3O7 as a green, low cost anode material for NIBs.

  2. Towards environmentally friendly Na-ion batteries: Moisture and water stability of Na2Ti3O7

    NASA Astrophysics Data System (ADS)

    Zarrabeitia, M.; Castillo-Martínez, E.; López Del Amo, J. M.; Eguía-Barrio, A.; Muñoz-Márquez, M. A.; Rojo, T.; Casas-Cabanas, M.

    2016-08-01

    We report here on the moisture and water stability of the promising Na-ion anode material Na2Ti3O7. Spontaneous Na+/H+ exchange is detected by PXRD after air exposure, forming solid solution compounds of the form Na2-xHxTi3O7 (0 < x < 2). By controlled ion exchange in aqueous solution two mixed compositions are prepared and their composition and structure are characterized with a panel of techniques. Both mixed compositions crystallize in C2/m space group like H2Ti3O7, and therefore Na+/H+ exchange is found to involve a structural transition from AA stacking of [TiO6] layers to AB stacking sequence. The electrochemical behaviour of the mixed compositions vs. Na+/Na is studied as well as that of an electrode of pure Na2Ti3O7 prepared in water media. The water-processed electrode is shown to exhibit a superior cycling stability and therefore the results obtained highlight the potential of Na2Ti3O7 as a green, low cost anode material for NIBs.

  3. Advanced Intermediate-Temperature Na-S Battery

    SciTech Connect

    Lu, Xiaochuan; Kirby, Brent W.; Xu, Wu; Li, Guosheng; Kim, Jin Yong; Lemmon, John P.; Sprenkle, Vincent L.; Yang, Zhenguo

    2012-11-12

    In this study, we reported an intermediate-temperature (~150°C) sodium-sulfur (Na-S) battery. With a reduced operating temperature, this novel battery can potentially reduce the cost and safety issues associated with the conventional high-temperature (300~350°C) Na-S battery. A dense β"-Al2O3 solid membrane and tetraglyme were utilized as the electrolyte separator and catholyte solvent in this battery. Solubility tests indicated that cathode mixture of Na2S4 and S exhibited extremely high solubility in tetraglyme (e.g., > 4.1 M for Na2S4 + 4 S). CV scans of Na2S4 in tetraglyme revealed two pairs of redox couples with peaks at around 2.22 and 1.75 V, corresponding to the redox reactions of polysulfide species. The discharge/charge profiles of the Na-S battery showed a slope region and a plateau, indicating multiple steps and cell reactions. In-situ Raman measurements during battery operation suggested that polysulfide species were formed in the sequence of Na2S5 + S → Na2S5 + Na2S4Na2S4 + Na2S2 during discharge and in a reverse order during charge. This battery showed dramatic improvement in rate capacity and cycling stability over room-temperature Na-S batteries, which makes it attractive for renewable energy integration and other grid related applications.

  4. The generalized quaternion sequence

    NASA Astrophysics Data System (ADS)

    Deveci, Ömür

    2016-04-01

    In this work, we define the recurrence sequence by using the relation matrix of the generalized quaternion group and then, we obtain miscellaneous properties of this sequence. Also, we obtain the cyclic groups and the semigroups which are produced by generating matrix of the sequence defined when read modulo m. Furthermore, we study this sequence modulo m, and then we derive the relationship among the order the cyclic groups obtained and the periods of the sequence defined.

  5. NaN, a novel voltage-gated Na channel, is expressed preferentially in peripheral sensory neurons and down-regulated after axotomy

    PubMed Central

    Dib-Hajj, S. D.; Tyrrell, L.; Black, J. A.; Waxman, S. G.

    1998-01-01

    Although physiological and pharmacological evidence suggests the presence of multiple tetrodotoxin-resistant (TTX-R) Na channels in neurons of peripheral nervous system ganglia, only one, SNS/PN3, has been identified in these cells to date. We have identified and sequenced a novel Na channel α-subunit (NaN), predicted to be TTX-R and voltage-gated, that is expressed preferentially in sensory neurons within dorsal root ganglia (DRG) and trigeminal ganglia. The predicted amino acid sequence of NaN can be aligned with the predicted structure of known Na channel α-subunits; all relevant landmark sequences, including positively charged S4 and pore-lining SS1–SS2 segments, and the inactivation tripeptide IFM, are present at predicted positions. However, NaN exhibits only 42–53% similarity to other mammalian Na channels, including SNS/PN3, indicating that it is a novel channel, and suggesting that it may represent a third subfamily of Na channels. NaN transcript levels are reduced significantly 7 days post axotomy in DRG neurons, consistent with previous findings of a reduction in TTX-R Na currents. The preferential expression of NaN in DRG and trigeminal ganglia and the reduction of NaN mRNA levels in DRG after axonal injury suggest that NaN, together with SNS/PN3, may produce TTX-R currents in peripheral sensory neurons and may influence the generation of electrical activity in these cells. PMID:9671787

  6. The pea gene NA encodes ent-kaurenoic acid oxidase.

    PubMed

    Davidson, Sandra E; Elliott, Robert C; Helliwell, Chris A; Poole, Andrew T; Reid, James B

    2003-01-01

    The gibberellin (GA)-deficient dwarf na mutant in pea (Pisum sativum) has severely reduced internode elongation, reduced root growth, and decreased leaflet size. However, the seeds develop normally. Two genes, PsKAO1 and PsKAO2, encoding cytochrome P450 monooxygenases of the subfamily CYP88A were isolated. Both PsKAO1 and PsKAO2 had ent-kaurenoic acid oxidase (KAO) activity, catalyzing the three steps of the GA biosynthetic pathway from ent-kaurenoic acid to GA(12) when expressed in yeast (Saccharomyces cerevisiae). In addition to the intermediates ent-7alpha-hydroxykaurenoic acid and GA(12)-aldehyde, some additional products of the pea KAO activity were detected, including ent-6alpha,7alpha-dihydroxykaurenoic acid and 7beta-hydroxykaurenolide. The NA gene encodes PsKAO1, because in two independent mutant alleles, na-1 and na-2, PsKAO1 had altered sequences and the five-base deletion in PsKAO1 associated with the na-1 allele cosegregated with the dwarf na phenotype. PsKAO1 was expressed in the stem, apical bud, leaf, pod, and root, organs in which GA levels have previously been shown to be reduced in na plants. PsKAO2 was expressed only in seeds and this may explain the normal seed development and normal GA biosynthesis in seeds of na plants.

  7. Genome Sequence Databases (Overview): Sequencing and Assembly

    SciTech Connect

    Lapidus, Alla L.

    2009-01-01

    From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

  8. Contamination of sequence databases with adaptor sequences

    SciTech Connect

    Yoshikawa, Takeo; Sanders, A.R.; Detera-Wadleigh, S.D.

    1997-02-01

    Because of the exponential increase in the amount of DNA sequences being added to the public databases on a daily basis, it has become imperative to identify sources of contamination rapidly. Previously, contaminations of sequence databases have been reported to alert the scientific community to the problem. These contaminations can be divided into two categories. The first category comprises host sequences that have been difficult for submitters to manage or control. Examples include anomalous sequences derived from Escherichia coli, which are inserted into the chromosomes (and plasmids) of the bacterial hosts. Insertion sequences are highly mobile and are capable of transposing themselves into plasmids during cloning manipulation. Another example of the first category is the infection with yeast genomic DNA or with bacterial DNA of some commercially available cDNA libraries from Clontech. The second category of database contamination is due to the inadvertent inclusion of nonhost sequences. This category includes incorporation of cloning-vector sequences and multicloning sites in the database submission. M13-derived artifacts have been common, since M13-based vectors have been widely used for subcloning DNA fragments. Recognizing this problem, the National Center for Biotechnology Information (NCBI) started to screen, in April 1994, all sequences directly submitted to GenBank, against a set of vector data retrieved from GenBank by use of key-word searches, such as {open_quotes}vector.{close_quotes} In this report, we present evidence for another sequence artifact that is widespread but that, to our knowledge, has not yet been reported. 11 refs., 1 tab.

  9. Automated DNA Sequencing System

    SciTech Connect

    Armstrong, G.A.; Ekkebus, C.P.; Hauser, L.J.; Kress, R.L.; Mural, R.J.

    1999-04-25

    Oak Ridge National Laboratory (ORNL) is developing a core DNA sequencing facility to support biological research endeavors at ORNL and to conduct basic sequencing automation research. This facility is novel because its development is based on existing standard biology laboratory equipment; thus, the development process is of interest to the many small laboratories trying to use automation to control costs and increase throughput. Before automation, biology Laboratory personnel purified DNA, completed cycle sequencing, and prepared 96-well sample plates with commercially available hardware designed specifically for each step in the process. Following purification and thermal cycling, an automated sequencing machine was used for the sequencing. A technician handled all movement of the 96-well sample plates between machines. To automate the process, ORNL is adding a CRS Robotics A- 465 arm, ABI 377 sequencing machine, automated centrifuge, automated refrigerator, and possibly an automated SpeedVac. The entire system will be integrated with one central controller that will direct each machine and the robot. The goal of this system is to completely automate the sequencing procedure from bacterial cell samples through ready-to-be-sequenced DNA and ultimately to completed sequence. The system will be flexible and will accommodate different chemistries than existing automated sequencing lines. The system will be expanded in the future to include colony picking and/or actual sequencing. This discrete event, DNA sequencing system will demonstrate that smaller sequencing labs can achieve cost-effective the laboratory grow.

  10. Sequence information signal processor

    DOEpatents

    Peterson, John C.; Chow, Edward T.; Waterman, Michael S.; Hunkapillar, Timothy J.

    1999-01-01

    An electronic circuit is used to compare two sequences, such as genetic sequences, to determine which alignment of the sequences produces the greatest similarity. The circuit includes a linear array of series-connected processors, each of which stores a single element from one of the sequences and compares that element with each successive element in the other sequence. For each comparison, the processor generates a scoring parameter that indicates which segment ending at those two elements produces the greatest degree of similarity between the sequences. The processor uses the scoring parameter to generate a similar scoring parameter for a comparison between the stored element and the next successive element from the other sequence. The processor also delivers the scoring parameter to the next processor in the array for use in generating a similar scoring parameter for another pair of elements. The electronic circuit determines which processor and alignment of the sequences produce the scoring parameter with the highest value.

  11. Cellulases and coding sequences

    DOEpatents

    Li, Xin-Liang; Ljungdahl, Lars G.; Chen, Huizhong

    2001-02-20

    The present invention provides three fungal cellulases, their coding sequences, recombinant DNA molecules comprising the cellulase coding sequences, recombinant host cells and methods for producing same. The present cellulases are from Orpinomyces PC-2.

  12. Cellulases and coding sequences

    DOEpatents

    Li, Xin-Liang; Ljungdahl, Lars G.; Chen, Huizhong

    2001-01-01

    The present invention provides three fungal cellulases, their coding sequences, recombinant DNA molecules comprising the cellulase coding sequences, recombinant host cells and methods for producing same. The present cellulases are from Orpinomyces PC-2.

  13. Roles of repetitive sequences

    SciTech Connect

    Bell, G.I.

    1991-12-31

    The DNA of higher eukaryotes contains many repetitive sequences. The study of repetitive sequences is important, not only because many have important biological function, but also because they provide information on genome organization, evolution and dynamics. In this paper, I will first discuss some generic effects that repetitive sequences will have upon genome dynamics and evolution. In particular, it will be shown that repetitive sequences foster recombination among, and turnover of, the elements of a genome. I will then consider some examples of repetitive sequences, notably minisatellite sequences and telomere sequences as examples of tandem repeats, without and with respectively known function, and Alu sequences as an example of interspersed repeats. Some other examples will also be considered in less detail.

  14. Nonparametric Combinatorial Sequence Models

    NASA Astrophysics Data System (ADS)

    Wauthier, Fabian L.; Jordan, Michael I.; Jojic, Nebojsa

    This work considers biological sequences that exhibit combinatorial structures in their composition: groups of positions of the aligned sequences are "linked" and covary as one unit across sequences. If multiple such groups exist, complex interactions can emerge between them. Sequences of this kind arise frequently in biology but methodologies for analyzing them are still being developed. This paper presents a nonparametric prior on sequences which allows combinatorial structures to emerge and which induces a posterior distribution over factorized sequence representations. We carry out experiments on three sequence datasets which indicate that combinatorial structures are indeed present and that combinatorial sequence models can more succinctly describe them than simpler mixture models. We conclude with an application to MHC binding prediction which highlights the utility of the posterior distribution induced by the prior. By integrating out the posterior our method compares favorably to leading binding predictors.

  15. DNA sequencing conference, 2

    SciTech Connect

    Cook-Deegan, R.M.; Venter, J.C.; Gilbert, W.; Mulligan, J.; Mansfield, B.K.

    1991-06-19

    This conference focused on DNA sequencing, genetic linkage mapping, physical mapping, informatics and bioethics. Several were used to study this sequencing and mapping. This article also discusses computer hardware and software aiding in the mapping of genes.

  16. Electronic structure and properties of isoelectronically substituted compounds Y{sub 1}Ba{sub 2-m}M{sub m}Cu{sub 3}O{sub 7} and Y{sub 1}Ba{sub 2-m}M{sub m}Cu{sub 4}O{sub 8} (M = Be, Mg, Ca, Sr, Ba, Ra)

    SciTech Connect

    Ermakov, A.I.; Zharikova, E.A.; Markushin, N.A.

    1994-09-01

    According to cluster calculations, the electronic structures of compounds based on Y{sub 1}Ba{sub 2}Cu{sub 3}O{sub 7} and Y{sub 1}Ba{sub 2}Cu{sub 4}O{sub 8} with isoelectronically substituted barium have some qualitative distinctions. These compounds behave differently upon barium substitution by other elements due to differences in the character of their highest occupied and lowest unoccupied molecular orbitals. Substitution of barium by radium is expected to lead to an increase in oxygen stability without a significant decrease in the critical temperature of superconduction transition T{sub s}. In order to raise T{sub s}, it is of interest to study the systems YBa{sub 2-m}(Be or Mg){sub m}Cu{sub 3}O{sub x} and YBa{sub 2-m}(Ca, Sr){sub m}Cu{sub 3}O{sub x}. On partial substitution of barium by calcium in YBa{sub 2}Cu{sub 4}O{sub 8}, the mechanism of T{sub s} elevation may involve contraction of the forbidden band due to oxygen sublattice distortions in the vicinity of Ba centers.

  17. Enhanced virome sequencing using targeted sequence capture

    PubMed Central

    Wylie, Todd N.; Wylie, Kristine M.; Herter, Brandi N.; Storch, Gregory A.

    2015-01-01

    Metagenomic shotgun sequencing (MSS) is an important tool for characterizing viral populations. It is culture independent, requires no a priori knowledge of the viruses in the sample, and may provide useful genomic information. However, MSS can lack sensitivity and may yield insufficient data for detailed analysis. We have created a targeted sequence capture panel, ViroCap, designed to enrich nucleic acid from DNA and RNA viruses from 34 families that infect vertebrate hosts. A computational approach condensed ∼1 billion bp of viral reference sequence into <200 million bp of unique, representative sequence suitable for targeted sequence capture. We compared the effectiveness of detecting viruses in standard MSS versus MSS following targeted sequence capture. First, we analyzed two sets of samples, one derived from samples submitted to a diagnostic virology laboratory and one derived from samples collected in a study of fever in children. We detected 14 and 18 viruses in the two sets, comprising 19 genera from 10 families, with dramatic enhancement of genome representation following capture enrichment. The median fold-increases in percentage viral reads post-capture were 674 and 296. Median breadth of coverage increased from 2.1% to 83.2% post-capture in the first set and from 2.0% to 75.6% in the second set. Next, we analyzed samples containing a set of diverse anellovirus sequences and demonstrated that ViroCap could be used to detect viral sequences with up to 58% variation from the references used to select capture probes. ViroCap substantially enhances MSS for a comprehensive set of viruses and has utility for research and clinical applications. PMID:26395152

  18. Enhanced virome sequencing using targeted sequence capture.

    PubMed

    Wylie, Todd N; Wylie, Kristine M; Herter, Brandi N; Storch, Gregory A

    2015-12-01

    Metagenomic shotgun sequencing (MSS) is an important tool for characterizing viral populations. It is culture independent, requires no a priori knowledge of the viruses in the sample, and may provide useful genomic information. However, MSS can lack sensitivity and may yield insufficient data for detailed analysis. We have created a targeted sequence capture panel, ViroCap, designed to enrich nucleic acid from DNA and RNA viruses from 34 families that infect vertebrate hosts. A computational approach condensed ∼1 billion bp of viral reference sequence into <200 million bp of unique, representative sequence suitable for targeted sequence capture. We compared the effectiveness of detecting viruses in standard MSS versus MSS following targeted sequence capture. First, we analyzed two sets of samples, one derived from samples submitted to a diagnostic virology laboratory and one derived from samples collected in a study of fever in children. We detected 14 and 18 viruses in the two sets, comprising 19 genera from 10 families, with dramatic enhancement of genome representation following capture enrichment. The median fold-increases in percentage viral reads post-capture were 674 and 296. Median breadth of coverage increased from 2.1% to 83.2% post-capture in the first set and from 2.0% to 75.6% in the second set. Next, we analyzed samples containing a set of diverse anellovirus sequences and demonstrated that ViroCap could be used to detect viral sequences with up to 58% variation from the references used to select capture probes. ViroCap substantially enhances MSS for a comprehensive set of viruses and has utility for research and clinical applications.

  19. Career Academy Course Sequences.

    ERIC Educational Resources Information Center

    Markham, Thom; Lenz, Robert

    This career academy course sequence guide is designed to give teachers a quick overview of the course sequences of well-known career academy and career pathway programs from across the country. The guide presents a variety of sample course sequences for the following academy themes: (1) arts and communication; (2) business and finance; (3)…

  20. Uncorrectable sequences and telecommand

    NASA Technical Reports Server (NTRS)

    Ekroot, Laura; Mceliece, R.; Dolinar, S.; Swanson, L.

    1993-01-01

    The purpose of a tail sequence for command link transmission units is to fail to decode, so that the command decoder will begin searching for the start of the next unit. A tail sequence used by several missions and recommended for this purpose by the Consultative Committee on Space Data Standards is analyzed. A single channel error can cause the sequence to decode. An alternative sequence requiring at least two channel errors before it can possibly decode is presented. (No sequence requiring more than two channel errors before it can possibly decode exists for this code.)

  1. Low autocorrelation binary sequences

    NASA Astrophysics Data System (ADS)

    Packebusch, Tom; Mertens, Stephan

    2016-04-01

    Binary sequences with minimal autocorrelations have applications in communication engineering, mathematics and computer science. In statistical physics they appear as groundstates of the Bernasconi model. Finding these sequences is a notoriously hard problem, that so far can be solved only by exhaustive search. We review recent algorithms and present a new algorithm that finds optimal sequences of length N in time O(N {1.73}N). We computed all optimal sequences for N≤slant 66 and all optimal skewsymmetric sequences for N≤slant 119.

  2. Regulatory sequence analysis tools.

    PubMed

    van Helden, Jacques

    2003-07-01

    The web resource Regulatory Sequence Analysis Tools (RSAT) (http://rsat.ulb.ac.be/rsat) offers a collection of software tools dedicated to the prediction of regulatory sites in non-coding DNA sequences. These tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Alternative formats are supported for the representation of regulatory motifs (strings or position-specific scoring matrices) and several algorithms are proposed for pattern discovery. RSAT currently holds >100 fully sequenced genomes and these data are regularly updated from GenBank.

  3. Na+ coordination at the Na2 site of the Na+/I- symporter.

    PubMed

    Ferrandino, Giuseppe; Nicola, Juan Pablo; Sánchez, Yuly E; Echeverria, Ignacia; Liu, Yunlong; Amzel, L Mario; Carrasco, Nancy

    2016-09-13

    The sodium/iodide symporter (NIS) mediates active I(-) transport in the thyroid-the first step in thyroid hormone biosynthesis-with a 2 Na(+): 1 I(-) stoichiometry. The two Na(+) binding sites (Na1 and Na2) and the I(-) binding site interact allosterically: when Na(+) binds to a Na(+) site, the affinity of NIS for the other Na(+) and for I(-) increases significantly. In all Na(+)-dependent transporters with the same fold as NIS, the side chains of two residues, S353 and T354 (NIS numbering), were identified as the Na(+) ligands at Na2. To understand the cooperativity between the substrates, we investigated the coordination at the Na2 site. We determined that four other residues-S66, D191, Q194, and Q263-are also involved in Na(+) coordination at this site. Experiments in whole cells demonstrated that these four residues participate in transport by NIS: mutations at these positions result in proteins that, although expressed at the plasma membrane, transport little or no I(-) These residues are conserved throughout the entire SLC5 family, to which NIS belongs, suggesting that they serve a similar function in the other transporters. Our findings also suggest that the increase in affinity that each site displays when an ion binds to another site may result from changes in the dynamics of the transporter. These mechanistic insights deepen our understanding not only of NIS but also of other transporters, including many that, like NIS, are of great medical relevance.

  4. Indexing Similar DNA Sequences

    NASA Astrophysics Data System (ADS)

    Huang, Songbo; Lam, T. W.; Sung, W. K.; Tam, S. L.; Yiu, S. M.

    To study the genetic variations of a species, one basic operation is to search for occurrences of patterns in a large number of very similar genomic sequences. To build an indexing data structure on the concatenation of all sequences may require a lot of memory. In this paper, we propose a new scheme to index highly similar sequences by taking advantage of the similarity among the sequences. To store r sequences with k common segments, our index requires only O(n + NlogN) bits of memory, where n is the total length of the common segments and N is the total length of the distinct regions in all texts. The total length of all sequences is rn + N, and any scheme to store these sequences requires Ω(n + N) bits. Searching for a pattern P of length m takes O(m + m logN + m log(rk)psc(P) + occlogn), where psc(P) is the number of prefixes of P that appear as a suffix of some common segments and occ is the number of occurrences of P in all sequences. In practice, rk ≤ N, and psc(P) is usually a small constant. We have implemented our solution and evaluated our solution using real DNA sequences. The experiments show that the memory requirement of our solution is much less than that required by BWT built on the concatenation of all sequences. When compared to the other existing solution (RLCSA), we use less memory with faster searching time.

  5. A putative fourth Na+,K(+)-ATPase alpha-subunit gene is expressed in testis.

    PubMed Central

    Shamraj, O I; Lingrel, J B

    1994-01-01

    The Na+,K(+)-ATPase alpha subunit has three known isoforms, alpha 1, alpha 2 and alpha 3, each encoded by a separate gene. This study was undertaken to determine the functional status of a fourth human alpha-like gene, ATP1AL2. Partial genomic sequence analysis revealed regions exhibiting sequence similarity with exons 3-6 of the Na+,K(+)-ATPase alpha isoform genes. ATP1AL2 cDNAs spanning the coding sequence of a novel P-type ATPase alpha subunit were isolated from a rat testis library. The predicted polypeptide is 1028 amino acids long and exhibits 76-78% identity with the rat Na+,K(+)-ATPase alpha 1, alpha 2 and alpha 3 isoforms, indicating that ATP1AL2 may encode a fourth Na+,K(+)-ATPase alpha isoform. A 3.9-kb mRNA is expressed abundantly in human and rat testis. Images Fig. 2 Fig. 5 PMID:7809153

  6. Light-driven Na(+) pump from Gillisia limnaea: a high-affinity Na(+) binding site is formed transiently in the photocycle.

    PubMed

    Balashov, Sergei P; Imasheva, Eleonora S; Dioumaev, Andrei K; Wang, Jennifer M; Jung, Kwang-Hwan; Lanyi, Janos K

    2014-12-01

    A group of microbial retinal proteins most closely related to the proton pump xanthorhodopsin has a novel sequence motif and a novel function. Instead of, or in addition to, proton transport, they perform light-driven sodium ion transport, as reported for one representative of this group (KR2) from Krokinobacter. In this paper, we examine a similar protein, GLR from Gillisia limnaea, expressed in Escherichia coli, which shares some properties with KR2 but transports only Na(+). The absorption spectrum of GLR is insensitive to Na(+) at concentrations of ≤3 M. However, very low concentrations of Na(+) cause profound differences in the decay and rise time of photocycle intermediates, consistent with a switch from a "Na(+)-independent" to a "Na(+)-dependent" photocycle (or photocycle branch) at ∼60 μM Na(+). The rates of photocycle steps in the latter, but not the former, are linearly dependent on Na(+) concentration. This suggests that a high-affinity Na(+) binding site is created transiently after photoexcitation, and entry of Na(+) from the bulk to this site redirects the course of events in the remainder of the cycle. A greater concentration of Na(+) is needed for switching the reaction path at lower pH. The data suggest therefore competition between H(+) and Na(+) to determine the two alternative pathways. The idea that a Na(+) binding site can be created at the Schiff base counterion is supported by the finding that upon perturbation of this region in the D251E mutant, Na(+) binds without photoexcitation. Binding of Na(+) to the mutant shifts the chromophore maximum to the red like that of H(+), which occurs in the photocycle of the wild type.

  7. Complete Genome Sequence of Pseudomonas balearica DSM 6083T

    PubMed Central

    Salvà-Serra, Francisco; Jaén-Luchoro, Daniel; Seguí, Carolina; Aliaga, Francisco; Busquets, Antonio; Gomila, Margarita; Lalucat, Jorge

    2016-01-01

    The whole-genome sequence of Pseudomonas balearica SP1402 (DSM 6083T) has been completed and annotated. It was isolated as a naphthalene degrader from water of a lagooning wastewater treatment plant. P. balearica strains tolerate up to 8.5% NaCl and are considered true marine denitrifiers. PMID:27103708

  8. Effect of NaCl and Na2SO4 on the biodecolourization of K-2BP by Halomonas sp. GYW

    PubMed Central

    Lian, Jing; Xu, Zhifang; Guo, Jianbo; Yue, Lin; Guo, Yankai; Zhang, Chenxiao; Yang, Jingliang

    2014-01-01

    In this paper, the effect of NaCl and Na2SO4 on the biodecolourization of reactive brilliant red K-2BP by a Halomonas sp. GYW (EF188281) was investigated in details. The decolourisation efficiency and the oxidation–reduction potential (ORP) change were explored during the decolourization process. The results from sequencing batch tests showed that Na2SO4 influenced the decolourization efficiency more slightly than NaCl in different synthetic dye solutions with different mixtures of Na2SO4 and NaCl. In the dye solutions with the same salt concentration or the same Na+ concentration, high Na2SO4 concentration did not inhibit the decolourization process and even stimulated the decolourization efficiency of reactive brilliant red K-2BP. Compared to NaCl system, the addition of Na2SO4 increased the ORP values about 35 mV, which agreed with the theoretic analysis of Gibbs function. This study improved our knowledge of azo dye decolourization under high salinity conditions and provided efficient option for the treatment of azo dye wastewater. PMID:27594796

  9. Sequences for Student Investigation

    ERIC Educational Resources Information Center

    Barton, Jeffrey; Feil, David; Lartigue, David; Mullins, Bernadette

    2004-01-01

    We describe two classes of sequences that give rise to accessible problems for undergraduate research. These problems may be understood with virtually no prerequisites and are well suited for computer-aided investigation. The first sequence is a variation of one introduced by Stephen Wolfram in connection with his study of cellular automata. The…

  10. Agriculture: Scope and Sequence.

    ERIC Educational Resources Information Center

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This guide, which was written as an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System, outlines the suggested scope and sequence of a 3-year program in agriculture. The guide consists of a course description; general course objectives;…

  11. M&m Sequences

    ERIC Educational Resources Information Center

    Schultz, Harris S.; Shiflett, Ray C.

    2005-01-01

    Consider a sequence recursively formed as follows: Start with three real numbers, and then when k are known, let the (k +1)st be such that the mean of all k +1 equals the median of the first k. The authors conjecture that every such sequence eventually becomes stable. This article presents results related to their conjecture.

  12. Cosmetology: Scope and Sequence.

    ERIC Educational Resources Information Center

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This scope and sequence guide, developed for a cosmetology vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents, and the…

  13. Lichenase and coding sequences

    DOEpatents

    Li, Xin-Liang; Ljungdahl, Lars G.; Chen, Huizhong

    2000-08-15

    The present invention provides a fungal lichenase, i.e., an endo-1,3-1,4-.beta.-D-glucanohydrolase, its coding sequence, recombinant DNA molecules comprising the lichenase coding sequences, recombinant host cells and methods for producing same. The present lichenase is from Orpinomyces PC-2.

  14. Twin Mitochondrial Sequence Analysis.

    PubMed

    Bouhlal, Yosr; Martinez, Selena; Gong, Henry; Dumas, Kevin; Shieh, Joseph T C

    2013-09-01

    When applying genome-wide sequencing technologies to disease investigation, it is increasingly important to resolve sequence variation in regions of the genome that may have homologous sequences. The human mitochondrial genome challenges interpretation given the potential for heteroplasmy, somatic variation, and homologous nuclear mitochondrial sequences (numts). Identical twins share the same mitochondrial DNA (mtDNA) from early life, but whether the mitochondrial sequence remains similar is unclear. We compared an adult monozygotic twin pair using high throughput-sequencing and evaluated variants with primer extension and mitochondrial pre-enrichment. Thirty-seven variants were shared between the twin individuals, and the variants were verified on the original genomic DNA. These studies support highly identical genetic sequence in this case. Certain low-level variant calls were of high quality and homology to the mitochondrial DNA, and they were further evaluated. When we assessed calls in pre-enriched mitochondrial DNA templates, we found that these may represent numts, which can be differentiated from mtDNA variation. We conclude that twin identity extends to mitochondrial DNA, and it is critical to differentiate between numts and mtDNA in genome sequencing, particularly since significant heteroplasmy could influence genome interpretation. Further studies on mtDNA and numts will aid in understanding how variation occurs and persists. PMID:24040623

  15. Sequence History Update Tool

    NASA Technical Reports Server (NTRS)

    Khanampompan, Teerapat; Gladden, Roy; Fisher, Forest; DelGuercio, Chris

    2008-01-01

    The Sequence History Update Tool performs Web-based sequence statistics archiving for Mars Reconnaissance Orbiter (MRO). Using a single UNIX command, the software takes advantage of sequencing conventions to automatically extract the needed statistics from multiple files. This information is then used to populate a PHP database, which is then seamlessly formatted into a dynamic Web page. This tool replaces a previous tedious and error-prone process of manually editing HTML code to construct a Web-based table. Because the tool manages all of the statistics gathering and file delivery to and from multiple data sources spread across multiple servers, there is also a considerable time and effort savings. With the use of The Sequence History Update Tool what previously took minutes is now done in less than 30 seconds, and now provides a more accurate archival record of the sequence commanding for MRO.

  16. Na Cauda do Cometa

    NASA Astrophysics Data System (ADS)

    Voelzke, M. R.

    2009-01-01

    Quando viam um cometa, os antigos gregos imaginavam uma estrela com uma vasta cabeleira. Não à toa, a palavra deriva do termo koma, que significa cabelo. Constituídos por fragmentos de gelo e gases, os cometas possuem um núcleo sólido, que pode ter vários quilômetros de diâmetro, e uma cauda que sempre aponta na direção contrária ao Sol, devido aos ventos solares. Graças à aparência de pontos luminosos em movimento (ao contrário de outros astros, que parecem estáticos), esses corpos celestes foram interpretados por diferentes povos com muito misticismo, inspirando mitos tanto de boas-novas como de maus presságios. Conheça algumas dessas histórias:

  17. Regulation of persistent Na current by interactions between β subunits of voltage-gated Na channels

    PubMed Central

    Aman, Teresa K.; Grieco-Calub, Tina M.; Chen, Chunling; Rusconi, Raffaella; Slat, Emily A.; Isom, Lori L.; Raman, Indira M.

    2009-01-01

    The β subunits of voltage-gated Na channels (Scnxb) regulate the gating of pore-forming α subunits, as well as their trafficking and localization. In heterologous expression systems, β1, β2, and β3 subunits influence inactivation and persistent current in different ways. To test how the β4 protein regulates Na channel gating, we transfected β4 into HEK cells stably expressing NaV1.1. Unlike a free peptide with a sequence from the β4 cytoplasmic domain, the full-length β4 protein did not block open channels. Instead, β4 expression favored open states by shifting activation curves negative, decreasing the slope of the inactivation curve, and increasing the percentage of non-inactivating current. Consequently, persistent current tripled in amplitude. Expression of β1 or chimeric subunits including the β1 extracellular domain, however, favored inactivation. Co-expressing NaV1.1 and β4 with β1 produced tiny persistent currents, indicating that β1 overcomes the effects of β4 in heterotrimeric channels. In contrast, β1C121W, which contains an extracellular epilepsy-associated mutation, did not counteract the destabilization of inactivation by β4, and also required unusually large depolarizations for channel opening. In cultured hippocampal neurons transfected with β4, persistent current was slightly but significantly increased. Moreover, in β4-expressing neurons from Scn1b and Scn1b/Scn2b null mice, entry into inactivated states was slowed. These data suggest that β1 and β4 have antagonistic roles, the former favoring inactivation and the latter favoring activation. Because increased Na channel availability may facilitate action potential firing, these results suggest a mechanism for seizure susceptibility of both mice and humans with disrupted β1 subunits. PMID:19228957

  18. HIV Sequence Compendium 2015

    SciTech Connect

    Foley, Brian Thomas; Leitner, Thomas Kenneth; Apetrei, Cristian; Hahn, Beatrice; Mizrachi, Ilene; Mullins, James; Rambaut, Andrew; Wolinsky, Steven; Korber, Bette Tina Marie

    2015-10-05

    This compendium is an annual printed summary of the data contained in the HIV sequence database. We try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2015. Hence, though it is published in 2015 and called the 2015 Compendium, its contents correspond to the 2014 curated alignments on our website. The number of sequences in the HIV database is still increasing. In total, at the end of 2014, there were 624,121 sequences in the HIV Sequence Database, an increase of 7% since the previous year. This is the first year that the number of new sequences added to the database has decreased compared to the previous year. The number of near complete genomes (>7000 nucleotides) increased to 5834 by end of 2014. However, as in previous years, the compendium alignments contain only a fraction of these. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/ content/sequence/NEWALIGN/align.html As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  19. Evolution of DNA sequencing.

    PubMed

    Tipu, Hamid Nawaz; Shabbir, Ambreen

    2015-03-01

    Sanger and coworkers introduced DNA sequencing in 1970s for the first time. It principally relied on termination of growing nucleotide chain when a dideoxythymidine triphosphate (ddTTP) was inserted in it. Detection of terminated sequences was done radiographically on Polyacrylamide Gel Electrophoresis (PAGE). Improvements that have evolved over time in original Sanger sequencing include replacement of radiography with fluorescence, use of separate fluorescent markers for each nucleotide, use of capillary electrophoresis instead of polyacrylamide gel electrophoresis and then introduction of capillary array electrophoresis. However, this technique suffered from few inherent limitations like decreased sensitivity for low level mutant alleles, complexities in analyzing highly polymorphic regions like Major Histocompatibility Complex (MHC) and high DNA concentrations required. Several Next Generation Sequencing (NGS) technologies have been introduced by Roche, Illumina and other commercial manufacturers that tend to overcome Sanger sequencing limitations and have been reviewed. Introduction of NGS in clinical research and medical diagnostics is expected to change entire diagnostic approach. These include study of cancer variants, detection of minimal residual disease, exome sequencing, detection of Single Nucleotide Polymorphisms (SNPs) and their disease association, epigenetic regulation of gene expression and sequencing of microorganisms genome.

  20. Automatic Command Sequence Generation

    NASA Technical Reports Server (NTRS)

    Fisher, Forest; Gladded, Roy; Khanampompan, Teerapat

    2007-01-01

    Automatic Sequence Generator (Autogen) Version 3.0 software automatically generates command sequences for the Mars Reconnaissance Orbiter (MRO) and several other JPL spacecraft operated by the multi-mission support team. Autogen uses standard JPL sequencing tools like APGEN, ASP, SEQGEN, and the DOM database to automate the generation of uplink command products, Spacecraft Command Message Format (SCMF) files, and the corresponding ground command products, DSN Keywords Files (DKF). Autogen supports all the major multi-mission mission phases including the cruise, aerobraking, mapping/science, and relay mission phases. Autogen is a Perl script, which functions within the mission operations UNIX environment. It consists of two parts: a set of model files and the autogen Perl script. Autogen encodes the behaviors of the system into a model and encodes algorithms for context sensitive customizations of the modeled behaviors. The model includes knowledge of different mission phases and how the resultant command products must differ for these phases. The executable software portion of Autogen, automates the setup and use of APGEN for constructing a spacecraft activity sequence file (SASF). The setup includes file retrieval through the DOM (Distributed Object Manager), an object database used to store project files. This step retrieves all the needed input files for generating the command products. Depending on the mission phase, Autogen also uses the ASP (Automated Sequence Processor) and SEQGEN to generate the command product sent to the spacecraft. Autogen also provides the means for customizing sequences through the use of configuration files. By automating the majority of the sequencing generation process, Autogen eliminates many sequence generation errors commonly introduced by manually constructing spacecraft command sequences. Through the layering of commands into the sequence by a series of scheduling algorithms, users are able to rapidly and reliably construct the

  1. Regulation of the epithelial Na(+) channel by intracellular Na(+).

    PubMed

    Awayda, M S

    1999-08-01

    The hypothesis that the intracellular Na(+) concentration ([Na(+)](i)) is a regulator of the epithelial Na(+) channel (ENaC) was tested with the Xenopus oocyte expression system by utilizing a dual-electrode voltage clamp. [Na(+)](i) averaged 48.1 +/- 2.2 meq (n = 27) and was estimated from the amiloride-sensitive reversal potential. [Na(+)](i) was increased by direct injection of 27.6 nl of 0.25 or 0.5 M Na(2)SO(4). Within minutes of injection, [Na(+)](i) stabilized and remained elevated at 97.8 +/- 6.5 meq (n = 9) and 64. 9 +/- 4.4 (n = 5) meq 30 min after the initial injection of 0.5 and 0.25 M Na(2)SO(4), respectively. This increase of [Na(+)](i) caused a biphasic inhibition of ENaC currents. In oocytes injected with 0.5 M Na(2)SO(4) (n = 9), a rapid decrease of inward amiloride-sensitive slope conductance (g(Na)) to 0.681 +/- 0.030 of control within the first 3 min and a secondary, slower decrease to 0.304 +/- 0.043 of control at 30 min were observed. Similar but smaller inhibitions were also observed with the injection of 0.25 M Na(2)SO(4). Injection of isotonic K(2)SO(4) (70 mM) or isotonic K(2)SO(4) made hypertonic with sucrose (70 mM K(2)SO(4)-1.2 M sucrose) was without effect. Injection of a 0.5 M concentration of either K(2)SO(4), N-methyl-D-glucamine (NMDG) sulfate, or 0.75 M NMDG gluconate resulted in a much smaller initial inhibition (<14%) and little or no secondary decrease. Thus increases of [Na(+)](i) have multiple specific inhibitory effects on ENaC that can be temporally separated into a rapid phase that was complete within 2-3 min and a delayed slow phase that was observed between 5 and 30 min. PMID:10444397

  2. Scope and Sequence.

    ERIC Educational Resources Information Center

    Callison, Daniel

    2002-01-01

    Discusses scope and sequence plans for curriculum coordination in elementary and secondary education related to school libraries. Highlights include library skills; levels of learning objectives; technology skills; media literacy skills; and information inquiry skills across disciplines by grade level. (LRW)

  3. Pierre Robin sequence

    MedlinePlus

    Pierre Robin syndrome; Pierre Robin complex; Pierre Robin anomaly ... The exact causes of Pierre Robin sequence are unknown. It may be part of many genetic syndromes. The lower jaw develops slowly before birth, but ...

  4. SINGLE CELL GENOME SEQUENCING

    PubMed Central

    Yilmaz, Suzan; Singh, Anup K.

    2011-01-01

    Whole genome amplification and next-generation sequencing of single cells has become a powerful approach for studying uncultivated microorganisms that represent 90–99 % of all environmental microbes. Single cell sequencing enables not only the identification of microbes but also linking of functions to species, a feat not achievable by metagenomic techniques. Moreover, it allows the analysis of low abundance species that may be missed in community-based analyses. It has also proved very useful in complementing metagenomics in the assembly and binning of single genomes. With the advent of drastically cheaper and higher throughput sequencing technologies, it is expected that single cell sequencing will become a standard tool in studying the genome and transcriptome of microbial communities. PMID:22154471

  5. Sequencing Complex Genomic Regions

    SciTech Connect

    Eichler, Evan

    2009-05-28

    Evan Eichler, Howard Hughes Medical Investigator at the University of Washington, gives the May 28, 2009 keynote speech at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM. Part 2 of 2

  6. Sequencing Complex Genomic Regions

    SciTech Connect

    Eichler, Evan

    2009-05-28

    Evan Eichler, Howard Hughes Medical Investigator at the University of Washington, gives the May 28, 2009 keynote speech at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM. Part 1 of 2

  7. Authentication of byte sequences

    SciTech Connect

    Stearns, S.D.

    1991-06-01

    Algorithms for the authentication of byte sequences are described. The algorithms are designed to authenticate data in the Storage, Retrieval, Analysis, and Display (SRAD) Test Data Archive of the Radiation Effects and Testing Directorate (9100) at Sandia National Laboratories, and may be used in similar situations where authentication of stored data is required. The algorithms use a well-known error detection method called the Cyclic Redundancy Check (CRC). When a byte sequence is authenticated and stored, CRC bytes are generated and attached to the end of the sequence. When the authenticated data is retrieved, the authentication check consists of processing the entire sequence, including the CRC bytes, and checking for a remainder of zero. The error detection properties of the CRC are extensive and result in a reliable authentication of SRAD data.

  8. HIV Sequence Compendium 2010

    SciTech Connect

    Kuiken, Carla; Foley, Brian; Leitner, Thomas; Apetrei, Christian; Hahn, Beatrice; Mizrachi, Ilene; Mullins, James; Rambaut, Andrew; Wolinsky, Steven; Korber, Bette

    2010-12-31

    This compendium is an annual printed summary of the data contained in the HIV sequence database. In these compendia we try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2010. Hence, though it is called the 2010 Compendium, its contents correspond to the 2009 curated alignments on our website. The number of sequences in the HIV database is still increasing exponentially. In total, at the time of printing, there were 339,306 sequences in the HIV Sequence Database, an increase of 45% since last year. The number of near complete genomes (>7000 nucleotides) increased to 2576 by end of 2009, reflecting a smaller increase than in previous years. However, as in previous years, the compendium alignments contain only a small fraction of these. Included in the alignments are a small number of sequences representing each of the subtypes and the more prevalent circulating recombinant forms (CRFs) such as 01 and 02, as well as a few outgroup sequences (group O and N and SIV-CPZ). Of the rarer CRFs we included one representative each. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html. Reprints are available from our website in the form of both HTML and PDF files. As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  9. Genome sequencing conference II

    SciTech Connect

    Not Available

    1990-01-01

    Genome Sequencing Conference 2 was held September 30 to October 30, 1990. 26 speaker abstracts and 33 poster presentations were included in the program report. New and improved methods for DNA sequencing and genetic mapping were presented. Many of the papers were concerned with accuracy and speed of acquisition of data with computers and automation playing an increasing role. Individual papers have been processed separately for inclusion on the database.

  10. Pairwise Sequence Alignment Library

    SciTech Connect

    Jeff Daily, PNNL

    2015-05-20

    Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.

  11. Nanapore Sequencing with MSPA

    NASA Astrophysics Data System (ADS)

    Gundlach, Jens H.

    2011-10-01

    Nanopore sequencing is the simplest concept of converting the sequence of a single DNA molecule directly into an electronic signal. We introduced the protein pore MspA. derived from Mycobacterium smegmatis, to nanpore sequencing [1]. MspA has a single, narrow (-1.2nm) and short (<1nm) constriction, ideal to identify single nucleotides. Compared to solid state devices, MspA is reproducible with sub-nanometer precision and is engineerable using genetic mutations. DNA moves through the pore at rates exceeding 1nt/microsec. too fast to observe the passage of each nucleotide. However, when DNA is held with double stranded DNA sections or an avidin anchor, single nucleotides resident in MspA's constriction can be identified with highly resolved current differences. We have provided proof of principle of a nanopore sequencing method [2] in which we use DNA modified by inserting double stranded DNA-sections between every nucleotide. The double stranded sections are designed to halt translocation for long enough to sequentially read the sequence of the original DNA molecule. Prospects and developments to sequence unmodified native DNA using MspA will be discussed.[4pt] [1] T.Z. Butler, et al, PNAS 105 20647 (2008)[0pt] [2] I.M. Derrington, et al, PNAS 107 16060 (2010).

  12. Pairwise Sequence Alignment Library

    2015-05-20

    Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprintmore » that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.« less

  13. Solidification of NaCl-NaF eutectic in space

    NASA Technical Reports Server (NTRS)

    Yue, A. S.; Yu, J. G.

    1974-01-01

    Continuous and discontinuous NaF fibers, embedded in a NaCl matrix, have been produced in space and on earth, respectively. The production of continuous fibers in a eutectic mixture was attributed to the absence of convection current in the liquid during solidification in space. Image transmission and optical transmittance measurements of transverse sections of the space-grown and earth-grown ingots were made with a light microscope and a spectrometer. It was found that better optical properties were obtained from samples grown in space. This was attributed to a better alignment of NaF fibers along the ingot axis.

  14. Complete genome sequence of strain Lentibacillus amyloliquefaciens LAM0015(T) isolated from saline sediment.

    PubMed

    Wang, Jing-Li; Li, Yan-Bin; Ruan, Zhi-Yong; You, Yang; Wang, Lu-Shan; Qin, Han; Liu, Song; Shui, Zong-Xia; Wang, Yan-Wei; Tan, Fu-Rong; Wu, Bo; Dai, Li-Chun; Hu, Guo-Quan; Ma, Ke-Dong; He, Ming-Xiong

    2016-02-20

    The type strain Lentibacillus amyloliquefaciens LAM0015(T) with considerably highly NaCl tolerance is a member of halophiles. Here we report its genome sequence, the first to publish complete genome sequence of the Lentibacillus genus. It contains 3,858,520bp with an average GC content of 42.12%, encoding multiple valuable proteins academically and industrially. The genome sequence of strain LAM0015(T) provides basic information for further elucidation of halophilic mechanism and wider exploitation of functional genes.

  15. Optical properties of NaCl-NaF eutectics

    NASA Technical Reports Server (NTRS)

    Yue, A. S.; Yu, J. G.

    1976-01-01

    A new concept is advanced to explain the phenomenon of transmittance versus far-field infrared wavelength of the directionally solidified NaCl-NaF eutectic in terms of the two-dimensional Bragg Scattering and the polarization effect of Rayleigh scattering. This concept can be applied to other eutectic systems as long as the index of refraction of the matrix over a range of wavelength is known. Experimental data are in excellent agreement with the theoretical prediction.

  16. Program Synthesizes UML Sequence Diagrams

    NASA Technical Reports Server (NTRS)

    Barry, Matthew R.; Osborne, Richard N.

    2006-01-01

    A computer program called "Rational Sequence" generates Universal Modeling Language (UML) sequence diagrams of a target Java program running on a Java virtual machine (JVM). Rational Sequence thereby performs a reverse engineering function that aids in the design documentation of the target Java program. Whereas previously, the construction of sequence diagrams was a tedious manual process, Rational Sequence generates UML sequence diagrams automatically from the running Java code.

  17. Controlled processing during sequencing

    PubMed Central

    Thothathiri, Malathi; Rattinger, Michelle

    2015-01-01

    Longstanding evidence has identified a role for the frontal cortex in sequencing within both linguistic and non-linguistic domains. More recently, neuropsychological studies have suggested a specific role for the left premotor-prefrontal junction (BA 44/6) in selection between competing alternatives during sequencing. In this study, we used neuroimaging with healthy adults to confirm and extend knowledge about the neural correlates of sequencing. Participants reproduced visually presented sequences of syllables and words using manual button presses. Items in the sequence were presented either consecutively or concurrently. Concurrent presentation is known to trigger the planning of multiple responses, which might compete with one another. Therefore, we hypothesized that regions involved in controlled processing would show greater recruitment during the concurrent than the consecutive condition. Whole-brain analysis showed concurrent > consecutive activation in sensory, motor and somatosensory cortices and notably also in rostral-dorsal anterior cingulate cortex. Region of interest analyses showed increased activation within left BA 44/6 and correlation between this region’s activation and behavioral response times. Functional connectivity analysis revealed increased connectivity between left BA 44/6 and the posterior lobe of the cerebellum during the concurrent than the consecutive condition. These results corroborate recent evidence and demonstrate the involvement of BA 44/6 and other control regions when ordering co-activated representations. PMID:26578941

  18. Controlled processing during sequencing.

    PubMed

    Thothathiri, Malathi; Rattinger, Michelle

    2015-01-01

    Longstanding evidence has identified a role for the frontal cortex in sequencing within both linguistic and non-linguistic domains. More recently, neuropsychological studies have suggested a specific role for the left premotor-prefrontal junction (BA 44/6) in selection between competing alternatives during sequencing. In this study, we used neuroimaging with healthy adults to confirm and extend knowledge about the neural correlates of sequencing. Participants reproduced visually presented sequences of syllables and words using manual button presses. Items in the sequence were presented either consecutively or concurrently. Concurrent presentation is known to trigger the planning of multiple responses, which might compete with one another. Therefore, we hypothesized that regions involved in controlled processing would show greater recruitment during the concurrent than the consecutive condition. Whole-brain analysis showed concurrent > consecutive activation in sensory, motor and somatosensory cortices and notably also in rostral-dorsal anterior cingulate cortex. Region of interest analyses showed increased activation within left BA 44/6 and correlation between this region's activation and behavioral response times. Functional connectivity analysis revealed increased connectivity between left BA 44/6 and the posterior lobe of the cerebellum during the concurrent than the consecutive condition. These results corroborate recent evidence and demonstrate the involvement of BA 44/6 and other control regions when ordering co-activated representations.

  19. Associated proteins and renal epithelial Na+ channel function.

    PubMed

    Ismailov, I I; Berdiev, B K; Bradford, A L; Awayda, M S; Fuller, C M; Benos, D J

    1996-01-01

    The hypothesis that amiloride-sensitive Na+ channel complexes immunopurified from bovine renal papillary collecting tubules contain, as their core conduction component, an ENaC subunit, was tested by functional and immunological criteria. Disulfide bond reduction with dithiothreitol (DTT) of renal Na+ channels incorporated into planar lipid bilayers caused a reduction of single channel conductance from 40 pS to 13 pS, and uncoupled PKA regulation of this channel. The cation permeability sequence, as assessed from bi-ionic reversal potential measurements, and apparent amiloride equilibrium dissociation constant (K(amil)i) of the Na+ channels were unaltered by DTT treatment. Like ENaC, the DTT treated renal channel became mechanosensitive, and displayed a substantial decrease in K(amil)i following stretch (0.44 +/- 0.12 microM versus 6.9 +/- 1.0 microM). Moreover, stretch activation induced a loss in the channel's ability to discriminate between monovalent cations, and even allowed Ca2+ to permeate. Polyclonal antibodies generated against a fusion protein of alpha bENaC recognized a 70 kDa polypeptide component of the renal Na+ channel complex. These data suggest that ENaC is present in the immunopurified renal Na+ channel protein complex, and that PKA sensitivity is conferred by other associated proteins. PMID:8834119

  20. Generations of sequencing technologies.

    PubMed

    Pettersson, Erik; Lundeberg, Joakim; Ahmadian, Afshin

    2009-02-01

    Advancements in the field of DNA sequencing are changing the scientific horizon and promising an era of personalized medicine for elevated human health. Although platforms are improving at the rate of Moore's Law, thereby reducing the sequencing costs by a factor of two or three each year, we find ourselves at a point in history where individual genomes are starting to appear but where the cost is still too high for routine sequencing of whole genomes. These needs will be met by miniaturized and parallelized platforms that allow a lower sample and template consumption thereby increasing speed and reducing costs. Current massively parallel, state-of-the-art systems are providing significantly improved throughput over Sanger systems and future single-molecule approaches will continue the exponential improvements in the field.

  1. Ranking and Sequencing Model

    2009-08-13

    This database application (commonly called the Supermodel) provides a repository for managing critical facility/project information, allows the user to subjectively an objectively assess key criteria , quantify project risks, develop ROM cost estimates, determine facility/project end states, ultimately performing risk-based modeling to rank facilities/project based on risk, sequencing project schedules and provides an optimized recommended sequencing/scheduling of these projects which maximize the S&M cost savings to perform closure projects which benefit all stakeholders.

  2. Microchips for DNA sequencing

    NASA Astrophysics Data System (ADS)

    Mastrangelo, Carlos H.; Palaniappan, S.; Man, Piu Francis; Burns, Mark A.; Burke, David T.

    1999-08-01

    Genetic information is vital for understanding features and response of an organism. In humans, genetic errors are linked to the development of major diseases such as cancer and diabetes. In order to maximally exploit this information it is necessary to develop miniature sequencing assays that are rapid and inexpensive. In this paper we show how this could be attained with microfluidic chips that contain integrated assays. To date simple silicon/glass chips aimed for sequencing purpose have been realized; but these chips are not yet practical. Some of the solutions that are used to bring these devices closer to commercial applications are discussed.

  3. Additives and solvents-induced phase and morphology modification of NaYF4 for improving up-conversion emission

    NASA Astrophysics Data System (ADS)

    Zhuang, Jianle; Yang, Xianfeng; Wang, Jing; Lei, Bingfu; Liu, Yingliang; Wu, Mingmei

    2016-01-01

    Both cubic and hexagonal NaYF4 were synthesized in different reaction systems via hydro/solvo-thermal route. The effects of reaction temperature, solvents, and additives on the synthesis of NaYF4 have been studied in detail. It has been shown that phase transformation from cubic NaYF4 to hexagonal NaYF4 always occurred. The sequence of the ability for inducing the phase transformation was ethanol>H2O>acetic acid. It is found that ethanol can not only facilitate the formation of hexagonal NaYF4 but also control the growth of the crystal. This is quite unusual for the growth of H-NaYF4. The up-conversion emission properties of Yb/Er co-doped NaYF4 have also been investigated and the results demonstrated some general principles for improving up-conversion emission.

  4. Method to amplify variable sequences without imposing primer sequences

    DOEpatents

    Bradbury, Andrew M.; Zeytun, Ahmet

    2006-11-14

    The present invention provides methods of amplifying target sequences without including regions flanking the target sequence in the amplified product or imposing amplification primer sequences on the amplified product. Also provided are methods of preparing a library from such amplified target sequences.

  5. Na+ recirculation and isosmotic transport.

    PubMed

    Larsen, E H; Møbjerg, N

    2006-01-01

    The Na(+) recirculation theory for solute-coupled fluid absorption is an expansion of the local osmosis concept introduced by Curran and analyzed by Diamond & Bossert. Based on studies on small intestine the theory assumes that the observed recirculation of Na(+) serves regulation of the osmolarity of the absorbate. Mathematical modeling reproducing bioelectric and hydrosmotic properties of small intestine and proximal tubule, respectively, predicts a significant range of observations such as isosmotic transport, hyposmotic transport, solvent drag, anomalous solvent drag, the residual hydraulic permeability in proximal tubule of AQP1 (-/-) mice, and the inverse relationship between hydraulic permeability and the concentration difference needed to reverse transepithelial water flow. The model reproduces the volume responses of cells and lateral intercellular space (lis) following replacement of luminal NaCl by sucrose as well as the linear dependence of volume absorption on luminal NaCl concentration. Analysis of solvent drag on Na(+) in tight junctions provides explanation for the surprisingly high metabolic efficiency of Na(+) reabsorption. The model predicts and explains low metabolic efficiency in diluted external baths. Hyperosmolarity of lis is governed by the hydraulic permeability of the apical plasma membrane and tight junction with 6-7 mOsm in small intestine and < or = 1 mOsm in proximal tubule. Truly isosmotic transport demands a Na(+) recirculation of 50-70% in small intestine but might be barely measurable in proximal tubule. The model fails to reproduce a certain type of observations: The reduced volume absorption at transepithelial osmotic equilibrium in AQP1 knockout mice, and the stimulated water absorption by gallbladder in diluted external solutions. Thus, it indicates cellular regulation of apical Na(+) uptake, which is not included in the mathematical treatment. PMID:17206513

  6. Na+ recirculation and isosmotic transport.

    PubMed

    Larsen, E H; Møbjerg, N

    2006-01-01

    The Na(+) recirculation theory for solute-coupled fluid absorption is an expansion of the local osmosis concept introduced by Curran and analyzed by Diamond & Bossert. Based on studies on small intestine the theory assumes that the observed recirculation of Na(+) serves regulation of the osmolarity of the absorbate. Mathematical modeling reproducing bioelectric and hydrosmotic properties of small intestine and proximal tubule, respectively, predicts a significant range of observations such as isosmotic transport, hyposmotic transport, solvent drag, anomalous solvent drag, the residual hydraulic permeability in proximal tubule of AQP1 (-/-) mice, and the inverse relationship between hydraulic permeability and the concentration difference needed to reverse transepithelial water flow. The model reproduces the volume responses of cells and lateral intercellular space (lis) following replacement of luminal NaCl by sucrose as well as the linear dependence of volume absorption on luminal NaCl concentration. Analysis of solvent drag on Na(+) in tight junctions provides explanation for the surprisingly high metabolic efficiency of Na(+) reabsorption. The model predicts and explains low metabolic efficiency in diluted external baths. Hyperosmolarity of lis is governed by the hydraulic permeability of the apical plasma membrane and tight junction with 6-7 mOsm in small intestine and < or = 1 mOsm in proximal tubule. Truly isosmotic transport demands a Na(+) recirculation of 50-70% in small intestine but might be barely measurable in proximal tubule. The model fails to reproduce a certain type of observations: The reduced volume absorption at transepithelial osmotic equilibrium in AQP1 knockout mice, and the stimulated water absorption by gallbladder in diluted external solutions. Thus, it indicates cellular regulation of apical Na(+) uptake, which is not included in the mathematical treatment.

  7. Bayesian classification for promoter prediction in human DNA sequences

    NASA Astrophysics Data System (ADS)

    Bercher, J.-F.; Jardin, P.; Duriez, B.

    2006-11-01

    Many Computational methods are yet available for data retrieval and analysis of genomic sequences, but some functional sites are difficult to characterize. In this work, we examine the problem of promoter localization in human DNA sequences. Promoters are regulatory regions that governs the expression of genes, and their prediction is reputed difficult, so that this issue is still open. We present the Chaos Game representation (CGR) of DNA sequences which has many interesting properties, and the notion of `genomic signature' that proved relevant in phylogeny applications. Based on this notion, we develop a (naïve) bayesian classifier, evaluate its performances, and show that its adaptive implementation enable to reveal or assess core-promoter positions along a DNA sequence.

  8. Sequences close to periodic

    NASA Astrophysics Data System (ADS)

    Muchnik, Andrei A.; Pritykin, Yurii L.; Semenov, Aleksei L.

    2009-10-01

    This paper is a survey of concepts and results connected with generalizations of the notion of a periodic sequence, both classical and new. The topics discussed relate to almost periodicity in such areas as combinatorics on words, symbolic dynamics, expressibility in logical theories, computability, Kolmogorov complexity, and number theory. Bibliography: 124 titles.

  9. Lining up Arithmetic Sequences

    ERIC Educational Resources Information Center

    Bell, Carol J.

    2011-01-01

    Most future teachers are familiar with number patterns that represent an arithmetic sequence, and most are able to determine the general representation of the "n"th number in the pattern. However, when they are given a visual representation instead of the numbers in the pattern, it is not always easy for them to make the connection between the…

  10. Drugs preventing Na+ and Ca2+ overload.

    PubMed

    Ravens, U; Himmel, H M

    1999-03-01

    Cardiac intracellular Na+and Ca2+homeostasis is regulated by the concerted action of ion channels, pumps and exchangers. The Na+, K+-ATPase produces the electrochemical concentration gradient for Na+, which is the driving force for Ca2+removal from the cytosol via the Na+/Ca2+exchange. Reduction of this gradient by increased intracellular Na+concentration leads to cellular Ca2+overload resulting in arrhythmias and contractile dysfunction. Na+and Ca2+overload-associated arrhythmias can be produced experimentally by inhibition of Na+efflux (digitalis-induced intoxication) and by abnormal Na+influx via modulated Na+channels (veratridine, DPI 201-106; hypoxia) or via the Na+, H+exchanger. Theoretically, blockers of Na+and Ca2+channels, inhibitors of abnormal oscillatory release of Ca2+from internal stores or modulators of the Na+, Ca2+and Na+, H+exchanger activities could protect against cellular Na+and Ca2+overload. Three exemplary drugs that prevent Na+and Ca2+overload, i.e. the benzothiazolamine R56865, the methylenephenoxydioxy-derivative CP-060S, and the benzoyl-guanidine Hoe 642, a Na+, H+exchange blocker, are briefly reviewed with respect to their efficacy on digitalis-, veratridine- and ischaemia/reperfusion-induced arrhythmias. PMID:10094840

  11. Na Deposition on MnO(100)

    NASA Astrophysics Data System (ADS)

    Feng, Xu; Cox, David F.

    2016-03-01

    Na deposition on the MnO(100) surface was investigated by temperature programmed desorption (TPD), X-ray photoelectron spectroscopy (XPS) and low energy electron diffraction (LEED). Na TPD and XPS results indicate that adsorbed Na interacts strongly with the MnO substrate to form an irreversibly-adsorbed, oxidic Na compound on the surface for coverages up to 1 monolayer (ML). This strongly-bound Na diffuses into the MnO subsurface and bulk at elevated temperatures above 500 K. For Na coverages above 1 ML, metallic Na is present and desorbs from the surface below 500 K. The deposition of Na on MnO(100) follows a Stranski-Krastanov (SK) growth mode, with the formation of metallic Na islands following completion of the first Na monolayer. After Na deposition, the surface exhibits a diffuse (1 × 1) LEED pattern, suggesting the formation of disordered Na overlayers. After heating to 1000 K, the surface presents a (2 × 2) LEED pattern indicating that a surface reconstruction is induced by the diffusion of Na into the near surface region. CO2 can be used as a probe molecule in TPD to distinguish between metallic Na islands and oxidic Na in the first ML, and to indicate when Na that is still observable by XPS goes subsurface.

  12. Epitaxial NaCl structure {delta}-TaN{sub x}(001): Electronic transport properties, elastic modulus, and hardness versus N/Ta ratio

    SciTech Connect

    Shin, C.-S.; Gall, D.; Kim, Y.-W.; Desjardins, P.; Petrov, I.; Greene, J. E.; Oden, M.; Hultman, L.

    2001-09-15

    While metastable B1-NaCl-structure {delta}-TaN{sub x} is presently used in a variety of hard coating, wear-resistant, and diffusion barrier applications, it is a complex material exhibiting a wide single-phase field, x{approx_equal}0.94--1.37, and little is known about its fundamental properties. Here, we report physical properties of epitaxial {delta}-TaN{sub x} layers grown as a function of x on MgO(001) by ultrahigh vacuum reactive magnetron sputter deposition. The room-temperature resistivity ({rho}=225 {mu}{Omega} cm), hardness (H=30.9 GPa), and elastic modulus (E=455 GPa) of {delta}-TaN{sub x}(001) are independent of x over the range 0.94--1.22. However, changes in the electronic structure associated with increasing x>1.22 lead to an increase in {rho} with a decrease in H and E. All {delta}-TaN{sub x}(001) layers exhibit negative temperature coefficients of resistivity between 20 and 400 K due to weak carrier localization. {delta}-TaN{sub x} is superconducting with the highest critical temperature, 8.45 K, obtained for layers with the lowest N/Ta ratio, x=0.94. Based upon the above results, combined with the fact that the relaxed lattice constant a{sub 0} shows only a very weak dependence on x, we propose that the wide phase field in {delta}-TaN{sub x} is due primarily to antisite substitutions of Ta on N (and N on Ta) sites, rather than to cation and anion vacancies. To first order, antisite substitutions in TaN{sub x} are isoelectronic and hence have little effect on charge carrier density. At sufficiently high N/Ta ratios, however, simple electron-counting arguments are no longer valid since large deviations from stoichiometry alter the character of the band structure itself.

  13. Methods for comparing a DNA sequence with a protein sequence.

    PubMed

    Huang, X; Zhang, J

    1996-12-01

    We describe two methods for constructing an optimal global alignment of, and an optimal local alignment between, a DNA sequence and a protein sequence. The alignment model of the methods addresses the problems of frameshifts and introns in the DNA sequence. The methods require computer memory proportional to the sequence lengths, so they can rigorously process very huge sequences. The simplified versions of the methods were implemented as computer programs named NAP and LAP. The experimental results demonstrate that the programs are sensitive and powerful tools for finding genes by DNA-protein sequence homology.

  14. Membrane-integral pyrophosphatase subfamily capable of translocating both Na+ and H+.

    PubMed

    Luoto, Heidi H; Baykov, Alexander A; Lahti, Reijo; Malinen, Anssi M

    2013-01-22

    One of the strategies used by organisms to adapt to life under conditions of short energy supply is to use the by-product pyrophosphate to support cation gradients in membranes. Transport reactions are catalyzed by membrane-integral pyrophosphatases (PPases), which are classified into two homologous subfamilies: H(+)-transporting (found in prokaryotes, protists, and plants) and Na(+)-transporting (found in prokaryotes). Transport activities have been believed to require specific machinery for each ion, in accordance with the prevailing paradigm in membrane transport. However, experiments using a fluorescent pH probe and (22)Na(+) measurements in the current study revealed that five bacterial PPases expressed in Escherichia coli have the ability to simultaneously translocate H(+) and Na(+) into inverted membrane vesicles under physiological conditions. Consistent with data from phylogenetic analyses, our results support the existence of a third, dual-specificity bacterial Na(+),H(+)-PPase subfamily, which apparently evolved from Na(+)-PPases. Interestingly, genes for Na(+),H(+)-PPase have been found in the major microbes colonizing the human gastrointestinal tract. The Na(+),H(+)-PPases require Na(+) for hydrolytic and transport activities and are further activated by K(+). Based on ionophore effects, we conclude that the Na(+) and H(+) transport reactions are electrogenic and do not result from secondary antiport effects. Sequence comparisons further disclosed four Na(+),H(+)-PPase signature residues located outside the ion conductance channel identified earlier in PPases using X-ray crystallography. Our results collectively support the emerging paradigm that both Na(+) and H(+) can be transported via the same mechanism, with switching between Na(+) and H(+) specificities requiring only subtle changes in the transporter structure.

  15. HIV sequence compendium 2002

    SciTech Connect

    Kuiken, Carla; Foley, Brian; Freed, Eric; Hahn, Beatrice; Marx, Preston; McCutchan, Francine; Mellors, John; Wolinsky, Steven; Korber, Bette

    2002-12-31

    This compendium is an annual printed summary of the data contained in the HIV sequence database. In these compendia we try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Traditionally, we present the sequence data themselves in the form of alignments: Section II, an alignment of a selection of HIV-1/SIVcpz full-length genomes (a lot of LAI-like sequences, for example, have been omitted because they are so similar that they bias the alignment); Section III, a combined HIV-1/HIV-2/SIV whole genome alignment; Sections IV–VI, amino acid alignments for HIV-1/SIV-cpz, HIV-2/SIV, and SIVagm. The HIV-2/SIV and SIVagm amino acid alignments are separate because the genetic distances between these groups are so great that presenting them in one alignment would make it very elongated because of the large number of gaps that have to be inserted. As always, tables with extensive background information gathered from the literature accompany the whole genome alignments. The collection of whole-gene sequences in the database is now large enough that we have abundant representation of most subtypes. For many subtypes, and especially for subtype B, a large number of sequences that span entire genes were not included in the printed alignments to conserve space. A more complete version of all alignments is available on our website, http://hiv-web.lanl.gov/content/hiv-db/ALIGN_CURRENT/ALIGN-INDEX.html. Importantly, all these alignments have been edited to include only one sequence per person, based on phylogenetic trees that were created for all of them, as well as on the literature. Because of the number of sequences available, we have decided to use a different selection principle this year, based on the epidemiological importance of the subtypes. Subtypes A–D and CRFs 01 and 02 are by far the most widespread variants, and for these (when available) we have included 8–10 representatives in the alignments. The other

  16. Rapid Polymer Sequencer

    NASA Technical Reports Server (NTRS)

    Stolc, Viktor (Inventor); Brock, Mathew W. (Inventor)

    2011-01-01

    Method and system for rapid and accurate determination of each of a sequence of unknown polymer components, such as nucleic acid components. A self-assembling monolayer of a selected substance is optionally provided on an interior surface of a pipette tip, and the interior surface is immersed in a selected liquid. A selected electrical field is impressed in a longitudinal or transverse direction at the tip, a polymer sequence is passed through the tip, and a change in an electrical current signal is measured as each polymer component passes through the tip. Each measured change in electrical current signals is compared with a database of reference signals, with each reference signal identified with a polymer component, to identify the unknown polymer component. The tip preferably has a pore inner diameter of no more than about 40 nm and is prepared by heating and pulling a very small section of a glass tubing.

  17. RNA Sequencing in Schizophrenia

    PubMed Central

    Li, Xin; Teng, Shaolei

    2015-01-01

    Schizophrenia (SCZ) is a serious psychiatric disorder that affects 1% of general population and places a heavy burden worldwide. The underlying genetic mechanism of SCZ remains unknown, but studies indicate that the disease is associated with a global gene expression disturbance across many genes. Next-generation sequencing, particularly of RNA sequencing (RNA-Seq), provides a powerful genome-scale technology to investigate the pathological processes of SCZ. RNA-Seq has been used to analyze the gene expressions and identify the novel splice isoforms and rare transcripts associated with SCZ. This paper provides an overview on the genetics of SCZ, the advantages of RNA-Seq for transcriptome analysis, the accomplishments of RNA-Seq in SCZ cohorts, and the applications of induced pluripotent stem cells and RNA-Seq in SCZ research. PMID:27053919

  18. Transposon facilitated DNA sequencing

    SciTech Connect

    Berg, D.E.; Berg, C.M.; Huang, H.V.

    1990-01-01

    The purpose of this research is to investigate and develop methods that exploit the power of bacterial transposable elements for large scale DNA sequencing: Our premise is that the use of transposons to put primer binding sites randomly in target DNAs should provide access to all portions of large DNA fragments, without the inefficiencies of methods involving random subcloning and attendant repetitive sequencing, or of sequential synthesis of many oligonucleotide primers that are used to match systematically along a DNA molecule. Two unrelated bacterial transposons, Tn5 and {gamma}{delta}, are being used because they have both proven useful for molecular analyses, and because they differ sufficiently in mechanism and specificity of transposition to merit parallel development.

  19. Rod sequence advisor

    SciTech Connect

    Wood, R.M. ); Lu, Yi ); Furia, R.V.; Thompson, R.J. ); Lin, Ching-lu )

    1992-01-01

    During startup and power shaping maneuvers of boiling water reactors (BWR's), control rods are sequentially withdrawn from the reactor core. The withdrawal sequences determine the overall reactor power and the local core power density and are based on the knowledge of station engineers. It is important that the control rods are withdrawn in such a manner that the local power level does not become excessive while the desired reactor power is generated. Rules that constrain the relative positions of control rod groups have been developed to do this. While these rules are relatively simple, applying them to all possible movements of the 17 control rod groups in a typical BWR is complex and time consuming. SMARTRODS, is a rule based pilot expert system, was developed in LISP for the determination of the rod sequences.

  20. From Artificial Amino Acids to Sequence-Defined Targeted Oligoaminoamides.

    PubMed

    Morys, Stephan; Wagner, Ernst; Lächelt, Ulrich

    2016-01-01

    Artificial oligoamino acids with appropriate protecting groups can be used for the sequential assembly of oligoaminoamides on solid-phase. With the help of these oligoamino acids multifunctional nucleic acid (NA) carriers can be designed and produced in highly defined topologies. Here we describe the synthesis of the artificial oligoamino acid Fmoc-Stp(Boc3)-OH, the subsequent assembly into sequence-defined oligomers and the formulation of tumor-targeted plasmid DNA (pDNA) polyplexes. PMID:27436323

  1. Multiview image sequence enhancement

    NASA Astrophysics Data System (ADS)

    Jovanov, Ljubomir; Luong, Hiêp; Ružic, Tijana; Philips, Wilfried

    2015-03-01

    Realistic visualization is crucial for more intuitive representation of complex data, medical imaging, simulation and entertainment systems. Multiview autostereoscopic displays are great step towards achieving complete immersive user experience. However, providing high quality content for this type of displays is still a great challenge. Due to the different characteristics/settings of the cameras in the multivew setup and varying photometric characteristics of the objects in the scene, the same object may have different appearance in the sequences acquired by the different cameras. Images representing views recorded using different cameras in practice have different local noise, color and sharpness characteristics. View synthesis algorithms introduce artefacts due to errors in disparity estimation/bad occlusion handling or due to erroneous warping function estimation. If the input multivew images are not of sufficient quality and have mismatching color and sharpness characteristics, these artifacts may become even more disturbing. The main goal of our method is to simultaneously perform multiview image sequence denoising, color correction and the improvement of sharpness in slightly blurred regions. Results show that the proposed method significantly reduces the amount of the artefacts in multiview video sequences resulting in a better visual experience.

  2. Sequencing BPS spectra

    DOE PAGESBeta

    Gukov, Sergei; Nawata, Satoshi; Saberi, Ingmar; Stošić, Marko; Sułkowski, Piotr

    2016-03-02

    In this article, we provide both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explainmore » from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincar e polynomials in numerous examples. Among these structural properties is a novel "sliding" property, which can be explained by using (re fined) modular S-matrix. This leads to the identi fication of modular transformations in Chern-Simons theory and 3d N = 2 theory via the 3d/3d correspondence. In conclusion, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.« less

  3. Sequencing BPS spectra

    NASA Astrophysics Data System (ADS)

    Gukov, Sergei; Nawata, Satoshi; Saberi, Ingmar; Stošić, Marko; Sułkowski, Piotr

    2016-03-01

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel "sliding" property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d {N}=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  4. Genetic Architecture of NaCl Tolerance in Arabidopsis1

    PubMed Central

    Quesada, Víctor; García-Martínez, Santiago; Piqueras, Pedro; Ponce, María Rosa; Micol, José Luis

    2002-01-01

    The little success of breeding approaches toward the improvement of salt tolerance in crop species is thought to be attributable to the quantitative nature of most, if not all the processes implicated. Hence, the identification of some of the quantitative trait loci (QTL) that contribute to natural variation in salt tolerance should be instrumental in eventually manipulating the perception of salinity and the corresponding responses. A good choice to reach this goal is the plant model system Arabidopsis, whose complete genome sequence is now available. Aiming to analyze natural variability in salt tolerance, we have compared the ability of 102 wild-type races (named ecotypes or accessions) of Arabidopsis to germinate on 250 mm NaCl, finding a wide range of variation among them. Accessions displaying extremely different responses to NaCl were intercrossed, and the phenotypes found in their F2 progenies suggested that natural variation in NaCl tolerance during germination was under polygenic controls. Genetic distances calculated on the basis of variations in repeat number at 22 microsatellites, were analyzed in a group of either extremely salt-tolerant or extremely salt-sensitive accessions. We found that most but not all accessions with similar responses to NaCl are phylogenetically related. NaCl tolerance was also studied in 100 recombinant inbred lines derived from a cross between the Columbia-4 and Landsberg erecta accessions. We detected 11 QTL harboring naturally occurring alleles that contribute to natural variation in NaCl tolerance in Arabidopsis, six at the germination and five at the vegetative growth stages, respectively. At least five of these QTL are likely to represent loci not yet described by their relationship with salt stress. PMID:12376659

  5. Bound excitons at nitrogen and bismuth isoelectronic impurities

    NASA Astrophysics Data System (ADS)

    Christian, Theresa; Alberi, Kirstin; Beaton, Daniel; Fluegel, Brian; Mascarenhas, Angelo

    When nitrogen and bismuth dopants are simultaneously incorporated into a host lattice such as gallium arsenide (GaAs) or gallium phosphide (GaP), each dopant species contributes to the evolution of the electronic structure. Bound excitons in these systems luminescence from localized states whose distinctive radiative signatures provide invaluable clues into the nature of impurity clustering and inter-impurity interactions within the host lattice. Spectroscopic studies of these states will be presented for a series of samples grown by molecular beam epitaxy. Research was supported by the U. S. Department of Energy, Basic Energy Sciences, Materials Sciences and Engineering Division under contract DE-AC36-08GO28308 and by the Department of Energy Office of Science Graduate Fellowship Program (DOE SCGF), made possible in part by the American Recovery and Reinvestment Act of 2009, administered by ORISE-ORAU under Contract No. DE-AC05-06OR23100.

  6. Light- and heavy-hole trions bound to isoelectronic centers

    NASA Astrophysics Data System (ADS)

    Éthier-Majcher, G.; St-Jean, P.; Francoeur, S.

    2015-10-01

    Optical control strategies in semiconductor nanostructures have almost exclusively relied on heavy-hole exciton and trion states. Interestingly, optical access to both light- and heavy-hole trions may provide the missing resource for consolidating all single qubit operations in a single magnetic field configuration. In this work, we describe the conditions in which nearly degenerate light- and heavy-hole trions can be exploited for implementing electron spin initialization, control, and single-shot readout in systems of Cs or higher symmetry. Then, we experimentally demonstrate that a previously unidentified nitrogen pair configuration in GaAs exhibiting Cs symmetry binds both light- and heavy-hole excitons and negative trions. A detailed analysis of the energy and polarization of the emission allows determining the crystal-field and exchange coefficients, the electron, hole, and exciton Zeeman coefficients, and the light- and heavy-hole character of all states. This analysis also reveals that light- and heavy-hole trion states provide the Λ level structure necessary for initialization and control along with an energetically protected cycling transition compatible with single-shot readout.

  7. Bioinformatic characterizations and prediction of K+ and Na+ ion channels effector toxins

    PubMed Central

    Soli, Rima; Kaabi, Belhassen; Barhoumi, Mourad; El-Ayeb, Mohamed; Srairi-Abid, Najet

    2009-01-01

    Background K+ and Na+ channel toxins constitute a large set of polypeptides, which interact with their ion channel targets. These polypeptides are classified in two different structural groups. Recently a new structural group called birtoxin-like appeared to contain both types of toxins has been described. We hypothesized that peptides of this group may contain two conserved structural motifs in K+ and/or Na+ channels scorpion toxins, allowing these birtoxin-like peptides to be active on K+ and/or Na+ channels. Results Four multilevel motifs, overrepresented and specific to each group of K+ and/or Na+ ion channel toxins have been identified, using GIBBS and MEME and based on a training dataset of 79 sequences judged as representative of K+ and Na+ toxins. Unexpectedly birtoxin-like peptides appeared to present a new structural motif distinct from those present in K+ and Na+ channels Toxins. This result, supported by previous experimental data, suggests that birtoxin-like peptides may exert their activity on different sites than those targeted by classic K+ or Na+ toxins. Searching, the nr database with these newly identified motifs using MAST, retrieved several sequences (116 with e-value < 1) from various scorpion species (test dataset). The filtering process left 30 new and highly likely ion channel effectors. Phylogenetic analysis was used to classify the newly found sequences. Alternatively, classification tree analysis, using CART algorithm adjusted with the training dataset, using the motifs and their 2D structure as explanatory variables, provided a model for prediction of the activity of the new sequences. Conclusion The phylogenetic results were in perfect agreement with those obtained by the CART algorithm. Our results may be used as criteria for a new classification of scorpion toxins based on functional motifs. PMID:19284552

  8. Hebbian learning for olfactory sequences.

    PubMed

    Johnson, Andrew J; Cauchi, Laura; Miles, Christopher

    2013-06-01

    The present paper explores the generality of the Hebb repetition effect to the learning of olfactory sequences in order to assess commonality of memory functioning across sensory modalities. Participants completed a serial-order reconstruction task comprising sequences of four olfactory stimuli. Following presentation of each sequence, participants were re-presented with the odours and were required to reconstruct their order of presentation. Surreptitious re-presentation of the repeated sequence occurred on every third trial. This order reconstruction task produced a serial-position function comprising recency only for both the non-repeated and the repeated sequences. Importantly, serial-order reconstruction for the repeated odour sequence produced improved performance for that sequence compared to the non-repeated sequences. This observation of a Hebb repetition effect for olfactory sequences further supports the proposition that sequential learning can operate amodally.

  9. CRISPR interference and priming varies with individual spacer sequences

    PubMed Central

    Xue, Chaoyou; Seetharam, Arun S.; Musharova, Olga; Severinov, Konstantin; J. Brouns, Stan J.; Severin, Andrew J.; Sashital, Dipali G.

    2015-01-01

    CRISPR–Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated) systems allow bacteria to adapt to infection by acquiring ‘spacer’ sequences from invader DNA into genomic CRISPR loci. Cas proteins use RNAs derived from these loci to target cognate sequences for destruction through CRISPR interference. Mutations in the protospacer adjacent motif (PAM) and seed regions block interference but promote rapid ‘primed’ adaptation. Here, we use multiple spacer sequences to reexamine the PAM and seed sequence requirements for interference and priming in the Escherichia coli Type I-E CRISPR–Cas system. Surprisingly, CRISPR interference is far more tolerant of mutations in the seed and the PAM than previously reported, and this mutational tolerance, as well as priming activity, is highly dependent on spacer sequence. We identify a large number of functional PAMs that can promote interference, priming or both activities, depending on the associated spacer sequence. Functional PAMs are preferentially acquired during unprimed ‘naïve’ adaptation, leading to a rapid priming response following infection. Our results provide numerous insights into the importance of both spacer and target sequences for interference and priming, and reveal that priming is a major pathway for adaptation during initial infection. PMID:26586800

  10. CRISPR interference and priming varies with individual spacer sequences.

    PubMed

    Xue, Chaoyou; Seetharam, Arun S; Musharova, Olga; Severinov, Konstantin; Brouns, Stan J J; Severin, Andrew J; Sashital, Dipali G

    2015-12-15

    CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated) systems allow bacteria to adapt to infection by acquiring 'spacer' sequences from invader DNA into genomic CRISPR loci. Cas proteins use RNAs derived from these loci to target cognate sequences for destruction through CRISPR interference. Mutations in the protospacer adjacent motif (PAM) and seed regions block interference but promote rapid 'primed' adaptation. Here, we use multiple spacer sequences to reexamine the PAM and seed sequence requirements for interference and priming in the Escherichia coli Type I-E CRISPR-Cas system. Surprisingly, CRISPR interference is far more tolerant of mutations in the seed and the PAM than previously reported, and this mutational tolerance, as well as priming activity, is highly dependent on spacer sequence. We identify a large number of functional PAMs that can promote interference, priming or both activities, depending on the associated spacer sequence. Functional PAMs are preferentially acquired during unprimed 'naïve' adaptation, leading to a rapid priming response following infection. Our results provide numerous insights into the importance of both spacer and target sequences for interference and priming, and reveal that priming is a major pathway for adaptation during initial infection.

  11. β decay of Na32

    NASA Astrophysics Data System (ADS)

    Mattoon, C. M.; Sarazin, F.; Hackman, G.; Cunningham, E. S.; Austin, R. A. E.; Ball, G. C.; Chakrawarthy, R. S.; Finlay, P.; Garrett, P. E.; Grinyer, G. F.; Hyland, B.; Koopmans, K. A.; Leslie, J. R.; Phillips, A. A.; Schumaker, M. A.; Scraggs, H. C.; Schwarzenberg, J.; Smith, M. B.; Svensson, C. E.; Waddington, J. C.; Walker, P. M.; Washbrook, B.; Zganjar, E.

    2007-01-01

    The β-decay of Na32 has been studied using β-γ coincidences. New transitions and levels are tentatively placed in the level scheme of Mg32 from an analysis of γ-γ and β-γ-γ coincidences. The observation of the indirect feeding of the 2321 keV state in Mg32 removes some restrictions previously placed on the spin assignment for this state. No evidence of a state at 2117 keV in Mg32 is found. Previously unobserved weak transitions up to 5.4 MeV were recorded but could not be placed in the decay scheme of Na32.

  12. Interactions of external and internal H+ and Na+ with Na+/Na+ and Na+/H+ exchange of rabbit red cells: evidence for a common pathway.

    PubMed

    Morgan, K; Canessa, M

    1990-12-01

    We have studied the kinetic properties of rabbit red cell (RRBC) Na+/Na+ and Na+/H+ exchanges (EXC) in order to define whether or not both transport functions are conducted by the same molecule. The strategy has been to determine the interactions of Na+ and H+ at the internal (i) and external (o) sites for both exchanges modes. RRBC containing varying Nai and Hi were prepared by nystatin and DIDS treatment of acid-loaded cells. Na+/Na+ EXC was measured as Nao-stimulated Na+ efflux and Na+/H+ EXC as Nao-stimulated H+ efflux and delta pHo-stimulated Na+ influx into acid-loaded cells. The activation of Na+/Na+ EXC by Nao at pHi 7.4 did not follow simple hyperbolic kinetics. Testing of different kinetic models to obtain the best fit for the experimental data indicated the presence of high (Km 2.2 mM) and low affinity (Km 108 mM) sites for a single- or two-carrier system. The activation of Na+/H+ EXC by Nao (pHi 6.6, Nai less than 1 mM) also showed high (Km 11 mM) and low (Km 248 mM) affinity sites. External H+ competitively inhibited Na+/Na+ EXC at the low affinity Nao site (KH 52 nM) while internally H+ were competitive inhibitors (pK 6.7) at low Nai and allosteric activators (pK 7.0) at high Nai. Na+/H+ EXC was also inhibited by acid pHo and allosterically activated by Hi (pK 6.4). We also established the presence of a Nai regulatory site which activates Na+/H+ and Na+/Na+ EXC modifying the affinity for Nao of both pathways. At low Nai, Na+/Na+ EXC was inhibited by acid pHi and Na+/H+ stimulated but at high Nai, Na+/Na+ EXC was stimulated and Na+/H+ inhibited being the sum of both pathways kept constant. Both exchange modes were activated by two classes of Nao sites, cis-inhibited by external Ho, allosterically modified by the binding of H+ to a Hi regulatory site and regulated by Nai. These findings are consistent with Na+/Na+ EXC being a mode of operation of the Na+/H+ exchanger. Na+/H+ EXC was partially inhibited (80-100%) by dimethyl-amiloride (DMA) but basal or

  13. A vision for ubiquitous sequencing.

    PubMed

    Erlich, Yaniv

    2015-10-01

    Genomics has recently celebrated reaching the $1000 genome milestone, making affordable DNA sequencing a reality. With this goal successfully completed, the next goal of the sequencing revolution can be sequencing sensors--miniaturized sequencing devices that are manufactured for real-time applications and deployed in large quantities at low costs. The first part of this manuscript envisions applications that will benefit from moving the sequencers to the samples in a range of domains. In the second part, the manuscript outlines the critical barriers that need to be addressed in order to reach the goal of ubiquitous sequencing sensors.

  14. A vision for ubiquitous sequencing

    PubMed Central

    Erlich, Yaniv

    2015-01-01

    Genomics has recently celebrated reaching the $1000 genome milestone, making affordable DNA sequencing a reality. With this goal successfully completed, the next goal of the sequencing revolution can be sequencing sensors—miniaturized sequencing devices that are manufactured for real-time applications and deployed in large quantities at low costs. The first part of this manuscript envisions applications that will benefit from moving the sequencers to the samples in a range of domains. In the second part, the manuscript outlines the critical barriers that need to be addressed in order to reach the goal of ubiquitous sequencing sensors. PMID:26430149

  15. High-Throughput Sequencing Technologies

    PubMed Central

    Reuter, Jason A.; Spacek, Damek; Snyder, Michael P.

    2015-01-01

    Summary The human genome sequence has profoundly altered our understanding of biology, human diversity and disease. The path from the first draft sequence to our nascent era of personal genomes and genomic medicine has been made possible only because of the extraordinary advancements in DNA sequencing technologies over the past ten years. Here, we discuss commonly used high-throughput sequencing platforms, the growing array of sequencing assays developed around them as well as the challenges facing current sequencing platforms and their clinical application. PMID:26000844

  16. Lyotropic anions. Na channel gating and Ca electrode response

    PubMed Central

    1983-01-01

    The effects of external anions on gating of Na channels of frog skeletal muscle were studied under voltage clamp. Anions reversibly shift the voltage dependence of peak sodium permeability and of steady state sodium inactivation towards more negative potentials in the sequence: methanesulfonate less than or equal to Cl- less than or equal to acetate less than Br- less than or equal to NO-3 less than or equal to SO2-4 less than benzenesulfonate less than SCN- less than ClO-4; approximately the lyotropic sequence. Voltage shifts are graded with mole fraction in mixtures and are roughly additive to calcium shifts. The peak PNa is not greatly affected. Except for SO2-4, these anions did not change the Ca++ activity of the solutions as measured with the dye murexide. Shifts of gating can be explained as the electrostatic effect of anion adsorption to the Na channel or to nearby lipid. Such adsorption is expected to follow the lyotropic series. Anions also interfere significantly with the response of a Ca-sensitive membrane electrode following the same sequence of effectiveness as the shifts of gating. The lyotropic anions decrease the Ca++ sensitivity and cause anomalously negative responses of the Ca electrode because these anions are somewhat permeant in the hydrophobic detector membrane. PMID:6302198

  17. Cloning and expression of a FMRFamide-gated Na+ channel from Helisoma trivolvis and comparison with the native neuronal channel

    PubMed Central

    Jeziorski, Michael C; Green, Kevin A; Sommerville, John; Cottrell, Glen A

    2000-01-01

    We have cloned a cDNA encoding a Phe-Met-Arg-Phe-NH2 (FMRFamide)-gated Na+ channel from nervous tissue of the pond snail Helisoma trivolvis (HtFaNaC) and expressed the channel in Xenopus oocytes. The deduced amino acid sequence of the protein expressed by HtFaNaC is 65 % identical to that of the FMRFamide-gated channel cloned from Helix aspersa (HaFaNaC). HtFaNaC expressed in oocytes was less sensitive to FMRFamide (EC50 = 70 μM) than HaFaNaC (EC50 = 2 μM). The two had a similar selectivity for Na+. The amplitude of the FMRFamide response of HtFaNaC was increased by reducing the extracellular concentration of divalent cations. The conductance of the two channels was similar, but the mean open time of unitary events was shorter for expressed HtFaNaC compared to expressed HaFaNaC. Each channel was susceptible to peptide block by high agonist concentrations. In marked contrast to HaFaNaC and other amiloride-sensitive Na+ channels, amiloride, and the related drugs benzamil and 5-(N-ethyl-N-isopropyl)-amiloride (EIPA), enhanced the FMRFamide response in oocytes expressing HtFaNaC cRNA. The potentiating effects of EIPA and benzamil were greater than those of amiloride. Unitary current analysis showed that with such drugs, there was channel blockade as well as an increased probability of channel opening. The similar permeability of the oocyte-expressed HtFaNaC and the Helisoma neuronal channel, and the susceptibility of both to agonist blockade and blockade by divalent cations, suggest that the channels are the same. However, neuronal channels were less susceptible to enhancement by amiloride analogues and in some patches were more sensitive to FMRFamide than expressed HtFaNaC. PMID:10878095

  18. Nutrient transport in the small intestine: Na+,K+-ATPase expression and activity in the small intestine of the chicken as influenced by dietary sodium.

    PubMed

    Gal-Garber, O; Mabjeesh, S J; Sklan, D; Uni, Z

    2003-07-01

    The Na+-K+-ATPase, localized in the basolateral membrane of enterocytes plays a major role in nutrient transport in the small intestine by transferring K+ ions into and Na+ out of the cell. Within the enterocyte, homeostasis is maintained by active exclusion of Na from the cell by the Na+,K+-adenosine triphosphatase (ATPase) or sodium pump. Because much of the intestinal nutrient transport is by Na cotransporters, Na+,K+-ATPase may be used to evaluate nutrient uptake. In this study, nutrient transport was evaluated by determining expression and activity of Na+-K+-ATPase in the jejunum of chicks fed diets with different concentrations of Na. Expression of the chicken Na+-K+-ATPase gene was examined following isolation of an 1,140 bp cDNA fragment of the alpha-subunit using a reverse transcription (RT)-PCR reaction with specific primers. This fragment was sequenced and showed 95 to 98% homology with the mammalian alpha-subunit of the Na+-K+-ATPase genes. This cDNA fragment was used as a specific probe in Northern blot hybridization for determination of expression in the chicken jejunum. Expression of mRNA of Na+-K+-ATPase was enhanced at low dietary Na but was unchanged at high dietary Na concentrations. In contrast, activity of the enzyme was low with low dietary Na and unchanged at high dietary Na. The Vmax of the Na+-K+-ATPase was unchanged, but affinity was altered by dietary Na concentrations. Thus, determination of expression and activity of intestinal Na+-K+-ATPase allows clearer understanding of changes in intestinal uptake due to dietary Na.

  19. Reprever: resolving low-copy duplicated sequences using template driven assembly.

    PubMed

    Kim, Sangwoo; Medvedev, Paul; Paton, Tara A; Bafna, Vineet

    2013-07-01

    Genomic sequence duplication is an important mechanism for genome evolution, often resulting in large sequence variations with implications for disease progression. Although paired-end sequencing technologies are commonly used for structural variation discovery, the discovery of novel duplicated sequences remains an unmet challenge. We analyze duplicons starting from identified high-copy number variants. Given paired-end mapped reads, and a candidate high-copy region, our tool, Reprever, identifies (a) the insertion breakpoints where the extra duplicons inserted into the donor genome and (b) the actual sequence of the duplicon. Reprever resolves ambiguous mapping signatures from existing homologs, repetitive elements and sequencing errors to identify breakpoint. At each breakpoint, Reprever reconstructs the inserted sequence using profile hidden Markov model (PHMM)-based guided assembly. In a test on 1000 artificial genomes with simulated duplication, Reprever could identify novel duplicates up to 97% of genomes within 3 bp positional and 1% sequence errors. Validation on 680 fosmid sequences identified and reconstructed eight duplicated sequences with high accuracy. We applied Reprever to reanalyzing a re-sequenced data set from the African individual NA18507 to identify >800 novel duplicates, including insertions in genes and insertions with additional variation. polymerase chain reaction followed by capillary sequencing validated both the insertion locations of the strongest predictions and their predicted sequence. PMID:23658221

  20. Correspondence: Searching sequence space

    SciTech Connect

    Youvan, D.C.

    1995-08-01

    This correspondence debates the efficiency and application of genetic algorithms (GAs) to search protein sequence space. The important experimental point is that such sparse searches utilize physically realistic syntheses. In this regard, all GA-based technologies are very similar; they {open_quotes}learn{close_quotes} from their initial sparse search and then generate interesting new proteins within a few iterations. Which GA-based technology is best? That probably depends on the protein and the specific engineering goal. Given the fact that the field of combinatorial chemistry is still in its infancy, it is probably wise to consider all of the proven mutagenesis methods. 19 refs.

  1. DNA Sequencing apparatus

    DOEpatents

    Tabor, Stanley; Richardson, Charles C.

    1992-01-01

    An automated DNA sequencing apparatus having a reactor for providing at least two series of DNA products formed from a single primer and a DNA strand, each DNA product of a series differing in molecular weight and having a chain terminating agent at one end; separating means for separating the DNA products to form a series bands, the intensity of substantially all nearby bands in a different series being different, band reading means for determining the position an This invention was made with government support including a grant from the U.S. Public Health Service, contract number AI-06045. The U.S. government has certain rights in the invention.

  2. Sequencing the Unrearranged Human Immunoglobin

    SciTech Connect

    Warren, Rene

    2010-06-03

    Rene Warren from Canada's Michael Smith Genome Sciences Centre discusses sequencing and finishing the IgH heavy chain locus on June 3, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  3. Marks of Change in Sequences

    NASA Astrophysics Data System (ADS)

    Jürgensen, H.

    2011-12-01

    Given a sequence of events, how does one recognize that a change has occurred? We explore potential definitions of the concept of change in a sequence and propose that words in relativized solid codes might serve as indicators of change.

  4. Next-Generation Sequencing Platforms

    NASA Astrophysics Data System (ADS)

    Mardis, Elaine R.

    2013-06-01

    Automated DNA sequencing instruments embody an elegant interplay among chemistry, engineering, software, and molecular biology and have built upon Sanger's founding discovery of dideoxynucleotide sequencing to perform once-unfathomable tasks. Combined with innovative physical mapping approaches that helped to establish long-range relationships between cloned stretches of genomic DNA, fluorescent DNA sequencers produced reference genome sequences for model organisms and for the reference human genome. New types of sequencing instruments that permit amazing acceleration of data-collection rates for DNA sequencing have been developed. The ability to generate genome-scale data sets is now transforming the nature of biological inquiry. Here, I provide an historical perspective of the field, focusing on the fundamental developments that predated the advent of next-generation sequencing instruments and providing information about how these instruments work, their application to biological research, and the newest types of sequencers that can extract data from single DNA molecules.

  5. The NA62 trigger system

    NASA Astrophysics Data System (ADS)

    Krivda, M.; NA62 Collaboration

    2013-08-01

    The main aim of the NA62 experiment (NA62 Technical Design Report, na62.web.cern.ch/NA62/Documents/TD_Full_doc_v1.pdf> [1]) is to study ultra-rare Kaon decays. In order to select rare events over the overwhelming background, central systems with high-performance, high bandwidth, flexibility and configurability are necessary, that minimize dead time while maximizing data collection reliability. The NA62 experiment consists of 12 sub-detector systems and several trigger and control systems, for a total channel count of less than 100,000. The GigaTracKer (GTK) has the largest number of channels (54,000), and the Liquid Krypton (LKr) calorimeter shares with it the largest raw data rate (19 GB/s). The NA62 trigger system works with 3 trigger levels. The first trigger level is based on a hardware central trigger unit, so-called L0 Trigger Processor (L0TP), and Local Trigger Units (LTU), which are all located in the experimental cavern. Other two trigger levels are based on software, and done with a computer farm located on surface. The L0TP receives information from triggering sub-detectors asynchronously via Ethernet; it processes the information, and then transmits a final trigger decision synchronously to each sub-detector through the Trigger and Timing Control (TTC) system. The interface between L0TP and the TTC system, which is used for trigger and clock distribution, is provided by the Local Trigger Unit board (LTU). The LTU can work in two modes: global and stand-alone. In the global mode, the LTU provides an interface between L0TP and TTC system. In the stand-alone mode, the LTU can fully emulate L0TP and so provides an independent way for each sub-detector for testing or calibration purposes. In addition to the emulation functionality, a further functionality is implemented that allows to synchronize the clock of the LTU with the L0TP and the TTC system. For testing and debugging purposes, a Snap Shot Memory (SSM) interface is implemented, that can work

  6. Europlanet NA2 Science Networking

    NASA Astrophysics Data System (ADS)

    Harri, Ari-Matti; Szego, Karoly; Genzer, Maria; Schmidt, Walter; Krupp, Norbert; Lammer, Helmut; Kallio, Esa; Haukka, Harri

    2013-04-01

    Europlanet RI / NA2 Science Networking [1] focused on determining the major goals of current and future European planetary science, relating them to the Research Infrastructure that the Europlanet RI project [2] developed, and placing them in a more global context. NA2 also enhanced the ability of European planetary scientists to participate on the global scene with their own agenda-setting projects and ideas. The Networking Activity NA2 included five working groups, aimed at identifying key science issues and producing reference books on major science themes that will bridge the gap between the results of present and past missions and the scientific preparation of the future ones. Within the Europlanet RI project (2009-2012) the NA2 and NA2-WGs organized thematic workshops, an expert exchange program and training groups to improve the scientific impact of this Infrastructure. The principal tasks addressed by NA2 were: • Science activities in support to the optimal use of data from past and present space missions, involving the broad planetary science community beyond the "space club" • Science activities in support to the preparation of future planetary missions: Earth-based preparatory observations, laboratory studies, R&D on advanced instrumentation and exploration technologies for the future, theory and modeling etc. • Develop scientific activities, joint publications, dedicated meetings, tools and services, education activities, engaging the public and industries • Update science themes and addressing the two main scientific objectives • Prepare and support workshops of the International Space Science Institute (ISSI) in Bern and • Support Trans National Activities (TNAs), Joined Research Activities (JRAs) and the Integrated and Distributed Information Service (IDIS) of the Europlanet project These tasks were achieved by WG workshops organized by the NA2 working groups, by ISSI workshops and by an Expert Exchange Program. There were 17 official WG

  7. Sodium iron hexacyanoferrate with high Na content as a Na-rich cathode material for Na-ion batteries

    SciTech Connect

    You, Ya; Yu, Xi -Qian; Yin, Ya -Xia; Nam, Kyung -Wan; Guo, Yu -Guo

    2014-10-27

    Owing to the worldwide abundance and low-cost of Na, room-temperature Na-ion batteries are emerging as attractive energy storage systems for large-scale grids. Increasing the Na content in cathode material is one of the effective ways to achieve high energy density. Prussian blue and its analogues (PBAs) are promising Na-rich cathode materials since they can theoretically store two Na ions per formula. However, increasing the Na content in PBAs cathode materials is a big challenge in the current. Here we show that sodium iron hexacyanoferrate with high Na content could be obtained by simply controlling the reducing agent and reaction atmosphere during synthesis. The Na content can reach as high as 1.63 per formula, which is the highest value for sodium iron hexacyanoferrate. This Na-rich sodium iron hexacyanoferrate demonstrates a high specific capacity of 150 mA h g-1 and remarkable cycling performance with 90% capacity retention after 200 cycles. Furthermore, the Na intercalation/de-intercalation mechanism is systematically studied by in situ Raman, X-ray diffraction and X-ray absorption spectroscopy analysis for the first time. As a result, the Na-rich sodium iron hexacyanoferrate could function as a plenteous Na reservoir and has great potential as a cathode material toward practical Na-ion batteries.

  8. Sodium iron hexacyanoferrate with high Na content as a Na-rich cathode material for Na-ion batteries

    DOE PAGESBeta

    You, Ya; Yu, Xi -Qian; Yin, Ya -Xia; Nam, Kyung -Wan; Guo, Yu -Guo

    2014-10-27

    Owing to the worldwide abundance and low-cost of Na, room-temperature Na-ion batteries are emerging as attractive energy storage systems for large-scale grids. Increasing the Na content in cathode material is one of the effective ways to achieve high energy density. Prussian blue and its analogues (PBAs) are promising Na-rich cathode materials since they can theoretically store two Na ions per formula. However, increasing the Na content in PBAs cathode materials is a big challenge in the current. Here we show that sodium iron hexacyanoferrate with high Na content could be obtained by simply controlling the reducing agent and reaction atmospheremore » during synthesis. The Na content can reach as high as 1.63 per formula, which is the highest value for sodium iron hexacyanoferrate. This Na-rich sodium iron hexacyanoferrate demonstrates a high specific capacity of 150 mA h g-1 and remarkable cycling performance with 90% capacity retention after 200 cycles. Furthermore, the Na intercalation/de-intercalation mechanism is systematically studied by in situ Raman, X-ray diffraction and X-ray absorption spectroscopy analysis for the first time. As a result, the Na-rich sodium iron hexacyanoferrate could function as a plenteous Na reservoir and has great potential as a cathode material toward practical Na-ion batteries.« less

  9. Sanger dideoxy sequencing of DNA.

    PubMed

    Walker, Sarah E; Lorsch, Jon

    2013-01-01

    While the ease and reduced cost of automated DNA sequencing has largely obviated the need for manual dideoxy sequencing for routine purposes, specific applications require manual DNA sequencing. For instance, in studies of enzymes or proteins that bind or modify DNA, a DNA ladder is often used to map the site at which an enzyme is bound or a modification occurs. In these cases, the Sanger method for dideoxy sequencing provides a rapid and facile method for producing a labeled DNA ladder.

  10. Skeletal Muscle-specific Calpain Is an Intracellular Na+-dependent Protease*

    PubMed Central

    Ono, Yasuko; Ojima, Koichi; Torii, Fukuyo; Takaya, Emi; Doi, Naoko; Nakagawa, Kazuhiro; Hata, Shoji; Abe, Keiko; Sorimachi, Hiroyuki

    2010-01-01

    Because intracellular [Na+] is kept low by Na+/K+-ATPase, Na+ dependence is generally considered a property of extracellular enzymes. However, we found that p94/calpain 3, a skeletal-muscle-specific member of the Ca2+-activated intracellular “modulator proteases” that is responsible for a limb-girdle muscular dystrophy (“calpainopathy”), underwent Na+-dependent, but not Cs+-dependent, autolysis in the absence of Ca2+. Furthermore, Na+ and Ca2+ complementarily activated autolysis of p94 at physiological concentrations. By blocking Na+/K+-ATPase, we confirmed intracellular autolysis of p94 in cultured cells. This was further confirmed using inactive p94:C129S knock-in (p94CS-KI) mice as negative controls. Mutagenesis studies showed that much of the p94 molecule contributed to its Na+/Ca2+-dependent autolysis, which is consistent with the scattered location of calpainopathy-associated mutations, and that a conserved Ca2+-binding sequence in the protease acted as a Na+ sensor. Proteomic analyses using Cs+/Mg2+ and p94CS-KI mice as negative controls revealed that Na+ and Ca2+ direct p94 to proteolyze different substrates. We propose three roles for Na+ dependence of p94; 1) to increase sensitivity of p94 to changes in physiological [Ca2+], 2) to regulate substrate specificity of p94, and 3) to regulate contribution of p94 as a structural component in muscle cells. Finally, this is the first example of an intracellular Na+-dependent enzyme. PMID:20460380

  11. Sodium Kinetics of Na,K-ATPase α Isoforms in Intact Transfected HeLa Cells

    PubMed Central

    Zahler, Raphael; Zhang, Zhong-Ting; Manor, Mira; Boron, Walter F.

    1997-01-01

    By participating in the regulation of ion and voltage gradients, the Na-K pump (i.e., Na,K-ATPase) influences many aspects of cellular physiology. Of the four α isoforms of the pump, α1 is ubiquitous, α2 is predominant in skeletal muscle, and α3 is found in neurons and the cardiac conduction system. To determine whether the isoforms have different intracellular Na+ affinities, we used the Na+-sensitive dye sodium-binding benzofuran isophthalate (SBFI) to measure pump-mediated Na+ efflux as a function of [Na+]i in human HeLa cells stably transfected with rat Na-K pump isoforms. We Na+-loaded the cells, and then monitored the time course of the decrease in [Na+]i after removing external Na+. All transfected rat α subunits were highly ouabain resistant: the α1 isoform is naturally resistant, whereas the α2 and α3 isoforms had been mutagenized to render them resistant. Thus, the Na+ efflux mediated by endogenous and transfected pumps could be separated by studying the cells at low (1 μM) and high (4 mM) ouabain concentrations. We found that the apparent Km for Na+ efflux attributable to the native human α1 isoform was 12 mM, which was similar to the Km of rat α1. The α2 and α3 isoforms had apparent Km's of 22 and 33 mM, respectively. The cells expressing α3 had a high resting [Na+]i. The maximal activity of native α1 in the α3-transfected cells was only ∼56% of native α1 activity in untransfected HeLa cells, suggesting that transfection with α3 led to a compensatory decrease in endogenous α1 pumps. We conclude that the apparent Km(Na+) for rat Na-K pump isoforms increases in the sequence α1 < α2 < α3. The α3 isoform may be suited for handling large Na+ loads in electrically active cells. PMID:9236212

  12. Ionic regulation of Na absorption in proximal colon: cation inhibition of electroneutral Na absorption

    SciTech Connect

    Sellin, J.H.; De Soignie, R.

    1987-01-01

    Active Na absorption (J/sub net//sup NA/) in rabbit proximal colon in vitro is paradoxically stimulated as (Na) in the bathing media is lowered with constant osmolarity. J/sub m..-->..s//sup Na/ increases almost linearly from 0 to 50 mM (Na)/sub 0/ but then plateaus and actually decreases from 50 to 140 mM (Na)/sub 0/, consistent with inhibition of an active transport process. Both lithium and Na are equally effective inhibitors of J/sub net//sup Na/, whereas choline and mannitol do not block the high rate of J/sub net//sup Na/ observed in decreased (Na)/sub 0/. Either gluconate or proprionate replacement of Cl inhibits J/sub net//sup Na/. J/sub net//sup Na/ at lowered (Na)/sub 0/ is electrically silent and is accompanied by increased Cl absorption; it is inhibited by 10/sup -3/ M amiloride and 10/sup -3/ theophylline but not by 10/sup -4/ M bumetanide. Epinephrine is equally effective at stimulating Na absorption at 50 and 140 mM (Na). Na gradient experiments are consistent with a predominantly serosal effect of the decreased (Na)/sub 0/. These results suggest that 1) Na absorption in rabbit proximal colon in vitro is stimulated by decreased (Na); 2) the effect is cation specific, both Na and Li blocking the stimulatory effect; 3) the transport is mediated by Na-H exchange and is Cl dependent but 4) is under different regulatory mechanisms than the epinephrine-sensitive Na-Cl cotransport previously described in proximal colon. Under the appropriate conditions, proximal colon absorbs Na extremely efficiently. Na-H exchange in this epithelium is cation inhibitable, either directly or by a secondary regulatory process.

  13. Automated Identification of Nucleotide Sequences

    NASA Technical Reports Server (NTRS)

    Osman, Shariff; Venkateswaran, Kasthuri; Fox, George; Zhu, Dian-Hui

    2007-01-01

    STITCH is a computer program that processes raw nucleotide-sequence data to automatically remove unwanted vector information, perform reverse-complement comparison, stitch shorter sequences together to make longer ones to which the shorter ones presumably belong, and search against the user s choice of private and Internet-accessible public 16S rRNA databases. ["16S rRNA" denotes a ribosomal ribonucleic acid (rRNA) sequence that is common to all organisms.] In STITCH, a template 16S rRNA sequence is used to position forward and reverse reads. STITCH then automatically searches known 16S rRNA sequences in the user s chosen database(s) to find the sequence most similar to (the sequence that lies at the smallest edit distance from) each spliced sequence. The result of processing by STITCH is the identification of the most similar well-described bacterium. Whereas previously commercially available software for analyzing genetic sequences operates on one sequence at a time, STITCH can manipulate multiple sequences simultaneously to perform the aforementioned operations. A typical analysis of several dozen sequences (length of the order of 103 base pairs) by use of STITCH is completed in a few minutes, whereas such an analysis performed by use of prior software takes hours or days.

  14. Chromosome specific repetitive DNA sequences

    DOEpatents

    Moyzis, Robert K.; Meyne, Julianne

    1991-01-01

    A method is provided for determining specific nucleotide sequences useful in forming a probe which can identify specific chromosomes, preferably through in situ hybridization within the cell itself. In one embodiment, chromosome preferential nucleotide sequences are first determined from a library of recombinant DNA clones having families of repetitive sequences. Library clones are identified with a low homology with a sequence of repetitive DNA families to which the first clones respectively belong and variant sequences are then identified by selecting clones having a pattern of hybridization with genomic DNA dissimilar to the hybridization pattern shown by the respective families. In another embodiment, variant sequences are selected from a sequence of a known repetitive DNA family. The selected variant sequence is classified as chromosome specific, chromosome preferential, or chromosome nonspecific. Sequences which are classified as chromosome preferential are further sequenced and regions are identified having a low homology with other regions of the chromosome preferential sequence or with known sequences of other family me This invention is the result of a contract with the Department of Energy (Contract No. W-7405-ENG-36).

  15. Novel sequences propel familiar folds.

    PubMed

    Jawad, Zahra; Paoli, Massimo

    2002-04-01

    Recent structure determinations have made new additions to a set of strikingly different sequences that give rise to the same topology. Proteins with a beta propeller fold are characterized by extreme sequence diversity despite the similarity in their three-dimensional structures. Several fold predictions, based in part on sequence repeats thought to match modular beta sheets, have been proved correct.

  16. Sequencing Technologies Panel at SFAF

    SciTech Connect

    Turner, Steve; Fiske, Haley; Knight, Jim; Rhodes, Michael; Vander Horn, Peter

    2010-06-02

    From left to right: Steve Turner of Pacific Biosciences, Haley Fiske of Illumina, Jim Knight of Roche, Michael Rhodes of Life Technologies and Peter Vander Horn of Life Technologies' Single Molecule Sequencing group discuss new sequencing technologies and applications on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  17. Sequence Factorial and Its Applications

    ERIC Educational Resources Information Center

    Asiru, Muniru A.

    2012-01-01

    In this note, we introduce sequence factorial and use this to study generalized M-bonomial coefficients. For the sequence of natural numbers, the twin concepts of sequence factorial and generalized M-bonomial coefficients, respectively, extend the corresponding concepts of factorial of an integer and binomial coefficients. Some latent properties…

  18. Rapid Polymer Sequencer

    NASA Technical Reports Server (NTRS)

    Stolc, Viktor (Inventor); Brock, Matthew W (Inventor)

    2013-01-01

    Method and system for rapid and accurate determination of each of a sequence of unknown polymer components, such as nucleic acid components. A self-assembling monolayer of a selected substance is optionally provided on an interior surface of a pipette tip, and the interior surface is immersed in a selected liquid. A selected electrical field is impressed in a longitudinal direction, or in a transverse direction, in the tip region, a polymer sequence is passed through the tip region, and a change in an electrical current signal is measured as each polymer component passes through the tip region. Each of the measured changes in electrical current signals is compared with a database of reference electrical change signals, with each reference signal corresponding to an identified polymer component, to identify the unknown polymer component with a reference polymer component. The nanopore preferably has a pore inner diameter of no more than about 40 nm and is prepared by heating and pulling a very small section of a glass tubing.

  19. Single crystal growth of type I Na-Si clathrate by using Na-Sn flux

    NASA Astrophysics Data System (ADS)

    Morito, Haruhiko; Shimoda, Masashi; Yamane, Hisanori

    2016-09-01

    Single crystals of type I Na-Si clathrate, Na8Si46, were synthesized by heating Na, Na4Si4, and Na15Sn4 at 723 K under an Ar gas pressure of 104 Pa for 12 h. The single crystals having {110} habit planes grew up to 1.5 mm in size due to Na evaporation from a Na-Si-Sn melt with a starting compositional molar ratio of Na/Si/Sn=5.75:2:1.

  20. Deliquescence of NaCl-NaNO3 and KNO3-NaNO3 Salt Mixtures at 90C

    SciTech Connect

    Carroll, S; Craig, L; Wolery, T

    2003-12-29

    We conducted reversed deliquescence experiments in saturated NaCl-NaNO3-H2O and KNO{sub 3}-NaNO{sub 3}-H{sub 2}O systems at 90 C to determine relative humidity and solution composition. NaCl, NaNO{sub 3}, and KNO{sub 3} represent members of dust salt assemblages that are likely to deliquesce and form concentrated brines on high-level radioactive waste package surfaces in a repository environment at Yucca Mountain, NV, USA. Model predictions agree with experimental results for the NaCl-NaNO{sub 3}-H{sub 2}O system, but underestimate relative humidity by as much as 8% and solution composition by as much as 50% in the KNO{sub 3}-NaNO{sub 3}-H{sub 2}O system.

  1. Application of the Photomodeler software and Matlab environment for analysisof objects movement parameters based on image sequences. (Polish Title: Wykorzystanie pakietu Photomodeler oraz środowiska Matlab, do badania parametrów ruchu obiektów na podstawie obrazów sekwencyjnych)

    NASA Astrophysics Data System (ADS)

    Markowski, T.

    2013-12-01

    Analysis of objects movement parameters is the area of interest of scientists representing many disciplines. Technological progress provides improvement of research methods. One of them is photogrammetry, and more specifically, close-range image sequences processing. Much research on different approaches to this issue are conducted all over the world. Proposed solution is to carry out photogrammetric measurements using one of the standard programs for close-range objects 3D modeling - PhotoModeler software and their mathematical processing using popular computing environment - Matlab software. Application of existing software's functionality, in many cases seems to be less costly than development and then implementation of specialized measuring and computing applications, dedicated to analysis of movement parameters. Considered solution is based primarily on the appropriate transformations of the frame of reference with respect to which the movement takes place. Automatic coded targets measurements and bundle adjustment, carried out using PhotoModeler software, were used in the research. In order to calculate objects movements parameters, there were further repeated isometric coordinates transformations, numerical differentiation in method of difference quotient and orientation by iterative tabulation with intervals narrowing additionally applied by building own Matlab environment functions. A number of experiments were performed using registration in the form of films from JVC GZ-HD5 digital video camera and films and series of photographs from Nikon D5000 digital photographic camera. Accomplished experiments covered different objects of movement parameters analysis and also distinct movement types. There were also three different versions of established frame of reference -movement of the camera in relation to surroundings, movement of the object in relation to the camera and movement of the object in relation to surrounding. Carried out research revealed that

  2. Sequence of a cDNA encoding pancreatic preprosomatostatin-22.

    PubMed

    Magazin, M; Minth, C D; Funckes, C L; Deschenes, R; Tavianini, M A; Dixon, J E

    1982-09-01

    We report the nucleotide sequence of a precursor to somatostatin that upon proteolytic processing may give rise to a hormone of 22 amino acids. The nucleotide sequence of a cDNA from the channel catfish (Ictalurus punctatus) encodes a precursor to somatostatin that is 105 amino acids (Mr, 11,500). The cDNA coding for somatostatin-22 consists of 36 nucleotides in the 5' untranslated region, 315 nucleotides that code for the precursor to somatostatin-22, 269 nucleotides at the 3' untranslated region, and a variable length of poly(A). The putative preprohormone contains a sequence of hydrophobic amino acids at the amino terminus that has the properties of a "signal" peptide. A connecting sequence of approximately 57 amino acids is followed by a single Arg-Arg sequence, which immediately precedes the hormone. Somatostatin-22 is homologous to somatostatin-14 in 7 of the 14 amino acids, including the Phe-Trp-Lys sequence. Hybridization selection of mRNA, followed by its translation in a wheat germ cell-free system, resulted in the synthesis of a single polypeptide having a molecular weight of approximately 10,000 as estimated on Na-DodSO4/polyacrylamide gels. PMID:6127673

  3. Sequence of a cDNA encoding pancreatic preprosomatostatin-22.

    PubMed Central

    Magazin, M; Minth, C D; Funckes, C L; Deschenes, R; Tavianini, M A; Dixon, J E

    1982-01-01

    We report the nucleotide sequence of a precursor to somatostatin that upon proteolytic processing may give rise to a hormone of 22 amino acids. The nucleotide sequence of a cDNA from the channel catfish (Ictalurus punctatus) encodes a precursor to somatostatin that is 105 amino acids (Mr, 11,500). The cDNA coding for somatostatin-22 consists of 36 nucleotides in the 5' untranslated region, 315 nucleotides that code for the precursor to somatostatin-22, 269 nucleotides at the 3' untranslated region, and a variable length of poly(A). The putative preprohormone contains a sequence of hydrophobic amino acids at the amino terminus that has the properties of a "signal" peptide. A connecting sequence of approximately 57 amino acids is followed by a single Arg-Arg sequence, which immediately precedes the hormone. Somatostatin-22 is homologous to somatostatin-14 in 7 of the 14 amino acids, including the Phe-Trp-Lys sequence. Hybridization selection of mRNA, followed by its translation in a wheat germ cell-free system, resulted in the synthesis of a single polypeptide having a molecular weight of approximately 10,000 as estimated on Na-DodSO4/polyacrylamide gels. Images PMID:6127673

  4. The evolution of nanopore sequencing

    PubMed Central

    Wang, Yue; Yang, Qiuping; Wang, Zhimin

    2014-01-01

    The “$1000 Genome” project has been drawing increasing attention since its launch a decade ago. Nanopore sequencing, the third-generation, is believed to be one of the most promising sequencing technologies to reach four gold standards set for the “$1000 Genome” while the second-generation sequencing technologies are bringing about a revolution in life sciences, particularly in genome sequencing-based personalized medicine. Both of protein and solid-state nanopores have been extensively investigated for a series of issues, from detection of ionic current blockage to field-effect-transistor (FET) sensors. A newly released protein nanopore sequencer has shown encouraging potential that nanopore sequencing will ultimately fulfill the gold standards. In this review, we address advances, challenges, and possible solutions of nanopore sequencing according to these standards. PMID:25610451

  5. Solid phase sequencing of biopolymers

    DOEpatents

    Cantor, Charles; Koster, Hubert

    2010-09-28

    This invention relates to methods for detecting and sequencing target nucleic acid sequences, to mass modified nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probes comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Nucleic acids whose sequences can be determined include DNA or RNA in biological samples such as patient biopsies and environmental samples. Probes may be fixed to a solid support such as a hybridization chip to facilitate automated molecular weight analysis and identification of the target sequence.

  6. ISHAN: sequence homology analysis package.

    PubMed

    Shil, Pratip; Dudani, Niraj; Vidyasagar, Pandit B

    2006-01-01

    Sequence based homology studies play an important role in evolutionary tracing and classification of proteins. Various methods are available to analyze biological sequence information. However, with the advent of proteomics era, there is a growing demand for analysis of huge amount of biological sequence information, and it has become necessary to have programs that would provide speedy analysis. ISHAN has been developed as a homology analysis package, built on various sequence analysis tools viz FASTA, ALIGN, CLUSTALW, PHYLIP and CODONW (for DNA sequences). This JAVA application offers the user choice of analysis tools. For testing, ISHAN was applied to perform phylogenetic analysis for sets of Caspase 3 DNA sequences and NF-kappaB p105 amino acid sequences. By integrating several tools it has made analysis much faster and reduced manual intervention. PMID:17274766

  7. Asteroid Ida Rotation Sequence

    NASA Technical Reports Server (NTRS)

    1994-01-01

    This montage of 14 images (the time order is right to left, bottom to top) shows Ida as it appeared in the field of view of Galileo's camera on August 28, 1993. Asteroid Ida rotates once every 4 hours, 39 minutes and clockwise when viewed from above the north pole; these images cover about one Ida 'day.' This sequence has been used to create a 3-D model that shows Ida to be almost croissant shaped. The earliest view (lower right) was taken from a range of 240,000 kilometers (150,000 miles), 5.4 hours before closest approach. The asteroid Ida draws its name from mythology, in which the Greek god Zeus was raised by the nymph Ida.

  8. Adversary Sequence Interruption Model

    1985-11-15

    PC EASI is an IBM personal computer or PC-compatible version of an analytical technique for measuring the effectiveness of physical protection systems. PC EASI utilizes a methodology called Estimate of Adversary Sequence Interruption (EASI) which evaluates the probability of interruption (PI) for a given sequence of adversary tasks. Probability of interruption is defined as the probability that the response force will arrive before the adversary force has completed its task. The EASI methodology is amore » probabilistic approach that analytically evaluates basic functions of the physical security system (detection, assessment, communications, and delay) with respect to response time along a single adversary path. It is important that the most critical scenarios for each target be identified to ensure that vulnerabilities have not been overlooked. If the facility is not overly complex, this can be accomplished by examining all paths. If the facility is complex, a global model such as Safeguards Automated Facility Evaluation (SAFE) may be used to identify the most vulnerable paths. PC EASI is menu-driven with screen forms for entering and editing the basic scenarios. In addition to evaluating PI for the basic scenario, the sensitivities of many of the parameters chosen in the scenario can be analyzed. These sensitivities provide information to aid the analyst in determining the tradeoffs for reducing the probability of interruption. PC EASI runs under the Micro Data Base Systems'' proprietary database management system Knowledgeman. KMAN provides the user environment and file management for the specified basic scenarios, and KGRAPH the graphical output of the sensitivity calculations. This software is not included. Due to errors in release 2 of KMAN, PC EASI will not execute properly; release 1.07 of KMAN is required.« less

  9. Identification and Phylogenetic Analysis of Tityus pachyurus and Tityus obscurus Novel Putative Na+-Channel Scorpion Toxins

    PubMed Central

    Guerrero-Vargas, Jimmy A.; Mourão, Caroline B. F.; Quintero-Hernández, Verónica; Possani, Lourival D.; Schwartz, Elisabeth F.

    2012-01-01

    Background Colombia and Brazil are affected by severe cases of scorpionism. In Colombia the most dangerous accidents are caused by Tityus pachyurus that is widely distributed around this country. In the Brazilian Amazonian region scorpion stings are a common event caused by Tityus obscurus. The main objective of this work was to perform the molecular cloning of the putative Na+-channel scorpion toxins (NaScTxs) from T. pachyurus and T. obscurus venom glands and to analyze their phylogenetic relationship with other known NaScTxs from Tityus species. Methodology/Principal Findings cDNA libraries from venom glands of these two species were constructed and five nucleotide sequences from T. pachyurus were identified as putative modulators of Na+-channels, and were named Tpa4, Tpa5, Tpa6, Tpa7 and Tpa8; the latter being the first anti-insect excitatory β-class NaScTx in Tityus scorpion venom to be described. Fifteen sequences from T. obscurus were identified as putative NaScTxs, among which three had been previously described, and the others were named To4 to To15. The peptides Tpa4, Tpa5, Tpa6, To6, To7, To9, To10 and To14 are closely related to the α-class NaScTxs, whereas Tpa7, Tpa8, To4, To8, To12 and To15 sequences are more related to the β-class NaScTxs. To5 is possibly an arthropod specific toxin. To11 and To13 share sequence similarities with both α and β NaScTxs. By means of phylogenetic analysis using the Maximum Parsimony method and the known NaScTxs from Tityus species, these toxins were clustered into 14 distinct groups. Conclusions/Significance This communication describes new putative NaScTxs from T. pachyurus and T. obscurus and their phylogenetic analysis. The results indicate clear geographic separation between scorpions of Tityus genus inhabiting the Amazonian and Mountain Andes regions and those distributed over the Southern of the Amazonian rainforest. Based on the consensus sequences for the different clusters, a new nomenclature for the Na

  10. Quantum-Sequencing: Fast electronic single DNA molecule sequencing

    NASA Astrophysics Data System (ADS)

    Casamada Ribot, Josep; Chatterjee, Anushree; Nagpal, Prashant

    2014-03-01

    A major goal of third-generation sequencing technologies is to develop a fast, reliable, enzyme-free, high-throughput and cost-effective, single-molecule sequencing method. Here, we present the first demonstration of unique ``electronic fingerprint'' of all nucleotides (A, G, T, C), with single-molecule DNA sequencing, using Quantum-tunneling Sequencing (Q-Seq) at room temperature. We show that the electronic state of the nucleobases shift depending on the pH, with most distinct states identified at acidic pH. We also demonstrate identification of single nucleotide modifications (methylation here). Using these unique electronic fingerprints (or tunneling data), we report a partial sequence of beta lactamase (bla) gene, which encodes resistance to beta-lactam antibiotics, with over 95% success rate. These results highlight the potential of Q-Seq as a robust technique for next-generation sequencing.

  11. Advances in nanopore sequencing technology.

    PubMed

    Yang, Yongqiang; Liu, Ruoyu; Xie, Haiqiang; Hui, Yanting; Jiao, Rengang; Gong, Yu; Zhang, Yiyu

    2013-07-01

    Much tremendous break through have been obtained in recent years for nanopore sequencing to achieve the goal of $1000 genome. As a method of single molecule sequencing, nanopore sequencing can discriminate the individual molecules of the target DNA strand rapidly due to the current blockages by translocating the nucleotides through a nano-scale pore. Both the protein-pores and solid-state nanopore channels which called single nanopore sequencing have been studied widely for the application of nanopore sequencing technology. This review will give a detail representation to protein nanopore and solid-state nanopore sequencing. For protein nanopore sequencing technology, we will introduce different nanopore types, device assembly and some challenges still exist at present. We will focus on more research fields for solid-state nanopore sequencing in terms of materials, device assembly, fabricated methods, translocation process and some specific challenges. The review also covers some of the technical advances in the union nanopore sequencing, which include nanopore sequencing combine with exonuclease, hybridization, synthesis and design polymer.

  12. Nax loci affect SOS1-like Na+/H+ exchanger expression and activity in wheat

    PubMed Central

    Zhu, Min; Shabala, Lana; Cuin, Tracey A; Huang, Xin; Zhou, Meixue; Munns, Rana; Shabala, Sergey

    2016-01-01

    Salinity stress tolerance in durum wheat is strongly associated with a plant’s ability to control Na+ delivery to the shoot. Two loci, termed Nax1 and Nax2, were recently identified as being critical for this process and the sodium transporters HKT1;4 and HKT1;5 were identified as the respective candidate genes. These transporters retrieve Na+ from the xylem, thus limiting the rates of Na+ transport from the root to the shoot. In this work, we show that the Nax loci also affect activity and expression levels of the SOS1-like Na+/H+ exchanger in both root cortical and stelar tissues. Net Na+ efflux measured in isolated steles from salt-treated plants, using the non-invasive ion flux measuring MIFE technique, decreased in the sequence: Tamaroi (parental line)>Nax1=Nax2>Nax1:Nax2 lines. This efflux was sensitive to amiloride (a known inhibitor of the Na+/H+ exchanger) and was mirrored by net H+ flux changes. TdSOS1 relative transcript levels were 6–10-fold lower in Nax lines compared with Tamaroi. Thus, it appears that Nax loci confer two highly complementary mechanisms, both of which contribute towards reducing the xylem Na+ content. One enhances the retrieval of Na+ back into the root stele via HKT1;4 or HKT1;5, whilst the other reduces the rate of Na+ loading into the xylem via SOS1. It is suggested that such duality plays an important adaptive role with greater versatility for responding to a changing environment and controlling Na+ delivery to the shoot. PMID:26585227

  13. Genetic analysis of HLA, NA and HPA typing in type 2 diabetes and ASO

    PubMed Central

    Nomura, S; Shouzu, A; Omoto, S; Matsuzaki, T; Yamaoka, M; Abe, M; Hosokawa, M; Nishikawa, M; Iwasaka, T; Fukuhara, S

    2006-01-01

    Summary We examined the genetic status of human leucocyte antigens (HLA), human platelet alloantigens (HPA) and neutrophil-specific antigens (NA) in patients with type 2 diabetes mellitus and diabetic arteriosclerosis obliterans (ASO). To our knowledge, the present study is the first report showing the relationship among three genetic factors in type 2 diabetes mellitus and ASO patients. HLA typing was performed by the polymerase chain reaction (PCR)–restriction fragment length polymorphism method. HPA-typing and NA-typing were by a PCR-sequence-specific primer method. The incidence of HLA-DRB1* 1501 was found to be significant in type 2 diabetes and non-diabetic, particularly ASO-positive patients, compared to control subjects. There were no differences in NA1/NA2 between the control and diabetic or non-diabetic ASO groups. However, the frequency of NA2/NA2 in ASO-positive diabetes and non-diabetic ASO patients was significantly higher than controls. The a/b genotype of HPA-5a/5b was significantly lower in type 2 diabetes and non-diabetic ASO-positive patients than in controls. These findings suggest that genetic studies of HLA, NA and HPA could be useful to understand the pathogenesis of type 2 diabetes and ASO. PMID:16611256

  14. Compensatory regulation of Na+ absorption by Na+/H+ exchanger and Na+-Cl- cotransporter in zebrafish (Danio rerio)

    PubMed Central

    2013-01-01

    Introduction In mammals, internal Na+ homeostasis is maintained through Na+ reabsorption via a variety of Na+ transport proteins with mutually compensating functions, which are expressed in different segments of the nephrons. In zebrafish, Na+ homeostasis is achieved mainly through the skin/gill ionocytes, namely Na+/H+ exchanger (NHE3b)-expressing H+-ATPase rich (HR) cells and Na+-Cl- cotransporter (NCC)-expressing NCC cells, which are functionally homologous to mammalian proximal and distal convoluted tubular cells, respectively. The present study aimed to investigate whether or not the functions of HR and NCC ionocytes are differentially regulated to compensate for disruptions of internal Na+ homeostasis and if the cell differentiation of the ionocytes is involved in this regulation pathway. Results Translational knockdown of ncc caused an increase in HR cell number and a resulting augmentation of Na+ uptake in zebrafish larvae, while NHE3b loss-of-function caused an increase in NCC cell number with a concomitant recovery of Na+ absorption. Environmental acid stress suppressed nhe3b expression in HR cells and decreased Na+ content, which was followed by up-regulation of NCC cells accompanied by recovery of Na+ content. Moreover, knockdown of ncc resulted in a significant decrease of Na+ content in acid-acclimated zebrafish. Conclusions These results provide evidence that HR and NCC cells exhibit functional redundancy in Na+ absorption, similar to the regulatory mechanisms in mammalian kidney, and suggest this functional redundancy is a critical strategy used by zebrafish to survive in a harsh environment that disturbs body fluid Na+ homeostasis. PMID:23924428

  15. Turtle Graphics of Morphic Sequences

    NASA Astrophysics Data System (ADS)

    Zantema, Hans

    2016-02-01

    The simplest infinite sequences that are not ultimately periodic are pure morphic sequences: fixed points of particular morphisms mapping single symbols to strings of symbols. A basic way to visualize a sequence is by a turtle curve: for every alphabet symbol fix an angle, and then consecutively for all sequence elements draw a unit segment and turn the drawing direction by the corresponding angle. This paper investigates turtle curves of pure morphic sequences. In particular, criteria are given for turtle curves being finite (consisting of finitely many segments), and for being fractal or self-similar: it contains an up-scaled copy of itself. Also space-filling turtle curves are considered, and a turtle curve that is dense in the plane. As a particular result we give an exact relationship between the Koch curve and a turtle curve for the Thue-Morse sequence, where until now for such a result only approximations were known.

  16. Solid phase sequencing of biopolymers

    SciTech Connect

    Cantor, Charles R.; Hubert, Koster

    2014-06-24

    This invention relates to methods for detecting and sequencing target nucleic acid sequences, to mass modified nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probes comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Probes may be affixed to a solid support such as a hybridization chip to facilitate automated molecular weight analysis and identification of the target sequence.

  17. Graphene nanodevices for DNA sequencing

    NASA Astrophysics Data System (ADS)

    Heerema, Stephanie J.; Dekker, Cees

    2016-02-01

    Fast, cheap, and reliable DNA sequencing could be one of the most disruptive innovations of this decade, as it will pave the way for personalized medicine. In pursuit of such technology, a variety of nanotechnology-based approaches have been explored and established, including sequencing with nanopores. Owing to its unique structure and properties, graphene provides interesting opportunities for the development of a new sequencing technology. In recent years, a wide range of creative ideas for graphene sequencers have been theoretically proposed and the first experimental demonstrations have begun to appear. Here, we review the different approaches to using graphene nanodevices for DNA sequencing, which involve DNA passing through graphene nanopores, nanogaps, and nanoribbons, and the physisorption of DNA on graphene nanostructures. We discuss the advantages and problems of each of these key techniques, and provide a perspective on the use of graphene in future DNA sequencing technology.

  18. Nuclear RNA Isolation and Sequencing.

    PubMed

    Dhaliwal, Navroop K; Mitchell, Jennifer A

    2016-01-01

    Most transcriptome studies involve sequencing and quantification of steady-state mRNA by isolating and sequencing poly (A) RNA. Although this type of sequencing data is informative to determine steady-state mRNA levels it does not provide information on transcriptional output and thus may not always reflect changes in transcriptional regulation of gene expression. Furthermore, sequencing poly (A) RNA may miss transcribed regions of the genome not usually modified by polyadenylation which includes many long noncoding RNAs. Here, we describe nuclear-RNA sequencing (nucRNA-seq) which investigates the transcriptional landscape through sequencing and quantification of nuclear RNAs which are both unspliced and spliced transcripts for protein-coding genes and nuclear-retained long noncoding RNAs.

  19. Seismic sequences in the Sombrero Seismic Zone

    NASA Astrophysics Data System (ADS)

    Pulliam, J.; Huerfano, V. A.; ten Brink, U.; von Hillebrandt, C.

    2007-05-01

    unrelated events in plots of the general catalog. One characteristic of these sequences is that their magnitudes tend to be consistently small (1.0 - 3.5 mb, with only five events greater than 3.5 mb) and they typically do not include an event that could confidently be identified as a "main" shock. Nevertheless, the numbers of events, temporal and geographic distribution of shocks in each sequence suggests that these are aftershock sequences, yet none includes an event that could confidently be identified as a "main" shock. This observation suggests several questions. Do these sequences truly represent aftershocks? If so, where are the main events? Are they perhaps related to "silent" or "slow" earthquakes in the subduction zone? If so, could such slow earthquakes be related to the dropping away of the subducting slab beneath the deep Puerto Rico Trench? Or do the sequences indicate tearing of the NA lithosphere of the North America plate as it subducts beneath the Caribbean plate?

  20. Identification of transcribed sequences

    SciTech Connect

    Hochgeschwender, U.; Gardiner, K.

    1994-12-31

    The international Human Genome Project is providing three essential ingredients for the efficient identification of diseases genes. One is the high density of polymorphic markers that are critical for the mapping of disease genes to defined chromosomal regions. The second is a physical map in the form of overlapping genomic clones in YACs or cosmids that will allow detailed analysis of the critical region. The third is a transcription map (gene map) that will provide a bank of regionally mapped candidate genes to test for mutations once a disease gene is mapped. In the past 5 years the identification and mapping of several thousand simple-sequence-repeat polymorphisms has provided the first ingredient, and the physical maps of many chromosomes are approaching completion. However, the transcription map is problematic and a long way from being a useful tool. A detailed analysis of the technology involved in building the requisite transcription maps is found in this book, the published proceedings of the third international workshop on the topic, held October 2-4, 1993, in association with the American Society of Human Genetics meeting in New Orleans.

  1. The hydrogen storage properties of Na decorated small boron cluster B6Na8

    NASA Astrophysics Data System (ADS)

    Tang, Chunmei; Wang, Zhiguo; Zhang, Xue; Wen, Ninghua

    2016-09-01

    The binding energy of the Na atoms to the hollow sites of the B6 cage is larger than the experimental cohesive energy of bulk Na, so the clustering of Na atoms can be avoided. The polarization interaction dominates the adsorption of H2 by the B6Na8 cluster. The Na-coated B6Na8sbnd B8sbnd B6Na8 complex with the dispersive Na atoms and four H2 molecules adsorbed per Na can serve as better building blocks of polymers than the (B6Na8)2 dimer. These findings suggest a new route to design cluster-assembled hydrogen storage materials based on sp2-terminated boron chains.

  2. Short sequence motifs, overrepresented in mammalian conservednon-coding sequences

    SciTech Connect

    Minovitsky, Simon; Stegmaier, Philip; Kel, Alexander; Kondrashov,Alexey S.; Dubchak, Inna

    2007-02-21

    Background: A substantial fraction of non-coding DNAsequences of multicellular eukaryotes is under selective constraint. Inparticular, ~;5 percent of the human genome consists of conservednon-coding sequences (CNSs). CNSs differ from other genomic sequences intheir nucleotide composition and must play important functional roles,which mostly remain obscure.Results: We investigated relative abundancesof short sequence motifs in all human CNSs present in the human/mousewhole-genome alignments vs. three background sets of sequences: (i)weakly conserved or unconserved non-coding sequences (non-CNSs); (ii)near-promoter sequences (located between nucleotides -500 and -1500,relative to a start of transcription); and (iii) random sequences withthe same nucleotide composition as that of CNSs. When compared tonon-CNSs and near-promoter sequences, CNSs possess an excess of AT-richmotifs, often containing runs of identical nucleotides. In contrast, whencompared to random sequences, CNSs contain an excess of GC-rich motifswhich, however, lack CpG dinucleotides. Thus, abundance of short sequencemotifs in human CNSs, taken as a whole, is mostly determined by theiroverall compositional properties and not by overrepresentation of anyspecific short motifs. These properties are: (i) high AT-content of CNSs,(ii) a tendency, probably due to context-dependent mutation, of A's andT's to clump, (iii) presence of short GC-rich regions, and (iv) avoidanceof CpG contexts, due to their hypermutability. Only a small number ofshort motifs, overrepresented in all human CNSs are similar to bindingsites of transcription factors from the FOX family.Conclusion: Human CNSsas a whole appear to be too broad a class of sequences to possess strongfootprints of any short sequence-specific functions. Such footprintsshould be studied at the level of functional subclasses of CNSs, such asthose which flank genes with a particular pattern of expression. Overallproperties of CNSs are affected by patterns in

  3. 23Na Magnetic Resonance Imaging of the Lower Leg of Acute Heart Failure Patients during Diuretic Treatment

    PubMed Central

    Hammon, Matthias; Grossmann, Susan; Linz, Peter; Kopp, Christoph; Dahlmann, Anke; Garlichs, Christoph; Janka, Rolf; Cavallaro, Alexander; Luft, Friedrich C.; Uder, Michael; Titze, Jens

    2015-01-01

    Objective Na+ can be stored in muscle and skin without commensurate water accumulation. The aim of this study was to assess Na+ and H2O in muscle and skin with MRI in acute heart failure patients before and after diuretic treatment and in a healthy cohort. Methods Nine patients (mean age 78 years; range 58–87) and nine age and gender-matched controls were studied. They underwent 23Na/1H-MRI at the calf with a custom-made knee coil. Patients were studied before and after diuretic therapy. 23Na-MRI gray-scale measurements of Na+-phantoms served to quantify Na+-concentrations. A fat-suppressed inversion recovery sequence was used to quantify H2O content. Results Plasma Na+-levels did not change during therapy. Mean Na+-concentrations in muscle and skin decreased after furosemide therapy (before therapy: 30.7±6.4 and 43.5±14.5 mmol/L; after therapy: 24.2±6.1 and 32.2±12.0 mmol/L; p˂0.05 and p˂0.01). Water content measurements did not differ significantly before and after furosemide therapy in muscle (p = 0.17) and only tended to be reduced in skin (p = 0.06). Na+-concentrations in calf muscle and skin of patients before and after diuretic therapy were significantly higher than in healthy subjects (18.3±2.5 and 21.1±2.3 mmol/L). Conclusions 23Na-MRI shows accumulation of Na+ in muscle and skin in patients with acute heart failure. Diuretic treatment can mobilize this Na+-deposition; however, contrary to expectations, water and Na+-mobilization are poorly correlated. PMID:26501774

  4. Nonlinear analysis of biological sequences

    SciTech Connect

    Torney, D.C.; Bruno, W.; Detours, V.

    1998-11-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The main objectives of this project involved deriving new capabilities for analyzing biological sequences. The authors focused on tabulating the statistical properties exhibited by Human coding DNA sequences and on techniques of inferring the phylogenetic relationships among protein sequences related by descent.

  5. Sequence factorial and its applications

    NASA Astrophysics Data System (ADS)

    Asiru, Muniru A.

    2012-06-01

    In this note, we introduce sequence factorial and use this to study generalized M-bonomial coefficients. For the sequence of natural numbers, the twin concepts of sequence factorial and generalized M-bonomial coefficients, respectively, extend the corresponding concepts of factorial of an integer and binomial coefficients. Some latent properties of generalized M-bonomial coefficients by which a vast majority of practical problems involving generalized M-bonomial coefficients can be solved are derived.

  6. Quasi-Random Sequence Generators.

    1994-03-01

    Version 00 LPTAU generates quasi-random sequences. The sequences are uniformly distributed sets of L=2**30 points in the N-dimensional unit cube: I**N=[0,1]. The sequences are used as nodes for multidimensional integration, as searching points in global optimization, as trial points in multicriteria decision making, as quasi-random points for quasi Monte Carlo algorithms.

  7. Biosensors for DNA sequence detection

    NASA Technical Reports Server (NTRS)

    Vercoutere, Wenonah; Akeson, Mark

    2002-01-01

    DNA biosensors are being developed as alternatives to conventional DNA microarrays. These devices couple signal transduction directly to sequence recognition. Some of the most sensitive and functional technologies use fibre optics or electrochemical sensors in combination with DNA hybridization. In a shift from sequence recognition by hybridization, two emerging single-molecule techniques read sequence composition using zero-mode waveguides or electrical impedance in nanoscale pores.

  8. Venter wins sequencing race - twice

    SciTech Connect

    Nowak, R.

    1995-06-02

    This article discusses the end of the race to sequence the first complete genome of a free-living organism. Craig Venter of the Institute for Geonomic Research unveiled the complete sequences of two bacteria: Haemophilus influenzae and Mycoplasma genitalium at the American Society of Microbiology Meeting in May 1995. Because there are many similarities in bacterial and human biochemistry, the sequences will be useful for searching for human genes.

  9. Fungal Genome Sequencing and Bioenergy

    SciTech Connect

    Baker, Scott E.; Thykaer, Jette; Adney, William S.; Brettin, T.; Brockman, Fred J.; D'haeseleer, Patrik; Martinez, Antonio D.; Miller, R. M.; Rokhsar, Daniel S.; Schadt, Christopher W.; Torok, Tamas; Tuskan, Gerald; Bennett, Joan W.; Berka, Randy; Briggs, Steve; Heitman, Joseph; Taylor, John; Turgeon, Barbara G.; Werner-Washburne, Maggie; Himmel, Michael E.

    2008-09-30

    To date, the number of ongoing filamentous fungal genome sequencing projects is almost tenfold fewer than those of bacterial and archaeal genome projects. The fungi chosen for sequencing represent narrow kingdom diversity; most are pathogens or models. We advocate an ambitious, forward-looking phylogenetic-based genome sequencing program, designed to capture metabolic diversity within the fungal kingdom, thereby enhancing research into alternative bioenergy sources, bioremediation, and fungal-environment interactions.

  10. Fungal Genome Sequencing and Bioenergy

    SciTech Connect

    Baker, Scott; Thykaer, Jette; Adney, William S; Brettin, Tom; Brockman, Fred; Dhaeseleer, Patrick; Martinez, A diego; Miller, R michael; Rokhsar, Daniel; Schadt, Christopher Warren; Torok, Tamas; Tuskan, Gerald A; Bennett, Joan; Berka, Randy; Briggs, Steven; Heitman, Joseph; Taylor, John; Turgeon, Gillian; Werner-Washburne, Maggie; Himmel, Michael E

    2008-01-01

    To date, the number of ongoing filamentous fungal genome sequencing projects is almost tenfold fewer than those of bacterial and archaeal genome projects. The fungi chosen for sequencing represent narrow kingdom diversity; most are pathogens or models. We advocate an ambitious, forward-looking phylogenetic-based genome sequencing program, designed to capture metabolic diversity within the fungal kingdom, thereby enhancing research into alternative bioenergy sources, bioremediation, and fungal-environment interactions. Published by Elsevier Ltd on behalf of The British Mycological Society.

  11. Fungal Genome Sequencing and Bioenergy

    SciTech Connect

    Schadt, Christopher Warren; Baker, Scott; Thykaer, Jette; Adney, William S; Brettin, Tom; Brockman, Fred; Dhaeseleer, Patrick; Martinez, A diego; Miller, R michael; Rokhsar, Daniel; Torok, Tamas; Tuskan, Gerald A; Bennett, Joan; Berka, Randy; Briggs, Steven; Heitman, Joseph; Rizvi, L; Taylor, John; Turgeon, Gillian; Werner-Washburne, Maggie; Himmel, Michael

    2008-01-01

    To date, the number of ongoing filamentous fungal genome sequencing projects is almost tenfold fewer than those of bacterial and archaeal genome projects. The fungi chosen for sequencing represent narrow kingdom diversity; most are pathogens or models. We advocate an ambitious, forward-looking phylogenetic-based genome sequencing program, designed to capture metabolic diversity within the fungal kingdom, thereby enhancing research into alternative bioenergy sources, bioremediation, and fungal-environment interactions.

  12. Establishing homologies in protein sequences

    NASA Technical Reports Server (NTRS)

    Dayhoff, M. O.; Barker, W. C.; Hunt, L. T.

    1983-01-01

    Computer-based statistical techniques used to determine homologies between proteins occurring in different species are reviewed. The technique is based on comparison of two protein sequences, either by relating all segments of a given length in one sequence to all segments of the second or by finding the best alignment of the two sequences. Approaches discussed include selection using printed tabulations, identification of very similar sequences, and computer searches of a database. The use of the SEARCH, RELATE, and ALIGN programs (Dayhoff, 1979) is explained; sample data are presented in graphs, diagrams, and tables and the construction of scoring matrices is considered.

  13. Sequence independent amplification of DNA

    DOEpatents

    Bohlander, Stefan K.

    1998-01-01

    The present invention is a rapid sequence-independent amplification procedure (SIA). Even minute amounts of DNA from various sources can be amplified independent of any sequence requirements of the DNA or any a priori knowledge of any sequence characteristics of the DNA to be amplified. This method allows, for example the sequence independent amplification of microdissected chromosomal material and the reliable construction of high quality fluorescent in situ hybridization (FISH) probes from YACs or from other sources. These probes can be used to localize YACs on metaphase chromosomes but also--with high efficiency--in interphase nuclei.

  14. Sequence independent amplification of DNA

    DOEpatents

    Bohlander, S.K.

    1998-03-24

    The present invention is a rapid sequence-independent amplification procedure (SIA). Even minute amounts of DNA from various sources can be amplified independent of any sequence requirements of the DNA or any a priori knowledge of any sequence characteristics of the DNA to be amplified. This method allows, for example, the sequence independent amplification of microdissected chromosomal material and the reliable construction of high quality fluorescent in situ hybridization (FISH) probes from YACs or from other sources. These probes can be used to localize YACs on metaphase chromosomes but also--with high efficiency--in interphase nuclei. 25 figs.

  15. SNMR pulse sequence phase cycling

    DOEpatents

    Walsh, David O; Grunewald, Elliot D

    2013-11-12

    Technologies applicable to SNMR pulse sequence phase cycling are disclosed, including SNMR acquisition apparatus and methods, SNMR processing apparatus and methods, and combinations thereof. SNMR acquisition may include transmitting two or more SNMR pulse sequences and applying a phase shift to a pulse in at least one of the pulse sequences, according to any of a variety cycling techniques. SNMR processing may include combining SNMR from a plurality of pulse sequences comprising pulses of different phases, so that desired signals are preserved and indesired signals are canceled.

  16. Multiple sequence alignment with DIALIGN.

    PubMed

    Morgenstern, Burkhard

    2014-01-01

    DIALIGN is a software tool for multiple sequence alignment by combining global and local alignment features. It composes multiple alignments from local pairwise sequence similarities. This approach is particularly useful to discover conserved functional regions in sequences that share only local homologies but are otherwise unrelated. An anchoring option allows to use external information and expert knowledge in addition to primary-sequence similarity alone. The latest version of DIALIGN optionally uses matches to the PFAM database to detect weak homologies. Various versions of the program are available through Göttingen Bioinformatics Compute Server (GOBICS) at http://www.gobics.de/department/software.

  17. Silicene for Na-ion battery applications

    NASA Astrophysics Data System (ADS)

    Zhu, Jiajie; Schwingenschlögl, Udo

    2016-09-01

    Na-ion batteries are promising candidates to replace Li-ion batteries in large scale applications because of the advantages in natural abundance and cost of Na. Silicene has potential as the anode in Li-ion batteries but so far has not received attention with respect to Na-ion batteries. In this context, freestanding silicene, a graphene-silicene-graphene heterostructure, and a graphene-silicene superlattice are investigated for possible application in Na-ion batteries, using first-principles calculations. The calculated Na capacities of 954 mAh/g for freestanding silicene and 730 mAh/g for the graphene-silicene superlattice (10% biaxial tensile strain) are highly competitive and potentials of \\gt 0.3 {{V}} against the Na{}+/Na potential exceed the corresponding value of graphite. In addition, the diffusion barriers are predicted to be \\lt 0.3 {eV}.

  18. Automated Sequence Preprocessing in a Large-Scale Sequencing Environment

    PubMed Central

    Wendl, Michael C.; Dear, Simon; Hodgson, Dave; Hillier, LaDeana

    1998-01-01

    A software system for transforming fragments from four-color fluorescence-based gel electrophoresis experiments into assembled sequence is described. It has been developed for large-scale processing of all trace data, including shotgun and finishing reads, regardless of clone origin. Design considerations are discussed in detail, as are programming implementation and graphic tools. The importance of input validation, record tracking, and use of base quality values is emphasized. Several quality analysis metrics are proposed and applied to sample results from recently sequenced clones. Such quantities prove to be a valuable aid in evaluating modifications of sequencing protocol. The system is in full production use at both the Genome Sequencing Center and the Sanger Centre, for which combined weekly production is ∼100,000 sequencing reads per week. PMID:9750196

  19. Identification of Nocobactin NA Biosynthetic Gene Clusters in Nocardia farcinica▿ §

    PubMed Central

    Hoshino, Yasutaka; Chiba, Kazuhiro; Ishino, Keiko; Fukai, Toshio; Igarashi, Yasuhiro; Yazawa, Katsukiyo; Mikami, Yuzuru; Ishikawa, Jun

    2011-01-01

    We identified the biosynthetic gene clusters of the siderophore nocobactin NA. The nbt clusters, which were discovered as genes highly homologous to the mycobactin biosynthesis genes by the genomic sequencing of Nocardia farcinica IFM 10152, consist of 10 genes separately located at two genomic regions. The gene organization of the nbt clusters and the predicted functions of the nbt genes, particularly the cyclization and epimerization domains, were in good agreement with the chemical structure of nocobactin NA. Disruptions of the nbtA and nbtE genes, respectively, reduced and abolished the productivity of nocobactin NA. The heterologous expression of the nbtS gene revealed that this gene encoded a salicylate synthase. These results indicate that the nbt clusters are responsible for the biosynthesis of nocobactin NA. We also found putative IdeR-binding sequences upstream of the nbtA, -G, -H, -S, and -T genes, whose expression was more than 10-fold higher in the low-iron condition than in the high-iron condition. These results suggest that nbt genes are regulated coordinately by IdeR protein in an iron-dependent manner. The ΔnbtE mutant was found to be impaired in cytotoxicity against J774A.1 cells, suggesting that nocobactin NA production is required for virulence of N. farcinica. PMID:21097631

  20. Quantifying Population Genetic Differentiation from Next-Generation Sequencing Data

    PubMed Central

    Fumagalli, Matteo; Vieira, Filipe G.; Korneliussen, Thorfinn Sand; Linderoth, Tyler; Huerta-Sánchez, Emilia; Albrechtsen, Anders; Nielsen, Rasmus

    2013-01-01

    Over the past few years, new high-throughput DNA sequencing technologies have dramatically increased speed and reduced sequencing costs. However, the use of these sequencing technologies is often challenged by errors and biases associated with the bioinformatical methods used for analyzing the data. In particular, the use of naïve methods to identify polymorphic sites and infer genotypes can inflate downstream analyses. Recently, explicit modeling of genotype probability distributions has been proposed as a method for taking genotype call uncertainty into account. Based on this idea, we propose a novel method for quantifying population genetic differentiation from next-generation sequencing data. In addition, we present a strategy for investigating population structure via principal components analysis. Through extensive simulations, we compare the new method herein proposed to approaches based on genotype calling and demonstrate a marked improvement in estimation accuracy for a wide range of conditions. We apply the method to a large-scale genomic data set of domesticated and wild silkworms sequenced at low coverage. We find that we can infer the fine-scale genetic structure of the sampled individuals, suggesting that employing this new method is useful for investigating the genetic relationships of populations sampled at low coverage. PMID:23979584

  1. Evaluating techniques for metagenome annotation using simulated sequence data.

    PubMed

    Randle-Boggis, Richard J; Helgason, Thorunn; Sapp, Melanie; Ashton, Peter D

    2016-07-01

    The advent of next-generation sequencing has allowed huge amounts of DNA sequence data to be produced, advancing the capabilities of microbial ecosystem studies. The current challenge is to identify from which microorganisms and genes the DNA originated. Several tools and databases are available for annotating DNA sequences. The tools, databases and parameters used can have a significant impact on the results: naïve choice of these factors can result in a false representation of community composition and function. We use a simulated metagenome to show how different parameters affect annotation accuracy by evaluating the sequence annotation performances of MEGAN, MG-RAST, One Codex and Megablast. This simulated metagenome allowed the recovery of known organism and function abundances to be quantitatively evaluated, which is not possible for environmental metagenomes. The performance of each program and database varied, e.g. One Codex correctly annotated many sequences at the genus level, whereas MG-RAST RefSeq produced many false positive annotations. This effect decreased as the taxonomic level investigated increased. Selecting more stringent parameters decreases the annotation sensitivity, but increases precision. Ultimately, there is a trade-off between taxonomic resolution and annotation accuracy. These results should be considered when annotating metagenomes and interpreting results from previous studies. PMID:27162180

  2. Evaluating techniques for metagenome annotation using simulated sequence data

    PubMed Central

    Randle-Boggis, Richard J.; Helgason, Thorunn; Sapp, Melanie; Ashton, Peter D.

    2016-01-01

    The advent of next-generation sequencing has allowed huge amounts of DNA sequence data to be produced, advancing the capabilities of microbial ecosystem studies. The current challenge is to identify from which microorganisms and genes the DNA originated. Several tools and databases are available for annotating DNA sequences. The tools, databases and parameters used can have a significant impact on the results: naïve choice of these factors can result in a false representation of community composition and function. We use a simulated metagenome to show how different parameters affect annotation accuracy by evaluating the sequence annotation performances of MEGAN, MG-RAST, One Codex and Megablast. This simulated metagenome allowed the recovery of known organism and function abundances to be quantitatively evaluated, which is not possible for environmental metagenomes. The performance of each program and database varied, e.g. One Codex correctly annotated many sequences at the genus level, whereas MG-RAST RefSeq produced many false positive annotations. This effect decreased as the taxonomic level investigated increased. Selecting more stringent parameters decreases the annotation sensitivity, but increases precision. Ultimately, there is a trade-off between taxonomic resolution and annotation accuracy. These results should be considered when annotating metagenomes and interpreting results from previous studies. PMID:27162180

  3. Dryland soil chemical properties and crop yields affected by long-term tillage and cropping sequence

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Information on the effect of long-term management on soil nutrients and chemical properties is scanty. We examined the 30-yr effect of tillage frequency and cropping sequence combination on dryland soil Olsen-P, K, Ca, Mg, Na, SO4-S, and Zn concentrations, pH, electrical conductivity (EC), and catio...

  4. Semiempirical studies of atomic structure. Progress report, July 1, 1994--October 1, 1996

    SciTech Connect

    Curtis, L.J.

    1996-12-31

    Brief summaries are given for significant results of research in the following areas: line strength isoelectronic extrapolations; lifetime measurement in few times ionized states; determination of dipole polarizabilities from precision lifetime measurements and transition moment calculations; spectra and intensity ratio studies in the Al isoelectronic sequence; and experimental studies of energy levels and lifetimes in very high ionized two electron systems.

  5. The natural product domain seeker NaPDoS: a phylogeny based bioinformatic tool to classify secondary metabolite gene diversity.

    PubMed

    Ziemert, Nadine; Podell, Sheila; Penn, Kevin; Badger, Jonathan H; Allen, Eric; Jensen, Paul R

    2012-01-01

    New bioinformatic tools are needed to analyze the growing volume of DNA sequence data. This is especially true in the case of secondary metabolite biosynthesis, where the highly repetitive nature of the associated genes creates major challenges for accurate sequence assembly and analysis. Here we introduce the web tool Natural Product Domain Seeker (NaPDoS), which provides an automated method to assess the secondary metabolite biosynthetic gene diversity and novelty of strains or environments. NaPDoS analyses are based on the phylogenetic relationships of sequence tags derived from polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) genes, respectively. The sequence tags correspond to PKS-derived ketosynthase domains and NRPS-derived condensation domains and are compared to an internal database of experimentally characterized biosynthetic genes. NaPDoS provides a rapid mechanism to extract and classify ketosynthase and condensation domains from PCR products, genomes, and metagenomic datasets. Close database matches provide a mechanism to infer the generalized structures of secondary metabolites while new phylogenetic lineages provide targets for the discovery of new enzyme architectures or mechanisms of secondary metabolite assembly. Here we outline the main features of NaPDoS and test it on four draft genome sequences and two metagenomic datasets. The results provide a rapid method to assess secondary metabolite biosynthetic gene diversity and richness in organisms or environments and a mechanism to identify genes that may be associated with uncharacterized biochemistry.

  6. The Natural Product Domain Seeker NaPDoS: A Phylogeny Based Bioinformatic Tool to Classify Secondary Metabolite Gene Diversity

    PubMed Central

    Ziemert, Nadine; Podell, Sheila; Penn, Kevin; Badger, Jonathan H.; Allen, Eric; Jensen, Paul R.

    2012-01-01

    New bioinformatic tools are needed to analyze the growing volume of DNA sequence data. This is especially true in the case of secondary metabolite biosynthesis, where the highly repetitive nature of the associated genes creates major challenges for accurate sequence assembly and analysis. Here we introduce the web tool Natural Product Domain Seeker (NaPDoS), which provides an automated method to assess the secondary metabolite biosynthetic gene diversity and novelty of strains or environments. NaPDoS analyses are based on the phylogenetic relationships of sequence tags derived from polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) genes, respectively. The sequence tags correspond to PKS-derived ketosynthase domains and NRPS-derived condensation domains and are compared to an internal database of experimentally characterized biosynthetic genes. NaPDoS provides a rapid mechanism to extract and classify ketosynthase and condensation domains from PCR products, genomes, and metagenomic datasets. Close database matches provide a mechanism to infer the generalized structures of secondary metabolites while new phylogenetic lineages provide targets for the discovery of new enzyme architectures or mechanisms of secondary metabolite assembly. Here we outline the main features of NaPDoS and test it on four draft genome sequences and two metagenomic datasets. The results provide a rapid method to assess secondary metabolite biosynthetic gene diversity and richness in organisms or environments and a mechanism to identify genes that may be associated with uncharacterized biochemistry. PMID:22479523

  7. VOE Accounting: Scope and Sequence.

    ERIC Educational Resources Information Center

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This guide, which was written as an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System, outlines the suggested scope and sequence of a 2-year program in accounting. The guide consists of a course description; general course objectives;…

  8. Sequence conserved for subcellular localization

    PubMed Central

    Nair, Rajesh; Rost, Burkhard

    2002-01-01

    The more proteins diverged in sequence, the more difficult it becomes for bioinformatics to infer similarities of protein function and structure from sequence. The precise thresholds used in automated genome annotations depend on the particular aspect of protein function transferred by homology. Here, we presented the first large-scale analysis of the relation between sequence similarity and identity in subcellular localization. Three results stood out: (1) The subcellular compartment is generally more conserved than what might have been expected given that short sequence motifs like nuclear localization signals can alter the native compartment; (2) the sequence conservation of localization is similar between different compartments; and (3) it is similar to the conservation of structure and enzymatic activity. In particular, we found the transition between the regions of conserved and nonconserved localization to be very sharp, although the thresholds for conservation were less well defined than for structure and enzymatic activity. We found that a simple measure for sequence similarity accounting for pairwise sequence identity and alignment length, the HSSP distance, distinguished accurately between protein pairs of identical and different localizations. In fact, BLAST expectation values outperformed the HSSP distance only for alignments in the subtwilight zone. We succeeded in slightly improving the accuracy of inferring localization through homology by fine tuning the thresholds. Finally, we applied our results to the entire SWISS-PROT database and five entirely sequenced eukaryotes. PMID:12441382

  9. Auto Mechanics: Scope and Sequence.

    ERIC Educational Resources Information Center

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This scope and sequence guide, developed for an auto mechanics vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents, and the…

  10. Commercial Photography: Scope and Sequence.

    ERIC Educational Resources Information Center

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This scope and sequence guide, developed for a commercial photography vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents,…

  11. Commercial Art: Scope and Sequence.

    ERIC Educational Resources Information Center

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This scope and sequence guide, developed for a commercial art vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents, and the…

  12. Urban Horticulture: Scope and Sequence.

    ERIC Educational Resources Information Center

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This guide, which was written as an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System, outlines the suggested scope and sequence of a 4-year program in urban horticulture. The guide consists of a course description; general course…

  13. AMPLIFICATION OF RIBOSOMAL RNA SEQUENCES

    EPA Science Inventory

    This book chapter offers an overview of the use of ribosomal RNA sequences. A history of the technology traces the evolution of techniques to measure bacterial phylogenetic relationships and recent advances in obtaining rRNA sequence information. The manual also describes procedu...

  14. Diesel Mechanics: Scope and Sequence.

    ERIC Educational Resources Information Center

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This scope and sequence guide, developed for a diesel mechanics vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents, and the…

  15. Health Occupations: Scope and Sequence.

    ERIC Educational Resources Information Center

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This guide, which was written as an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System, outlines the suggested scope and sequence of a 3-year program in health occupations. The guide consists of a course description; general course…

  16. Commercial Foods: Scope and Sequence.

    ERIC Educational Resources Information Center

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This scope and sequence guide, developed for a commercial food service vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents,…

  17. Aircraft Mechanics: Scope and Sequence.

    ERIC Educational Resources Information Center

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This scope and sequence guide, developed for an aircraft mechanics vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents, and…

  18. Complete genome sequence of strain Lentibacillus amyloliquefaciens LAM0015(T) isolated from saline sediment.

    PubMed

    Wang, Jing-Li; Li, Yan-Bin; Ruan, Zhi-Yong; You, Yang; Wang, Lu-Shan; Qin, Han; Liu, Song; Shui, Zong-Xia; Wang, Yan-Wei; Tan, Fu-Rong; Wu, Bo; Dai, Li-Chun; Hu, Guo-Quan; Ma, Ke-Dong; He, Ming-Xiong

    2016-02-20

    The type strain Lentibacillus amyloliquefaciens LAM0015(T) with considerably highly NaCl tolerance is a member of halophiles. Here we report its genome sequence, the first to publish complete genome sequence of the Lentibacillus genus. It contains 3,858,520bp with an average GC content of 42.12%, encoding multiple valuable proteins academically and industrially. The genome sequence of strain LAM0015(T) provides basic information for further elucidation of halophilic mechanism and wider exploitation of functional genes. PMID:26806488

  19. Rapid Diagnostics of Onboard Sequences

    NASA Technical Reports Server (NTRS)

    Starbird, Thomas W.; Morris, John R.; Shams, Khawaja S.; Maimone, Mark W.

    2012-01-01

    Keeping track of sequences onboard a spacecraft is challenging. When reviewing Event Verification Records (EVRs) of sequence executions on the Mars Exploration Rover (MER), operators often found themselves wondering which version of a named sequence the EVR corresponded to. The lack of this information drastically impacts the operators diagnostic capabilities as well as their situational awareness with respect to the commands the spacecraft has executed, since the EVRs do not provide argument values or explanatory comments. Having this information immediately available can be instrumental in diagnosing critical events and can significantly enhance the overall safety of the spacecraft. This software provides auditing capability that can eliminate that uncertainty while diagnosing critical conditions. Furthermore, the Restful interface provides a simple way for sequencing tools to automatically retrieve binary compiled sequence SCMFs (Space Command Message Files) on demand. It also enables developers to change the underlying database, while maintaining the same interface to the existing applications. The logging capabilities are also beneficial to operators when they are trying to recall how they solved a similar problem many days ago: this software enables automatic recovery of SCMF and RML (Robot Markup Language) sequence files directly from the command EVRs, eliminating the need for people to find and validate the corresponding sequences. To address the lack of auditing capability for sequences onboard a spacecraft during earlier missions, extensive logging support was added on the Mars Science Laboratory (MSL) sequencing server. This server is responsible for generating all MSL binary SCMFs from RML input sequences. The sequencing server logs every SCMF it generates into a MySQL database, as well as the high-level RML file and dictionary name inputs used to create the SCMF. The SCMF is then indexed by a hash value that is automatically included in all command

  20. Structural analysis of the α subunit of Na(+)/K(+) ATPase genes in invertebrates.

    PubMed

    Thabet, Rahma; Rouault, J-D; Ayadi, Habib; Leignel, Vincent

    2016-01-01

    The Na(+)/K(+) ATPase is a ubiquitous pump coordinating the transport of Na(+) and K(+) across the membrane of cells and its role is fundamental to cellular functions. It is heteromer in eukaryotes including two or three subunits (α, β and γ which is specific to the vertebrates). The catalytic functions of the enzyme have been attributed to the α subunit. Several complete α protein sequences are available, but only few gene structures were characterized. We identified the genomic sequences coding the α-subunit of the Na(+)/K(+) ATPase, from the whole-genome shotgun contigs (WGS), NCBI Genomes (chromosome), Genomic Survey Sequences (GSS) and High Throughput Genomic Sequences (HTGS) databases across distinct phyla. One copy of the α subunit gene was found in Annelida, Arthropoda, Cnidaria, Echinodermata, Hemichordata, Mollusca, Placozoa, Porifera, Platyhelminthes, Urochordata, but the nematodes seem to possess 2 to 4 copies. The number of introns varied from 0 (Platyhelminthes) to 26 (Porifera); and their localization and length are also highly variable. Molecular phylogenies (Maximum Likelihood and Maximum Parsimony methods) showed some clusters constituted by (Chordata/(Echinodermata/Hemichordata)) or (Plathelminthes/(Annelida/Mollusca)) and a basal position for Porifera. These structural analyses increase our knowledge about the evolutionary events of the α subunit genes in the invertebrates.

  1. Structural analysis of the α subunit of Na(+)/K(+) ATPase genes in invertebrates.

    PubMed

    Thabet, Rahma; Rouault, J-D; Ayadi, Habib; Leignel, Vincent

    2016-01-01

    The Na(+)/K(+) ATPase is a ubiquitous pump coordinating the transport of Na(+) and K(+) across the membrane of cells and its role is fundamental to cellular functions. It is heteromer in eukaryotes including two or three subunits (α, β and γ which is specific to the vertebrates). The catalytic functions of the enzyme have been attributed to the α subunit. Several complete α protein sequences are available, but only few gene structures were characterized. We identified the genomic sequences coding the α-subunit of the Na(+)/K(+) ATPase, from the whole-genome shotgun contigs (WGS), NCBI Genomes (chromosome), Genomic Survey Sequences (GSS) and High Throughput Genomic Sequences (HTGS) databases across distinct phyla. One copy of the α subunit gene was found in Annelida, Arthropoda, Cnidaria, Echinodermata, Hemichordata, Mollusca, Placozoa, Porifera, Platyhelminthes, Urochordata, but the nematodes seem to possess 2 to 4 copies. The number of introns varied from 0 (Platyhelminthes) to 26 (Porifera); and their localization and length are also highly variable. Molecular phylogenies (Maximum Likelihood and Maximum Parsimony methods) showed some clusters constituted by (Chordata/(Echinodermata/Hemichordata)) or (Plathelminthes/(Annelida/Mollusca)) and a basal position for Porifera. These structural analyses increase our knowledge about the evolutionary events of the α subunit genes in the invertebrates. PMID:26812300

  2. The Na+-motive terminal oxidase activity in an alkalo- and halo-tolerant Bacillus.

    PubMed

    Semeykina, A L; Skulachev, V P; Verkhovskaya, M L; Bulygina, E S; Chumakov, K M

    1989-08-15

    An alkalo- and halo-tolerant aerobic microorganism has been isolated which, according to microbiological analysis data and the ribosomal 5S RNA sequence, is a Bacillus similar, but not identical, to B. licheniformis and B. subtilis. The microorganism, called Bacillus FTU, proved to be resistant to the protonophorous uncoupler carbonylcyanide m-chlorophenylhydrazone (CCCP). The fast growth of Bacillus FTU in the presence of CCCP was shown to require a high Na+ concentration in the medium. A procedure was developed to exhaust endogenous respiratory substrates in Bacillus FTU cells so that fast oxygen consumption by the cells was observed only when an exogenous respiratory substrate was added. The exhausted cells were found to oxidize ascorbate in the presence of N,N,N',N'-tetramethyl-p-phenylenediamine (TMPD) in a cyanide-sensitive fashion. The ascorbate oxidation was coupled to the uphill Na+ extrusion which was stimulated by CCCP and a penetrating weak base, diethylamine, as well as by valinomycin with or without diethylamine. Operation of the Bacillus FTU terminal oxidase resulted in the generation of a delta psi which, in the Na+ medium, was slightly decreased by CCCP and strongly decreased by CCCP + diethylamine. In the K+ medium, CCCP discharged delta psi even without diethylamine. Ascorbate oxidation was competent in ATP synthesis which was resistant to CCCP in the Na+ medium and sensitive to CCCP in the K+ medium as if Na+- and H+-coupled oxidative phosphorylations were operative in the Na+ and K+ media, respectively. Inside-out subcellular vesicles of Bacillus FTU were found to be competent in the Na+ uptake supported by oxidation of ascorbate + TMPD or diaminodurene. CCCP or valinomycin + K+ increased the Na+ uptake very strongly. The process was completely inhibited by cyanide or monensin, the former, but not the latter, being inhibitory for respiration. The data obtained indicate that in Bacillus FTU there is not only H+-motive but also Na

  3. Functional characterization of a plasma membrane Na+/H+ antiporter from alkali grass (Puccinellia tenuiflora).

    PubMed

    Wang, Xin; Yang, Ru; Wang, Baichen; Liu, Guifeng; Yang, Chuanping; Cheng, Yuxiang

    2011-10-01

    We have cloned a Na(+)/H(+) antiporter gene (GenBank accession no EF440291, PtNHA1) from Puccinellia tenuiflora (so-called alkali grass in Chinese) roots under NaCl salt stress. Its cDNA is 3775 bp and contains a 3414 bp open reading frame. The amino acid sequences of PtNHA1 show high identities with a putative plasma membrane Na(+)/H(+) antiporter from wheat. PtNHA1 was predicted to contain 11 hypothetical transmembrane domains in the N-terminal part and to localize in the plasma membrane. Genomic DNA gel blot analysis shows that PtNHA1 is a single-copy gene in the alkali grass genome. PtNHA1 is highly expressed in leaves, roots and shoots by RNA gel blot analysis. Furthermore, PtNHA1 gene expression of alkali grass was clearly up-regulated by NaCl salt stress. Overexpression of PtNHA1 in Arabidopsis resulted in enhanced tolerance of transgenic plants to NaCl stress. The ion contents analysis shows that, compared with the wild-type (WT), less Na(+) and more K(+) were accumulated in transgenic plants under NaCl stress. The results indicate that PtNHA1 play an important role in NaCl salt stress. Additionally, compared with the WT, total activities of ascorbate peroxidase (APX) and catalase (CAT), two key reactive oxygen species (ROS) detoxifying enzymes were high in transgenic plants under salt stress, respectively. The transcript levels of two APX genes (Apx1, s/mApx) and two CAT genes (Cat1, Cat2) in transgenic plants were higher than those in WT. This suggests that overexpression of PtNHA1 results in enhanced ROS-scavenging enzymes of transgenic plants under NaCl salt stress.

  4. Analysis of the Na+/Ca2+ exchanger gene family within the phylum Nematoda.

    PubMed

    He, Chao; O'Halloran, Damien M

    2014-01-01

    Na+/Ca2+ exchangers are low affinity, high capacity transporters that rapidly transport calcium at the plasma membrane, mitochondrion, endoplasmic (and sarcoplasmic) reticulum, and the nucleus. Na+/Ca2+ exchangers are widely expressed in diverse cell types where they contribute homeostatic balance to calcium levels. In animals, Na+/Ca2+ exchangers are divided into three groups based upon stoichiometry: Na+/Ca2+ exchangers (NCX), Na+/Ca2+/K+ exchangers (NCKX), and Ca2+/Cation exchangers (CCX). In mammals there are three NCX genes, five NCKX genes and one CCX (NCLX) gene. The genome of the nematode Caenorhabditis elegans contains ten Na+/Ca2+ exchanger genes: three NCX; five CCX; and two NCKX genes. Here we set out to characterize structural and taxonomic specializations within the family of Na+/Ca2+ exchangers across the phylum Nematoda. In this analysis we identify Na+/Ca2+ exchanger genes from twelve species of nematodes and reconstruct their phylogenetic and evolutionary relationships. The most notable feature of the resulting phylogenies was the heterogeneous evolution observed within exchanger subtypes. Specifically, in the case of the CCX exchangers we did not detect members of this class in three Clade III nematodes. Within the Caenorhabditis and Pristionchus lineages we identify between three and five CCX representatives, whereas in other Clade V and also Clade IV nematode taxa we only observed a single CCX gene in each species, and in the Clade III nematode taxa that we sampled we identify NCX and NCKX encoding genes but no evidence of CCX representatives using our mining approach. We also provided re-annotation for predicted CCX gene structures from Heterorhabditis bacteriophora and Caenorhabditis japonica by RT-PCR and sequencing. Together, these findings reveal a complex picture of Na+/Ca2+ transporters in nematodes that suggest an incongruent evolutionary history of proteins that provide central control of calcium dynamics.

  5. Recent advances in nanopore sequencing

    PubMed Central

    Maitra, Raj D.; Kim, Jungsuk; Dunbar, William B.

    2013-01-01

    The prospect of nanopores as a next-generation sequencing (NGS) platform has been a topic of growing interest and considerable government-sponsored research for more than a decade. Oxford Nanopore Technologies recently announced the first commercial nanopore sequencing devices, to be made available by the end of 2012, while other companies (Life, Roche, IBM) are also pursuing nanopore sequencing approaches. In this paper, the state of the art in nanopore sequencing is reviewed, focusing on the most recent contributions that have or promise to have NGS commercial potential. We consider also the scalability of the circuitry to support multichannel arrays of nanopores in future sequencing devices, which is critical to commercial viability. PMID:23138639

  6. The EMBL nucleotide sequence database.

    PubMed Central

    Stoesser, G; Moseley, M A; Sleep, J; McGowran, M; Garcia-Pastor, M; Sterk, P

    1998-01-01

    The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl. html ) constitutes Europe's primary nucleotide sequence resource. DNA and RNA sequences are directly submitted from researchers and genome sequencing groups and collected from the scientific literature and patent applications (Fig. 1). In collaboration with DDBJ and GenBank the database is produced, maintained and distributed at the European Bioinformatics Institute. Database releases are produced quarterly and are distributed on CD-ROM. EBI's network services allow access to the most up-to-date data collection via Internet and World Wide Web interface, providing database searching and sequence similarity facilities plus access to a large number of additional databases. PMID:9399791

  7. The effect of Na vapor on the Na content of chondrules

    NASA Technical Reports Server (NTRS)

    Lewis, R. Dean; Lofgren, Gary E.; Franzen, Hugo F.; Windom, Kenneth E.

    1993-01-01

    Chondrules contain higher concentrations of volatiles (Na) than expected for melt droplets in the solar nebula. Recent studies have proposed that chondrules may have formed under non-canonical nebular conditions such as in particle/gas-rich clumps. Such chondrule formation areas may have contained significant Na vapor. To test the hypothesis of whether a Na-rich vapor would minimize Na volatilization reaction rates in a chondrule analog and maintain the Na value of the melt, experiments were designed where a Na-rich vapor could be maintained around the sample. A starting material with a melting point lower that typical chondrules was required to keep the logistics of working with Na volatilization from NaCl within the realm of feasibility. The Knippa basalt, a MgO-rich alkali olivine basalt with a melting temperature of 1325 +/- 5 C and a Na2O content of 3.05 wt%, was used as the chondrule analog. Experiments were conducted in a 1 atm, gas-mixing furnace with the fO2 controlled by a CO/CO2 gas mixture and fixed at the I-W buffer curve. To determine the extent of Na loss from the sample, initial experiments were conducted at high temperatures (1300 C - 1350 C) for duration of up to 72 h without a Na-rich vapor present. Almost all (up to 98%) Na was volatilized in runs of 72 h. Subsequent trials were conducted at 1330 C for 16 h in the presence of a Na-rich vapor, supplied by a NaCl-filled crucible placed in the bottom of the furnace. Succeeding Knudsen cell weight-loss mass-spectrometry analysis of NaCl determined the P(sub Na) for these experimental conditions to be in the 10(exp -6) atm range. This value is considered high for nebula conditions but is still plausible for non-canonical environments. In these trials the Na2O content of the glass was maintained or in some cases increased; Na2O values ranged from 2.62% wt to 4.37% wt. The Na content of chondrules may be controlled by the Na vapor pressure in the chondrule formation region. Most heating events capable

  8. Poisson process approximation for sequence repeats, and sequencing by hybridization.

    PubMed

    Arratia, R; Martin, D; Reinert, G; Waterman, M S

    1996-01-01

    Sequencing by hybridization is a tool to determine a DNA sequence from the unordered list of all l-tuples contained in this sequence; typical numbers for l are l = 8, 10, 12. For theoretical purposes we assume that the multiset of all l-tuples is known. This multiset determines the DNA sequence uniquely if none of the so-called Ukkonen transformations are possible. These transformations require repeats of (l-1)-tuples in the sequence, with these repeats occurring in certain spatial patterns. We model DNA as an i.i.d. sequence. We first prove Poisson process approximations for the process of indicators of all leftmost long repeats allowing self-overlap and for the process of indicators of all left-most long repeats without self-overlap. Using the Chen-Stein method, we get bounds on the error of these approximations. As a corollary, we approximate the distribution of longest repeats. In the second step we analyze the spatial patterns of the repeats. Finally we combine these two steps to prove an approximation for the probability that a random sequence is uniquely recoverable from its list of l-tuples. For all our results we give some numerical examples including error bounds. PMID:8891959

  9. The Offline Software Framework of the NA61/SHINE Experiment

    NASA Astrophysics Data System (ADS)

    Sipos, Roland; Laszlo, Andras; Marcinek, Antoni; Paul, Tom; Szuba, Marek; Unger, Michael; Veberic, Darko; Wyszynski, Oskar

    2012-12-01

    NA61/SHINE (SHINE = SPS Heavy Ion and Neutrino Experiment) is an experiment at the CERN SPS using the upgraded NA49 hadron spectrometer. Among its physics goals are precise hadron production measurements for improving calculations of the neutrino beam flux in the T2K neutrino oscillation experiment as well as for more reliable simulations of cosmic-ray air showers. Moreover, p+p, p+Pb and nucleus+nucleus collisions will be studied extensively to allow for a study of properties of the onset of deconfinement and search for the critical point of strongly interacting matter. Currently NA61/SHINE uses the old NA49 software framework for reconstruction, simulation and data analysis. The core of this legacy framework was developed in the early 1990s. It is written in different programming and scripting languages (C, pgi-Fortran, shell) and provides several concurrent data formats for the event data model, which includes also obsolete parts. In this contribution we will introduce the new software framework, called Shine, that is written in C++ and designed to comprise three principal parts: a collection of processing modules which can be assembled and sequenced by the user via XML files, an event data model which contains all simulation and reconstruction information based on STL and ROOT streaming, and a detector description which provides data on the configuration and state of the experiment. To assure a quick migration to the Shine framework, wrappers were introduced that allow to run legacy code parts as modules in the new framework and we will present first results on the cross validation of the two frameworks.

  10. Identification and characterization of the antifungal substances of a novel Streptomyces cavourensis NA4.

    PubMed

    Pan, Hua-Qi; Yu, Su-Ya; Song, Chun-Feng; Wang, Nan; Hua, Hui-Ming; Hu, Jiang-Chun; Wang, Shu-Jin

    2015-03-01

    A new actinomycete strain NA4 was isolated from a deep-sea sediment collected from the South China Sea and showed promising antifungal activities against soilborne fungal pathogens. It was identified as Streptomyces cavourensis by morphological, physiological, and phylogenetic analyses based on its 16S rRNA gene sequence. The main antifungal components were isolated and identified from the fermentation culture as bafilomycins B1 and C1. These compounds exhibited significant antifungal activities and a broad antifungal spectrum. The results suggest that the Streptomyces cavourensis NA4 and bafilomycins B1 and C1 could be used as potential biocontrol agents for soilborne fungal diseases of plants.

  11. Multilocus sequence typing of total-genome-sequenced bacteria.

    PubMed

    Larsen, Mette V; Cosentino, Salvatore; Rasmussen, Simon; Friis, Carsten; Hasman, Henrik; Marvig, Rasmus Lykke; Jelsbak, Lars; Sicheritz-Pontén, Thomas; Ussery, David W; Aarestrup, Frank M; Lund, Ole

    2012-04-01

    Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the "gold standard" of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS) continue to decline, it becomes increasingly available to scientists and routine diagnostic laboratories. Currently, the cost is below that of traditional MLST. The new challenges will be how to extract the relevant information from the large amount of data so as to allow for comparison over time and between laboratories. Ideally, this information should also allow for comparison to historical data. We developed a Web-based method for MLST of 66 bacterial species based on WGS data. As input, the method uses short sequence reads from four sequencing platforms or preassembled genomes. Updates from the MLST databases are downloaded monthly, and the best-matching MLST alleles of the specified MLST scheme are found using a BLAST-based ranking method. The sequence type is then determined by the combination of alleles identified. The method was tested on preassembled genomes from 336 isolates covering 56 MLST schemes, on short sequence reads from 387 isolates covering 10 schemes, and on a small test set of short sequence reads from 29 isolates for which the sequence type had been determined by traditional methods. The method presented here enables investigators to determine the sequence types of their isolates on the basis of WGS data. This method is publicly available at www.cbs.dtu.dk/services/MLST. PMID:22238442

  12. Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

    PubMed Central

    Cosentino, Salvatore; Rasmussen, Simon; Friis, Carsten; Hasman, Henrik; Marvig, Rasmus Lykke; Jelsbak, Lars; Sicheritz-Pontén, Thomas; Ussery, David W.; Aarestrup, Frank M.; Lund, Ole

    2012-01-01

    Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the “gold standard” of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS) continue to decline, it becomes increasingly available to scientists and routine diagnostic laboratories. Currently, the cost is below that of traditional MLST. The new challenges will be how to extract the relevant information from the large amount of data so as to allow for comparison over time and between laboratories. Ideally, this information should also allow for comparison to historical data. We developed a Web-based method for MLST of 66 bacterial species based on WGS data. As input, the method uses short sequence reads from four sequencing platforms or preassembled genomes. Updates from the MLST databases are downloaded monthly, and the best-matching MLST alleles of the specified MLST scheme are found using a BLAST-based ranking method. The sequence type is then determined by the combination of alleles identified. The method was tested on preassembled genomes from 336 isolates covering 56 MLST schemes, on short sequence reads from 387 isolates covering 10 schemes, and on a small test set of short sequence reads from 29 isolates for which the sequence type had been determined by traditional methods. The method presented here enables investigators to determine the sequence types of their isolates on the basis of WGS data. This method is publicly available at www.cbs.dtu.dk/services/MLST. PMID:22238442

  13. Effect of colchicine on sensitivity of duck salt gland Na,K-ATPase to Na+.

    PubMed

    Yakushev, S S; Kumskova, E M; Rubtsov, A M; Lopina, O D

    2008-09-01

    Low molecular mass proteins of the FXYD family that affect the sensitivity of Na,K-ATPase to Na+ and K+ are known to be present in Na,K-ATPases in various tissues. In particular, in Na,K-ATPase from kidney a gamma-subunit (with electrophoretic mobility corresponding to molecular mass of about 10 kD) is present, and Na,K-ATPase preparations from heart contain phospholemman (electrophoretic mobility of this protein corresponds to molecular mass of 13-14 kD), which provides for the interaction of heart Na,K-ATPase with cytoskeletal microtubules. Disruption of microtubules by colchicine removes phospholemman from heart Na,K-ATPase preparations. The goal of the present study was to reveal a low molecular mass protein (probably a member of FXYD family) in preparation of Na,K-ATPase from duck salt glands. Immunoprecipitation of solubilized duck salt gland Na,K-ATPase using antibodies against alpha1-subunit results in the coprecipitation of a 13 kD protein with the Na,K-ATPase complex. Treatment of homogenate from duck salt glands with colchicine removes this protein from the purified preparation of Na,K-ATPase. Simultaneously, we observed a decrease in the sensitivity of Na,K-ATPase to Na+ at pH 6.5. However, colchicine treatment of homogenate from rabbit kidney does not affect either the sensitivity of Na,K-ATPase obtained from this homogenate to Na+ or the content of 10 kD protein (presumably gamma-subunit). The data suggest that phospholemman (or a similar member of the FXYD family) tightly interacts with Na,K-ATPase from duck salt glands and binds it to microtubules, simultaneously participating in the regulation of the sensitivity of Na,K-ATPase to Na+. PMID:18976215

  14. Growth of binary organic NLO crystals: m.NA-p.NA and m.NA-CNA system

    NASA Technical Reports Server (NTRS)

    Singh, N. B.; Henningsen, T.; Hopkins, R. H.; Mazelsky, R.

    1993-01-01

    Experiments were carried out to grow 3.Nitroaniline (m.NA) crystals doped with 4.Nitroaniline (p.NA) and 2.chloro 4.Nitroaniline (CNA). The measured undercooling for m.NA, p.NA, and CNA were 0.21 tm K, 0.23 tm K, and 0.35 tm K respectively, where tm represents the melting temperature of the pure component. Because of the crystals' large heat of fusion and large undercooling, it was not possible to grow good quality crystals with low thermal gradients. In the conventional two-zone Bridgman furnace we had to raise the temperature of the hot zone above the decomposition temperature of CNA, p.NA, and m.NA to achieve the desired thermal gradient. To avoid decomposition, we used an unconventional Bridgman furnace. Two immiscible liquids, silicone oil and ethylene glycol, were used to build a special two-zone Bridgman furnace. A temperature gradient of 18 K/cm was achieved without exceeding the decomposition temperature of the crystal. The binary crystals, m.NA-p.NA and m.NA-CNA, were grown in centimeter size in this furnace. X-ray and optical characterization showed good optical quality.

  15. Ossification sequence heterochrony among amphibians.

    PubMed

    Harrington, Sean M; Harrison, Luke B; Sheil, Christopher A

    2013-01-01

    Heterochrony is an important mechanism in the evolution of amphibians. Although studies have centered on the relationship between size and shape and the rates of development, ossification sequence heterochrony also may have been important. Rigorous, phylogenetic methods for assessing sequence heterochrony are relatively new, and a comprehensive study of the relative timing of ossification of skeletal elements has not been used to identify instances of sequence heterochrony across Amphibia. In this study, a new version of the program Parsimov-based genetic inference (PGi) was used to identify shifts in ossification sequences across all extant orders of amphibians, for all major structural units of the skeleton. PGi identified a number of heterochronic sequence shifts in all analyses, the most interesting of which seem to be tied to differences in metamorphic patterns among major clades. Early ossification of the vomer, premaxilla, and dentary is retained by Apateon caducus and members of Gymnophiona and Urodela, which lack the strongly biphasic development seen in anurans. In contrast, bones associated with the jaws and face were identified as shifting late in the ancestor of Anura. The bones that do not shift late, and thereby occupy the earliest positions in the anuran cranial sequence, are those in regions of the skull that undergo the least restructuring throughout anuran metamorphosis. Additionally, within Anura, bones of the hind limb and pelvic girdle were also identified as shifting early in the sequence of ossification, which may be a result of functional constraints imposed by the drastic metamorphosis of most anurans.

  16. Image analysis for DNA sequencing

    NASA Astrophysics Data System (ADS)

    Palaniappan, Kannappan; Huang, Thomas S.

    1991-07-01

    There is a great deal of interest in automating the process of DNA (deoxyribonucleic acid) sequencing to support the analysis of genomic DNA such as the Human and Mouse Genome projects. In one class of gel-based sequencing protocols autoradiograph images are generated in the final step and usually require manual interpretation to reconstruct the DNA sequence represented by the image. The need to handle a large volume of sequence information necessitates automation of the manual autoradiograph reading step through image analysis in order to reduce the length of time required to obtain sequence data and reduce transcription errors. Various adaptive image enhancement, segmentation and alignment methods were applied to autoradiograph images. The methods are adaptive to the local characteristics of the image such as noise, background signal, or presence of edges. Once the two-dimensional data is converted to a set of aligned one-dimensional profiles waveform analysis is used to determine the location of each band which represents one nucleotide in the sequence. Different classification strategies including a rule-based approach are investigated to map the profile signals, augmented with the original two-dimensional image data as necessary, to textual DNA sequence information.

  17. Maintaining the Na atmosphere of Mercury

    NASA Technical Reports Server (NTRS)

    Killen, Rosemary M.; Morgan, Thomas H.

    1993-01-01

    The possible sources of the Na atmosphere of Mercury are calculatively studied. The likely structure, composition, and temperature of the planet's upper crust is examined along with the probable flux of Na from depth by grain boundary diffusion and by Knudsen flow. The creation of fresh regolith is considered along with mechanisms for supplying Na from the surface to the exosphere. The implications of the calculations for the probable abundances in the regolith are discussed.

  18. From mapping to sequencing, post-sequencing and beyond.

    PubMed

    Sasaki, Takuji; Matsumoto, Takashi; Antonio, Baltazar A; Nagamura, Yoshiaki

    2005-01-01

    The Rice Genome Research Program (RGP) in Japan has been collaborating with the international community in elucidating a complete high-quality sequence of the rice genome. As the pioneer in large-scale analysis of the rice genome, the RGP has successfully established the fundamental tools for genome research such as a genetic map, a yeast artificial chromosome (YAC)-based physical map, a transcript map and a phage P1 artificial chromosome (PAC)/bacterial artificial chromosome (BAC) sequence-ready physical map, which serve as common resources for genome sequencing. Among the 12 rice chromosomes, the RGP is in charge of sequencing six chromosomes covering 52% of the 390 Mb total length of the genome. The contribution of the RGP to the realization of decoding the rice genome sequence with high accuracy and deciphering the genetic information in the genome will have a great impact in understanding the biology of the rice plant that provides a major food source for almost half of the world's population. A high-quality draft sequence (phase 2) was completed in December 2002. Since then, much of the finished quality sequence (phase 3) has become available in public databases. With the completion of sequencing in December 2004, it is expected that the genome sequence would facilitate innovative research in functional and applied genomics. A map-based genome sequence is indispensable for further improvement of current rice varieties and for development of novel varieties carrying agronomically important traits such as high yield potential and tolerance to both biotic and abiotic stresses. In addition to genome sequencing, various related projects have been initiated to generate valuable resources, which could serve as indispensable tools in clarifying the structure and function of the rice genome. These resources have been made available to the scientific community through the Rice Genome Resource Center (RGRC) of the National Institute of Agrobiological Sciences (NIAS) to

  19. Colonic H(+)-K(+)-ATPase in K(+) conservation and electrogenic Na(+) absorption during Na(+) restriction.

    PubMed

    Spicer, Z; Clarke, L L; Gawenis, L R; Shull, G E

    2001-12-01

    Upregulation of the colonic H(+)-K(+)- ATPase (cHKA) during hyperaldosteronism suggests that it functions in both K(+) conservation and electrogenic Na(+) absorption in the colon when Na(+)-conserving mechanisms are activated. To test this hypothesis, wild-type (cHKA(+/+)) and cHKA-deficient (cHKA(-/-)) mice were fed Na(+)-replete and Na(+)-restricted diets and their responses were analyzed. In both genotypes, Na(+) restriction led to reduced plasma Na(+) and increased serum aldosterone, and mRNAs for the epithelial Na(+) channel (ENaC) beta- and gamma-subunits, channel-inducing factor, and cHKA were increased in distal colon. Relative to wild-type controls, cHKA(-/-) mice on a Na(+)-replete diet had elevated fecal K(+) excretion. Dietary Na(+) restriction led to increased K(+) excretion in knockout but not in wild-type mice. The amiloride-sensitive, ENaC-mediated short-circuit current in distal colon was significantly reduced in knockout mice maintained on either the Na(+)-replete or Na(+)-restricted diet. These results demonstrate that cHKA plays an important role in K(+) conservation during dietary Na(+) restriction and suggest that cHKA-mediated K(+) recycling across the apical membrane is required for maximum electrogenic Na(+) absorption. PMID:11705741

  20. Ionic dependence of active Na-K transport: "clamping" of cellular Na+ with monensin.

    PubMed

    Haber, R S; Pressley, T A; Loeb, J N; Ismail-Beigi, F

    1987-07-01

    The Na+ ionophore monensin was used to study the Na+- and K+-dependence of ouabain-inhibitable 86Rb+ uptake in ARL 15 cells, a rat liver cell line. Graded concentrations of monensin rapidly induced incremental elevations of cellular Na+ that were stable for up to 2 h. In experiments in which cellular Na+ was thus "clamped" at various levels, the activation curve for ouabain-inhibitable 86Rb+ uptake as a function of intracellular Na+ was found to be steepest near basal Na+ levels (Hill coefficient approximately equal to 2.4), indicating that these cells can respond to relatively large changes in passive Na+ entry by increasing the race of Na-K pump function with only minimal increases in cellular Na+. Exposure of cells to monensin also permitted examination of the extracellular-K+ dependence of ouabain-inhibitable 86Rb+ uptake in the presence of saturating intracellular Na+ and yielded a Hill coefficient of approximately 1.5. The rate of ATP hydrolysis calculated from measurements of the maximal rate of ouabain-inhibitable 86Rb+ uptake in intact cells was similar to the enzymatic Vmax of the Na+-K+-ATPase in cell lysates, suggesting that the Na+-K+-ATPase activity in these broken-cell preparations closely reflects the functional transport capacity of the Na-K pump.

  1. Leishmania amazonensis: PKC-like protein kinase modulates the (Na++K+)ATPase activity.

    PubMed

    Almeida-Amaral, Elmo Eduardo de; Caruso-Neves, Celso; Lara, Lucienne Silva; Pinheiro, Carla Mônica; Meyer-Fernandes, José Roberto

    2007-08-01

    The present study aimed to identify the presence of protein kinase C-like (PKC-like) in Leishmania amazonensis and to elucidate its possible role in the modulation of the (Na(+)+K(+))ATPase activity. Immunoblotting experiments using antibody against a consensus sequence (Ac 543-549) of rabbit protein kinase C (PKC) revealed the presence of a protein kinase of 80 kDa in L. amazonensis. Measurements of protein kinase activity showed the presence of both (Ca(2+)-dependent) and (Ca(2+)-independent) protein kinase activity in plasma membrane and cytosol. Phorbol ester (PMA) activation of the Ca(2+)-dependent protein kinase stimulated the (Na(+)+K(+))ATPase activity, while activation of the Ca(2+)-independent protein kinase was inhibitory. Both effects of protein kinase on the (Na(+)+K(+))ATPase of the plasma membrane were lower than that observed in intact cells. PMA induced the translocation of protein kinase from cytosol to plasma membrane, indicating that the maximal effect of protein kinase on the (Na(+)+K(+))ATPase activity depends on the synergistic action of protein kinases from both plasma membrane and cytosol. This is the first demonstration of a protein kinase activated by PMA in L. amazonensis and the first evidence for a possible role in the regulation of the (Na(+)+K(+))ATPase activity in this trypanosomatid. Modulation of the (Na(+)+K(+))ATPase by protein kinase in a trypanosomatid opens up new possibilities to understand the regulation of ion homeostasis in this parasite. PMID:17475255

  2. NA-NET numerical analysis net

    SciTech Connect

    Dongarra, J. |; Rosener, B.

    1991-12-01

    This report describes a facility called NA-NET created to allow numerical analysts (na) an easy method of communicating with one another. The main advantage of the NA-NET is uniformity of addressing. All mail is addressed to the Internet host ``na-net.ornl.gov`` at Oak Ridge National Laboratory. Hence, members of the NA-NET do not need to remember complicated addresses or even where a member is currently located. As long as moving members change their e-mail address in the NA-NET everything works smoothly. The NA-NET system is currently located at Oak Ridge National Laboratory. It is running on the same machine that serves netlib. Netlib is a separate facility that distributes mathematical software via electronic mail. For more information on netlib consult, or send the one-line message ``send index`` to netlib{at}ornl.gov. The following report describes the current NA-NET system from both a user`s perspective and from an implementation perspective. Currently, there are over 2100 members in the NA-NET. An average of 110 mail messages pass through this facility daily.

  3. NA-NET numerical analysis net

    SciTech Connect

    Dongarra, J. . Dept. of Computer Science Oak Ridge National Lab., TN ); Rosener, B. . Dept. of Computer Science)

    1991-12-01

    This report describes a facility called NA-NET created to allow numerical analysts (na) an easy method of communicating with one another. The main advantage of the NA-NET is uniformity of addressing. All mail is addressed to the Internet host na-net.ornl.gov'' at Oak Ridge National Laboratory. Hence, members of the NA-NET do not need to remember complicated addresses or even where a member is currently located. As long as moving members change their e-mail address in the NA-NET everything works smoothly. The NA-NET system is currently located at Oak Ridge National Laboratory. It is running on the same machine that serves netlib. Netlib is a separate facility that distributes mathematical software via electronic mail. For more information on netlib consult, or send the one-line message send index'' to netlib{at}ornl.gov. The following report describes the current NA-NET system from both a user's perspective and from an implementation perspective. Currently, there are over 2100 members in the NA-NET. An average of 110 mail messages pass through this facility daily.

  4. Painful Na-channelopathies: an expanding universe.

    PubMed

    Waxman, Stephen G

    2013-07-01

    The universe of painful Na-channelopathies--human disorders caused by mutations in voltage-gated sodium channels--has recently expanded in three dimensions. We now know that mutations of sodium channels cause not only rare genetic 'model disorders' such as inherited erythromelalgia and channelopathy-associated insensitivity to pain but also common painful neuropathies. We have learned that mutations of NaV1.8, as well as mutations of NaV1.7, can cause painful Na-channelopathies. Moreover, recent studies combining atomic level structural models and pharmacogenomics suggest that the goal of genomically guided pain therapy may not be unrealistic.

  5. NaHCO3 and NaC1 tolerance in chronic renal failure.

    PubMed

    Husted, F C; Nolph, K D; Maher, J F

    1975-08-01

    In patients with chronic renal failure, NaHCO3 therapy may correct or prevent acidemia. It has been proposed that the NaHCO3 required will not result in clinically significant Na retention comparable to that from similar increases in NaC1 intake. In each of ten patients with chronic renal failure, creatinine clearance (Ccr) range 2.5-16.8 ml/min, on an estimated 10-meq Na and C1 diet, electrolyte excretion was compared on NaHCO3 vs NaC1 supplements of 200 meq/day. Periods of NaHCO3 and NaC1 (in alternate order for successive patients) lasted 4 days, separated by reequilibration to base-line weight. Mean +/- SEM excretion (ex) of Na, C1, and HCO3 and deltaCcr and deltaweight (day 4-1) are compared below for the 4th day of NaC1 vs. NaHCO3 intake. Mean Ccr +/-SEM on day 4 of NaC1 and NaHCO3 were 10.8 +/-1.6 and 9.0 +/-1.4 ml/min, respectively (P less than 0.02). Mean systolic blood pressure (but not diastolic) increased significantly on NaC1 (P less than 0.05). No significant blood pressure changes were seen on NaHCO3. Net positive HCO3 balance occurred on NaHCO3 as indicated above and reflected a rise in mean serum HCO3 from 19 to 30 meq/liter (day 1 vs. 4) (P less than 0.01). Mechanisms for the greater excretion of Na on NaHCO3 may relate to C1 wasting as noted above on low C1 intake and limited HCO3 reabsorptive capacity. Thus, Na excretion by day 4 was greater on NaHCO3 than on NaHCO3 did Na excretion near intake (210 meq/day).

  6. Phylogenetic Analysis of Poliovirus Sequences.

    PubMed

    Jorba, Jaume

    2016-01-01

    Comparative genomic sequencing is a major surveillance tool in the Polio Laboratory Network. Due to the rapid evolution of polioviruses (~1 % per year), pathways of virus transmission can be reconstructed from the pathways of genomic evolution. Here, we describe three main phylogenetic methods; estimation of genetic distances, reconstruction of a maximum-likelihood (ML) tree, and estimation of substitution rates using Bayesian Markov chain Monte Carlo (MCMC). The data set used consists of complete capsid sequences from a survey of poliovirus sequences available in GenBank. PMID:26983737

  7. Voltage dependence of Na/K pump current in Xenopus oocytes.

    PubMed

    Rakowski, R F; Paxson, C L

    1988-12-01

    Stage V and VI (Dumont, J.N., 1972, J. Morphol. 136:153-180) oocytes of Xenopus laevis were treated with collagenase to remove follicular cells and were placed in K-free solution for 2 to 4 days to elevate internal [Na]. Na/K pump activity was studied by restoring the eggs to normal 3 mM K Barth's solution and measuring membrane current-voltage (I-V) relationships before and after the addition of 10 microM dihydroouabain (DHO) using a two-microelectrode voltage clamp. Two pulse protocols were used to measure membrane I-V relationships, both allowing membrane currents to be determined twice at each of a series of membrane potentials: (i) a down-up-down sequence of 5 mV, 1-sec stair steps and (ii) a similar sequence of 1-sec voltage pulses but with consecutive pulses separated by 4-sec recovery periods at the holding potential (-40 mV). The resulting membrane I-V relationships determined both before and during exposure to DHO showed significant hysteresis between the first and second current measurements at each voltage. DHO difference curves also usually showed hysteresis indicating that DHO caused a change in a component of current that varied with time. Since, by definition, the steady-state Na/K pump I-V relationship must be free of hysteresis, the presence of hysteresis in DHO difference I-V curves can be used as a criterion for excluding such data from consideration as a valie measure of the Na/K pump I-V relationship. DHO difference I-V relationships that did not show hysteresis were sigmoid functions of membrane potential when measured in normal (90 mM) external Na solution. The Na/K pump current magnitude saturated near 0 mV at a value of 1.0-1.5 microA cm-2, without evidence of negative slope conductance for potentials up to +55 mV. The Na/K pump current magnitude in Na-free external solution was approximately voltage independent. Since these forward-going Na/K pump I-V relationships do not show a region of negative slope over the voltage range -110 to +55

  8. Guitars, Violins, and Geometric Sequences

    ERIC Educational Resources Information Center

    Barger, Rita; Haehl, Martha

    2007-01-01

    This article describes middle school mathematics activities that relate measurement, ratios, and geometric sequences to finger positions or the placement of frets on stringed musical instruments. (Contains 2 figures and 2 tables.)

  9. Paucity of moderately repetitive sequences

    SciTech Connect

    Schmid, C.W.

    1991-01-01

    We examined clones of renatured repetitive human DNA to find novel repetitive DNAs. After eliminating known repeats, the remaining clones were subjected to sequence analysis. These clones also corresponded to known repeats, but with greater sequence diversity. This indicates that either these libraries were depleted of short interspersed repeats in construction, or these repeats are much less prevalent in the human genome than is indicated by data from {und Xenopus} or sea urchin studies. We directly investigated the sequence composition of human DNA through traditional renaturation techniques with the goal of estimating the limits of abundance of repetitive sequence classes in human DNA. Our results sharply limit the maximum possible abundance to 1--2% of the human genome. Our estimate, minus the known repeats in this fraction, leaves about 1% (3 {times} 10{sup 7} nucleotides) of the human genome for novel repetitive elements. 2 refs. (MHB)

  10. Molecular beacon sequence design algorithm.

    PubMed

    Monroe, W Todd; Haselton, Frederick R

    2003-01-01

    A method based on Web-based tools is presented to design optimally functioning molecular beacons. Molecular beacons, fluorogenic hybridization probes, are a powerful tool for the rapid and specific detection of a particular nucleic acid sequence. However, their synthesis costs can be considerable. Since molecular beacon performance is based on its sequence, it is imperative to rationally design an optimal sequence before synthesis. The algorithm presented here uses simple Microsoft Excel formulas and macros to rank candidate sequences. This analysis is carried out using mfold structural predictions along with other free Web-based tools. For smaller laboratories where molecular beacons are not the focus of research, the public domain algorithm described here may be usefully employed to aid in molecular beacon design.

  11. The Dynamics of DNA Sequencing.

    ERIC Educational Resources Information Center

    Morvillo, Nancy

    1997-01-01

    Describes a paper-and-pencil activity that helps students understand DNA sequencing and expands student understanding of DNA structure, replication, and gel electrophoresis. Appropriate for advanced biology students who are familiar with the Sanger method. (DDR)

  12. Polymorphix: a sequence polymorphism database.

    PubMed

    Bazin, Eric; Duret, Laurent; Penel, Simon; Galtier, Nicolas

    2005-01-01

    Within-species sequence variation data are of special interest since they contain information about recent population/species history, and the molecular evolutionary forces currently in action in natural populations. These data, however, are presently dispersed within generalist databases, and are difficult to access. To solve this problem, we have developed Polymorphix, a database dedicated to sequence polymorphism. It contains within-species homologous sequence families built using EMBL/GenBank under suitable similarity and bibliographic criteria. Polymorphix is an ACNUC structured database allowing both simple and complex queries for population genomic studies. Alignments within families as well as phylogenetic trees can be download. When available, outgroups are included in the alignment. Polymorphix contains sequences from the nuclear, mitochondrial and chloroplastic genomes of every eukaryote species represented in EMBL. It can be accessed by a web interface (http://pbil.univ-lyon1.fr/polymorphix/query.php).

  13. Rover Sequencing and Visualization Program

    NASA Technical Reports Server (NTRS)

    Cooper, Brian; Hartman, Frank; Maxwell, Scott; Yen, Jeng; Wright, John; Balacuit, Carlos

    2005-01-01

    The Rover Sequencing and Visualization Program (RSVP) is the software tool for use in the Mars Exploration Rover (MER) mission for planning rover operations and generating command sequences for accomplishing those operations. RSVP combines three-dimensional (3D) visualization for immersive exploration of the operations area, stereoscopic image display for high-resolution examination of the downlinked imagery, and a sophisticated command-sequence editing tool for analysis and completion of the sequences. RSVP is linked with actual flight-code modules for operations rehearsal to provide feedback on the expected behavior of the rover prior to committing to a particular sequence. Playback tools allow for review of both rehearsed rover behavior and downlinked results of actual rover operations. These can be displayed simultaneously for comparison of rehearsed and actual activities for verification. The primary inputs to RSVP are downlink data products from the Operations Storage Server (OSS) and activity plans generated by the science team. The activity plans are high-level goals for the next day s activities. The downlink data products include imagery, terrain models, and telemetered engineering data on rover activities and state. The Rover Sequence Editor (RoSE) component of RSVP performs activity expansion to command sequences, command creation and editing with setting of command parameters, and viewing and management of rover resources. The HyperDrive component of RSVP performs 2D and 3D visualization of the rover s environment, graphical and animated review of rover-predicted and telemetered state, and creation and editing of command sequences related to mobility and Instrument Deployment Device (IDD) operations. Additionally, RoSE and HyperDrive together evaluate command sequences for potential violations of flight and safety rules. The products of RSVP include command sequences for uplink that are stored in the Distributed Object Manager (DOM) and predicted rover

  14. Na+/Ca2+ exchange and Na+/K+-ATPase in the heart

    PubMed Central

    Shattock, Michael J; Ottolia, Michela; Bers, Donald M; Blaustein, Mordecai P; Boguslavskyi, Andrii; Bossuyt, Julie; Bridge, John H B; Chen-Izu, Ye; Clancy, Colleen E; Edwards, Andrew; Goldhaber, Joshua; Kaplan, Jack; Lingrel, Jerry B; Pavlovic, Davor; Philipson, Kenneth; Sipido, Karin R; Xie, Zi-Jian

    2015-01-01

    This paper is the third in a series of reviews published in this issue resulting from the University of California Davis Cardiovascular Symposium 2014: Systems approach to understanding cardiac excitation–contraction coupling and arrhythmias: Na+ channel and Na+ transport. The goal of the symposium was to bring together experts in the field to discuss points of consensus and controversy on the topic of sodium in the heart. The present review focuses on cardiac Na+/Ca2+ exchange (NCX) and Na+/K+-ATPase (NKA). While the relevance of Ca2+ homeostasis in cardiac function has been extensively investigated, the role of Na+ regulation in shaping heart function is often overlooked. Small changes in the cytoplasmic Na+ content have multiple effects on the heart by influencing intracellular Ca2+ and pH levels thereby modulating heart contractility. Therefore it is essential for heart cells to maintain Na+ homeostasis. Among the proteins that accomplish this task are the Na+/Ca2+ exchanger (NCX) and the Na+/K+ pump (NKA). By transporting three Na+ ions into the cytoplasm in exchange for one Ca2+ moved out, NCX is one of the main Na+ influx mechanisms in cardiomyocytes. Acting in the opposite direction, NKA moves Na+ ions from the cytoplasm to the extracellular space against their gradient by utilizing the energy released from ATP hydrolysis. A fine balance between these two processes controls the net amount of intracellular Na+ and aberrations in either of these two systems can have a large impact on cardiac contractility. Due to the relevant role of these two proteins in Na+ homeostasis, the emphasis of this review is on recent developments regarding the cardiac Na+/Ca2+ exchanger (NCX1) and Na+/K+ pump and the controversies that still persist in the field. PMID:25772291

  15. The Na-O anticorrelation in horizontal branch stars. I. NGC 2808

    NASA Astrophysics Data System (ADS)

    Gratton, R. G.; Lucatello, S.; Carretta, E.; Bragaglia, A.; D'Orazi, V.; Momany, Y. Al

    2011-10-01

    Globular clusters have been recognized to host multiple stellar populations. A spectacular example of this is the massive cluster NGC 2808, where multiple populations have been found along the horizontal branch (HB) and the main sequence (MS). Studies of red giants showed that this cluster appears homogeneous insofar Fe abundance is concerned, but it shows an extended anticorrelation between Na and O abundances. The Na-poor, O-rich population can be identified with the red MS, and the Na-rich, O-poor one with the blue one. This may be understood in terms of different He content, He being correlated with Na. A prediction of this scenario is that He-rich, Na-rich He-core burning stars, because they are less massive, will end up on the bluer part of the HB, while He-poor, Na-poor stars will reside on the red HB. The aim of this paper is to verify this prediction. To this purpose, we acquired high-resolution spectra of regions including strong O and Na lines in several tens of HB stars of NGC 2808, sampling both the red and blue parts of the HB. We limited our analysis to those blue HB stars cooler than the gap at 11 500 K, because diffusion and radiative pressure are known to strongly modify the atmospheric composition of warmer stars. We indeed found a strict correspondence between the colour of the HB stars and their Na and O abundances: all blue HB stars are very O-poor and Na-rich. In addition, we found that while all the red HB stars are more O-rich and Na-poor than the blue ones, there is a moderate Na-O anticorrelation among them as well. This anticorrelation is in turn related to the colour of the red HB stars. These results reinforce the connection between Na and O abundances and the second parameter phenomenon, and show that there are more than three stellar populations in NGC 2808 because only a fraction of the red HB stars belong to the primordial population of this cluster. Based on observations collected at ESO telescopes under programme 386.D-0086.

  16. DNA sequences at a glance.

    PubMed

    Pinho, Armando J; Garcia, Sara P; Pratas, Diogo; Ferreira, Paulo J S G

    2013-01-01

    Data summarization and triage is one of the current top challenges in visual analytics. The goal is to let users visually inspect large data sets and examine or request data with particular characteristics. The need for summarization and visual analytics is also felt when dealing with digital representations of DNA sequences. Genomic data sets are growing rapidly, making their analysis increasingly more difficult, and raising the need for new, scalable tools. For example, being able to look at very large DNA sequences while immediately identifying potentially interesting regions would provide the biologist with a flexible exploratory and analytical tool. In this paper we present a new concept, the "information profile", which provides a quantitative measure of the local complexity of a DNA sequence, independently of the direction of processing. The computation of the information profiles is computationally tractable: we show that it can be done in time proportional to the length of the sequence. We also describe a tool to compute the information profiles of a given DNA sequence, and use the genome of the fission yeast Schizosaccharomyces pombe strain 972 h(-) and five human chromosomes 22 for illustration. We show that information profiles are useful for detecting large-scale genomic regularities by visual inspection. Several discovery strategies are possible, including the standalone analysis of single sequences, the comparative analysis of sequences from individuals from the same species, and the comparative analysis of sequences from different organisms. The comparison scale can be varied, allowing the users to zoom-in on specific details, or obtain a broad overview of a long segment. Software applications have been made available for non-commercial use at http://bioinformatics.ua.pt/software/dna-at-glance.

  17. Sequencing Centers Panel at SFAF

    SciTech Connect

    Schilkey, Faye; Ali, Johar; Grafham, Darren; Muzny, Donna; Fulton, Bob; Fitzgerald, Mike; Hostetler, Jessica; Daum, Chris

    2010-06-02

    From left to right: Faye Schilkey of NCGR, Johar Ali of OICR, Darren Grafham of Wellcome Trust Sanger Institute, Donna Muzny of the Baylor College of Medicine, Bob Fulton of Washington University, Mike Fitzgerald of the Broad Institute, Jessica Hostetler of the J. Craig Venter Institute and Chris Daum of the DOE Joint Genome Institute discuss sequencing technologies, applications and pipelines on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  18. Structural complexity of DNA sequence.

    PubMed

    Liou, Cheng-Yuan; Tseng, Shen-Han; Cheng, Wei-Chen; Tsai, Huai-Ying

    2013-01-01

    In modern bioinformatics, finding an efficient way to allocate sequence fragments with biological functions is an important issue. This paper presents a structural approach based on context-free grammars extracted from original DNA or protein sequences. This approach is radically different from all those statistical methods. Furthermore, this approach is compared with a topological entropy-based method for consistency and difference of the complexity results. PMID:23662161

  19. DNA Sequences at a Glance

    PubMed Central

    Pinho, Armando J.; Garcia, Sara P.; Pratas, Diogo; Ferreira, Paulo J. S. G.

    2013-01-01

    Data summarization and triage is one of the current top challenges in visual analytics. The goal is to let users visually inspect large data sets and examine or request data with particular characteristics. The need for summarization and visual analytics is also felt when dealing with digital representations of DNA sequences. Genomic data sets are growing rapidly, making their analysis increasingly more difficult, and raising the need for new, scalable tools. For example, being able to look at very large DNA sequences while immediately identifying potentially interesting regions would provide the biologist with a flexible exploratory and analytical tool. In this paper we present a new concept, the “information profile”, which provides a quantitative measure of the local complexity of a DNA sequence, independently of the direction of processing. The computation of the information profiles is computationally tractable: we show that it can be done in time proportional to the length of the sequence. We also describe a tool to compute the information profiles of a given DNA sequence, and use the genome of the fission yeast Schizosaccharomyces pombe strain 972 h− and five human chromosomes 22 for illustration. We show that information profiles are useful for detecting large-scale genomic regularities by visual inspection. Several discovery strategies are possible, including the standalone analysis of single sequences, the comparative analysis of sequences from individuals from the same species, and the comparative analysis of sequences from different organisms. The comparison scale can be varied, allowing the users to zoom-in on specific details, or obtain a broad overview of a long segment. Software applications have been made available for non-commercial use at http://bioinformatics.ua.pt/software/dna-at-glance. PMID:24278218

  20. Sequenced drive for rotary valves

    DOEpatents

    Mittell, Larry C.

    1981-01-01

    A sequenced drive for rotary valves which provides the benefits of applying rotary and linear motions to the movable sealing element of the valve. The sequenced drive provides a close approximation of linear motion while engaging or disengaging the movable element with the seat minimizing wear and damage due to scrubbing action. The rotary motion of the drive swings the movable element out of the flowpath thus eliminating obstruction to flow through the valve.

  1. Mycobacterium abscessus multispacer sequence typing

    PubMed Central

    2013-01-01

    Background Mycobacterium abscessus group includes antibiotic-resistant, opportunistic mycobacteria that are responsible for sporadic cases and outbreaks of cutaneous, pulmonary and disseminated infections. However, because of their close genetic relationships, accurate discrimination between the various strains of these mycobacteria remains difficult. In this report, we describe the development of a multispacer sequence typing (MST) analysis for the simultaneous identification and typing of M. abscessus mycobacteria. We also compared MST with the reference multilocus sequence analysis (MLSA) typing method. Results Based on the M. abscessus CIP104536T genome, eight intergenic spacers were selected, PCR amplified and sequenced in 21 M. abscessus isolates and analysed in 48 available M. abscessus genomes. MST and MLSA grouped 37 M. abscessus organisms into 12 and nine types, respectively; four formerly “M. bolletii” organisms and M. abscessus M139 into three and four types, respectively; and 27 formerly “M. massiliense” organisms grouped into nine and five types, respectively. The Hunter-Gaston index was off 0.912 for MST and of 0.903 for MLSA. The MST-derived tree was similar to that based on MLSA and rpoB gene sequencing and yielded three main clusters comprising each the type strain of the respective M. abscessus sub-species. Two isolates exhibited discordant MLSA- and rpoB gene sequence-derived position, one isolate exhibited discordant MST- and rpoB gene sequence-derived position and one isolate exhibited discordant MST- and MLSA-derived position. MST spacer n°2 sequencing alone allowed for the accurate identification of the different isolates at the sub-species level. Conclusions MST is a new sequencing-based approach for both identifying and genotyping M. abscessus mycobacteria that clearly differentiates formerly “M. massiliense” organisms from other M. abscessus subsp. bolletii organisms. PMID:23294800

  2. Structural Complexity of DNA Sequence

    PubMed Central

    Liou, Cheng-Yuan; Cheng, Wei-Chen; Tsai, Huai-Ying

    2013-01-01

    In modern bioinformatics, finding an efficient way to allocate sequence fragments with biological functions is an important issue. This paper presents a structural approach based on context-free grammars extracted from original DNA or protein sequences. This approach is radically different from all those statistical methods. Furthermore, this approach is compared with a topological entropy-based method for consistency and difference of the complexity results. PMID:23662161

  3. Determining orientation and direction of DNA sequences

    DOEpatents

    Goodwin, Edwin H.; Meyne, Julianne

    2000-01-01

    Determining orientation and direction of DNA sequences. A method by which fluorescence in situ hybridization can be made strand specific is described. Cell cultures are grown in a medium containing a halogenated nucleotide. The analog is partially incorporated in one DNA strand of each chromatid. This substitution takes place in opposite strands of the two sister chromatids. After staining with the fluorescent DNA-binding dye Hoechst 33258, cells are exposed to long-wavelength ultraviolet light which results in numerous strand nicks. These nicks enable the substituted strand to be denatured and solubilized by heat, treatment with high or low pH aqueous solutions, or by immersing the strands in 2.times.SSC (0.3M NaCl+0.03M sodium citrate), to name three procedures. It is unnecessary to enzymatically digest the strands using Exo III or another exonuclease in order to excise and solubilize nucleotides starting at the sites of the nicks. The denaturing/solubilizing process removes most of the substituted strand while leaving the prereplication strand largely intact. Hybridization of a single-stranded probe of a tandem repeat arranged in a head-to-tail orientation will result in hybridization only to the chromatid with the complementary strand present.

  4. Genome Sequence of Canine Herpesvirus

    PubMed Central

    Papageorgiou, Konstantinos V.; Suárez, Nicolás M.; Wilkie, Gavin S.; McDonald, Michael; Graham, Elizabeth M.; Davison, Andrew J.

    2016-01-01

    Canine herpesvirus is a widespread alphaherpesvirus that causes a fatal haemorrhagic disease of neonatal puppies. We have used high-throughput methods to determine the genome sequences of three viral strains (0194, V777 and V1154) isolated in the United Kingdom between 1985 and 2000. The sequences are very closely related to each other. The canine herpesvirus genome is estimated to be 125 kbp in size and consists of a unique long sequence (97.5 kbp) and a unique short sequence (7.7 kbp) that are each flanked by terminal and internal inverted repeats (38 bp and 10.0 kbp, respectively). The overall nucleotide composition is 31.6% G+C, which is the lowest among the completely sequenced alphaherpesviruses. The genome contains 76 open reading frames predicted to encode functional proteins, all of which have counterparts in other alphaherpesviruses. The availability of the sequences will facilitate future research on the diagnosis and treatment of canine herpesvirus-associated disease. PMID:27213534

  5. Reduced Na+ uptake in the NaCl-hypersensitive sos1 mutant of Arabidopsis thaliana.

    PubMed Central

    Ding, L; Zhu, J K

    1997-01-01

    Sos1 is an Arabidopsis thaliana mutant with > 20 times higher sensitivity toward Na+ inhibition due to a defective high-affinity potassium-uptake system. We report here that sos1 accumulates less Na+ than the wild type in response to NaCl stress. The Na+ contents in sos1 seedlings exposed to 25 mM NaCl for 2 or more d are about 43% lower than those in the wild type. When assayed at 20 mM external NaCl, sos1 seedlings pretreated with low potassium have 32% lower Na+ uptake than the wild type. However, little difference in Na+ uptake could be measured when the seedlings were not pretreated with low potassium. Low-potassium treatment was shown to induce high-affinity potassium-uptake activity in Arabidopsis seedlings. No substantial difference in Na+ efflux between sos1 and the wild type was detected. The results show that the reduced Na+ accumulation in sos1 is due to a lower Na+ influx rate. Therefore, the sos1 mutation appears to disrupt low-affinity Na+ uptake in addition to its impairment of high-affinity K+ uptake. PMID:9085573

  6. Long-range barcode labeling-sequencing

    DOEpatents

    Chen, Feng; Zhang, Tao; Singh, Kanwar K.; Pennacchio, Len A.; Froula, Jeff L.; Eng, Kevin S.

    2016-10-18

    Methods for sequencing single large DNA molecules by clonal multiple displacement amplification using barcoded primers. Sequences are binned based on barcode sequences and sequenced using a microdroplet-based method for sequencing large polynucleotide templates to enable assembly of haplotype-resolved complex genomes and metagenomes.

  7. Sequence dependence of isothermal DNA amplification via EXPAR

    PubMed Central

    Qian, Jifeng; Ferguson, Tanya M.; Shinde, Deepali N.; Ramírez-Borrero, Alissa J.; Hintze, Arend; Adami, Christoph; Niemz, Angelika

    2012-01-01

    Isothermal nucleic acid amplification is becoming increasingly important for molecular diagnostics. Therefore, new computational tools are needed to facilitate assay design. In the isothermal EXPonential Amplification Reaction (EXPAR), template sequences with similar thermodynamic characteristics perform very differently. To understand what causes this variability, we characterized the performance of 384 template sequences, and used this data to develop two computational methods to predict EXPAR template performance based on sequence: a position weight matrix approach with support vector machine classifier, and RELIEF attribute evaluation with Naïve Bayes classification. The methods identified well and poorly performing EXPAR templates with 67–70% sensitivity and 77–80% specificity. We combined these methods into a computational tool that can accelerate new assay design by ruling out likely poor performers. Furthermore, our data suggest that variability in template performance is linked to specific sequence motifs. Cytidine, a pyrimidine base, is over-represented in certain positions of well-performing templates. Guanosine and adenosine, both purine bases, are over-represented in similar regions of poorly performing templates, frequently as GA or AG dimers. Since polymerases have a higher affinity for purine oligonucleotides, polymerase binding to GA-rich regions of a single-stranded DNA template may promote non-specific amplification in EXPAR and other nucleic acid amplification reactions. PMID:22416064

  8. Inelastic processes in Na+-Ne, Na+-Ar, Ne+-Na, and Ar+-Na collisions in the energy range 0.5-14 keV

    NASA Astrophysics Data System (ADS)

    Lomsadze, R. A.; Gochitashvili, M. R.; Kezerashvili, R. Ya.

    2015-12-01

    Absolute cross sections for charge-exchange, ionization, and excitation in Na+-Ne and Na+-Ar collisions were measured in the ion energy range 0.5 -10 keV using a refined version of a capacitor method and collision and optical spectroscopy methods simultaneously in the same experimental setup. Ionization cross sections for Ne+-Na and Ar+-Na collisions are measured at energies of 2 -14 keV using a crossed-beam spectroscopy method. The experimental data and the schematic correlation diagrams are used to analyze and determine the mechanisms for these processes. For the charge-exchange process in Na+-Ar collisions two nonadiabatic regions are revealed and mechanisms responsible for these regions are explained. Structural peculiarity on the excitation function for the resonance lines of argon atoms in Na+-Ar collisions are observed and the possible mechanisms of this phenomenon are explored. The measured ionization cross sections for Na+-Ne and Ne+-Na collisions in conjunction with the Landau-Zener formula are used to determine the coupling matrix element and transition probability in a region of pseudocrossing of the potential curves.

  9. Regulation of Na+ fluxes in plants

    PubMed Central

    Maathuis, Frans J. M.; Ahmad, Izhar; Patishtan, Juan

    2014-01-01

    When exposed to salt, every plant takes up Na+ from the environment. Once in the symplast, Na+ is distributed within cells and between different tissues and organs. There it can help to lower the cellular water potential but also exert potentially toxic effects. Control of Na+ fluxes is therefore crucial and indeed, research shows that the divergence between salt tolerant and salt sensitive plants is not due to a variation in transporter types but rather originates in the control of uptake and internal Na+ fluxes. A number of regulatory mechanisms has been identified based on signaling of Ca2+, cyclic nucleotides, reactive oxygen species, hormones, or on transcriptional and post translational changes of gene and protein expression. This review will give an overview of intra- and intercellular movement of Na+ in plants and will summarize our current ideas of how these fluxes are controlled and regulated in the early stages of salt stress. PMID:25278946

  10. High NA Nicrostepper Final Optical Design Report

    SciTech Connect

    Hudyma, R

    1999-09-24

    The development of a new EUV high NA small-field exposure tool has been proposed for obtaining mask defect printability data in a timeframe several years before beta-tools are available. The imaging system for this new Micro-Exposure Tool (MET), would have a numerical aperture (NA) of about 0.3, similar to the NA for a beta-tool, but substantially larger than the 0.10 NA for the Engineering Test Stand (ETS) and 0.088 NA for the existing 10x Microstepper. This memorandum discusses the development and summarizes the performance of the camera for the MET and includes a listing of the design prescription, detailed analysis of the distortion, and analysis demonstrating the capability to resolution 30 nm features under the conditions of partially coherent illumination.

  11. Negative electrodes for Na-ion batteries.

    PubMed

    Dahbi, Mouad; Yabuuchi, Naoaki; Kubota, Kei; Tokiwa, Kazuyasu; Komaba, Shinichi

    2014-08-01

    Research interest in Na-ion batteries has increased rapidly because of the environmental friendliness of sodium compared to lithium. Throughout this Perspective paper, we report and review recent scientific advances in the field of negative electrode materials used for Na-ion batteries. This paper sheds light on negative electrode materials for Na-ion batteries: carbonaceous materials, oxides/phosphates (as sodium insertion materials), sodium alloy/compounds and so on. These electrode materials have different reaction mechanisms for electrochemical sodiation/desodiation processes. Moreover, not only sodiation-active materials but also binders, current collectors, electrolytes and electrode/electrolyte interphase and its stabilization are essential for long cycle life Na-ion batteries. This paper also addresses the prospect of Na-ion batteries as low-cost and long-life batteries with relatively high-energy density as their potential competitive edge over the commercialized Li-ion batteries.

  12. Sequence Factorization with Multiple References

    PubMed Central

    Wandelt, Sebastian; Leser, Ulf

    2015-01-01

    The success of high-throughput sequencing has lead to an increasing number of projects which sequence large populations of a species. Storage and analysis of sequence data is a key challenge in these projects, because of the sheer size of the datasets. Compression is one simple technology to deal with this challenge. Referential factorization and compression schemes, which store only the differences between input sequence and a reference sequence, gained lots of interest in this field. Highly-similar sequences, e.g., Human genomes, can be compressed with a compression ratio of 1,000:1 and more, up to two orders of magnitude better than with standard compression techniques. Recently, it was shown that the compression against multiple references from the same species can boost the compression ratio up to 4,000:1. However, a detailed analysis of using multiple references is lacking, e.g., for main memory consumption and optimality. In this paper, we describe one key technique for the referential compression against multiple references: The factorization of sequences. Based on the notion of an optimal factorization, we propose optimization heuristics and identify parameter settings which greatly influence 1) the size of the factorization, 2) the time for factorization, and 3) the required amount of main memory. We evaluate a total of 30 setups with a varying number of references on data from three different species. Our results show a wide range of factorization sizes (optimal to an overhead of up to 300%), factorization speed (0.01 MB/s to more than 600 MB/s), and main memory usage (few dozen MB to dozens of GB). Based on our evaluation, we identify the best configurations for common use cases. Our evaluation shows that multi-reference factorization is much better than single-reference factorization. PMID:26422374

  13. Dissociation pathways of alkali-cationized peptides: opportunities for C-terminal peptide sequencing.

    PubMed

    Lin, T; Payne, A H; Glish, G L

    2001-05-01

    Dissociation pathways of alkali-cationized peptides have been studied using multiple stages of mass spectrometry (MSx) with a quadrupole ion trap mass spectrometer. Over 100 peptide ions ranging from 2 to 10 residues in length and containing each of the 20 common amino acids have been examined. The formation of the [b(n-1) + Na + OH]+ product ion is the predominant dissociation pathway for the majority of the common amino acids. This product corresponds to a sodium-cationized peptide one residue shorter in length than the original peptide. In a few cases, product ions such as [b(n-1) + Na - H]+ and those formed by loss, or partial loss, of a sidechain are observed. Both [b(n-1) + Na + OH]+ and [b(n-1) + Na - H]+ product ions can be selected as parent ions for a subsequent stage of tandem mass spectrometry (MS/MS). It is shown that these dissociation patterns provide opportunities for peptide sequencing by successive dissociation from the C-terminus of alkali-cationized peptides. Up to seven stages of MS/MS have been performed on a series of [b + Na + OH]+ ions to provide sequence information from the C-terminus. This method is analogous to Edman degradation except that the cleavage occurs from the C-terminus instead of the N-terminus, making it more attractive for N-terminal blocked peptides. The isomers leucine and isoleucine cannot be differentiated by this method but the isobars lysine and glutamine can.

  14. Sequence change and phylogenetic signal in muscoid COII DNA sequences.

    PubMed

    Szalanski, Allen L; Owens, Carrie B

    2003-08-01

    The complete DNA sequence of the mtDNA cytochrome oxidase II gene from house fly, Musca domestica, face fly, Musca autumnalis, stable fly, Stomoxys calcitrans, horn fly, Haematobia irritans, and black garbage fly, Hydrotaea aenescens, are reported. The nucleotide sequence codes for a 229 amino acid peptide. The COII sequence is A + T rich (74.1%), with up to 12.3% nucleotide and 8.4% amino acid divergence among the five taxa. Of the 688 nucleotides encoding for the gene, 135 nucleotide sites (19.6%) are variable, and 55 (8.0%) are phylogenetically informative. A phylogenetic analysis using three calliphorids as the outgroup taxa, indicates that the two haematophagus species, horn fly and stable fly, form a sister group.

  15. Na-doped optical Germanium bulk crystals

    NASA Astrophysics Data System (ADS)

    Pekar, G. S.; Singaevsky, A. F.

    2012-09-01

    In an effort to develop a material for infrared (IR) optics with improved parameters, bulk crystals of optical germanium doped with Na have been first grown and studied. Single-crystalline and coarse-crystalline Ge:Na boules of different shapes and dimensions, up to 10 kg by weight, have been grown. Sodium was incorporated into the Ge crystal during the crystal growing from the melt. Despite the fact that Na contamination in the source material was not strictly controlled, the density of Na in the grown crystals determined by the neutron activation analysis as well as by the glow discharge mass spectrometry did not exceed 1015 cm-3. Just this value may be supposed to be close to the solubility limit of Na incorporated in Ge in the course of bulk crystal growth. A first demonstration of donor behavior of Na in bulk Ge crystals is made by means of a thermoelectric type of testing. An interstitial location of Na impurity has been verified by experiments on donor drift in the dc electric field. The crystals are grown with free electron density in the range from 5ṡ1013 to 4ṡ1014 cm-3 which is optimal for using Ge crystals as an optical material for fabricating passive elements of the IR technique. A comparison between the properties of Ge:Na crystals and Ge crystals doped with Sb, a conventional impurity in optical germanium, grown under the same technological conditions and from the same intrinsic Ge as a source material, revealed a number of advantages of Ge:Na crystals; among them, the higher transparency in the IR region, smaller radiation scattering and higher regular optical transmission, lower dislocation density, more uniform distribution of electrical and optical characteristics over the crystal volume, the identity of optical parameters in the single-crystalline, and coarse-crystalline boules. No degradation of optical elements fabricated from Ge:Na crystals was detected in the course of their commercial application, starting from 1998.

  16. Polarization dependence of Na/emph>+Na/emph> associative ionization revisited

    NASA Astrophysics Data System (ADS)

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

    1986-02-01

    The dependence of the associative ionization process Na 3 2P3/2+Na 3 2P3/2-->Na2 ++e- on the polarization of the laser light used for Na excitation was independently investigated in Utrecht and Berlin. The purpose of this paper is to clarify discrepancies between earlier experimental results of Kircz, Morgenstern, and Nienhuis, on one hand, and Rothe, Theyunni, Reck, and Tung on the other hand. The new results confirm in general the data of Kircz, Morgenstern, and Nienhuis, and also indicate a dependence of the anisotropy ratios on the relative velocity of the interacting Na* atoms.

  17. Complete genome sequence of Desulfomicrobium baculatum type strain (XT)

    SciTech Connect

    Copeland, A; Spring, Stefan; Goker, Markus; Schneider, Susan; Lapidus, Alla L.; Glavina Del Rio, Tijana; Tice, Hope; Cheng, Jan-Fang; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne A.; Pitluck, Sam; Ivanova, N; Mavromatis, K; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Meincke, Linda; Sims, David; Brettin, Tom; Detter, J. Chris; Han, Cliff; Chain, Patrick S. G.; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2009-01-01

    Desulfomicrobium baculatum is the type species of the genus Desulfomicrobium, which is the type genus of the family Desulfomicrobiaceae. It is of phylogenetic interest because of the isolated location of the family Desulfomicrobiaceae within the order Desulfovibrionales. D. baculatum strain XT is a Gram-negative, motile, sulfate-reducing bacterium isolated from wa-ter-saturated manganese carbonate ore. It is strictly anaerobic and does not require NaCl for growth, although NaCl concentrations up to 6% (w/v) are tolerated. The metabolism is respi-ratory or fermentative. In the presence of sulfate, pyruvate and lactate are incompletely oxi-dized to acetate and CO2. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the deltaproteobacterial family Desulfomicrobiaceae, and this 3,942,657 bp long single replicon genome with its 3494 protein-coding and 72 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  18. Complete genome sequence of Desulfomicrobium baculatum type strain (XT)

    SciTech Connect

    Copeland, Alex; Spring, Stefan; Goker, Markus; Schneider, Susanne; Lapidus, Alla; Glavina Del Rio, Tijana; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavrommatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jefferies, Cynthia C; Meincke, Linda; Sims, David; Brettin, Thomas; Detter, John C; Han, Cliff; Chain, Patrick; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Klenk, Hans-Peter; Kyrpides, Nikos C; Lucas, Susan

    2009-05-20

    Desulfomicrobium baculatum is the type species of the genus Desulfomicrobium, which is the type genus of the family Desulfomicrobiaceae. It is of phylogenetic interest because of the isolated location of the family Desulfomicrobiaceae within the order Desulfovibrionales. D. baculatum strain XT is a Gram-negative, motile, sulfate-reducing bacterium isolated from water-saturated manganese carbonate ore. It is strictly anaerobic and does not require NaCl for growth, although NaCl concentrations up to 6percent (w/v) are tolerated. The metabolism is respiratory or fermentative. In the presence of sulfate, pyruvate and lactate are incompletely oxidized to acetate and CO2. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the deltaproteobacterial family Desulfomicrobiaceae, and this 3,942,657 bp long single replicon genome with its 3494 protein-coding and 72 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  19. Complete genome sequence of Desulfomicrobium baculatum type strain (XT)

    PubMed Central

    Copeland, Alex; Spring, Stefan; Göker, Markus; Schneider, Susanne; Lapidus, Alla; Del Rio, Tijana Glavina; Tice, Hope; Cheng, Jan-Fang; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavrommatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia C.; Meincke, Linda; Sims, David; Brettin, Thomas; Detter, John C.; Han, Cliff; Chain, Patrick; Bristow, Jim; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter; Lucas, Susan

    2009-01-01

    Desulfomicrobium baculatum is the type species of the genus Desulfomicrobium, which is the type genus of the family Desulfomicrobiaceae. It is of phylogenetic interest because of the isolated location of the family Desulfomicrobiaceae within the order Desulfovibrionales. D. baculatum strain XT is a Gram-negative, motile, sulfate-reducing bacterium isolated from water-saturated manganese carbonate ore. It is strictly anaerobic and does not require NaCl for growth, although NaCl concentrations up to 6% (w/v) are tolerated. The metabolism is respiratory or fermentative. In the presence of sulfate, pyruvate and lactate are incompletely oxidized to acetate and CO2. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the deltaproteobacterial family Desulfomicrobiaceae, and this 3,942,657 bp long single replicon genome with its 3494 protein-coding and 72 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. PMID:21304634

  20. A Demonstration of Automated DNA Sequencing.

    ERIC Educational Resources Information Center

    Latourelle, Sandra; Seidel-Rogol, Bonnie

    1998-01-01

    Details a simulation that employs a paper-and-pencil model to demonstrate the principles behind automated DNA sequencing. Discusses the advantages of automated sequencing as well as the chemistry of automated DNA sequencing. (DDR)

  1. The NA62 RICH detector

    SciTech Connect

    Cassese, A.

    2011-07-01

    The NA62 experiment is designed to measure the very rare kaon decay K{sup +} {yields} {pi}{sup +} at the CERN SPS with a 10% accuracy. The Standard Model prediction for the Branching Ratio is (8.5 {+-} 0.7) x 10{sup -11}. One of the challenging aspect of the experiment is the suppression of the K{sup +} {yields} {mu}{sup +} v{sub {mu}} background at the 10{sup -12} level. To satisfy this requirement a Ring Imaging Cherenkov Detector (RICH), able to separate {pi}{sup {+-}} from {mu}{sup {+-}} in the momentum range between 15 and 35 GeV/c, with a {mu}, rejection factor better than 10{sup -2}, is needed. The RICH must also have a time resolution of about 100 ps to disentangle accidental time associations of beam particles with pions. The RICH will have a very long focal length (17 m) and will be filled with Ne gas at atmospheric pressure. Two test beams were held at CERN in 2007 and 2009 with a RICH prototype. The results of the two test beams will be presented: the {mu}, mis-identification probability is found to be about 0.7% and the time resolution better than 100 ps in the whole momentum range. (authors)

  2. Analysis of Pteridium ribosomal RNA sequences by rapid direct sequencing.

    PubMed

    Tan, M K

    1991-08-01

    A total of 864 bases from 5 regions interspersed in the 18S and 26S rRNA molecules from various clones of Pteridium covering the general geographical distribution of the genus was analysed using a rapid rRNA sequencing technique. No base difference has been detected amongst the three major lineages, two of which apparently separated before the breakup of the ancient supercontinent, Pangaea. These regions of the rRNA sequences have thus been conserved for at least 160 million years and are here compared with other eukaryotic, especially plant rRNAs.

  3. Predicting the molecular complexity of sequencing libraries.

    PubMed

    Daley, Timothy; Smith, Andrew D

    2013-04-01

    Predicting the molecular complexity of a genomic sequencing library is a critical but difficult problem in modern sequencing applications. Methods to determine how deeply to sequence to achieve complete coverage or to predict the benefits of additional sequencing are lacking. We introduce an empirical bayesian method to accurately characterize the molecular complexity of a DNA sample for almost any sequencing application on the basis of limited preliminary sequencing. PMID:23435259

  4. Statistical properties of DNA sequences

    NASA Technical Reports Server (NTRS)

    Peng, C. K.; Buldyrev, S. V.; Goldberger, A. L.; Havlin, S.; Mantegna, R. N.; Simons, M.; Stanley, H. E.

    1995-01-01

    We review evidence supporting the idea that the DNA sequence in genes containing non-coding regions is correlated, and that the correlation is remarkably long range--indeed, nucleotides thousands of base pairs distant are correlated. We do not find such a long-range correlation in the coding regions of the gene. We resolve the problem of the "non-stationarity" feature of the sequence of base pairs by applying a new algorithm called detrended fluctuation analysis (DFA). We address the claim of Voss that there is no difference in the statistical properties of coding and non-coding regions of DNA by systematically applying the DFA algorithm, as well as standard FFT analysis, to every DNA sequence (33301 coding and 29453 non-coding) in the entire GenBank database. Finally, we describe briefly some recent work showing that the non-coding sequences have certain statistical features in common with natural and artificial languages. Specifically, we adapt to DNA the Zipf approach to analyzing linguistic texts. These statistical properties of non-coding sequences support the possibility that non-coding regions of DNA may carry biological information.

  5. Sequencing Needs for Viral Diagnostics

    SciTech Connect

    Gardner, S N; Lam, M; Mulakken, N J; Torres, C L; Smith, J R; Slezak, T

    2004-01-26

    We built a system to guide decisions regarding the amount of genomic sequencing required to develop diagnostic DNA signatures, which are short sequences that are sufficient to uniquely identify a viral species. We used our existing DNA diagnostic signature prediction pipeline, which selects regions of a target species genome that are conserved among strains of the target (for reliability, to prevent false negatives) and unique relative to other species (for specificity, to avoid false positives). We performed simulations, based on existing sequence data, to assess the number of genome sequences of a target species and of close phylogenetic relatives (''near neighbors'') that are required to predict diagnostic signature regions that are conserved among strains of the target species and unique relative to other bacterial and viral species. For DNA viruses such as variola (smallpox), three target genomes provide sufficient guidance for selecting species-wide signatures. Three near neighbor genomes are critical for species specificity. In contrast, most RNA viruses require four target genomes and no near neighbor genomes, since lack of conservation among strains is more limiting than uniqueness. SARS and Ebola Zaire are exceptional, as additional target genomes currently do not improve predictions, but near neighbor sequences are urgently needed. Our results also indicate that double stranded DNA viruses are more conserved among strains than are RNA viruses, since in most cases there was at least one conserved signature candidate for the DNA viruses and zero conserved signature candidates for the RNA viruses.

  6. Na-site substitution effects on the thermoelectric properties of NaCo2O4

    NASA Astrophysics Data System (ADS)

    Kawata, T.; Iguchi, Y.; Itoh, T.; Takahata, K.; Terasaki, I.

    1999-10-01

    The resistivity and thermopower of Na1+xCo2O4 and Na1.1-xCaxCo2O4 are measured and analyzed. In Na1+xCo2O4, whereas the resistivity increases with x, the thermopower is nearly independent of x. This suggests that the excess Na is unlikely to supply carriers, and decreases effective conduction paths in the sample. In Na1.1-xCaxCo2O4, the resistivity and the thermopower increase with x, and the Ca2+ substitution for Na+ reduces the majority carriers in NaCo2O4. This means that they are holes, which is consistent with the positive sign of the thermopower. Strong correlation in this compound is evidenced by the peculiar temperature dependence of the resistivity.

  7. Extracellular Na+ levels regulate formation and activity of the NaX/alpha1-Na+/K+-ATPase complex in neuronal cells

    PubMed Central

    Berret, Emmanuelle; Smith, Pascal Y.; Henry, Mélaine; Soulet, Denis; Hébert, Sébastien S.; Toth, Katalin; Mouginot, Didier; Drolet, Guy

    2014-01-01

    MnPO neurons play a critical role in hydromineral homeostasis regulation by acting as sensors of extracellular sodium concentration ([Na+]out). The mechanism underlying Na+-sensing involves Na+-flow through the NaX channel, directly regulated by the Na+/K+-ATPase α1-isoform which controls Na+-influx by modulating channel permeability. Together, these two partners form a complex involved in the regulation of intracellular sodium ([Na+]in). Here we aim to determine whether environmental changes in Na+ could actively modulate the NaX/Na+/K+-ATPase complex activity. We investigated the complex activity using patch-clamp recordings from rat MnPO neurons and Neuro2a cells. When the rats were fed with a high-salt-diet, or the [Na+] in the culture medium was increased, the activity of the complex was up-regulated. In contrast, drop in environmental [Na+] decreased the activity of the complex. Interestingly under hypernatremic condition, the colocalization rate and protein level of both partners were up-regulated. Under hyponatremic condition, only NaX protein expression was increased and the level of NaX/Na+/K+-ATPase remained unaltered. This unbalance between NaX and Na+/K+-ATPase pump proportion would induce a bigger portion of Na+/K+-ATPase-control-free NaX channel. Thus, we suggest that hypernatremic environment increases NaX/Na+/K+-ATPase α1-isoform activity by increasing the number of both partners and their colocalization rate, whereas hyponatremic environment down-regulates complex activity via a decrease in the relative number of NaX channels controlled by the pump. PMID:25538563

  8. Genetic variability of Echinococcus granulosus from the Tibetan plateau inferred by mitochondrial DNA sequences.

    PubMed

    Yan, Ning; Nie, Hua-Ming; Jiang, Zhong-Rong; Yang, Ai-Guo; Deng, Shi-Jin; Guo, Li; Yu, Hua; Yan, Yu-Bao; Tsering, Dawa; Kong, Wei-Shu; Wang, Ning; Wang, Jia-Hai; Xie, Yue; Fu, Yan; Yang, De-Ying; Wang, Shu-Xian; Gu, Xiao-Bin; Peng, Xue-Rong; Yang, Guang-You

    2013-09-01

    To analyse genetic variability and population structure, 84 isolates of Echinococcus granulosus (Cestoda: Taeniidae) collected from various host species at different sites of the Tibetan plateau in China were sequenced for the whole mitochondrial nad1 (894 bp) and atp6 (513 bp) genes. The vast majority were classified as G1 genotype (n=82), and two samples from human patients in Sichuan province were identified as G3 genotype. Based on the concatenated sequences of nad1+atp6, 28 different haplotypes (NA1-NA28) were identified. A parsimonious network of the concatenated sequence haplotypes showed star-like features in the overall population, with NA1 as the major haplotype in the population networks. By AMOVA it was shown that variation of E. granulosus within the overall population was the main pattern of the total genetic variability. Neutrality indexes of the concatenated sequence (nad1+atp6) were computed by Tajima's D and Fu's Fs tests and showed high negative values for E. granulosus, indicating significant deviations from neutrality. FST and Nm values suggested that the populations were not genetically differentiated.

  9. Twenty years of bacterial genome sequencing.

    PubMed

    Loman, Nicholas J; Pallen, Mark J

    2015-12-01

    Twenty years ago, the publication of the first bacterial genome sequence, from Haemophilus influenzae, shook the world of bacteriology. In this Timeline, we review the first two decades of bacterial genome sequencing, which have been marked by three revolutions: whole-genome shotgun sequencing, high-throughput sequencing and single-molecule long-read sequencing. We summarize the social history of sequencing and its impact on our understanding of the biology, diversity and evolution of bacteria, while also highlighting spin-offs and translational impact in the clinic. We look forward to a 'sequencing singularity', where sequencing becomes the method of choice for as-yet unthinkable applications in bacteriology and beyond.

  10. Graph Partitioning and Sequencing Software

    1995-09-19

    Graph partitioning is a fundemental problem in many scientific contexts. CHACO2.0 is a software package designed to partition and sequence graphs. CHACO2.0 allows for recursive application of several methods for finding small edge separators in weighted graphs. These methods include inertial, spectral, Kernighan Lin and multilevel methods in addition to several simpler strategies. Each of these approaches can be used to partition the graph into two, four, or eight pieces at each level of recursion.more » In addition, the Kernighan Lin method can be used to improve partitions generated by any of the other algorithms. CHACO2.0 can also be used to address various graph sequencing problems, with applications to scientific computing, database design, gene sequencing and other problems.« less

  11. The Extrapolation of Elementary Sequences

    NASA Technical Reports Server (NTRS)

    Laird, Philip; Saul, Ronald

    1992-01-01

    We study sequence extrapolation as a stream-learning problem. Input examples are a stream of data elements of the same type (integers, strings, etc.), and the problem is to construct a hypothesis that both explains the observed sequence of examples and extrapolates the rest of the stream. A primary objective -- and one that distinguishes this work from previous extrapolation algorithms -- is that the same algorithm be able to extrapolate sequences over a variety of different types, including integers, strings, and trees. We define a generous family of constructive data types, and define as our learning bias a stream language called elementary stream descriptions. We then give an algorithm that extrapolates elementary descriptions over constructive datatypes and prove that it learns correctly. For freely-generated types, we prove a polynomial time bound on descriptions of bounded complexity. An especially interesting feature of this work is the ability to provide quantitative measures of confidence in competing hypotheses, using a Bayesian model of prediction.

  12. Multilocus sequence typing of bacteria.

    PubMed

    Maiden, Martin C J

    2006-01-01

    Multilocus sequence typing (MLST) was proposed in 1998 as a portable, universal, and definitive method for characterizing bacteria, using the human pathogen Neisseria meningitidis as an example. In addition to providing a standardized approach to data collection, by examining the nucleotide sequences of multiple loci encoding housekeeping genes, or fragments of them, MLST data are made freely available over the Internet to ensure that a uniform nomenclature is readily available to all those interested in categorizing bacteria. At the time of writing, over thirty MLST schemes have been published and made available on the Internet, mostly for pathogenic bacteria, although there are schemes for pathogenic fungi and some nonpathogenic bacteria. MLST data have been employed in epidemiological investigations of various scales and in studies of the population biology, pathogenicity, and evolution of bacteria. The increasing speed and reduced cost of nucleotide sequence determination, together with improved web-based databases and analysis tools, present the prospect of increasingly wide application of MLST.

  13. Numerical classification of coding sequences

    NASA Technical Reports Server (NTRS)

    Collins, D. W.; Liu, C. C.; Jukes, T. H.

    1992-01-01

    DNA sequences coding for protein may be represented by counts of nucleotides or codons. A complete reading frame may be abbreviated by its base count, e.g. A76C158G121T74, or with the corresponding codon table, e.g. (AAA)0(AAC)1(AAG)9 ... (TTT)0. We propose that these numerical designations be used to augment current methods of sequence annotation. Because base counts and codon tables do not require revision as knowledge of function evolves, they are well-suited to act as cross-references, for example to identify redundant GenBank entries. These descriptors may be compared, in place of DNA sequences, to extract homologous genes from large databases. This approach permits rapid searching with good selectivity.

  14. Gasotransmitters: novel regulators of epithelial na(+) transport?

    PubMed

    Althaus, Mike

    2012-01-01

    The vectorial transport of Na(+) across epithelia is crucial for the maintenance of Na(+) and water homeostasis in organs such as the kidneys, lung, or intestine. Dysregulated Na(+) transport processes are associated with various human diseases such as hypertension, the salt-wasting syndrome pseudohypoaldosteronism type 1, pulmonary edema, cystic fibrosis, or intestinal disorders, which indicate that a precise regulation of epithelial Na(+) transport is essential. Novel regulatory signaling molecules are gasotransmitters. There are currently three known gasotransmitters: nitric oxide (NO), carbon monoxide (CO), and hydrogen sulfide (H(2)S). These molecules are endogenously produced in mammalian cells by specific enzymes and have been shown to regulate various physiological processes. There is a growing body of evidence which indicates that gasotransmitters may also regulate Na(+) transport across epithelia. This review will summarize the available data concerning NO, CO, and H(2)S dependent regulation of epithelial Na(+) transport processes and will discuss whether or not these mediators can be considered as true physiological regulators of epithelial Na(+) transport biology.

  15. Analysis of DNA Sequence Variants Detected by High Throughput Sequencing

    PubMed Central

    Adams, David R; Sincan, Murat; Fajardo, Karin Fuentes; Mullikin, James C; Pierson, Tyler M; Toro, Camilo; Boerkoel, Cornelius F; Tifft, Cynthia J; Gahl, William A; Markello, Tom C

    2014-01-01

    The Undiagnosed Diseases Program at the National Institutes of Health uses High Throughput Sequencing (HTS) to diagnose rare and novel diseases. HTS techniques generate large numbers of DNA sequence variants, which must be analyzed and filtered to find candidates for disease causation. Despite the publication of an increasing number of successful exome-based projects, there has been little formal discussion of the analytic steps applied to HTS variant lists. We present the results of our experience with over 30 families for whom HTS sequencing was used in an attempt to find clinical diagnoses. For each family, exome sequence was augmented with high-density SNP-array data. We present a discussion of the theory and practical application of each analytic step and provide example data to illustrate our approach. The paper is designed to provide an analytic roadmap for variant analysis, thereby enabling a wide range of researchers and clinical genetics practitioners to perform direct analysis of HTS data for their patients and projects. PMID:22290882

  16. A repetitive sequence assembler based on next-generation sequencing.

    PubMed

    Lian, S; Tu, Y; Wang, Y; Chen, X; Wang, L

    2016-01-01

    Repetitive sequences of variable length are common in almost all eukaryotic genomes, and most of them are presumed to have important biomedical functions and can cause genomic instability. Next-generation sequencing (NGS) technologies provide the possibility of identifying capturing these repetitive sequences directly from the NGS data. In this study, we assessed the performances in identifying capturing repeats of leading assemblers, such as Velvet, SOAPdenovo, SGA, MSR-CA, Bambus2, ALLPATHS-LG, and AByss using three real NGS datasets. Our results indicated that most of them performed poorly in capturing the repeats. Consequently, we proposed a repetitive sequence assembler, named NGSReper, for capturing repeats from NGS data. Simulated datasets were used to validate the feasibility of NGSReper. The results indicate that the completeness of capturing repeat is up to 99%. Cross validation was performed in three real NGS datasets, and extensive comparisons indicate that NGSReper performed best in terms of completeness and accuracy in capturing repeats. In conclusion, NGSReper is an appropriate and suitable tool for capturing repeats directly from NGS data. PMID:27525861

  17. Composition for nucleic acid sequencing

    SciTech Connect

    Korlach, Jonas; Webb, Watt W.; Levene, Michael; Turner, Stephen; Craighead, Harold G.; Foquet, Mathieu

    2008-08-26

    The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is followed in real time. The sequence is deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions. A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site. A plurality of labelled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The steps of providing labelled nucleotide analogs, polymerizing the growing nucleic acid strand, and identifying the added nucleotide analog are repeated so that the nucleic acid strand is further extended and the sequence of the target nucleic acid is determined.

  18. BFC: correcting Illumina sequencing errors

    PubMed Central

    2015-01-01

    Summary: BFC is a free, fast and easy-to-use sequencing error corrector designed for Illumina short reads. It uses a non-greedy algorithm but still maintains a speed comparable to implementations based on greedy methods. In evaluations on real data, BFC appears to correct more errors with fewer overcorrections in comparison to existing tools. It particularly does well in suppressing systematic sequencing errors, which helps to improve the base accuracy of de novo assemblies. Availability and implementation: https://github.com/lh3/bfc Contact: hengli@broadinstitute.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25953801

  19. Data compression for sequencing data

    PubMed Central

    2013-01-01

    Post-Sanger sequencing methods produce tons of data, and there is a general agreement that the challenge to store and process them must be addressed with data compression. In this review we first answer the question “why compression” in a quantitative manner. Then we also answer the questions “what” and “how”, by sketching the fundamental compression ideas, describing the main sequencing data types and formats, and comparing the specialized compression algorithms and tools. Finally, we go back to the question “why compression” and give other, perhaps surprising answers, demonstrating the pervasiveness of data compression techniques in computational biology. PMID:24252160

  20. DNA Sequencing Using capillary Electrophoresis

    SciTech Connect

    Dr. Barry Karger

    2011-05-09

    The overall goal of this program was to develop capillary electrophoresis as the tool to be used to sequence for the first time the Human Genome. Our program was part of the Human Genome Project. In this work, we were highly successful and the replaceable polymer we developed, linear polyacrylamide, was used by the DOE sequencing lab in California to sequence a significant portion of the human genome using the MegaBase multiple capillary array electrophoresis instrument. In this final report, we summarize our efforts and success. We began our work by separating by capillary electrophoresis double strand oligonucleotides using cross-linked polyacrylamide gels in fused silica capillaries. This work showed the potential of the methodology. However, preparation of such cross-linked gel capillaries was difficult with poor reproducibility, and even more important, the columns were not very stable. We improved stability by using non-cross linked linear polyacrylamide. Here, the entangled linear chains could move when osmotic pressure (e.g. sample injection) was imposed on the polymer matrix. This relaxation of the polymer dissipated the stress in the column. Our next advance was to use significantly lower concentrations of the linear polyacrylamide that the polymer could be automatically blown out after each run and replaced with fresh linear polymer solution. In this way, a new column was available for each analytical run. Finally, while testing many linear polymers, we selected linear polyacrylamide as the best matrix as it was the most hydrophilic polymer available. Under our DOE program, we demonstrated initially the success of the linear polyacrylamide to separate double strand DNA. We note that the method is used even today to assay purity of double stranded DNA fragments. Our focus, of course, was on the separation of single stranded DNA for sequencing purposes. In one paper, we demonstrated the success of our approach in sequencing up to 500 bases. Other

  1. High speed nucleic acid sequencing

    SciTech Connect

    Korlach, Jonas; Webb, Watt W.; Levene, Michael; Turner, Stephen; Craighead, Harold G.; Foquet, Mathieu

    2011-05-17

    The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid. Each type of labeled nucleotide comprises an acceptor fluorophore attached to a phosphate portion of the nucleotide such that the fluorophore is removed upon incorporation into a growing strand. Fluorescent signal is emitted via fluorescent resonance energy transfer between the donor fluorophore and the acceptor fluorophore as each nucleotide is incorporated into the growing strand. The sequence is deduced by identifying which base is being incorporated into the growing strand.

  2. Myocardial Na,K-ATPase: Clinical aspects

    PubMed Central

    Kjeldsen, Keld

    2003-01-01

    The specific binding of digitalis glycosides to Na,K-ATPase is used as a tool for Na,K-ATPase quantification with high accuracy and precision. In myocardial biopsies from patients with heart failure, total Na,K-ATPase concentration is decreased by around 40%; a correlation exists between a decrease in heart function and a decrease in Na,K-ATPase concentration. During digitalization, around 30% of remaining pumps are occupied by digoxin. Myocardial Na,K-ATPase is also influenced by other drugs used for the treatment of heart failure. Thus, potassium loss during diuretic therapy has been found to reduce myocardial Na,K-ATPase, whereas angiotensin-converting enzyme inhibitors may stimulate Na,K pump activity. Furthermore, hyperaldosteronism induced by heart failure has been found to decrease Na,K-ATPase activity. Accordingly, treatment with the aldosterone antagonist, spironolactone, may also influence Na,K-ATPase activity. The importance of Na,K pump modulation with heart disease, inhibition in digitalization and other effects of medication should be considered in the context of sodium, potassium and calcium regulation. It is recommended that digoxin be administered to heart failure patients who, after institution of mortality-reducing therapy, still have heart failure symptoms, and that the therapy be continued if symptoms are revealed or reduced. Digitalis glycosides are the only safe inotropic drugs for oral use that improve hemodynamics in heart failure. An important aspect of myocardial Na,K pump affection in heart disease is its influence on extracellular potassium (Ke) homeostasis. Two important aspects should be considered: potassium handling among myocytes, and effects of potassium entering the extracellular space of the heart via the bloodstream. It should be noted that both of these aspects of Ke homeostasis are affected by regulatory aspects, eg, regulation of the Na,K pump by physiological and pathophysiological conditions, as well as by medical

  3. Evolutionarily divergent, Na+-regulated H+-transporting membrane-bound pyrophosphatases.

    PubMed

    Luoto, Heidi H; Nordbo, Erika; Malinen, Anssi M; Baykov, Alexander A; Lahti, Reijo

    2015-04-15

    Membrane-bound pyrophosphatase (mPPases) of various types consume pyrophosphate (PPi) to drive active H+ or Na+ transport across membranes. H+-transporting PPases are divided into phylogenetically distinct K+-independent and K+-dependent subfamilies. In the present study, we describe a group of 46 bacterial proteins and one archaeal protein that are only distantly related to known mPPases (23%-34% sequence identity). Despite this evolutionary divergence, these proteins contain the full set of 12 polar residues that interact with PPi, the nucleophilic water and five cofactor Mg2+ ions found in 'canonical' mPPases. They also contain a specific lysine residue that confers K+ independence on canonical mPPases. Two of the proteins (from Chlorobium limicola and Cellulomonas fimi) were expressed in Escherichia coli and shown to catalyse Mg2+-dependent PPi hydrolysis coupled with electrogenic H+, but not Na+ transport, in inverted membrane vesicles. Unique features of the new H+-PPases include their inhibition by Na+ and inhibition or activation, depending on PPi concentration, by K+ ions. Kinetic analyses of PPi hydrolysis over wide ranges of cofactor (Mg2+) and substrate (Mg2-PPi) concentrations indicated that the alkali cations displace Mg2+ from the enzyme, thereby arresting substrate conversion. These data define the new proteins as a novel subfamily of H+-transporting mPPases that partly retained the Na+ and K+ regulation patterns of their precursor Na+-transporting mPPases.

  4. Evolutionarily divergent, Na+-regulated H+-transporting membrane-bound pyrophosphatases.

    PubMed

    Luoto, Heidi H; Nordbo, Erika; Malinen, Anssi M; Baykov, Alexander A; Lahti, Reijo

    2015-04-15

    Membrane-bound pyrophosphatase (mPPases) of various types consume pyrophosphate (PPi) to drive active H+ or Na+ transport across membranes. H+-transporting PPases are divided into phylogenetically distinct K+-independent and K+-dependent subfamilies. In the present study, we describe a group of 46 bacterial proteins and one archaeal protein that are only distantly related to known mPPases (23%-34% sequence identity). Despite this evolutionary divergence, these proteins contain the full set of 12 polar residues that interact with PPi, the nucleophilic water and five cofactor Mg2+ ions found in 'canonical' mPPases. They also contain a specific lysine residue that confers K+ independence on canonical mPPases. Two of the proteins (from Chlorobium limicola and Cellulomonas fimi) were expressed in Escherichia coli and shown to catalyse Mg2+-dependent PPi hydrolysis coupled with electrogenic H+, but not Na+ transport, in inverted membrane vesicles. Unique features of the new H+-PPases include their inhibition by Na+ and inhibition or activation, depending on PPi concentration, by K+ ions. Kinetic analyses of PPi hydrolysis over wide ranges of cofactor (Mg2+) and substrate (Mg2-PPi) concentrations indicated that the alkali cations displace Mg2+ from the enzyme, thereby arresting substrate conversion. These data define the new proteins as a novel subfamily of H+-transporting mPPases that partly retained the Na+ and K+ regulation patterns of their precursor Na+-transporting mPPases. PMID:25662511

  5. Characteristics and pharmacological regulation of epithelial Na+ channel (ENaC) and epithelial Na+ transport.

    PubMed

    Marunaka, Yoshinori

    2014-01-01

    Epithelial Na(+) transport participates in control of various body functions and conditions: e.g., homeostasis of body fluid content influencing blood pressure, control of amounts of fluids covering the apical surface of alveolar epithelial cells at appropriate levels for normal gas exchange, and prevention of bacterial/viral infection. Epithelial Na(+) transport via the transcellular pathway is mediated by the entry step of Na(+) across the apical membrane via Epithelial Na(+) Channel (ENaC) located at the apical membrane, and the extrusion step of Na(+) across the basolateral membrane via the Na(+),K(+)-ATPase located at the basolateral membrane. The rate-limiting step of the epithelial Na(+) transport via the transcellular pathway is generally recognized to be the entry step of Na(+) across the apical membrane via ENaC. Thus, up-/down-regulation of ENaC essentially participates in regulatory systems of blood pressure and normal gas exchange. Amount of ENaC-mediated Na(+) transport is determined by the number of ENaCs located at the apical membrane, activity (open probability) of individual ENaC located at the apical membrane, single channel conductance of ENaC located at the apical membrane, and driving force for the Na(+) entry via ENaCs across the apical membrane. In the present review article, I discuss the characteristics of ENaC and how these factors are regulated.

  6. Glutathionylation-Dependence of Na(+)-K(+)-Pump Currents Can Mimic Reduced Subsarcolemmal Na(+) Diffusion.

    PubMed

    Garcia, Alvaro; Liu, Chia-Chi; Cornelius, Flemming; Clarke, Ronald J; Rasmussen, Helge H

    2016-03-01

    The existence of a subsarcolemmal space with restricted diffusion for Na(+) in cardiac myocytes has been inferred from a transient peak electrogenic Na(+)-K(+) pump current beyond steady state on reexposure of myocytes to K(+) after a period of exposure to K(+)-free extracellular solution. The transient peak current is attributed to enhanced electrogenic pumping of Na(+) that accumulated in the diffusion-restricted space during pump inhibition in K(+)-free extracellular solution. However, there are no known physical barriers that account for such restricted Na(+) diffusion, and we examined if changes of activity of the Na(+)-K(+) pump itself cause the transient peak current. Reexposure to K(+) reproduced a transient current beyond steady state in voltage-clamped ventricular myocytes as reported by others. Persistence of it when the Na(+) concentration in patch pipette solutions perfusing the intracellular compartment was high and elimination of it with K(+)-free pipette solution could not be reconciled with restricted subsarcolemmal Na(+) diffusion. The pattern of the transient current early after pump activation was dependent on transmembrane Na(+)- and K(+) concentration gradients suggesting the currents were related to the conformational poise imposed on the pump. We examined if the currents might be accounted for by changes in glutathionylation of the β1 Na(+)-K(+) pump subunit, a reversible oxidative modification that inhibits the pump. Susceptibility of the β1 subunit to glutathionylation depends on the conformational poise of the Na(+)-K(+) pump, and glutathionylation with the pump stabilized in conformations equivalent to those expected to be imposed on voltage-clamped myocytes supported this hypothesis. So did elimination of the transient K(+)-induced peak Na(+)-K(+) pump current when we included glutaredoxin 1 in patch pipette solutions to reverse glutathionylation. We conclude that transient K(+)-induced peak Na(+)-K(+) pump current reflects the effect

  7. Dependence of Na-K pump current on internal Na+ in mammalian cardiac myocytes.

    PubMed

    Mogul, D J; Singer, D H; Ten Eick, R E

    1990-08-01

    Na-K pump current (Ipump) is a function of the intracellular Na+ concentration [( Na+]i). We examined the quantitative relationship between Ipump and [Na+]i in isolated guinea pig ventricular myocytes under steady-state conditions. [Na+]i was controlled and "clamped" at several selected concentrations using wide-tipped pipette microelectrodes, and membrane current was measured using the whole cell patch voltage-clamp technique. Ipump generated at a holding potential of -40 mV was determined by measuring the change in steady-state holding current before and during exposure to dihydroouabain (1 mM); Ipump was measured at 11 levels of [Na+]i ranging from 0 to 80 mM (n = 63) with only one measurement per cell and normalized to cell capacitance to account for differences between myocytes in sarcolemmal surface area. Ipump exhibited a nonlinear dependence on [Na+]i; a Hill analysis of the relationship yielded a half-maximal [Na+]i for pump stimulation of 43.2 mM and a Hill coefficient of 1.53. An alternative analysis of the experimental data was performed assuming that occupation of three internal binding sites by Na+ is required for enzyme turnover. Regression analysis gave the best fit when only two different binding affinities (KD) are postulated. The values are KD1 = 1 mM, KD2 = KD3 = 29 mM. From the analysis using the latter model, the level of [Na+]i at which Ipump saturated closely approximated the theoretical saturation level calculated from published estimates of pump turnover rate and density. The maximal sensitivity of the Na-K pump to changes in [Na+]i occurs when internal [Na+] is within the range for the normal resting physiological level. PMID:2167023

  8. Single-Cell Semiconductor Sequencing

    PubMed Central

    Kohn, Andrea B.; Moroz, Tatiana P.; Barnes, Jeffrey P.; Netherton, Mandy; Moroz, Leonid L.

    2014-01-01

    RNA-seq or transcriptome analysis of individual cells and small-cell populations is essential for virtually any biomedical field. It is especially critical for developmental, aging, and cancer biology as well as neuroscience where the enormous heterogeneity of cells present a significant methodological and conceptual challenge. Here we present two methods that allow for fast and cost-efficient transcriptome sequencing from ultra-small amounts of tissue or even from individual cells using semiconductor sequencing technology (Ion Torrent, Life Technologies). The first method is a reduced representation sequencing which maximizes capture of RNAs and preserves transcripts’ directionality. The second, a template-switch protocol, is designed for small mammalian neurons. Both protocols, from cell/tissue isolation to final sequence data, take up to 4 days. The efficiency of these protocols has been validated with single hippocampal neurons and various invertebrate tissues including individually identified neurons within a simpler memory-forming circuit of Aplysia californica and early (1-, 2-, 4-, 8-cells) embryonic and developmental stages from basal metazoans. PMID:23929110

  9. [Multilocus sequence typing (MLST) analysis].

    PubMed

    Matsumura, Yasufumi

    2013-12-01

    Multilocus sequence typing (MLST) analysis has been emerging as a powerful tool for genotyping specific bacterial species. MLST utilizes internal fragments of multiple housekeeping genes and the combination of each allele defines the sequence type for each isolate. MLST databases contain reference data and are freely accessible via internet websites. The standard method for investigating short-term hospital outbreaks is still pulse-field gel-electrophoresis and MLST analysis is not a substitute. However, analysis of sequence types and clonal complexes (closely related sequence types) enables identification and understanding of a specific clone that is widely spreading among drug-resistant organisms, or a key clone that is important for evolution of the organism. In the case of Escherichia coli, CTX-M-15 or CTX-M-14 extended-spectrum beta-lactamase producing ST131 clone has emerged and spread globally in the last 10 years. MLST analysis is an unambiguous procedure and is becoming a common typing method to characterize isolates. PMID:24605545

  10. Genome Sequence of Spizellomyces punctatus

    PubMed Central

    Russ, Carsten; Lang, B. Franz; Chen, Zehua; Gujja, Sharvari; Shea, Terrance; Zeng, Qiandong; Young, Sarah; Nusbaum, Chad

    2016-01-01

    Spizellomyces punctatus is a basally branching chytrid fungus that is found in the Chytridiomycota phylum. Spizellomyces species are common in soil and of importance in terrestrial ecosystems. Here, we report the genome sequence of S. punctatus, which will facilitate the study of this group of early diverging fungi. PMID:27540072

  11. Ideal statistically quasi Cauchy sequences

    NASA Astrophysics Data System (ADS)

    Savas, Ekrem; Cakalli, Huseyin

    2016-08-01

    An ideal I is a family of subsets of N, the set of positive integers which is closed under taking finite unions and subsets of its elements. A sequence (xk) of real numbers is said to be S(I)-statistically convergent to a real number L, if for each ɛ > 0 and for each δ > 0 the set { n ∈N :1/n | { k ≤n :| xk-L | ≥ɛ } | ≥δ } belongs to I. We introduce S(I)-statistically ward compactness of a subset of R, the set of real numbers, and S(I)-statistically ward continuity of a real function in the senses that a subset E of R is S(I)-statistically ward compact if any sequence of points in E has an S(I)-statistically quasi-Cauchy subsequence, and a real function is S(I)-statistically ward continuous if it preserves S(I)-statistically quasi-Cauchy sequences where a sequence (xk) is called to be S(I)-statistically quasi-Cauchy when (Δxk) is S(I)-statistically convergent to 0. We obtain results related to S(I)-statistically ward continuity, S(I)-statistically ward compactness, Nθ-ward continuity, and slowly oscillating continuity.

  12. Why Visual Sequences Come First.

    ERIC Educational Resources Information Center

    Barley, Steven D.

    Visual sequences should be the first visual literacy exercises for reasons that are physio-psychological, semantic, and curricular. In infancy, vision is undifferentiated and undetailed. The number of details a child sees increases with age. Therefore, a series of pictures, rather than one photograph which tells a whole story, is more appropriate…

  13. Genome Sequence of Spizellomyces punctatus.

    PubMed

    Russ, Carsten; Lang, B Franz; Chen, Zehua; Gujja, Sharvari; Shea, Terrance; Zeng, Qiandong; Young, Sarah; Cuomo, Christina A; Nusbaum, Chad

    2016-01-01

    Spizellomyces punctatus is a basally branching chytrid fungus that is found in the Chytridiomycota phylum. Spizellomyces species are common in soil and of importance in terrestrial ecosystems. Here, we report the genome sequence of S. punctatus, which will facilitate the study of this group of early diverging fungi. PMID:27540072

  14. Image Sequence Coding by Octrees

    NASA Astrophysics Data System (ADS)

    Leonardi, Riccardo

    1989-11-01

    This work addresses the problem of representing an image sequence as a set of octrees. The purpose is to generate a flexible data structure to model video signals, for applications such as motion estimation, video coding and/or analysis. An image sequence can be represented as a 3-dimensional causal signal, which becomes a 3 dimensional array of data when the signal has been digitized. If it is desirable to track long-term spatio-temporal correlation, a series of octree structures may be embedded on this 3D array. Each octree looks at a subset of data in the spatio-temporal space. At the lowest level (leaves of the octree), adjacent pixels of neighboring frames are captured. A combination of these is represented at the parent level of each group of 8 children. This combination may result in a more compact representation of the information of these pixels (coding application) or in a local estimate of some feature of interest (e.g., velocity, classification, object boundary). This combination can be iterated bottom-up to get a hierarchical description of the image sequence characteristics. A coding strategy using such data structure involves the description of the octree shape using one bit per node except for leaves of the tree located at the lowest level, and the value (or parametric model) assigned to each one of these leaves. Experiments have been performed to represent Common Image Format (CIF) sequences.

  15. Foreign Language Scope and Sequence.

    ERIC Educational Resources Information Center

    Raven, Patrick T.; And Others

    The scope and sequence format for foreign language instruction in Waukesha, Wisconsin's public schools is presented. It charts the specific concepts, skills, and objectives to be included in foreign language exploration (FLEX) courses and courses in French, German, Latin, and Spanish at each of five levels. Each concept, skill, and objective is…

  16. Single-cell semiconductor sequencing.

    PubMed

    Kohn, Andrea B; Moroz, Tatiana P; Barnes, Jeffrey P; Netherton, Mandy; Moroz, Leonid L

    2013-01-01

    RNA-seq or transcriptome analysis of individual cells and small-cell populations is essential for virtually any biomedical field. It is especially critical for developmental, aging, and cancer biology as well as neuroscience where the enormous heterogeneity of cells present a significant methodological and conceptual challenge. Here we present two methods that allow for fast and cost-efficient transcriptome sequencing from ultra-small amounts of tissue or even from individual cells using semiconductor sequencing technology (Ion Torrent, Life Technologies). The first method is a reduced representation sequencing which maximizes capture of RNAs and preserves transcripts' directionality. The second, a template-switch protocol, is designed for small mammalian neurons. Both protocols, from cell/tissue isolation to final sequence data, take up to 4 days. The efficiency of these protocols has been validated with single hippocampal neurons and various invertebrate tissues including individually identified neurons within a simpler memory-forming circuit of Aplysia californica and early (1-, 2-, 4-, 8-cells) embryonic and developmental stages from basal metazoans.

  17. RSAT: regulatory sequence analysis tools.

    PubMed

    Thomas-Chollier, Morgane; Sand, Olivier; Turatsinze, Jean-Valéry; Janky, Rekin's; Defrance, Matthieu; Vervisch, Eric; Brohée, Sylvain; van Helden, Jacques

    2008-07-01

    The regulatory sequence analysis tools (RSAT, http://rsat.ulb.ac.be/rsat/) is a software suite that integrates a wide collection of modular tools for the detection of cis-regulatory elements in genome sequences. The suite includes programs for sequence retrieval, pattern discovery, phylogenetic footprint detection, pattern matching, genome scanning and feature map drawing. Random controls can be performed with random gene selections or by generating random sequences according to a variety of background models (Bernoulli, Markov). Beyond the original word-based pattern-discovery tools (oligo-analysis and dyad-analysis), we recently added a battery of tools for matrix-based detection of cis-acting elements, with some original features (adaptive background models, Markov-chain estimation of P-values) that do not exist in other matrix-based scanning tools. The web server offers an intuitive interface, where each program can be accessed either separately or connected to the other tools. In addition, the tools are now available as web services, enabling their integration in programmatic workflows. Genomes are regularly updated from various genome repositories (NCBI and EnsEMBL) and 682 organisms are currently supported. Since 1998, the tools have been used by several hundreds of researchers from all over the world. Several predictions made with RSAT were validated experimentally and published.

  18. Interrogating the relationship between naïve and immune antiviral T cell repertoires.

    PubMed

    La Gruta, Nicole L; Thomas, Paul G

    2013-08-01

    Understanding how naïve virus-specific CD8+ T cells influence the type of immune response generated after virus infection is critical for the development of enhanced therapeutic and vaccination strategies to exploit CD8+ T cell-mediated immunity. Recent technological advances in T cell isolation and T receptor sequencing have allowed for greater understanding of the basic structure of immune T cell repertoires, the diversity of responses within and between individuals, and changes in repertoires over time and in response to infection conditions. In this review, we discuss the current understanding of how T cell repertoires contribute to potent antiviral responses. Additionally we compare the state of the art in receptor sequencing, highlighting the advantages and disadvantages of the three most common approaches: next-generation sequencing, template-switch anchored RT-PCR, and multiplex single cell PCR. Finally, we describe how TCR sequencing has delineated the relationship between naïve and immune T cell repertoires.

  19. [Na+/H+- and Na+/Na+-countertransport in human, rabbit, and rat erythrocytes: evidence for the existence of two independent ion-transporting systems].

    PubMed

    Orlov, S N; Kuznetsov, S R; Kolosova, I A; Makarov, V L

    1994-05-01

    The activity and regulatory features of the Na+/H(+)- and Na+/Na(+)-exchange were studied in human, rabbit and rat red blood cells. No basal activity of the Na+/H(+)-exchange (the amyloride-inhibited component of the 22Na+ influx) in erythrocytes of these species was observed. The rate of 22Na+ influx increased rapidly when the experiments were carried out on acid-loaded cells in an alkaline (pH0 = 8.0) incubation medium (delta mu H(+)-induced Na+/H(+)-exchange). The ratio of delta mu H(+)-induced Na+/H(+)-exchange activities in human, rabbit and rat red blood cells was 1.0 : 1.1 : 2.3, respectively, whereas that of the Na+/Na(+)-exchange activities (the phloretin-inhibited component of the 22Na+ influx) in erythrocytes of these species was 1.0 : 4.6 : 0.2. The osmotic shrinkage of rat and rabbit erythrocytes led to the stimulation of the Na+/H(+)- (but not Na+/Na+) exchange. Amyloride (1 mM) inhibited the shrinkage-induced 22Na+ entry as well as the delta mu H(+)-induced 22Na+ entry--by 95 and 10-20%, respectively. Heat treatment (10 min, 49-51 degrees C), disturbing the membrane cytoskeleton suppressed both the shrinkage-induced activation and the delta mu H(+)-induced activation of the Na+/H(+)-exchange. The data obtained indicate that the both transport systems are mediated by two distinct transport carriers. It may be suggested that the delta mu H(+)-induced Na+/H(+)-exchange, on the one hand, and the shrinkage-induced Na+/H(+)-exchange, on the other, are mediated by two different Na+/H(+)-exchanger subtypes. PMID:8043690

  20. Anamorphic high-NA EUV lithography optics

    NASA Astrophysics Data System (ADS)

    Migura, Sascha; Kneer, Bernhard; Neumann, Jens Timo; Kaiser, Winfried; van Schoot, Jan

    2015-09-01

    EUV lithography (EUVL) for a limit resolution below 8 nm requires the numerical aperture (NA) of the projection optics to be larger than 0.50. For such a high-NA optics a configuration of 4x magnification, full field size of 26 x 33 mm² and 6'' mask is not feasible anymore. The increased chief ray angle and higher NA at reticle lead to non-acceptable mask shadowing effects. These shadowing effects can only be controlled by increasing the magnification, hence reducing the system productivity or demanding larger mask sizes. We demonstrate that the best compromise in imaging, productivity and field split is a so-called anamorphic magnification and a half field of 26 x 16.5 mm² but utilizing existing 6'' mask infrastructure. We discuss the optical solutions for such anamorphic high-NA EUVL.

  1. Searches for New Physics at NA62

    NASA Astrophysics Data System (ADS)

    Palladino, Vito

    2011-10-01

    We present the latest NA62 results in the search for physics beyond Standard Model (SM). NA62 aims to have indirect evidences of new physics, measuring rare K decays. NA62 phase I took place in 2007 when we collected data in order to measure the ratio RK = Ke2/Kμ2 (were Kl2 means K → lνl) at few per mill level. A brief experimental layout description will be followed by analysis strategy and preliminary results. The last part of present paper will be devoted to the description of NA62 phase II, which has the main goal of measuring the ultra-rare K -> π ^ + ν bar ν decay Branching Ratio.

  2. Nanosegregation in Na2C60

    SciTech Connect

    Klupp, G.; Kamaras, K.; Matus, P.; Kiss, L.F.; Kovats, E.; Pekker, S.; Nemes, N.M.; Quintavalle, D.; Janossy, A.

    2005-09-27

    There is continuous interest in the nature of alkali metal fullerides containing C{sub 60}{sup 4-} and C{sub 60}{sup 2-}, because these compounds are believed to be nonmagnetic Mott-Jahn-Teller insulators. This idea could be verified in the case of A4C60, but Na2C60 is more controversial. By comparing the results of infrared spectroscopy and X-ray diffraction, we found that Na2C60 is segregated into 3-10 nm large regions. The two main phases of the material are insulating C60 and metallic Na3C60. We found by neutron scattering that the diffusion of sodium ions becomes faster on heating. Above 470 K Na2C60 is homogeneous and we show IR spectroscopic evidence of a Jahn-Teller distorted C{sub 60}{sup 2-} anion.

  3. Recent Scope-and-Sequence Models.

    ERIC Educational Resources Information Center

    Beem, Ronald

    1990-01-01

    Presents scope-and-sequence models from the National Commission on Social Studies in the Schools, the Bradley Commission on History in Schools, and three from the National Council for the Social Studies (NCSS) Ad Hoc Committee on Scope and Sequence. Provides NCSS's criteria on scope and sequence and notes that sequence of the five models varies…

  4. Multiple Strand Sequencing Using the Elaboration Theory.

    ERIC Educational Resources Information Center

    Beissner, Katherine; Reigeluth, Charles M.

    This study examined the sequencing of instruction in a course in physical therapy. In the first phase, a procedural elaboration sequence was designed using the Simplifying Assumptions Method. In the second phase, a prescriptive-theoretical elaboration sequence independent of the procedural sequence was designed. A descriptive-theoretical…

  5. Direct evidence of an incommensurate phase in NaNbO{sub 3} and its implication in NaNbO{sub 3}-based lead-free antiferroelectrics

    SciTech Connect

    Guo, Hanzheng; Randall, Clive A.; Shimizu, Hiroyuki

    2015-09-14

    Hot-stage in situ transmission electron microscopy was employed to investigate the temperature-induced complex sequence of phase transitions in NaNbO{sub 3} polycrystalline. In addition to the commonly recognized P (Pbma) → R (Pmnm) → S (Pnmm) phase transitions, incommensurate phases were observed to exist in P and R phase regions. The former (in the P → R transition region) is coincident with a diffused dielectric peak appearing at ∼170 °C, and the latter (in the R → S transition region) serves as an intermediate structure to bridge the two sub-phases in the R phase region. The incommensurate phase in the P phase region can be inferred from the polarization current density and differential dielectric permittivity anomalies, and it provides the bridge structure during the electric field-induced polarization reversal and antiferroelectric-to-ferroelectric transition in NaNbO{sub 3} solid solutions.

  6. Targeted capture enrichment and sequencing identifies extensive nucleotide variation in the turkey MHC-B.

    PubMed

    Reed, Kent M; Mendoza, Kristelle M; Settlage, Robert E

    2016-03-01

    Variation in the major histocompatibility complex (MHC) is increasingly associated with disease susceptibility and resistance in avian species of agricultural importance. This variation includes sequence polymorphisms but also structural differences (gene rearrangement) and copy number variation (CNV). The MHC has now been described for multiple galliform species including the best defined assemblies of the chicken (Gallus gallus) and domestic turkey (Meleagris gallopavo). Using this sequence resource, this study applied high-throughput sequencing to investigate MHC variation in turkeys of North America (NA turkeys). An MHC-specific SureSelect (Agilent) capture array was developed, and libraries were created for 14 turkeys representing domestic (commercial bred), heritage breed, and wild turkeys. In addition, a representative of the Ocellated turkey (M. ocellata) and chicken (G. gallus) was included to test cross-species applicability of the capture array allowing for identification of new species-specific polymorphisms. Libraries were hybridized to ∼12 K cRNA baits and the resulting pools were sequenced. On average, 98% of processed reads mapped to the turkey whole genome sequence and 53% to the MHC target. In addition to the MHC, capture hybridization recovered sequences corresponding to other MHC regions. Sequence alignment and de novo assembly indicated the presence of several additional BG genes in the turkey with evidence for CNV. Variant detection identified an average of 2245 polymorphisms per individual for the NA turkeys, 3012 for the Ocellated turkey, and 462 variants in the chicken (RJF-256). This study provides an extensive sequence resource for examining MHC variation and its relation to health of this agriculturally important group of birds.

  7. Deliquescence of NaCl-NaNO3, KNO3-NaNO3, and NaCl-KNO3 Salt Mixtures From 90 to 120?C

    SciTech Connect

    Carroll, S A; Craig, L; Wolery, T J

    2004-10-20

    We conducted reversed deliquescence experiments in saturated NaCl-NaNO{sub 3}-H{sub 2}O, KNO{sub 3}-NaNO{sub 3}-H{sub 2}O, and NaCl-KNO{sub 3}-H{sub 2}O systems from 90 to 120 C as a function of relative humidity and solution composition. NaCl, NaNO{sub 3}, and KNO{sub 3} represent members of dust salt assemblages that are likely to deliquesce and form concentrated brines on high-level radioactive waste package surfaces in a repository environment at Yucca Mountain, NV, USA. Discrepancy between model prediction and experimental code can be as high as 8% for relative humidity and 50% for dissolved ion concentration. The discrepancy is attributed primarily to the use of 25 C models for Cl-NO{sub 3} and K-NO{sub 3} ion interactions in the current Yucca Mountain Project high-temperature Pitzer model to describe the non-ideal behavior of these highly concentrated solutions.

  8. Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features

    PubMed Central

    Mohammad-Noori, Morteza; Beer, Michael A.

    2014-01-01

    Abstract Oligomers of length k, or k-mers, are convenient and widely used features for modeling the properties and functions of DNA and protein sequences. However, k-mers suffer from the inherent limitation that if the parameter k is increased to resolve longer features, the probability of observing any specific k-mer becomes very small, and k-mer counts approach a binary variable, with most k-mers absent and a few present once. Thus, any statistical learning approach using k-mers as features becomes susceptible to noisy training set k-mer frequencies once k becomes large. To address this problem, we introduce alternative feature sets using gapped k-mers, a new classifier, gkm-SVM, and a general method for robust estimation of k-mer frequencies. To make the method applicable to large-scale genome wide applications, we develop an efficient tree data structure for computing the kernel matrix. We show that compared to our original kmer-SVM and alternative approaches, our gkm-SVM predicts functional genomic regulatory elements and tissue specific enhancers with significantly improved accuracy, increasing the precision by up to a factor of two. We then show that gkm-SVM consistently outperforms kmer-SVM on human ENCODE ChIP-seq datasets, and further demonstrate the general utility of our method using a Naïve-Bayes classifier. Although developed for regulatory sequence analysis, these methods can be applied to any sequence classification problem. PMID:25033408

  9. A somatic reference standard for cancer genome sequencing.

    PubMed

    Craig, David W; Nasser, Sara; Corbett, Richard; Chan, Simon K; Murray, Lisa; Legendre, Christophe; Tembe, Waibhav; Adkins, Jonathan; Kim, Nancy; Wong, Shukmei; Baker, Angela; Enriquez, Daniel; Pond, Stephanie; Pleasance, Erin; Mungall, Andrew J; Moore, Richard A; McDaniel, Timothy; Ma, Yussanne; Jones, Steven J M; Marra, Marco A; Carpten, John D; Liang, Winnie S

    2016-04-20

    Large-scale multiplexed identification of somatic alterations in cancer has become feasible with next generation sequencing (NGS). However, calibration of NGS somatic analysis tools has been hampered by a lack of tumor/normal reference standards. We thus performed paired PCR-free whole genome sequencing of a matched metastatic melanoma cell line (COLO829) and normal across three lineages and across separate institutions, with independent library preparations, sequencing, and analysis. We generated mean mapped coverages of 99X for COLO829 and 103X for the paired normal across three institutions. Results were combined with previously generated data allowing for comparison to a fourth lineage on earlier NGS technology. Aggregate variant detection led to the identification of consensus variants, including key events that represent hallmark mutation types including amplified BRAF V600E, a CDK2NA small deletion, a 12 kb PTEN deletion, and a dinucleotide TERT promoter substitution. Overall, common events include >35,000 point mutations, 446 small insertion/deletions, and >6,000 genes affected by copy number changes. We present this reference to the community as an initial standard for enabling quantitative evaluation of somatic mutation pipelines across institutions.

  10. A somatic reference standard for cancer genome sequencing.

    PubMed

    Craig, David W; Nasser, Sara; Corbett, Richard; Chan, Simon K; Murray, Lisa; Legendre, Christophe; Tembe, Waibhav; Adkins, Jonathan; Kim, Nancy; Wong, Shukmei; Baker, Angela; Enriquez, Daniel; Pond, Stephanie; Pleasance, Erin; Mungall, Andrew J; Moore, Richard A; McDaniel, Timothy; Ma, Yussanne; Jones, Steven J M; Marra, Marco A; Carpten, John D; Liang, Winnie S

    2016-01-01

    Large-scale multiplexed identification of somatic alterations in cancer has become feasible with next generation sequencing (NGS). However, calibration of NGS somatic analysis tools has been hampered by a lack of tumor/normal reference standards. We thus performed paired PCR-free whole genome sequencing of a matched metastatic melanoma cell line (COLO829) and normal across three lineages and across separate institutions, with independent library preparations, sequencing, and analysis. We generated mean mapped coverages of 99X for COLO829 and 103X for the paired normal across three institutions. Results were combined with previously generated data allowing for comparison to a fourth lineage on earlier NGS technology. Aggregate variant detection led to the identification of consensus variants, including key events that represent hallmark mutation types including amplified BRAF V600E, a CDK2NA small deletion, a 12 kb PTEN deletion, and a dinucleotide TERT promoter substitution. Overall, common events include >35,000 point mutations, 446 small insertion/deletions, and >6,000 genes affected by copy number changes. We present this reference to the community as an initial standard for enabling quantitative evaluation of somatic mutation pipelines across institutions. PMID:27094764

  11. A somatic reference standard for cancer genome sequencing

    PubMed Central

    Craig, David W.; Nasser, Sara; Corbett, Richard; Chan, Simon K.; Murray, Lisa; Legendre, Christophe; Tembe, Waibhav; Adkins, Jonathan; Kim, Nancy; Wong, Shukmei; Baker, Angela; Enriquez, Daniel; Pond, Stephanie; Pleasance, Erin; Mungall, Andrew J.; Moore, Richard A.; McDaniel, Timothy; Ma, Yussanne; Jones, Steven J. M.; Marra, Marco A.; Carpten, John D.; Liang, Winnie S.

    2016-01-01

    Large-scale multiplexed identification of somatic alterations in cancer has become feasible with next generation sequencing (NGS). However, calibration of NGS somatic analysis tools has been hampered by a lack of tumor/normal reference standards. We thus performed paired PCR-free whole genome sequencing of a matched metastatic melanoma cell line (COLO829) and normal across three lineages and across separate institutions, with independent library preparations, sequencing, and analysis. We generated mean mapped coverages of 99X for COLO829 and 103X for the paired normal across three institutions. Results were combined with previously generated data allowing for comparison to a fourth lineage on earlier NGS technology. Aggregate variant detection led to the identification of consensus variants, including key events that represent hallmark mutation types including amplified BRAF V600E, a CDK2NA small deletion, a 12 kb PTEN deletion, and a dinucleotide TERT promoter substitution. Overall, common events include >35,000 point mutations, 446 small insertion/deletions, and >6,000 genes affected by copy number changes. We present this reference to the community as an initial standard for enabling quantitative evaluation of somatic mutation pipelines across institutions. PMID:27094764

  12. Draft Genome Sequence of Arthrobacter enclensis NCIM 5488T for Secondary Metabolism

    PubMed Central

    Neurgaonkar, Priya S.; Dharne, Mahesh S.

    2016-01-01

    Here, we report the draft genome sequence of Arthrobacter enclensis NCIM 5488T, an actinobacterium isolated from a marine sediment sample from Chorao Island, Goa, India. This draft genome sequence consists of 4,226,231 bp with a G+C content of 67.08%, 3,888 protein-coding genes, 50 tRNAs, and 10 rRNAs. Analysis of the genome using bioinformatics tools such as antiSMASH and NaPDoS showed the presence of many unique natural product biosynthetic gene clusters. PMID:27257206

  13. Partial genome sequence of the haloalkaliphilic soda lake bacterium Thioalkalivibrio thiocyanoxidans ARh 2T

    DOE PAGESBeta

    Berben, Tom; Sorokin, Dimitry Y.; Ivanova, Natalia; Pati, Amrita; Kyrpides, Nikos; Goodwin, Lynne A.; Woyke, Tanja; Muyzer, Gerard

    2015-10-26

    Thioalkalivibrio thiocyanoxidans strain ARh 2T is a sulfur-oxidizing bacterium isolated from haloalkaline soda lakes. It is a motile, Gram-negative member of the Gammaproteobacteria. Remarkable properties include the ability to grow on thiocyanate as the sole energy, sulfur and nitrogen source, and the capability of growth at salinities of up to 4.3 M total Na+. This draft genome sequence consists of 61 scaffolds comprising 2,765,337 bp, and contains 2616 protein-coding and 61 RNA-coding genes. In conclusion, this organism was sequenced as part of the Community Science Program of the DOE Joint Genome Institute.

  14. Partial genome sequence of the haloalkaliphilic soda lake bacterium Thioalkalivibrio thiocyanoxidans ARh 2(T).

    PubMed

    Berben, Tom; Sorokin, Dimitry Y; Ivanova, Natalia; Pati, Amrita; Kyrpides, Nikos; Goodwin, Lynne A; Woyke, Tanja; Muyzer, Gerard

    2015-01-01

    Thioalkalivibrio thiocyanoxidans strain ARh 2(T) is a sulfur-oxidizing bacterium isolated from haloalkaline soda lakes. It is a motile, Gram-negative member of the Gammaproteobacteria. Remarkable properties include the ability to grow on thiocyanate as the sole energy, sulfur and nitrogen source, and the capability of growth at salinities of up to 4.3 M total Na(+). This draft genome sequence consists of 61 scaffolds comprising 2,765,337 bp, and contains 2616 protein-coding and 61 RNA-coding genes. This organism was sequenced as part of the Community Science Program of the DOE Joint Genome Institute.

  15. Draft Genome Sequence of Aquamicrobium defluvii Strain W13Z1, a Psychrotolerant Halotolerant Hydrocarbon-Degrading Bacterium

    PubMed Central

    Jin, Decai; Zhou, Lisha; Zhang, Zhuo

    2015-01-01

    Aquamicrobium defluvii W13Z1 was isolated from petroleum-contaminated drill cuttings from the Bohai Sea and could degrade petroleum hydrocarbon with 5% NaCl at 15°C. Here, we present the 4.8-Mb draft genome sequence of this strain, which may provide useful information about the mechanism of petroleum degradation in drill cuttings. PMID:26316640

  16. Performance comparison of Next Generation sequencing platforms.

    PubMed

    Erguner, Bekir; Ustek, Duran; Sagiroglu, Mahmut S

    2015-01-01

    Next Generation DNA Sequencing technologies offer ultra high sequencing throughput for very low prices. The increase in throughput and diminished costs open up new research areas. Moreover, number of clinicians utilizing DNA sequencing keeps growing. One of the main concern for researchers and clinicians who are adopting these platforms is their sequencing accuracy. We compared three of the most commonly used Next Generation Sequencing platforms; Ion Torrent from Life Technologies, GS FLX+ from Roche and HiSeq 2000 from Illumina.

  17. Structure and Properties of Modified and Charge-Compensated Chalcogenide Glasses in the Na/Ba-Ga-Ge Selenide System

    NASA Astrophysics Data System (ADS)

    Mao, Alvin W.

    Chalcogenide glasses exhibit unique optical properties such as infrared transparency owing to the low-phonon energies, optical non-linearity, and photo-induced effects that have important consequences for a wide range of technological applications. However, to fully utilize these properties, it is necessary to better understand the atomic-scale structure and structure-property relationships in this important class of materials. Of particular interest in this regard are glasses in the stoichiometric system Na2Se/BaSe--Ga 2Se3--GeSe2 as they are isoelectronic with the well-studied, oxide glasses of the type M2O(M'O)--Al 2O3--SiO2 (M = alkali, M' = alkaline earth). This dissertation investigates the structure of stoichiometric Na 2Se/BaSe--Ga2Se3--GeSe2 and off-stoichiometric BaSe--Ga2Se3--GeSe 2+/-Se glasses using a combination of Fourier-transform Raman and solid state nuclear magnetic resonance (NMR) spectroscopies. The spectroscopic data is then compared to composition-dependent trends in physical properties such as density, optical band gap, glass transition temperature, and melt fragility to develop predictive structural models of the short- and intermediate-range order in the glass network. These models significantly improve our current understanding of the effects of modifier addition on the structure and properties of chalcogenide glasses, and thus enable a more efficient engineering of these highly functional materials for applications as solid electrolytes in batteries or as optical components in infrared photonics. In general, the underlying stoichiometric Ga2Se3--GeSe 2 network consists primarily of corner-sharing (Ga/Ge)Se4 tetrahedra, where the coordination numbers of Ga, Ge, and Se are 4, 4, and 2, respectively. Some edge-sharing exists, but this configuration is relatively unstable and its concentration tends to decrease with any deviation from the GeSe2 composition. Due to the tetrahedral coordination of Ga, the initial addition of Se-deficient Ga2Se

  18. Protein sequence analysis using Hewlett-Packard biphasic sequencing cartridges in an applied biosystems 473A protein sequencer.

    PubMed

    Tang, S; Mozdzanowski, J; Anumula, K R

    1999-01-01

    Protein sequence analysis using an adsorptive biphasic sequencing cartridge, a set of two coupled columns introduced by Hewlett-Packard for protein sequencing by Edman degradation, in an Applied Biosystems 473A protein sequencer has been demonstrated. Samples containing salts, detergents, excipients, etc. (e.g., formulated protein drugs) can be easily analyzed using the ABI sequencer. Simple modifications to the ABI sequencer to accommodate the cartridge extend its utility in the analysis of difficult samples. The ABI sequencer solvents and reagents were compatible with the HP cartridge for sequencing. Sequence information up to ten residues can be easily generated by this nonoptimized procedure, and it is sufficient for identifying proteins by database search and for preparing a DNA probe for cloning novel proteins.

  19. Molecular phylogenetics of North American phoxinins (Actinopterygii: Cypriniformes: Leuciscidae) based on RAG1 and S7 nuclear DNA sequence data.

    PubMed

    Bufalino, Angelo P; Mayden, Richard L

    2010-04-01

    Most molecular phylogenetic hypotheses for North American (NA) phoxinins are based on mitochondrial DNA sequences (mtDNA) and the resulting hypotheses are rather variable, though there is general support for three major lineages of NA phoxinins: western, creek chub-plagopterin (CC-P), and open posterior myodome (OPM) clades. Support for a monophyletic NA phoxinin group has varied among studies. This study utilizes nuclear DNA (nDNA) sequences from the RAG1 (exon 3) and S7 (intron 1) gene regions to evaluate the phylogenetic relationships and monophyly of NA phoxinins. Results from the nDNA analyses provide overall support for the western, CC-P, and OPM clades. The CC-P clade had the best overall resolution and support in the individual and combined analyses of the nDNA data. Resolution of the western clade was fairly good, with most analyses recovering a monophyletic Gila clade. The OPM clade demonstrated the highest degree of topological variability among the analyses. The RAG1 analyses failed to recover a monophyletic NA phoxinin group by resolving the European leuciscins, inclusive Notemigonus crysoleucas, within the NA phoxinin topology. Most analyses recovered a strongly supported shiner clade though, similar to several mtDNA studies; there was a high degree of topological variability among the results.

  20. Program for Editing Spacecraft Command Sequences

    NASA Technical Reports Server (NTRS)

    Gladden, Roy; Waggoner, Bruce; Kordon, Mark; Hashemi, Mahnaz; Hanks, David; Salcedo, Jose

    2006-01-01

    Sequence Translator, Editor, and Expander Resource (STEER) is a computer program that facilitates construction of sequences and blocks of sequences (hereafter denoted generally as sequence products) for commanding a spacecraft. STEER also provides mechanisms for translating among various sequence product types and quickly expanding activities of a given sequence in chronological order for review and analysis of the sequence. To date, construction of sequence products has generally been done by use of such clumsy mechanisms as text-editor programs, translating among sequence product types has been challenging, and expanding sequences to time-ordered lists has involved arduous processes of converting sequence products to "real" sequences and running them through Class-A software (defined, loosely, as flight and ground software critical to a spacecraft mission). Also, heretofore, generating sequence products in standard formats has been troublesome because precise formatting and syntax are required. STEER alleviates these issues by providing a graphical user interface containing intuitive fields in which the user can enter the necessary information. The STEER expansion function provides a "quick and dirty" means of seeing how a sequence and sequence block would expand into a chronological list, without need to use of Class-A software.

  1. Transcriptomic Analysis of Petunia hybrida in Response to Salt Stress Using High Throughput RNA Sequencing

    PubMed Central

    Villarino, Gonzalo H.; Bombarely, Aureliano; Giovannoni, James J.; Scanlon, Michael J.; Mattson, Neil S.

    2014-01-01

    Salinity and drought stress are the primary cause of crop losses worldwide. In sodic saline soils sodium chloride (NaCl) disrupts normal plant growth and development. The complex interactions of plant systems with abiotic stress have made RNA sequencing a more holistic and appealing approach to study transcriptome level responses in a single cell and/or tissue. In this work, we determined the Petunia transcriptome response to NaCl stress by sequencing leaf samples and assembling 196 million Illumina reads with Trinity software. Using our reference transcriptome we identified more than 7,000 genes that were differentially expressed within 24 h of acute NaCl stress. The proposed transcriptome can also be used as an excellent tool for biological and bioinformatics in the absence of an available Petunia genome and it is available at the SOL Genomics Network (SGN) http://solgenomics.net. Genes related to regulation of reactive oxygen species, transport, and signal transductions as well as novel and undescribed transcripts were among those differentially expressed in response to salt stress. The candidate genes identified in this study can be applied as markers for breeding or to genetically engineer plants to enhance salt tolerance. Gene Ontology analyses indicated that most of the NaCl damage happened at 24 h inducing genotoxicity, affecting transport and organelles due to the high concentration of Na+ ions. Finally, we report a modification to the library preparation protocol whereby cDNA samples were bar-coded with non-HPLC purified primers, without affecting the quality and quantity of the RNA-seq data. The methodological improvement presented here could substantially reduce the cost of sample preparation for future high-throughput RNA sequencing experiments. PMID:24722556

  2. Elastic Coulomb breakup of 34Na

    NASA Astrophysics Data System (ADS)

    Singh, G.; Shubhchintak, Chatterjee, R.

    2016-08-01

    Background: 34Na is conjectured to play an important role in the production of seed nuclei in the alternate r -process paths involving light neutron rich nuclei very near the β -stability line, and as such, it is important to know its ground state properties and structure to calculate rates of the reactions it might be involved in, in the stellar plasma. Found in the region of `island of inversion', its ground state might not be in agreement with normal shell model predictions. Purpose: The aim of this paper is to study the elastic Coulomb breakup of 34Na on 208Pb to give us a core of 33Na with a neutron and in the process we try and investigate the one neutron separation energy and the ground state configuration of 34Na. Method: A fully quantum mechanical Coulomb breakup theory within the architecture of post-form finite range distorted wave Born approximation extended to include the effects of deformation is used to research the elastic Coulomb breakup of 34Na on 208Pb at 100 MeV/u. The triple differential cross section calculated for the breakup is integrated over the desired components to find the total cross-section, momentum, and angular distributions as well as the average momenta, along with the energy-angular distributions. Results: The total one neutron removal cross section is calculated to test the possible ground state configurations of 34Na. The average momentum results along with energy-angular calculations indicate 34Na to have a halo structure. The parallel momentum distributions with narrow full widths at half-maxima signify the same. Conclusion: We have attempted to analyze the possible ground state configurations of 34Na and in congruity with the patterns in the `island of inversion' conclude that even without deformation, 34Na should be a neutron halo with a predominant contribution to its ground state most probably coming from 33Na(3 /2+)⊗ 2 p3 /2ν configuration. We also surmise that it would certainly be useful and rewarding to test our

  3. HCO3(-)-coupled Na+ influx is a major determinant of Na+ turnover and Na+/K+ pump activity in rat hepatocytes

    SciTech Connect

    Fitz, J.G.; Lidofsky, S.D.; Weisiger, R.A.; Xie, M.H.; Cochran, M.; Grotmol, T.; Scharschmidt, B.F. )

    1991-05-01

    Recent studies in hepatocytes indicate that Na(+)-coupled HCO3- transport contributes importantly to regulation of intracellular pH and membrane HCO3- transport. However, the direction of net coupled Na+ and HCO3- movement and the effect of HCO3- on Na+ turnover and Na+/K+ pump activity are not known. In these studies, the effect of HCO3- on Na+ influx and turnover were measured in primary rat hepatocyte cultures with 22Na+, and (Na+)i was measured in single hepatocytes using the Na(+)-sensitive fluorochrome SBFI. Na+/K+ pump activity was measured in intact perfused rat liver and hepatocyte monolayers as Na(+)-dependent or ouabain-suppressible 86Rb uptake, and was measured in single hepatocytes as the effect of transient pump inhibition by removal of extracellular K+ on membrane potential difference (PD) and (Na+)i. In hepatocyte monolayers, HCO3- increased 22Na+ entry and turnover rates by 50-65%, without measurably altering 22Na+ pool size or cell volume, and HCO3- also increased Na+/K+ pump activity by 70%. In single cells, exposure to HCO3- produced an abrupt and sustained rise in (Na+)i from approximately 8 to 12 mM. Na+/K+ pump activity assessed in single cells by PD excursions during transient K+ removal increased congruent to 2.5-fold in the presence of HCO3-, and the rise in (Na+)i produced by inhibition of the Na+/K+ pump was similarly increased congruent to 2.5-fold in the presence of HCO3-. In intact perfused rat liver, HCO3- increased both Na+/K+ pump activity and O2 consumption. These findings indicate that, in hepatocytes, net coupled Na+ and HCO3- movement is inward and represents a major determinant of Na+ influx and Na+/K+ pump activity. About half of hepatic Na+/K+ pump activity appears dedicated to recycling Na+ entering in conjunction with HCO3- to maintain (Na+)i within the physiologic range.

  4. Cassini Mission Sequence Subsystem (MSS)

    NASA Technical Reports Server (NTRS)

    Alland, Robert

    2011-01-01

    This paper describes my work with the Cassini Mission Sequence Subsystem (MSS) team during the summer of 2011. It gives some background on the motivation for this project and describes the expected benefit to the Cassini program. It then introduces the two tasks that I worked on - an automatic system auditing tool and a series of corrections to the Cassini Sequence Generator (SEQ_GEN) - and the specific objectives these tasks were to accomplish. Next, it details the approach I took to meet these objectives and the results of this approach, followed by a discussion of how the outcome of the project compares with my initial expectations. The paper concludes with a summary of my experience working on this project, lists what the next steps are, and acknowledges the help of my Cassini colleagues.

  5. Triple helix purification and sequencing

    DOEpatents

    Wang, R.; Smith, L.M.; Tong, X.E.

    1995-03-28

    Disclosed herein are methods, kits, and equipment for purifying single stranded circular DNA and then using the DNA for DNA sequencing purposes. Templates are provided with an insert having a hybridization region. An elongated oligonucleotide has two regions that are complementary to the insert and the oligo is bound to a magnetic anchor. The oligo hybridizes to the insert on two sides to form a stable triple helix complex. The anchor can then be used to drag the template out of solution using a magnet. The system can purify sequencing templates, and if desired the triple helix complex can be opened up to a double helix so that the oligonucleotide will act as a primer for further DNA synthesis. 4 figures.

  6. Triple helix purification and sequencing

    DOEpatents

    Wang, Renfeng; Smith, Lloyd M.; Tong, Xinchun E.

    1995-01-01

    Disclosed herein are methods, kits, and equipment for purifying single stranded circular DNA and then using the DNA for DNA sequencing purposes. Templates are provided with an insert having a hybridization region. An elongated oligonucleotide has two regions that are complementary to the insert and the oligo is bound to a magnetic anchor. The oligo hybridizes to the insert on two sides to form a stable triple helix complex. The anchor can then be used to drag the template out of solution using a magnet. The system can purify sequencing templates, and if desired the triple helix complex can be opened up to a double helix so that the oligonucleotide will act as a primer for further DNA synthesis.

  7. Apparatus for improved DNA sequencing

    DOEpatents

    Douthart, Richard J.; Crowell, Shannon L.

    1996-01-01

    This invention is a means for the rapid sequencing of DNA samples. More specifically, it consists of a new design direct blotting electrophoresis unit. The DNA sequence is deposited on a membrane attached to a rotating drum. Initial data compaction is facilitated by the use of a machined multi-channeled plate called a ribbon channel plate. Each channel is an isolated mini gel system much like a gel filled capillary. The system as a whole, however, is in a slab gel like format with the advantages of uniformity and easy reusability. The system can be used in different embodiments. The drum system is unique in that after deposition the drum rotates the deposited DNA into a large non-buffer open space where processing and detection can occur. The drum can also be removed in toto to special workstations for downstream processing, multiplexing and detection.

  8. Apparatus for improved DNA sequencing

    DOEpatents

    Douthart, R.J.; Crowell, S.L.

    1996-05-07

    This invention is a means for the rapid sequencing of DNA samples. More specifically, it consists of a new design direct blotting electrophoresis unit. The DNA sequence is deposited on a membrane attached to a rotating drum. Initial data compaction is facilitated by the use of a machined multi-channeled plate called a ribbon channel plate. Each channel is an isolated mini gel system much like a gel filled capillary. The system as a whole, however, is in a slab gel like format with the advantages of uniformity and easy reusability. The system can be used in different embodiments. The drum system is unique in that after deposition the drum rotates the deposited DNA into a large non-buffer open space where processing and detection can occur. The drum can also be removed in toto to special workstations for downstream processing, multiplexing and detection. 18 figs.

  9. Visual mislocalization during saccade sequences

    PubMed Central

    Morrone, Maria Concetta; Burr, David

    2016-01-01

    Visual objects briefly presented around the time of saccadic eye movements are perceived compressed towards the saccade target. Here, we investigated perisaccadic mislocalization with a double-step saccade paradigm, measuring localization of small probe dots briefly flashed at various times around the sequence of the two saccades. At onset of the first saccade, probe dots were mislocalized towards the first and, to a lesser extent, also towards the second saccade target. However, there was very little mislocalization at the onset of the second saccade. When we increased the presentation duration of the saccade targets prior to onset of the saccade sequence, perisaccadic mislocalization did occur at the onset of the second saccade. PMID:25370348

  10. Extrapolation methods for vector sequences

    NASA Technical Reports Server (NTRS)

    Smith, David A.; Ford, William F.; Sidi, Avram

    1987-01-01

    This paper derives, describes, and compares five extrapolation methods for accelerating convergence of vector sequences or transforming divergent vector sequences to convergent ones. These methods are the scalar epsilon algorithm (SEA), vector epsilon algorithm (VEA), topological epsilon algorithm (TEA), minimal polynomial extrapolation (MPE), and reduced rank extrapolation (RRE). MPE and RRE are first derived and proven to give the exact solution for the right 'essential degree' k. Then, Brezinski's (1975) generalization of the Shanks-Schmidt transform is presented; the generalized form leads from systems of equations to TEA. The necessary connections are then made with SEA and VEA. The algorithms are extended to the nonlinear case by cycling, the error analysis for MPE and VEA is sketched, and the theoretical support for quadratic convergence is discussed. Strategies for practical implementation of the methods are considered.

  11. Channel plate for DNA sequencing

    DOEpatents

    Douthart, R.J.; Crowell, S.L.

    1998-01-13

    This invention is a channel plate that facilitates data compaction in DNA sequencing. The channel plate has a length, a width and a thickness, and further has a plurality of channels that are parallel. Each channel has a depth partially through the thickness of the channel plate. Additionally an interface edge permits electrical communication across an interface through a buffer to a deposition membrane surface. 15 figs.

  12. Channel plate for DNA sequencing

    DOEpatents

    Douthart, Richard J.; Crowell, Shannon L.

    1998-01-01

    This invention is a channel plate that facilitates data compaction in DNA sequencing. The channel plate has a length, a width and a thickness, and further has a plurality of channels that are parallel. Each channel has a depth partially through the thickness of the channel plate. Additionally an interface edge permits electrical communication across an interface through a buffer to a deposition membrane surface.

  13. Genome Sequence of Mycobacteriophage Momo.

    PubMed

    Pope, Welkin H; Bina, Elizabeth A; Brahme, Indraneel S; Hill, Amy B; Himmelstein, Philip H; Hunsicker, Sara M; Ish, Amanda R; Le, Tinh S; Martin, Mary M; Moscinski, Catherine N; Shetty, Sameer A; Swierzewski, Tomasz; Iyengar, Varun B; Kim, Hannah; Schafer, Claire E; Grubb, Sarah R; Warner, Marcie H; Bowman, Charles A; Russell, Daniel A; Hatfull, Graham F

    2015-06-18

    Momo is a newly discovered phage of Mycobacterium smegmatis mc(2)155. Momo has a double-stranded DNA genome 154,553 bp in length, with 233 predicted protein-encoding genes, 34 tRNA genes, and one transfer-messenger RNA (tmRNA) gene. Momo has a myoviral morphology and shares extensive nucleotide sequence similarity with subcluster C1 mycobacteriophages.

  14. Genome Sequence of Mycobacteriophage Momo

    PubMed Central

    Bina, Elizabeth A.; Brahme, Indraneel S.; Hill, Amy B.; Himmelstein, Philip H.; Hunsicker, Sara M.; Ish, Amanda R.; Le, Tinh S.; Martin, Mary M.; Moscinski, Catherine N.; Shetty, Sameer A.; Swierzewski, Tomasz; Iyengar, Varun B.; Kim, Hannah; Schafer, Claire E.; Grubb, Sarah R.; Warner, Marcie H.; Bowman, Charles A.; Russell, Daniel A.; Hatfull, Graham F.

    2015-01-01

    Momo is a newly discovered phage of Mycobacterium smegmatis mc2155. Momo has a double-stranded DNA genome 154,553 bp in length, with 233 predicted protein-encoding genes, 34 tRNA genes, and one transfer-messenger RNA (tmRNA) gene. Momo has a myoviral morphology and shares extensive nucleotide sequence similarity with subcluster C1 mycobacteriophages. PMID:26089415

  15. Robot navigation using image sequences

    SciTech Connect

    Rasmussen, C.; Hager, G.D.

    1996-12-31

    We describe a framework for robot navigation that exploits the continuity of image sequences. Tracked visual features both guide the robot and provide predictive information about subsequent features to track. Our hypothesis is that image-based techniques will allow accurate motion without a precise geometric model of the world, while using predictive information will add speed and robustness. A basic component of our framework is called a scene, which is the set of image features stable over some segment of motion. When the scene changes, it is appended to a stored sequence. As the robot moves, correspondences and dissimilarities between current, remembered, and expected scenes provide cues to join and split scene sequences, forming a map-like directed graph. Visual servoing on features in successive scenes is used to traverse a path between robot and goal map locations. In our framework, a human guide serves as a scene recognition oracle during a map-learning phase; thereafter, assuming a known starting position, the robot can independently determine its location without general scene recognition ability. A prototype implementation of this framework uses as features color patches, sum-of-squared differences (SSD) subimages, or image projections of rectangles.

  16. Incidental sequence learning across the lifespan.

    PubMed

    Weiermann, Brigitte; Meier, Beat

    2012-06-01

    The purpose of the present study was to investigate incidental sequence learning across the lifespan. We tested 50 children (aged 7-16), 50 young adults (aged 20-30), and 50 older adults (aged >65) with a sequence learning paradigm that involved both a task and a response sequence. After several blocks of practice, all age groups slowed down when the training sequences were removed, providing indirect evidence for sequence learning. This performance slowing was comparable between groups, indicating no age-related differences. However, when explicit sequence knowledge was considered, age effects were found. For both children and older adults with no or only little explicit knowledge, incidental sequence learning was largely reduced and statistically not significant. In contrast, young adults showed sequence learning irrespective of the amount of explicit knowledge. These results indicate that different learning processes are involved in incidental sequence learning depending on age.

  17. Shaping Action Sequences in Basal Ganglia Circuits

    PubMed Central

    Jin, Xin; Costa, Rui M

    2015-01-01

    Many behaviors necessary for organism survival are learned anew and become organized as complex sequences of actions. Recent studies suggest that cortico-basal ganglia circuits are important for chunking isolated movements into precise and robust action sequences that permit the achievement of particular goals. During sequence learning many neurons in the basal ganglia develop sequence-related activity - related to the initiation, execution, and termination of sequences - suggesting that action sequences are processed as action units. Corticostriatal plasticity is critical for the crystallization of action sequences, and for the development of sequence-related neural activity. Furthermore, this sequence-related activity is differentially expressed in direct and indirect basal ganglia pathways. These findings have implications for understanding the symptoms associated with movement and psychiatric disorders. PMID:26189204

  18. Method and apparatus for biological sequence comparison

    DOEpatents

    Marr, Thomas G.; Chang, William I-Wei

    1997-01-01

    A method and apparatus for comparing biological sequences from a known source of sequences, with a subject (query) sequence. The apparatus takes as input a set of target similarity levels (such as evolutionary distances in units of PAM), and finds all fragments of known sequences that are similar to the subject sequence at each target similarity level, and are long enough to be statistically significant. The invention device filters out fragments from the known sequences that are too short, or have a lower average similarity to the subject sequence than is required by each target similarity level. The subject sequence is then compared only to the remaining known sequences to find the best matches. The filtering member divides the subject sequence into overlapping blocks, each block being sufficiently large to contain a minimum-length alignment from a known sequence. For each block, the filter member compares the block with every possible short fragment in the known sequences and determines a best match for each comparison. The determined set of short fragment best matches for the block provide an upper threshold on alignment values. Regions of a certain length from the known sequences that have a mean alignment value upper threshold greater than a target unit score are concatenated to form a union. The current block is compared to the union and provides an indication of best local alignment with the subject sequence.

  19. Method and apparatus for biological sequence comparison

    DOEpatents

    Marr, T.G.; Chang, W.I.

    1997-12-23

    A method and apparatus are disclosed for comparing biological sequences from a known source of sequences, with a subject (query) sequence. The apparatus takes as input a set of target similarity levels (such as evolutionary distances in units of PAM), and finds all fragments of known sequences that are similar to the subject sequence at each target similarity level, and are long enough to be statistically significant. The invention device filters out fragments from the known sequences that are too short, or have a lower average similarity to the subject sequence than is required by each target similarity level. The subject sequence is then compared only to the remaining known sequences to find the best matches. The filtering member divides the subject sequence into overlapping blocks, each block being sufficiently large to contain a minimum-length alignment from a known sequence. For each block, the filter member compares the block with every possible short fragment in the known sequences and determines a best match for each comparison. The determined set of short fragment best matches for the block provide an upper threshold on alignment values. Regions of a certain length from the known sequences that have a mean alignment value upper threshold greater than a target unit score are concatenated to form a union. The current block is compared to the union and provides an indication of best local alignment with the subject sequence. 5 figs.

  20. Memory and learning with rapid audiovisual sequences

    PubMed Central

    Keller, Arielle S.; Sekuler, Robert

    2015-01-01

    We examined short-term memory for sequences of visual stimuli embedded in varying multisensory contexts. In two experiments, subjects judged the structure of the visual sequences while disregarding concurrent, but task-irrelevant auditory sequences. Stimuli were eight-item sequences in which varying luminances and frequencies were presented concurrently and rapidly (at 8 Hz). Subjects judged whether the final four items in a visual sequence identically replicated the first four items. Luminances and frequencies in each sequence were either perceptually correlated (Congruent) or were unrelated to one another (Incongruent). Experiment 1 showed that, despite encouragement to ignore the auditory stream, subjects' categorization of visual sequences was strongly influenced by the accompanying auditory sequences. Moreover, this influence tracked the similarity between a stimulus's separate audio and visual sequences, demonstrating that task-irrelevant auditory sequences underwent a considerable degree of processing. Using a variant of Hebb's repetition design, Experiment 2 compared musically trained subjects and subjects who had little or no musical training on the same task as used in Experiment 1. Test sequences included some that intermittently and randomly recurred, which produced better performance than sequences that were generated anew for each trial. The auditory component of a recurring audiovisual sequence influenced musically trained subjects more than it did other subjects. This result demonstrates that stimulus-selective, task-irrelevant learning of sequences can occur even when such learning is an incidental by-product of the task being performed. PMID:26575193

  1. Memory and learning with rapid audiovisual sequences.

    PubMed

    Keller, Arielle S; Sekuler, Robert

    2015-01-01

    We examined short-term memory for sequences of visual stimuli embedded in varying multisensory contexts. In two experiments, subjects judged the structure of the visual sequences while disregarding concurrent, but task-irrelevant auditory sequences. Stimuli were eight-item sequences in which varying luminances and frequencies were presented concurrently and rapidly (at 8 Hz). Subjects judged whether the final four items in a visual sequence identically replicated the first four items. Luminances and frequencies in each sequence were either perceptually correlated (Congruent) or were unrelated to one another (Incongruent). Experiment 1 showed that, despite encouragement to ignore the auditory stream, subjects' categorization of visual sequences was strongly influenced by the accompanying auditory sequences. Moreover, this influence tracked the similarity between a stimulus's separate audio and visual sequences, demonstrating that task-irrelevant auditory sequences underwent a considerable degree of processing. Using a variant of Hebb's repetition design, Experiment 2 compared musically trained subjects and subjects who had little or no musical training on the same task as used in Experiment 1. Test sequences included some that intermittently and randomly recurred, which produced better performance than sequences that were generated anew for each trial. The auditory component of a recurring audiovisual sequence influenced musically trained subjects more than it did other subjects. This result demonstrates that stimulus-selective, task-irrelevant learning of sequences can occur even when such learning is an incidental by-product of the task being performed. PMID:26575193

  2. Milk protein-gum tragacanth mixed gels: effect of heat-treatment sequence.

    PubMed

    Hatami, Masoud; Nejatian, Mohammad; Mohammadifar, Mohammad Amin; Pourmand, Hanieh

    2014-01-30

    The aim of this study was to investigate the role of the heat-treatment sequence of biopolymer mixtures as a formulation parameter on the acid-induced gelation of tri-polymeric systems composed of sodium caseinate (Na-caseinate), whey protein concentrate (WPC), and gum tragacanth (GT). This was studied by applying four sequences of heat treatment: (A) co-heating all three biopolymers; (B) heating the milk-protein dispersion and the GT dispersion separately; (C) heating the dispersion containing Na-caseinate and GT together and heating whey protein alone; and (D) co-heating whey protein with GT and heating Na-caseinate alone. According to small-deformation rheological measurements, the strength of the mixed-gel network decreased in the order: C>B>D>A samples. SEM micrographs show that the network of sample C is much more homogenous, coarse and dense than sample A, while the networks of samples B and D are of intermediate density. The heat-treatment sequence of the biopolymer mixtures as a formulation parameter thus offers an opportunity to control the microstructure and rheological properties of mixed gels.

  3. The transvaal sequence: an overview

    NASA Astrophysics Data System (ADS)

    Eriksson, P. G.; Schweitzer, J. K.; Bosch, P. J. A.; Schereiber, U. M.; Van Deventer, J. L.; Hatton, C. J.

    1993-02-01

    The 15 000 m of relatively unmetamorphosed clastic and chemical sedimentary and volcanic rocks of the 2550-2050 Ma Transvaal Sequence as preserved within the Transvaal and correlated Griqualand West basins of South Africa, and in the Kanye basin of Botswana are described. Immature clastic sedimentary and largely andesitic volcanic rocks of the Wolkberg, Godwan and Buffelsfontein Groups and the Bloempoort and Wachteenbeetje Formations probably represent rift-related sequences of Ventersdorp age. The thin sandstones of the Black Reef Formation, developed at the base of both the Kanye and Transvaal basin successions and correlated with the basal Vryburg siltstones of the Griqualand West Sequence, are considered here to be the basal unit of the Transvaal Sequence. The Black Reef fluvial deposits grade up into the epeiric marine carbonates of the Malmani Subgroup. These stromatolitic dolomites and interdbedded cherts were laid down within a steepened carbonate ramp setting; transgressions from an initial Griqualand West compartment towards the northeast covered both the Kanye and Transvaal basins. Iron formations of the succeeding Penge Formation and Griqualand West correlates are envisaged as relatively shallow water shelf deposits within the carbonate platform model; siliceous breccias of the Kanye basin are interpreted as reflecting subaerial brecciation of exposed silica gels. The Duitschland Formation overlying the Penge iron formations is seen as a final, regressive clastic and chemical sedimentary deposits as the Malmani-Penge sea retreated from the Transvaal basin. The interbedded sandstones and mudstones of the uncomformity-bounded Pretoria Group probably represent a combination of alluvial fan and fluviodeltaic complexes debouching into the largely lacustrine Transvaal and Kanye basins. A strong glacial influence in the lower Pretoria Group is reflected in the correlated Makganyene diamicities of the Griqualand West Sequence. Sedimentation across all three

  4. Electrophysiological Determination of Submembrane Na(+) Concentration in Cardiac Myocytes.

    PubMed

    Hegyi, Bence; Bányász, Tamás; Shannon, Thomas R; Chen-Izu, Ye; Izu, Leighton T

    2016-09-20

    In the heart, Na(+) is a key modulator of the action potential, Ca(2+) homeostasis, energetics, and contractility. Because Na(+) currents and cotransport fluxes depend on the Na(+) concentration in the submembrane region, it is necessary to accurately estimate the submembrane Na(+) concentration ([Na(+)]sm). Current methods using Na(+)-sensitive fluorescent indicators or Na(+) -sensitive electrodes cannot measure [Na(+)]sm. However, electrophysiology methods are ideal for measuring [Na(+)]sm. In this article, we develop patch-clamp protocols and experimental conditions to determine the upper bound of [Na(+)]sm at the peak of action potential and its lower bound at the resting state. During the cardiac cycle, the value of [Na(+)]sm is constrained within these bounds. We conducted experiments in rabbit ventricular myocytes at body temperature and found that 1) at a low pacing frequency of 0.5 Hz, the upper and lower bounds converge at 9 mM, constraining the [Na(+)]sm value to ∼9 mM; 2) at 2 Hz pacing frequency, [Na(+)]sm is bounded between 9 mM at resting state and 11.5 mM; and 3) the cells can maintain [Na(+)]sm to the above values, despite changes in the pipette Na(+) concentration, showing autoregulation of Na(+) in beating cardiomyocytes. PMID:27653489

  5. Molecular cloning and expression of a cDNA encoding the rabbit ileal villus cell basolateral membrane Na+/H+ exchanger.

    PubMed Central

    Tse, C M; Ma, A I; Yang, V W; Watson, A J; Levine, S; Montrose, M H; Potter, J; Sardet, C; Pouyssegur, J; Donowitz, M

    1991-01-01

    A cDNA clone encoding a rabbit ileal villus cell Na+/H+ exchanger was isolated and its complete nucleotide sequence was determined. The cDNA is 4 kb long and contains 322 bp of 5'-untranslated region, 2451 bp of open reading frame and 1163 bp of 3'-untranslated area, with 70%, 91% and 40% identity to the human sequence, respectively. Amino acid sequence deduced from the longest open reading frame indicated a protein of 816 residues (predicted Mr 90,716) which exhibits 95% amino acid identity to the human Na+/H+ exchanger. The two putative glycosylation sites in the human Na+/H+ exchanger are conserved in this protein, suggesting that it is a glycoprotein. Stable transfection of the cDNA into an Na+/H+ exchanger deficient fibroblast cell line, established Na+/H+ exchange. The Na+/H+ exchanger was stimulated by serum and a phorbol ester but not by 8-Br-cAMP. In Northern blot analysis, the cDNA hybridized to a 4.8 kb message in rabbit ileal villus cells, kidney cortex, kidney medulla, adrenal gland, brain and descending colon and to a 5.2 kb message in cultured human colonic cancer cell lines, HT29-18 and Caco-2. In immunoblotting, a polyclonal antibody raised against a fusion protein of beta-galactosidase and the C-terminal 158 amino acids of the human Na+/H+ exchanger identified a rabbit ileal basolateral membrane protein of 94 kd and only weakly interacted with the ileal brush border membrane. In immunocytochemical studies using ileal villus and crypt epithelial cells, the same antibody identified basolateral and not brush border epitopes. Restriction analysis of genomic DNA with a 462 bp PstI-AccI fragment of the rabbit Na+/H+ exchanger strongly suggests the existence of closely related Na+/H+ exchanger genes. The near identity of the basolateral Na+/H+ exchanger and the human Na+/H+ exchanger plus the ubiquitous expression of this message suggests that the ileal basolateral Na+/H+ exchanger is the 'housekeeping' Na+/H+ exchanger. Images PMID:1712287

  6. Interaction of NaCl(g) and HCl(g) with condensed NA2SO4

    NASA Technical Reports Server (NTRS)

    Stearns, C. A.; Kohl, F. J.; Fryburg, G. C.; Miller, R. A.

    1977-01-01

    The interaction of Na2SO4(l) with NaCl(g), HCl(g) and H2O(g) was studied in atmospheric pressure flowing air and oxygen at Na2SO4(l) temperatures of 900 and 1000 C. Thermomicrogravimetric and high pressure mass spectrometric sampling techniques were used. Experimental results establish that previously reported enhanced rates of weight loss of Na2SO4(l) in the presence of NaCl(g) are due to the reaction: Na2SO4(c) + 2HCl(g) = 2NaCl(g) + SO2(g) + H2O(g) + 1/2O2(g) being driven to the right in flowing gas systems. The HCl(g) is the product of hydrolysis of NaCl caused by small but significant amounts of H2O(g) present in the system. Thermochemical calculations are used to show that even with sub-ppm levels of H2O(g) present, significant quantities of HCl(g) are produced.

  7. Sequencing Voyager II for the Uranus encounter

    NASA Technical Reports Server (NTRS)

    Morris, R. B.

    1986-01-01

    The process of developing the programmed sequence of events necessary for the Voyager 2 spacecraft to return desired data from its Uranus encounter is discussed. The major steps in the sequence process are reviewed, and the elements of the Mission Sequence Software are described. The design phase and the implementation phase of the sequence process are discussed, and the Computer Command Subsystem architecture is examined in detail. The software's role in constructing the sequences and converting them into onboard programs is elucidated, and the problems unique to the Uranus encounter sequences are considered.

  8. Lotus tenuis tolerates combined salinity and waterlogging: maintaining O2 transport to roots and expression of an NHX1-like gene contribute to regulation of Na+ transport.

    PubMed

    Teakle, Natasha L; Amtmann, Anna; Real, Daniel; Colmer, Timothy D

    2010-08-01

    Salinity and waterlogging interact to reduce growth for most crop and pasture species. The combination of these stresses often cause a large increase in the rate of Na(+) and Cl(-) transport to shoots; however, the mechanisms responsible for this are largely unknown. To identify mechanisms contributing to the adverse interaction between salinity and waterlogging, we compared two Lotus species with contrasting tolerances when grown under saline (200 mM NaCl) and O(2)-deficient (stagnant) treatments. Measurements of radial O(2) loss (ROL) under stagnant conditions indicated that more O(2) reaches root tips of Lotus tenuis, compared with Lotus corniculatus. Better internal aeration would contribute to maintaining Na(+) and Cl(-) transport processes in roots of L. tenuis exposed to stagnant-plus-NaCl treatments. L. tenuis root Na(+) concentrations after stagnant-plus-NaCl treatment (200 mM) were 17% higher than L. corniculatus, with 55% of the total plant Na(+) being accumulated in roots, compared with only 39% for L. corniculatus. L. tenuis accumulated more Na(+) in roots, presumably in vacuoles, thereby reducing transport to the shoot (25% lower than L. corniculatus). A candidate gene for vacuole Na(+) accumulation, an NHX1-like gene, was cloned from L. tenuis and identity established via sequencing and yeast complementation. Transcript levels of NHX1 in L. tenuis roots under stagnant-plus-NaCl treatment were the same as for aerated NaCl, whereas L. corniculatus roots had reduced transcript levels. Enhanced O(2) transport to roots enables regulation of Na(+) transport processes in L. tenuis roots, contributing to tolerance to combined salinity and waterlogging stresses.

  9. Direct Measurement of ^21Na+α Stellar Reaction

    NASA Astrophysics Data System (ADS)

    Binh Dam, Nguyen; Yamaguchi, H.; Wakabayashi, Y.; Hayakawa, S.; Hashimoto, T.; Kahl, D.; Kubono, S.; Le, H. K.; Nguyen, T. T.; Iwasa, N.; Kume, N.; Kato, S.; Teranishi, T.

    2009-10-01

    Nucleosynthesis of ^22Na is an interesting subject because of possible γ-ray observation and isotopic anomalies in presolar grain. ^22Na would have been mainly produced in the NeNa cycle. At high temperature conditions, ^21Na(α,p)^24Mg reaction could play a significant role to make flow from the NeNa cycle to the next MgAl cycle and beyond. Clearly, the ^21Na(α,p)^24Mg stellar reaction would bypass ^22Na, resulting in reduction of ^22Na production, therefore, it is strongly coupled to the Ne-E problem. It could be also important to understand the early stage of the rp-process. Experiment was performed using a 39 MeV ^21Na radioactive beam obtained by the CNS Radio Isotope Beam separator CRIB of the University of Tokyo. Both protons and alphas were measured from α+^21Na scattering with a thick ^4He gas target.

  10. Characterization of the 70 kDa polypeptide of the Na/Ca exchanger.

    PubMed Central

    Saba, R I; Bollen, A; Herchuelz, A

    1999-01-01

    The Na/Ca exchanger is associated with 160, 120 and 70 kDa polypeptides whose nature is poorly understood. We have purified and characterized the Na/Ca exchanger from bovine cardiac sarcolemmal vesicles (SLVs) by using ion-exchange and affinity chromatographies. The Na/Ca exchanger-enriched fraction was reconstituted into asolectin liposomes [lipid to protein ratio 10:1 (w/w)] that showed Na/Ca exchange activity. Under non-reducing conditions, SDS/PAGE showed a single 70 kDa polypeptide, which was further characterized by immunoblots with different antibodies: SWant, raised against the purified exchanger protein; NH2-terminus, residues 1-21; NCX1, residues 393-406; and Exon F, residues 622-644. Immunoblots under reducing conditions with SWant, NH2-terminus and NCX1 showed three bands migrating at 160, 120 and 70 kDa for SLV preparations, whereas Exon F reacted only with the 160 and 120 kDa bands. Under non-reducing conditions, immunoblots with purified reconstituted Na/Ca exchanger showed a single band at 70 kDa reacting with SWant, NH2-terminus and NCX1 but not with Exon F. We conclude that the 70 kDa protein is associated with Na/Ca exchange activity, has the same N-terminal sequence as the cloned bovine cardiac exchanger, and has its length decreased by at least 35% from its C-terminal portion as compared with that of the wild-type exchanger. PMID:9931309

  11. Biomolecule Sequencer: Nanopore Sequencing Technology for In-Situ Environmental Monitoring and Astrobiology

    NASA Astrophysics Data System (ADS)

    John, K. K.; Botkin, D. J.; Burton, A. S.; Castro-Wallace, S. L.; Chaput, J. D.; Dworkin, J. P.; Lupisella, M. L.; Mason, C. E.; Rubins, K. H.; Smith, D. J.; Stahl, S.; Switzer, C.

    2016-10-01

    Biomolecule Sequencer will demonstrate, for the first time, that DNA sequencing is feasible as a tool for in-situ environmental monitoring and astrobiology. A space-based sequencer could identify microbes, diseases, and help detect DNA-based life.

  12. Functional coupling of renal K+ and Na+ handling causes high blood pressure in Na+ replete mice

    PubMed Central

    Vitzthum, Helga; Seniuk, Anika; Schulte, Laura Helene; Müller, Maxie Luise; Hetz, Hannah; Ehmke, Heimo

    2014-01-01

    A network of kinases, including WNKs, SPAK and Sgk1, is critical for the independent regulation of K+ and Na+ transport in the distal nephron. Angiotensin II is thought to act as a key hormone in orchestrating these kinases to switch from K+ secretion during hyperkalaemia to Na+ reabsorption during intravascular volume depletion, thus keeping disturbances in electrolyte and blood pressure homeostasis at a minimum. It remains unclear, however, how K+ and Na+ transport are regulated during a high Na+ intake, which is associated with suppressed angiotensin II levels and a high distal tubular Na+ load. We therefore investigated the integrated blood pressure, renal, hormonal and gene and protein expression responses to large changes of K+ intake in Na+ replete mice. Both low and high K+ intake increased blood pressure and caused Na+ retention. Low K+ intake was accompanied by an upregulation of the sodium-chloride cotransporter (NCC) and its activating kinase SPAK, and inhibition of NCC normalized blood pressure. Renal responses were unaffected by angiotensin AT1 receptor antagonism, indicating that low K+ intake activates the distal nephron by an angiotensin-independent mode of action. High K+ intake was associated with elevated plasma aldosterone concentrations and an upregulation of the epithelial sodium channel (ENaC) and its activating kinase Sgk1. Surprisingly, high K+ intake increased blood pressure even during ENaC or mineralocorticoid receptor antagonism, suggesting the contribution of aldosterone-independent mechanisms. These findings show that in a Na+ replete state, changes in K+ intake induce specific molecular and functional adaptations in the distal nephron that cause a functional coupling of renal K+ and Na+ handling, resulting in Na+ retention and high blood pressure when K+ intake is either restricted or excessively increased. PMID:24396058

  13. NaCd excimer emission bands

    NASA Astrophysics Data System (ADS)

    Pichler, G.; Veža, D.; Fijan, D.

    1988-06-01

    The analysis of the visible spectrum of a high pressure sodium lamp filled with sodium, cadium and xenon revealed the existence of NaCd excimer spectral features. These are four red satellite bands at 691, 697, 709 and 726.5 nm and diffuse bands peaking at 479.1 and 484.3 nm. Both spectral phenomena are related to those found earlier for the NaHg system. An interpretation of the red satellite bands origin is given in terms of a qualitative model for the four lowest potential curves of the NaCd excimer. In this model the essential feature is the avoided crossing between B 2∑ 1/2 and A 2∏ 1/2 electronic states, which causes a complex structure of the satellite bands in the very far red wing of the sodium D lines broadened by cadmium.

  14. Proline-rich Sequence Recognition

    PubMed Central

    Schlundt, Andreas; Sticht, Jana; Piotukh, Kirill; Kosslick, Daniela; Jahnke, Nadin; Keller, Sandro; Schuemann, Michael; Krause, Eberhard; Freund, Christian

    2009-01-01

    The tumor maintenance protein Tsg101 has recently gained much attention because of its involvement in endosomal sorting, virus release, cytokinesis, and cancerogenesis. The ubiquitin-E2-like variant (UEV) domain of the protein interacts with proline-rich sequences of target proteins that contain P(S/T)AP amino acid motifs and weakly binds to the ubiquitin moiety of proteins committed to sorting or degradation. Here we performed peptide spot analysis and phage display to refine the peptide binding specificity of the Tsg101 UEV domain. A mass spectrometric proteomics approach that combines domain-based pulldown experiments, binding site inactivation, and stable isotope labeling by amino acids in cell culture (SILAC) was then used to delineate the relative importance of the peptide and ubiquitin binding sites. Clearly “PTAP” interactions dominate target recognition, and we identified several novel binders as for example the poly(A)-binding protein 1 (PABP1), Sec24b, NFκB2, and eIF4b. For PABP1 and eIF4b the interactions were confirmed in the context of the corresponding full-length proteins in cellular lysates. Therefore, our results strongly suggest additional roles of Tsg101 in cellular regulation of mRNA translation. Regulation of Tsg101 itself by the ubiquitin ligase TAL (Tsg101-associated ligase) is most likely conferred by a single PSAP binding motif that enables the interaction with Tsg101 UEV. Together with the results from the accompanying article (Kofler, M., Schuemann, M., Merz, C., Kosslick, D., Schlundt, A., Tannert, A., Schaefer, M., Lührmann, R., Krause, E., and Freund, C. (2009) Proline-rich sequence recognition: I. Marking GYF and WW domain assembly sites in early spliceosomal complexes. Mol. Cell. Proteomics 8, 2461–2473) on GYF and WW domain pathways our work defines major proline-rich sequence-mediated interaction networks that contribute to the modular assembly of physiologically relevant protein complexes. PMID:19542561

  15. Benchmarking short sequence mapping tools

    PubMed Central

    2013-01-01

    Background The development of next-generation sequencing instruments has led to the generation of millions of short sequences in a single run. The process of aligning these reads to a reference genome is time consuming and demands the development of fast and accurate alignment tools. However, the current proposed tools make different compromises between the accuracy and the speed of mapping. Moreover, many important aspects are overlooked while comparing the performance of a newly developed tool to the state of the art. Therefore, there is a need for an objective evaluation method that covers all the aspects. In this work, we introduce a benchmarking suite to extensively analyze sequencing tools with respect to various aspects and provide an objective comparison. Results We applied our benchmarking tests on 9 well known mapping tools, namely, Bowtie, Bowtie2, BWA, SOAP2, MAQ, RMAP, GSNAP, Novoalign, and mrsFAST (mrFAST) using synthetic data and real RNA-Seq data. MAQ and RMAP are based on building hash tables for the reads, whereas the remaining tools are based on indexing the reference genome. The benchmarking tests reveal the strengths and weaknesses of each tool. The results show that no single tool outperforms all others in all metrics. However, Bowtie maintained the best throughput for most of the tests while BWA performed better for longer read lengths. The benchmarking tests are not restricted to the mentioned tools and can be further applied to others. Conclusion The mapping process is still a hard problem that is affected by many factors. In this work, we provided a benchmarking suite that reveals and evaluates the different factors affecting the mapping process. Still, there is no tool that outperforms all of the others in all the tests. Therefore, the end user should clearly specify his needs in order to choose the tool that provides the best results. PMID:23758764

  16. Integration of retinal image sequences

    NASA Astrophysics Data System (ADS)

    Ballerini, Lucia

    1998-10-01

    In this paper a method for noise reduction in ocular fundus image sequences is described. The eye is the only part of the human body where the capillary network can be observed along with the arterial and venous circulation using a non invasive technique. The study of the retinal vessels is very important both for the study of the local pathology (retinal disease) and for the large amount of information it offers on systematic haemodynamics, such as hypertension, arteriosclerosis, and diabetes. In this paper a method for image integration of ocular fundus image sequences is described. The procedure can be divided in two step: registration and fusion. First we describe an automatic alignment algorithm for registration of ocular fundus images. In order to enhance vessel structures, we used a spatially oriented bank of filters designed to match the properties of the objects of interest. To evaluate interframe misalignment we adopted a fast cross-correlation algorithm. The performances of the alignment method have been estimated by simulating shifts between image pairs and by using a cross-validation approach. Then we propose a temporal integration technique of image sequences so as to compute enhanced pictures of the overall capillary network. Image registration is combined with image enhancement by fusing subsequent frames of a same region. To evaluate the attainable results, the signal-to-noise ratio was estimated before and after integration. Experimental results on synthetic images of vessel-like structures with different kind of Gaussian additive noise as well as on real fundus images are reported.

  17. Targeting voltage gated sodium channels NaV1.7, Na V1.8, and Na V1.9 for treatment of pathological cough.

    PubMed

    Muroi, Yukiko; Undem, Bradley J

    2014-02-01

    Recent advances in our understanding of voltage-gated sodium channels (NaVs) lead to the rational hypothesis that drugs capable of selective blockade of NaV subtypes may be a safe and effective strategy for the treatment of unwanted cough. Among the nine NaV subtypes (NaV1.1-NaV1.9), the afferent nerves involved in initiating cough, in common with nociceptive neurons in the somatosensory system, express mainly NaV1.7, NaV1.8, and NaV1.9. Although knowledge about the effect of selectively blocking these channels on the cough reflex is limited, their biophysical properties indicate that each may contribute to the hypertussive and allotussive state that typifies subacute and chronic nonproductive cough.

  18. Concentration dependence of Li+/Na+ diffusion in manganese hexacyanoferrates

    NASA Astrophysics Data System (ADS)

    Takachi, Masamitsu; Fukuzumi, Yuya; Moritomo, Yutaka

    2016-06-01

    Manganese hexacyanoferrates (Mn-HCFs) with a jungle-gym-type structure are promising cathode materials for Li+/Na+ secondary batteries (LIBs/SIBs). Here, we investigated the diffusion constants D Li/D Na of Li+/Na+ against the Li+/Na+ concentration x Na/x Li and temperature (T) of A 1.32Mn[Fe(CN)6]0.833.6H2O (A = Li and Na). We evaluated the activation energy E\\text{a}\\text{Li}/E\\text{a}\\text{Na} of D Li/D Na against x Na/x Li. We found that E\\text{a}\\text{Na} steeply increases with x Na from 0.41 eV at x Na = 0.69 to 0.7 eV at 1.1. The increase in E\\text{a}\\text{Na} is ascribed to the occupancy effect of the Na+ site. The increase in E\\text{a}\\text{Li} is suppressed, probably because the number of Li+ sites is three times that of Na+ sites.

  19. Cold-aggravated pain in humans caused by a hyperactive NaV1.9 channel mutant.

    PubMed

    Leipold, Enrico; Hanson-Kahn, Andrea; Frick, Miya; Gong, Ping; Bernstein, Jonathan A; Voigt, Martin; Katona, Istvan; Oliver Goral, R; Altmüller, Janine; Nürnberg, Peter; Weis, Joachim; Hübner, Christian A; Heinemann, Stefan H; Kurth, Ingo

    2015-01-01

    Gain-of-function mutations in the human SCN11A-encoded voltage-gated Na(+) channel NaV1.9 cause severe pain disorders ranging from neuropathic pain to congenital pain insensitivity. However, the entire spectrum of the NaV1.9 diseases has yet to be defined. Applying whole-exome sequencing we here identify a missense change (p.V1184A) in NaV1.9, which leads to cold-aggravated peripheral pain in humans. Electrophysiological analysis reveals that p.V1184A shifts the voltage dependence of channel opening to hyperpolarized potentials thereby conferring gain-of-function characteristics to NaV1.9. Mutated channels diminish the resting membrane potential of mouse primary sensory neurons and cause cold-resistant hyperexcitability of nociceptors, suggesting a mechanistic basis for the temperature dependence of the pain phenotype. On the basis of direct comparison of the mutations linked to either cold-aggravated pain or pain insensitivity, we propose a model in which the physiological consequence of a mutation, that is, augmented versus absent pain, is critically dependent on the type of NaV1.9 hyperactivity. PMID:26645915

  20. Cold-aggravated pain in humans caused by a hyperactive NaV1.9 channel mutant

    PubMed Central

    Leipold, Enrico; Hanson-Kahn, Andrea; Frick, Miya; Gong, Ping; Bernstein, Jonathan A.; Voigt, Martin; Katona, Istvan; Oliver Goral, R.; Altmüller, Janine; Nürnberg, Peter; Weis, Joachim; Hübner, Christian A.; Heinemann, Stefan H.; Kurth, Ingo

    2015-01-01

    Gain-of-function mutations in the human SCN11A-encoded voltage-gated Na+ channel NaV1.9 cause severe pain disorders ranging from neuropathic pain to congenital pain insensitivity. However, the entire spectrum of the NaV1.9 diseases has yet to be defined. Applying whole-exome sequencing we here identify a missense change (p.V1184A) in NaV1.9, which leads to cold-aggravated peripheral pain in humans. Electrophysiological analysis reveals that p.V1184A shifts the voltage dependence of channel opening to hyperpolarized potentials thereby conferring gain-of-function characteristics to NaV1.9. Mutated channels diminish the resting membrane potential of mouse primary sensory neurons and cause cold-resistant hyperexcitability of nociceptors, suggesting a mechanistic basis for the temperature dependence of the pain phenotype. On the basis of direct comparison of the mutations linked to either cold-aggravated pain or pain insensitivity, we propose a model in which the physiological consequence of a mutation, that is, augmented versus absent pain, is critically dependent on the type of NaV1.9 hyperactivity. PMID:26645915

  1. Molecular and functional comparisons of the vacuolar Na+/H+ exchangers originated from glycophytic and halophytic species.

    PubMed

    Li, Jin-yao; He, Xiao-wei; Xu, Li; Zhou, Jie; Wu, Ping; Shou, Hui-xia; Zhang, Fu-chun

    2008-02-01

    A novel vacuolar Na+/H+ exchanger, CgNHX1, was cloned from a halophytic species Chenopodium glaucum by using reverse transcriptase-polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE) technique. Sequence alignment and phylogenetic analysis of 22 NHX genes from GenBank as well as the new CgNHX1 gene indicate that NHX genes shared a great degree of similarity, regardless of their glycophytic or halophytic origin. Expression of the CgNHX1 gene was induced by NaCl and peaked at 400 mmol/L NaCl. Overexpression of NHX1 genes in rice enhanced their tolerance to salt stress. However, there is no significant difference in salt tolerance among the transgenic rice plants overexpressing the NHX1 genes from either glycophytic or halophytic species. The Na+ content of both the wild type (WT) and transgenic plants increased when exposed to 50 and 100 mmol/L NaCl, and the Na+ concentration in transgenic plants was marginally higher than that of WT. Our data demonstrate that the overexpression of the NHX1 gene from either glycophytic or halophytic species resulted in the enhanced tolerance to salt stress at a similar level, suggesting that NHX gene per se might not be the reason accounting for the difference in salt tolerance between glycophytes and halophytes. PMID:18257135

  2. Crystal structure of a Na+-bound Na+,K+-ATPase preceding the E1P state.

    PubMed

    Kanai, Ryuta; Ogawa, Haruo; Vilsen, Bente; Cornelius, Flemming; Toyoshima, Chikashi

    2013-10-10

    Na(+),K(+)-ATPase pumps three Na(+) ions out of cells in exchange for two K(+) taken up from the extracellular medium per ATP molecule hydrolysed, thereby establishing Na(+) and K(+) gradients across the membrane in all animal cells. These ion gradients are used in many fundamental processes, notably excitation of nerve cells. Here we describe 2.8 Å-resolution crystal structures of this ATPase from pig kidney with bound Na(+), ADP and aluminium fluoride, a stable phosphate analogue, with and without oligomycin that promotes Na(+) occlusion. These crystal structures represent a transition state preceding the phosphorylated intermediate (E1P) in which three Na(+) ions are occluded. Details of the Na(+)-binding sites show how this ATPase functions as a Na(+)-specific pump, rejecting K(+) and Ca(2+), even though its affinity for Na(+) is low (millimolar dissociation constant). A mechanism for sequential, cooperative Na(+) binding can now be formulated in atomic detail. PMID:24089211

  3. Na+/K+-ATPase: Activity and inhibition

    NASA Astrophysics Data System (ADS)

    Čolović, M.; Krstić, D.; Krinulović, K.; Momić, T.; Savić, J.; Vujačić, A.; Vasić, V.

    2009-09-01

    The aim of the study was to give an overview of the mechanism of inhibition of Na+/K+-ATPase activity induced by some specific and non specific inhibitors. For this purpose, the effects of some ouabain like compounds (digoxin, gitoxin), noble metals complexes ([PtCl2DMSO2], [AuCl4]-, [PdCl4]2-, [PdCl(dien)]+, [PdCl(Me4dien)]+), transition metal ions (Cu2+, Zn2+, Fe2+, Co2+), and heavy metal ions (Hg2+, Pb2+, Cd2+) on the activity of Na+/K+-ATPase from rat synaptic plasma membranes (SPM), porcine cerebral cortex and human erythrocytes were discussed.

  4. An Assignment Sequence for Underprepared Writers.

    ERIC Educational Resources Information Center

    Nimmo, Kristi

    2000-01-01

    Presents a sequenced writing assignment on shopping to aid basic writers. Describes a writing assignment focused around online and mail-order shopping. Notes steps in preparing for the assignment, the sequence, and discusses responses to the assignments. (SC)

  5. Genome sequences of eight morphologically diverse Alphaproteobacteria.

    PubMed

    Brown, Pamela J B; Kysela, David T; Buechlein, Aaron; Hemmerich, Chris; Brun, Yves V

    2011-09-01

    The Alphaproteobacteria comprise morphologically diverse bacteria, including many species of stalked bacteria. Here we announce the genome sequences of eight alphaproteobacteria, including the first genome sequences of species belonging to the genera Asticcacaulis, Hirschia, Hyphomicrobium, and Rhodomicrobium. PMID:21705585

  6. The Genome Sequencing Center at NCGR

    SciTech Connect

    Schilkey, Faye

    2010-06-02

    Faye Schilkey from the National Center for Genome Resources discusses NCGR's research, sequencing and analysis experience on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  7. NaOH-Debittering Induces Changes in Bacterial Ecology during Table Olives Fermentation

    PubMed Central

    Cocolin, Luca; Alessandria, Valentina; Botta, Cristian; Gorra, Roberta; De Filippis, Francesca; Ercolini, Danilo; Rantsiou, Kalliopi

    2013-01-01

    Limited information is available on the impact of the NaOH treatment on table olive fermentations, and for this reason a polyphasic approach has been adopted here to investigate its effect on the fermentation dynamics and bacterial biodiversity. The microbial counts of the main groups involved in the transformation have not shown any differences, apart from a more prompt start of the fermentation when the olives were subjected to the NaOH treatment. The data produced by culture-independent analyses highlighted that the fermentation of table olives not treated with NaOH is the result of the coexistence of two different ecosystems: the surface of the olives and the brines. A sodium hydroxide treatment not only eliminates this difference, but also affects the bacterial ecology of the olives to a great extent. As proved by high-throughput sequencing, the fermentation of the olives not treated with NaOH was characterized by the presence of halophilic bacteria, which were substituted by Lactobacillus at the later stages of the fermentation, while enterobacteria were dominant when the olives were treated with sodium hydroxide. Higher biodiversity was found for Lactobacillus plantarum isolated during untreated fermentation. Different biotypes were found on the olive surface and in the brines. When the debittering process was carried out, a decrease in the number of L. plantarum biotypes were observed and those originating from the surface of the olive did not differentiate from the ones present in the brines. PMID:23935928

  8. Ordered and disordered polymorphs of Na(Ni2/3Sb1/3)O₂: Honeycomb-ordered cathodes for Na-ion batteries

    DOE PAGESBeta

    Ma, Jeffrey; Wu, Lijun; Bo, Shou -Hang; Khalifah, Peter G.; Grey, Clare P.; Zhu, Yimei

    2015-04-14

    Na-ion batteries are appealing alternatives to Li-ion battery systems for large-scale energy storage applications in which elemental cost and abundance are important. Although it is difficult to find Na-ion batteries which achieve substantial specific capacities at voltages above 3 V (vs Na⁺/Na), the honeycomb-layered compound Na(Ni2/3Sb1/3)O₂ can deliver up to 130 mAh/g of capacity at voltages above 3 V with this capacity concentrated in plateaus at 3.27 and 3.64 V. Comprehensive crystallographic studies have been carried out in order to understand the role of disorder in this system which can be prepared in both “disordered” and “ordered” forms, depending onmore » the synthesis conditions. The average structure of Na(Ni2/3Sb1/3)O₂ is always found to adopt an O3-type stacking sequence, though different structures for the disordered (R3¯m, #166, a = b = 3.06253(3) Å and c = 16.05192(7) Å) and ordered variants (C2/m, #12, a = 5.30458(1) Å, b = 9.18432(1) Å, c = 5.62742(1) Å and β = 108.2797(2)°) are demonstrated through the combined Rietveld refinement of synchrotron X-ray and time-of-flight neutron powder diffraction data. However, pair distribution function studies find that the local structure of disordered Na(Ni2/3Sb1/3)O₂ is more correctly described using the honeycomb-ordered structural model, and solid state NMR studies confirm that the well-developed honeycomb ordering of Ni and Sb cations within the transition metal layers is indistinguishable from that of the ordered phase. The disorder is instead found to mainly occur perpendicular to the honeycomb layers with an observed coherence length of not much more than 1 nm seen in electron diffraction studies. When the Na environment is probed through ²³Na solid state NMR, no evidence is found for prismatic Na environments, and a bulk diffraction analysis finds no evidence of conventional stacking faults. The lack of long range coherence is instead attributed to disorder among the

  9. Data structures for DNA sequence manipulation.

    PubMed Central

    Lawrence, C B

    1986-01-01

    Two data structures designated Fragment and Construct are described. The Fragment data structure defines a continuous nucleic acid sequence from a unique genetic origin. The Construct defines a continuous sequence composed of sequences from multiple genetic origins. These data structures are manipulated by a set of software tools to simulate the construction of mosaic recombinant DNA molecules. They are also used as an interface between sequence data banks and analytical programs. PMID:3753765

  10. Sequencing crop genomes: approaches and applications

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plant genome sequencing methodology parrallels the sequencing of the human genome. The first projects were slow and very expensive. BAC by BAC approaches were utilized first and whole-genome shotgun sequencing rapidly replaced that approach. So called 'next generation' technologies such as short rea...

  11. PacBio Sequencing and Its Applications

    PubMed Central

    Rhoads, Anthony; Au, Kin Fai

    2015-01-01

    Single-molecule, real-time sequencing developed by Pacific BioSciences offers longer read lengths than the second-generation sequencing (SGS) technologies, making it well-suited for unsolved problems in genome, transcriptome, and epigenetics research. The highly-contiguous de novo assemblies using PacBio sequencing can close gaps in current reference assemblies and characterize structural variation (SV) in personal genomes. With longer reads, we can sequence through extended repetitive regions and detect mutations, many of which are associated with diseases. Moreover, PacBio transcriptome sequencing is advantageous for the identification of gene isoforms and facilitates reliable discoveries of novel genes and novel isoforms of annotated genes, due to its ability to sequence full-length transcripts or fragments with significant lengths. Additionally, PacBio’s sequencing technique provides information that is useful for the direct detection of base modifications, such as methylation. In addition to using PacBio sequencing alone, many hybrid sequencing strategies have been developed to make use of more accurate short reads in conjunction with PacBio long reads. In general, hybrid sequencing strategies are more affordable and scalable especially for small-size laboratories than using PacBio Sequencing alone. The advent of PacBio sequencing has made available much information that could not be obtained via SGS alone. PMID:26542840

  12. Incidental Sequence Learning across the Lifespan

    ERIC Educational Resources Information Center

    Weiermann, Brigitte; Meier, Beat

    2012-01-01

    The purpose of the present study was to investigate incidental sequence learning across the lifespan. We tested 50 children (aged 7-16), 50 young adults (aged 20-30), and 50 older adults (aged >65) with a sequence learning paradigm that involved both a task and a response sequence. After several blocks of practice, all age groups slowed down…

  13. Automated Sequence Generation Process and Software

    NASA Technical Reports Server (NTRS)

    Gladden, Roy

    2007-01-01

    "Automated sequence generation" (autogen) signifies both a process and software used to automatically generate sequences of commands to operate various spacecraft. The autogen software comprises the autogen script plus the Activity Plan Generator (APGEN) program. APGEN can be used for planning missions and command sequences.

  14. The recurrence sequence via the Fibonacci groups

    NASA Astrophysics Data System (ADS)

    Aküzüm, Yeşim; Deveci, Ömür

    2016-04-01

    This work develops properties of the recurrence sequence defined by the aid of the relation matrix of the Fibonacci groups. The study of this sequence modulo m yields cyclic groups and semigroups from generating matrix. Finally, we extend the sequence defined to groups and then, we obtain its period in the Fibonacci groups.

  15. SP8 Sequencing Extinct Genomes

    PubMed Central

    Poinar, H.

    2007-01-01

    Nucleic acids, which hold clues to the evolution of various animal and hominid taxa, are comparatively weak molecules from other cellular debris, and thus evolutionary biologists are in essence time trapped. Fortunately, DNA and protein fragments do exist in fossil remains beyond what theoretical experimentation would suggest. Sequestering of DNA molecules in humic or Maillard-like complexes likely represents a rich source of DNA molecules from the past, which have yet to be tapped. These molecules were impossible to acquire due to the selective nature of the polymerase chain reaction. Recently, however, rapid parallel pyrosequencing techniques, such as those used in metagenomics-based research, which, in theory, allow for the identification of all short nucleotide sequences in a sample in a non-selective approach, have the potential to allow the identification of all nucleic acids in a sample, and thus represent the way forward for ancient DNA. In theory, this new technology will allow the completion of genomes of extinct animals, plants, and microbes. I will discuss the benefits and pitfalls of this metagenomics approach to ancient DNA, highlighting our recent efforts underway to sequence the wooly mammoth genome as well as other fossil remains.

  16. Na+ Inhibits the Epithelial Na+ Channel by Binding to a Site in an Extracellular Acidic Cleft*

    PubMed Central

    Kashlan, Ossama B.; Blobner, Brandon M.; Zuzek, Zachary; Tolino, Michael; Kleyman, Thomas R.

    2015-01-01

    The epithelial Na+ channel (ENaC) has a key role in the regulation of extracellular fluid volume and blood pressure. ENaC belongs to a family of ion channels that sense the external environment. These channels have large extracellular regions that are thought to interact with environmental cues, such as Na+, Cl−, protons, proteases, and shear stress, which modulate gating behavior. We sought to determine the molecular mechanism by which ENaC senses high external Na+ concentrations, resulting in an inhibition of channel activity. Both our structural model of an ENaC α subunit and the resolved structure of an acid-sensing ion channel (ASIC1) have conserved acidic pockets in the periphery of the extracellular region of the channel. We hypothesized that these acidic pockets host inhibitory allosteric Na+ binding sites. Through site-directed mutagenesis targeting the acidic pocket, we modified the inhibitory response to external Na+. Mutations at selected sites altered the cation inhibitory preference to favor Li+ or K+ rather than Na+. Channel activity was reduced in response to restraining movement within this region by cross-linking structures across the acidic pocket. Our results suggest that residues within the acidic pocket form an allosteric effector binding site for Na+. Our study supports the hypothesis that an acidic cleft is a key ligand binding locus for ENaC and perhaps other members of the ENaC/degenerin family. PMID:25389295

  17. Study on Na layer response to geomagnetic activities based on Odin/OSIRIS Na density data

    NASA Astrophysics Data System (ADS)

    Tsuda, Takuo; Nakamura, Takuji; Hedin, Jonas; Gumbel, Jorg; Hosokawa, Keisuke; Ejiri, Mitsumu K.; Nishiyama, Takanori; Takahashi, Toru

    2016-07-01

    The Na layer is normally distributed from 80 to 110 km, and the height range is corresponding to the ionospheric D and E region. In the polar region, the energetic particles precipitating from the magnetosphere can often penetrate into the E region and even into the D region. Thus, the influence of the energetic particles to the Na layer is one of interests in the aspect of the atmospheric composition change accompanied with the auroral activity. There are several previous studies in this issue. For example, recently, we have reported an initial result on a clear relationship between the electron density increase (due to the energetic particles) and the Na density decrease from observational data sets obtained by Na lidar, EISCAT VHF radar, and optical instruments at Tromsoe, Norway on 24-25 January 2012. However, all of the previous studies had been carried out based on case studies by ground-based lidar observations. In this study, we have performed, for the first time, statistical analysis using Na density data from 2004 to 2009 obtained with the Optical Spectrograph and InfraRed Imager System (OSIRIS) onboard Odin satellite. In the presentation, we will show relationship between the Na density and geomagnetic activities, and its latitudinal variation. Based on these results, the Na layer response to the energetic particles will be discussed.

  18. Na+ inhibits the epithelial Na+ channel by binding to a site in an extracellular acidic cleft.

    PubMed

    Kashlan, Ossama B; Blobner, Brandon M; Zuzek, Zachary; Tolino, Michael; Kleyman, Thomas R

    2015-01-01

    The epithelial Na(+) channel (ENaC) has a key role in the regulation of extracellular fluid volume and blood pressure. ENaC belongs to a family of ion channels that sense the external environment. These channels have large extracellular regions that are thought to interact with environmental cues, such as Na(+), Cl(-), protons, proteases, and shear stress, which modulate gating behavior. We sought to determine the molecular mechanism by which ENaC senses high external Na(+) concentrations, resulting in an inhibition of channel activity. Both our structural model of an ENaC α subunit and the resolved structure of an acid-sensing ion channel (ASIC1) have conserved acidic pockets in the periphery of the extracellular region of the channel. We hypothesized that these acidic pockets host inhibitory allosteric Na(+) binding sites. Through site-directed mutagenesis targeting the acidic pocket, we modified the inhibitory response to external Na(+). Mutations at selected sites altered the cation inhibitory preference to favor Li(+) or K(+) rather than Na(+). Channel activity was reduced in response to restraining movement within this region by cross-linking structures across the acidic pocket. Our results suggest that residues within the acidic pocket form an allosteric effector binding site for Na(+). Our study supports the hypothesis that an acidic cleft is a key ligand binding locus for ENaC and perhaps other members of the ENaC/degenerin family. PMID:25389295

  19. Role of the Na(+)-translocating NADH:quinone oxidoreductase in voltage generation and Na(+) extrusion in Vibrio cholerae.

    PubMed

    Vorburger, Thomas; Nedielkov, Ruslan; Brosig, Alexander; Bok, Eva; Schunke, Emina; Steffen, Wojtek; Mayer, Sonja; Götz, Friedrich; Möller, Heiko M; Steuber, Julia

    2016-04-01

    For Vibrio cholerae, the coordinated import and export of Na(+) is crucial for adaptation to habitats with different osmolarities. We investigated the Na(+)-extruding branch of the sodium cycle in this human pathogen by in vivo (23)Na-NMR spectroscopy. The Na(+) extrusion activity of cells was monitored after adding glucose which stimulated respiration via the Na(+)-translocating NADH:quinone oxidoreductase (Na(+)-NQR). In a V. cholerae deletion mutant devoid of the Na(+)-NQR encoding genes (nqrA-F), rates of respiratory Na(+) extrusion were decreased by a factor of four, but the cytoplasmic Na(+) concentration was essentially unchanged. Furthermore, the mutant was impaired in formation of transmembrane voltage (ΔΨ, inside negative) and did not grow under hypoosmotic conditions at pH8.2 or above. This growth defect could be complemented by transformation with the plasmid encoded nqr operon. In an alkaline environment, Na(+)/H(+) antiporters acidify the cytoplasm at the expense of the transmembrane voltage. It is proposed that, at alkaline pH and limiting Na(+) concentrations, the Na(+)-NQR is crucial for generation of a transmembrane voltage to drive the import of H(+) by electrogenic Na(+)/H(+) antiporters. Our study provides the basis to understand the role of the Na(+)-NQR in pathogenicity of V. cholerae and other pathogens relying on this primary Na(+) pump for respiration. PMID:26721205

  20. High dense structure boosts stability of antiferroelectric phase of NaNbO3 polycrystalline ceramics

    NASA Astrophysics Data System (ADS)

    Chao, Lumen; Hou, Yudong; Zheng, Mupeng; Zhu, Mankang

    2016-05-01

    For NaNbO3, its intrinsic phase transition sequence is still controversial in literature. In this paper, high-densified NaNbO3 ceramics derived from mechanochemical nanostructures presented a stabilized antiferroelectric characteristic. In addition to the Tc of 360 °C, another diffuse dielectric anomaly appeared around 100 °C, which did not vanish after O2 annealing treatment. The fine structure analysis indicated that this dielectric anomaly belongs to first order phase transition from P phase to Q phase. Moreover, even exerting the strong electric field close to breakdown value, the normal ferroelectric loops cannot be induced, proving the large free energy difference between these two phases.

  1. Electrochemistry of selenium in a basic AlCl{sub 3}-NaCl melt

    SciTech Connect

    Matsunaga, M.; Morimitsu, M.; Hosokawa, K.

    1995-09-01

    Sodium/molten-salt secondary batteries composed of a liquid sodium and chloroaluminate melt have been widely studied for electric vehicle and load-leveling applications. The authors have been interested in developing new cathode materials to be used in this type of battery. The electrochemical reactions of selenium species in a basic AlCl{sub 3}-NaCl melt has been studied by measuring EMF of an Na/SeCl{sub 4} cell. The reaction mechanism between elemental and tetravalent selenium consists of at least four electrochemical steps, including intermediates such as Se{sup 2+}, Se{sub 2}{sup 2+}, and Se{sub 8}{sup 2+}. The reaction sequence from Se{sup 4+} to Se{sub 8}{sup 2+} is discussed. The formal potential for each reaction is also determined.

  2. Estimating evolution of temporal sequence changes: a practical approach to inferring ancestral developmental sequences and sequence heterochrony.

    PubMed

    Harrison, Luke B; Larsson, Hans C E

    2008-06-01

    Developmental biology often yields data in a temporal context. Temporal data in phylogenetic systematics has important uses in the field of evolutionary developmental biology and, in general, comparative biology. The evolution of temporal sequences, specifically developmental sequences, has proven difficult to examine due to the highly variable temporal progression of development. Issues concerning the analysis of temporal sequences and problems with current methods of analysis are discussed. We present here an algorithm to infer ancestral temporal sequences, quantify sequence heterochronies, and estimate pseudoreplicate consensus support for sequence changes using Parsimov-based genetic inference [PGi]. Real temporal developmental sequence data sets are used to compare PGi with currently used approaches, and PGi is shown to be the most efficient, accurate, and practical method to examine biological data and infer ancestral states on a phylogeny. The method is also expandable to address further issues in developmental evolution, namely modularity. PMID:18570033

  3. Na+ Regulation in the Malaria Parasite Plasmodiumfalciparum Involves the Cation ATPase PfATP4 and Is a Target of the Spiroindolone Antimalarials

    PubMed Central

    Spillman, Natalie J.; Allen, Richard J.W.; McNamara, Case W.; Yeung, Bryan K.S.; Winzeler, Elizabeth A.; Diagana, Thierry T.; Kirk, Kiaran

    2013-01-01

    Summary The malaria parasite Plasmodium falciparum establishes in the host erythrocyte plasma membrane new permeability pathways that mediate nutrient uptake into the infected cell. These pathways simultaneously allow Na+ influx, causing [Na+] in the infected erythrocyte cytosol to increase to high levels. The intraerythrocytic parasite itself maintains a low cytosolic [Na+] via unknown mechanisms. Here we present evidence that the intraerythrocytic parasite actively extrudes Na+ against an inward gradient via PfATP4, a parasite plasma membrane protein with sequence similarities to Na+-ATPases of lower eukaryotes. Mutations in PfATP4 confer resistance to a potent class of antimalarials, the spiroindolones. Consistent with this, the spiroindolones cause a profound disruption in parasite Na+ homeostasis, which is attenuated in parasites bearing resistance-conferring mutations in PfATP4. The mutant parasites also show some impairment of Na+ regulation. Taken together, our results are consistent with PfATP4 being a Na+ efflux ATPase and a target of the spiroindolones. PMID:23414762

  4. Mechanisms contributing to the cardiac inotropic effect of Na pump inhibition and reduction of extracellular Na

    PubMed Central

    1987-01-01

    Reduction of the transsarcolemmal [Na] gradient in rabbit cardiac muscle leads to an increase in the force of contraction. This has frequently been attributed to alteration of Ca movements via the sarcolemmal Na/Ca exchange system. However, the specific mechanisms that mediate the increased force at individual contractions have not been clearly established. In the present study, the [Na] gradient was decreased by reduction of extracellular [Na] or inhibition of the Na pump by either the cardioactive steroid acetylstrophanthidin or by reduction of extracellular [K]. Contractile performance and changes in extracellular Ca (sensed by double-barreled Ca-selective microelectrodes) were studied in order to elucidate the underlying basis for the increase in force. In the presence of agents that inhibit sarcoplasmic reticulum (SR) function (10 mM caffeine, 100-500 nM ryanodine), reduction of the [Na] gradient produced increases in contractile force similar to that observed in the absence of caffeine or ryanodine. It is concluded that an intact, functioning SR is not required for the inotropic effect of [Na] gradient reduction (at least in rabbit ventricle). However, this does not exclude a possible contribution of enhanced SR Ca release in the inotropic response to [Na] gradient reduction in the absence of caffeine or ryanodine. Acetylstrophanthidin (3-5 microM) usually leads to an increase in the magnitude of extracellular Ca depletions associated with individual contractions. However, acetylstrophanthidin can also increase extracellular Ca accumulation during the contraction, especially at potentiated contractions. This extracellular Ca accumulation can be suppressed by ryanodine and it is suggested that this apparent enhancement of Ca efflux is secondary to an enhanced release of Ca from the SR. Under conditions where Ca efflux during contractions is minimized (after a rest interval in the presence of ryanodine), acetylstrophanthidin increased both the rate and the

  5. Nucleotide Sequence-Based Multitarget Identification

    PubMed Central

    Vinayagamoorthy, T.; Mulatz, Kirk; Hodkinson, Roger

    2003-01-01

    MULTIGEN technology (T. Vinayagamoorthy, U.S. patent 6,197,510, March 2001) is a modification of conventional sequencing technology that generates a single electropherogram consisting of short nucleotide sequences from a mixture of known DNA targets. The target sequences may be present on the same or different nucleic acid molecules. For example, when two DNA targets are sequenced, the first and second sequencing primers are annealed to their respective target sequences, and then a polymerase causes chain extension by the addition of new deoxyribose nucleotides. Since the electrophoretic separation depends on the relative molecular weights of the truncated molecules, the molecular weight of the second sequencing primer was specifically designed to be higher than the combined molecular weight of the first sequencing primer plus the molecular weight of the largest truncated molecule generated from the first target sequence. Thus, the series of truncated molecules produced by the second sequencing primer will have higher molecular weights than those produced by the first sequencing primer. Hence, the truncated molecules produced by these two sequencing primers can be effectively separated in a single lane by standard gel electrophoresis in a single electropherogram without any overlapping of the nucleotide sequences. By using sequencing primers with progressively higher molecular weights, multiple short DNA sequences from a variety of targets can be determined simultaneously. We describe here the basic concept of MULTIGEN technology and three applications: detection of sexually transmitted pathogens (Neisseria gonorrhoeae, Chlamydia trachomatis, and Ureaplasma urealyticum), detection of contaminants in meat samples (coliforms, fecal coliforms, and Escherichia coli O157:H7), and detection of single-nucleotide polymorphisms in the human N-acetyltransferase (NAT1) gene (S. Fronhoffs et al., Carcinogenesis 22:1405-1412, 2001). PMID:12843076

  6. Screening a novel Na+/H+ antiporter gene from a metagenomic library of halophiles colonizing in the Dagong Ancient Brine Well in China.

    PubMed

    Xiang, Wenliang; Zhang, Jie; Li, Lin; Liang, Huazhong; Luo, Hai; Zhao, Jian; Yang, Zhirong; Sun, Qun

    2010-05-01

    Metagenomic DNA libraries constructed from the Dagong Ancient Brine Well were screened for genes with Na(+)/H(+) antiporter activity on the antiporter-deficient Escherichia coli KNabc strain. One clone with a stable Na(+)-resistant phenotype was obtained and its Na(+)/H(+) antiporter gene was sequenced and designated as m-nha. The deduced amino acid sequence of M-Nha protein consists of 523 residues with a calculated molecular weight of 58 147 Da and a pI of 5.50, which is homologous with NhaH from Halobacillus dabanensis D-8(T) (92%) and Halobacillus aidingensis AD-6(T) (86%), and with Nhe2 from Bacillus sp. NRRL B-14911 (64%). It had a hydropathy profile with 10 putative transmembrane domains and a long carboxyl terminal hydrophilic tail of 140 amino acid residues, similar to Nhap from Synechocystis sp. and Aphanothece halophytica, as well as NhaG from Bacillus subtilis. The m-nha gene in the antiporter-negative mutant E. coli KNabc conferred resistance to Na(+) and the ability to grow under alkaline conditions. The difference in amino acid sequence and the putative secondary structure suggested that the m-nha isolated from the Dagong Ancient Brine Well in this study was a novel Na(+)/H(+) antiporter gene.

  7. Complete genome sequence of Haloterrigena turkmenica type strain (4kT)

    SciTech Connect

    Saunders, Elizabeth H; Tindall, Brian; Fahnrich, Regine; Lapidus, Alla L.; Copeland, A; Glavina Del Rio, Tijana; Lucas, Susan; Chen, Feng; Tice, Hope; Cheng, Jan-Fang; Han, Cliff; Detter, J C; Bruce, David; Goodwin, Lynne A.; Chain, Patrick S. G.; Pitluck, Sam; Pati, Amrita; Ivanova, N; Mavromatis, K; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Brettin, Tom; Rohde, Manfred; Goker, Markus; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Klenk, Hans-Peter; Kyrpides, Nikos C

    2010-01-01

    Haloterrigena turkmenica (Zvyagintseva and Tarasov 1987) Ventosa et al. 1999, comb. nov. is the type species of the genus Haloterrigena in the euryarchaeal family Halobacteriaceae. It is of phylogenetic interest because of the yet unclear position of the genera Haloterrigena and Natrinema within the Halobacteriaceae, which created some taxonomic problems historically. H. turkmenica, was isolated from sulfate saline soil in Turkmenistan, is a relatively fast growing, chemoorganotrophic, carotenoid-containing, extreme halophile, requiring at least 2 M NaCl for growth. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the genus Haloterrigena, but the eighth genome sequence from a member of the family Halobacteriaceae. The 5,440,782 bp genome (including six plasmids) with its 5,287 protein-coding and 63 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  8. Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing.

    PubMed

    Reumers, Joke; De Rijk, Peter; Zhao, Hui; Liekens, Anthony; Smeets, Dominiek; Cleary, John; Van Loo, Peter; Van Den Bossche, Maarten; Catthoor, Kirsten; Sabbe, Bernard; Despierre, Evelyn; Vergote, Ignace; Hilbush, Brian; Lambrechts, Diether; Del-Favero, Jurgen

    2012-01-01

    Distinguishing single-nucleotide variants (SNVs) from errors in whole-genome sequences remains challenging. Here we describe a set of filters, together with a freely accessible software tool, that selectively reduce error rates and thereby facilitate variant detection in data from two short-read sequencing technologies, Complete Genomics and Illumina. By sequencing the nearly identical genomes from monozygotic twins and considering shared SNVs as 'true variants' and discordant SNVs as 'errors', we optimized thresholds for 12 individual filters and assessed which of the 1,048 filter combinations were effective in terms of sensitivity and specificity. Cumulative application of all effective filters reduced the error rate by 290-fold, facilitating the identification of genetic differences between monozygotic twins. We also applied an adapted, less stringent set of filters to reliably identify somatic mutations in a highly rearranged tumor and to identify variants in the NA19240 HapMap genome relative to a reference set of SNVs. PMID:22178994

  9. Sequence of a probable potassium channel component encoded at shaker locus of drosophila

    SciTech Connect

    Tempel, B.L.; Papazian, D.M.; Schwarz, T.L.; Jan, Y.N.; Jan, L.Y.

    1987-08-24

    Potassium currents are crucial for the repolarization of electrically excitable membranes, a role that makes potassium channels a target for physiological modifications that alter synaptic efficacy. The Shaker locus of Drosophila is thought to encode a K/sup +/ channel. The sequence of two complementary DNA clones from the Shaker locus is reported here. The sequence predicts an integral membrane protein of 70,200 daltons containing seven potential membrane-spanning sequences. In addition, the predicted protein is homologous to the vertebrate sodium channel in a region previously proposed to be involved in the voltage-dependent activation of the Na/sup +/ channel. These results support the hypothesis that Shaker encodes a structural component of a voltage-dependent K/sup +/ channel and suggest a conserved mechanism for voltage activation.

  10. Structure of the fully modified left-handed cyclohexene nucleic acid sequence GTGTACAC.

    PubMed

    Robeyns, Koen; Herdewijn, Piet; Van Meervelt, Luc

    2008-02-13

    CeNA oligonucleotides consist of a phosphorylated backbone where the deoxyribose sugars are replaced by cyclohexene moieties. The X-ray structure determination and analysis of a fully modified octamer sequence GTGTACAC, which is the first crystal structure of a carbocyclic-based nucleic acid, is presented. This particular sequence was built with left-handed building blocks and crystallizes as a left-handed double helix. The helix can be characterized as belonging to the (mirrored) A-type family. Crystallographic data were processed up to 1.53 A, and the octamer sequence crystallizes in the space group R32. The sugar puckering is found to adopt the 3H2 half-chair conformation which mimics the C3'-endo conformation of the ribose sugar. The double helices stack on top of each other to form continuous helices, and static disorder is observed due to this end-to-end stacking.

  11. Phylogenetic relationships of North American phoxinins (Actinopterygii: Cypriniformes: Leuciscidae) as inferred from S7 nuclear DNA sequences.

    PubMed

    Bufalino, Angelo P; Mayden, Richard L

    2010-04-01

    The phylogenetic systematics of North American (NA) phoxinins, and family Leuciscidae (formerly Cyprinidae, in part) in general, have had a very dynamic history marked by uncertainty regarding the validity of many taxonomic designations. Recent molecular studies, based on mitochondrial DNA sequences, of NA phoxinins have provided the first comprehensive hypotheses for the group and suggest that they are comprised of three major lineages: creek chub-plagopterin (CC-P), western, and open posterior myodome clades. A number of phylogenetic evaluations, using both mitochondrial and nuclear DNA sequences, of the formerly recognized family Cyprinidae (=Cyprinoidea) have failed to support the traditional subfamily designations. This study, based on sequences from the first intron of the nuclear gene S7, supports many of the findings of the earlier molecular studies of NA phoxinins, but also suggests that European Leuciscidae evolved within the NA phoxinin lineage and are most likely descended from the common ancestor of the CC-P clade. As in some other recent phylogenetic studies of the Cyprinoidea, analyses of this study fail to support the broader subfamily designations within the formerly recognized family Cyprinidae.

  12. Magnetic and thermoelectric properties of layered Li{sub x}Na{sub y}CoO{sub 2}

    SciTech Connect

    Bos, J.W.G. Hertz, J.T.; Morosan, E.; Cava, R.J.

    2007-11-15

    The magnetic, thermoelectric, and structural properties of Li{sub x}Na{sub y}CoO{sub 2}, prepared by intercalation and deintercalation chemistry from the thermodynamically stable phase Li{sub 0.41}Na{sub 0.31}CoO{sub 2}, which has an alternating Li/Na sequence along the c-axis, are reported. For the high Li-Na content phases Li{sub 0.41}Na{sub 0.31}CoO{sub 2} and Li{sub 0.40}Na{sub 0.43}CoO{sub 2}, a sudden increase in susceptibility is seen below 50 K, whereas for Li{sub 0.21}Na{sub 0.14}CoO{sub 2} an antiferromagnetic-like transition is seen at 10 K, in spite of a change from dominantly antiferromagnetic to dominantly ferromagnetic interactions with decreasing alkali content. The Curie constant decreases linearly with decreasing alkali content, at the same time the temperature-independent contribution to the susceptibility increases, indicating that as the Co becomes more oxidized the electronic states become more delocalized. Consistent with this observation, the low alkali containing phases have metallic-like resistivities. The 300 K thermopowers fall between 30 {mu}V/K (x+y=0.31) and 150 {mu}V/K (x+y=0.83). - Graphical abstract: The ordered layered arrangement of Li{sup +} and Na{sup +} ions between CoO{sub 2} sheets.

  13. Cloning of a Na+-driven Cl/HCO3 exchanger from squid giant fiber lobe.

    PubMed

    Virkki, Leila V; Choi, Inyeong; Davis, Bruce A; Boron, Walter F

    2003-10-01

    We extracted RNA from the giant fiber lobe (GFL) of the squid Loligo pealei and performed PCR with degenerate primers that were based on highly conserved regions of Na+-coupled HCO3- transporters. This approach yielded a novel, 290-bp sequence related to the bicarbonate transporter superfamily. Using an L. opalescens library, we extended the initial fragment in the 3' and 5' directions by a combination of library screening and PCR and obtained the full-length clone (1,198 amino acids) by PCR from L. pealei GFL. The amino acid sequence is 46% identical to mammalian electrogenic and electroneutral Na-HCO3 cotransporters and 33% identical to the anion exchanger AE1. Northern blot analysis showed strong signals in L. pealei GFL, optic lobe, and heart and weaker signals in gill and stellate ganglion. To assess function, we injected in vitro-transcribed cRNA into Xenopus oocytes and subsequently used microelectrodes to monitor intracellular pH (pHi) and membrane voltage (Vm). Superfusing these oocytes with 5% CO2-33 mM HCO3- caused a CO2-induced fall in pHi, followed by a slow recovery. The absence of a rapid HCO3- -induced hyperpolarization indicates that the pHi recovery mechanism is electroneutral. Ion substitutions showed that Na+ and Cl- are required on opposite sides of the membrane. Transport was blocked by 50 microM 4,4'-diisothiocyanostilbene-2,2'-disulfonic acid (DIDS). The characteristics of our novel clone fit those of a Na+-driven Cl/HCO3 exchanger (NDCBE).

  14. Dispersed repetitive DNA sequence of Mucor racemosus.

    PubMed Central

    Dewar, R; Katayama, C; Sypherd, P S; Cihlar, R L

    1985-01-01

    A dispersed repetitive DNA sequence has been identified within the genome of the fungus Mucor racemosus. Recombinant phage clones, as well as a plasmid harboring the sequence, have been isolated. Examination of cloned fragments comprising part of the repetitive sequence has led to a partial characterization of the element. The sequence has been detected in other Mucor species, and although the apparent number and chromosomal position of the repetitive sequence vary from strain to strain, it is clear that at least portions of the element have been conserved. Images PMID:3980442

  15. Chip-based sequencing nucleic acids

    SciTech Connect

    Beer, Neil Reginald

    2014-08-26

    A system for fast DNA sequencing by amplification of genetic material within microreactors, denaturing, demulsifying, and then sequencing the material, while retaining it in a PCR/sequencing zone by a magnetic field. One embodiment includes sequencing nucleic acids on a microchip that includes a microchannel flow channel in the microchip. The nucleic acids are isolated and hybridized to magnetic nanoparticles or to magnetic polystyrene-coated beads. Microreactor droplets are formed in the microchannel flow channel. The microreactor droplets containing the nucleic acids and the magnetic nanoparticles are retained in a magnetic trap in the microchannel flow channel and sequenced.

  16. Differences in shoot Na+ accumulation between two tomato species are due to differences in ion affinity of HKT1;2.

    PubMed

    Almeida, Pedro; de Boer, Gert-Jan; de Boer, Albertus H

    2014-03-15

    HKT1 has been shown to be essential in Na(+) homeostasis in plants. In this paper, we report the analysis of Na(+) accumulation in different plant organs of two tomato species with contrasting salt tolerances: Solanum lycopersicum and Solanum pennellii. Furthermore, we relate these differences in Na(+) accumulation between the two species to the differences in HKT1;2 transport kinetics and HKT1;2 expression. S. lycopersicum showed "Na(+) excluder" behaviour, whereas S. pennellii showed "Na(+) includer" behaviour. SlHKT1;2 expression, in contrast to SpHKT1;2 expression showed a significant effect of NaCl treatment, especially stems had a high increase in SlHKT1;2 expression. SlHKT1;2 promoter-GUS reporter gene analysis showed that SlHKT1;2 is expressed in the vasculature surrounding the roots and shoots of transformed Arabidopsis plants. In this paper, we present HKT1;2 protein sequences of both tomato species and provide evidence that both SlHKT1;2 and SpHKT1;2 are Na(+) transporters. Our kinetic studies showed that SpHKT1;2, in comparison with SlHKT1;2, had a lower affinity for Na(+). This low affinity of SpHKT1;2 correlated with higher xylem Na(+) and higher accumulation of Na(+) in stems and leaves of S. pennellii. Our findings demonstrate the importance of the understanding of transport characteristics of HKT1;2 transporters to improve the understanding of Na(+) homeostasis in plants.

  17. Overexpression of a novel soybean gene modulating Na+ and K+ transport enhances salt tolerance in transgenic tobacco plants.

    PubMed

    Chen, Huatao; He, Hui; Yu, Deyue

    2011-01-01

    Salt is an important factor affecting the growth and development of soybean in saline soil. In this study, a novel soybean gene encoding a transporter (GmHKT1) was identified and its function analyzed using transgenic plants. GmHKT1 encoded a protein of 419 amino acids, with a potential molecular mass of 47.06 kDa and a predicted pI value of 8.59. Comparison of the genomic and cDNA sequences of GmHKT1 identified no intron. The deduced amino acid sequence of GmHKT1 showed 38-49% identity with other plant HKT-like sequences. RT-PCR analysis showed that the expression of GmHKT1 was upregulated by salt stress (150 mM NaCl) in roots and leaves but not in stems. Overexpression of GmHKT1 significantly enhanced the tolerance of transgenic tobacco plants to salt stress, compared with non-transgenic plants. To investigate the role of GmHKT1 in K(+) and Na(+) transport, we compared K(+) and Na(+) accumulation in roots and shoots of wild-type and transgenic tobacco plants. The results suggested that GmHKT1 is a transporter that affected K(+) and Na(+) transport in roots and shoots, and regulated Na(+) /K(+) homeostasis in these organs. Our findings suggest that GmHKT1 plays an important role in response to salt stress and would be useful in engineering crop plants for enhanced tolerance to salt stress.

  18. Local structure analysis of NaNbO3 and AgNbO3 modified by Li substitution

    NASA Astrophysics Data System (ADS)

    Yoneda, Yasuhiro; Aoyagi, Rintaro; Fu, Desheng

    2016-10-01

    We analyzed the local structures of NaNbO3 and AgNbO3 by combining the X-ray absorption fine structure (XAFS) and atomic pair-distribution function (PDF) techniques. NaNbO3 is known to be an antiferroelectric material at room temperature. It also undergoes a diffuse phase transition, in which orthorhombic and rhombohedral phases coexist over a wide temperature range. We found a disordered feature in the nearest-neighbor bond distance corresponding to the Nb-O bonds. The disordered bond distribution disappeared when Li was substituted for Na. A similar disorder feature was found in AgNbO3. The disordered site can be specified by combining XAFS and PDF techniques. The sequences of disordered and complex phase transitions are attributable to the competition between the tolerance of the AO12 cage and the tilt of NbO6 octahedra.

  19. Laser trapping of {sup 21}Na atoms

    SciTech Connect

    Lu, Zheng-Tian

    1994-09-01

    This thesis describes an experiment in which about four thousand radioactive {sup 21}Na (t{sub l/2} = 22 sec) atoms were trapped in a magneto-optical trap with laser beams. Trapped {sup 21}Na atoms can be used as a beta source in a precision measurement of the beta-asymmetry parameter of the decay of {sup 21}Na {yields} {sup 21}Ne + {Beta}{sup +} + v{sub e}, which is a promising way to search for an anomalous right-handed current coupling in charged weak interactions. Although the number o trapped atoms that we have achieved is still about two orders of magnitude lower than what is needed to conduct a measurement of the beta-asymmetry parameter at 1% of precision level, the result of this experiment proved the feasibility of trapping short-lived radioactive atoms. In this experiment, {sup 21}Na atoms were produced by bombarding {sup 24}Mg with protons of 25 MeV at the 88 in. Cyclotron of Lawrence Berkeley Laboratory. A few recently developed techniques of laser manipulation of neutral atoms were applied in this experiment. The {sup 21}Na atoms emerging from a heated oven were first transversely cooled. As a result, the on-axis atomic beam intensity was increased by a factor of 16. The atoms in the beam were then slowed down from thermal speed by applying Zeeman-tuned slowing technique, and subsequently loaded into a magneto-optical trap at the end of the slowing path. The last two chapters of this thesis present two studies on the magneto-optical trap of sodium atoms. In particular, the mechanisms of magneto-optical traps at various laser frequencies and the collisional loss mechanisms of these traps were examined.

  20. Role of phylogenetically conserved amino acids in folding of Na,K-ATPase.

    PubMed

    Jørgensen, J R; Pedersen, P A

    2001-06-19

    This paper focuses on the amino acid sequence 708-TGDGVNDSPALKK in pig kidney Na,K-ATPase as one of the best conserved among P-type ATPases. In Ca-ATPase this sequence forms a strand-loop-helix structure as part of a Rossman fold next to the phosphorylation site. Substitution of polar residues in the investigated sequence interfered with high-level accumulation of mutant protein. Mutant alpha1-subunit protein only accumulated in membranes from yeast cells grown at 15 degrees C whereas wild-type protein accumulated at both 15 and 35 degrees C. A systematic screen for the molecular mechanism behind lack of accumulation of mutant protein at 35 degrees C showed that transcription and translation were unaffected by the mutations. To demonstrate in vivo protein folding problems, an unfolded protein response reporter system was constructed in yeast. In this strain, only expression of mutant Na,K-ATPase alpha1-subunit caused induction of the unfolded protein response at 35 degrees C, indicating folding problems in the ER. Lowering the expression temperature to 15 degrees C prevented induction of the unfolded protein response after mutant protein expression, indicating correct folding at this temperature. At the permissive temperature mutant proteins were able to escape the endoplasmic reticulum quality control, reach the plasma membrane, and bind ouabain with high affinity. Since mutants in the 708-TGDGVNDSPALKK segment had a thermo inactivation profile identical to that of wild type, they were classified as temperature-sensitive synthesis mutants. The results indicate that this segment contributes side chains of importance for overall folding and maturation of Na,K-ATPase and all other P-type ATPases.