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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. Atomic data for opacity calculations. XI - The carbon isoelectronic sequence

    NASA Technical Reports Server (NTRS)

    Luo, D.; Pradhan, A. K.

    1989-01-01

    Close-coupling calculations are carried out for radiative processes in neutral carbon and a number of carbon-like ions; energy levels, oscillator strengths, and photoionization cross sections have been computed for all bound states of the type 2 s(j)2p(k)nl with n not above 10 and 1 not above 3. The R-matrix method is employed to solve the coupled equations with a ten-state eigenfunction expansion for the parent ion C II and an eight-state expansion for the other boron-like target ions. A number of selected results for oscillator strengths are presented and compared with earlier data, as well as for photoionization cross sections with autoionizing resonance structures. Isoelectronic trends are discussed. The present results for the oscillator strengths of C I and N II are found to differ significantly from some earlier theoretical works for a number of transitions. However, the present C I f values are in excellent agreement with recent calculations and experimental results.

  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. 2s -> np Autoionizing Resonances of the Neon Isoelectronic Sequence using RRPA and RMQDT

    NASA Astrophysics Data System (ADS)

    Madugula, Nrisimha Murty; Rundhe, Milind V.; Aravind, Gopalan; Deshmukh, Pranawa C.; Manson, Steven T.

    2012-06-01

    Extensive theoretical and experimental studies of the photoionization of various atoms and ions have been carried out over long period of time [1, 2] owing both to the fundamental importance of the process and to the many applications, e.g., astrophysical and atmospheric modeling, plasma dynamics, etc. In the present work, we report our studies of the 2s -> np autoionizing resonances in the Ne isoelectronic sequence, of significance due to the cosmic abundance of these systems [2-4]. In particular, Ne, Na^+, Mg^2+, Al^3+ and Sc^11+ have been studied. The study has been performed within the framework of the relativistic random-phase approximation (RRPA) [5] and relativistic multichannel quantum defect theory (RMQDT) [6]. The resonances have been characterized in terms of position, width and shape, i.e., Fano profiles [7, 8], and the evolution of the parameters of the resonances along the sequence has been investigated.[4pt] [1] A. Neogi et al, Phys. Rev. A 67, 042707 (2003). [2] H. S. Chakraborty et al, Phys. Rev. Lett. 83, 2151 (1999). [3] H. S. Chakraborty et al, Ap. J. 595, 1307 (2003). [4] G. Nasreen Haque, Ph.D. thesis (unpublished), Georgia State University, Atlanta, USA (1991). [5] W.R. Johnson et al, Phys. Scr. 21, 409 (1980). [6] C. M. Lee and W.R. Johnson, Phys. Rev. A 22, 979 (1980). [7] U. Fano and J. W. Cooper, Phys. Rev. A 40, 441 (1968). [8] W.R. Johnson, et al, Phys. Rev. A 22, 989 (1980).

  8. Photoionization dominated by doubly excited resonances for Be and its isoelectronic sequence

    SciTech Connect

    Chang, T.N.; Zhu, L.

    1993-05-01

    We present the photoionization cross sections the ground and a few selected bound excited states of Be using a B-spline based configuration-interaction procedure for continuum (CIC). The resonant structures dominated by the doubly excited autoionization series will be examined in detail. Our calculation has shown that the strong overlap between the 2p(n+1)s and 2pnd {sup 1}P resonances seen in the ground state photoionization spectrum is completely removed in the spectrum originated from the bound excited state. Our calculated resonant widths vary smoothly as functions of the effective quantum number v and approach approximately an {nu}{sup 3}-dependence. We will also present the variation of the doubly excited resonance structures as Z increases along the Be-isoelectronic sequence.

  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. Extensive computation of allowed and forbidden transition probabilities in the potassium isoelectronic sequence

    NASA Astrophysics Data System (ADS)

    Dixit, Gopal; Deshmukh, Pranawa C.; Manson, Steven T.; Majumder, Sonjoy

    2007-06-01

    Our primary aim in this work is to present both allowed and forbidden transition amplitudes and corresponding wavelengths and oscillator strengths for a few ions in the 19-electron potassium isoelectronic sequence. All of these ions have the configuration [Ar] 3^2D3/2 as their ground state, except in the case of K and Ca^+, where it is [Ar] 4^2S1/2.This difference in ground state configuration arises due to strong contributions of correlation effects in the energy levels of these systems [1]. Allowed and forbidden transitions in these systems are of great importance in astrophysics [2] and in laboratory plasma research [3]. We apply in the present work the relativistic coupled-cluster (RCC) theory [4] to evaluate the energy levels and wave functions of these systems and study amplitudes for electric and magnetic dipole transition amplitudes and also the electric quadrupole transition amplitudes. The contributions of various electron correlation effects to the transition amplitudes are estimated in some detail using the RCC theory. [1] Gopal Dixit et al., Astrophys. J (submitted); arXiv.org: physics/0702066. [2] C. R. Cowley and G. M. Wahlgern, Astronomy & Astrophysics, 447, 681 (2002). [3] J. E. Vernazza, E. M. Reeves, Astrophys. J. Suppl. 37, 485 (1978) [4] I. Lindgren, Physics Scripta, 36, 591 (1987).

  11. 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.

  12. [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

  13. Hylleraas-configuration-interaction nonrelativistic energies for the 1S ground states of the beryllium isoelectronic sequence

    NASA Astrophysics Data System (ADS)

    Sims, James S.; Hagstrom, Stanley A.

    2014-06-01

    In a previous work, Sims and Hagstrom ["Hylleraas-configuration-interaction study of the 1 1S ground state of neutral beryllium," Phys. Rev. A 83, 032518 (2011)] reported Hylleraas-configuration-interaction (Hy-CI) method variational calculations for the 1S 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 1S isoelectronic sequence. The best nonrelativistic energies for Be, B+, and C++ 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.

  14. Ab initio estimations of the isotope shift for the first three elements of the K isoelectronic sequence

    NASA Astrophysics Data System (ADS)

    Roy, Sourav; Majumder, Sonjoy

    2015-07-01

    Isotope shifts (ISs) of D1(n s S1/22 →n p P1/22 ) and D2(n s S1/22 →n p P3/22 ) transitions for the first three elements of the K isoelectronic sequence are calculated with all-order correlated relativistic coupled-cluster theory. To get precise ab initio results, all the orbitals of the reference states have been optimized by a linear regression technique. Some of the important IS estimations reported here were not available in literature. Interesting features of odd-even staggering and magic neutron number effects are also observed in the case of volume shift calculations. Energy-level corrections for a few levels due to a change in the nuclear model from a point nucleus to a Fermi nucleus have been studied with interesting correlation features and compared with other theoretical results available in literature.

  15. 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.

  16. Proton collisional excitation in the lowest lying 3P terms of ions in the Be and Mg isoelectronic sequences

    NASA Technical Reports Server (NTRS)

    Landman, D. A.; Brown, T.

    1979-01-01

    Proton collisional excitation cross sections and rate constants are presented for transitions between the 3P(J) fine-structure levels of the lowest-lying sp configurations in a number of astrophysically important ions belonging to the Be and Mg isoelectronic sequences. The calculations were made by direct integration of the Schroedinger equation resulting from semiclassical Coulomb excitation theory. The cross sections and rate constants for the 3P(J) transitions in the lowest-lying P(2) configurations are expected to be similar to those for the corresponding sp configuration transitions, and this is illustrated for C III. For the high-temperature ion Ca XVII alpha particle excitation is shown to be unimportant for situations involving ordinary values of the He/H abundance ratio. A simple, but apparently accurate method for determining certain radial integrals for low-lying excited configurations is proposed.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. Short wavelength laser calculations for electron pumping in Be I and B I isoelectronic sequences (Z greater than or equal to 18 and less than or equal to 36)

    NASA Technical Reports Server (NTRS)

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

    1985-01-01

    There has been considerable interest in creating large laser gains in the X-ray region from atomic transitions in ne-like ions formed in high-temperature plasmas. Although the Ne-like ions habe received the most attention, it is also possible to produce population inversions in ions of other isoelectronic sequences. Accordingly, it is shown that certain levels of the 2s3p and 2s(2)3p configurations in the Be I and B I isoelectronic sequences can be inverted by collisional pumping relative to levels of the 2s3s and 2s(2)3s configurations. Level populations and gain coefficients were calculated for the most promising transitions, and opacities were calculated for 2s2p-2s3s and 2s(2)2p-2s(2)3s transitions.

  2. 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.

  3. 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.

  4. 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.

  5. 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)

  6. Isoelectronic Traps in Gallium Phosphide

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

    Isoelectronic substitutional dopants can result in strongly localized exciton traps within a host bandstructure such as gallium arsenide (GaAs) or gallium phosphide (GaP). These traps have received great attention for their role in the anomalous bandgap bowing of nitrogen or bismuth-doped GaAs, creating the dramatic bandgap tunability of these unusual dilute alloys. In the wider, indirect-bandgap host material GaP, these same isoelectronic dopants create bound states within the gap that can have very high radiative efficiency and a wealth of discrete spectral transitions illuminating the symmetry of the localized excitonic trap state. We will present a comparative study of nitrogen and bismuth isoelectronic traps in GaP. 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.

  7. Be I isoelectronic ions embedded in hot plasma.

    PubMed

    Saha, B; Fritzsche, S

    2006-03-01

    The influence of plasma screening on the 2s(2 1)S0-->2s2p(3)p(0)1 intercombination and the 2s(2 1)S0-->2s2p(1)p(0)1 allowed transitions is investigated theoretically for several ions along the isoelectronic sequence (C III, N IV, O V, Si XI, Fe XXIII, and Mo XXXIX). For the case of a weakly coupled hot plasma, multiconfiguration Dirac-Fock computations have been carried out for these ions by considering a (time averaged) Debye-Hückel potential for both the "electron-nucleus" and "electron-electron" interaction. The plasma screening is found to enlarge the 2s(2 1)S0-->2s2p(3)p(0)1 excitation energy uniformly along the Be I isoelectronic sequence, leading to an increasing blueshift of this intercombination line as the nuclear charge is increased. For the 2s(2 1)S0-->2s2p(1)p(0)1 resonance line, in contrast, the transition energy is either blueshifted or redshifted in dependence of the screening parameter and owing to a cancellation of the plasma screening on the electron-nucleus and electron-electron interaction. This interplay of the (external) plasma screening with the internal interactions in the berylliumlike ions leads, for instance, to a shift of the resonance transition from red to blue in going from O V to Si XI ions. Apart from the screening effects on the transition energies, we also investigate their influence on the oscillator strengths and emission rates along the Be I isoelectronic sequence. PMID:16605666

  8. F values for isoelectronic ions of carbon

    NASA Astrophysics Data System (ADS)

    Ganas, P. S.

    1981-10-01

    An analytic atomic independent particle model is used to generate wave functions for the valence and excited states of isoelectronic ions of carbon up to Z = 20. Using these wave functions in conjunction with the Born approximation and the Russell-Saunders LS-coupling scheme, f values are calculated for various transitions from the 2p2(3P0) ground state. The results are compared with those from other works.

  9. 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.

  10. 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. PMID:25059868

  11. 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

  12. Sequence of subunit c of the Na(+)-translocating F1F0 ATPase of Acetobacterium woodii: proposal for determinants of Na+ specificity as revealed by sequence comparisons.

    PubMed

    Rahlfs, S; Müller, V

    1997-03-10

    A 3.2 kb EcoRI fragment carrying genes for Na(+)-F1F0 ATPase was cloned from chromosomal DNA of Acetobacterium woodii. DNA sequence analysis revealed the presence of an open reading frame which was identified by data base searches and comparison with the experimentally derived N-terminal amino acid sequence to code for subunit c of Na(+)-F1F0 ATPase. A comparison of the primary sequences of the two well established Na(+)-translocating F1F0 ATPases from Acetobacterium woodii and Propionigenium modestum with H(+)-translocating enzymes indicates the length of the C-terminus as well as specific residues located in the cytoplasmic membrane to be important for Na+ transport. PMID:9119076

  13. 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…

  14. Diagnosing Te of NIF plasmas using the isoelectronic ratios of microdot tracer elements

    NASA Astrophysics Data System (ADS)

    Barrios, M. A.; Regan, S. P.; Fournier, K. B.; Schneider, M. B.; Liedahl, D. A.; Kemp, G. E.; Moody, J. D.; Brown, G. V.; Chen, H.; Landen, O.; Bradley, D.; Jones, O.; Epstein, R.; LLNL Collaboration; LLE Collaboration

    2014-10-01

    Experiments planned on NIF will diagnose the electron temperature (Te) of the hohlraum in the vicinity of the laser entrance hole (LEH) using x-ray spectroscopy. A microdot consisting of Ti and Cr will be coated on the surface of a CH implosion capsule and centered on the symmetry axis of the hohlraum. As the microdot is ablated it is ionized by the hohlraum plasma and flows into the LEH region. The experimental plan to use the isoelectronic line ratio technique to diagnose Te of the hohlraum plasma near the LEH will be presented. Exploratory experiments at NIF tested the Te sensitivity of the technique by recording time resolved K-shell emission of direct-drive spherical targets coated with a CrNiZn alloy. Application of the isoelectronic technique to the coronal plasma of these targets will be presented. This work was performed under the auspices of the U.S. Department of Energy by LLNL under Contract DE-AC52-07NA27344.

  15. Isoelectronic apparatus to probe the thermal Casimir force

    NASA Astrophysics Data System (ADS)

    Bimonte, Giuseppe

    2015-05-01

    Isoelectronic differential force measurements provide a unique opportunity to probe controversial features of the thermal Casimir effect that are still much debated in the current literature. Isolectronic setups offer two major advantages over conventional Casimir setups. On the one hand, they are immune from electrostatic forces caused by potential patches on the plates surfaces that plague present Casimir experiments, especially for separations in the micron range. On the other hand, they can strongly enhance the discrepancy between alternative theoretical models that have been proposed to estimate the thermal Casimir force for metallic and magnetic surfaces. Thanks to these two features, isoelectronic differential experiments should allow one to establish conclusively which among these models correctly describes the thermal Casimir force.

  16. Complete quantum control of exciton qubits bound to isoelectronic centres.

    PubMed

    Éthier-Majcher, G; St-Jean, P; Boso, G; Tosi, A; Klem, J F; Francoeur, S

    2014-01-01

    In recent years, impressive demonstrations related to quantum information processing have been realized. The scalability of quantum interactions between arbitrary qubits within an array remains however a significant hurdle to the practical realization of a quantum computer. Among the proposed ideas to achieve fully scalable quantum processing, the use of photons is appealing because they can mediate long-range quantum interactions and could serve as buses to build quantum networks. Quantum dots or nitrogen-vacancy centres in diamond can be coupled to light, but the former system lacks optical homogeneity while the latter suffers from a low dipole moment, rendering their large-scale interconnection challenging. Here, through the complete quantum control of exciton qubits, we demonstrate that nitrogen isoelectronic centres in GaAs combine both the uniformity and predictability of atomic defects and the dipole moment of semiconductor quantum dots. This establishes isoelectronic centres as a promising platform for quantum information processing. PMID:24875932

  17. Energy transfer among isoelectronic dopants in GaP

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

    Although GaP is an indirect-bandgap material, it can also be an efficient light-emitter at visible wavelengths when isoelectronic impurities mediate radiative recombination via states within the bandgap. Since these states also provide a medium for energy transfer via exciton hopping among localized isoelectronic trap sites, the carrier dynamics in doped GaP are strongly dependent on the distribution and density of impurity species. We present spectroscopic data demonstrating the role of energy transfer among isoelectronic states in GaP via temperature-dependent and time-resolved photoluminescence. 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.

  18. Sequence of subunit a of the Na(+)-translocating F1F0-ATPase of Acetobacterium woodii: proposal for residues involved in Na+ binding.

    PubMed

    Rahlfs, S; Müller, V

    1999-06-18

    Na+ transport through the F0 domain of Na(+)-F1F0-ATPases involves the combined action of subunits c and a but the residues involved in Na+ liganding in subunit a are unknown. As a first step towards the identification of these residues, we have cloned and sequenced the gene encoding subunit a of the Na(+)-F1F0-ATPase of Acetobacterium woodii. This is the second sequence available now for this subunit from Na(+)-F1F0-ATPases. A comparison of subunit a from Na(+)-F1F0-ATPases with those from H(+)-translocating enzymes unraveled structural similarity in a C-terminal segment including the ultimate and penultimate transmembrane helix. Seven residues are conserved in this region and, therefore, likely to be involved in Na+ liganding. PMID:10403370

  19. 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.

  20. Initialization of a hole spin bound to an isoelectronic center

    NASA Astrophysics Data System (ADS)

    St-Jean, Philippe; Ethier-Majcher, Gabriel; Francoeur, Sebastien

    2015-03-01

    Hole spins are promising candidates for solid-state qubits because they interact weakly with nuclear spins, leading to long relaxation and coherence times. In this work, we demonstrate the ability to optically initialize a single hole spin bound to an isoelectronic center, which is an atomic defect formed from a small number of isovalent impurities in a semiconductor host. Using time-resolved magneto-photoluminescence of a positive trion bound to a Te dyad in ZnSe, we measured the degree of polarization of the emission under various conditions of excitation and magnetic field. Under non-resonant excitation, the trion emission is partially polarized and becomes completely unpolarized under a longitudinal magnetic field. In contrast, resonant excitation of the heavy-hole valence band of the ZnSe host leads to highly polarized emission, implying that the hole has been initialized in a known spin state.

  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. Fisher-Shannon analysis of ionization processes and isoelectronic series

    SciTech Connect

    Sen, K. D.; Antolin, J.; Angulo, J. C.

    2007-09-15

    The Fisher-Shannon plane which embodies the Fisher information measure in conjunction with the Shannon entropy is tested in its ability to quantify and compare the informational behavior of the process of atomic ionization. We report the variation of such an information measure and its constituents for a comprehensive set of neutral atoms, and their isoelectronic series including the mononegative ions, using the numerical data generated on 320 atomic systems in position, momentum, and product spaces at the Hartree-Fock level. It is found that the Fisher-Shannon plane clearly reveals shell-filling patterns across the periodic table. Compared to position space, a significantly higher resolution is exhibited in momentum space. Characteristic features in the Fisher-Shannon plane accompanying the ionization process are identified, and the physical reasons for the observed patterns are described.

  3. The role of isoelectronic dopants in organic light emitting diodes

    NASA Astrophysics Data System (ADS)

    Crone, B. K.; Campbell, I. H.; Smith, D. L.

    2007-09-01

    Power efficiency is an important parameter for all OLEDs, and is particularly critical for lighting applications. To maximize the power efficiency one must optimize charge injection, carrier transport, and radiative quantum efficiency, while minimizing energy losses. In this work we discuss how isoelectronic dopants can be used to address these problems. It can be difficult to produce efficient electrical contacts, particularly to large energy gap organic materials, and thus the contacts often limit the performance and stability of OLEDs . Recent results by several groups have attributed improved hole injection in poly (9,9' dioctylfluorene) [PFO] based LEDs to charge trapping, but the origin of the traps is unknown. In order to understand the role of traps in improving injection we studied poly[2-methoxy, 5-(2'- ethyl-hexyloxy)-1,4-phenylene vinylene] (MEH-PPV) devices with C 60 molecules at the anode to improve hole injection. Isoelectronic dopants are used widely as recombination centers in organic light emitting diodes (OLEDs). In these systems one wants to maximize quantum efficiency by effectively trapping charges on the emitting dopants, while at the same time maximizing power efficiency by maintaining good charge transport. An understanding of the influence of the depth of the dopant on charge capture, and charge transport will aid in optimizing doped organic LEDs. We have looked at the OLED system consisting of the polymer PFO, and the organometallic molecule PhqIr. We show that PhqIr acts as a shallow hole trap in PFO, and that the charge transport and luminescence properties of this system are described by quasi-equilibrium statistics.

  4. The Hg isoelectronic defect in ZnO

    NASA Astrophysics Data System (ADS)

    Cullen, J.; Johnston, K.; Dunker, D.; McGlynn, E.; Yakovlev, D. R.; Bayer, M.; Henry, M. O.

    2013-11-01

    We report a study of the luminescence due to Hg in ZnO, concentrating on the main zero phonon line (ZPL) at 3.2766(1) eV and its associated phonon sidebands. For a sample implanted with radioactive 192Hg, the ZPL intensity, normalised to that of shallow bound exciton emission, is observed to decrease with an equivalent half-life of 4.5(1) h, very close to the 4.85(20) h half-life of 192Hg. ZnO implanted with stable Hg impurities produces the same luminescence spectrum. Temperature dependent measurements confirm that the zero phonon line is a thermalizing doublet involving one allowed and one largely forbidden transition from excited states separated by 0.91(1) meV to a common ground state. Uniaxial stress measurements show that the allowed transition takes place from an orbitally degenerate excited state to a non-degenerate ground state in a centre of trigonal (C3v) symmetry while the magneto-optical properties are characteristic of electron-hole pair recombination at an isoelectronic defect. The doublet luminescence is assigned to bound exciton recombination involving exchange-split Γ5 and Γ1,2 excited states (using C6v symmetry labels; Γ3 and Γ1,2 using C3v labels) at isoelectronic Hg impurities substituting for Zn in the crystal. The electron and hole g values deduced from the magneto-optical data indicate that this Hg impurity centre in ZnO is hole-attractive.

  5. The Hg isoelectronic defect in ZnO

    SciTech Connect

    Cullen, J.; McGlynn, E. Henry, M. O.; Johnston, K.; Dunker, D.; Bayer, M.; Yakovlev, D. R.

    2013-11-21

    We report a study of the luminescence due to Hg in ZnO, concentrating on the main zero phonon line (ZPL) at 3.2766(1) eV and its associated phonon sidebands. For a sample implanted with radioactive {sup 192}Hg, the ZPL intensity, normalised to that of shallow bound exciton emission, is observed to decrease with an equivalent half-life of 4.5(1) h, very close to the 4.85(20) h half-life of {sup 192}Hg. ZnO implanted with stable Hg impurities produces the same luminescence spectrum. Temperature dependent measurements confirm that the zero phonon line is a thermalizing doublet involving one allowed and one largely forbidden transition from excited states separated by 0.91(1) meV to a common ground state. Uniaxial stress measurements show that the allowed transition takes place from an orbitally degenerate excited state to a non-degenerate ground state in a centre of trigonal (C{sub 3v}) symmetry while the magneto-optical properties are characteristic of electron-hole pair recombination at an isoelectronic defect. The doublet luminescence is assigned to bound exciton recombination involving exchange-split Γ{sub 5} and Γ{sub 1,2} excited states (using C{sub 6v} symmetry labels; Γ{sub 3} and Γ{sub 1,2} using C{sub 3v} labels) at isoelectronic Hg impurities substituting for Zn in the crystal. The electron and hole g values deduced from the magneto-optical data indicate that this Hg impurity centre in ZnO is hole-attractive.

  6. 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

  7. 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.

  8. Complete nucleotide sequence of plasmid pNA6 reveals the high plasticity of IncU family plasmids.

    PubMed

    Dang, Bingjun; Xu, Yan; Mao, Daqing; Luo, Yi

    2016-10-10

    Antibiotic resistance is a serious problem in health care and is of widespread public concern. Conjugative plasmids are the most important vectors in the dissemination of antibiotic resistance genes. In this study, we determined the complete sequence of plasmid pNA6, a plasmid which was isolated from the sediments of Haihe River. This plasmid confers reduced susceptibility to ampicillin, erythromycin and sulfamethoxazole. The complete sequence of plasmid pNA6 was 52,210bp in length with an average G+C content of 52.70%. Plasmid pNA6 belongs to the IncU group by sequence queries against the GenBank database. This plasmid has a typical IncU backbone and shows the highest similarities with plasmid RA3 and plasmid pFBAOT6. Plasmid pNA6 carries a class 1 integron consisting of aacA4, ereA and dfrA1 genes. Moreover, plasmid pNA6 also harbors a blaTEM-1-containing complex structure which inserted into the replication region and maintenance region. This insertion site has never been found on other IncU plasmids. The sequencing of plasmid pNA6 will add new sequence information to IncU family plasmids and enhance our understanding of the plasticity of IncU family plasmids. PMID:27374151

  9. 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

  10. Isoelectronic analogues of PN: Remarkably stable multiply charged cations

    SciTech Connect

    Wong, Ming Wah; Radom, L. )

    1990-01-25

    The structures and stabilities of PN and its 27 isoelectronic analogues, CS, SiO, BCl, AlF, BeAr, MgNe, Sn{sup +}, PO{sup +}, CCl{sup +}, SiF{sup +}, BAr{sup +}, AlNe{sup +}, SO{sup 2+}, NCl{sup 2+}, PF{sup 2+}, CAr{sup 2+}, SiNe{sup 2+}, OCl{sup 3+}, SF{sup 3+}, NAr{sup 3+}, PNe{sup 3+}, FCl{sup 4+}, OAr{sup 4+}, SNe{sup 4+}, FAr{sup 5+}, ClNe{sup 5+}, and ArNe{sup 6+}, have been examined by ab initio molecular orbital theory. The CASSCF/6-311G(MC)(d) level was used to determine the ground-state potential energy curves and spectroscopic constants for the 28 diatomic systems. Equilibrium structures were also obtained with the 6-311G(MC)(d) basis set at the MP3 and ST4CCD levels, and dissociation energies were determined at the MP4/6-311 + G(MC)(2df) and MP4/6-311 + G(MC)(3d2f) levels. For the neutral and monocation analogues of PN, the calculated equilibrium geometries (at MP3/6-311G(MC)(d)) and dissociation energies (at MP4/6-311 + G(MC)(3d2f)) are in very good agreement with available experimental values. All the dication analogues of PN, namely, SO{sup 2+}, NCl{sup 2+}, PF{sup 2+}, CAr{sup 2+}, and SiNe{sup 2+}, are predicted to be experimentally observable species. Of these, the SO{sup 2+}, NCl{sup 2+}, and CAr{sup 2+} dications are calculated to be kinetically stable species, with large barriers associated with the exothermic charge-separation reactions, while the PF{sup 2+} and SiNe{sup 2+} dications are predicted not only to be kinetically stable but also to be thermodynamically stable species.

  11. Effects of isoelectronic and halide surfactants on compound semiconductors

    NASA Astrophysics Data System (ADS)

    Howard, Alexander David

    Isoelectronic surfactants Sb, Bi, and N, have proven to increase the doping efficiency of Zn while concurrently reducing the unintentional impurities C, Si, and S in GaP. Additionally, surfactant Sb and N have demonstrated that altering the incorporation efficiency in GaP is also possible with a surfactant surface coverage of less than one. Halide surfactants Br and Cl were shown to systematically destroy ordering in GaInP. Furthermore, a distinct correlation between increasing surfactant Br or Cl in the vapor and surface roughness was evident. This work is presented in three main sections. First, surfactants Sb and Bi, from the pyrolysis of TMSb and TMBi, were examined to determine the effect on Zn doping in GaP. The data demonstrate that the incorporation of Zn can be increased by an order of magnitude in GaP to a value of approximately 1020 cm-3, the highest value reported to date. Additionally, these same surfactants lead to significant decreases in carbon contamination during growth. At high growth temperatures, the reduction can be as large as 100 x in GaP. Second, the role of steps versus the singular surface between steps was studied by using a surfactant fractional surface coverage of less than one. When surfactant Sb was used, the Zn concentration was increased and C was reduced. However, there was no discernable change in incorporation efficiency over the entire range of surfactant Sb studied. Interestingly, surfactant N showed a linear increase in the Zn doping the with amount of surfactant present during growth resulting in an increase of 2 x at the highest flow rate used. Third, halide surfactants Br and Cl, carbon-tetrabromide and carbon-tetrachloride, were studied for their effects on ordering in GaInP. Bromine systematically decreased the amount of CuPt ordering observed by photoluminescence and transmission electron microscopy. Both surfactants Br and Cl were shown to significantly increase the surface roughness, which is postulated to be the

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

    PubMed Central

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

    2010-01-01

    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. PMID:20080555

  13. 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.

  14. 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.

  15. VizieR Online Data Catalog: Boron isoelectronic sequence data (Jonsson+, 2013)

    NASA Astrophysics Data System (ADS)

    Jonsson, P.; Ekman, J.; Gustafsson, S.; Hartman, H.; Karlsson, L. B.; du Rietz, R.; Gaigalas, G.; Godefroid, M. R.; Froese Fischer, C.

    2013-11-01

    Relativistic configuration interaction (RCI) calculations are performed for 291 states belonging to the configurations 1s22s22p, 1s22s2p2, 1s22p3, 1s22s23l, 1s22s2p3l, 1s22p23l, 1s22s24l', 1s22s2p4l', and 1s22p24l' (l=0, 1, 2 and l'=0, 1, 2, 3) in boronlike ions Si X and Ti XVIII to Cu XXV. Electron correlation effects are represented in the wave functions by large configuration state function (CSF) expansions. States are transformed from j j-coupling to LS -coupling, and the LS -percentage compositions are used for labeling the levels. Radiative electric dipole transition rates are given for all ions, leading to massive data sets. Calculated energy levels are compared with other theoretical predictions and crosschecked against the Chianti database, NIST recommended values, and other observations. The accuracy of the calculations are high enough to facilitate the identification of observed spectral lines. (19 data files).

  16. 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.

  17. VizieR Online Data Catalog: Carbon isoelectronic sequence data (Ekman+, 2014)

    NASA Astrophysics Data System (ADS)

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

    2014-02-01

    Extensive self-consistent multiconfiguration Dirac-Hartree-Fock (MCDHF) calculations and subsequent relativistic configuration interaction (RCI) 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 (CSF) expansions. Calculated energy levels are compared with existing theoretical calculations and data from the Chianti and NIST databases. In addition, Lande 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. Complete online tables of energy levels and transition rates are available. (22 data files).

  18. Energy levels and transition rates for the boron isoelectronic sequence: Si X, Ti XVIII - Cu XXV

    NASA Astrophysics Data System (ADS)

    Jönsson, P.; Ekman, J.; Gustafsson, S.; Hartman, H.; Karlsson, L. B.; du Rietz, R.; Gaigalas, G.; Godefroid, M. R.; Froese Fischer, C.

    2013-11-01

    Relativistic configuration interaction (RCI) calculations are performed for 291 states belonging to the configurations 1s22s22p, 1s22s2p2, 1s22p3, 1s22s23l, 1s22s2p3l, 1s22p23l, 1s22s24l', 1s22s2p4l', and 1s22p24l' (l = 0,1,2 and l' = 0,1,2,3) in boron-like ions Si X and Ti XVIII to Cu XXV. Electron correlation effects are represented in the wave functions by large configuration state function (CSF) expansions. States are transformed from jj-coupling to LS-coupling, and the LS-percentage compositions are used for labeling the levels. Radiative electric dipole transition rates are given for all ions, leading to massive data sets. Calculated energy levels are compared with other theoretical predictions and crosschecked against the Chianti database, NIST recommended values, and other observations. 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 and the Swedish Institute. Part of this work was supported by the Communauté française of Belgium, the Belgian National Fund for Scientific Research (FRFC/IISN Convention) and by the IUAP-Belgian State Science Policy (BriX network P7/12).Tables of energy levels and transition rates (Tables 3-19) 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/559/A100

  19. 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.

  20. Isoelectronic sequence fits to configuration-averaged photoionization cross sections and ionization energies

    SciTech Connect

    Clark, R.E.H.; Cowan, R.D.; Bobrowicz, F.W.

    1986-05-01

    Hartree--Fock wave functions have been used to calculate configuration -averaged photoionization cross sections and ionization energies for orbitals 1s< or =nl< or =5g in He-like through Al-like isoelectroni csequences. The photoionization cross sections have been fitted as a function of the nuclear charge, Z, and photon energy, X, in threshold units, with average error of less than 10%. The ionization energies have been fitted as a function of Z with errors of less than 0.5%

  1. VizieR Online Data Catalog: Silicon isoelectronic sequence data (Jonsson+, 2016)

    NASA Astrophysics Data System (ADS)

    Jonsson, P.; Radziute, L.; Gaigalas, G.; Godefroid, M. R.; Marques, J. P.; Brage, T.; Froese Fischer, C.; Grant, I. P.

    2015-11-01

    Calculations were performed for the five states belonging to the 3s23p2 even configuration and the 22 states belonging to the 3s3p3 and 3s23p3d odd configurations. The calculations were made by parity, meaning that the even and odd states were determined in separate calculations in the EOL scheme. (3 data files).

  2. Electron temperature in transient plasmas from quasi-steady ratio of isoelectronic lines: application to picosecond and subpicosecond plasmas

    NASA Astrophysics Data System (ADS)

    Marjoribanks, R. S.; Budnik, F. W.; Chen, H.; Meyerhofer, D. D.

    1996-02-01

    We have extended the technique of plasma temperature measurement by ratio of isoelectronic lines, recently developed with nanosecond laser plasmas, to the diagnosis of picosecond and subpicosecond plasmas. We have found a major benefit-particularly for short-pulse laser plasmas-that even where level populations are far from steady-state values, the ratio of isoelectronic lines may be nearly steady state, which considerably simplifies interpretation. We describe theoretical and experimental investigations for plasmas created from solid targets by 100-fs-10-ps high-intensity laser pulses and report the experimental application of the technique to lambda =1.05 - mu m laser pulses at 1016 W cm -2 .

  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. 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.

  6. 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

  7. 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

  8. Nearly degenerate light- and heavy-hole trions bound to isoelectronic centers

    NASA Astrophysics Data System (ADS)

    Ethier-Majcher, Gabriel; St-Jean, Philippe; Francoeur, Sebastien

    2015-03-01

    Many optical quantum control schemes of spin qubits in semiconductors rely on the existence of trion states. In this work, we investigate the fine structure of negative trions bound to isoelectronic centers formed from a pair of nitrogen isovalent impurities in GaAs, which represent interesting candidates for optical quantum information processing. Using polarization resolved microluminescence, we find that the fine structure is composed of two unpolarized lines, characteristic of light- and heavy-hole trion states, evolving into two quadruplets under a longitudinal magnetic field. The availability of both light- and heavy-hole states on the same trion could lead to new powerful optical quantum control schemes where both spin initialization and single-shot readout could be conveniently realized.

  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. 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

  11. An asymptotic expression for the dipole oscillator strength for transitions of the He sequence

    NASA Technical Reports Server (NTRS)

    Khandelwal, G. S.; Khan, F.; Wilson, J. W.

    1989-01-01

    The radial integral for 1s2 1S-1s np 1P transitions of the He isoelectronic sequence is asymptotically expanded to order n exp -7 to facilitate calculations of the dipole oscillator strength for large n. The threshold differential oscillator strength values are obtained for ions up to Z = 30 within the screened hydrogenic model.

  12. 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

  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. Antiferromagnetism and Hidden Order in Isoelectronic Doping of URu2Si2

    NASA Astrophysics Data System (ADS)

    Wilson, Murray; Williams, Travis; Cai, Yipeng; Hallas, Alannah; Medina, Teresa; Munsie, Timothy; Cheung, Sky; Liu, Lian; Frandsen, Benjamen; Uemura, Yasutomo; Luke, Graeme

    URu2Si2 has been studied for three decades to understand its unusual hidden order state. Doping of this compound on the Ru site usually causes the transition temperature to decrease and hidden order to transition to magnetic order. In contrast, the isoelectronic dopings Fe and Os cause a substantial increase in the transition temperature over a wide range of dopings, with Fe in particular mimicking applied hydrostatic pressure. However, until recently, the magnetic states of these dopings have not been well characterized. In the past year, neutron scattering results have been reported on Fe doping that show antiferromagnetism with moments that are twice as large as those measured for pure URu2Si2 under pressure. In this talk we present an investigation of the magnetic properties of single crystal samples of URu-xFexSi2 and URu2-xOsxSi2 by muon spin rotation (μSR) and susceptibility. Our μSR results demonstrate that both of these dopings show an antiferromagnetic ground state with internal fields comparable to pure URu2Si2 under pressure. Interpretation of our data indicates that the evolution of magnetism with doping for both Fe and Os is driven by changes in hybridization.

  16. Physical properties and intermolecular dynamics of an ionic liquid compared with its isoelectronic neutral binary solution.

    PubMed

    Shirota, Hideaki; Castner, Edward W

    2005-10-27

    In this study, we address the following question about room-temperature ionic liquids (RTILs). Are the properties of a RTIL more dependent on the charges of the molecular ions or on the fact that the liquid is a complex mixture of two species, one or both of which are asymmetric? To address this question and to better understand the interactions and dynamics in RTILs, we have prepared the organic ionic liquid 1-methoxyethylpyridinium dicyanoamide (MOEPy(+)/DCA(-)) and compared this RTIL with the analogous isoelectronic binary solution, comprised of equal parts of 1-methoxyethylbenzene (MOEBz) and dicyanomethane (DCM). In essence, we have created a RTIL and a nearly identical neutral pair in which we have effectively turned off the charges. To understand the intermolecular interactions in both of these liquids, we have characterized the bulk density and shear viscosity. Using femtosecond optical Kerr effect spectroscopy, we have also characterized the intermolecular vibrational dynamics and diffusive reorientation. To verify that the shape, polarizability, and electronic structure of the RTIL ions and the components of the neutral pair are truly quite similar, we have carried out density functional theory calculations on the individual molecular ion and neutral species. PMID:16866386

  17. 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.

  18. Oxygen-Boron Vacancy Defect in Cubic Boron Nitride: A Diamond NV- Isoelectronic Center

    NASA Astrophysics Data System (ADS)

    Abtew, Tesfaye; Gao, Weiwei; Gao, Xiang; Sun, Yiyang; Zhang, Shengbai; Zhang, Peihong

    2015-03-01

    The promises of NV? center in diamond for quantum information application have inspired unprecedented research interests in optical manipulations of defect states, and have stimulated the search for alternative isoelectronic defect systems. In this talk, we present a diamond NV- like color center in c-BN based on first-principles electronic structure calculations using the Heyd-Scuseria-Ernzerhof hybrid functional. The defect consists of an substitutional oxygen and an adjacent boron vacancy (ON -VB). We discuss the electronic and optical properties of this center in comparison with the NV- center GC-2 defect center in c-BN. We acknowledge the computational support provided by the Center for Computational Research at the University at Buffalo, SUNY. This work is supported by the US Department of Energy under Grant No. DE-SC0002623 and by the National Science Foundation under Grant No. DMR-0946404. Work at Beijing CSRC is supported by the National Natural Science Foundation of China (Grant No. 11328401).

  19. Extended Bis(benzothia)quinodimethanes and Their Dications: From Singlet Diradicaloids to Isoelectronic Structures of Long Acenes.

    PubMed

    Dong, Shaoqiang; Herng, Tun Seng; Gopalakrishna, Tullimilli Y; Phan, Hoa; Lim, Zheng Long; Hu, Pan; Webster, Richard D; Ding, Jun; Chi, Chunyan

    2016-08-01

    Extended bis(benzothia)quinodimethanes and their dications were synthesized as stable species. The neutral compounds mainly have a quinoidal structure in the ground state but show increased diradical character with extension of the central quinodimethane unit. The dications exhibit similar electronic absorption spectra, NMR spectra, NICS values, and diatropic ring currents to their aromatic all-carbon acene analogues and thus can be regarded as genuine isoelectronic structures of pentacene, hexacene, and heptacene, respectively. Our research gave some insights into the design and synthesis of stable longer acene analogues. PMID:27356244

  20. 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.

  1. Solving the Schrodinger equation for helium atom and its isoelectronic ions with the free iterative complement interaction (ICI) method.

    PubMed

    Nakashima, Hiroyuki; Nakatsuji, Hiroshi

    2007-12-14

    The Schrodinger equation was solved very accurately for helium atom and its isoelectronic ions (Z=1-10) with the free iterative complement interaction (ICI) method followed by the variational principle. We obtained highly accurate wave functions and energies of helium atom and its isoelectronic ions. For helium, the calculated energy was -2.903,724,377,034,119,598,311,159,245,194,404,446,696,905,37 a.u., correct over 40 digit accuracy, and for H(-), it was -0.527,751,016,544,377,196,590,814,566,747,511,383,045,02 a.u. These results prove numerically that with the free ICI method, we can calculate the solutions of the Schrodinger equation as accurately as one desires. We examined several types of scaling function g and initial function psi(0) of the free ICI method. The performance was good when logarithm functions were used in the initial function because the logarithm function is physically essential for three-particle collision area. The best performance was obtained when we introduce a new logarithm function containing not only r(1) and r(2) but also r(12) in the same logarithm function. PMID:18081387

  2. 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.

  3. Linear coupled-cluster method. II. Analysis of local exchange-correlation potentials in beryllium and its isoelectronic series

    NASA Astrophysics Data System (ADS)

    Shankar, S.; Narasimhan, P. T.

    1984-01-01

    The Slater Xα method and its local-potential modifications are examined with reference to the many-electron exchange-correlation effects in the beryllium atom and its isoelectronic series. The linear coupled-cluster method and a hierarchy of approximations to it are employed for this purpose. The role of the exchange parameter α in providing an accurate description of the exchange-correlation effects is analyzed in the light of the electron-gas model. It is found that for Be atoms an α value of 0.768, that which causes the local potential to mimic the Hartree-Fock potential, is the best suited reference state for many-body calculations. The impact of the.α variation on the exchange-correlation corrections in the Be isoelectronic series is assessed. With increase in the nuclear charge Z, exchange-correlation corrections favor the use of α values closer to 23, the Gaspar-Kohn-Sham limit, in the Xα model. The instabilities in the cluster equations induced by ringdiagram terms are also noted. The futility of using gradient corrections to the Xα model to account for exchange-correlation effects is brought out in the calculations. It is found that a simple scaling of the electron-gas potential results in excellent single-particle reference states for many-body calculations.

  4. 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.

  5. 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.

  6. 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

  7. Direct measurement of T cell receptor affinity and sequence from naïve antiviral T cells.

    PubMed

    Zhang, Shu-Qi; Parker, Patricia; Ma, Ke-Yue; He, Chenfeng; Shi, Qian; Cui, Zhonghao; Williams, Chad M; Wendel, Ben S; Meriwether, Amanda I; Salazar, Mary Alice; Jiang, Ning

    2016-06-01

    T cells recognize and kill a myriad of pathogen-infected or cancer cells using a diverse set of T cell receptors (TCRs). The affinity of TCR to cognate antigen is of high interest in adoptive T cell transfer immunotherapy and antigen-specific T cell repertoire immune profiling because it is widely known to correlate with downstream T cell responses. We introduce the in situ TCR affinity and sequence test (iTAST) for simultaneous measurement of TCR affinity and sequence from single primary CD8(+) T cells in human blood. We demonstrate that the repertoire of primary antigen-specific T cells from pathogen-inexperienced individuals has a surprisingly broad affinity range of 1000-fold composed of diverse TCR sequences. Within this range, samples from older individuals contained a reduced frequency of high-affinity T cells compared to young individuals, demonstrating an age-related effect of T cell attrition that could cause holes in the repertoire. iTAST should enable the rapid selection of high-affinity TCRs ex vivo for adoptive immunotherapy and measurement of T cell response for immune monitoring applications. PMID:27252176

  8. TCR sequences and tissue distribution discriminate the subsets of naïve and activated/memory Treg cells in mice.

    PubMed

    Bergot, Anne-Sophie; Chaara, Wahiba; Ruggiero, Eliana; Mariotti-Ferrandiz, Encarnita; Dulauroy, Sophie; Schmidt, Manfred; von Kalle, Christof; Six, Adrien; Klatzmann, David

    2015-05-01

    Analyses of the regulatory T (Treg) cell TCR repertoire should help elucidate the nature and diversity of their cognate antigens and thus how Treg cells protect us from autoimmune diseases. We earlier identified CD44(hi) CD62L(low) activated/memory (am) Treg cells as a Treg-cell subset with a high turnover and possible self-specificity. We now report that amTreg cells are predominantly distributed in lymph nodes (LNs) draining deep tissues. Multivariate analyses of CDR3 spectratyping first revealed that amTreg TCR repertoire is different from that of naïve Treg cells (nTreg cells) and effector T (Teff) cells. Furthermore, in deep- versus superficial LNs, TCR-β deep sequencing further revealed diversified nTreg-cell and amTreg-cell repertoires, although twofold less diverse than that of Teff cells, and with repertoire richness significantly lower in deep-LN versus superficial-LN Treg cells. Importantly, expanded clonotypes were mostly detected in deep-LN amTreg cells, some accounting for 20% of the repertoire. Strikingly, these clonotypes were absent from nTreg cells, but found at low frequency in Teff cells. Our results, obtained in nonmanipulated mice, indicate different antigenic targets for naïve and amTreg cells and that amTreg cells are self-specific. The data we present are consistent with an instructive component in Treg-cell differentiation. PMID:25726757

  9. Effect of hot implantation on ON-current enhancement utilizing isoelectronic trap in Si-based tunnel field-effect transistors

    NASA Astrophysics Data System (ADS)

    Mori, Takahiro; Mizubayashi, Wataru; Morita, Yukinori; Migita, Shinji; Fukuda, Koichi; Miyata, Noriyuki; Yasuda, Tetsuji; Masahara, Meishoku; Ota, Hiroyuki

    2015-03-01

    A tunneling-current enhancement technology for Si-based tunnel field-effect transistors (TFETs) utilizing an Al-N isoelectronic trap (IET) has been proposed recently. In this study, we investigate hot implantation as a doping technique for Al-N isoelectronic impurity. Hot implantation reduces the damage induced by Al and N implantation processes, resulting in performance improvement of IET-assisted TFETs, e.g., a 12-fold enhancement in the driving current at an operation voltage of 0.5 V and an approximately one-third reduction in the subthreshold slope. By hot implantation, we can achieve a higher driving current in Si-based TFETs using the IET technology.

  10. Solving the electron-nuclear Schrodinger equation of helium atom and its isoelectronic ions with the free iterative-complement-interaction method.

    PubMed

    Nakashima, Hiroyuki; Nakatsuji, Hiroshi

    2008-04-21

    Our previous paper [J. Chem. Phys. 127, 224104 (2007)] revealed that the Schrodinger equation in the fixed-nucleus approximation could be very accurately solved for helium atom and its isoelectronic ions (Z=1-10) with the free iterative-complement-interaction (ICI) method combined with the variation principle. In this report, the quantum effect of nuclear motion has further been variationally considered by the free ICI formalism for the Hamiltonian including mass-polarization operator. We obtained -2.903 304 557 729 580 294 733 816 943 892 697 752 659 273 965 a.u. for helium atom, which is over 40 digits in accuracy, similarly to the previous result for the fixed-nucleus level. Similar accuracy was also obtained for the helium isoelectronic ions. The present results may be regarded to be the nonrelativistic limits. We have further analyzed the physics of the free ICI wave function by applying it to an imaginary atom called "eneon," [e(-)e(10+)e(-)](8+), in which both of the quantum effect of nuclear motion and the three-particle collisions are differently important from the helium and its isoelectronic ions. This revealed the accurate physics automatically generated by the free ICI formalism. PMID:18433190

  11. 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

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

    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- 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.

  13. Ambiphilic diphosphine-borane ligands: metal-->borane interactions within isoelectronic complexes of rhodium, platinum and palladium.

    PubMed

    Bontemps, Sébastien; Sircoglou, Marie; Bouhadir, Ghenwa; Puschmann, Horst; Howard, Judith A K; Dyer, Philip W; Miqueu, Karinne; Bourissou, Didier

    2008-01-01

    Coordination of an ambiphilic diphosphine-borane (DPB) ligand to the RhCl(CO) fragment affords two isomeric complexes. According to X-ray diffraction analysis, each complex adopts a square-pyramidal geometry with trans coordination of the two phosphine buttresses and axial RhB contacts, but the two differ in the relative orientations around the rhodium and boron centres. DFT calculations on the actual complexes provide insight into the influence of the pi-accepting CO co-ligand, compared with previously reported complexes [Rh(mu-Cl)(dpb)]2 and [RhCl(dmap)(dpb)]. In addition, comparison of the nu(CO) frequency of [RhCl(CO)(dpb)] with that of the related borane-free complex [RhCl(CO)(iPr2PPh)2] substantiates the significant electron-withdrawing effect that the sigma-accepting borane moiety exerts on the metal. Valence isoelectronic [PtCl2(dpb)] and [PdCl2(dpb)] complexes have also been prepared and characterized spectroscopically and structurally. The pronounced influence of the transition metal on the magnitude of the M-->B interaction is highlighted by geometric considerations and NBO analyses. PMID:17948327

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. Ab initio rates of multiphoton ionization of the isoelectronic species H, He+, and Li2+ in the vuv and xuv frequency regions

    NASA Astrophysics Data System (ADS)

    Lambrecht, U.; Dimou, L.; Faisal, F. H. M.

    1998-04-01

    Ab initio theoretical investigation of two- and three-photon ionization of the isoelectronic species H, He+, and Li2+ in the vacuum ultraviolet and x-ray ultraviolet frequency regions, is carried out using the fully nonperturbative Floquet-coupled-channel method. We present the results for the total ionization rates in the wavelength region between approximately 260 to 10 nm, and in the intensity domain between about 1010 and 1017 W/cm2, depending on the member of the isoelectronic species investigated. Comparison with the perturbation theoretical results at moderate intensities is made, a corresponding scaling law is tested, and the finite values of the rates of ionization at the resonance frequencies are obtained. The dependence of the rates on the intensity of the field shows the presence of the so-called ``stability windows,'' for all three species investigated here. The role of polarization on the ionization rates shows a general dominance of the linear polarization over the circular polarization in the intensity and frequency domains investigated, for all the three species concerned.

  20. 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.

    2016-06-01

    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.

  1. 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

  2. HIV-1 Transmission Patterns in Antiretroviral Therapy-Naïve, HIV-Infected North Americans Based on Phylogenetic Analysis by Population Level and Ultra-Deep DNA Sequencing

    PubMed Central

    Ross, Lisa L.; Horton, Joseph; Hasan, Samiul; Brown, James R.; Murphy, Daniel; DeJesus, Edwin; Potter, Martin; LaMarca, Anthony; Melendez-Rivera, Ivan; Ward, Douglas; Uy, Jonathon; Shaefer, Mark S.

    2014-01-01

    Factors that contribute to the transmission of human immunodeficiency virus type 1 (HIV-1), especially drug-resistant HIV-1 variants remain a significant public health concern. In-depth phylogenetic analyses of viral sequences obtained in the screening phase from antiretroviral-naïve HIV-infected patients seeking enrollment in EPZ108859, a large open-label study in the USA, Canada and Puerto Rico (ClinicalTrials.gov NCT00440947) were examined for insights into the roles of drug resistance and epidemiological factors that could impact disease dissemination. Viral transmission clusters (VTCs) were initially predicted from a phylogenetic analysis of population level HIV-1 pol sequences obtained from 690 antiretroviral-naïve subjects in 2007. Subsequently, the predicted VTCs were tested for robustness by ultra deep sequencing (UDS) using pyrosequencing technology and further phylogenetic analyses. The demographic characteristics of clustered and non-clustered subjects were then compared. From 690 subjects, 69 were assigned to 1 of 30 VTCs, each containing 2 to 5 subjects. Race composition of VTCs were significantly more likely to be white (72% vs. 60%; p = 0.04). VTCs had fewer reverse transcriptase and major PI resistance mutations (9% vs. 24%; p = 0.002) than non-clustered sequences. Both men-who-have-sex-with-men (MSM) (68% vs. 48%; p = 0.001) and Canadians (29% vs. 14%; p = 0.03) were significantly more frequent in VTCs than non-clustered sequences. Of the 515 subjects who initiated antiretroviral therapy, 33 experienced confirmed virologic failure through 144 weeks while only 3/33 were from VTCs. Fewer VTCs subjects (as compared to those with non-clustering virus) had HIV-1 with resistance-associated mutations or experienced virologic failure during the course of the study. Our analysis shows specific geographical and drug resistance trends that correlate well with transmission clusters defined by HIV sequences of similarity. Furthermore, our

  3. The study of the 4s4p configuration of the Zn isoelectronic sequence using the relativistic jj-coupling approach

    NASA Astrophysics Data System (ADS)

    Aguiar, Julio C.; Raineri, Mónica; Di Rocco, Héctor O.

    2013-08-01

    The 4 s4 p configuration of Zn is analyzed using the Relativistic jj-coupling approach. The experimentally determined relativistic Slater integrals are compared with the results of numerical codes, both quasi- and fully-relativistic ones. In this work, they are estimated, semi-empirically, the two J = 1 levels up Z = 70 and the 1P1 level up Z = 92 by judicious interpolation and extrapolation of energies. The comparison with extensive relativistic configuration-interaction calculations indicates that differences between both approaches are of the order of measurement accuracies.

  4. 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

  5. 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

  6. Accurate multiconfiguration calculations of energy levels, lifetimes, and transition rates for the silicon isoelectronic sequence. Ti IX - Ge XIX, Sr XXV, Zr XXVII, Mo XXIX

    NASA Astrophysics Data System (ADS)

    Jönsson, P.; Radžiūtė, L.; Gaigalas, G.; Godefroid, M. R.; Marques, J. P.; Brage, T.; Froese Fischer, C.; Grant, I. P.

    2016-01-01

    Multiconfiguration Dirac-Hartree-Fock (MCDHF) calculations and relativistic configuration interaction (RCI) calculations are performed for states of the 3s23p2, 3s3p3 and 3s23p3d configurations in the Si-like ions Ti IX - Ge XIX, Sr XXV, Zr XXVII and Mo XXIX. Valence and core-valence 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 reference databases. Lifetime and transition rates along with uncertainty estimations are given for all ions. Energies from the calculations are in excellent agreement with observations and computed wavelength are almost of spectroscopic accuracy, aiding line identification in spectra. Full Tables 2, 3, and 5 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/585/A26

  7. 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.

  8. DFT Study of the Reaction Mechanisms of Carbon Dioxide and its Isoelectronic Molecules CS2 and OCS Dissolved in Pyrrolidinium and Imidazolium Acetate Ionic Liquids.

    PubMed

    Danten, Y; Cabaço, M I; Coutinho, J A P; Pinaud, Noël; Besnard, M

    2016-06-16

    The reaction mechanisms of CO2 and its isoelectronic molecules OCS and CS2 dissolved in N-butyl-N-methylpyrrolidinium acetate and in 1-butyl-3-methylimidazolium acetate were investigated by DFT calculations in "gas phase". The analysis of predicted multistep pathways allowed calculating energies of reaction and energy barriers of the processes. The major role played by the acetate anion in the degradation of the solutes CS2 and OCS as well as in the capture of OCS and CO2 by the imidazolium ring is highlighted. In both ionic liquids, this anion governs the conversion of CS2 into OCS and of OCS into CO2 through interatomic S-O exchanges between the anion and the solutes with formation of thioacetate anions. In imidazolium acetate, the selective capture of CS2 and OCS by the imidazolium ring competes with the S-O exchanges. From the calculated values of the energy barriers a basicity scale of the anions is proposed. The (13)C NMR chemical shifts of the predicted adducts were calculated and agree well with the experimental observations. It is argued that the scenario issued from the calculated pathways is shown qualitatively to be independent from the functionals and basis set used, constitute a valuable tool in the understanding of chemical reactions taking place in liquid phase. PMID:27186961

  9. Improved thermoelectric performance in the Zintl phase compounds YbZn2-xMnxSb2 via isoelectronic substitution in the anionic framework

    NASA Astrophysics Data System (ADS)

    Yu, C.; Zhu, T. J.; Zhang, S. N.; Zhao, X. B.; He, J.; Su, Z.; Tritt, Terry M.

    2008-07-01

    It has been shown previously that the thermoelectric properties of the Zintl phase compound, YbZn2Sb2 can be finely tuned via substitution at the cationic Yb-site. Here we report the results of the investigation of isoelectronic substitution of Zn by Mn in the anionic (Zn2Sb2)2- framework. The p-type YbZn2-xMnxSb2 (0.0⩽x ⩽0.4) samples have been synthesized via a solid-state reaction followed by suitable cooling, annealing, grounding, and hot-pressing densification processes. In samples with x =0.0, 0.05, 0.10, 0.15, 0.2, 0.3, and 0.4, the electrical conductivity, Seebeck coefficient, and thermal conductivity measurements have been performed as a function of temperature from 300to750K. It is found that the Mn substitution effectively lowers the thermal conductivity for all samples, while it significantly increases the power factor for x ⩽0.15. As a result, a dimensionless figure of merit ZT of ˜0.61-0.65 has been attained at 726K for x =0.05-0.15 as compared to the ZT of ˜0.48 in the unsubstituted YbZn2Sb2.

  10. Relative energies, structures, vibrational frequencies, and electronic spectra of pyrylium cation, an oxygen-containing carbocyclic ring isoelectronic with benzene, and its isomers

    NASA Astrophysics Data System (ADS)

    Bera, Partha P.; Head-Gordon, Martin; Lee, Timothy J.

    2013-11-01

    We have studied relative energies, structures, rotational, vibrational, and electronic spectra of the pyrylium cation, an oxygen-containing six-membered carbocyclic ring, and its six isomers, using ab initio quantum chemical methods. Isoelectronic with benzene, the pyrylium cation has a benzenoid structure and is the global minimum on the singlet potential energy surface of C5H5O+. The second lowest energy isomer, the furfuryl cation, has a five membered backbone akin to a sugar, and is only 16 kcal mol-1 above the global minimum computed using coupled cluster theory with singles, doubles, and perturbative triple excitations (CCSD(T)) with the correlation consistent cc-pVTZ basis set. Other isomers are 25, 26, 37, 60, and 65 kcal mol-1 above the global minimum, respectively, at the same level of theory. Lower level methods such as density functional theory (B3LYP) and second order Møller-Plesset perturbation theory performed well when tested against the CCSD(T) results. The pyrylium and furfuryl cations, although separated by only 16 kcal mol-1, are not easily interconverted, as multiple bonds must be broken and formed, and the existence of more than one transition state is likely. Additionally, we have also investigated the asymptotes for the barrierless ion-molecule association of molecules known to exist in the interstellar medium that may lead to formation of the pyrylium cation.

  11. On the LS coupling along the boron sequence.

    NASA Astrophysics Data System (ADS)

    Blagojević, B.; Popović, M. V.; Konjević, N.

    1995-08-01

    LS or Russell-Saunders coupling is dominant for many transitions in the spectra of light elements. The spin-orbit interaction in atomic Hamiltonian becomes more important in comparison to the electrostatic separation between levels of the same principal quantum number n but different orbital angular moments. Electrostatic separation increases as Z while the spin-orbit interaction grows as Z4·α2 where α is fine structure constant, Z is nuclear charge, so the LS-coupling approximation is expected from lower to higher elements of an isoelectronic sequence for nl-nl' transitions. The aim of this paper is to test the validity of experimental data for the LS-coupling approproximation in N III and O IV ions (3s-3p and 3p-3d transitions) with the theory and experimental data in Glenzer et al. (1994).

  12. 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

  13. Simple wave functions for (1s)(ns) {sup 1,3}S and (1s)(np) {sup 1,3}P states of He and isoelectronic ions

    SciTech Connect

    Patil, S.H.

    2003-10-01

    Model wave functions are developed for the excited (1s)(ns) {sup 1,3}S and (1s)(np) {sup 1,3}P states of He and isoelectronic ions, incorporating the asymptotic behavior when one of the electrons is far away, coalescence property when it is close to the nucleus, and cusp property when the two electrons are close to each other. They lead to accurate values for the energies and other properties, and provide an insight into their physical structure.

  14. Repetitive Sequences

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Repetitive sequences, or repeats, account for a substantial portion of the eukaryotic genomes. These sequences include very different types of DNA with respect to mode of origin, function, structure, and genomic distribution. Two large families of repetitive sequences can be readily recognized, ta...

  15. First-principles relativistic calculations of the fine-structure intervals and magnetic dipole transition probabilities in the 1 s sup 2 2 p configuration of the lithium isoelectric sequence

    SciTech Connect

    Das, B.P.; Venugopal, E.P. ); Idrees, M. )

    1990-12-01

    We present the results of our first-principles relativistic calculations of the fine-structure intervals and magnetic dipole transition probabilities for the 1{ital s}{sup 2}2{ital p} configuration of the lithium isoelectronic sequence using a variational approach. The contributions of the Breit interaction and approximate Lamb-shift corrections are incorporated via first-order perturbation theory. Our results of the fine-structure intervals are in good agreement with experiment, but experimental data for the magnetic dipole transition probabilities are not available for comparison with our calculations.

  16. Analysis of Bonding Patterns in the Valence Isoelectronic series O3, S3, SO2 and OS2 in Terms of Oriented Quasi-Atomic Molecular Orbitals

    SciTech Connect

    Glezakou, Vassiliki Alexandra; Elbert, Stephen T; Xantheas, Sotiris S; Ruedenberg, Klaus

    2010-08-26

    A novel analysis of the chemical bonding pattern in the valence isoelectronic series of triatomic molecules O3, S3, SO2 and OS2 is reported. The analysis is based on examining the bond order matrix elements between the Oriented Localized Molecular Orbitals (OLMOs) that are localized on the three individual left (L), center (C) and right (R) atoms. The analysis indicates that there is a (L-C) and (C-R) π-bonding interaction and a (L-R) π-antibonding interaction. This finding supports the previously proposed "partial biradical" interpretation of these triatomic systems, which had recently been challenged.

  17. 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.

  18. 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.

  19. Spectra of germanium and selenium in the 50-350 A region from the PLT tokamak plasma

    SciTech Connect

    Stratton, B.C.; Hodge, W.L.; Moos, H.W.; Schwob, J.L.; Suckewer, S.; Finkenthal, M.; Cohen, S.

    1983-03-01

    Spectra of germanium and selenium injected into the PLT tokamak plasma were observed in the 50 to 350 A region for GeXIV-XXV (KI to OI-like) and SeXVI-XXIV (KI to NaI-like). A number of 3p/sup k/-3p/sup k-1/3d transitions predicted by isoelectronic sequence extrapolation have been identified. Also, previously identified lines from ions in the AlI to OI-like and KI-like isoelectronic sequences have been observed in the tokamak plasma.

  20. [Sequencing babies?].

    PubMed

    Jordan, Bertrand

    2015-10-01

    An extension of newborn screening to genome sequencing is now feasible but raises a number of scientific, organisational and ethical issues. This is being explored in discussions and in several funded trials, in order to maximize benefits and avoid some identified risks. As some companies are already offering such a service, this is quite an urgent matter. PMID:26481033

  1. 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

  2. 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

  3. 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.

  4. Reconstructing of a Sequence Using Similar Sequences

    Energy Science and Technology Software Center (ESTSC)

    1995-11-28

    SIMSEQ reconstructs sequences from oligos. Similar known sequences are used as a reference. At present, simulated data are being used to develop the algorithm. SIMSEQ generates an initial random sequence, then generates a second sequence that is 60 to 90 percent similar to the first. Next, the second sequence is chopped into its appropriate oligos. All possible sequences are reconstructed to determine the most similar. Those with the highest similarity are printed as output.

  5. REPEATED SEQUENCES INCLUDING RS1100 FROM PSEUDOMONAS CEPACIA AC100 FUNCTION AS IS ELEMENTS

    EPA Science Inventory

    Several lines of evidence were obtained that the previously identified, repeated sequence RS1100 of Pseudomonas cepacia strain AC1100 undergoes transposition events. NA sequences flanking the chlorohydroxy hydroquinone (CHQ) degradative genes of this organism were examined from s...

  6. Epithelial Na(+) channels are regulated by flow.

    PubMed

    Satlin, L M; Sheng, S; Woda, C B; Kleyman, T R

    2001-06-01

    Na(+) absorption in the renal cortical collecting duct (CCD) is mediated by apical epithelial Na(+) channels (ENaCs). The CCD is subject to continuous variations in intraluminal flow rate that we speculate alters hydrostatic pressure, membrane stretch, and shear stress. Although ENaCs share limited sequence homology with putative mechanosensitive ion channels in Caenorhabditis elegans, controversy exists as to whether ENaCs are regulated by biomechanical forces. We examined the effect of varying the rate of fluid flow on whole cell Na(+) currents (I(Na)) in oocytes expressing mouse alpha,beta,gamma-ENaC (mENaC) and on net Na(+) absorption in microperfused rabbit CCDs. Oocytes injected with mENaC but not water responded to the initiation of superfusate flow (to 4-6 ml/min) with a reversible threefold stimulation of I(Na) without a change in reversal potential. The increase in I(Na) was variable among oocytes. CCDs responded to a threefold increase in rate of luminal flow with a twofold increase in the rate of net Na(+) absorption. An increase in luminal viscosity achieved by addition of 5% dextran to the luminal perfusate did not alter the rate of net Na(+) absorption, suggesting that shear stress does not influence Na(+) transport in the CCD. In sum, our data suggest that flow stimulation of ENaC activity and Na(+) absorption is mediated by an increase in hydrostatic pressure and/or membrane stretch. We propose that intraluminal flow rate may be an important regulator of channel activity in the CCD. PMID:11352841

  7. Chemical Bonding in Si52- and NaSi5- via Photoelectron Spectroscopy and Ab Initio Calculations

    SciTech Connect

    Yu, Dmitry; Boldyrev, Zubarev; Boldyrev, Alexander I.; Li, Xi; Cui, Lifeng; Wang, Lai S.

    2005-12-22

    Photoelectron spectroscopy and ab initio calculations are used to investigate the electronic structure and chemical bonding of Si5 - and Si5 2- in NaSi5 -. Photoelectron spectra of Si5 - and NaSi5 - are obtained at several photon energies and are compared with theoretical calculations at four different levels of theory, TD-B3LYP, R(U)OVGF, UCCSD(T), and EOM-CCSD(T), all with 6-311+G(2df) basis sets. Excellent agreement is observed between experiment and theory, confirming the obtained ground-state structures for Si5 - and Si5 2-, which are both found to be trigonal bipyramid with D3h symmetry at several levels of theory. Chemical bonding in Si5, Si5 -, and Si5 2- is analyzed using NPA, molecular orbitals, ELF, and NICS indices. The bonding in Si5 2- is compared with that in the isoelectronic and isostructural B5H5 2- species, but they are found to differ due to the involvement of electron densities, which are supposed to be lone pairs in the skeletal bonding in Si5 2-.

  8. The Third Dimension of a More O’Ferrall-Jencks Diagram for Hydrogen Atom Transfer in the Isoelectronic Hydrogen Exchange Reactions of (PhX)2H• with X = O, NH, and CH2

    PubMed Central

    Cembran, Alessandro; Provorse, Makenzie R.; Wang, Changwei

    2012-01-01

    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)2H•, where X = O, NH, and CH2, 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 PhNH2 and PhNH• has a mechanism intermediate of CPET and HAT. The electronically nonadiabatic

  9. 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

  10. Pulse sequences in photoassociation via adiabatic passage

    NASA Astrophysics Data System (ADS)

    Li, Xuan; Dupre, William; Parker, Gregory A.

    2012-07-01

    We perform a detailed study of pulse sequences in a photoassociation via adiabatic passage (PAP) process to transfer population from an ensemble of ultracold atomic clouds to a vibrationally cold molecular state. We show that an appreciable final population of ultracold NaCs molecules can be achieved with optimized pulses in either the ‘counter-intuitive’ (tP > tS) or ‘intuitive’ (tP < tS) PAP pulse sequences, with tP and tS denoting the temporal centers of the pump and Stokes pulses, respectively. By investigating the dependence of the reactive yield on pulse sequences, in a wide range of tP-tS, we show that there is not a fundamental preference to either pulse sequence in a PAP process. We explain this no-sequence-preference phenomenon by analyzing a multi-bound model so that an analogy can be drawn to the conventional stimulated Raman adiabatic passage.

  11. 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.

  12. 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

  13. 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 ...

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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)…

  7. T. cacao Transcriptome Sequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To compliment the T. cacao genome sequencing initiative and to build a reference set of expressed genes for functional studies, a broad and state-of-the-art approach to transcriptome sequencing is underway. Using newly optimized methods, transcriptome sequencing libraries were prepared from RNA of o...

  8. 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

  9. 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

  10. 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.

  11. 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.

  12. 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.)

  13. 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.

  14. Unlocking hidden genomic sequence

    PubMed Central

    Keith, Jonathan M.; Cochran, Duncan A. E.; Lala, Gita H.; Adams, Peter; Bryant, Darryn; Mitchelson, Keith R.

    2004-01-01

    Despite the success of conventional Sanger sequencing, significant regions of many genomes still present major obstacles to sequencing. Here we propose a novel approach with the potential to alleviate a wide range of sequencing difficulties. The technique involves extracting target DNA sequence from variants generated by introduction of random mutations. The introduction of mutations does not destroy original sequence information, but distributes it amongst multiple variants. Some of these variants lack problematic features of the target and are more amenable to conventional sequencing. The technique has been successfully demonstrated with mutation levels up to an average 18% base substitution and has been used to read previously intractable poly(A), AT-rich and GC-rich motifs. PMID:14973330

  15. Multiplexed Fragaria Chloroplast Genome Sequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A method to sequence multiple chloroplast genomes that uses the sequencing depth of ultra high throughput sequencing technologies was recently described. Sequencing complete chloroplast genomes can resolve phylogenetic relationships at low taxonomic levels and identify point mutations and indels tha...

  16. 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

  17. 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.

  18. 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.

  19. 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…

  20. 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

  1. 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…

  2. 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;…

  3. Protein sequence databases.

    PubMed

    Apweiler, Rolf; Bairoch, Amos; Wu, Cathy H

    2004-02-01

    A variety of protein sequence databases exist, ranging from simple sequence repositories, which store data with little or no manual intervention in the creation of the records, to expertly curated universal databases that cover all species and in which the original sequence data are enhanced by the manual addition of further information in each sequence record. As the focus of researchers moves from the genome to the proteins encoded by it, these databases will play an even more important role as central comprehensive resources of protein information. Several the leading protein sequence databases are discussed here, with special emphasis on the databases now provided by the Universal Protein Knowledgebase (UniProt) consortium. PMID:15036160

  4. 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.

  5. Nucleosome dynamics: Sequence matters.

    PubMed

    Eslami-Mossallam, Behrouz; Schiessel, Helmut; van Noort, John

    2016-06-01

    About three quarter of all eukaryotic DNA is wrapped around protein cylinders, forming nucleosomes. Even though the histone proteins that make up the core of nucleosomes are highly conserved in evolution, nucleosomes can be very different from each other due to posttranslational modifications of the histones. Another crucial factor in making nucleosomes unique has so far been underappreciated: the sequence of their DNA. This review provides an overview of the experimental and theoretical progress that increasingly points to the importance of the nucleosomal base pair sequence. Specifically, we discuss the role of the underlying base pair sequence in nucleosome positioning, sliding, breathing, force-induced unwrapping, dissociation and partial assembly and also how the sequence can influence higher-order structures. A new view emerges: the physical properties of nucleosomes, especially their dynamical properties, are determined to a large extent by the mechanical properties of their DNA, which in turn depends on DNA sequence. PMID:26896338

  6. 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.

  7. Automated DNA sequencing.

    PubMed

    Wallis, Yvonne; Morrell, Natalie

    2011-01-01

    Fluorescent cycle sequencing of PCR products is a multistage process and several methodologies are available to perform each stage. This chapter will describe the more commonly utilised dye-terminator cycle sequencing approach using BigDye® terminator chemistry (Applied Biosystems) ready for analysis on a 3730 DNA genetic analyzer. Even though DNA sequencing is one of the most common and robust techniques performed in molecular laboratories it may not always produce desirable results. The causes of the most common problems will also be discussed in this chapter. PMID:20938839

  8. 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

  9. Photofragmentation of Na

    SciTech Connect

    Assion, A.; Baumert, T.; Weichmann, U.; Gerber, G.

    2001-06-18

    Photofragmentation of Na{sup +}{sub 2} molecules in well prepared vibrational levels has been studied employing intense (10{sup 11}{endash}10{sup 14} W/cm{sup 2} ) and ultrashort (80fs) 790nm laser fields. Four fragmentation channels with different released kinetic energies are observed. Depending on the applied laser intensity, the fragmentation of Na{sup +}{sub 2} is governed by photodissociation on light-induced potentials and field ionization followed by Coulomb explosion. Below 1{times}10{sup 12} W /cm{sup 2} , only photodissociation on light-induced potentials is seen. For intermediate laser intensities, field ionization at large internuclear distances competes with photodissociation, thus preventing the observation of above threshold dissociation. Field ionization at small internuclear distances dominates for the highest laser intensities used.

  10. Compact rotary sequencer

    NASA Technical Reports Server (NTRS)

    Appleberry, W. T.

    1980-01-01

    Rotary sequencer is assembled from conventional planetary differential gearset and latching mechanism utilizing inputs and outputs which are coaxial. Applications include automated production-line equipment in home appliances and in vehicles.

  11. 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

  12. 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

  13. 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.

  14. 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

  15. 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.

  16. Burst diaphragm sequence valve

    NASA Astrophysics Data System (ADS)

    Wisneskie, Bradley D.; Hyman, Sheldon; Hallum, Charles E.

    1991-11-01

    A burst diaphragm sequence valve which effectively combines the structure of a burst diaphragm with that of an ordinary swing check valve, the pivot of the ordinary swing check valve being replaced by an integral flexural hinge. The sequence valve provides a way to sequentially burn solid propellant hot gas generators which exit into a common gas manifold, thereby enabling gas-powered devices to operate for a longer time than the duration of one gas generator burn.

  17. Pairwise Sequence Alignment Library

    Energy Science and Technology Software Center (ESTSC)

    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

  18. 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.

  19. 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).

  20. Light-Driven Na+ Pump from Gillisia limnaea: A High-Affinity Na+ Binding Site Is Formed Transiently in the Photocycle

    PubMed Central

    2015-01-01

    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. PMID:25375769

  1. 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.

  2. 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.

  3. 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

  4. DNA sequencing: chemical methods

    SciTech Connect

    Ambrose, B.J.B.; Pless, R.C.

    1987-01-01

    Limited base-specific or base-selective cleavage of a defined DNA fragment yields polynucleotide products, the length of which correlates with the positions of the particular base (or bases) in the original fragment. Sverdlov and co-workers recognized the possibility of using this principle for the determination of DNA sequences. In 1977 a fully elaborated method was introduced based on this principle, which allowed routine analysis of DNA sequences over distances greater than 100 nucleotide unite from a defined, radiolabeled terminus. Six procedures for partial cleavage were described. Simultaneous parallel resolution of an appropriate set of partial cleavage mixtures by polyacrylamide gel electrophoresis, followed by visualization of the radioactive bands by autoradiography, allows the deduction of nucleotide sequence.

  5. Sequencing the Connectome

    PubMed Central

    Zador, Anthony M.; Dubnau, Joshua; Oyibo, Hassana K.; Zhan, Huiqing; Cao, Gang; Peikon, Ian D.

    2012-01-01

    Connectivity determines the function of neural circuits. Historically, circuit mapping has usually been viewed as a problem of microscopy, but no current method can achieve high-throughput mapping of entire circuits with single neuron precision. Here we describe a novel approach to determining connectivity. We propose BOINC (“barcoding of individual neuronal connections”), a method for converting the problem of connectivity into a form that can be read out by high-throughput DNA sequencing. The appeal of using sequencing is that its scale—sequencing billions of nucleotides per day is now routine—is a natural match to the complexity of neural circuits. An inexpensive high-throughput technique for establishing circuit connectivity at single neuron resolution could transform neuroscience research. PMID:23109909

  6. 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.

  7. Regulation of persistent Na current by interactions between beta subunits of voltage-gated Na channels.

    PubMed

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

    2009-02-18

    The beta subunits of voltage-gated Na channels (Scnxb) regulate the gating of pore-forming alpha subunits, as well as their trafficking and localization. In heterologous expression systems, beta1, beta2, and beta3 subunits influence inactivation and persistent current in different ways. To test how the beta4 protein regulates Na channel gating, we transfected beta4 into HEK (human embryonic kidney) cells stably expressing Na(V)1.1. Unlike a free peptide with a sequence from the beta4 cytoplasmic domain, the full-length beta4 protein did not block open channels. Instead, beta4 expression favored open states by shifting activation curves negative, decreasing the slope of the inactivation curve, and increasing the percentage of noninactivating current. Consequently, persistent current tripled in amplitude. Expression of beta1 or chimeric subunits including the beta1 extracellular domain, however, favored inactivation. Coexpressing Na(V)1.1 and beta4 with beta1 produced tiny persistent currents, indicating that beta1 overcomes the effects of beta4 in heterotrimeric channels. In contrast, beta1(C121W), which contains an extracellular epilepsy-associated mutation, did not counteract the destabilization of inactivation by beta4 and also required unusually large depolarizations for channel opening. In cultured hippocampal neurons transfected with beta4, persistent current was slightly but significantly increased. Moreover, in beta4-expressing neurons from Scn1b and Scn1b/Scn2b null mice, entry into inactivated states was slowed. These data suggest that beta1 and beta4 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 beta1 subunits. PMID:19228957

  8. 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

  9. Ranking and Sequencing Model

    Energy Science and Technology Software Center (ESTSC)

    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.

  10. 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.

  11. 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.

  12. The Compliment Sequence.

    ERIC Educational Resources Information Center

    Sims, Anntarie L.

    1989-01-01

    Describes and examines 150 tape-recorded compliment sequences. Reports that the course and outcome of compliments and compliment responses are affected by: (1) the way a compliment is worded; (2) the type of statement that precedes or follows the compliment; and (3) the status and sex of the compliment participants. (RAE)

  13. A Sequence of Cylinders

    ERIC Educational Resources Information Center

    Johnson, Erica

    2006-01-01

    Hoping to develop in her students an understanding of mathematics as a way of thinking more than a way of doing, the author of this article describes how her students worked on a spatial reasoning problem stemming from an iteratively constructed sequence of cylinders. She presents an activity of making cylinders out of paper models, and for every…

  14. Effect of ADP on Na+-Na+ Exchange Reaction Kinetics of Na,K-ATPase

    PubMed Central

    Peluffo, R. Daniel

    2004-01-01

    The whole-cell voltage-clamp technique was used in rat cardiac myocytes to investigate the kinetics of ADP binding to phosphorylated states of Na,K-ATPase and its effects on presteady-state Na+-dependent charge movements by this enzyme. Ouabain-sensitive transient currents generated by Na,K-ATPase functioning in electroneutral Na+-Na+ exchange mode were measured at 23°C with pipette ADP concentrations ([ADP]) of up to 4.3 mM and extracellular Na+ concentrations ([Na]o) between 36 and 145 mM at membrane potentials (VM) from −160 to +80 mV. Analysis of charge-VM curves showed that the midpoint potential of charge distribution was shifted toward more positive VM both by increasing [ADP] at constant Na+o and by increasing [Na]o at constant ADP. The total quantity of mobile charge, on the other hand, was found to be independent of changes in [ADP] or [Na]o. The presence of ADP increased the apparent rate constant for current relaxation at hyperpolarizing VM but decreased it at depolarizing VM as compared to control (no added ADP), an indication that ADP binding facilitates backward reaction steps during Na+-Na+ exchange while slowing forward reactions. Data analysis using a pseudo three-state model yielded an apparent Kd of ∼6 mM for ADP binding to and release from the Na,K-ATPase phosphoenzyme; a value of 130 s−1 for k2, a rate constant that groups Na+ deocclusion/release and the enzyme conformational transition E1∼P → E2-P; a value of 162 s−1M−1 for k−2, a lumped second-order VM-independent rate constant describing the reverse reactions; and a Hill coefficient of ∼1 for Na+o binding to E2-P. The results are consistent with electroneutral release of ADP before Na+ is deoccluded and released through an ion well. The same approach can be used to study additional charge-moving reactions and associated electrically silent steps of the Na,K-pump and other transporters. PMID:15298896

  15. 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:

  16. Molecular cloning of a putative tetrodotoxin-resistant rat heart Na+ channel isoform.

    PubMed Central

    Rogart, R B; Cribbs, L L; Muglia, L K; Kephart, D D; Kaiser, M W

    1989-01-01

    Voltage-gated Na+ channels in mammalian heart differ from those in nerve and skeletal muscle. One major difference is that tetrodotoxin (TTX)-resistant cardiac Na+ channels are blocked by 1-10 microM TTX, whereas TTX-sensitive nerve Na+ channels are blocked by nanomolar TTX concentrations. We constructed a cDNA library from 6-day-old rat hearts, where only low-affinity [3H]saxitoxin receptors, corresponding to TTX-resistant Na+ channels, were detected. We isolated several overlapping cDNA clones encompassing 7542 nucleotides and encoding the entire alpha subunit of a cardiac-specific Na+ channel isoform (designated rat heart I) as well as several rat brain I Na+ channel cDNA clones. The derived amino acid sequence of rat heart I was highly homologous to, but distinct from, previous Na+ channel clones. RNase protection studies showed that the corresponding mRNA species is abundant in newborn and adult rat hearts, but not detectable in brain or innervated skeletal muscle. The same mRNA species appears upon denervation of skeletal muscle, likely accounting for expression of new TTX-resistant Na+ channels. Thus, this cardiac-specific Na+ channel clone appears to encode a distinct TTX-resistant isoform and is another member of the mammalian Na+ channel multigene family, found in newborn heart and denervated skeletal muscles. Images PMID:2554302

  17. 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.

  18. 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

  19. 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.

  20. 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

  1. 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

  2. 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.

  3. 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.

  4. 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

  5. Sequence logos: a new way to display consensus sequences.

    PubMed Central

    Schneider, T D; Stephens, R M

    1990-01-01

    A graphical method is presented for displaying the patterns in a set of aligned sequences. The characters representing the sequence are stacked on top of each other for each position in the aligned sequences. The height of each letter is made proportional to its frequency, and the letters are sorted so the most common one is on top. The height of the entire stack is then adjusted to signify the information content of the sequences at that position. From these 'sequence logos', one can determine not only the consensus sequence but also the relative frequency of bases and the information content (measured in bits) at every position in a site or sequence. The logo displays both significant residues and subtle sequence patterns. PMID:2172928

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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.

  11. Music Sequencing and Printing Software.

    ERIC Educational Resources Information Center

    Kassner, Kirk

    2000-01-01

    States that sequencing and printing software eliminates the barriers to students composing music. Describes "Master Tracks Pro," a sequencing program, and "Rhapsody," a printing program. Includes a lesson plan for setting pentatonic music to a poem. (CMK)

  12. Sequence repeats and protein structure

    NASA Astrophysics Data System (ADS)

    Hoang, Trinh X.; Trovato, Antonio; Seno, Flavio; Banavar, Jayanth R.; Maritan, Amos

    2012-11-01

    Repeats are frequently found in known protein sequences. The level of sequence conservation in tandem repeats correlates with their propensities to be intrinsically disordered. We employ a coarse-grained model of a protein with a two-letter amino acid alphabet, hydrophobic (H) and polar (P), to examine the sequence-structure relationship in the realm of repeated sequences. A fraction of repeated sequences comprises a distinct class of bad folders, whose folding temperatures are much lower than those of random sequences. Imperfection in sequence repetition improves the folding properties of the bad folders while deteriorating those of the good folders. Our results may explain why nature has utilized repeated sequences for their versatility and especially to design functional proteins that are intrinsically unstructured at physiological temperatures.

  13. 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.

  14. Cement sequence stratigraphy in carbonates

    SciTech Connect

    Braithwaite, C.J.R. )

    1993-03-01

    Conventional paragenesis analysis commonly fails to describe the subtleties of regional variation found in carbonate cement sequences. Application of the concept of sequence stratigraphy to diagenetic studies allows grouping of the products of depositional (precipitation or crystallization) events into sequences. The boundaries to these sequences are surfaces reflecting erosion (dissolution), non-deposition (renucleation), compaction or imposed fracture events. The pattern of chemical changes within a diagenetic sequence provides a fingerprint which allows that sequence to be recognized among others. Diagenetic sequences may be grouped into temporal series to provide an overall view of the diagenesis of the unit which takes account of local unconformities. The belief that lateral stratigraphical equivalence can serve as a proxy for diagenetic time equivalence is evidently mistaken; diagenetic boundaries may cross stratigraphic boundaries. The application of sequence stratigraphy concepts provides a valuable tool for interpreting regional diagenesis in carbonates and potentially offers insight into the pathways of hydrocarbon or ore fluid migration.

  15. An Na+-pumping V1V0-ATPase complex in the thermophilic bacterium Clostridium fervidus.

    PubMed Central

    Höner zu Bentrup, K; Ubbink-Kok, T; Lolkema, J S; Konings, W N

    1997-01-01

    Energy transduction in the anaerobic, thermophilic bacterium Clostridium fervidus relies exclusively on Na+ as the coupling ion. The Na+ ion gradient across the membrane is generated by a membrane-bound ATPase (G. Speelmans, B. Poolman, T. Abee, and W. N. Konings, J. Bacteriol. 176:5160-5162, 1994). The Na+-ATPase complex was purified to homogeneity. It migrates as a single band in native polyacrylamide gel electrophoresis and catalyzes Na+-stimulated ATPase activity. Denaturing gel electrophoresis showed that the complex consists of at least six different polypeptides with apparent molecular sizes of 66, 61, 51, 37, 26, and 17 kDa. The N-terminal sequences of the 66- and 51-kDa subunits were found to be significantly homologous to subunits A and B, respectively, of the Na+-translocating V-type ATPase of Enterococcus hirae. The purified V1V0 protein complex was reconstituted in a mixture of Escherichia coli phosphatidylethanolamine and egg yolk phosphatidylcholine and shown to catalyze the uptake of Na+ ions upon hydrolysis of ATP. Na+ transport was completely abolished by monensin, whereas valinomycin stimulated the uptake rate. This is indicative of electrogenic sodium transport. The presence of the protonophore SF6847 had no significant effect on the uptake, indicating that Na+ translocation is a primary event and in the cell is not accomplished by an H+-translocating pump in combination with an Na+-H+ antiporter. PMID:9023212

  16. Biological activity of mRNA immobilized on nitrocellulose in NaI.

    PubMed Central

    Bresser, J; Hubbell, H R; Gillespie, D

    1983-01-01

    In 12.2 molal NaI and at 25 degrees C or below, mRNA bound to nitrocellulose while DNA and rRNA did not. Neither the poly(A) tract nor the cap were required for binding. The immobilized RNA could be translated, reverse transcribed, hybridized with radioactive probes, or released for further manipulation. mRNA was efficiently transferred from polyacrylamide to nitrocellulose in NaI. Baking was not required to fix NaI-immobilized mRNA to nitrocellulose. When cells dissolved in 12.2 molal NaI were filtered through nitrocellulose, mRNA became selectively bound (quickblot). The quick-blot system utilizing protease and detergents to prepare cells for NaI solubilization was especially suitable in quantitative, rapid screening of cells for expression of specific genes. Expression of highly repeated DNA sequences was detected in human leukemia cells. Images PMID:6579539

  17. 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.

  18. 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.

  19. Nucleotide sequences 1986/1987

    SciTech Connect

    Not Available

    1987-01-01

    These eight volumes are the third annual published compendium of nucleic acid sequences included in the European Molecular Biology Laboratory Nucleotide Sequence Data Library and the GenBank Genetic Sequences Data Bank. Each volume surveys one or more subdivisions of the database. The volume subtitles are: Primates; Rodents; Other Vertebrates and Invertebrates, Plants and Organelles, Bacteria and Bacteriophage, Viruses, Structural RNA, Synthetic and Unannotated Sequences, and Database Directory and Master Indices.

  20. 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

  1. 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…

  2. 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.

  3. 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).

  4. Natural protein sequences are more intrinsically disordered than random sequences.

    PubMed

    Yu, Jia-Feng; Cao, Zanxia; Yang, Yuedong; Wang, Chun-Ling; Su, Zhen-Dong; Zhao, Ya-Wei; Wang, Ji-Hua; Zhou, Yaoqi

    2016-08-01

    Most natural protein sequences have resulted from millions or even billions of years of evolution. How they differ from random sequences is not fully understood. Previous computational and experimental studies of random proteins generated from noncoding regions yielded inclusive results due to species-dependent codon biases and GC contents. Here, we approach this problem by investigating 10,000 sequences randomized at the amino acid level. Using well-established predictors for protein intrinsic disorder, we found that natural sequences have more long disordered regions than random sequences, even when random and natural sequences have the same overall composition of amino acid residues. We also showed that random sequences are as structured as natural sequences according to contents and length distributions of predicted secondary structure, although the structures from random sequences may be in a molten globular-like state, according to molecular dynamics simulations. The bias of natural sequences toward more intrinsic disorder suggests that natural sequences are created and evolved to avoid protein aggregation and increase functional diversity. PMID:26801222

  5. Sequence Maneuverer: tool for sequence extraction from genomes

    PubMed Central

    Yasmin, Tayyaba; Rehman, Inayat Ur; Ansari, Adnan Ahmad; liaqat, Khurrum; khan, Muhammad Irfan

    2012-01-01

    The availability of genomic sequences of many organisms has opened new challenges in many aspects particularly in terms of genome analysis. Sequence extraction is a vital step and many tools have been developed to solve this issue. These tools are available publically but have limitations with reference to the sequence extraction, length of the sequence to be extracted, organism specificity and lack of user friendly interface. We have developed a java based software package having three modules which can be used independently or sequentially. The tool efficiently extracts sequences from large datasets with few simple steps. It can efficiently extract multiple sequences of any desired length from a genome of any organism. The results are crosschecked by published data. Availability URL 1: http://ww3.comsats.edu.pk/bio/ResearchProjects.aspx URL 2: http://ww3.comsats.edu.pk/bio/SequenceManeuverer.aspx PMID:23275734

  6. 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.

  7. 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. PMID:23297210

  8. The EMBL Nucleotide Sequence Database.

    PubMed

    Stoesser, G; Tuli, M A; Lopez, R; Sterk, P

    1999-01-01

    The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl.html) constitutes Europe's primary nucleotide sequence resource. Main sources for DNA and RNA sequences are direct submissions from individual researchers, genome sequencing projects and patent applications. While automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO), the preferred submission tool for individual submitters is Webin (WWW). Through all stages, dataflow is monitored by EBI biologists communicating with the sequencing groups. In collaboration with DDBJ and GenBank the database is produced, maintained and distributed at the European Bioinformatics Institute (EBI). Database releases are produced quarterly and are distributed on CD-ROM. Network services allow access to the most up-to-date data collection via Internet and World Wide Web interface. EBI's Sequence Retrieval System (SRS) is a Network Browser for Databanks in Molecular Biology, integrating and linking the main nucleotide and protein databases, plus many specialised databases. For sequence similarity searching a variety of tools (e.g. Blitz, Fasta, Blast etc) are available for external users to compare their own sequences against the most currently available data in the EMBL Nucleotide Sequence Database and SWISS-PROT. PMID:9847133

  9. Sequence analysis on microcomputers.

    PubMed

    Cannon, G C

    1987-10-01

    Overall, each of the program packages performed their tasks satisfactorily. For analyses where there was a well-defined answer, such as a search for a restriction site, there were few significant differences between the program sets. However, for tasks in which a degree of flexibility is desirable, such as homology or similarity determinations and database searches, DNASTAR consistently afforded the user more options in conducting the required analysis than did the other two packages. However, for laboratories where sequence analysis is not a major effort and the expense of a full sequence analysis workstation cannot be justified, MicroGenie and IBI-Pustell offer a satisfactory alternative. MicroGenie is a polished program system. Many may find that its user interface is more "user friendly" than the standard menu-driven interfaces. Its system of filing sequences under individual passwords facilitates use by more than one person. MicroGenie uses a hardware device for software protection that occupies a card slot in the computer on which it is used. Although I am sympathetic to the problem of software piracy, I feel that a less drastic solution is in order for a program likely to be sharing limited computer space with other software packages. The IBI-Pustell package performs the required analysis functions as accurately and quickly as MicroGenie but it lacks the clearness and ease of use. The menu system seems disjointed, and new or infrequent users often find themselves at apparent "dead-end menus" where the only clear alternative is to restart the entire program package. It is suggested from published accounts that the user interface is going to be upgraded and perhaps when that version is available, use of the system will be improved. The documentation accompanying each package was relatively clear as to how to run the programs, but all three packages assumed that the user was familiar with the computational techniques employed. MicroGenie and IBI-Pustell further

  10. The evolution of nanopore sequencing.

    PubMed

    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

  11. 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

  12. 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

  13. 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.

  14. Making sense of deep sequencing.

    PubMed

    Goldman, D; Domschke, K

    2014-10-01

    This review, the first of an occasional series, tries to make sense of the concepts and uses of deep sequencing of polynucleic acids (DNA and RNA). Deep sequencing, synonymous with next-generation sequencing, high-throughput sequencing and massively parallel sequencing, includes whole genome sequencing but is more often and diversely applied to specific parts of the genome captured in different ways, for example the highly expressed portion of the genome known as the exome and portions of the genome that are epigenetically marked either by DNA methylation, the binding of proteins including histones, or that are in different configurations and thus more or less accessible to enzymes that cleave DNA. Deep sequencing of RNA (RNASeq) reverse-transcribed to complementary DNA is invaluable for measuring RNA expression and detecting changes in RNA structure. Important concepts in deep sequencing include the length and depth of sequence reads, mapping and assembly of reads, sequencing error, haplotypes, and the propensity of deep sequencing, as with other types of 'big data', to generate large numbers of errors, requiring monitoring for methodologic biases and strategies for replication and validation. Deep sequencing yields a unique genetic fingerprint that can be used to identify a person, and a trove of predictors of genetic medical diseases. Deep sequencing to identify epigenetic events including changes in DNA methylation and RNA expression can reveal the history and impact of environmental exposures. Because of the power of sequencing to identify and deliver biomedically significant information about a person and their blood relatives, it creates ethical dilemmas and practical challenges in research and clinical care, for example the decision and procedures to report incidental findings that will increasingly and frequently be discovered. PMID:24925306

  15. 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.

  16. Relay Sequence Generation Software

    NASA Technical Reports Server (NTRS)

    Gladden, Roy E.; Khanampompan, Teerapat

    2009-01-01

    Due to thermal and electromagnetic interactivity between the UHF (ultrahigh frequency) radio onboard the Mars Reconnaissance Orbiter (MRO), which performs relay sessions with the Martian landers, and the remainder of the MRO payloads, it is required to integrate and de-conflict relay sessions with the MRO science plan. The MRO relay SASF/PTF (spacecraft activity sequence file/ payload target file) generation software facilitates this process by generating a PTF that is needed to integrate the periods of time during which MRO supports relay activities with the rest of the MRO science plans. The software also generates the needed command products that initiate the relay sessions, some features of which are provided by the lander team, some are managed by MRO internally, and some being derived.

  17. Isotropic sequence order learning.

    PubMed

    Porr, Bernd; Wörgötter, Florentin

    2003-04-01

    In this article, we present an isotropic unsupervised algorithm for temporal sequence learning. No special reward signal is used such that all inputs are completely isotropic. All input signals are bandpass filtered before converging onto a linear output neuron. All synaptic weights change according to the correlation of bandpass-filtered inputs with the derivative of the output. We investigate the algorithm in an open- and a closed-loop condition, the latter being defined by embedding the learning system into a behavioral feedback loop. In the open-loop condition, we find that the linear structure of the algorithm allows analytically calculating the shape of the weight change, which is strictly heterosynaptic and follows the shape of the weight change curves found in spike-time-dependent plasticity. Furthermore, we show that synaptic weights stabilize automatically when no more temporal differences exist between the inputs without additional normalizing measures. In the second part of this study, the algorithm is is placed in an environment that leads to closed sensor-motor loop. To this end, a robot is programmed with a prewired retraction reflex reaction in response to collisions. Through isotropic sequence order (ISO) learning, the robot achieves collision avoidance by learning the correlation between his early range-finder signals and the later occurring collision signal. Synaptic weights stabilize at the end of learning as theoretically predicted. Finally, we discuss the relation of ISO learning with other drive reinforcement models and with the commonly used temporal difference learning algorithm. This study is followed up by a mathematical analysis of the closed-loop situation in the companion article in this issue, "ISO Learning Approximates a Solution to the Inverse-Controller Problem in an Unsupervised Behavioral Paradigm" (pp. 865-884). PMID:12689389

  18. Adversary Sequence Interruption Model

    Energy Science and Technology Software Center (ESTSC)

    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

  19. 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

  20. 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.

  1. 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

  2. BAC sequencing using pooled methods.

    PubMed

    Saski, Christopher A; Feltus, F Alex; Parida, Laxmi; Haiminen, Niina

    2015-01-01

    Shotgun sequencing and assembly of a large, complex genome can be both expensive and challenging to accurately reconstruct the true genome sequence. Repetitive DNA arrays, paralogous sequences, polyploidy, and heterozygosity are main factors that plague de novo genome sequencing projects that typically result in highly fragmented assemblies and are difficult to extract biological meaning. Targeted, sub-genomic sequencing offers complexity reduction by removing distal segments of the genome and a systematic mechanism for exploring prioritized genomic content through BAC sequencing. If one isolates and sequences the genome fraction that encodes the relevant biological information, then it is possible to reduce overall sequencing costs and efforts that target a genomic segment. This chapter describes the sub-genome assembly protocol for an organism based upon a BAC tiling path derived from a genome-scale physical map or from fine mapping using BACs to target sub-genomic regions. Methods that are described include BAC isolation and mapping, DNA sequencing, and sequence assembly. PMID:25239741

  3. 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.

  4. Solid phase sequencing of biopolymers

    DOEpatents

    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.

  5. Graphene nanodevices for DNA sequencing.

    PubMed

    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. PMID:26839258

  6. 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.

  7. 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?

  8. AB118. Validation of next generation sequencing by Sanger sequencing

    PubMed Central

    Low, Meow Hong Wendy; Lai, Hwei Meeng Angeline; Jamuar, Saumya Shekhar; Law, Hai Yang

    2015-01-01

    Background and objective Development of the next generation sequencing (NGS) platform was driven by the completion of the Human Genome Project in 2003. With the availability of NGS, the time taken for sequencing of humongous genomic regions was greatly reduced and data generated per unit DNA was also significantly increased. Though the cost to use NGS in a clinically setting is far from ideal, economically speaking, there is a significant decrease in the average cost per sequenced base. To validate findings of NGS on mutation detected for FBN1, TGFBR2, RAF1, RTEL1, LMNA, MID2, KCNK9, DMD, SMARCA2 and IQSEC2 by using gold standard, Sanger Sequencing. Methods The coordinate of the mutation identified by NGS was used to retrieve the adjacent genomic sequence in UCSC Genome Browser (Available from URL: https://genome.ucsc.edu/). Targeted primers were designed with Primer 3 software (Available from URL: http://primer3.ut.ee/) based on the genomic sequence obtained from UCSC. The following step involves the optimization of a Polymerase Chain Reaction (PCR) with the designed primers to amplify the desired DNA template for the targeted region. Upon optimization, the template is purified and subjected to dye terminator sequencing to generate multiple DNA fragments of varying sizes. Lastly, the DNA fragments will be purified and analysed with an automated sequencer. The sequencer separates the DNA fragments based on their size by carrying out capillary electrophoresis. Results A total of 28 cases were validated with Sanger sequencing. Of them, 25 (89.3%) cases concur with the findings from NGS and 3 (10.7%) cases were false-positive calls. Conclusions NGS shows promise in the future molecular diagnostic regime, however, at the present moment, it needs to be done concurrently with Sanger sequencing for clinical applications.

  9. 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

  10. Functional role of polar amino acid residues in Na+/H+ exchangers.

    PubMed Central

    Wiebe, C A; Dibattista, E R; Fliegel, L

    2001-01-01

    Na(+)/H(+) exchangers are a family of ubiquitous membrane proteins. In higher eukaryotes they regulate cytosolic pH by removing an intracellular H(+) in exchange for an extracellular Na(+). In yeast and Escherichia coli, Na(+)/H(+) exchangers function in the opposite direction to remove intracellular Na(+) in exchange for extracellular H(+). Na(+)/H(+) exchangers display an internal pH-sensitivity that varies with the different antiporter types. Only recently have investigations examined the amino acids involved in pH-sensitivity and in cation binding and transport. Histidine residues are good candidates for H(+)-sensing amino acids, since they can ionize within the physiological pH range. Histidine residues have been shown to be important in the function of the E. coli Na(+)/H(+) exchanger NhaA and in the yeast Na(+)/H(+) exchanger sod2. In E. coli, His(225) of NhaA may function to interact with, or regulate, the pH-sensory region of NhaA. In sod2, His(367) is also critical to transport and may be a functional analogue of His(225) of NhaA. Histidine residues are not critical for the function of the mammalian Na(+)/H(+) exchanger, although an unusual histidine-rich sequence of the C-terminal tail has some influence on activity. Other amino acids involved in cation binding and transport by Na(+)/H(+) exchangers are only beginning to be studied. Amino acids with polar side chains such as aspartate and glutamate have been implicated in transport activity of NhaA and sod2, but have not been studied in the mammalian Na(+)/H(+) exchanger. Further studies are needed to elucidate the mechanisms involved in pH-sensitivity and cation binding and transport by Na(+)/H(+) exchangers. PMID:11415429

  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. 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.

  13. 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.

  14. Quasi-Random Sequence Generators.

    Energy Science and Technology Software Center (ESTSC)

    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.

  15. 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.

  16. 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

  17. Representations of mechanical assembly sequences

    NASA Astrophysics Data System (ADS)

    Homem de Mello, Luiz S.; Sanderson, Arthur C.

    1991-04-01

    Five types of representations for assembly sequences are reviewed: the directed graph of feasible assembly sequences, the AND/OR graph of feasible assembly sequences, the set of establishment conditions, and two types of sets of precedence relationships. (precedence relationships between the establishment of one connection between parts and the establishment of another connection, and precedence relationships between the establishment of one connection and states of the assembly process). The mappings of one representation into the others are established. The correctness and completeness of these representations are established. The results presented are needed in the proof of correctness and completeness of algorithms for the generation of mechanical assembly sequences.

  18. 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.

  19. 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.

  20. 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.

  1. Representations of mechanical assembly sequences

    NASA Technical Reports Server (NTRS)

    Homem De Mello, Luiz S.; Sanderson, Arthur C.

    1991-01-01

    Five types of representations for assembly sequences are reviewed: the directed graph of feasible assembly sequences, the AND/OR graph of feasible assembly sequences, the set of establishment conditions, and two types of sets of precedence relationships. (precedence relationships between the establishment of one connection between parts and the establishment of another connection, and precedence relationships between the establishment of one connection and states of the assembly process). The mappings of one representation into the others are established. The correctness and completeness of these representations are established. The results presented are needed in the proof of correctness and completeness of algorithms for the generation of mechanical assembly sequences.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. Slow inactivation of Na(+) channels.

    PubMed

    Silva, Jonathan

    2014-01-01

    Prolonged depolarizing pulses that last seconds to minutes cause slow inactivation of Na(+) channels, which regulates neuron and myocyte excitability by reducing availability of inward current. In neurons, slow inactivation has been linked to memory of previous excitation and in skeletal muscle it ensures myocytes are able to contract when K(+) is elevated. The molecular mechanisms underlying slow inactivation are unclear even though it has been studied for 50+ years. This chapter reviews what is known to date regarding the definition, measurement, and mechanisms of voltage-gated Na(+) channel slow inactivation. PMID:24737231

  7. Complementary DNA sequencing: Expressed sequence tags and human genome project

    SciTech Connect

    Adams, M.D.; Kelley, J.M.; Gocayne, J.D.; Dubnick, M.; Wu, A.; Olde, B.; Moreno, R.F.; Kerlavage, A.R.; McCombie, W.R.; Venter, J.C. ); Polymeropoulos, M.H.; Hong Xiao; Merril, C.R. )

    1991-06-21

    Automated partial DNA sequencing was conducted on more than 600 randomly selected human brain complementary DNA (cDNA) clones to generate expressed sequence tags (ESTs). ESTs have applications in the discovery of new human genes, mapping of the human genome, and identification of coding regions in genomic sequences. Of the sequences generated, 337 represent new genes, including 48 with significant similarity to genes from other organisms, such as a yeast RNA polymerase II subunit; Drosophila kinesin, Notch, and Enhancer of split; and a murine tyrosine kinase receptor. Forty-six ESTs were mapped to chromosomes after amplification by the polymerase chain reaction. This fast approach to cDNA characterization will facilitate the tagging of most human genes in a few years at a fraction of the cost of complete genomic sequencing, provide new genetic markers, and serve as a resource in diverse biological research fields.

  8. 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

  9. 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

  10. Halvade: scalable sequence analysis with MapReduce

    PubMed Central

    Decap, Dries; Reumers, Joke; Herzeel, Charlotte; Costanza, Pascal; Fostier, Jan

    2015-01-01

    Motivation: Post-sequencing DNA analysis typically consists of read mapping followed by variant calling. Especially for whole genome sequencing, this computational step is very time-consuming, even when using multithreading on a multi-core machine. Results: We present Halvade, a framework that enables sequencing pipelines to be executed in parallel on a multi-node and/or multi-core compute infrastructure in a highly efficient manner. As an example, a DNA sequencing analysis pipeline for variant calling has been implemented according to the GATK Best Practices recommendations, supporting both whole genome and whole exome sequencing. Using a 15-node computer cluster with 360 CPU cores in total, Halvade processes the NA12878 dataset (human, 100 bp paired-end reads, 50× coverage) in <3 h with very high parallel efficiency. Even on a single, multi-core machine, Halvade attains a significant speedup compared with running the individual tools with multithreading. Availability and implementation: Halvade is written in Java and uses the Hadoop MapReduce 2.0 API. It supports a wide range of distributions of Hadoop, including Cloudera and Amazon EMR. Its source is available at http://bioinformatics.intec.ugent.be/halvade under GPL license. Contact: jan.fostier@intec.ugent.be Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25819078

  11. 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

  12. Astrocytes generate Na+-mediated metabolic waves

    NASA Astrophysics Data System (ADS)

    Bernardinelli, Yann; Magistretti, Pierre J.; Chatton, Jean-Yves

    2004-10-01

    Glutamate-evoked Na+ increase in astrocytes has been identified as a signal coupling synaptic activity to glucose consumption. Astrocytes participate in multicellular signaling by transmitting intercellular Ca2+ waves. Here we show that intercellular Na+ waves are also evoked by activation of single cultured cortical mouse astrocytes in parallel with Ca2+ waves; however, there are spatial and temporal differences. Indeed, maneuvers that inhibit Ca2+ waves also inhibit Na+ waves; however, inhibition of the Na+/glutamate cotransporters or enzymatic degradation of extracellular glutamate selectively inhibit the Na+ wave. Thus, glutamate released by a Ca2+ wave-dependent mechanism is taken up by the Na+/glutamate cotransporters, resulting in a regenerative propagation of cytosolic Na+ increases. The Na+ wave gives rise to a spatially correlated increase in glucose uptake, which is prevented by glutamate transporter inhibition. Therefore, astrocytes appear to function as a network for concerted neurometabolic coupling through the generation of intercellular Na+ and metabolic waves.

  13. 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...

  14. 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

  15. 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.

  16. 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

  17. 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...

  18. Mass genotyping by sequencing technology

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Large scale genotyping of a moderate number of loci is cost prohibitive with current chip-based technologies. We demonstrate the ability to use next generation sequencing technologies to genotype many DNA samples for a moderate number of loci – a mass genotyping by sequencing technology (MGST). Ou...

  19. Sequence in the Social Studies

    ERIC Educational Resources Information Center

    Ediger, Marlow

    2010-01-01

    Quality sequence in the social studies is of utmost importance. Sequence emphasizes "when" selected concepts should be stressed in ongoing lessons and units of study. The social studies teacher needs to observe pupils carefully in teaching and learning situations to ascertain suitable, ordered experiences for pupils. Pupils face frustration if the…

  20. 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…

  1. Assembly of shotgun sequencing data

    SciTech Connect

    Huang, Xiaoqiu

    1996-12-31

    We present a simple algorithm for construction of the DNA sequence from a set of fragments generated in a shotgun sequencing project. The algorithm is based on rigorous detection of overlaps among fragments. We report assembly results of the algorithm on two genomic data sets. 14 refs., 1 fig.

  2. 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…

  3. 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…

  4. DNA Sequencing by Capillary Electrophoresis

    PubMed Central

    Karger, Barry L.; Guttman, Andras

    2009-01-01

    Sequencing of human and other genomes has been at the center of interest in the biomedical field over the past several decades and is now leading toward an era of personalized medicine. During this time, DNA sequencing methods have evolved from the labor intensive slab gel electrophoresis, through automated multicapillary electrophoresis systems using fluorophore labeling with multispectral imaging, to the “next generation” technologies of cyclic array, hybridization based, nanopore and single molecule sequencing. Deciphering the genetic blueprint and follow-up confirmatory sequencing of Homo sapiens and other genomes was only possible by the advent of modern sequencing technologies that was a result of step by step advances with a contribution of academics, medical personnel and instrument companies. While next generation sequencing is moving ahead at break-neck speed, the multicapillary electrophoretic systems played an essential role in the sequencing of the Human Genome, the foundation of the field of genomics. In this prospective, we wish to overview the role of capillary electrophoresis in DNA sequencing based in part of several of our articles in this journal. PMID:19517496

  5. 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…

  6. 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;…

  7. 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…

  8. Recently published protein sequences. I.

    NASA Technical Reports Server (NTRS)

    Jukes, T. H.; Holmquist, R.

    1972-01-01

    Some polypeptide sequences that have been published in the 1972 scientific literature are listed. Only selected sequences are included. The compilation has two objectives. Current information between periods when more comprehensive compilations are published is to be assembled and the use of data that do not include arrangements of unsequenced peptides for 'maximum homology' is to be encouraged.

  9. Sequence Learning and Selection Difficulty

    ERIC Educational Resources Information Center

    Rowland, Lee A.; Shanks, David R.

    2006-01-01

    The authors studied the role of attention as a selection mechanism in implicit learning by examining the effect on primary sequence learning of performing a demanding target-selection task. Participants were trained on probabilistic sequences in a novel version of the serial reaction time (SRT) task, with dual- and triple-stimulus participants…

  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. Direct Detection of Unnatural DNA Nucleotides dNaM and d5SICS using the MspA Nanopore.

    PubMed

    Craig, Jonathan M; Laszlo, Andrew H; Derrington, Ian M; Ross, Brian C; Brinkerhoff, Henry; Nova, Ian C; Doering, Kenji; Tickman, Benjamin I; Svet, Mark T; Gundlach, Jens H

    2015-01-01

    Malyshev et al. showed that the four-letter genetic code within a living organism could be expanded to include the unnatural DNA bases dNaM and d5SICS. However, verification and detection of these unnatural bases in DNA requires new sequencing techniques. Here we provide proof of concept detection of dNaM and d5SICS in DNA oligomers via nanopore sequencing using the nanopore MspA. We find that both phi29 DNA polymerase and Hel308 helicase are capable of controlling the motion of DNA containing dNaM and d5SICS through the pore and that single reads are sufficient to detect the presence and location of dNaM and d5SICS within single molecules. PMID:26588074

  12. Direct Detection of Unnatural DNA Nucleotides dNaM and d5SICS using the MspA Nanopore

    PubMed Central

    Craig, Jonathan M.; Laszlo, Andrew H.; Derrington, Ian M.; Ross, Brian C.; Brinkerhoff, Henry; Nova, Ian C.; Doering, Kenji; Tickman, Benjamin I.; Svet, Mark T.; Gundlach, Jens H.

    2015-01-01

    Malyshev et al. showed that the four-letter genetic code within a living organism could be expanded to include the unnatural DNA bases dNaM and d5SICS. However, verification and detection of these unnatural bases in DNA requires new sequencing techniques. Here we provide proof of concept detection of dNaM and d5SICS in DNA oligomers via nanopore sequencing using the nanopore MspA. We find that both phi29 DNA polymerase and Hel308 helicase are capable of controlling the motion of DNA containing dNaM and d5SICS through the pore and that single reads are sufficient to detect the presence and location of dNaM and d5SICS within single molecules. PMID:26588074

  13. 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

  14. Decoding the human genome sequence.

    PubMed

    Bentley, D R

    2000-10-01

    The year 2000 is marked by the production of the sequence of the human genome. A 'working draft' of high quality sequence covering 90% of the genome has been determined and a quarter is in finished form, including the first two completed chromosomes. All sequence data from the project is made freely available to the community via the Internet, for further analysis and exploitation. The challenge which lies ahead is to decipher the information. Knowledge of the human genome sequence will enable us to understand how the genetic information determines the development, structure and function of the human body. We will be able to explore how variations within our DNA sequence cause disease, how they affect our interaction with our environment and ultimately to develop new and effective ways to improve human health. PMID:11005789

  15. 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.

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  1. 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.

  2. Na+-stimulated ATPase of alkaliphilic halotolerant cyanobacterium Aphanothece halophytica translocates Na+ into proteoliposomes via Na+ uniport mechanism

    PubMed Central

    2010-01-01

    Background When cells are exposed to high salinity conditions, they develop a mechanism to extrude excess Na+ from cells to maintain the cytoplasmic Na+ concentration. Until now, the ATPase involved in Na+ transport in cyanobacteria has not been characterized. Here, the characterization of ATPase and its role in Na+ transport of alkaliphilic halotolerant Aphanothece halophytica were investigated to understand the survival mechanism of A. halophytica under high salinity conditions. Results The purified enzyme catalyzed the hydrolysis of ATP in the presence of Na+ but not K+, Li+ and Ca2+. The apparent Km values for Na+ and ATP were 2.0 and 1.2 mM, respectively. The enzyme is likely the F1F0-ATPase based on the usual subunit pattern and the protection against N,N'-dicyclohexylcarbodiimide inhibition of ATPase activity by Na+ in a pH-dependent manner. Proteoliposomes reconstituted with the purified enzyme could take up Na+ upon the addition of ATP. The apparent Km values for this uptake were 3.3 and 0.5 mM for Na+ and ATP, respectively. The mechanism of Na+ transport mediated by Na+-stimulated ATPase in A. halophytica was revealed. Using acridine orange as a probe, alkalization of the lumen of proteoliposomes reconstituted with Na+-stimulated ATPase was observed upon the addition of ATP with Na+ but not with K+, Li+ and Ca2+. The Na+- and ATP-dependent alkalization of the proteoliposome lumen was stimulated by carbonyl cyanide m - chlorophenylhydrazone (CCCP) but was inhibited by a permeant anion nitrate. The proteoliposomes showed both ATPase activity and ATP-dependent Na+ uptake activity. The uptake of Na+ was enhanced by CCCP and nitrate. On the other hand, both CCCP and nitrate were shown to dissipate the preformed electric potential generated by Na+-stimulated ATPase of the proteoliposomes. Conclusion The data demonstrate that Na+-stimulated ATPase from A. halophytica, a likely member of F-type ATPase, functions as an electrogenic Na+ pump which transports only

  3. 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

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

    PubMed

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

    2016-02-01

    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

  5. Default processing of event sequences.

    PubMed

    Hymel, Alicia; Levin, Daniel T; Baker, Lewis J

    2016-02-01

    In a wide range of circumstances, it is important to perceive and represent the sequence of events. For example, sequence perception is necessary to learn statistical contingencies between events, and to generate predictions about events when segmenting actions. However, viewer's awareness of event sequence is rarely tested, and at least some means of encoding event sequence are likely to be resource-intensive. Therefore, previous research may have overestimated the degree to which viewers are aware of specific event sequences. In the experiments reported here, we tested viewers' ability to detect anomalies during visual event sequences. Participants viewed videos containing events that either did or did not contain an out-of-order action. Participants were unable to consistently detect the misordered events, and performance on the task decreased significantly to very low levels when performing a secondary task. In addition, participants almost never detected misorderings in an incidental version of the task, and performance increased when videos ended immediately after the misordering, We argue that these results demonstrate that viewers can effectively perceive the elements of events, but do not consistently test their expectations about the specific sequence of natural events unless bidden to do so by task-specific demands. (PsycINFO Database Record PMID:26348070

  6. 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.

  7. 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

  8. 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

  9. Study Design for Sequencing Studies.

    PubMed

    Honaas, Loren A; Altman, Naomi S; Krzywinski, Martin

    2016-01-01

    Once a biochemical method has been devised to sample RNA or DNA of interest, sequencing can be used to identify the sampled molecules with high fidelity and low bias. High-throughput sequencing has therefore become the primary data acquisition method for many genomics studies and is being used more and more to address molecular biology questions. By applying principles of statistical experimental design, sequencing experiments can be made more sensitive to the effects under study as well as more biologically sound, hence more replicable. PMID:27008009

  10. 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.

  11. 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

  12. Complete Genome Sequences of Caldicellulosiruptor sp. Strain Rt8.B8, Caldicellulosiruptor sp. Strain Wai35.B1, and "Thermoanaerobacter cellulolyticus".

    PubMed

    Lee, Laura L; Izquierdo, Javier A; Blumer-Schuette, Sara E; Zurawski, Jeffrey V; Conway, Jonathan M; Cottingham, Robert W; Huntemann, Marcel; Copeland, Alex; Chen, I-Min A; Kyrpides, Nikos; Markowitz, Victor; Palaniappan, Krishnaveni; Ivanova, Natalia; Mikhailova, Natalia; Ovchinnikova, Galina; Andersen, Evan; Pati, Amrita; Stamatis, Dimitrios; Reddy, T B K; Shapiro, Nicole; Nordberg, Henrik P; Cantor, Michael N; Hua, Susan X; Woyke, Tanja; Kelly, Robert M

    2015-01-01

    The genus Caldicellulosiruptor contains extremely thermophilic, cellulolytic bacteria capable of lignocellulose deconstruction. Currently, complete genome sequences for eleven Caldicellulosiruptor species are available. Here, we report genome sequences for three additional Caldicellulosiruptor species: Rt8.B8 DSM 8990 (New Zealand), Wai35.B1 DSM 8977 (New Zealand), and "Thermoanaerobacter cellulolyticus" strain NA10 DSM 8991 (Japan). PMID:25977428

  13. Pythagorean Triples from Harmonic Sequences.

    ERIC Educational Resources Information Center

    DiDomenico, Angelo S.; Tanner, Randy J.

    2001-01-01

    Shows how all primitive Pythagorean triples can be generated from harmonic sequences. Use inductive and deductive reasoning to explore how Pythagorean triples are connected with another area of mathematics. (KHR)

  14. 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)

  15. Mining protein sequences for motifs.

    PubMed

    Narasimhan, Giri; Bu, Changsong; Gao, Yuan; Wang, Xuning; Xu, Ning; Mathee, Kalai

    2002-01-01

    We use methods from Data Mining and Knowledge Discovery to design an algorithm for detecting motifs in protein sequences. The algorithm assumes that a motif is constituted by the presence of a "good" combination of residues in appropriate locations of the motif. The algorithm attempts to compile such good combinations into a "pattern dictionary" by processing an aligned training set of protein sequences. The dictionary is subsequently used to detect motifs in new protein sequences. Statistical significance of the detection results are ensured by statistically determining the various parameters of the algorithm. Based on this approach, we have implemented a program called GYM. The Helix-Turn-Helix motif was used as a model system on which to test our program. The program was also extended to detect Homeodomain motifs. The detection results for the two motifs compare favorably with existing programs. In addition, the GYM program provides a lot of useful information about a given protein sequence. PMID:12487759

  16. 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)

  17. Expressed sequence tags: an overview.

    PubMed

    Parkinson, John; Blaxter, Mark

    2009-01-01

    Expressed sequence tags (ESTs) are fragments of mRNA sequences derived through single sequencing reactions performed on randomly selected clones from cDNA libraries. To date, over 45 million ESTs have been generated from over 1400 different species of eukaryotes. For the most part, EST projects are used to either complement existing genome projects or serve as low-cost alternatives for purposes of gene discovery. However, with improvements in accuracy and coverage, they are beginning to find application in fields such as phylogenetics, transcript profiling and proteomics. This volume provides practical details on the generation and analysis of ESTs. Chapters are presented which cover creation of cDNA libraries; generation and processing of sequence data; bioinformatics analysis of ESTs; and their application to phylogenetics and transcript profiling. PMID:19277571

  18. 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.)

  19. Thermodynamics of dissolution of lead oxide in NaOH-Na2CO3 melts

    NASA Astrophysics Data System (ADS)

    Barbin, N. M.; Barbina, T. M.

    2016-08-01

    The solubility of lead oxide in NaOH + (20%)Na2CO3 and NaOH + (40%)Na2CO3 melts was studied by the isothermal saturation method. The model mechanisms of dissolution were considered. The thermodynamic parameters were calculated.

  20. 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

  1. 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

  2. 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. PMID:24278218

  3. 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.

  4. 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

  5. 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

  6. Poultry Genome Sequences: Progress and Outstanding Challenges

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The first build of the chicken genome sequence appeared in March 2004 – the first genome sequence of any animal agriculture species. That sequence was done primarily by whole genome shotgun Sanger sequencing, along with the use of an extensive BAC contig-based physical map to assemble the sequence ...

  7. Genomic sequencing in clinical trials

    PubMed Central

    2011-01-01

    Human genome sequencing is the process by which the exact order of nucleic acid base pairs in the 24 human chromosomes is determined. Since the completion of the Human Genome Project in 2003, genomic sequencing is rapidly becoming a major part of our translational research efforts to understand and improve human health and disease. This article reviews the current and future directions of clinical research with respect to genomic sequencing, a technology that is just beginning to find its way into clinical trials both nationally and worldwide. We highlight the currently available types of genomic sequencing platforms, outline the advantages and disadvantages of each, and compare first- and next-generation techniques with respect to capabilities, quality, and cost. We describe the current geographical distributions and types of disease conditions in which these technologies are used, and how next-generation sequencing is strategically being incorporated into new and existing studies. Lastly, recent major breakthroughs and the ongoing challenges of using genomic sequencing in clinical research are discussed. PMID:22206293

  8. Elimination sequence optimization for SPAR

    NASA Technical Reports Server (NTRS)

    Hogan, Harry A.

    1986-01-01

    SPAR is a large-scale computer program for finite element structural analysis. The program allows user specification of the order in which the joints of a structure are to be eliminated since this order can have significant influence over solution performance, in terms of both storage requirements and computer time. An efficient elimination sequence can improve performance by over 50% for some problems. Obtaining such sequences, however, requires the expertise of an experienced user and can take hours of tedious effort to affect. Thus, an automatic elimination sequence optimizer would enhance productivity by reducing the analysts' problem definition time and by lowering computer costs. Two possible methods for automating the elimination sequence specifications were examined. Several algorithms based on the graph theory representations of sparse matrices were studied with mixed results. Significant improvement in the program performance was achieved, but sequencing by an experienced user still yields substantially better results. The initial results provide encouraging evidence that the potential benefits of such an automatic sequencer would be well worth the effort.

  9. 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

  10. 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.

  11. 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

  12. PANDAseq: paired-end assembler for illumina sequences

    PubMed Central

    2012-01-01

    Background Illumina paired-end reads are used to analyse microbial communities by targeting amplicons of the 16S rRNA gene. Publicly available tools are needed to assemble overlapping paired-end reads while correcting mismatches and uncalled bases; many errors could be corrected to obtain higher sequence yields using quality information. Results PANDAseq assembles paired-end reads rapidly and with the correction of most errors. Uncertain error corrections come from reads with many low-quality bases identified by upstream processing. Benchmarks were done using real error masks on simulated data, a pure source template, and a pooled template of genomic DNA from known organisms. PANDAseq assembled reads more rapidly and with reduced error incorporation compared to alternative methods. Conclusions PANDAseq rapidly assembles sequences and scales to billions of paired-end reads. Assembly of control libraries showed a 4-50% increase in the number of assembled sequences over naïve assembly with negligible loss of "good" sequence. PMID:22333067

  13. 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

  14. Sequencing and comparative analysis of the gorilla MHC genomic sequence.

    PubMed

    Wilming, Laurens G; Hart, Elizabeth A; Coggill, Penny C; Horton, Roger; Gilbert, James G R; Clee, Chris; Jones, Matt; Lloyd, Christine; Palmer, Sophie; Sims, Sarah; Whitehead, Siobhan; Wiley, David; Beck, Stephan; Harrow, Jennifer L

    2013-01-01

    Major histocompatibility complex (MHC) genes play a critical role in vertebrate immune response and because the MHC is linked to a significant number of auto-immune and other diseases it is of great medical interest. Here we describe the clone-based sequencing and subsequent annotation of the MHC region of the gorilla genome. Because the MHC is subject to extensive variation, both structural and sequence-wise, it is not readily amenable to study in whole genome shotgun sequence such as the recently published gorilla genome. The variation of the MHC also makes it of evolutionary interest and therefore we analyse the sequence in the context of human and chimpanzee. In our comparisons with human and re-annotated chimpanzee MHC sequence we find that gorilla has a trimodular RCCX cluster, versus the reference human bimodular cluster, and additional copies of Class I (pseudo)genes between Gogo-K and Gogo-A (the orthologues of HLA-K and -A). We also find that Gogo-H (and Patr-H) is coding versus the HLA-H pseudogene and, conversely, there is a Gogo-DQB2 pseudogene versus the HLA-DQB2 coding gene. Our analysis, which is freely available through the VEGA genome browser, provides the research community with a comprehensive dataset for comparative and evolutionary research of the MHC. PMID:23589541

  15. Analysis of the Na+/Ca2+ Exchanger Gene Family within the Phylum Nematoda

    PubMed Central

    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. PMID:25397810

  16. 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. PMID:25397810

  17. 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

  18. Distribution of sequence variation in the mtDNA control region of Native North Americans.

    PubMed

    Lorenz, J G; Smith, D G

    1997-12-01

    The distributions of mtDNA diversity within and/or among North American haplogroups, language groups, and tribes were used to characterize the process of tribalization that followed the colonization of the New World. Approximately 400 bp from the mtDNA control region of 1 Na-Dene and 33 Amerind individuals representing a wide variety of languages and geographic origins were sequenced. With the inclusion of data from previous studies, 225 native North American (284 bp) sequences representing 85 distinct mtDNA lineages were analyzed. Mean pairwise sequence differences between (and within) tribes and language groups were primarily due to differences in the distribution of three of the four major haplogroups that evolved before settlement of the New World. Pairwise sequence differences within each of these three haplogroups were more similar than previous studies based on restriction enzyme analysis have indicated. The mean of pairwise sequence differences between Amerind members of haplogroup A, the most common of the four haplogroups in North America, was only slightly higher than that for the Eskimo, providing no evidence of separate ancestry, but was about two-thirds higher than that for the Na-Dene. However, analysis of pairwise sequence divergence between only tribal-specific lineages, unweighted for sample size, suggests that random evolutionary processes have reduced sequence diversity within the Na-Dene and that members of all three language groups possess approximately equally diverse mtDNA lineages. Comparisons of diversity within and between specific ethnic groups with the largest sample size were also consistent with this outcome. These data are not consistent with the hypothesis that the New World was settled by more than a single migration. Because lineages tended not to cluster by tribe and because lineage sharing among linguistically unrelated groups was restricted to geographically proximate groups, the tribalization process probably did not occur

  19. A model of random sequences for de novo peptide sequencing

    SciTech Connect

    Jarman, Kenneth D.; Cannon, William R.; Jarman, Kristin H.; Heredia-Langner, Alejandro

    2003-04-15

    We present a model for the probability of random sequences appearing in product ion spectra obtained from tandem mass spectrometry experiments using collision-induced dissociation. We demonstrate the use of these probabilities for ranking candidate peptide sequences obtained using a de novo algorithm. Sequence candidates are obtained from a spectrum graph that is greatly reduced in size from those in previous graph-theoretical de novo approaches. Evidence of multiple instances of subsequences of each candidate, due to different fragment ion type series as well as isotopic peaks, is incorporated in a hierarchical scoring scheme. This approach is shown to be useful for confirming results from database search and as a first step towards a statistically rigorous de novo algorithm.

  20. 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. PMID:14631656

  1. Whole Chloroplast Genome Sequencing in Fragaria Using Deep Sequencing: A Comparison of Three Methods

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Chloroplast sequences previously investigated in Fragaria revealed low amounts of variation. Deep sequencing technologies enable economical sequencing of complete chloroplast genomes. These sequences can potentially provide robust phylogenetic resolution, even at low taxonomic levels within plant gr...

  2. 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.

  3. 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.

  4. 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

  5. Engineered DNA sequence syntax inspector.

    PubMed

    Hsiau, Timothy Hwei-Chung; Anderson, J Christopher

    2014-02-21

    DNAs encoding polypeptides often contain design errors that cause experiments to prematurely fail. One class of design errors is incorrect or missing elements in the DNA, here termed syntax errors. We have identified three major causes of syntax errors: point mutations from sequencing or manual data entry, gene structure misannotation, and unintended open reading frames (ORFs). The Engineered DNA Sequence Syntax Inspector (EDSSI) is an online bioinformatics pipeline that checks for syntax errors through three steps. First, ORF prediction in input DNA sequences is done by GeneMark; next, homologous sequences are retrieved by BLAST, and finally, syntax errors in the protein sequence are predicted by using the SIFT algorithm. We show that the EDSSI is able to identify previously published examples of syntactical errors and also show that our indel addition to the SIFT program is 97% accurate on a test set of Escherichia coli proteins. The EDSSI is available at http://andersonlab.qb3.berkeley.edu/Software/EDSSI/ . PMID:24364864

  6. 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.

  7. 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.

  8. Detecting selection in immunoglobulin sequences.

    PubMed

    Uduman, Mohamed; Yaari, Gur; Hershberg, Uri; Stern, Jacob A; Shlomchik, Mark J; Kleinstein, Steven H

    2011-07-01

    The ability to detect selection by analyzing mutation patterns in experimentally derived immunoglobulin (Ig) sequences is a critical part of many studies. Such techniques are useful not only for understanding the response to pathogens, but also to determine the role of antigen-driven selection in autoimmunity, B cell cancers and the diversification of pre-immune repertoires in certain species. Despite its importance, quantifying selection in experimentally derived sequences is fraught with difficulties. The necessary parameters for statistical tests (such as the expected frequency of replacement mutations in the absence of selection) are non-trivial to calculate, and results are not easily interpretable when analyzing more than a handful of sequences. We have developed a web server that implements our previously proposed Focused binomial test for detecting selection. Several features are integrated into the web site in order to facilitate analysis, including V(D)J germline segment identification with IMGT alignment, batch submission of sequences and integration of additional test statistics proposed by other groups. We also implement a Z-score-based statistic that increases the power of detecting selection while maintaining specificity, and further allows for the combined analysis of sequences from different germlines. The tool is freely available at http://clip.med.yale.edu/selection. PMID:21665923

  9. Statistical properties of DNA sequences

    NASA Astrophysics Data System (ADS)

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

    1995-02-01

    We review evidence supporting the idea that the DNA sequence in genese 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 (33 301 coding and 29 453 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.

  10. 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

  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. 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.

  13. Statistical analysis of nucleotide sequences.

    PubMed Central

    Stückle, E E; Emmrich, C; Grob, U; Nielsen, P J

    1990-01-01

    In order to scan nucleic acid databases for potentially relevant but as yet unknown signals, we have developed an improved statistical model for pattern analysis of nucleic acid sequences by modifying previous methods based on Markov chains. We demonstrate the importance of selecting the appropriate parameters in order for the method to function at all. The model allows the simultaneous analysis of several short sequences with unequal base frequencies and Markov order k not equal to 0 as is usually the case in databases. As a test of these modifications, we show that in E. coli sequences there is a bias against palindromic hexamers which correspond to known restriction enzyme recognition sites. PMID:2251125

  14. Sequence alignment with tandem duplication

    SciTech Connect

    Benson, G.

    1997-12-01

    Algorithm development for comparing and aligning biological sequences has, until recently, been based on the SI model of mutational events which assumes that modification of sequences proceeds through any of the operations of substitution, insertion or deletion (the latter two collectively termed indels). While this model has worked farily well, it has long been apparent that other mutational events occur. In this paper, we introduce a new model, the DSI model which includes another common mutational event, tandem duplication. Tandem duplication produces tandem repeats which are common in DNA, making up perhaps 10% of the human genome. They are responsible for some human diseases and may serve a multitude of functions in DNA regulation and evolution. Using the DSI model, we develop new exact and heuristic algorithms for comparing and aligning DNA sequences when they contain tandem repeats. 30 refs., 3 figs.

  15. Sequence-invariant state machines

    NASA Astrophysics Data System (ADS)

    Whitaker, Sterling R.; Manjunath, Shamanna K.; Maki, Gary K.

    1991-08-01

    A synthesis method and an MOS VLSI architecture are presented to realize sequential circuits that have the ability to implement any state machine having N states and m inputs, regardless of the actual sequence specified in the flow table. The design method utilizes binary tree structured (BTS) logic to implement regular and dense circuits. The desired state sequence can be hardwired with power supply connections or can be dynamically reallocated if stored in a register. This allows programmable VLSI controllers to be designed with a compact size and performance approaching that of dedicated logic. Results of ICV implementations are reported and an example sequence-invariant state machine is contrasted with implementations based on traditional methods.

  16. Graph Partitioning and Sequencing Software

    Energy Science and Technology Software Center (ESTSC)

    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

  17. Composition for nucleic acid sequencing

    DOEpatents

    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. 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

  19. 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

  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. Regulation of next generation sequencing.

    PubMed

    Javitt, Gail H; Carner, Katherine Strong

    2014-01-01

    Next generation sequencing raises new questions within the context of an existing and still evolving regulatory landscape for device manufacturers and clinical laboratories. FDA cleared the first NGS sequencing platform in November 2013, but it is unclear what lies ahead for this technology. NGS will require new types of training and expertise to interpret the vast quantities of genetic data so as to provide meaningful clinical information to physicians and patients. This paper will describe the current regulatory landscape for NGS technologies, identify the regulatory challenges they present, and consider whether new regulatory paradigms are needed to accommodate NGS technologies and services. PMID:25298288

  2. Endogenized viral sequences in mammals.

    PubMed

    Parrish, Nicholas F; Tomonaga, Keizo

    2016-06-01

    Reverse-transcribed RNA molecules compose a significant portion of the human genome. Many of these RNA molecules were retrovirus genomes either infecting germline cells or having done so in a previous generation but retaining transcriptional activity. This mechanism itself accounts for a quarter of the genomic sequence information of mammals for which there is data. We understand relatively little about the causes and consequences of retroviral endogenization. This review highlights functions ascribed to sequences of viral origin endogenized into mammalian genomes and suggests some of the most pressing questions raised by these observations. PMID:27128186

  3. High speed nucleic acid sequencing

    DOEpatents

    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.

  4. Detection of latent sequence periodicities.

    PubMed Central

    Pizzi, E; Liuni, S; Frontali, C

    1990-01-01

    A method is proposed for the automatic detection of serial periodicities in a linear sequence. Its application to DNA subtelomeric sequences from two lower eukaryotes, P.falciparum and S.cerevisiae, reveals ordered patterns organised in hierarchical periodicities, not easily recognizable by other methods. The possible implications concerning the evolution of tandemly repetitive arrays are discussed in light of a model which involves, as successive steps, random repeat modification, the fusion of differently modified repeat versions into longer units, and the amplification of (and/or homogenization to) the more recent repeat units. PMID:2197595

  5. 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

  6. 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.

  7. Maintaining the NA atmosphere of Mercury

    NASA Astrophysics Data System (ADS)

    Killen, R. M.; Morgan, T. H.

    1993-02-01

    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.

  8. 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.

  9. The effect of NA vapor on the NA content of chondrules

    NASA Astrophysics Data System (ADS)

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

    1993-12-01

    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 PNa for these experimental conditions to be in the 10-6 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 of producing

  10. Tracking simple and complex sequences.

    PubMed

    Large, Edward W; Fink, Philip; Kelso, J A Scott

    2002-02-01

    We address issues of synchronization to rhythms of musical complexity. In two experiments, synchronization to simple and more complex rhythmic sequences was investigated. Experiment 1 examined responses to phase and tempo perturbations within simple, structurally isochronous sequences, presented at different base rates. Experiment 2 investigated responses to similar perturbations embedded within more complex, metrically structured sequences; participants were explicitly instructed to synchronize at different metrical levels (i.e., tap at different rates to the same rhythmic patterns) on different trials. We found evidence that (1) the intrinsic tapping frequency adapts in response to temporal perturbations in both simple (isochronous) and complex (metrically structured) rhythms, (2) people can synchronize with unpredictable, metrically structured rhythms at different metrical levels, with qualitatively different patterns of synchronization seen at higher versus lower levels of metrical structure, and (3) synchronization at each tapping level reflects information from other metrical levels. The latter finding provides evidence for a dynamic and flexible internal representation of the sequence's metrical structure. PMID:11963276

  11. 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…

  12. 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. PMID:18495751

  13. Crop Sequence Calculator, v. 3

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Producers need to know how to sequence crops to develop sustainable dynamic cropping systems that take advantage of inherent internal resources, such as crop synergism, nutrient cycling, and soil water, and capitalize on external resources, such as weather, markets, and government programs. Version ...

  14. 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

  15. [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

  16. 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…

  17. Teaching Task Sequencing via Verbal Mediation.

    ERIC Educational Resources Information Center

    Rusch, Frank R.; And Others

    1987-01-01

    Verbal sequence training was used to teach a moderately mentally retarded woman to sequence job-related tasks. Learning to say the tasks in the proper sequence resulted in the employee performing her tasks in that sequence, and the employee was capable of mediating her own work behavior when scheduled changes occurred. (Author/JDD)

  18. 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…

  19. 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.

  20. 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.

  1. Extracellular Vesicles of the Hyperthermophilic Archaeon “Thermococcus onnurineus” NA1T

    PubMed Central

    Choi, Dong Hee; Kwon, Yong Min; Chiura, Hiroshi Xavier; Yang, Eun Chan; Bae, Seung Seob; Kang, Sung Gyun; Lee, Jung-Hyun; Yoon, Hwan Su

    2015-01-01

    Extracellular vesicles (EVs) produced by a sulfur-reducing, hyperthermophilic archaeon, “Thermococcus onnurineus” NA1T, were purified and characterized. A maximum of four EV bands, showing buoyant densities between 1.1899 and 1.2828 g cm−3, were observed after CsCl ultracentrifugation. The two major EV bands, B (buoyant density at 25°C [ρ25] = 1.2434 g cm−3) and C (ρ25 = 1.2648 g cm−3), were separately purified and counted using a qNano particle analyzer. These EVs, showing different buoyant densities, were identically spherical in shape, and their sizes varied from 80 to 210 nm in diameter, with 120- and 190-nm sizes predominant. The average size of DNA packaged into EVs was about 14 kb. The DNA of the EVs in band C was sequenced and assembled. Mapping of the T. onnurineus NA1T EV (ToEV) DNA sequences onto the reference genome of the parent archaeon revealed that most genes of T. onnurineus NA1T were packaged into EVs, except for an ∼9.4-kb region from TON_0536 to TON_0544. The absence of this specific region of the genome in the EVs was confirmed from band B of the same culture and from bands B and C purified from a different batch culture. The presence of the 3′-terminal sequence and the absence of the 5′-terminal sequence of TON_0536 were repeatedly confirmed. On the basis of these results, we hypothesize that the unpackaged part of the T. onnurineus NA1T genome might be related to the process that delivers DNA into ToEVs and/or the mechanism generating the ToEVs themselves. PMID:25934618

  2. 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. PMID:26729471

  3. 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

  4. 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

  5. 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

  6. Draft Genome Sequence of Arthrobacter enclensis NCIM 5488T for Secondary Metabolism.

    PubMed

    Neurgaonkar, Priya S; Dharne, Mahesh S; Dastager, Syed G

    2016-01-01

    Here, we report the draft genome sequence of Arthrobacter enclensis NCIM 5488(T), 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

  7. 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.

  8. 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

  9. Gene Discovery through Expressed Sequence Tag Sequencing in Trypanosoma cruzi

    PubMed Central

    Verdun, Ramiro E.; Di Paolo, Nelson; Urmenyi, Turan P.; Rondinelli, Edson; Frasch, Alberto C. C.; Sanchez, Daniel O.

    1998-01-01

    Analysis of expressed sequence tags (ESTs) constitutes a useful approach for gene identification that, in the case of human pathogens, might result in the identification of new targets for chemotherapy and vaccine development. As part of the Trypanosoma cruzi genome project, we have partially sequenced the 5′ ends of 1,949 clones to generate ESTs. The clones were randomly selected from a normalized CL Brener epimastigote cDNA library. A total of 14.6% of the clones were homologous to previously identified T. cruzi genes, while 18.4% had significant matches to genes from other organisms in the database. A total of 67% of the ESTs had no matches in the database, and thus, some of them might be T. cruzi-specific genes. Functional groups of those sequences with matches in the database were constructed according to their putative biological functions. The two largest categories were protein synthesis (23.3%) and cell surface molecules (10.8%). The information reported in this paper should be useful for researchers in the field to analyze genes and proteins of their own interest. PMID:9784549

  10. 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

  11. Genome Sequence and Comparative Genomics Analysis of a Vibrio cholerae O1 Strain Isolated from a Cholera Patient in Malaysia

    PubMed Central

    Osama, Abdulrazak; Gan, Han Ming; Teh, Cindy Shuan Ju; Yap, Kien-Pong

    2012-01-01

    The genome sequence analysis of a clinical Vibrio cholerae VC35 strain from an outbreak case in Malaysia indicates multiple genes involved in host adaptation and a novel Na+-driven multidrug efflux pump-coding gene in the genome of Vibrio cholerae with the highest similarity to VMA_001754 of Vibrio mimicus VMA223. PMID:23209200

  12. 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.

  13. 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

  14. 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

  15. Partial Antiviral Activities Detection of Chicken Mx Jointing with Neuraminidase Gene (NA) against Newcastle Disease Virus

    PubMed Central

    Zhang, Yani; Fu, Dezhi; Chen, Hao; Zhang, Zhentao; Shi, Qingqing; Elsayed, Ahmed Kamel; Li, Bichun

    2013-01-01

    As an attempt to increase the resistance to Newcastle Disease Virus (NDV) and so further reduction of its risk on the poultry industry. This work aimed to build the eukaryotic gene co-expression plasmid of neuraminidase (NA) gene and myxo-virus resistance (Mx) and detect the gene expression in transfected mouse fibroblasts (NIH-3T3) cells, it is most important to investigate the influence of the recombinant plasmid on the chicken embryonic fibroblasts (CEF) cells. cDNA fragment of NA and mutant Mx gene were derived from pcDNA3.0-NA and pcDNA3.0-Mx plasmid via PCR, respectively, then NA and Mx cDNA fragment were inserted into the multiple cloning sites of pVITRO2 to generate the eukaryotic co-expression plasmid pVITRO2-Mx-NA. The recombinant plasmid was confirmed by restriction endonuclease treatment and sequencing, and it was transfected into the mouse fibroblasts (NIH-3T3) cells. The expression of genes in pVITRO2-Mx-NA were measured by RT-PCR and indirect immunofluorescence assay (IFA). The recombinant plasmid was transfected into CEF cells then RT-PCR and the micro-cell inhibition tests were used to test the antiviral activity for NDV. Our results showed that co-expression vector pVITRO2-Mx-NA was constructed successfully; the expression of Mx and NA could be detected in both NIH-3T3 and CEF cells. The recombinant proteins of Mx and NA protect CEF cells from NDV infection until after 72 h of incubation but the individually mutagenic Mx protein or NA protein protects CEF cells from NDV infection till 48 h post-infection, and co-transfection group decreased significantly NDV infection compared with single-gene transfection group (P<0. 05), indicating that Mx-NA jointing contributed to delaying the infection of NDV in single-cell level and the co-transfection of the jointed genes was more powerful than single one due to their synergistic effects. PMID:23977111

  16. Visual mislocalization during saccade sequences.

    PubMed

    Zimmermann, Eckart; Morrone, Maria Concetta; Burr, David

    2015-02-01

    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

  17. 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.

  18. 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.

  19. Sequence correlations shape protein promiscuity

    NASA Astrophysics Data System (ADS)

    Lukatsky, David B.; Afek, Ariel; Shakhnovich, Eugene I.

    2011-08-01

    We predict analytically that diagonal correlations of amino acid positions within protein sequences statistically enhance protein propensity for nonspecific binding. We use the term "promiscuity" to describe such nonspecific binding. Diagonal correlations represent statistically significant repeats of sequence patterns where amino acids of the same type are clustered together. The predicted effect is qualitatively robust with respect to the form of the microscopic interaction potentials and the average amino acid composition. Our analytical results provide an explanation for the enhanced diagonal correlations observed in hubs of eukaryotic organismal proteomes [J. Mol. Biol. 409, 439 (2011)], 10.1016/j.jmb.2011.03.056. We suggest experiments that will allow direct testing of the predicted effect.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. Na3DyCl6

    PubMed Central

    Schurz, Christian M.; Meyer, Gerd; Schleid, Thomas

    2011-01-01

    Single crystals of the title compound, tris­odium hexa­chloridodysprosate, Na3DyCl6, were obtained as a by-product of synthesis using dysprosium(III) chloride and sodium chloride among others. The monoclinic structure with its typical β angle close to 90° [90.823 (4)°] is isotypic with the mineral cryolite (Na3AlF6) and the high-temperature structure of the Na3 MCl6 series, with M = Eu–Lu, Y and Sc. The isolated, almost perfect [DyCl6]3− octa­hedra are inter­connected via two crystallographically different Na+ cations: while one Na+ resides on centres of symmetry (as well as Dy3+) and also builds almost perfect, isolated [NaCl6]5− octa­hedra, the other Na+ is surrounded by seven chloride anions forming a distorted [NaCl7]6− trigonal prism with just one cap as close secondary contact. PMID:21754259

  5. Na(3)DyCl(6).

    PubMed

    Schurz, Christian M; Meyer, Gerd; Schleid, Thomas

    2011-05-01

    Single crystals of the title compound, tris-odium hexa-chloridodysprosate, Na(3)DyCl(6), were obtained as a by-product of synthesis using dysprosium(III) chloride and sodium chloride among others. The monoclinic structure with its typical β angle close to 90° [90.823 (4)°] is isotypic with the mineral cryolite (Na(3)AlF(6)) and the high-temperature structure of the Na(3)MCl(6) series, with M = Eu-Lu, Y and Sc. The isolated, almost perfect [DyCl(6)](3-) octa-hedra are inter-connected via two crystallographically different Na(+) cations: while one Na(+) resides on centres of symmetry (as well as Dy(3+)) and also builds almost perfect, isolated [NaCl(6)](5-) octa-hedra, the other Na(+) is surrounded by seven chloride anions forming a distorted [NaCl(7)](6-) trigonal prism with just one cap as close secondary contact. PMID:21754259

  6. 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.

  7. 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.

  8. Dynamical model for DNA sequences

    NASA Astrophysics Data System (ADS)

    Allegrini, P.; Barbi, M.; Grigolini, P.; West, B. J.

    1995-11-01

    We address the problem of DNA sequences, developing a ``dynamical'' method based on the assumption that the statistical properties of DNA paths are determined by the joint action of two processes, one deterministic with long-range correlations, and the other random and δ-function correlated. The generator of the deterministic evolution is a nonlinear map, belonging to a class of maps recently tailored to mimic the processes of weak chaos that are responsible for the birth of anomalous diffusion. It is assumed that the deterministic process corresponds to unknown biological rules that determine the DNA path, whereas the noise mimics the influence of an infinite-dimensional environment on the biological process under study. We prove that the resulting diffusion process, if the effect of the random process is neglected, is an α-stable Lévy process with 1<α<2. We also show that, if the diffusion process is determined by the joint action of the deterministic and the random process, the correlation effects of the ``deterministic dynamics'' are cancelled on the short-range scale, but show up in the long-range one. We denote our prescription to generate statistical sequences as the copying mistake map (CMM). We carry out our analysis of several DNA sequences and their CMM realizations with a variety of techniques, and we especially focus on a method of regression to equilibrium, which we call the Onsager analysis. With these techniques we establish the statistical equivalence of the real DNA sequences with their CMM realizations. We show that long-range correlations are present in exons as well as in introns, but are difficult to detect, since the exon ``dynamics'' is shown to be determined by the entanglement of three distinct and independent CMM's.

  9. Insertion Sequence Diversity in Archaea

    PubMed Central

    Filée, J.; Siguier, P.; Chandler, M.

    2007-01-01

    Insertion sequences (ISs) can constitute an important component of prokaryotic (bacterial and archaeal) genomes. Over 1,500 individual ISs are included at present in the ISfinder database (www-is.biotoul.fr), and these represent only a small portion of those in the available prokaryotic genome sequences and those that are being discovered in ongoing sequencing projects. In spite of this diversity, the transposition mechanisms of only a few of these ubiquitous mobile genetic elements are known, and these are all restricted to those present in bacteria. This review presents an overview of ISs within the archaeal kingdom. We first provide a general historical summary of the known properties and behaviors of archaeal ISs. We then consider how transposition might be regulated in some cases by small antisense RNAs and by termination codon readthrough. This is followed by an extensive analysis of the IS content in the sequenced archaeal genomes present in the public databases as of June 2006, which provides an overview of their distribution among the major archaeal classes and species. We show that the diversity of archaeal ISs is very great and comparable to that of bacteria. We compare archaeal ISs to known bacterial ISs and find that most are clearly members of families first described for bacteria. Several cases of lateral gene transfer between bacteria and archaea are clearly documented, notably for methanogenic archaea. However, several archaeal ISs do not have bacterial equivalents but can be grouped into Archaea-specific groups or families. In addition to ISs, we identify and list nonautonomous IS-derived elements, such as miniature inverted-repeat transposable elements. Finally, we present a possible scenario for the evolutionary history of ISs in the Archaea. PMID:17347521

  10. 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.

  11. Partial reactions of the Na,K-ATPase: determination of rate constants

    PubMed Central

    1994-01-01

    , which were performed at various Na concentrations in the absence and presence of strophanthidin, we found that the transition (Na3).E1-P-->P-E2.(Na2) is the major charge translocating step in the reaction sequence Na3.E1-->(Na3).E1-P-->P-E2.(Na2)-->P-E2. The subsequent release of 2 Na+ ions contributed less than 25% to the total electric current transient. (d) The well known antagonism between cardiotonic steroids and K+ binding can be explained by a kinetic model. A quantitative description has been obtained under the assumption that these inhibitors bind only to the states P-E2(Na2) and P-E2(K2).(ABSTRACT TRUNCATED AT 400 WORDS) PMID:7807047

  12. 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

  13. RNA sequence analysis using covariance models.

    PubMed Central

    Eddy, S R; Durbin, R

    1994-01-01

    We describe a general approach to several RNA sequence analysis problems using probabilistic models that flexibly describe the secondary structure and primary sequence consensus of an RNA sequence family. We call these models 'covariance models'. A covariance model of tRNA sequences is an extremely sensitive and discriminative tool for searching for additional tRNAs and tRNA-related sequences in sequence databases. A model can be built automatically from an existing sequence alignment. We also describe an algorithm for learning a model and hence a consensus secondary structure from initially unaligned example sequences and no prior structural information. Models trained on unaligned tRNA examples correctly predict tRNA secondary structure and produce high-quality multiple alignments. The approach may be applied to any family of small RNA sequences. Images PMID:8029015

  14. Biological sequence classification with multivariate string kernels.

    PubMed

    Kuksa, Pavel P

    2013-01-01

    String kernel-based machine learning methods have yielded great success in practical tasks of structured/sequential data analysis. They often exhibit state-of-the-art performance on many practical tasks of sequence analysis such as biological sequence classification, remote homology detection, or protein superfamily and fold prediction. However, typical string kernel methods rely on the analysis of discrete 1D string data (e.g., DNA or amino acid sequences). In this paper, we address the multiclass biological sequence classification problems using multivariate representations in the form of sequences of features vectors (as in biological sequence profiles, or sequences of individual amino acid physicochemical descriptors) and a class of multivariate string kernels that exploit these representations. On three protein sequence classification tasks, the proposed multivariate representations and kernels show significant 15-20 percent improvements compared to existing state-of-the-art sequence classification methods. PMID:24384708

  15. Biological Sequence Analysis with Multivariate String Kernels.

    PubMed

    Kuksa, Pavel P

    2013-03-01

    String kernel-based machine learning methods have yielded great success in practical tasks of structured/sequential data analysis. They often exhibit state-of-the-art performance on many practical tasks of sequence analysis such as biological sequence classification, remote homology detection, or protein superfamily and fold prediction. However, typical string kernel methods rely on analysis of discrete one-dimensional (1D) string data (e.g., DNA or amino acid sequences). In this work we address the multi-class biological sequence classification problems using multivariate representations in the form of sequences of features vectors (as in biological sequence profiles, or sequences of individual amino acid physico-chemical descriptors) and a class of multivariate string kernels that exploit these representations. On a number of protein sequence classification tasks proposed multivariate representations and kernels show significant 15-20\\% improvements compared to existing state-of-the-art sequence classification methods. PMID:23509193

  16. Factors That Affect Large Subunit Ribosomal DNA Amplicon Sequencing Studies of Fungal Communities: Classification Method, Primer Choice, and Error

    PubMed Central

    Porter, Teresita M.; Golding, G. Brian

    2012-01-01

    Nuclear large subunit ribosomal DNA is widely used in fungal phylogenetics and to an increasing extent also amplicon-based environmental sequencing. The relatively short reads produced by next-generation sequencing, however, makes primer choice and sequence error important variables for obtaining accurate taxonomic classifications. In this simulation study we tested the performance of three classification methods: 1) a similarity-based method (BLAST + Metagenomic Analyzer, MEGAN); 2) a composition-based method (Ribosomal Database Project naïve Bayesian classifier, NBC); and, 3) a phylogeny-based method (Statistical Assignment Package, SAP). We also tested the effects of sequence length, primer choice, and sequence error on classification accuracy and perceived community composition. Using a leave-one-out cross validation approach, results for classifications to the genus rank were as follows: BLAST + MEGAN had the lowest error rate and was particularly robust to sequence error; SAP accuracy was highest when long LSU query sequences were classified; and, NBC runs significantly faster than the other tested methods. All methods performed poorly with the shortest 50–100 bp sequences. Increasing simulated sequence error reduced classification accuracy. Community shifts were detected due to sequence error and primer selection even though there was no change in the underlying community composition. Short read datasets from individual primers, as well as pooled datasets, appear to only approximate the true community composition. We hope this work informs investigators of some of the factors that affect the quality and interpretation of their environmental gene surveys. PMID:22558215

  17. Fluorescence-detected DNA sequencing

    SciTech Connect

    Haugland, R.P.

    1990-01-01

    Our research effort funded by this grant primarily focused on development of suitable fluorescent dyes for DNA sequencing studies. Prior to our efforts, the dyes being sued in commercial DNA sequencers were various versions of fluorescein dyes for the shorter wavelengths and of rhodamine dyes for the longer wavelengths. Our initial goal was to synthesize a set of four dyes that could all be excited by the 488 and 514 nm line of the argon laser lines and that have emission spectra that minimize spectral overlap. The specific result sought was higher fluorescent intensity, particularly of the longest wavelength dyes than was available using existing dyes. Another important property of the desired set of dyes was uniform ionic charge in order to have minimum interference on the electrophoretic mobility during the sequencing. During the period of this grant we prepared and characterized four types of dyes: fluorescent bifluorophores, derivatives of rhodamine dyes, derivatives of rhodol dyes and derivatives of boron dipyrromethene difluoride (BODIPY{trademark}) dyes.

  18. Spectral clustering of protein sequences

    PubMed Central

    Paccanaro, Alberto; Casbon, James A.; Saqi, Mansoor A. S.

    2006-01-01

    An important problem in genomics is automatically clustering homologous proteins when only sequence information is available. Most methods for clustering proteins are local, and are based on simply thresholding a measure related to sequence distance. We first show how locality limits the performance of such methods by analysing the distribution of distances between protein sequences. We then present a global method based on spectral clustering and provide theoretical justification of why it will have a remarkable improvement over local methods. We extensively tested our method and compared its performance with other local methods on several subsets of the SCOP (Structural Classification of Proteins) database, a gold standard for protein structure classification. We consistently observed that, the number of clusters that we obtain for a given set of proteins is close to the number of superfamilies in that set; there are fewer singletons; and the method correctly groups most remote homologs. In our experiments, the quality of the clusters as quantified by a measure that combines sensitivity and specificity was consistently better [on average, improvements were 84% over hierarchical clustering, 34% over Connected Component Analysis (CCA) (similar to GeneRAGE) and 72% over another global method, TribeMCL]. PMID:16547200

  19. 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

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. The modular structure of informational sequences.

    PubMed

    Schmitt, A O; Ebeling, W; Herzel, H

    1996-01-01

    It is shown that DNA sequences can be decomposed into smaller units much the same as texts can be decomposed into syllables, words, or groups of words. Those smaller units (modules) are extracted from DNA sequences according to statistical criteria. Tests with sequences of known modular structure (two novels and a FORTRAN source code) were performed. The rate to which DNA sequences can be decomposed into modules (modularity) turns out to be a very sensitive measure to distinguish DNA sequences from random sequences. PMID:8924645

  6. 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.

  7. A simple method for global sequence comparison.

    PubMed Central

    Pizzi, E; Attimonelli, M; Liuni, S; Frontali, C; Saccone, C

    1992-01-01

    A simple method of sequence comparison, based on a correlation analysis of oligonucleotide frequency distributions, is here shown to be a reliable test of overall sequence similarity. The method does not involve sequence alignment procedures and permits the rapid screening of large amounts of sequence data. It identifies those sequences which deserve more careful analysis of sequence similarity at the level of resolution of the single nucleotide. It uses observed quantities only and does not involve the adoption of any theoretical model. PMID:1738591

  8. Cytosolic Na+ Controls an Epithelial Na+ Channel Via the Go Guanine Nucleotide-Binding Regulatory Protein

    NASA Astrophysics Data System (ADS)

    Komwatana, P.; Dinudom, A.; Young, J. A.; Cook, D. I.

    1996-07-01

    In tight Na+-absorbing epithelial cells, the rate of Na+ entry through amiloride-sensitive apical membrane Na+ channels is matched to basolateral Na+ extrusion so that cell Na+ concentration and volume remain steady. Control of this process by regulation of apical Na+ channels has been attributed to changes in cytosolic Ca2+ concentration or pH, secondary to changes in cytosolic Na+ concentration, although cytosolic Cl- seems also to be involved. Using mouse mandibular gland duct cells, we now demonstrate that increasing cytosolic Na+ concentration inhibits apical Na+ channels independent of changes in cytosolic Ca2+, pH, or Cl-, and the effect is blocked by GDP-β -S, pertussis toxin, and antibodies against the α -subunits of guanine nucleotide-binding regulatory proteins (Go). In contrast, the inhibitory effect of cytosolic anions is blocked by antibodies to inhibitory guanine nucleotide-binding regulatory proteins (Gi1/Gi2. It thus appears that apical Na+ channels are regulated by Go and Gi proteins, the activities of which are controlled, respectively, by cytosolic Na+ and Cl-.

  9. 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

  10. Na and K Dependence of the Na/K Pump in Cystic Fibrosis Fibroblasts

    NASA Astrophysics Data System (ADS)

    Reznik, Vivian M.; Schneider, Jerry A.; Mendoza, Stanley A.

    1981-11-01

    The Na and K dependence of the Na/K pump was measured in skin fibroblasts from patients with cystic fibrosis and age/sex-matched controls. Under basal conditions, there was no difference between control and cystic fibrosis cells in protein per cell, intracellular Na and K content, or Na/K pump activity (measured as ouabain-sensitive 86Rb uptake). There was no difference in the Na dependence of the Na/K pump between cystic fibrosis cells and control cells. In cells from patients with cystic fibrosis, the Na/K pump had a significantly lower affinity for K (Km = 1.6 mM) when compared to normals (Km = 0.9 mM). This difference was demonstrated by using two independent experimental designs.

  11. 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.

  12. Intracellular Na+ kinetically interferes with the rotation of the Na(+)-driven flagellar motors of Vibrio alginolyticus.

    PubMed

    Yoshida, S; Sugiyama, S; Hojo, Y; Tokuda, H; Imae, Y

    1990-11-25

    To understand the mechanism of Na+ movement through the force-generating units of the Na(+)-driven flagellar motors of Vibrio alginolyticus, the effect of intracellular Na+ concentration on motor rotation was investigated. Control cells containing about 50 mM Na+ showed good motility even at 10 mM Na+ in the medium, i.e. in the absence of an inwardly directed Na+ gradient. In contrast, Na(+)-loaded cells containing about 400 mM Na+ showed very poor motility at 500 mM Na+ in the medium, i.e. even in the presence of an inwardly directed Na+ gradient. The membrane potential of the cells, which is a major driving force for the motor under these conditions, was not detectably altered, and consistently with this, Na(+)-coupled sucrose transport was only partly reduced in the Na(+)-loaded cells. Motility of the Na(+)-loaded cells was restored by decreasing the intracellular Na+ concentration, and the rate of restoration of motility correlated with the rate of the Na+ decrease. These results indicate that the absolute concentration of the intracellular Na+ is a determinant of the rotation rate of the Na(+)-driven flagellar motors of V. alginolyticus. A simple explanation for this phenomenon is that the force-generating unit of the motor has an intracellular Na(+)-binding site, at which the intracellular Na+ kinetically interferes with the rate of Na+ influx for motor rotation. PMID:2243095

  13. Variational calculations of rotationally resolved infrared properties of Li 2Na +, LiNa 2+ and KLiNa +

    NASA Astrophysics Data System (ADS)

    Wang, Feng; Searles, Debra J.; von Nagy-Felsobuki, Ellak I.

    1992-10-01

    Ab initio variational rovibrational calculations have been performed for the ground electronic states of Li 2Na +, LiNa +2 and KLiNa +. Discrete potential and electric dipole moment surfaces were used to calculate rovibrational transition frequencies, absolute vibrational bands and line intensities. The variational rovibration calculations take into account a full description of the mechanical and electrical anharmonicity as well as vibration—rotation coupling effects. Absolute line intensities and square dipole matrix elements are given for some intense transitions within the P-, Q- and R-branches between the vibrational ground state and the lowest lying excited states.

  14. NHE3 Regulatory Factor 1 (NHERF1) Modulates Intestinal Sodium-dependent Phosphate Transporter (NaPi-2b) Expression in Apical Microvilli*

    PubMed Central

    Giral, Hector; Cranston, DeeAnn; Lanzano, Luca; Caldas, Yupanqui; Sutherland, Eileen; Rachelson, Joanna; Dobrinskikh, Evgenia; Weinman, Edward J.; Doctor, R. Brian; Gratton, Enrico; Levi, Moshe

    2012-01-01

    Pi uptake in the small intestine occurs predominantly through the NaPi-2b (SLC34a2) co-transporter. NaPi-2b is regulated by changes in dietary Pi but the mechanisms underlying this regulation are largely undetermined. Sequence analyses show NaPi-2b has a PDZ binding motif at its C terminus. Immunofluorescence imaging shows NaPi-2b and two PDZ domain containing proteins, NHERF1 and PDZK1, are expressed in the apical microvillar domain of rat small intestine enterocytes. Co-immunoprecipitation studies in rat enterocytes show that NHERF1 associates with NaPi-2b but not PDZK1. In HEK co-expression studies, GFP-NaPi-2b co-precipitates with FLAG-NHERF1. This interaction is markedly diminished when the C-terminal four amino acids are truncated from NaPi-2b. FLIM-FRET analyses using tagged proteins in CACO-2BBE cells show a distinct phasor shift between NaPi-2b and NHERF1 but not between NaPi-2b and the PDZK1 pair. This shift demonstrates that NaPi-2b and NHERF1 reside within 10 nm of each other. NHERF1−/− mice, but not PDZK1−/− mice, had a diminished adaptation of NaPi-2b expression in response to a low Pi diet. Together these studies demonstrate that NHERF1 associates with NaPi-2b in enterocytes and regulates NaPi-2b adaptation. PMID:22904329

  15. DNA sequencing: bench to bedside and beyond†

    PubMed Central

    Hutchison, Clyde A.

    2007-01-01

    Fifteen years elapsed between the discovery of the double helix (1953) and the first DNA sequencing (1968). Modern DNA sequencing began in 1977, with development of the chemical method of Maxam and Gilbert and the dideoxy method of Sanger, Nicklen and Coulson, and with the first complete DNA sequence (phage ϕX174), which demonstrated that sequence could give profound insights into genetic organization. Incremental improvements allowed sequencing of molecules >200 kb (human cytomegalovirus) leading to an avalanche of data that demanded computational analysis and spawned the field of bioinformatics. The US Human Genome Project spurred sequencing activity. By 1992 the first ‘sequencing factory’ was established, and others soon followed. The first complete cellular genome sequences, from bacteria, appeared in 1995 and other eubacterial, archaebacterial and eukaryotic genomes were soon sequenced. Competition between the public Human Genome Project and Celera Genomics produced working drafts of the human genome sequence, published in 2001, but refinement and analysis of the human genome sequence will continue for the foreseeable future. New ‘massively parallel’ sequencing methods are greatly increasing sequencing capacity, but further innovations are needed to achieve the ‘thousand dollar genome’ that many feel is prerequisite to personalized genomic medicine. These advances will also allow new approaches to a variety of problems in biology, evolution and the environment. PMID:17855400

  16. NMR studies on Na+ transport in Synechococcus PCC 6311

    NASA Technical Reports Server (NTRS)

    Nitschmann, W. H.; Packer, L.

    1992-01-01

    The freshwater cyanobacterium Synechococcus PCC 6311 is able to adapt to grow after sudden exposure to salt (NaCl) stress. We have investigated the mechanism of Na+ transport in these cells during adaptation to high salinity. Na+ influx under dark aerobic conditions occurred independently of delta pH or delta psi across the cytoplasmic membrane, ATPase activity, and respiratory electron transport. These findings are consistent with the existence of Na+/monovalent anion cotransport or simultaneous Na+/H+ +anion/OH- exchange. Na+ influx was dependent on Cl-, Br-, NO3-, or NO2-. No Na+ uptake occurred after addition of NaI, NaHCO3, or Na2SO4. Na+ extrusion was absolutely dependent on delta pH and on an ATPase activity and/or on respiratory electron transport. This indicates that Na+ extrusion via Na+/H+ exchange is driven by primary H+ pumps in the cytoplasmic membrane. Cells grown for 4 days in 0.5 m NaCl medium, "salt-grown cells," differ from control cells by a lower maximum velocity of Na+ influx and by lower steady-state ratios of [Na+]in/[Na+]out. These results indicate that cells grown in high-salt medium increase their capacity to extrude Na+. During salt adaptation Na+ extrusion driven by respiratory electron transport increased from about 15 to 50%.

  17. The Art of Gymnastics: Creating Sequences.

    ERIC Educational Resources Information Center

    Rovegno, Inez

    1988-01-01

    Offering students opportunities for creating movement sequences in gymnastics allows them to understand the essence of gymnastics, have creative experiences, and learn about themselves. The process of creating sequences is described. (MT)

  18. 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)

  19. A naïve Bayesian classifier for identifying plant microRNAs.

    PubMed

    Douglass, Stephen; Hsu, Ssu-Wei; Cokus, Shawn; Goldberg, Robert B; Harada, John J; Pellegrini, Matteo

    2016-06-01

    MicroRNAs (miRNAs) are important regulatory molecules in eukaryotic organisms. Existing methods for the identification of mature miRNA sequences in plants rely extensively on the search for stem-loop structures, leading to high false negative rates. Here, we describe a probabilistic method for ranking putative plant miRNAs using a naïve Bayes classifier and its publicly available implementation. We use a number of properties to construct the classifier, including sequence length, number of observations, existence of detectable predicted miRNA* sequences, the distribution of nearby reads and mapping multiplicity. We apply the method to small RNA sequence data from soybean, peach, Arabidopsis and rice and provide experimental validation of several predictions in soybean. The approach performs well overall and strongly enriches for known miRNAs over other types of sequences. By utilizing a Bayesian approach to rank putative miRNAs, our method is able to score miRNAs that would be eliminated by other methods, such as those that have low counts or lack detectable miRNA* sequences. As a result, we are able to detect several soybean miRNA candidates, including some that are 24 nucleotides long, a class that is almost universally eliminated by other methods. PMID:27061965

  20. Studies on the digitalis binding site in Na, K-ATPase

    SciTech Connect

    Ahmed, K.; McParland, R.; Becker, R.; From, A.; Schimerlik, M.; Fullerton, D.S.

    1986-05-01

    Na, K-ATPase is believed to be the receptor for digitalis glycosides. The authors have previously documented that C17 side group of the cardenolide molecule is crucial to ..cap alpha.. subunit receptor binding. They have attempted to identify the structure of this binding site by labelling the enzyme with a /sup 3/H-labelled photoactive probe localized in the C17 side group of the genin molecule. /sup 3/H-..cap alpha..-subunit was purified and subjected to tryptic digestion. The digest was fractionated by gel filtration on Sephadex G-100. Fractions containing /sup 3/H-labelled peptide were pooled and rechromatographed. The central peak fractions of /sup 3/H-peptide were pooled, analyzed by SDS-PAGE, and subjected to amino acid sequence analysis. The tryptic peptide containing the /sup 3/H-probe showed considerable sequence heterogeneity. Comparison of the sequence data with the published cDNA-based ..cap alpha..-subunit sequence revealed that this peptide material was indeed a mixture of two tryptic peptides of nearly identical size containing the sequences from residue 68 through residue 146, and residues 263 through 342. The latter peptide contains the sequence ... glu tyr thr try leu glu ... speculated by Shull et al. as a possible ouabain binding site.

  1. 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

  2. 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.

  3. Genetic mapping and DNA sequencing

    SciTech Connect

    Speed, T.; Waterman, M.S.

    1996-12-31

    The Human Genome Initiative has as its primary objective the characterization of the human genome. High-resolution linkage maps of genetic markers will play an important role in completing the human genome project. This is one of two volumes based on the proceedings of the 1994 IMA Summer Program on Molecular Biology and comprises Weeks 1 and 2 of the four-week program. This volume focuses on genetic mapping and DNA sequencing. Selected papers are indexed separately for inclusion in the Energy Science and Technology Database.

  4. Apollo: a sequence annotation editor

    PubMed Central

    Lewis, SE; Searle, SMJ; Harris, N; Gibson, M; Iyer, V; Richter, J; Wiel, C; Bayraktaroglu, L; Birney, E; Crosby, MA; Kaminker, JS; Matthews, BB; Prochnik, SE; Smith, CD; Tupy, JL; Rubin, GM; Misra, S; Mungall, CJ; Clamp, ME

    2002-01-01

    The well-established inaccuracy of purely computational methods for annotating genome sequences necessitates an interactive tool to allow biological experts to refine these approximations by viewing and independently evaluating the data supporting each annotation. Apollo was developed to meet this need, enabling curators to inspect genome annotations closely and edit them. FlyBase biologists successfully used Apollo to annotate the Drosophila melanogaster genome and it is increasingly being used as a starting point for the development of customized annotation editing tools for other genome projects. PMID:12537571

  5. The PIR-International Protein Sequence Database.

    PubMed Central

    George, D G; Barker, W C; Mewes, H W; Pfeiffer, F; Tsugita, A

    1994-01-01

    PIR-International is an association of macromolecular sequence data collection centers dedicated to fostering international cooperation as an essential element in the development of scientific databases. A major objective of PIR-International is to continue the development of the Protein Sequence Database as an essential public resource for protein sequence information. This paper briefly describes the architecture of the Protein Sequence Database and how it and associated data sets are distributed and can be accessed electronically. PMID:7937060

  6. Sequences of Rational Numbers Converging to Surds

    ERIC Educational Resources Information Center

    Fletcher, Rodney

    2010-01-01

    In this sequence 1/1, 7/5, 41/29, 239/169 and so on, Thomas notes that the sequence converges to square root of 2. By observation, the sequence of numbers in the numerator of the above sequence, have a pattern of generation which is the same as that in the denominator. That is, the next term is found by multiplying the previous term by six and…

  7. Capsazepine, a synthetic vanilloid that converts the Na,K-ATPase to Na-ATPase.

    PubMed

    Mahmmoud, Yasser A

    2008-02-01

    Capsazepine (CPZ), a synthetic capsaicin analogue, inhibits ATP hydrolysis by Na,K-ATPase in the presence but not in the absence of K(+). Studies with purified membranes revealed that CPZ reduced Na(+)-dependent phosphorylation by interference with Na(+) binding from the intracellular side of the membrane. Kinetic analyses showed that CPZ stabilized an enzyme species that constitutively occluded K(+). Low-affinity ATP interaction with the enzyme was strongly reduced after CPZ treatment; in contrast, indirectly measured interaction with ADP was much increased, which suggests that composite regulatory communication with nucleotides takes place during turnover. Studies with lipid vesicles revealed that CPZ reduced ATP-dependent digitoxigenin-sensitive (22)Na(+) influx into K(+)-loaded vesicles only at saturating ATP concentrations. The drug apparently abolishes the regulatory effect of ATP on the pump. Drawing on previous homology modeling studies of Na,K-ATPase to atomic models of sarcoplasmic reticulum Ca-ATPase and on kinetic data, we propose that CPZ uncouples an Na(+) cycle from an Na(+)/K(+) cycle in the pump. The Na(+) cycle possibly involves transport through the recently characterized Na(+)-specific site. A shift to such an uncoupled mode is believed to produce pumps mediating uncoupled Na(+) efflux by modifying the transport stoichiometry of single pump units. PMID:18230728

  8. 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

  9. 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

  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. 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…

  12. 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.

  13. Sequencing and mapping of the onion genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The cost of DNA sequencing continues to decline and, in the near future, it will become reasonable to undertake sequencing of the enormous nuclear genome of onion. We undertook sequencing of expressed and genomic regions of the onion genome to learn about the structure of the onion genome, as well a...

  14. 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

  15. Molecular cloning and functional expression of the bumetanide-sensitive Na-K-Cl cotransporter.

    PubMed Central

    Xu, J C; Lytle, C; Zhu, T T; Payne, J A; Benz, E; Forbush, B

    1994-01-01

    By mediating the coupled movement of Na, K, and Cl ions across the plasma membrane of most animal cells, the bumetanide-sensitive Na-K-Cl cotransporter (NKCC) plays a vital role in the regulation of ionic balance and cell volume. The transporter is a central element in the process of vectorial salt transport in secretory and absorptive epithelia. A cDNA encoding a Na-K-Cl cotransport protein was isolated from a shark rectal gland library by screening with monoclonal antibodies to the native shark cotransporter. The 1191-residue protein predicted from the cDNA sequence has 12 putative transmembrane domains flanked by large cytoplasmic N and C termini. Regulatory phosphoacceptor residues in isolated peptides are identified as Thr-189 and Thr-1114 in the predicted sequence. Northern blot analysis identified a 7.4-kb mRNA in rectal gland and most other shark tissues; a 5.2-kb mRNA was restricted to shark kidney. Homology with an uncharacterized gene from Caenorhabditis elegans and with the thiazide-sensitive Na-Cl cotransporter of flounder urinary bladder was found over most of the coding region; shorter stretches of homology were found with a C. elegans cDNA and with an uncharacterized gene of cyanobacterium. Human HEK-293 cells have been stably transfected with the shark cDNA and shown to express Na-K-Cl cotransport activity with the bumetanide sensitivity of the shark protein. The expressed transporter is functionally quiescent in the host cells and can be activated by depleting the cells of chloride. Images PMID:8134373

  16. Thermodynamic Model for the Solubility of Cr(OH)(3)(am) in Concentrated NaOH and NaOH-NaNO3 Solutions

    SciTech Connect

    Rai, Dhanpat ); Hess, Nancy J. ); Rao, Linfeng; Zhang, Zhicheng; Felmy, Andrew R. ); Moore, Dean A. ); Clark, Sue B.; Lumetta, Gregg J. )

    2001-12-01

    The objectives of this study were to develop a reliable thermodynamic model for predicting Cr(III) behavior in concentrated NaOH and in mixed NaOH-NaNO3 solutions for application to effective caustic leaching strategies for high-level tank sludges. To meet these objectives, the solubility of Cr(OH)3(am) was measured in 0.003 to 10.5 m NaOH, 3.0 m es in NaOH concentration...

  17. Artificial sequences and complexity measures

    NASA Astrophysics Data System (ADS)

    Baronchelli, Andrea; Caglioti, Emanuele; Loreto, Vittorio

    2005-04-01

    In this paper we exploit concepts of information theory to address the fundamental problem of identifying and defining the most suitable tools for extracting, in a automatic and agnostic way, information from a generic string of characters. We introduce in particular a class of methods which use in a crucial way data compression techniques in order to define a measure of remoteness and distance between pairs of sequences of characters (e.g. texts) based on their relative information content. We also discuss in detail how specific features of data compression techniques could be used to introduce the notion of dictionary of a given sequence and of artificial text and we show how these new tools can be used for information extraction purposes. We point out the versatility and generality of our method that applies to any kind of corpora of character strings independently of the type of coding behind them. We consider as a case study linguistic motivated problems and we present results for automatic language recognition, authorship attribution and self-consistent classification.

  18. Not All Sequence Tags Are Created Equal: Designing and Validating Sequence Identification Tags Robust to Indels

    PubMed Central

    Faircloth, Brant C.; Glenn, Travis C.

    2012-01-01

    Ligating adapters with unique synthetic oligonucleotide sequences (sequence tags) onto individual DNA samples before massively parallel sequencing is a popular and efficient way to obtain sequence data from many individual samples. Tag sequences should be numerous and sufficiently different to ensure sequencing, replication, and oligonucleotide synthesis errors do not cause tags to be unrecoverable or confused. However, many design approaches only protect against substitution errors during sequencing and extant tag sets contain too few tag sequences. We developed an open-source software package to validate sequence tags for conformance to two distance metrics and design sequence tags robust to indel and substitution errors. We use this software package to evaluate several commercial and non-commercial sequence tag sets, design several large sets (maxcount = 7,198) of edit metric sequence tags having different lengths and degrees of error correction, and integrate a subset of these edit metric tags to polymerase chain reaction (PCR) primers and sequencing adapters. We validate a subset of these edit metric tagged PCR primers and sequencing adapters by sequencing on several platforms and subsequent comparison to commercially available alternatives. We find that several commonly used sets of sequence tags or design methodologies used to produce sequence tags do not meet the minimum expectations of their underlying distance metric, and we find that PCR primers and sequencing adapters incorporating edit metric sequence tags designed by our software package perform as well as their commercial counterparts. We suggest that researchers evaluate sequence tags prior to use or evaluate tags that they have been using. The sequence tag sets we design improve on extant sets because they are large, valid across the set, and robust to the suite of substitution, insertion, and deletion errors affecting massively parallel sequencing workflows on all currently used platforms

  19. 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.

  20. Two-step melting of Na41+

    NASA Astrophysics Data System (ADS)

    Zamith, Sébastien; Labastie, Pierre; Chirot, Fabien; L'Hermite, Jean-Marc

    2010-10-01

    The heat capacity of the mass selected Na41+ cluster has been measured using a differential nanocalorimetry method. A two-peak structure appears in the heat capacity curve of Na41+, whereas Schmidt and co-workers [M. Schmidt, J. Donges, Th. Hippler, and H. Haberland, Phys. Rev. Lett. 90, 103401 (2003)] observed, within their experimental accuracy, a smooth caloric curve. They concluded from the absence of any structure that there is a second order melting transition in Na41+ with no particular feature such as premelting. The observed difference with the latter results is attributed to the better accuracy of our method owing to its differential character. The two structures in the heat capacity are ascribed to melting and premelting of Na41+. The peak at lower temperature is likely due to an anti-Mackay to Mackay solid-solid transition.

  1. Two-step melting of Na(41)(+).

    PubMed

    Zamith, Sébastien; Labastie, Pierre; Chirot, Fabien; L'hermite, Jean-Marc

    2010-10-21

    The heat capacity of the mass selected Na(41) (+) cluster has been measured using a differential nanocalorimetry method. A two-peak structure appears in the heat capacity curve of Na(41) (+), whereas Schmidt and co-workers [M. Schmidt, J. Donges, Th. Hippler, and H. Haberland, Phys. Rev. Lett. 90, 103401 (2003)] observed, within their experimental accuracy, a smooth caloric curve. They concluded from the absence of any structure that there is a second order melting transition in Na(41) (+) with no particular feature such as premelting. The observed difference with the latter results is attributed to the better accuracy of our method owing to its differential character. The two structures in the heat capacity are ascribed to melting and premelting of Na(41) (+). The peak at lower temperature is likely due to an anti-Mackay to Mackay solid-solid transition. PMID:20969397

  2. Triplet state photoassociation of LiNa

    NASA Astrophysics Data System (ADS)

    Rvachov, Timur; Jamison, Alan; Jing, Li; Jiang, Yijun; Zwierlein, Martin; Ketterle, Wolfgang

    2015-05-01

    Ultracold molecules have promise to become a useful tool for studies in quantum simulation and ultracold chemistry. We aim to produce ultracold fermionic 6Li23Na molecules in the triplet ground state. Due to the small mass, small spin-orbit coupling, and fermionic character of LiNa, the triplet ground state is expected to be long lived. We report on photoassociation spectra of LiNa to its triplet excited states from an ultracold mixture. This is the first observation of these excited triplet potentials, which have been previously difficult to observe in heat-pipe experiments due to the small spin-orbit coupling in the system. Determining the excited state potentials is a key milestone towards forming triplet ground state LiNa via two-photon STIRAP. Work supported by the NSF, AFOSR-MURI, ARO-MURI, and NSERC.

  3. Practical and Scalable Transmission of Segmented Video Sequences to Multiple Players Using H.264

    NASA Astrophysics Data System (ADS)

    Quax, Peter; di Fiore, Fabian; Issaris, Panagiotis; Lamotte, Wim; van Reeth, Frank

    We present a practical way to distribute viewports on the same video sequence to large amounts of players. Each of them has personal preferences to be met or is limited by the physical properties of his/her device (e.g., screen size of a PDA or processing power of a mobile phone). Instead of taking the naïve approach, in which sections of the video sequence are decoded and re-encoded for each of the clients, we have exploited advanced features offered by the H.264 codec to enable selection of parts of the video sequence by directly manipulating the encoder-generated bitstream. At the same time, we have overcome several practical issues presented by the fact that support for these features is sadly lacking from the state-of-the-art encoders available on the market. Two alternative solutions are discussed and have been implemented, enabling the generation of measurement results and comparison to alternative approaches.

  4. 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.

  5. Identification of DNA lesions using a third base pair for amplification and nanopore sequencing

    PubMed Central

    Riedl, Jan; Ding, Yun; Fleming, Aaron M.; Burrows, Cynthia J.

    2015-01-01

    Damage to the genome is implicated in the progression of cancer and stress-induced diseases. DNA lesions exist in low levels, and cannot be amplified by standard PCR because they are frequently strong blocks to polymerases. Here, we describe a method for PCR amplification of lesion-containing DNA in which the site and identity could be marked, copied and sequenced. Critical for this method is installation of either the dNaM or d5SICS nucleotides at the lesion site after processing via the base excision repair process. These marker nucleotides constitute an unnatural base pair, allowing large quantities of marked DNA to be made by PCR amplification. Sanger sequencing confirms the potential for this method to locate lesions by marking, amplifying and sequencing a lesion in the KRAS gene. Detection using the α-hemolysin nanopore is also developed to analyse the markers in individual DNA strands with the potential to identify multiple lesions per strand. PMID:26542210

  6. 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.

  7. Chip-based sequencing nucleic acids

    DOEpatents

    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.

  8. Na and K distribution in agpaitic pegmatites

    NASA Astrophysics Data System (ADS)

    Müller-Lorch, Daniel; Marks, Michael A. W.; Markl, Gregor

    2007-05-01

    Composition and zoning of amphibole in agpaitic pegmatites of the 1.16 Ga Ilímaussaq complex, South Greenland record the chemical evolution of the final stages of an already extremely fractionated melt. Our results show that the general differentiation trends found in the earlier rocks of the complex are continued in the pegmatites, albeit with some significant modifications: the dominating exchange mechanism of Na + Si ⇔ Ca + Al in the amphiboles of the magmatic stage changes to K + Si ⇔ Ca + Al and K ⇔ Na in some pegmatitic samples. Na/K ratios in amphiboles, which generally increase in the course of the Ilímaussaq fractionation, partly display a reversal during the crystallization of the most differentiated amphiboles. The alkali trends are probably related to the buffering of Na +and K +activity by the co-crystallization of albite and microcline. This buffering favors Na +in cooling fluids. This mechanism is lost when analcime replaces feldspar as a stable phase in the late stages of crystallization, e.g. due to locally elevated H 2O activity. Analcime does not incorporate significant amounts of K and accordingly, amphibole incorporates more K in analcime-bearing assemblages. The Na-K variation in amphiboles in the Ilímaussaq pegmatites allow a detailed view into the late-stage evolutionary trends of a textbook agpaitic complex. The transition from silicate melt to aqueous fluid is recorded by the change of the dominant alkali ion in the pegmatitic amphiboles from Na to K. Only in the very latest stage, virtually K-free mineral assemblages in analcime-aegirine veins support the existence of a Na-dominated aqueous fluid.

  9. Neural substrates of graphomotor sequence learning: a combined FMRI and kinematic study.

    PubMed

    Swett, Bruce A; Contreras-Vidal, Jose L; Birn, Rasmus; Braun, Allen

    2010-06-01

    The goal of this study was to characterize the dynamics and functional connectivity of brain networks associated with fast (short-term) learning of handwriting using functional magnetic resonance imaging. Participants (n = 12) performed a graphomotor sequence learning task (naïve subjects learning to draw simple, 3-stroke Chinese word characters), which focused the learning process on the kinematic aspects of sequence learning instead of on the production of the line segments. Learning of the graphomotor sequence was demonstrated by a progressive improvement in movement smoothness as assessed by normalized jerk scores. Examination of the patterns of regional neural activity and functional connectivity during sequence learning demonstrated that cortical regions, which may support visuomotor mapping components of the task, were active prior to subcortical areas that may play a role in encoding and refining the novel sequences. Importantly, differences in the time course of recruitment of basal ganglia and cerebellar networks suggest distinct but integrated roles in the encoding and refining of the handwritten sequences. This implies multiple kinematic representations of graphomotor trajectories may be encoded at various spatiotemporal scales. PMID:20375250

  10. An accurate clone-based haplotyping method by overlapping pool sequencing.

    PubMed

    Li, Cheng; Cao, Changchang; Tu, Jing; Sun, Xiao

    2016-07-01

    Chromosome-long haplotyping of human genomes is important to identify genetic variants with differing gene expression, in human evolution studies, clinical diagnosis, and other biological and medical fields. Although several methods have realized haplotyping based on sequencing technologies or population statistics, accuracy and cost are factors that prohibit their wide use. Borrowing ideas from group testing theories, we proposed a clone-based haplotyping method by overlapping pool sequencing. The clones from a single individual were pooled combinatorially and then sequenced. According to the distinct pooling pattern for each clone in the overlapping pool sequencing, alleles for the recovered variants could be assigned to their original clones precisely. Subsequently, the clone sequences could be reconstructed by linking these alleles accordingly and assembling them into haplotypes with high accuracy. To verify the utility of our method, we constructed 130 110 clones in silico for the individual NA12878 and simulated the pooling and sequencing process. Ultimately, 99.9% of variants on chromosome 1 that were covered by clones from both parental chromosomes were recovered correctly, and 112 haplotype contigs were assembled with an N50 length of 3.4 Mb and no switch errors. A comparison with current clone-based haplotyping methods indicated our method was more accurate. PMID:27095193

  11. An accurate clone-based haplotyping method by overlapping pool sequencing

    PubMed Central

    Li, Cheng; Cao, Changchang; Tu, Jing; Sun, Xiao

    2016-01-01

    Chromosome-long haplotyping of human genomes is important to identify genetic variants with differing gene expression, in human evolution studies, clinical diagnosis, and other biological and medical fields. Although several methods have realized haplotyping based on sequencing technologies or population statistics, accuracy and cost are factors that prohibit their wide use. Borrowing ideas from group testing theories, we proposed a clone-based haplotyping method by overlapping pool sequencing. The clones from a single individual were pooled combinatorially and then sequenced. According to the distinct pooling pattern for each clone in the overlapping pool sequencing, alleles for the recovered variants could be assigned to their original clones precisely. Subsequently, the clone sequences could be reconstructed by linking these alleles accordingly and assembling them into haplotypes with high accuracy. To verify the utility of our method, we constructed 130 110 clones in silico for the individual NA12878 and simulated the pooling and sequencing process. Ultimately, 99.9% of variants on chromosome 1 that were covered by clones from both parental chromosomes were recovered correctly, and 112 haplotype contigs were assembled with an N50 length of 3.4 Mb and no switch errors. A comparison with current clone-based haplotyping methods indicated our method was more accurate. PMID:27095193

  12. Na+ reabsorption in cultured rat epididymal epithelium via the Na+/nucleoside cotransporter.

    PubMed

    Leung, G P; Cheung, K H; Tse, C M; Wong, P Y

    2001-03-01

    The effect of nucleoside on Na+ reabsorption via Na+/nucleoside cotransporter in cultured rat epididymal epithelia was studied by short-circuit current (Isc) technique. Guanosine added apically stimulated Isc in a dose-dependent manner, with a median effective concentration (EC50) of 7 +/- 2 microM (mean +/- SEM). Removal of Na+ from the apical bathing solution or pretreatment with a nonspecific Na+/nucleoside cotransporter inhibitor, phloridzin, completely blocked the Isc response to guanosine. Moreover, the guanosine response was abolished by pretreatment of the tissue with ouabain, a Na+/K+-ATPase inhibitor, suggesting the involvement of Na+/nucleoside cotransporter on the apical side and Na+/K+-ATPase on the basolateral side in Na+ reabsorption. In contrast, the Isc response to guanosine was not affected after desensitization of purinoceptors by ATP. Addition of the Na+/K+/2Cl- symport inhibitor bumetanide to the basolateral side or the nonspecific Cl- channel blocker diphenylamine-2-carboxylate to the apical side showed no effect on the Isc response to guanosine, excluding stimulation of Cl- secretion by guanosine as the cause of the guanosine-induced Isc. The Isc response to purine nucleoside (guanosine and inosine) was much higher than that to pyrimidine nucleoside (thymidine and cytidine). Consistent with substrate specificity, results of reverse transcription-polymerase chain reaction revealed mRNA for concentrative nucleoside transporter (CNT2), which is a purine nucleoside-selective Na+/nucleoside cotransporter in the epididymis, but not for CNT1. It is suggested that the Na+/nucleoside cotransporter (i.e., CNT2) may be one of the elements involved in Na+ and fluid reabsorption in the epididymis, thereby providing an optimal microenvironment for the maturation and storage of spermatozoa. PMID:11207189

  13. Distinguishing Proteins From Arbitrary Amino Acid Sequences

    PubMed Central

    Yau, Stephen S.-T.; Mao, Wei-Guang; Benson, Max; He, Rong Lucy

    2015-01-01

    What kinds of amino acid sequences could possibly be protein sequences? From all existing databases that we can find, known proteins are only a small fraction of all possible combinations of amino acids. Beginning with Sanger's first detailed determination of a protein sequence in 1952, previous studies have focused on describing the structure of existing protein sequences in order to construct the protein universe. No one, however, has developed a criteria for determining whether an arbitrary amino acid sequence can be a protein. Here we show that when the collection of arbitrary amino acid sequences is viewed in an appropriate geometric context, the protein sequences cluster together. This leads to a new computational test, described here, that has proved to be remarkably accurate at determining whether an arbitrary amino acid sequence can be a protein. Even more, if the results of this test indicate that the sequence can be a protein, and it is indeed a protein sequence, then its identity as a protein sequence is uniquely defined. We anticipate our computational test will be useful for those who are attempting to complete the job of discovering all proteins, or constructing the protein universe. PMID:25609314

  14. Genotator: a workbench for sequence annotation.

    PubMed

    Harris, N L

    1997-07-01

    Sequencing centers such as the Human Genome Center at LBNL are producing an ever-increasing flood of genetic data. Annotation can greatly enhance the biological value of these sequences. Useful annotations include possible gene locations, homologies to known genes, and gene signal such as promoters and splice sites. Genotator is a workbench for automated sequence annotation and annotation browsing. The back end runs a series of sequence analysis tools on a DNA sequence, handling the various input and output formats required by the tools. Genotator currently runs five different gene-finding programs, three homology searches, and searches for promoters, splice sites, and ORFs. The results of the analyses run by Genotator can be viewed with the interactive graphical browser. The browser displays color-coded sequence annotations on a canvas that can be scrolled and zoomed, allowing the annotated sequence to be explored at multiple levels of detail. The user can view the actual DNA sequence in a separate window; when a region is selected in the map display, it is highlighted automatically in the sequence display, and vice versa. By displaying the output of all of the sequence analyses, Genotator provides an intuitive way to identify the significant regions (for example, probable exons) in a sequence. Users can interactively add personal annotations to label regions of interest. Additional capabilities of Genotator include primer design and pattern searching. PMID:9253604

  15. Experimental investigation of an RNA sequence space

    NASA Technical Reports Server (NTRS)

    Lee, Youn-Hyung; Dsouza, Lisa; Fox, George E.

    1993-01-01

    Modern rRNAs are the historic consequence of an ongoing evolutionary exploration of a sequence space. These extant sequences belong to a special subset of the sequence space that is comprised only of those primary sequences that can validly perform the biological function(s) required of the particular RNA. If it were possible to readily identify all such valid sequences, stochastic predictions could be made about the relative likelihood of various evolutionary pathways available to an RNA. Herein an experimental system which can assess whether a particular sequence is likely to have validity as a eubacterial 5S rRNA is described. A total of ten naturally occurring, and hence known to be valid, sequences and two point mutants of unknown validity were used to test the usefulness of the approach. Nine of the ten valid sequences tested positive whereas both mutants tested as clearly defective. The tenth valid sequence gave results that would be interpreted as reflecting a borderline status were the answer not known. These results demonstrate that it is possible to experimentally determine which sequences in local regions of the sequence space are potentially valid 5S rRNAs.

  16. 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.

  17. The evolution of the Voyager mission sequence software and trends for future mission sequence software systems

    NASA Technical Reports Server (NTRS)

    Brooks, Robert N., Jr.

    1988-01-01

    The historical background of the spacecraft sequence generation process as it is represented by the Voyager mission to the outer planets is discussed. Present plans for future sequencing methods are examined, including the emphasis on cutting costs and the contrast between the centralized and distributed systems for sequencing. The use of artificial intelligence in mission sequencing is addressed.

  18. RNAome sequencing delineates the complete RNA landscape.

    PubMed

    Derks, Kasper W J; Pothof, Joris

    2015-09-01

    Standard RNA expression profiling methods rely on enrichment steps for specific RNA classes, thereby not detecting all RNA species. For example, small and large RNAs from the same sample cannot be sequenced in a single sequence run. We designed RNAome sequencing, which is a strand-specific method to determine the expression of small and large RNAs from ribosomal RNA-depleted total RNA in a single sequence run. RNAome sequencing quantitatively preserves all RNA classes. This characteristic allows comparisons between RNA classes, thereby facilitating relationships between different RNA classes. Here, we describe in detail the experimental procedure associated with RNAome sequencing published by Derks and colleagues in RNA Biology (2015) [1]. We also provide the R code for the developed Total Rna Analysis Pipeline (TRAP), an algorithm to analyze RNAome sequencing datasets (deposited at the Gene Expression Omnibus data repository, accession number GSE48084). PMID:26484291

  19. Should the draft chimpanzee sequence be finished?

    PubMed

    Taudien, Stefan; Ebersberger, Ingo; Glöckner, Gernot; Platzer, Matthias

    2006-03-01

    Owing to the availability of genome working drafts (WDs), current comparative-sequence studies are frequently performed on a genome-wide scale. In this article, we appraise the utility of WD sequences in the detection of genomic differences in closely related species. We compared human DNA sequences with draft and high-quality versions of the corresponding chimpanzee loci to reveal the overall high quality of the chimp WD sequence. Nevertheless, a significant proportion of the differences between WD and high-quality sequences we observed can be attributed to sequencing errors in the draft. Although we suggest methods to reduce the number of such false positives efficiently, our study emphasizes the benefit expected from finishing the chimpanzee genome sequence. PMID:16406850

  20. Atypical regions in large genomic DNA sequences

    SciTech Connect

    Scherer, S. |; McPeek, M.S.; Speed, T.P.

    1994-07-19

    Large genomic DNA sequences contain regions with distinctive patterns of sequence organization. The authors describe a method using logarithms of probabilities based on seventh-order Markov chains to rapidly identify genomic sequences that do not resemble models of genome organization built from compilations of octanucleotide usage. Data bases have been constructed from Escherichia coli and Saccharomyces cerevisiae DNA sequences of >1000 nt and human sequences of >10,000 nt. Atypical genes and clusters of genes have been located in bacteriophage, yeast, and primate DNA sequences. The authors consider criteria for statistical significance of the results, offer possible explanations for the observed variation in genome organization, and give additional applications of these methods in DNA sequence analysis.

  1. Determination of Na acceptor level in Na+ ion-implanted ZnO single crystal

    NASA Astrophysics Data System (ADS)

    Wang, Zheng; Liu, Huibin; He, Haiping; Huang, Jingyun; Chen, Lingxiang; Ye, Zhizhen

    2015-03-01

    Ion implantation was used to dope Na acceptor into ZnO single crystals. With three mixed implantation energies, uniform depth distribution of Na ion in the surface region (~300 nm) of ZnO bulk crystals is achieved. Via post-implantation annealing, a donor-acceptor pair recombination band is identified in the low-temperature photoluminescence spectra, from which the energy level of Na-related acceptor in single crystalline ZnO is estimated to be 300 meV. A p-n junction based on this ZnO-Na layer shows rectifying characteristics, confirming the p-type conductivity.

  2. De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data

    PubMed Central

    DiGuistini, Scott; Liao, Nancy Y; Platt, Darren; Robertson, Gordon; Seidel, Michael; Chan, Simon K; Docking, T Roderick; Birol, Inanc; Holt, Robert A; Hirst, Martin; Mardis, Elaine; Marra, Marco A; Hamelin, Richard C; Bohlmann, Jörg; Breuil, Colette; Jones, Steven JM

    2009-01-01

    Sequencing-by-synthesis technologies can reduce the cost of generating de novo genome assemblies. We report a method for assembling draft genome sequences of eukaryotic organisms that integrates sequence information from different sources, and demonstrate its effectiveness by assembling an approximately 32.5 Mb draft genome sequence for the forest pathogen Grosmannia clavigera, an ascomycete fungus. We also developed a method for assessing draft assemblies using Illumina paired end read data and demonstrate how we are using it to guide future sequence finishing. Our results demonstrate that eukaryotic genome sequences can be accurately assembled by combining Illumina, 454 and Sanger sequence data. PMID:19747388

  3. Feedback shift register sequences versus uniformly distributed random sequences for correlation chromatography

    NASA Technical Reports Server (NTRS)

    Kaljurand, M.; Valentin, J. R.; Shao, M.

    1996-01-01

    Two alternative input sequences are commonly employed in correlation chromatography (CC). They are sequences derived according to the algorithm of the feedback shift register (i.e., pseudo random binary sequences (PRBS)) and sequences derived by using the uniform random binary sequences (URBS). These two sequences are compared. By applying the "cleaning" data processing technique to the correlograms that result from these sequences, we show that when the PRBS is used the S/N of the correlogram is much higher than the one resulting from using URBS.

  4. Secondary-task effects on sequence learning.

    PubMed

    Heuer, H; Schmidtke, V

    1996-01-01

    With a repeated sequence of stimuli, performance in a serial reaction-time task improves more than with a random sequence. The difference has been taken as a measure of implicit sequence learning. Implicit sequence learning is impaired when a secondary task is added to the serial RT task. In the first experiment, secondary-task effects on different types of sequences were studied to test the hypothesis that the learning of unique sequences (where each sequence element has a unique relation to the following one) is not impaired by the secondary task, while the learning of ambiguous sequences is. The sequences were random up to a certain order of sequential dependencies, where they became deterministic. Contrary to the hypothesis, secondary-task effects on the learning of unique sequences were as strong or stronger than such effects on the learning of ambiguous sequences. In the second experiment a hybrid sequence (with unique as well as ambiguous transitions) was used with different secondary tasks. A visuo-spatial and a verbal memory task did not interfere with the learning of the sequence, but interference was observed with an auditory go/no-go task in which high- and low-pitched tones were presented after each manual response and a foot pedal had to be pressed in response to high-pitched tones. Thus, interference seems to be specific to certain secondary tasks and may be related to memory processes (but most likely not to visuo-spatial and verbal memory) or to the organizations of sequences, consistent with previous suggestions. PMID:8810586

  5. Automatic Sequencing for Experimental Protocols

    NASA Astrophysics Data System (ADS)

    Hsieh, Paul F.; Stern, Ivan

    We present a paradigm and implementation of a system for the specification of the experimental protocols to be used for the calibration of AXAF mirrors. For the mirror calibration, several thousand individual measurements need to be defined. For each measurement, over one hundred parameters need to be tabulated for the facility test conductor and several hundred instrument parameters need to be set. We provide a high level protocol language which allows for a tractable representation of the measurement protocol. We present a procedure dispatcher which automatically sequences a protocol more accurately and more rapidly than is possible by an unassisted human operator. We also present back-end tools to generate printed procedure manuals and database tables required for review by the AXAF program. This paradigm has been tested and refined in the calibration of detectors to be used in mirror calibration.

  6. Replacement Sequence of Events Generator

    NASA Technical Reports Server (NTRS)

    Fisher, Forest; Gladden, Daniel Wenkert Roy; Khanampompan, Teerpat

    2008-01-01

    The soeWINDOW program automates the generation of an ITAR (International Traffic in Arms Regulations)-compliant sub-RSOE (Replacement Sequence of Events) by extracting a specified temporal window from an RSOE while maintaining page header information. RSOEs contain a significant amount of information that is not ITAR-compliant, yet that foreign partners need to see for command details to their instrument, as well as the surrounding commands that provide context for validation. soeWINDOW can serve as an example of how command support products can be made ITAR-compliant for future missions. This software is a Perl script intended for use in the mission operations UNIX environment. It is designed for use to support the MRO (Mars Reconnaissance Orbiter) instrument team. The tool also provides automated DOM (Distributed Object Manager) storage into the special ITAR-okay DOM collection, and can be used for creating focused RSOEs for product review by any of the MRO teams.

  7. Particle sizer and DNA sequencer

    DOEpatents

    Olivares, Jose A.; Stark, Peter C.

    2005-09-13

    An electrophoretic device separates and detects particles such as DNA fragments, proteins, and the like. The device has a capillary which is coated with a coating with a low refractive index such as Teflon.RTM. AF. A sample of particles is fluorescently labeled and injected into the capillary. The capillary is filled with an electrolyte buffer solution. An electrical field is applied across the capillary causing the particles to migrate from a first end of the capillary to a second end of the capillary. A detector light beam is then scanned along the length of the capillary to detect the location of the separated particles. The device is amenable to a high throughput system by providing additional capillaries. The device can also be used to determine the actual size of the particles and for DNA sequencing.

  8. Dynamic Denoising of Tracking Sequences

    PubMed Central

    Michailovich, Oleg; Tannenbaum, Allen

    2009-01-01

    In this paper, we describe an approach to the problem of simultaneously enhancing image sequences and tracking the objects of interest represented by the latter. The enhancement part of the algorithm is based on Bayesian wavelet denoising, which has been chosen due to its exceptional ability to incorporate diverse a priori information into the process of image recovery. In particular, we demonstrate that, in dynamic settings, useful statistical priors can come both from some reasonable assumptions on the properties of the image to be enhanced as well as from the images that have already been observed before the current scene. Using such priors forms the main contribution of the present paper which is the proposal of the dynamic denoising as a tool for simultaneously enhancing and tracking image sequences. Within the proposed framework, the previous observations of a dynamic scene are employed to enhance its present observation. The mechanism that allows the fusion of the information within successive image frames is Bayesian estimation, while transferring the useful information between the images is governed by a Kalman filter that is used for both prediction and estimation of the dynamics of tracked objects. Therefore, in this methodology, the processes of target tracking and image enhancement “collaborate” in an interlacing manner, rather than being applied separately. The dynamic denoising is demonstrated on several examples of SAR imagery. The results demonstrated in this paper indicate a number of advantages of the proposed dynamic denoising over “static” approaches, in which the tracking images are enhanced independently of each other. PMID:18482881

  9. Electrophysiological characterization of the rat epithelial Na+ channel (rENaC) expressed in MDCK cells. Effects of Na+ and Ca2+.

    PubMed

    Ishikawa, T; Marunaka, Y; Rotin, D

    1998-06-01

    The epithelial Na+ channel (ENaC), composed of three subunits (alpha, beta, and gamma), is expressed in several epithelia and plays a critical role in salt and water balance and in the regulation of blood pressure. Little is known, however, about the electrophysiological properties of this cloned channel when expressed in epithelial cells. Using whole-cell and single channel current recording techniques, we have now characterized the rat alpha beta gamma ENaC (rENaC) stably transfected and expressed in Madin-Darby canine kidney (MDCK) cells. Under whole-cell patch-clamp configuration, the alpha beta gamma rENaC-expressing MDCK cells exhibited greater whole cell Na+ current at -143 mV (-1,466.2 +/- 297.5 pA) than did untransfected cells (-47.6 +/- 10.7 pA). This conductance was completely and reversibly inhibited by 10 microM amiloride, with a Ki of 20 nM at a membrane potential of -103 mV; the amiloride inhibition was slightly voltage dependent. Amiloride-sensitive whole-cell current of MDCK cells expressing alpha beta or alpha gamma subunits alone was -115.2 +/- 41.4 pA and -52.1 +/- 24.5 pA at -143 mV, respectively, similar to the whole-cell Na+ current of untransfected cells. Relaxation analysis of the amiloride-sensitive current after voltage steps suggested that the channels were activated by membrane hyperpolarization. Ion selectivity sequence of the Na+ conductance was Li+ > Na+ > K+ = N-methyl-D-glucamine+ (NMDG+). Using excised outside-out patches, amiloride-sensitive single channel conductance, likely responsible for the macroscopic Na+ channel current, was found to be approximately 5 and 8 pS when Na+ and Li+ were used as a charge carrier, respectively. K+ conductance through the channel was undetectable. The channel activity, defined as a product of the number of active channel (n) and open probability (Po), was increased by membrane hyperpolarization. Both whole-cell Na+ current and conductance were saturated with increased extracellular Na

  10. 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

  11. Nanopore Detection of 8-Oxoguanine in the Human Telomere Repeat Sequence

    PubMed Central

    2015-01-01

    The human telomere repeat sequence 5′-TTAGGG-3′ is a hot spot for oxidation at guanine, yielding 8-oxo-7,8-dihydroguanine (OG), a biomarker of oxidative stress. Telomere shortening resulting from oxidation will ultimately induce cellular senescence. In this study, α-hemolysin (α-HL) nanopore technology was applied to detect and quantify OG in the human telomeric DNA sequence. This repeat sequence adopts a basket G-quadruplex in the NaCl electrolyte used for analysis that enters the α-HL channel, slowly unfolds, and translocates. The basket fold containing OG disrupts the structure, leading to >10× increase in the unfolding kinetics without yielding a detectable current pattern. Therefore, detection of OG with α-HL required labeling of OG with aminomethyl-[18-crown-6] using a mild oxidant. The labeled OG yielded a pulse-like signal in the current vs time trace when the DNA strand was electrophoretically passed through α-HL in NaCl electrolyte. However, the rate of translocation was too slow using NaCl salts, leading us to further refine the method. A mixture of NH4Cl and LiCl electrolytes induced the propeller fold that unravels quickly outside the α-HL channel. This electrolyte allowed observation of the labeled OG, while providing a faster recording of the currents. Lastly, OG distributions were probed with this method in a 120-mer stretch of the human telomere sequence exposed to the cellular oxidant 1O2. Single-molecule profiles determined the OG distributions to be random in this context. Application of the method in nanomedicine can potentially address many questions surrounding oxidative stress and telomere attrition observed in various disease phenotypes including prostate cancer and diabetes. PMID:25768204

  12. Application of Ion Torrent Sequencing to the Assessment of the Effect of Alkali Ballast Water Treatment on Microbial Community Diversity

    PubMed Central

    Fujimoto, Masanori; Moyerbrailean, Gregory A.; Noman, Sifat; Gizicki, Jason P.; Ram, Michal L.; Green, Phyllis A.; Ram, Jeffrey L.

    2014-01-01

    The impact of NaOH as a ballast water treatment (BWT) on microbial community diversity was assessed using the 16S rRNA gene based Ion Torrent sequencing with its new 400 base chemistry. Ballast water samples from a Great Lakes ship were collected from the intake and discharge of both control and NaOH (pH 12) treated tanks and were analyzed in duplicates. One set of duplicates was treated with the membrane-impermeable DNA cross-linking reagent propidium mono-azide (PMA) prior to PCR amplification to differentiate between live and dead microorganisms. Ion Torrent sequencing generated nearly 580,000 reads for 31 bar-coded samples and revealed alterations of the microbial community structure in ballast water that had been treated with NaOH. Rarefaction analysis of the Ion Torrent sequencing data showed that BWT using NaOH significantly decreased microbial community diversity relative to control discharge (p<0.001). UniFrac distance based principal coordinate analysis (PCoA) plots and UPGMA tree analysis revealed that NaOH-treated ballast water microbial communities differed from both intake communities and control discharge communities. After NaOH treatment, bacteria from the genus Alishewanella became dominant in the NaOH-treated samples, accounting for <0.5% of the total reads in intake samples but more than 50% of the reads in the treated discharge samples. The only apparent difference in microbial community structure between PMA-processed and non-PMA samples occurred in intake water samples, which exhibited a significantly higher amount of PMA-sensitive cyanobacteria/chloroplast 16S rRNA than their corresponding non-PMA total DNA samples. The community assembly obtained using Ion Torrent sequencing was comparable to that obtained from a subset of samples that were also subjected to 454 pyrosequencing. This study showed the efficacy of alkali ballast water treatment in reducing ballast water microbial diversity and demonstrated the application of new Ion Torrent

  13. Application of ion torrent sequencing to the assessment of the effect of alkali ballast water treatment on microbial community diversity.

    PubMed

    Fujimoto, Masanori; Moyerbrailean, Gregory A; Noman, Sifat; Gizicki, Jason P; Ram, Michal L; Green, Phyllis A; Ram, Jeffrey L

    2014-01-01

    The impact of NaOH as a ballast water treatment (BWT) on microbial community diversity was assessed using the 16S rRNA gene based Ion Torrent sequencing with its new 400 base chemistry. Ballast water samples from a Great Lakes ship were collected from the intake and discharge of both control and NaOH (pH 12) treated tanks and were analyzed in duplicates. One set of duplicates was treated with the membrane-impermeable DNA cross-linking reagent propidium mono-azide (PMA) prior to PCR amplification to differentiate between live and dead microorganisms. Ion Torrent sequencing generated nearly 580,000 reads for 31 bar-coded samples and revealed alterations of the microbial community structure in ballast water that had been treated with NaOH. Rarefaction analysis of the Ion Torrent sequencing data showed that BWT using NaOH significantly decreased microbial community diversity relative to control discharge (p<0.001). UniFrac distance based principal coordinate analysis (PCoA) plots and UPGMA tree analysis revealed that NaOH-treated ballast water microbial communities differed from both intake communities and control discharge communities. After NaOH treatment, bacteria from the genus Alishewanella became dominant in the NaOH-treated samples, accounting for <0.5% of the total reads in intake samples but more than 50% of the reads in the treated discharge samples. The only apparent difference in microbial community structure between PMA-processed and non-PMA samples occurred in intake water samples, which exhibited a significantly higher amount of PMA-sensitive cyanobacteria/chloroplast 16S rRNA than their corresponding non-PMA total DNA samples. The community assembly obtained using Ion Torrent sequencing was comparable to that obtained from a subset of samples that were also subjected to 454 pyrosequencing. This study showed the efficacy of alkali ballast water treatment in reducing ballast water microbial diversity and demonstrated the application of new Ion Torrent

  14. A Fast Na+/Ca2+-Based Action Potential in a Marine Diatom

    PubMed Central

    Taylor, Alison R.

    2009-01-01

    Background Electrical impulses in animals play essential roles in co-ordinating an array of physiological functions including movement, secretion, environmental sensing and development. Underpinning many of these electrical signals is a fast Na+-based action potential that has been fully characterised only in cells associated with the neuromuscular systems of multicellular animals. Such rapid action potentials are thought to have evolved with the first metazoans, with cnidarians being the earliest representatives. The present study demonstrates that a unicellular protist, the marine diatom Odontella sinensis, can also generate a fast Na+/Ca2+ based action potential that has remarkably similar biophysical and pharmacological properties to invertebrates and vertebrate cardiac and skeletal muscle cells. Methodology/Principal Findings The kinetic, ionic and pharmacological properties of the rapid diatom action potential were examined using single electrode current and voltage clamp techniques. Overall, the characteristics of the fast diatom currents most closely resemble those of vertebrate and invertebrate muscle Na+/Ca2+ currents. Conclusions/Significance This is the first demonstration of voltage-activated Na+ channels and the capacity to generate fast Na+-based action potentials in a unicellular photosynthetic organism. The biophysical and pharmacological characteristics together with the presence of a voltage activated Na+/Ca2+ channel homologue in the recently sequenced genome of the diatom Thalassiosira pseudonana, provides direct evidence supporting the hypothesis that this rapid signalling mechanism arose in ancestral unicellular eukaryotes and has been retained in at least two phylogenetically distant lineages of eukaryotes; opisthokonts and the stramenopiles. The functional role of the fast animal-like action potential in diatoms remains to be elucidated but is likely involved in rapid environmental sensing of these widespread and successful marine protists

  15. 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

  16. Sequences and Combinations of Multifaceted Therapy In Advanced Prostate Cancer

    PubMed Central

    Vaishampayan, Ulka

    2015-01-01

    Purpose of Review Multiple agents with very distinct mechanisms of actions and unique toxicities and efficacies have become available for use in advanced prostate cancer. The next wave of investigations is focused on development of combinations and optimal sequences of the currently available agents. The focus of this review paper is to provide an update on clinical developments in advanced prostate cancer occurring within the past year, and to highlight the ongoing investigations of promising novel targets and compounds. Recent Findings The clinical use of enzalutamide prior to chemotherapy, demonstrated improvement in progression free survival (PFS) and overall survival (OS) as compared to placebo in metastatic castrate resistant prostate cancer (CRPC). This report of the PREVAIL trial led to the FDA approval of this agent. Novel agents such as cabozantinib and custirsen that had shown promising results in phase II trials, revealed disappointing results in the phase III setting. The breakthrough report, of the ability of the ARV-7 mutation, detected in circulating tumor cells, to predict lack of response to abiraterone or enzalutamide, and the remarkable responses of poly ADP ribose polymerase (PARP) inhibitors in prostate cancer with BRCA1/2 mutations, have elevated hopes of a bright future in the biomarker driven therapeutic arena. Summary As the clinical application of the recently approved multifaceted therapies widens, trials addressing optimal sequences and combinations are gaining importance. In addition, exploring the utility of therapies in the hormone naïve or non-metastatic settings is an area of active investigation. Early use of available agents, optimal sequencing and aid of biomarkers to guide therapeutic choices will make the achievement of lifetime remissions in advanced prostate cancer a reachable goal. PMID:25811344

  17. Diotic and dichotic discrimination of binary sequences

    NASA Astrophysics Data System (ADS)

    Sheft, Stanley; Yost, William A.; Dye, Raymond H.

    2005-04-01

    Binary-sequence discrimination was compared for diotic and dichotic stimuli. Sequences consisted of 4 to 32 wideband-noise pulses with pulse duration ranging from 8 to 32 ms. Diotic sequences were distinguished by pulse-amplitude pattern, while dichotic patterns differed by their sequence of ear of presentation. Discrimination was measured as a function of the number of pattern elements that differed between the standard and comparison sequences with temporal location of the altered pulses randomly selected on each trial. Additional fringe pulses bracketed the target sequences to avoid onset and offset cuing. Neither diotic nor dichotic performance was monotonic with the ratio of the number of altered to sequence pulses, with greater exception noted in the dichotic results. Except at the shortest pulse duration, diotic performance was significantly better than that obtained in the dichotic condition with similar pulse duration and numbers of altered and sequence pulses. For the range of stimulus parameters used, sequence discrimination often relied on a global percept rather than processing of individual pulse attributes with timbre differences cuing diotic discrimination. Though exhibiting fine resolution, results suggest poorer ability of the binaural than monaural system at extracting a global percept to cue sequence discrimination. [Work supported by NIDCD.

  18. Randomness in Sequence Evolution Increases over Time

    PubMed Central

    Wang, Guangyu; Sun, Shixiang; Zhang, Zhang

    2016-01-01

    The second law of thermodynamics states that entropy, as a measure of randomness in a system, increases over time. Although studies have investigated biological sequence randomness from different aspects, it remains unknown whether sequence randomness changes over time and whether this change consists with the second law of thermodynamics. To capture the dynamics of randomness in molecular sequence evolution, here we detect sequence randomness based on a collection of eight statistical random tests and investigate the randomness variation of coding sequences with an application to Escherichia coli. Given that core/essential genes are more ancient than specific/non-essential genes, our results clearly show that core/essential genes are more random than specific/non-essential genes and accordingly indicate that sequence randomness indeed increases over time, consistent well with the second law of thermodynamics. We further find that an increase in sequence randomness leads to increasing randomness of GC content and longer sequence length. Taken together, our study presents an important finding, for the first time, that sequence randomness increases over time, which may provide profound insights for unveiling the underlying mechanisms of molecular sequence evolution. PMID:27224236

  19. Deciphering the RNA landscape by RNAome sequencing.

    PubMed

    Derks, Kasper W J; Misovic, Branislav; van den Hout, Mirjam C G N; Kockx, Christel E M; Gomez, Cesar Payan; Brouwer, Rutger W W; Vrieling, Harry; Hoeijmakers, Jan H J; van IJcken, Wilfred F J; Pothof, Joris

    2015-01-01

    Current RNA expression profiling methods rely on enrichment steps for specific RNA classes, thereby not detecting all RNA species in an unperturbed manner. We report strand-specific RNAome sequencing that determines expression of small and large RNAs from rRNA-depleted total RNA in a single sequence run. Since current analysis pipelines cannot reliably analyze small and large RNAs simultaneously, we developed TRAP, Total Rna Analysis Pipeline, a robust interface that is also compatible with existing RNA sequencing protocols. RNAome sequencing quantitatively preserved all RNA classes, allowing cross-class comparisons that facilitates the identification of relationships between different RNA classes. We demonstrate the strength of RNAome sequencing in mouse embryonic stem cells treated with cisplatin. MicroRNA and mRNA expression in RNAome sequencing significantly correlated between replicates and was in concordance with both existing RNA sequencing methods and gene expression arrays generated from the same samples. Moreover, RNAome sequencing also detected additional RNA classes such as enhancer RNAs, anti-sense RNAs, novel RNA species and numerous differentially expressed RNAs undetectable by other methods. At the level of complete RNA classes, RNAome sequencing also identified a specific global repression of the microRNA and microRNA isoform classes after cisplatin treatment whereas all other classes such as mRNAs were unchanged. These characteristics of RNAome sequencing will significantly improve expression analysis as well as studies on RNA biology not covered by existing methods. PMID:25826412

  20. Variable copy number DNA sequences in rice.

    PubMed

    Kikuchi, S; Takaiwa, F; Oono, K

    1987-12-01

    We have cloned two types of variable copy number DNA sequences from the rice embryo genome. One of these sequences, which was cloned in pRB301, was amplified about 50-fold during callus formation and diminished in copy number to the embryonic level during regeneration. The other clone, named pRB401, showed the reciprocal pattern. The copy numbers of both sequences were changed even in the early developmental stage and eliminated from nuclear DNA along with growth of the plant. Sequencing analysis of the pRB301 insert revealed some open reading frames and direct repeat structures, but corresponding sequences were not identified in the EMBL and LASL DNA databases. Sequencing of the nuclear genomic fragment cloned in pRB401 revealed the presence of the 3'rps12-rps7 region of rice chloroplast DNA. Our observations suggest that during callus formation (dedifferentiation), regeneration and the growth process the copy numbers of some DNA sequences are variable and that nuclear integrated chloroplast DNA acts as a variable copy number sequence in the rice genome. Based on data showing a common sequence in mitochondria and chloroplast DNA of maize (Stern and Lonsdale 1982) and that the rps12 gene of tobacco chloroplast DNA is a divided gene (Torazawa et al. 1986), it is suggested that the sequence on the inverted repeat structure of chloroplast DNA may have the character of a movable genetic element. PMID:3481021