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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

    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.

  2. Labeling conventions in isoelectronic sequences

    SciTech Connect

    Maniak, S.T.; Curtis, L.J. )

    1990-08-01

    The isoelectronic exposition of atomic structure properties involves labeling ambiguities when more than one level of the same total angular momentum and parity is present, and an energy ordered labeling of these levels can lead to apparent isoelectronic discontinuities. For example, in the recent oscillator strength calculations for S-like ions by Saloman and Kim (Phys. Rev. A 38, 577 (1988)), abrupt changes in the rates were sometimes observed between one isoelectronic element and the next. We suggest an alternative labeling scheme that removes these discontinuities and produces a smooth isoelectronic variation. This alternative labeling offers advantages for data exposition and for semiempirical interpolation and extrapolation.

  3. R-matrix electron-impact excitation data for the Na-like iso-electronic sequence

    NASA Astrophysics Data System (ADS)

    Liang, G. Y.; Whiteford, A. D.; Badnell, N. R.

    2009-06-01

    We present results for the outer-shell electron-impact excitation of all Na-like ions from Mg+ to Kr25+ obtained using the intermediate-coupling frame transformation R-matrix approach. For each ion's calculation, the target and close-coupling expansions are both taken to be the 18 LS terms (32 levels) belonging to configurations [ 1s^22s^22p^6] 3l, 4l, 5l and 6l (l = 0-5). Effective collision strengths (Upsilons;) are presented at temperatures ranging from 2×10^2(q+1)2 K to 2×10^6(q+1)2 K (where q is the residual charge of ions, i.e. Z-11). Detailed comparisons for the Upsilons; are made with the results of previous calculations for several ions, which span the sequence. Furthermore, we examine the iso-electronic trends of both low- and high-temperature effective collision strengths These data are made available in the archives of APAP via http://www.apap-network.org, OPEN-ADAS via http://open.adas.ac.uk as well as anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsweb.u-strasbg.fr/cgi-bin/qcat?J/A+A/500/1263

  4. 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.

  5. 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.

  6. Systematic in the relativistic oscillator strengths for fine-structure transitions in the aluminium isoelectronic sequence.

    NASA Astrophysics Data System (ADS)

    Lavin, C.; Alvarez, A. B.; Martin, I.

    1997-06-01

    Theoretical oscillator strengths for 3s23p 2P-3s23d 2D, 3s23p 2P-3s24s 2S and 3s24s 2S-3s24p 2P fine-structure transitions in some ions of the aluminium isoelectronic sequence are reported. The computations have been carried out with two formalisms within the context of quantum defect theory: the quantum defect orbital method (QDO) and its relativistic counterpart (RQDO). The advantages of including relativistic effects are made apparent. Some of these are reflected by the correct systematic trends displayed by the RQDO f-values along the isoelectronic sequence.

  7. Quantum-defect studies of transitions in the diffuse spectral series of the potassium isoelectronic sequence.

    NASA Astrophysics Data System (ADS)

    Lavin, C.; Barrientos, C.; Martín, I.

    1992-05-01

    Theoretical oscillator strengths are reported for transitions in the diffuse spectral series of some members of the potassium isoelectronic sequence (K I-Cr VI). The calculations have been performed with the Quantum Defect Orbital (QDO) method. A core-polarization correction to the dipole transition moment has also been included in the formalism.

  8. 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.

  9. 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).

  10. Relativistic oscillator strengths for transitions in the principal spectral series of the silver isoelectronic sequence

    NASA Astrophysics Data System (ADS)

    Martín, I.; Almaraz, M. A.; Lavin, C.

    1995-12-01

    In a very recent paper [1] we have reported oscillator strengths for fine structure transitions between levels belonging to the diffuse and sharp spectral series in the silver isoelectronic sequence. The calculations were performed with the quantum defect orbital method in both their non-relativistic (QDO) and relativistic (RQDO) formulations, with both implicit and explicit allowance for core-valence polarisation. We now present a parallel study of transitions belonging to the ns 2 S- n'2 P( n=5, 6; n'=5-10) spectral series of the AgI sequence, up to Z=63 in some cases.

  11. Kinetic Correlation In Photo-Double-Ionization Processes: The He-Isoelectronic Sequence

    SciTech Connect

    Otranto, S.; Garibotti, C. R.

    2006-01-09

    Analytical models proposed to represent the two-electron continuum are revisited. Main results obtained with these models are summarized. Recent studies of the photo-double-ionization (PDI) of the He-isoelectronic sequence by means of the recently introduced SC3 model are shown and compared with the results predicted by classical and semi-classical Wannier approaches. By fitting the triply differential cross sections (TDCSs) with the usual dipolar Gaussian form we find that the width has a power dependence on excess energy with exponent 0.25 in the near threshold region and departs from this law with increasing energy.

  12. 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.

  13. K-Shell Photoabsorption and Photoionisation of Trace Elements I. Isoelectronic Sequences With Electron Number 3< or = N < or = 11

    NASA Technical Reports Server (NTRS)

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

    2016-01-01

    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< or = N< or = 11. The Na sequence (N=11) is used to estimate the contributions from configurations with a 2s hole (i.e. [2s]) and those containing 3d orbitals, which will be crucial when considering sequences with N 11.Conclusions. It is found that the [2s/u] 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.

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

    NASA Astrophysics Data System (ADS)

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

    2012-09-01

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

  15. 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.

  16. Static electric dipole polarizabilities for isoelectronic sequences. II. Open-shell S statesa2

    NASA Astrophysics Data System (ADS)

    Koch, Volker; Andrae, Dirk

    2013-07-01

    We present static electric dipole polarizabilities α d( Z,N) from numerical nonrelativistic restricted Hartree-Fock (RHF) finite-field calculations for high-spin open-shell S states ( L = 0) of atoms and isoelectronic ions with N ≤ 55 electrons. All these S states result from one or more half-filled shells. For eight isoelectronic sequences, those with N = 3, 7, 11, 15, 23, 29, 33 or 41 electrons where the electronic ground state of the neutral or nearly neutral members is conserved upon increase of the nuclear charge number Z, polarizability data are given for ions with charge number Q = Z - N up to Q = 90. In addition, these data are represented in terms of rational functions of Q (with absolute value of the relative error of the fit always below 4%). The rational functions are comparable to the classical nonrelativistic result α d( Z,1) = 4.5 / Z 4 = 4.5 / ( Q + 1)4 for the polarizability of the 2S ground state of a hydrogen-like system. Our results also contribute to constitute a reference database (i) for algebraic approaches relying on basis functions, and (ii) for the discussion of relativistic and correlation effects on polarizabilities along isoelectronic sequences.

  17. K-shell photoabsorption and photoionization of trace elements. II. Isoelectronic sequences with electron number 12 ≤N ≤ 18

    NASA Astrophysics Data System (ADS)

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

    2017-08-01

    Context. We are concerned with improving the diagnostic potential of the K lines and edges of elements with low cosmic abundances, namely F, Na, P, Cl, K, Sc, Ti, V, Cr, Mn, Co, Cu, and Zn, that are observed in the X-ray spectra of supernova remnants, galaxy clusters, and accreting black holes and neutron stars. Aims: Since accurate photoabsorption and photoionization cross sections are needed in their spectral models, they have been computed for isoelectronic sequences with electron number 12 ≤ N ≤ 18 using a multi-channel method. Methods: Target representations are obtained with the atomic structure code autostructure, and ground-state cross sections are computed with the Breit-Pauli R-matrix method (bprm) in intermediate coupling, including damping (radiative and Auger) effects. Results: Following the findings in our earlier work on sequences with 2 ≤ N ≤ 11, the contributions from channels associated with the 2s-hole [2s] μ target configurations and those containing 3d orbitals are studied in the Mg (N = 12) and Ar (N = 18) isoelectronic sequences. Cross sections for the latter ions are also calculated in the isolated-resonance approximation as implemented in autostructure and compared with bprm to test their accuracy. Conclusions: It is confirmed that the collisional channels associated with the [2s] μ target configurations must be taken into account owing to significant increases in the monotonic background cross section between the L and K edges. Target configurations with 3d orbitals give rise to fairly conspicuous unresolved transition arrays in the L-edge region, but to a much lesser extent in the K-edge that is our main concern; therefore, they have been neglected throughout owing to their computationally intractable channel inventory, thus allowing the computation of cross sections for all the ions with 12 ≤ N ≤ 18 in intermediate coupling with bprm. We find that the isolated-resonance approximations performs satisfactorily and will be our

  18. R-matrix electron-impact excitation data for the Ne-like iso-electronic sequence

    NASA Astrophysics Data System (ADS)

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

    2010-07-01

    We present results for the electron-impact excitation of all Ne-like ions from Na+ to Kr26+ obtained using the intermediate-coupling frame transformation R-matrix approach. For each ion's calculation, the close-coupling expansion is taken to be the 113 LS terms (209 levels) belonging to the configurations [1s2] 2s22p6, 2s22p5{3, 4, 5}l, 2s2p6{3, 4, 5}l (l ∈ s, p, d, f, and g), and 2s22p5{6, 7}l' (l' ∈ s, p, and d). An additional configuration interaction effect arising from configurations of 2s22p43l{3, 4, 5}l'' (l'' ∈ s, p, d, f and g) was included in the target expansion. A detailed comparison of the target structure has been made for six specific ions (Si4+, Ar8+, Ca10+, Fe16+, Ni18+, and Kr26+) spanning the sequence to assess the accuracy for the entire sequence. Effective collision strengths (Υs) are presented at temperatures ranging from 2 × 102(q+1)2 K to 2 × 106(q + 1)2 K (where q is the residual charge of ions, i.e. Z - 10). Detailed comparisons for the Υs are made with the results of previous calculations for several ions, which span the sequence. Furthermore, we examine the iso-electronic trends of effective collision strengths as a function of temperature. The present results are the only R-matrix ones for the majority of the ions and the most extensive and complete data for modelling to-date. These data are made available in the archives of APAP via http://www.apap-network.org, OPEN-ADAS via http://open.adas.ac.uk as well as anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsweb.u-strasbg.fr/cgi-bin/qcat?J/A+A/518/A64

  19. Spectroscopic studies of highly ionized atoms: New results for the Ne, Mg, Mn, Fe, Co, Ga and Ge isoelectronic sequences

    NASA Astrophysics Data System (ADS)

    Zeng, Xiantang

    The electron structure of several highly charged ions, belonging to the Mg, Ne, Mn, Fe, Co, Ga and Ge isoelectronic sequences, has been experimentally studied by means of two techniques, beam-foil spectroscopy, BFS, and the spectroscopy of laser-produced plasmas, LPP. The investigations were carried out at Lund University, LU, in 1989-90 and at the China Institute of Atomic Energy, CIAE, Beijing, from 1990 on. In Lund the spectra Br IX - Br XI (belonging to Co, Fe and Mn sequences, respectively) were studied by BFS, using the 3 MV Pelletron tandem accelerator. The LPP investigations, in which a 1.5 GW Nd(YAG) laser system was utilized, dealt with highly charged ions belonging to the Ga and Ge isoelectronic sequences. Many previously unknown transitions were observed and new energy levels were established. The observations were corroborated by theoretical calculations with the relativistic Hartree- Fock code, HFR, by R. D. Cowan. At CIAE a beamline for atomic physics experiments was designed and constructed in the 14 MV tandem accelerator laboratory. The instrumentation includes a high- resolution 2.2 m grazing incidence monochromator for the spectral region 10-1000 Å. This monochromator, which compares favorably with commercially available instruments, was designed and built in China. Spectra of highly charged S, Ni, Cu, Ge and Br have already been recorded at CIAE. The thesis includes detailed results, for Ne-like Br XXVI and Mg-like Br XXIV. In both spectra about 20 previously unknown energy levels were established. Parallel with the experimental work HFR calculations were performed. Theory and experiment are in very satisfactory agreement. Also, future atomic physics investigations at CIAE are briefly discussed in the thesis.

  20. 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.

  1. 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.

  2. Electron-impact excitation-autoionization in the cadmium isoelectronic sequence: A case of target term dependence in scattering theory

    NASA Astrophysics Data System (ADS)

    Pindzola, M. S.; Griffin, D. C.; Bottcher, C.

    1983-05-01

    Excitation-autoionization contributions to electron-impact ionization are calculated for several atomic ions in the cadmium isoelectronic sequence. We calculate excitation cross sections in the distorted-wave approximation and compare them in one case to a calculation in the close-coupling approximation. We focus attention on the 4d105s2-->4d95s2nf innershell excitations in In+, Sb3+, and Xe6+. Hartree-Fock atomic structure calculations for the 4d95s2nf configurations are found to be highly term dependent. Thus our predictions for the total ionization cross section from the 5s subshell for these ions exhibit strong target term dependence. Our Xe6+ results are found to be in excellent agreement with the recent experimental crossed-beam measurements of Gregory and Crandall.

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

    PubMed

    Sims, James S; Hagstrom, Stanley A

    2014-06-14

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  5. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

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

  7. Calculation of levels, transition rates, and lifetimes for the arsenic isoelectronic sequence Sn XVIII-Ba XXIV, W XLII

    NASA Astrophysics Data System (ADS)

    Wang, K.; Chen, Z. B.; Chen, C. Y.; Yan, J.; Dang, W.; Zhao, X. H.; Yang, X.

    2017-09-01

    Multi-configuration Dirac-Fock (MCDF) calculations of energy levels, wavelengths, oscillator strengths, lifetimes, and electric dipole (E1), magnetic dipole (M1), electric quadrupole (E2), magnetic quadrupole (M2) transition rates are reported for the arsenic isoelectronic sequence Sn XVIII-Ba XXIV, W XLII. Results are presented among the 86 levels of the 4s2 4p3, 4 s 4p4, 4p5, 4s2 4p2 4 d, and 4 s 4p3 4 d configurations in each ion. The relativistic atomic structure package GRASP2K is adopted for the calculations, in which the contributions from the correlations within the n ≤ 7 complexes, Breit interaction (BI) and quantum electrodynamics (QED) effects are taking into account. The many-body perturbation theory (MBPT) method is also employed as an independent calculation for comparison purposes, taking W XLII as an example. Calculated results are compared with data from other calculations and the observed values from the Atomic Spectra Database (ASD) of the National Institute of Standards and Technology (NIST). Good agreements are obtained. i.e, the accuracy of our energy levels is assessed to be better than 0.6%. These accurate theoretical data should be useful for diagnostics of hot plasmas in fusion devices.

  8. Comparison of Theoretical and Experimental Level Values of the n = 2 Configurations in the Boron Isoelectronic Sequence

    NASA Astrophysics Data System (ADS)

    Edlén, Bengt

    1983-10-01

    The examination of the level values of the n = 2 configurations, which was recently carried through for ions iso-electronic with Li, Be, O and F, has now been extended to the configurations 2s22p, 2s2p2 and 2p3 of the boron sequence. In this study, expressions of the form A + B(Z - C)-1 + a(Z - s)x are derived for the difference between observed and theoretical values of selected level intervals, the theoretical values being based on the calculations of Cheng, Kim and Desclaux. By this procedure, accidental errors in the experimental data are smoothed out and missing data are interpolated or extrapolated beyond the range of observations. In the case of the two strongly interacting levels 2s2p2 2S1/2, 2P1/2, however, the theory fails to reproduce the effects of the "avoided crossing" well enough to provide a useful frame of reference, and a more primitive method of extrapolation had to be used. The results of the examination are summarized in a table of recommended values for the 14 excited levels of the n = 2 complex, covering the range from Z = 7 to Z = 36, and a corresponding table of recalculated wavelengths, including intersystem combinations. Some experimental data reported in the literature are found to need revision.

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

    NASA Astrophysics Data System (ADS)

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

    2012-11-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-04-01

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

  11. 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.

  12. Data-based methods for isoelectronic prediction of atomic lifetimes and energy levels

    NASA Astrophysics Data System (ADS)

    Curtis, Lorenzo J.

    1993-11-01

    The use of data-based semiempirical methods to produce high precision predictions and systematizations along isoelectronic sequences is discussed and applied to several examples. Applications include: studies of trends in the lifetimes of resonance transitions in alkali-like isoelectronic sequences; the combined systematization of spin-allowed and spin-forbidden transition probabilities in alkaline earth-like and inert gas-like isoelectronic sequences; the use of screening and quantum defect parametrizations to predict ionization potentials for the Be sequence.

  13. Energy levels, lifetimes, and transition rates for the selenium isoelectronic sequence Pd XIII-Te XIX, Xe XXI-Nd XXVII, W XLI

    NASA Astrophysics Data System (ADS)

    Wang, K.; Yang, X.; Chen, Z. B.; Si, R.; Chen, C. Y.; Yan, J.; Zhao, X. H.; Dang, W.

    2017-09-01

    Energy levels, wavelengths, lifetimes, oscillator strengths, and electric dipole (E1), magnetic dipole (M1), electric quadrupole (E2), magnetic quadrupole (M2) transition rates among the 46 fine structure levels belonging to the ([ Ar ] 3d10) 4s2 4p4, ([ Ar ] 3d10) 4s2 4p3 4 d, and ([ Ar ] 3d10) 4 s 4p5 configurations for the selenium isoelectronic sequence Pd XIII-Te XIX, Xe XXI-Nd XXVII, W XLI are reported. These data are determined in the multi-configuration Dirac-Fock (MCDF) approach, in which relativistic effects, main electron correlations within the n = 7 complex, Breit interaction (BI), and quantum electrodynamic (QED) corrections are included. The many-body perturbation theory (MBPT) method is also employed as an independent calculation to confirm the present accuracy, taking W XLI as an example. Comparisons and analysis are made between the present results and available experimental and theoretical ones, and good agreements are obtained. These accurate data are expected to be useful in nuclear fusion research and astrophysical applications.

  14. 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.

  15. Comparison of Theoretical and Experimental Level Values of the n = 2 Configurations in the Nitrogen Isoelectronic Sequence

    NASA Astrophysics Data System (ADS)

    Edlén, Bengt

    1984-08-01

    Observed level intervals within and between the configurations 2s2 2p3, 2s2p4 and 2p5 of the nitrogen sequence are compared with the corresponding theoretical values derived from the tables of Cheng, Kim and Desclaux. The differences are expressed by suitable functions of Z which give the systematic correction to the theoretical values and reveal the accidental errors in the experimental values. The technique is the same as was used in previous examinations of the Li, Be, B, O and F sequences. The results are summarized in tables of recommended level values (Z = 10-36) and recalculated wavelengths.

  16. Higher order two- and three-body dispersion coefficients for alkali isoelectronic sequences by a variationally stable procedure

    NASA Astrophysics Data System (ADS)

    Huang, Shi-Zhong; Sun, Qiu-Feng

    2011-04-01

    Using the variationally stable method of Gao and Starace, and the simple ground state wave function of the valence electron previously suggested by Patil and Tang, the multipolar polarizabilities of Li, Na, K, Rb, Cs, Be+, Mg+, Ca+, Sr+, Ba+, the two-body dispersion coefficients of homonuclear and heteronuclear interactions from C6 to C40, as well as the three-body dispersion coefficients Z(L1, L2, L3) (up to Li = 5), are investigated. Higher order van der Waals dispersion coefficients Cn (n > 24) and Z(L1, L2, L3) (Li > 3) are reported for the first time. Comparisons with previous calculations found in the literature show that this approach is capable of yielding precise and fast convergent values for higher order dispersion coefficients for alkali-metal atoms.

  17. 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.

  18. CALCULATIONS WITH SPECTROSCOPIC ACCURACY: ENERGIES AND TRANSITION RATES IN THE NITROGEN ISOELECTRONIC SEQUENCE FROM Ar XII TO Zn XXIV

    SciTech Connect

    Wang, K.; Dang, W.; Si, R.; Guo, X. L.; Hutton, R.; Chen, C. Y.; Jönsson, P.; Li, S.; Zhang, H.; Long, F. Y.; Liu, H. T.; Li, D. F.; Yan, J.; Chen, Z. B. E-mail: chychen@fudan.edu.cn

    2016-03-15

    Combined relativistic configuration interaction and many-body perturbation calculations are performed for the 359 fine-structure levels of the 2s{sup 2} 2p{sup 3}, 2 s2p{sup 4}, 2p{sup 5}, 2s{sup 2} 2p{sup 2} 3l, 2 s2p{sup 3} 3l, 2p{sup 4} 3l, and 2s{sup 2} 2p{sup 2} 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.

  19. Study of the 4p2, 5p2 and 5s5f excited configurations of the Zn and Cd isoelectronic sequences, using relativistic and non-relativistic semiempirical approaches

    NASA Astrophysics Data System (ADS)

    Di Rocco, Héctor O.; Raineri, Mónica; Reyna-Almandos, Jorge G.

    2016-11-01

    The consistency of the energy levels published for configurations 4p2, 5p2 and 5s5f belonging to Zn and Cd isoelectronic sequences is studied. Different semiempirical approaches considering the linearity of the Slater integrals for large Zc, the smoothness of the sF screening parameters, the energy values in terms of Z (or Zc), and the differences of the Ecalc - Eexp values are used, where Ecalc values are energies calculated with a Hartree-Hock method with relativistic corrections and superposition of configurations (HFR-SOC), and Eexp are the experimental values. For the np2 configurations both LS and relativistic jj expressions are considered. Configuration 5s5f is also analyzed taking into account the Landé's interval rule.

  20. 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)

  1. Excited states of Ne isoelectronic ions: SAC-CI study

    NASA Astrophysics Data System (ADS)

    Das, A. K.; Ehara, M.; Nakatsuji, H.

    2001-01-01

    Excited states of the s, p, and d symmetries up to principal quantum number n = 4 are studied for the first eight members of Ne isoelectronic sequence (Ne to Cl7+) by the SAC-CI (symmetry-adapted-cluster configuration-interaction) method. The valence STO basis sets of Clementi et al. and the optimized excited STO are used by the STO-6G expansion method. The calculated transition energies agree well with the experimental values wherever available.

  2. 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.

  3. Photoionization of isoelectronic ions: Mg{sup +} and Al{sup 2+}

    SciTech Connect

    Aguilar, A.; West, J.B.; Phaneuf, R.A.; Brooks, R. L.; Folkmann, F.; Kjeldsen, H.; Bozek, J.D.; Schlachter, A.S.; Cisneros, C.

    2003-01-01

    High-resolution measurements of the photoionization cross sections of the Na-isoelectronic ions Mg{sup +} and Al{sup 2+} are presented, to be compared with earlier measurements in which structure in the most prominent peaks was unresolved. These measurements have been normalized to the earlier ones in order to provide values of the oscillator strengths of the newly resolved peaks, and comparison is made with multiconfiguration Hartree-Fock calculations.

  4. 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…

  5. 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…

  6. The spectrum of NeH. A comparative isoelectronic study

    NASA Astrophysics Data System (ADS)

    Martin, I.; Pérez-Delgado, Y.; Lavín, C.

    1999-05-01

    Einstein coefficients and oscillator strengths for Rydberg-ground and Rydberg-Rydberg transitions in the rare-gas excimer NeH have been calculated with the quantum defect orbital (QDO) method. A comparative study of analogous transitions in NeH and in some of its isoelectronic Rydberg radicals has revealed clear similarities between them.

  7. Quantum defect orbital study of the sodium isoelectronic sequence

    NASA Astrophysics Data System (ADS)

    Martin, Inmaculada; Karwowski, Jacek; Lavin, Carmen; Diercksen, Geerd H. F.

    1991-12-01

    The quantum defect orbital (QDO) method and its relativistic (RQDO) counterpart have been applied to the calculation of oscillator strengths for the 3s 2S → 3p 2Po, 3p 2Po → 3d 2D, 3d 2D → 4f 2Fo, and 3d 2D → 5f 2Fo transitions in sodium-like atoms. The consequences of including relativistic effects are demonstrated.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  9. Divergence analysis of atomic ionization processes and isoelectronic series

    SciTech Connect

    Lopez-Rosa, S.; Angulo, J. C.; Antolin, J.; Esquivel, R. O.

    2009-07-15

    Fisher divergences (FDs) and Jensen-Shannon divergences (JSDs) are used in this work to quantify the informational discrepancies between the one-particle electron densities of neutral atoms, singly charged ions, and isoelectronic series. These dissimilarity magnitudes, computed for a set of 319 atomic systems in both position and momentum spaces, provide relevant information concerning pattern, structure, and periodicity properties of the ionization processes. In particular an apparent correlation between extremal values of the atomic ionization potential and the divergences is found. Results are compared with those obtained by quantum similarity techniques.

  10. Thermoelectric properties of isoelectronically substituted bismuth compounds: a computational study

    NASA Astrophysics Data System (ADS)

    Liangruksa, Monrudee

    2017-03-01

    This work focuses on using isoelectronic substitution to modify electronic density of states (DOS) of bismuth (Bi) compounds for thermoelectric property modification. The calculations include first-principle density functional theory (DFT) and analytical calculations based on Mott formula. The thermoelectric materials selected in the present study are Bi compounds, i.e. Bi2Te3, Bi2Se3, Bi2Se2Te, Bi2Te2Se, Bi2O2Te, and Bi2O2Se. The results reveal that isoelectronic substitution of Se and Te atoms with O atoms (Bi2O2Te and Bi2O2Se) introduces changes in DOS around the valence band maximum and the conduction band minimum, exhibiting the figure of merit (ZT) approaching the values 0.004 and 0.03 at room temperature, for Bi2O2Se and Bi2O2Te, respectively. Though the ZT of these oxide compounds are inferior to conventional thermoelectric materials, it is known that they show better stability and less toxicity which could be the alternative materials.

  11. Isoelectronic line intensity ratios for plasma electron temperature measurement (invited)

    NASA Astrophysics Data System (ADS)

    Marjoribanks, Robin S.; Budnik, Fredric; Kulcsár, Gábor; Zhao, Liang

    1995-01-01

    Strictly speaking, temperature is uniquely defined only in plasmas which are in complete thermodynamic equilibrium. In typical laser-produced plasmas, measurement of electron temperature amounts to a parametrization of some part of the distribution of electron energies, typically inferred from the recombination continuum, or from the ratio of spectral lines that are implicitly dependent on the electron distribution. Where the plasma is highly transient, suffers appreciable opacity, or is subject to a background radiation field, the interpretation of temperature from disparate spectral lines can become untrustworthy. For these complicated plasmas, a conceptually simpler spectral line diagnostic offers great advantages. A technique has been introduced that begins with plasmas that include two elements of similar atomic number, in a known ratio, and compares isoelectronic lines from ions that differ only in their nuclear charge Z, and thus in their ionization potentials χi. Since these two have different values of the same dimensionless parameter Te/χi, the ratio of intensities of isoelectronic lines can be interpreted to determine the temperature Te. The technique and its areas of advantage are described, the applications made to the special problems of laboratories elsewhere are summarized, and this particular progress in application to laser plasmas produced by high-intensity picosecond pulses are reported here.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. X-ray Emission Line Anisotropy Effects on the Isoelectronic Temperature Measurement Method

    NASA Astrophysics Data System (ADS)

    Liedahl, Duane; Barrios, Maria; Brown, Greg; Foord, Mark; Gray, William; Hansen, Stephanie; Heeter, Robert; Jarrott, Leonard; Mauche, Christopher; Moody, John; Schneider, Marilyn; Widmann, Klaus

    2016-10-01

    Measurements of the ratio of analogous emission lines from isoelectronic ions of two elements form the basis of the isoelectronic method of inferring electron temperatures in laser-produced plasmas, with the expectation that atomic modeling errors cancel to first order. Helium-like ions are a common choice in many experiments. Obtaining sufficiently bright signals often requires sample sizes with non-trivial line optical depths. For lines with small destruction probabilities per scatter, such as the 1s2p-1s2 He-like resonance line, repeated scattering can cause a marked angular dependence in the escaping radiation. Isoelectronic lines from near-Z equimolar dopants have similar optical depths and similar angular variations, which leads to a near angular-invariance for their line ratios. Using Monte Carlo simulations, we show that possible ambiguities associated with anisotropy in deriving electron temperatures from X-ray line ratios are minimized by exploiting this isoelectronic invariance.

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

    PubMed Central

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

    2016-01-01

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

  18. Draft Genome Sequence of a Pseudomonas aeruginosa NA04 Bacterium Isolated from an Entomopathogenic Nematode.

    PubMed

    Salgado-Morales, Rosalba; Rivera-Gómez, Nancy; Lozano-Aguirre Beltrán, Luis Fernando; Hernández-Mendoza, Armando; Dantán-González, Edgar

    2017-09-07

    We report the draft genome sequence of Gram-negative bacterium Pseudomonas aeruginosa NA04, isolated from the entomopathogenic nematode Heterorhabditis indica MOR03. The draft genome consists of 54 contigs, a length of 6.37 Mb, and a G+C content 66.49%. Copyright © 2017 Salgado-Morales et al.

  19. United atoms to superatoms and the isoelectronic principle

    NASA Astrophysics Data System (ADS)

    Peppernick, Samuel John

    The work described in this thesis pertains to the photoelectron spectroscopy of negatively charged atomic ions and their superatomic counterparts. The molecular ions studied in this work, TiO-, ZrO -, and WC- can be interpreted as superatomic manifestations of the respective isoelectronic elements appearing on the periodic table. The superposition principle, in the context of the unified atom picture from molecular orbital theory, allows for the assignment of molecular electronic transitions to be referenced to the atomic frame. This approach represents a novel method of determining the electronic state origins of transitions appearing in the photoelectron spectra of molecular anions by directly comparing the known spectroscopy for the isoelectronic element. In Chapter 3, a remarkable correspondence is presented between the separate PADs produced independently by TiO- and Ni- , suggesting the bound ionic state of the diatomic is mimicking that present in the negative atomic ion. Application of the beta-wave approach provides supporting evidence that the dominant photodetachment channel in TiO- arises from electron emission of the highest ocuupied 9sigma molecular orbital. This provides an immediate assignment of the ground electronic state of TiO- as the doublet 2Delta 3/2 configuration. Similarly, the ground electronic state of Ni - is 2D5/2 with 4s orbital ejection describing the ground state electron affinity transition. Obtained in Chapter 4 is an improved measurement of the electron affinity of ZrO-, determined to be 1.29(1) eV. This energy arises from the assigned anion to neutral ground state, 1Sigma + ← 2Sigma-, electronic transition. Further indentified are features assigned to the 2Delta 3/2 and 2Delta5/2 electronically excited states of the anion, with the 2Delta3/2 spin orbit component measured to lie ˜ 0.10 eV above the 2Sigma - ground state. The first measurement of the photoelectron binding energy spectrum of Pt-, at a fixed frequency photon

  20. 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.

  1. Evaluation of recombinant monoclonal antibody SVmab1 binding to Na V1.7 target sequences and block of human Na V1.7 currents

    PubMed Central

    Liu, Dong; Tseng, Mandy; Epstein, Linda F.; Green, Lydia; Chan, Brian; Soriano, Brian; Lim, Desiree; Pan, Oscar; Murawsky, Christopher M.; King, Chadwick T.; Moyer, Bryan D.

    2016-01-01

    Identification of small and large molecule pain therapeutics that target the genetically validated voltage-gated sodium channel Na V1.7 is a challenging endeavor under vigorous pursuit. The monoclonal antibody SVmab1 was recently published to bind the Na V1.7 DII voltage sensor domain and block human Na V1.7 sodium currents in heterologous cells. We produced purified SVmab1 protein based on publically available sequence information, and evaluated its activity in a battery of binding and functional assays. Herein, we report that our recombinant SVmAb1 does not bind peptide immunogen or purified Na V1.7 DII voltage sensor domain via ELISA, and does not bind Na V1.7 in live HEK293, U-2 OS, and CHO-K1 cells via FACS. Whole cell manual patch clamp electrophysiology protocols interrogating diverse Na V1.7 gating states in HEK293 cells, revealed that recombinant SVmab1 does not block Na V1.7 currents to an extent greater than observed with an isotype matched control antibody. Collectively, our results show that recombinant SVmab1 monoclonal antibody does not bind Na V1.7 target sequences or specifically inhibit Na V1.7 current. PMID:27990272

  2. Evaluation of recombinant monoclonal antibody SVmab1 binding to Na V1.7 target sequences and block of human Na V1.7 currents.

    PubMed

    Liu, Dong; Tseng, Mandy; Epstein, Linda F; Green, Lydia; Chan, Brian; Soriano, Brian; Lim, Desiree; Pan, Oscar; Murawsky, Christopher M; King, Chadwick T; Moyer, Bryan D

    2016-01-01

    Identification of small and large molecule pain therapeutics that target the genetically validated voltage-gated sodium channel Na V1.7 is a challenging endeavor under vigorous pursuit. The monoclonal antibody SVmab1 was recently published to bind the Na V1.7 DII voltage sensor domain and block human Na V1.7 sodium currents in heterologous cells. We produced purified SVmab1 protein based on publically available sequence information, and evaluated its activity in a battery of binding and functional assays. Herein, we report that our recombinant SVmAb1 does not bind peptide immunogen or purified Na V1.7 DII voltage sensor domain via ELISA, and does not bind Na V1.7 in live HEK293, U-2 OS, and CHO-K1 cells via FACS. Whole cell manual patch clamp electrophysiology protocols interrogating diverse Na V1.7 gating states in HEK293 cells, revealed that recombinant SVmab1 does not block Na V1.7 currents to an extent greater than observed with an isotype matched control antibody. Collectively, our results show that recombinant SVmab1 monoclonal antibody does not bind Na V1.7 target sequences or specifically inhibit Na V1.7 current.

  3. 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.

  4. Incorporation of the influenza A virus NA segment into virions does not require cognate non-coding sequences

    PubMed Central

    Crescenzo-Chaigne, Bernadette; Barbezange, Cyril V. S.; Léandri, Stéphane; Roquin, Camille; Berthault, Camille; van der Werf, Sylvie

    2017-01-01

    For each influenza virus genome segment, the coding sequence is flanked by non-coding (NC) regions comprising shared, conserved sequences and specific, non-conserved sequences. The latter and adjacent parts of the coding sequence are involved in genome packaging, but the precise role of the non-conserved NC sequences is still unclear. The aim of this study is to better understand the role of the non-conserved non-coding sequences in the incorporation of the viral segments into virions. The NA-segment NC sequences were systematically replaced by those of the seven other segments. Recombinant viruses harbouring two segments with identical NC sequences were successfully rescued. Virus growth kinetics and serial passages were performed, and incorporation of the viral segments was tested by real-time RT-PCR. An initial virus growth deficiency correlated to a specific defect in NA segment incorporation. Upon serial passages, growth properties were restored. Sequencing revealed that the replacing 5′NC sequence length drove the type of mutations obtained. With sequences longer than the original, point mutations in the coding region with or without substitutions in the 3′NC region were detected. With shorter sequences, insertions were observed in the 5′NC region. Restoration of viral fitness was linked to restoration of the NA segment incorporation. PMID:28240311

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

    PubMed

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

    2010-01-19

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

  6. 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.

  7. Generation and analysis of expressed sequence tags from NaCl-treated Glycine soja

    PubMed Central

    Ji, Wei; Li, Yong; Li, Jie; Dai, Cui-hong; Wang, Xi; Bai, Xi; Cai, Hua; Yang, Liang; Zhu, Yan-ming

    2006-01-01

    Background Salinization causes negative effects on plant productivity and poses an increasingly serious threat to the sustainability of agriculture. Wild soybean (Glycine soja) can survive in highly saline conditions, therefore provides an ideal candidate plant system for salt tolerance gene mining. Results As a first step towards the characterization of genes that contribute to combating salinity stress, we constructed a full-length cDNA library of Glycine soja (50109) leaf treated with 150 mM NaCl, using the SMART technology. Random expressed sequence tag (EST) sequencing of 2,219 clones produced 2,003 cleaned ESTs for gene expression analysis. The average read length of cleaned ESTs was 454 bp, with an average GC content of 40%. These ESTs were assembled using the PHRAP program to generate 375 contigs and 696 singlets. The resulting unigenes were categorized according to the Gene Ontology (GO) hierarchy. The potential roles of gene products associated with stress related ESTs were discussed. We compared the EST sequences of Glycine soja to that of Glycine max by using the blastn algorithm. Most expressed sequences from wild soybean exhibited similarity with soybean. All our EST data are available on the Internet (GenBank_Accn: DT082443~DT084445). Conclusion The Glycine soja ESTs will be used to mine salt tolerance gene, whose full-length cDNAs will be obtained easily from the full-length cDNA library. Comparison of Glycine soja ESTs with those of Glycine max revealed the potential to investigate the wild soybean's expression profile using the soybean's gene chip. This will provide opportunities to understand the genetic mechanisms underlying stress response of plants. PMID:16504061

  8. Excited states of boron isoelectronic series from explicitly correlated wave functions.

    PubMed

    Gálvez, F J; Buendía, E; Sarsa, A

    2005-04-15

    The ground state and some low-lying excited states arising from the 1s2 2s2p2 configuration of the boron isoelectronic series are studied starting from explicitly correlated multideterminant wave functions. One- and two-body densities in position space have been calculated and different expectation values such as , , , , , and , where r, r12, and R stand for the electron-nucleus, interelectronic, and two electron center of mass coordinates, respectively, have been obtained. The energetic ordering of the excited states and the fulfillment of the Hund's rules is analyzed systematically along the isoelectronic series in terms of the electron-electron and electron-nucleus potential energies. The effects of electronic correlations have been systematically studied by comparing the correlated results with the corresponding noncorrelated ones. All the calculations have been done by using the variational Monte Carlo method.

  9. Isoelectronic Tungsten Doping in Monolayer MoSe2 for Carrier Type Modulation.

    PubMed

    Li, Xufan; Lin, Ming-Wei; Basile, Leonardo; Hus, Saban M; Puretzky, Alexander A; Lee, Jaekwang; Kuo, Yen-Chien; Chang, Lo-Yueh; Wang, Kai; Idrobo, Juan C; Li, An-Ping; Chen, Chia-Hao; Rouleau, Christopher M; Geohegan, David B; Xiao, Kai

    2016-10-01

    Carrier-type modulation is demonstrated in 2D transition metal dichalcogenides as n-type monolayer MoSe2 is converted to nondegenerate p-type monolayer Mo1-x Wx Se2 through isoelectronic doping. Although the alloys are mesoscopically uniform, the p-type conduction in monolayer Mo1-x Wx Se2 appears to originate from the upshift of the valenceband maximum toward the Fermi level at highly localized "W-rich" regions in the lattice.

  10. Enhanced Photocatalytic Water Splitting in a C2 N Monolayer by C-Site Isoelectronic Substitution.

    PubMed

    Kishore, M R Ashwin; Ravindran, P

    2017-06-20

    Two-dimensional (2D) semiconductors have shown great promise as efficient photocatalysts for water splitting. Tailoring the band gap and band edge positions are the most crucial steps to further improve the photocatalytic activity of 2D materials. Here, we report an improved photocatalytic water splitting activity in a C2 N monolayer by isoelectronic substitutions at the C-site, based on density functional calculations. Our optical calculations show that the isoelectronic substitutions significantly reduce the band gap of the C2 N monolayer and thus strongly enhance the absorption of visible light, which is consistent with the observed redshift in the optical absorption spectra. Based on the HSE06 functional, the calculated band edge positions of C2-x Six N and C2-x Gex N monolayers are even more favorable than the pristine C2 N monolayer for the overall photocatalytic activity. On the other hand, for the C2-x Snx N monolayer, the conduction band minima is more positive than the oxygen reduction potential and, hence, Sn substitution in C2 N is unfavorable for the water decomposition reaction. In addition, the isoelectronic substitutions improve the separation of e(-) -h(+) pairs, which, in turn, suppress the recombination rate, thereby leading to enhanced photocatalytic activity in this material. Our results imply that Si-, and Ge-substituted C2 N monolayers will be a promising visible-light photocatalysts for water splitting. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    PubMed Central

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

    2012-01-01

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

  12. Suppression of Defects and Deep Levels Using Isoelectronic Tungsten Substitution in Monolayer MoSe2

    DOE PAGES

    Li, Xufan; Puretzky, Alexander A.; Sang, Xiahan; ...

    2017-05-18

    Chemical vapor deposition (CVD) is one of the most promising, scalable synthetic techniques to enable large-area synthesis of two-dimensional (2D) transition metal dichalcogenides (TMDs) for the realization of next generation optoelectronic devices. However, defects formed during the CVD growth process currently limit the quality and electronic properties of 2D TMDs. Effective synthesis and processing strategies to suppress defects and enhance the quality of 2D TMDs are urgently needed. In this work, isoelectrnic doping to produce stable alloy is presented as a new strategy to suppress defects and enhance photoluminescence (PL) in CVD-grown TMD monolayers. The random, isoelectronic substitution of Wmore » atoms for Mo atoms in CVD-grown monolayers of Mo1-xWxSe2 (02 monolayers. The resultant decrease in defect-medicated non-radiative recombination in the Mo0.82W0.18Se2 monolayers yielded ~10 times more intense PL and extended the carrier lifetime by a factor of 3 compared to pristine CVD-grown MoSe2 monolayers grown under similar conditions. Low temperatures (4 125 K) PL from defect-related localized states confirms theoretical predictions that isoelectronic W alloying should suppress deep levels in MoSe2, showing that the defect levels in Mo1-xWxSe2 monolayers are higher in energy and quenched more quickly than in MoSe2. Isoelectronic substitution therefore appears to be a promising synthetic method to control the heterogeneity of 2D TMDs to realize the scalable production of high performance optoelectronic and electronic devices.« less

  13. Paramagnetic closed-shell molecules: the isoelectronic series CH , BH and BeH-

    NASA Astrophysics Data System (ADS)

    Fowler, P. W.; Steiner, E.

    Coupled Hartree-Fock calculations predict CH+, like its isoelectronic analogue BH, to be paramagnetic. The calculated magnetizability has components χ∥(CH+) = - 1·44 and χ⊥(CH+) = + 10·54 a.u. with a mean value χ(CH+) = + 6·55 a.u. (5·17 × 10-28 J T-2). Predicted nuclear shieldings are σ(C) = - 1250 ppm and σ(H) = + 34·1 ppm. The isolated BeH- anion is predicted to lie on the diamagnetic/paramagnetic borderline, but when placed in a crystal lattice is likely to be weakly diamagnetic.

  14. On the systematics of line ratios along the helium isoelectronic sequence

    NASA Astrophysics Data System (ADS)

    Pradhan, A. K.

    1982-12-01

    Temperature and change dependence of the line ratios involving the forbidden, intercombination, and the resonance lines is investigated for helium-like ions of C, O, Ne, Si, S, Ca, and Fe. Systematic variations are found and should facilitate the interpretation of observed data. Calculations are carried out using more accurate atomic data than earlier works resulting in significant differences. A few recent observations from laboratory and astrophysical plasmas are discussed.

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

    SciTech Connect

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

    2006-08-15

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-08-01

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

  17. 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

  18. Excitation energies, oscillator strengths, and lifetimes of levels along the gold isoelectronic sequence

    SciTech Connect

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

    2004-05-01

    Energies of ns{sub 1/2}(n=6-9), np{sub j}(n=6-8), nd{sub j}(n=6-7), and 5f{sub j} states in neutral Au and Au-like ions with nuclear charges Z=80-83 are calculated using relativistic many-body perturbation theory. Reduced matrix elements, oscillator strengths, transition rates and lifetimes are determined for the 30 possible nl{sub j}-n{sup '}l{sub j{sup '}}{sup '} electric-dipole transitions. Results for a limited number states, ns{sub 1/2}, np{sub j}(n=6-7) and 6d{sub j} are obtained in the relativistic single-double (SD) approximation, where single and double excitations of Dirac-Fock wave functions are included to all orders in perturbation theory. Using SD wave functions, accurate values are obtained for energies of the eight lowest states and for the fourteen possible electric-dipole matrix elements between these states. With the aid of the SD wave functions, we also determine transition rates and oscillator strengths for the fourteen transitions together with lifetimes of 6p{sub j}, 7p{sub j}, and 6d{sub j} levels. We investigate the hyperfine structure in Hg II and Tl III. The hyperfine A values are determined for 6s{sub 1/2} and 6p{sub j} states in {sup 199}Hg{sup +}, {sup 201}Hg{sup +}, and {sup 205}Tl{sup 2+} isotopes. These calculations provide a theoretical benchmark for comparison with experiment and theory.

  19. Excitation energies, oscillator strengths, and lifetimes of levels along the gold isoelectronic sequence

    NASA Astrophysics Data System (ADS)

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

    2004-05-01

    Energies of n s1/2 ( n=6-9 ) , n pj ( n=6-8 ) , n dj ( n=6-7 ) , and 5 fj states in neutral Au and Au-like ions with nuclear charges Z=80 83 are calculated using relativistic many-body perturbation theory. Reduced matrix elements, oscillator strengths, transition rates and lifetimes are determined for the 30 possible n lj - n' l 'j' electric-dipole transitions. Results for a limited number states n s1/2 , n pj ( n=6 7 ) and 6 dj are obtained in the relativistic single-double (SD) approximation, where single and double excitations of Dirac-Fock wave functions are included to all orders in perturbation theory. Using SD wave functions, accurate values are obtained for energies of the eight lowest states and for the fourteen possible electric-dipole matrix elements between these states. With the aid of the SD wave functions, we also determine transition rates and oscillator strengths for the fourteen transitions together with lifetimes of 6 pj , 7 pj , and 6 dj levels. We investigate the hyperfine structure in Hg II and Tl III . The hyperfine A values are determined for 6 s1/2 and 6 pj states in 199 Hg+ , 201 Hg+ , and 205 Tl2+ isotopes. These calculations provide a theoretical benchmark for comparison with experiment and theory.

  20. 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.

  1. Anomalous diffusion of isoelectronic antimony implant induced defects in GaAs-AlGaAs multiquantum well structures

    NASA Astrophysics Data System (ADS)

    Rao, E. V. K.; Krauz, Ph.; Thibierge, H.; Azoulay, R.; Vieu, C.

    1994-03-01

    We present here evidence on the deep diffusion of isoelectronic Sb implant induced defects in thick GaAs-AlGaAs multiquantum well structures (MQW) to depths as far as ˜30 times the implant projected range (Rp). This observation has been confirmed by performing low temperature photoluminescence depth scanning measurements and cross-sectional transmission electron microscopy (XTEM) analysis on room temperature Sb implanted thick MQW samples. An explanation based on the isoelectronic nature of Sb and its substitution on As site (SbAs) has been proposed to understand the anomalous diffusion of defects during implant and their contribution to Al/Ga disordering during post-implant annealing.

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

    PubMed Central

    Palma, Leopoldo; Muñoz, Delia; Murillo, Jesús

    2014-01-01

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

  3. Isoelectronic x-ray spectroscopy to determine electron temperatures in long-scale-length inertial-confinement-fusion plasmas

    NASA Astrophysics Data System (ADS)

    Shepard, T. D.; Back, C. A.; Kalantar, D. H.; Kauffman, R. L.; Keane, C. J.; Klem, D. E.; Lasinski, B. F.; MacGowan, B. J.; Powers, L. V.; Suter, L. J.; Turner, R. E.; Failor, B. H.; Hsing, W. W.

    1996-05-01

    We have successfully employed isoelectronic line ratios to measure the electron temperature in gas-filled Hohlraum targets and gas bags shot with the Nova laser. These targets produce millimeter-scale-length plasmas with electron density Ne~1021 cm-3 and electron temperature Te~3 keV. The Hohlraum targets can also produce radiation temperature exceeding 200 eV. Isoelectronic line ratios are well suited to this measurement because they are relatively insensitive to radiation field effects in Hohlraum targets, opacity, transients, and variations in electron density compared to conventional line ratios. We survey the properties of isoelectronic line ratios formed from ratios of n-to-1 resonance transitions in heliumlike Cr to the same transitions in Ti and compare with conventional ratios of n-to-1 transitions in hydrogenlike Ti to the corresponding transitions in heliumlike Ti, concentrating on plasma parameter ranges of interest to the Nova experiments. We also consider the same ratios using K and Cl. Atomic kinetics are treated using collisional-radiative models and experimental data are analyzed with the aid of radiation-hydrodynamics calculations. When we apply isoelectronic techniques to the Nova experimental data, we find that the targets have electron temperatures of at least 3 keV.

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

    PubMed

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

    2015-10-19

    In the present study, the inorganic analogues of alkanes as well as their isoelectronic BN/CC counterparts that bridge the gap between organic and inorganic chemistry are comparatively studied on the grounds of static DFT and Car-Parrinello molecular dynamics simulations. The BN/CC butanes CH3 CH2 BH2 NH3 , BH3 CH2 NH2 CH3 , and NH3 CH2 BH2 CH3 were considered and compared with their isoelectronic counterparts NH3 BH2 NH2 BH3 and CH3 CH2 CH2 CH3 . In addition, systematical replacement of the NH2 BH2 fragment by the isoelectronic CH2 CH2 moiety is studied in the molecules H3 N(NH2 BH2 )3-m (CH2 CH2 )m BH3 (for m=0, 1, 2, or 3) and H3 N(NH2 BH2 )2-m (CH2 CH2 )m BH3 (for m=0, 1, or 2). The DFT and Car-Parrinello simulations show that the isosteres of the BN/CC butanes CH3 CH2 BH2 NH3 , BH3 CH2 NH2 CH3 , and NH3 CH2 BH2 CH3 and of larger oligomers of the type (BN)k (CC)l where k≥l are stable compounds. The BN/CC butane H3 NCH2 CH2 BH3 spontaneously produces molecular hydrogen at room temperature. The reaction, prompted by very strong dihydrogen bonding NH⋅⋅⋅HB, undergoes through the neutral, hypervalent, pentacoordinated boron dihydrogen complex RBH2 (H2 ) [R=(CH2 CH2 )n NH2 ]. The calculations suggest that such intermediate and the other BN/CC butanes CH3 CH2 BH2 NH3 , BH3 CH2 NH2 CH3 , and NH3 CH2 BH2 CH3 as well as larger BN/CC oligomers are viable experimentally. A simple recipe for the synthesis of CH3 CH2 BH2 NH3 is proposed. The strength of the dihydrogen bonding appeared to be crucial for the overall stability of the saturated BN/CC derivatives. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Antiferromagnetism and hidden order in isoelectronic doping of URu2Si2

    DOE PAGES

    Wilson, Murray N.; Williams, Travis J.; Cai, Yipeng; ...

    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

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

    DOE PAGES

    Li, Xufan; Lin, Ming -Wei; Basile, Leonardo; ...

    2016-07-06

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

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

    SciTech Connect

    Li, Xufan; Lin, Ming -Wei; Basile, Leonardo; Hus, Saban M.; Puretzky, Alexander A.; Lee, Jaekwang; Kuo, Yen -Chien; Chang, Lo -Yueh; Wang, Kai; Idrobo, Juan C.; Li, An -Ping; Chen, Chia-Hao; Rouleau, Christopher M.; Geohegan, David B.; Xiao, Kai

    2016-07-06

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

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

    SciTech Connect

    Li, Xufan; Lin, Ming -Wei; Basile, Leonardo; Hus, Saban M.; Puretzky, Alexander A.; Lee, Jaekwang; Kuo, Yen -Chien; Chang, Lo -Yueh; Wang, Kai; Idrobo, Juan C.; Li, An -Ping; Chen, Chia-Hao; Rouleau, Christopher M.; Geohegan, David B.; Xiao, Kai

    2016-07-06

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

  9. Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy▿ †

    PubMed Central

    Wang, Qiong; Garrity, George M.; Tiedje, James M.; Cole, James R.

    2007-01-01

    The Ribosomal Database Project (RDP) Classifier, a naïve Bayesian classifier, can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes (2nd ed., release 5.0, Springer-Verlag, New York, NY, 2004). It provides taxonomic assignments from domain to genus, with confidence estimates for each assignment. The majority of classifications (98%) were of high estimated confidence (≥95%) and high accuracy (98%). In addition to being tested with the corpus of 5,014 type strain sequences from Bergey's outline, the RDP Classifier was tested with a corpus of 23,095 rRNA sequences as assigned by the NCBI into their alternative higher-order taxonomy. The results from leave-one-out testing on both corpora show that the overall accuracies at all levels of confidence for near-full-length and 400-base segments were 89% or above down to the genus level, and the majority of the classification errors appear to be due to anomalies in the current taxonomies. For shorter rRNA segments, such as those that might be generated by pyrosequencing, the error rate varied greatly over the length of the 16S rRNA gene, with segments around the V2 and V4 variable regions giving the lowest error rates. The RDP Classifier is suitable both for the analysis of single rRNA sequences and for the analysis of libraries of thousands of sequences. Another related tool, RDP Library Compare, was developed to facilitate microbial-community comparison based on 16S rRNA gene sequence libraries. It combines the RDP Classifier with a statistical test to flag taxa differentially represented between samples. The RDP Classifier and RDP Library Compare are available online at http://rdp.cme.msu.edu/. PMID:17586664

  10. Integration of Ixodes ricinus genome sequencing with transcriptome and proteome annotation of the naïve midgut.

    PubMed

    Cramaro, Wibke J; Revets, Dominique; Hunewald, Oliver E; Sinner, Regina; Reye, Anna L; Muller, Claude P

    2015-10-28

    In Europe, Ixodes ricinus ticks are the most important vectors of diseases threatening humans, livestock, wildlife and companion animals. Nevertheless, genomic sequence information is missing and functional annotation of transcripts and proteins is limited. This lack of information is restricting studies of the vector and its interactions with pathogens and hosts. Here we present and integrate the first analysis of the I. ricinus genome with the transcriptome and proteome of the unfed I. ricinus midgut. Whole genome sequencing was performed on I. ricinus ticks and the sequences were de novo assembled. In parallel, I. ricinus ticks were dissected and the midgut transcriptome sequenced. Both datasets were integrated by transcript discovery analysis to identify putative genes and genome contigs were screened for homology. An alignment-based and a motif-search-based approach were combined for the annotation of the midgut transcriptome. Additionally, midgut proteins were identified and annotated by mass spectrometry with public databases and the in-house built transcriptome database as references and results were cross-validated. The de novo assembly of 1 billion DNA sequences to a reference genome of 393 Mb length provides an unprecedented insight into the I. ricinus genome. A homology search revealed sequences in the assembled genome contigs homologous to 89% of the I. scapularis genome scaffolds indicating coverage of most genome regions. We identified moreover 6,415 putative genes. More than 10,000 transcripts from naïve midgut were annotated with respect of predicted function and/or cellular localization. By combining an alignment-based with a motif-search-based annotation approach, we doubled the number of annotations throughout all functional categories. In addition, 574 gel spots were significantly identified by mass spectrometry (p<0.05) and 285 distinct proteins expressed in the naïve midgut were annotated functionally and/or for cellular localization. Our

  11. 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).

  12. 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).

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2013-10-16

    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).

  15. 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.

  16. 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).

  17. Comparison of Theoretical and Experimental Level Values of the n = 2 Complex in Ions Isoelectronic with Li, Be, O and F

    NASA Astrophysics Data System (ADS)

    Edlén, Bengt

    1983-07-01

    The differences between observed and theoretical values of level intervals within the n = 2 complex in ions isoelectronic with Li, Be, O and F have been studied as functions of Z. The theoretical values are based on the tables of Cheng, Kim and Desclaux. For spin-orbit intervals, σ (theor) is taken as their multiconfiguration Dirac-Fock value with Breit correction (MCDF + B), for other intervals within the same configuration the Z-independent correlation energy from Cheng, Froese Fischer and Kim is added, and for interconfiguration intervals a Lamb-shift correction is also included, obtained by transforming the values of Cheng et al. into a smooth function of Z. The difference σ (obs) - σ (theor) is then expressed by the formula A + B(Z - C)-1 + a(Z - s)x, where the first two terms account for the residual correlation energy and the last term comprises all additional relativistic and radiative corrections. In a few cases we had to use two such terms with opposite sign and exponents differing by 2 to 3 units. The constants A, B, C, a and x are adjusted to fit the observations within their error limits. As compared to a fitted polynomial, the present formula is much better suited for extrapolation and provides a sharper test of the experimental data, especially at the high-Z end of a sequence. It has revealed a number of incorrect line identifications in the Be sequence. The results of the analyses are summarized in tables of recommended level values and wavelengths, extending to Z = 36 and in some cases to Z = 42. The wavelengths obtained for the resonance lines in the Be, O and F sequences may become useful as wavelength standards.

  18. 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.

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

    PubMed

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

    2013-01-01

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

  20. 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.

  1. Pressure effects in the isoelectronic REFe0.85Ir0.15AsO system.

    PubMed

    Maroni, Beatrice; Di Castro, Daniele; Hanfland, Michael; Boby, Joseph; Vercesi, Cristiano; Mozzati, M Cristina; Weyeneth, Stephen; Keller, Hugo; Khasanov, Rustem; Drathen, Christina; Dore, Paolo; Postorino, Paolo; Malavasi, Lorenzo

    2011-03-16

    The effect of chemical and hydrostatic pressure has been studied systematically in a selected system belonging to the 1111 family of iron pnictide high-temperature superconductors. The results show a surprising similarity between the trend of critical temperature vs hydrostatic pressure for isoelectronic samples with different rare earths (RE) on the RE site and samples of the SmFeAsO(1-x)F(x) series with different doping levels. These results open new questions about the underlying mechanism for superconductivity in iron pnictides.

  2. First-principles study of SO2 sensors based on phosphorene and its isoelectronic counterparts: GeS, GeSe, SnS, SnSe

    NASA Astrophysics Data System (ADS)

    Guo, Shiying; Yuan, Lu; Liu, Xuhai; Zhou, Wenhan; Song, Xiufeng; Zhang, Shengli

    2017-10-01

    Phosphorene and its isoelectronic counterparts, such as GeS, GeSe, SnS and SnSe monolayers, show great potential in electrical and sensing applications. Here, we study the SO2 sensing properties of phosphorene and its isoelectronic counterparts by first-principles calculations. Results predict that the SO2 molecule as electron acceptor holds high adsorption strength with the five monolayer substrates, especially for SnS and SnSe monolayers. Moreover, the electronic properties of the five substrates can be modified by the SO2 molecule, together with distinct charge transfer, rendering them promising for application as a high-performance gas sensor.

  3. The heat of formation of chlorine-isocyanate and the relative stability of isoelectronic molecules: an experimental and theoretical study.

    PubMed

    Ji, Yuanyuan; Bobadova-Parvanova, Petia; Larson, Chris; Samartzis, Peter C; Morokuma, Keiji; Lin, Jim Jr-Min; Ching, Tao-Tsung; Chaudhuri, Chanchal; Lee, Shih-Huang; Wodtke, Alec M

    2006-06-28

    Accurate thermochemical data of small molecules are invaluable to the progress of every aspect of chemistry, especially in the atmosphere, combustion and industry. In this work, photofragmentation translational spectroscopy and 1st principles electronic structure theory reveal the literature value of the heat of formation of chlorine-isocyanate to be in error by more than 40 kcalmol. We report a revised experimental value for D0(Cl-NCO) = 51+/-3 kcal/mol which leads to a Delta Hf (ClNCO) = 8.5+/-3 kcal/mol. High level ab initio (CCSD(T)) electronic structure calculations extrapolated to the complete basis set limit give D0(Cl-NCO) = 6.3 kcal/mol, in good agreement with experiment. In light of the present results, the destabilization of azides relative to isoelectronic isocyanates has been evaluated empirically for three pairs of related molecules. It is found to be 90-110 kcal/mol, and has been attributed mainly to the weakening of the N-NN bond relative to the N-CO bond. Electronic structure calculations employing decomposition analysis suggest that, compared to homopolar N2, the (+delta)CO(-delta) pi polarity provides better orbital interaction (charge transfer) and electrostatic attraction and results in a closer encounter and larger stabilization between the fragments and that this is the origin of isoelectronic destabilization of azides relative to the isocyanates.

  4. 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.

  5. Photoionization of ions of the nitrogen isoelectronic sequence:experiment and theory for F2+ and Ne3+

    SciTech Connect

    Aguilar, A.; Emmons, E.D.; Gharaibeh, M.F.; Covington, A.M.; Bozek, J.D.; Ackerman, G.; Canton, S.; Rude, B.; Schlachter, A.S.; Hinojosa, G.; Alvarez, I.; Cisneros, C.; McLaughlin, B.M.; Phaneuf, R.A.

    2005-06-21

    Absolute photoionization measurements are reported for admixtures of the ground and metastable states of F2+ from 56.3 eV to 75.6 eV, and of Ne3+ from 89.3 eV to 113.8 eV. The 4So ground-state and the 2Do and 2Po metastable-state fractions present in the primary ion beams were estimated from photo ion yield measurements near the irrespective threshold energies. Most of the observed resonance structure has been spectroscopically assigned. The measurements are compared with new R-matrix theoretical calculations and with those in the TOP base astrophysical database. The systematic behaviour of the quantum-defect parameter is analyzed as a function of the nuclear charge for four Rydberg series observed in both species, and compared to published data for O+ and N.

  6. Antiferromagnetism and hidden order in isoelectronic doping of URu2Si2

    SciTech Connect

    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.; Luke, Graeme M.

    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 important in driving the evolution of magnetic order with doping.

  7. Ab initio calculation of infrared intensities for the linear isoelectronic series HCN, HNC, CO, HCO/+/, and HOC/+/. [in interstellar medium

    NASA Technical Reports Server (NTRS)

    Rogers, J. D.; Hillman, J. J.

    1982-01-01

    Ab initio infrared intensities and dipole moment derivatives expressed in atomic polar tensor form are calculated using the 4-31 and 6-31G(double asterisk) basis sets for the isoelectronic HCN, HNC, CO, HCO(+), and HOC(+) series of molecules. The calculated atomic polar tensors are analyzed in terms of the charge-charge flux-overlap model, which is found to be useful in explaining some of the trends observed in the dipole moment derivatives for this series of molecules. A detailed examination of the dipole moment derivatives for the structural isomers indicates some of the ways in which experimental atomic polar tensors for one isomer should be modified to predict infrared intensities for the other isomer. The absolute intensities calculated for the HCO(+) and HOC(+) ions are believed to be accurate to within a factor of 2 and thus should be useful in astrophysical applications.

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  9. 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.

  10. Correlating the optical properties of WS2 monolayers grown by CVD with isoelectronic Mo doping level(Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Wang, Kai; Cross, Nick; Boulesbaa, Abdelaziz; Pudasaini, Pushpa R.; Tian, Mengkun; Mahjouri-Samani, Masoud; Oxley, Mark P.; Rouleau, Christopher M.; Puretzky, Alexander A.; Rack, Philip D.; Xiao, Kai; Yoon, Mina; Eres, Gyula; Duscher, Gerd; Geohegan, David B.

    2017-02-01

    Incorporating dopants in monolayer transition metal dichalcogenides (TMD) can enable manipulations of their electrical and optical properties. Previous attempts in amphoteric doping in monolayer TMDs have proven to be challenging. Here we report the incorporation of molybdenum (Mo) atoms in monolayer WS2 during growth by chemical vapor deposition, and correlate the distribution of Mo atoms with the optical properties including photoluminescence and ultrafast transient absorption dynamics. Dark field scanning transmission electron microscopy imaging quantified the isoelectronic doping of Mo in WS2 and revealed its gradual distribution along a triangular WS2 monolayer crystal, increasing from 0% at the edge to 2% in the center of the triangular WS2 triangular crystals. This agrees well with the Raman spectra data that showed two obvious modes between 360 cm-1 and 400 cm-1 that corresponded to MoS2 in the center. This in-plane gradual distribution of Mo in WS2 was found to account for the spatial variations in photoluminescence intensity and emission energy. Transition absorption spectroscopy further indicated that the incorporation of Mo in WS2 regulate the amplitude ratio of XA and XB of WS2. The effect of Mo incorporation on the electronic structure of WS2 was further elucidated by density functional theory. Finally, we compared the electrical properties of Mo incorporated and pristine WS2 monolayers by fabricating field-effect transistors. The isoelectronic doping of Mo in WS2 provides an alternative approach to engineer the bandgap and also enriches our understanding the influence of the doping on the excitonic dynamics.

  11. Tuning the morphology, luminescence and magnetic properties of hexagonal-phase NaGdF4: Yb, Er nanocrystals via altering the addition sequence of the precursors

    NASA Astrophysics Data System (ADS)

    Zhao, Shuwen; Xia, Donglin; Zhao, Ruimin; Zhu, Hao; Zhu, Yiru; Xiong, Yuda; Wang, Youfa

    2017-01-01

    Hexagonal-phase NaGdF4: Yb, Er upconversion nanocrystals (UCNCs) with tunable morphology and properties were successfully prepared via a thermal decomposition method. The influences of the adding sequence of the precursors on the morphology, chemical composition, luminescence and magnetic properties were investigated by transmission electron microscopy (TEM), inductively coupled plasma-atomic emission spectrometry (ICP-AES), upconversion (UC) spectroscopy, and a vibrating sample magnetometer (VSM). It was found that the resulting nanocrystals, with different sizes ranging from 24 to 224 nm, are in the shape of spheres, hexagonal plates and flakes; moreover, the composition percentage of Yb3+-Er3+ and Gd3+ ions was found to vary in a regular pattern with the adding sequence. Furthermore, the intensity ratios of emission colors (f g/r, f g/p), and the magnetic mass susceptibility of hexagonal-phase NaGdF4: Yb, Er nanocrystals change along with the composition of the nanocrystals. A positive correlation between the susceptibility and f g/r of NaGdF4: Yb, Er was proposed. The decomposition processes of the precursors were investigated by a thermogravimetric (TG) analyzer. The result indicated that the decomposition of the resolved lanthanide trifluoroacetate is greatly different from lanthanide trifluoroacetate powder. It is of tremendous help to recognize the decomposition process of the precursors and to understand the related reaction mechanism.

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

    PubMed Central

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

    2015-01-01

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

  13. Benchmark values of chemical potential and chemical hardness for atoms and atomic ions (including unstable anions) from the energies of isoelectronic series.

    PubMed

    Cárdenas, Carlos; Heidar-Zadeh, Farnaz; Ayers, Paul W

    2016-09-14

    We present benchmark values for the electronic chemical potential and chemical hardness from reference data for ionization potentials and electron affinities. In cases where the energies needed to compute these quantities are not available, we estimate the ionization potential of the metastable (di)anions by extrapolation along the isoelectronic series, taking care to ensure that the extrapolated data satisfy reasonable intuitive rules to the maximum possible extent. We also propose suitable values for the chemical potential and chemical hardness of zero-electron species. Because the values we report are faithful to the trends in accurate data on atomic energies, we believe that our proposed values for the chemical potential and chemical hardness are ideally suited to conceptual studies of chemical trends across the periodic table. The critical nuclear charge (Z critical) of the isoelectronic series with 2 < N < 96 has also been reported for the first time.

  14. 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.

  15. Isoelectronic substitution from Si52- to Al5H52-: Exploration of the series Si5-n(AlH)n2- (n = 0-5)

    NASA Astrophysics Data System (ADS)

    Fuenzalida-Valdivia, Isabel; Beltran, Maria J.; Ferraro, Franklin; Vasquez-Espinal, Alejandro; Tiznado, William; Osorio, Edison

    2016-03-01

    We established that the transformation from Si52- to Al5H52- could be possible by the successive isoelectronic substitution of silicon atoms by Alsbnd H units. The potential energy surfaces for the series Si5-n(AlH)n2- (n = 0-5) systems were explored in detail, and the global minima maintained the same overall deltahedral structure as the one of the Si52- cluster. The conservation of the overall structure upon isoelectronic substitution was proven to happen due to the preservation of the chemical bonding pattern. Theoretical VDEs were calculated for the series LiSi5-n(AlH)n- (n = 1-4) systems to facilitate their experimental detection.

  16. 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

  17. Boronyl ligand as a member of the isoelectronic series BO(-) → CO → NO(+): viable cobalt carbonyl boronyl derivatives?

    PubMed

    Gong, Xiaoli; Li, Qian-Shu; Xie, Yaoming; King, R Bruce; Schaefer, Henry F

    2010-12-06

    Recently the first boronyl (oxoboryl) complex [(c-C(6)H(11))(3)P](2)Pt(BO)Br was synthesized. The boronyl ligand in this complex is a member of the isoelectronic series BO(-) → CO → NO(+). The cobalt carbonyl boronyls Co(BO)(CO)(4) and Co(2)(BO)(2)(CO)(7), with cobalt in the formal d(8) +1 oxidation state, are thus isoelectronic with the familiar homoleptic iron carbonyls Fe(CO)(5) and Fe(2)(CO)(9). Density functional theory predicts Co(BO)(CO)(4) to have a trigonal bipyramidal structure with the BO group in an axial position. The tricarbonyl Co(BO)(CO)(3) is predicted to have a distorted square planar structure, similar to those of other 16-electron complexes of d(8) transition metals. Higher energy Co(BO)(CO)(n) (n = 3, 2) structures may be derived by removal of one (for n = 3) or two (for n = 2) CO groups from a trigonal bipyramidal Co(BO)(CO)(4) structure. Structures with a CO group bridging 17-electron Co(CO)(4) and Co(BO)(2)(CO)(3) units and no Co-Co bond are found for Co(2)(BO)(2)(CO)(8). However, Co(2)(BO)(2)(CO)(8) is not viable because of the predicted exothermic loss of CO to give Co(2)(BO)(2)(CO)(7). The lowest lying Co(2)(BO)(2)(CO)(7) structure is a triply bridged (2BO + CO) structure closely related to the experimental Fe(2)(CO)(9) structure. However, other relatively low energy Co(2)(BO)(2)(CO)(7) structures are found, either with a single CO bridge, similar to the experimental Os(2)(CO)(8)(μ-CO) structure; or with 17-electron Co(CO)(4) and Co(BO)(2)(CO)(3) units joined by a single Co-Co bond with or without semibridging carbonyl groups. Both triplet and singlet Co(2)(BO)(2)(CO)(6) structures are found. The lowest lying triplet Co(2)(BO)(2)(CO)(6) structures have a Co(CO)(3)(BO)(2) unit coordinated to a Co(CO)(3) unit through the oxygen atoms of the boronyl groups with a non-bonding ∼4.3 Å Co···Co distance. The lowest lying singlet Co(2)(BO)(2)(CO)(6) structures have either two three-electron donor bridging η(2)-μ-BO groups and no Co

  18. Signal sequence cleavage and plasma membrane targeting of the retinal rod NCKX1 and cone NCKX2 Na+/Ca2+ - K+ exchangers.

    PubMed

    Kang, KyeongJin; Schnetkamp, Paul P M

    2003-08-12

    Retinal rod and cone photoreceptors express two distinct Na(+)/Ca(2+)-K(+) exchanger (NCKX) gene products. Both the rod NCKX1 and cone NCKX2 are polytopic membrane proteins thought to contain a putative cleavable signal peptide. A cleavable signal peptide is unusual for plasma membrane proteins; moreover, predictive algorithms suggest the presence of a cleavable signal peptide for all rod NCKX1 proteins and a noncleavable signal anchor for the cone NCKX2 proteins. In this study we have placed a peptide tag at different positions of the NCKX sequence to examine whether the putative signal sequence is indeed cleaved in either NCKX1 or NCKX2 proteins expressed in heterologous systems. The signal peptide was found to be, at least in part, cleaved in dolphin rod NCKX1 and in chicken and human cone NCKX2 expressed in HEK293 cells; no signal peptide cleavage was observed for chicken rod NCKX1 despite the fact that the SignalP predictive algorithm assigned this sequence to have the highest likelihood for a cleavable signal peptide among the three NCKX sequences tested here. For the two NCKX proteins that contained a cleavable signal peptide, only cleaved NCKX protein was found in the plasma membrane of HEK293 cells. Deletion of the signal sequence in both dolphin rod NCKX1 or cone NCKX2 did not affect NCKX protein synthesis but did disrupt plasma membrane targeting as judged from abolition of NCKX function and from lack of surface biotinylation. These results are consistent with delayed signal peptide cleavage for the rod and cone NCKX proteins.

  19. Direct Measurement of T Cell Receptor Affinity and Sequence from Naïve Anti-Viral T Cells

    PubMed Central

    Zhang, Shuqi; Parker, Patricia; Ma, Keyue; He, Chenfeng; Shi, Qian; Cui, Zhonghao; Williams, Chad; Wendel, Ben S.; Meriwether, Amanda; Salazar, Mary A.; Jiang, Ning

    2016-01-01

    T cells recognize and kill a myriad of pathogen-infected or cancer cells using a diverse set of T cell receptors (TCR). 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. Here, 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

  20. On the origin of the differences in the Cu K-edge XANES of isostructural and isoelectronic compounds.

    PubMed

    Sipr, O; Rocca, F; Fornasini, P

    2009-06-24

    Cu K-edge x-ray absorption near-edge structure (XANES) spectra of trigonal (3R) CuScO(2) and CuLaO(2) and of hexagonal (2H) CuScO(2) were investigated experimentally and theoretically, in order to study differences between spectra of isostructural and isoelectronic compounds. Significant differences were found in the Cu K-edge XANES of 3R CuScO(2) and 3R CuLaO(2); these differences can be understood by considering the calculated polarization dependence of the XANES spectra and the differences between the phaseshifts of Sc and La. Spectra of the 3R and 2H polytypes of CuScO(2) differ only weakly and the difference originates from the long-range order. The pre-edge peak around 8980 eV is generated by the same mechanism as the pre-edge peak in Cu(2)O, i.e. involving scattering by the Cu atoms in the plane which is perpendicular to the O-Cu-O axis.

  1. 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.

  2. Exploring the optimal sequence of abiraterone and enzalutamide in patients with chemotherapy-naïve castration-resistant prostate cancer: The Kyoto-Baltimore collaboration.

    PubMed

    Terada, Naoki; Maughan, Benjamin L; Akamatsu, Shusuke; Kobayashi, Takashi; Yamasaki, Toshinari; Inoue, Takahiro; Kamba, Tomomi; Ogawa, Osamu; Antonarakis, Emmanuel S

    2017-06-01

    To evaluate and compare the efficacy of sequential treatment with abiraterone followed by enzalutamide or vice versa for castration-resistant prostate cancer. We retrospectively evaluated data on 198 consecutive chemotherapy-naïve patients who had received both abiraterone and enzalutamide for castration-resistant prostate cancer at Kyoto University Hospital (including satellite hospitals) and at Johns Hopkins Cancer Center. Prostate-specific antigen progression-free survival and overall survival in patients treated with sequential abiraterone-to-enzalutamide versus enzalutamide-to-abiraterone without intervening therapies were compared. Overall, 113 patients were treated with the abiraterone-to-enzalutamide sequence and 85 with the enzalutamide-to-abiraterone sequence. Median prostate-specific antigen progression-free survival was not significantly different between abiraterone and enzalutamide in the first-line setting (hazard ratio 0.88, 95% confidence interval 0.66-1.19, P = 0.412), but there was an advantage favoring enzalutamide compared with abiraterone in the second-line setting (hazard ratio 0.67, 95% confidence interval 0.49-0.91, P = 0.009). Furthermore, the combined prostate-specific antigen progression-free survival was significantly longer in the abiraterone-to-enzalutamide sequence than in the enzalutamide-to-abiraterone sequence (hazard ratio 0.56, 95% confidence interval 0.41-0.76, P < 0.001). The difference was significant even in multivariate analyses (hazard ratio 0.65, 95% confidence interval 0.42-0.99, P = 0.044). There was no statistical difference in overall survival between the two sequences in univariate (hazard ratio 0.88, 95% confidence interval 0.53-1.43, P = 0.599) and multivariate analyses (hazard ratio 0.81, 95% confidence interval 0.49-1.35, P = 0.427). The abiraterone-to-enzalutamide sequence might have more favorable efficacy in terms of combined prostate-specific antigen progression-free survival than the

  3. 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.

  4. 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

  5. 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

  6. Effect of charge transfer on the local order in liquid group IV isoelectronic compounds: neutron diffraction data versus numerical tight-binding simulations

    SciTech Connect

    Prigent, G.; Bellissent, R.; Gaspard, J.-P.; Bichara, C.

    1999-06-15

    In a simple tight-binding approach, we consider the role of charge transfer and entropy in the semiconductor-to-metal transition which may occur upon melting group IV elements and their isoelectronic III-V and II-VI compounds. In the liquid state, entropy is shown to destabilise the diamond structure in favor of a metallic simple cubic-like local order, while charge transfer tends to keep the semiconducting tetrahedral local order of the solid state. These results are consistent with neutron diffraction data.

  7. One- and two-body densities of carbon isoelectronic series in their low-lying multiplet states from explicitly correlated wave functions.

    PubMed

    Gálvez, F J; Buendía, E; Sarsa, A

    2006-01-28

    The (3)P ground state and both the (1)D and (1)S excited states arising from the low-lying 1s(2)2s(2)2p(2) configuration of the carbon isoelectronic series are studied starting from explicitly correlated multiconfigurational wave functions. One- and two-body densities in position space have been calculated and different one- and two-body expectation values have been obtained. The effects of electronic correlations have been systematically studied. All the calculations have been done by means of variational Monte Carlo.

  8. Observation of the weak electronic correlations in KFeCoAs2 (3d 6): an isoelectronic to the parent compounds of 122 series of iron pnictides BaFe2As2

    NASA Astrophysics Data System (ADS)

    Liu, Z. H.; Yaresko, A. N.; Li, Y.; Dai, P. C.; Zhang, H.; Büchner, B.; Lin, C. T.; Borisenko, S. V.

    2017-03-01

    Using the angle-resolved photoemission spectroscopy and band structure calculations we study the electronic structure of KFeCoAs2, which is isoelectronic to the parent material of 122 series of iron-based superconductors BaFe2As2. Although band structure calculations predict nearly identical dispersions of the electronic states in both compounds, experiment reveals drastic differences in both the global renormalization and Fermi surfaces. On the basis of the comparison of electronic structures of these two isoelectronic compounds, we demonstrate local magnetic correlations as a vital role for the peculiar low-energy electron dynamics of iron-based superconductors.

  9. Planarization of B7- and B12- clusters by isoelectronic substitution: AlB6- and AlB11-.

    PubMed

    Romanescu, Constantin; Sergeeva, Alina P; Li, Wei-Li; Boldyrev, Alexander I; Wang, Lai-Sheng

    2011-06-08

    Small boron clusters have been shown to be planar from a series of combined photoelectron spectroscopy and theoretical studies. However, a number of boron clusters are quasiplanar, such as B(7)(-) and B(12)(-). To elucidate the nature of the nonplanarity in these clusters, we have investigated the electronic structure and chemical bonding of two isoelectronic Al-doped boron clusters, AlB(6)(-) and AlB(11)(-). Vibrationally resolved photoelectron spectra were obtained for AlB(6)(-), resulting in an accurate electron affinity (EA) for AlB(6) of 2.49 ± 0.03 eV. The photoelectron spectra of AlB(11)(-) revealed the presence of two isomers with EAs of 2.16 ± 0.03 and 2.33 ± 0.03 eV, respectively. Global minimum structures of both AlB(6)(-) and AlB(11)(-) were established from unbiased searches and comparison with the experimental data. The global minimum of AlB(6)(-) is nearly planar with a central B atom and an AlB(5) six membered ring, in contrast to that of B(7)(-), which possesses a C(2v) structure with a large distortion from planarity. Two nearly degenerate structures were found for AlB(11)(-) competing for the global minimum, in agreement with the experimental observation. One of these isomers with the lower EA can be viewed as substituting a peripheral B atom by Al in B(12)(-), which has a bowl shape with a B(9) outer ring and an out-of-plane inner B(3) triangle. The second isomer of AlB(11)(-) can be viewed as an Al atom interacting with a B(11)(-) cluster. Both isomers of AlB(11)(-) are perfectly planar. It is shown that Al substitution of a peripheral B atom in B(7)(-) and B(12)(-) induces planarization by slightly expanding the outer ring due to the larger size of Al.

  10. Theoretical Investigation of Methane Hydroxylation over Isoelectronic [FeO](2+)- and [MnO](+)-Exchanged Zeolites Activated by N2O.

    PubMed

    Mahyuddin, M Haris; Shiota, Yoshihito; Staykov, Aleksandar; Yoshizawa, Kazunari

    2017-09-05

    While the most likely structure of the active site in iron-containing zeolites has been recently identified as [FeO](2+) (Snyder et al. Nature 2016, 536, 317-321), the mechanism for the direct conversion of methane to methanol over this active species is still debatable between the direct-radical-rebound or nonradical (concerted) mechanism. Using density functional theory on periodic systems, we calculated the two reaction mechanisms over two d(4) isoelectronic systems, [FeO](2+) and [MnO](+) zeolites. We found that [FeO](2+) zeolites favor the direct-radical-rebound mechanism with low CH4 activation energies, while [MnO](+) zeolites prefer the nonradical mechanism with higher CH4 activation energies. These contrasts, despite their isoelectronic structures, are mainly due to the differences in the metal coordination number and Oα (oxo) spin density. Moreover, molecular orbital analyses suggest that the zeolite steric hindrance further degrades the reactivity of [MnO](+) zeolites toward methane. Two types of zeolite frameworks, i.e., medium-pore ZSM-5 (MFI framework) and small-pore SSZ-39 (AEI framework) zeolites, were evaluated, but no significant differences in the reactivity were found. The rate-determining reaction step is found to be methanol desorption instead of methane activation. Careful examination of the most stable sites hosting the active species and calculation for N2O decomposition over [Fe](2+)-MFI and -AEI zeolites were also performed.

  11. Direct access to [(Mes*P)2As](-), a 1,3-diphosphaarsa-2-allyl anion, isoelectronic with the allyl anion (Mes* = 2,4,6-(t)Bu3C6H2).

    PubMed

    Dixon, Lily S H; Allen, Lucy K; Less, Robert J; Wright, Dominic S

    2014-03-21

    The reaction of As(NMe2)3 with Mes*PHLi provides a direct source of the 1,3-diphosphaarsa-2-allyl anion, [(Mes*P)2As](-) (isoelectronic with the allyl anion). The equilibrium between the E,E and E,Z isomers of this anion depends on the extent of Li(+) ion-pairing.

  12. First-order transition between a small gap semiconductor and a ferromagnetic metal in the isoelectronic alloy FeSi1-xGex.

    PubMed

    Anisimov, V I; Hlubina, R; Korotin, M A; Mazurenko, V V; Rice, T M; Shorikov, A O; Sigrist, M

    2002-12-16

    The contrasting ground states of isoelectronic, isostructural FeSi and FeGe are explained within an extended local density approximation scheme (LDA+U) by an appropriate choice of the Coulomb repulsion U on the Fe sites. A minimal two-band model with interband interactions leads to a phase diagram for the alloys FeSi1-xGex. A mean field approximation gives a first-order transition between a small gap semiconductor and a ferromagnetic metal as a function of magnetic field, temperature, and concentration x. Unusually the transition from metal to insulator is driven by broadening, not narrowing, the bands and it is the metallic state that shows magnetic order.

  13. A DFT investigation on geometry and chemical bonding of isoelectronic Si8N6V-, Si8N6Cr, and Si8N6Mn+ clusters

    NASA Astrophysics Data System (ADS)

    Tam, Nguyen Minh; Pham, Hung Tan; Cuong, Ngo Tuan; Tung, Nguyen Thanh

    2017-10-01

    The geometric feature and chemical bonding of isoelectronic systems Si8N6Mq (M = V, Cr, Mn and q = -1, 0, 1, respectively) are investigated by means of density-functional-theory calculations. The encapsulated form is found for all ground-state structures, where the metal atom locates at the central site of the hollow Si8N6 cage. The Si8N6 cage is established by adding two Si atoms to a distorted Si6N6 prism, which is a combination of Si4N2 and Si2N4 strings. Chemical bonding of Si8N6Mq systems is explored by using the electron localization indicator and theory of atom in molecule, revealing the vital role of metal center in stabilizing the clusters.

  14. Sequence Based Prediction of DNA-Binding Proteins Based on Hybrid Feature Selection Using Random Forest and Gaussian Naïve Bayes

    PubMed Central

    Lou, Wangchao; Wang, Xiaoqing; Chen, Fan; Chen, Yixiao; Jiang, Bo; Zhang, Hua

    2014-01-01

    Developing an efficient method for determination of the DNA-binding proteins, due to their vital roles in gene regulation, is becoming highly desired since it would be invaluable to advance our understanding of protein functions. In this study, we proposed a new method for the prediction of the DNA-binding proteins, by performing the feature rank using random forest and the wrapper-based feature selection using forward best-first search strategy. The features comprise information from primary sequence, predicted secondary structure, predicted relative solvent accessibility, and position specific scoring matrix. The proposed method, called DBPPred, used Gaussian naïve Bayes as the underlying classifier since it outperformed five other classifiers, including decision tree, logistic regression, k-nearest neighbor, support vector machine with polynomial kernel, and support vector machine with radial basis function. As a result, the proposed DBPPred yields the highest average accuracy of 0.791 and average MCC of 0.583 according to the five-fold cross validation with ten runs on the training benchmark dataset PDB594. Subsequently, blind tests on the independent dataset PDB186 by the proposed model trained on the entire PDB594 dataset and by other five existing methods (including iDNA-Prot, DNA-Prot, DNAbinder, DNABIND and DBD-Threader) were performed, resulting in that the proposed DBPPred yielded the highest accuracy of 0.769, MCC of 0.538, and AUC of 0.790. The independent tests performed by the proposed DBPPred on completely a large non-DNA binding protein dataset and two RNA binding protein datasets also showed improved or comparable quality when compared with the relevant prediction methods. Moreover, we observed that majority of the selected features by the proposed method are statistically significantly different between the mean feature values of the DNA-binding and the non DNA-binding proteins. All of the experimental results indicate that the proposed DBPPred

  15. Sequence analysis of diamine oxidase gene from fava bean and its expression related to γ-aminobutyric acid accumulation in seeds germinating under hypoxia-NaCl stress.

    PubMed

    Yang, Runqiang; Yin, Yongqi; Guo, Liping; Han, Yongbin; Gu, Zhenxin

    2014-06-01

    γ-Aminobutyric acid (GABA) is synthesized via the polyamine degradation pathway in plants, with diamine oxidase (DAO) being the key enzyme. In this study the cDNA of DAO in fava bean was cloned and its expression in seeds germinating under hypoxia-NaCl stress was investigated. Fava bean DAO cDNA is 2199 bp long and contains 2025 bp of open reading frame that encodes 675 amino acid peptides with a calculated molecular weight of 76.31 kDa and a pI of 5.41. Hypoxia and hypoxia-NaCl stress enhanced DAO activity and resulted in GABA accumulation in germinating fava bean. However, DAO gene expression was down-regulated under hypoxia compared with non-stress condition, while its expression in the cotyledon and shoot was up-regulated under hypoxia-NaCl. In addition, DAO expression could be promoted to enhance GABA accumulation after increasing the stress intensity using NaCl. DAO gene expression was significantly inhibited by aminoguanidine treatment under hypoxia but increased under hypoxia-NaCl. Under hypoxia, GABA accumulation due to NaCl was mainly concentrated in the cotyledon. The GABA content increase under hypoxia did not result from DAO gene expression, but DAO existing in seeds was activated under hypoxia. DAO gene expression was up-regulated to enhance GABA accumulation after increasing the stress intensity. © 2013 Society of Chemical Industry.

  16. Extended Calculations with Spectroscopic Accuracy: Energy Levels and Transition Properties for the Fluorine-like Isoelectronic Sequence with Z = 24-30

    NASA Astrophysics Data System (ADS)

    Si, R.; Li, S.; Guo, X. L.; Chen, Z. B.; Brage, T.; Jönsson, P.; Wang, K.; Yan, J.; Chen, C. Y.; Zou, Y. M.

    2016-12-01

    We have performed extensive multiconfiguration Dirac-Hartree-Fock calculations and second-order many-body perturbation calculations for F-like ions with Z = 24-30. Energy levels and transition rates for electric dipole (E1), electric-quadrupole (E2), electric-octupole (E3), magnetic dipole (M1), and magnetic-quadrupole (M2) transitions, as well as radiative lifetimes, are provided for the lowest 200 levels belonging to the 1{s}22{s}22{p}5, 1{s}22s2{p}6, 1{s}22{s}22{p}43l, 1{s}22s2{p}53l, 1{s}22{p}63l, and 1{s}22{s}22{p}44l configurations of each ion. The results from the two sets of calculations are in excellent agreement. Extensive comparisons are also made with other theoretical results and observed data from the CHIANTI and NIST databases. The present energies and wavelengths are believed to be accurate enough to aid line identifications involving the n = 3 and n = 4 configurations, for which observations are largely missing. The calculated wavelengths and transition data will be useful in the modeling and diagnostics of astrophysical and fusion plasmas.

  17. 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

  18. 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

  19. Effects of isoelectronic Ru substitution at the Fe site on the energy gaps of optimally F-doped SmFeAsO

    NASA Astrophysics Data System (ADS)

    Daghero, D.; Tortello, M.; Ummarino, G. A.; Stepanov, V. A.; Bernardini, F.; Tropeano, M.; Putti, M.; Gonnelli, R. S.

    2012-08-01

    We studied the effects of isoelectronic Ru substitution at the Fe site on the energy gaps of optimally F-doped SmFeAsO by means of point-contact Andreev-reflection spectroscopy. The results show that the SmFe1-xRuxAsO0.85F0.15 system keeps a multigap character at least up to x = 0.50, and that the gap amplitudes Δ1 and Δ2 scale almost linearly with the local critical temperature {T}_{{c}}^{A}. The gap ratios 2Δi/kBTc remain approximately constant only as long as Tc ≥ 30 K, and increase dramatically when Tc decreases further. This trend seems to be common to many Fe-based superconductors, irrespective of their family. Based on first-principle calculations of the bandstructure and of the density of states projected on the different bands, we show that this trend, as well as the Tc dependence of the gaps and the reduction of Tc upon Ru doping, can be explained within an effective three-band Eliashberg model as being due to a suppression of the superfluid density at finite temperature that, in turn, modifies the temperature dependence of the characteristic spin-fluctuation energy.

  20. 1s22p3 and 1s22s23l, l = s,p,d, excited states of boron isoelectronic series from explicitly correlated wave functions.

    PubMed

    Gálvez, F J; Buendía, E; Sarsa, A

    2005-07-15

    For some members of the boron isoelectronic series and starting from explicitly correlated wave functions, six low-lying excited states have been studied. Three of them arise from the 1s(2)2p(3) configuration, and the other three from the 1s(2)2s(2)3l, l = s,p,d, configurations. This work follows a previous one on both the 1s(2)2s(2)2p-(2)P ground state and the four excited states coming from the 1s(2)2s2p(2) configuration. Energies, one- and two-body densities in position space and some other two-body properties in position and momentum spaces have been obtained. A systematic analysis of the energetic ordering of the states as a function of the total orbital angular momentum and spin is performed in terms of the electron-nucleus and electron-electron potential energies and the role of the angular correlation is discussed. All calculations have been carried out by using the Monte Carlo algorithm.

  1. 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.

  2. 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.

  3. Synthesis and structural characterization of C(OTeF5)4 and a comparative structural study of the isoelectronic B(OTeF5)4- anion.

    PubMed

    Moran, Matthew D; Mercier, Hélène P A; Schrobilgen, Gary J

    2007-06-11

    Tetrakis(pentafluoroorthotellurate)carbon(IV), C(OTeF5)4, was synthesized by reaction of CBr4 with BrOTeF5 in SO2ClF solution at -78 degrees C and was isolated as a colorless, crystalline solid that is room-temperature stable in SO2ClF and in the solid state. Both natural abundance and 99% 13C-enriched C(OTeF5)4 have been characterized in SO2ClF solution by 13C, 19F, and 125Te NMR spectroscopy. In contrast, C(OTeF5)4 undergoes rapid decomposition to O(TeF5)2 and CO2 in CH3CN at 10 degrees C but is stable at -40 degrees C. The X-ray crystal structures of C(OTeF5)4 and [N(CH3)4][B(OTeF5)4] were determined at -30 and -170 degrees C, respectively. The averages of four smaller C/B-O-Te bond angles and O...O contacts and two larger C/B-O-Te bond angles and O...O contacts of C(OTeF5)4 and the isoelectronic B(OTeF5)4- anion are consistent with local S4 symmetry, as predicted by ligand close packing considerations. The existence of three sets of Te-O-C/B-O torsion angles and the energy-minimized geometries of C(OTeF5)4 and B(OTeF5)4- also confirm their local S4 symmetries. The low-temperature, solid-state Raman spectra of 12/13C(OTeF5)4 and B(OTeF5)4- were assigned and compared. The energy-minimized geometries, vibrational frequencies, natural charges, and natural bond orders of both species have been calculated using density functional theory methods. The calculated geometries are in accord with the S4 symmetries assigned for the experimental structures.

  4. Theoretical study of the Si(5-n)(BH)n2- and Na(Si(5-n)(BH)n)- (n = 0-5) systems.

    PubMed

    Osorio, Edison; Sergeeva, Alina P; Santos, Juan Carlos; Tiznado, William

    2012-12-21

    The potential energy surfaces of the Na(Si(5-n)(BH)(n))(-) and Si(5-n)(BH)(n)(2-) (n = 0-5) systems have been explored in detail. We established that all the global minimum structures of anionic and dianionic systems can be obtained by substitution of one or more silicon atoms of the global minima of NaSi(5)(-) and Si(5)(2-) for B-H units. The conservation of the overall structure upon isoelectronic substitution was shown to be due to the preservation of the chemical bonding pattern. Theoretical VDEs were calculated for all of the sodiated Na(Si(5-n)(BH)(n))(-) (n = 0-5) systems to facilitate their experimental detection.

  5. Recognizing Sequences of Sequences

    PubMed Central

    Kiebel, Stefan J.; von Kriegstein, Katharina; Daunizeau, Jean; Friston, Karl J.

    2009-01-01

    The brain's decoding of fast sensory streams is currently impossible to emulate, even approximately, with artificial agents. For example, robust speech recognition is relatively easy for humans but exceptionally difficult for artificial speech recognition systems. In this paper, we propose that recognition can be simplified with an internal model of how sensory input is generated, when formulated in a Bayesian framework. We show that a plausible candidate for an internal or generative model is a hierarchy of ‘stable heteroclinic channels’. This model describes continuous dynamics in the environment as a hierarchy of sequences, where slower sequences cause faster sequences. Under this model, online recognition corresponds to the dynamic decoding of causal sequences, giving a representation of the environment with predictive power on several timescales. We illustrate the ensuing decoding or recognition scheme using synthetic sequences of syllables, where syllables are sequences of phonemes and phonemes are sequences of sound-wave modulations. By presenting anomalous stimuli, we find that the resulting recognition dynamics disclose inference at multiple time scales and are reminiscent of neuronal dynamics seen in the real brain. PMID:19680429

  6. Carbonic anhydrase inhibitors. Inhibition of isozymes I, II, IV, V, and IX with anions isosteric and isoelectronic with sulfate, nitrate, and carbonate.

    PubMed

    Innocenti, Alessio; Vullo, Daniela; Scozzafava, Andrea; Supuran, Claudiu T

    2005-02-01

    The inhibition of five human carbonic anhydrase (hCA, EC 4.2.1.1) isozymes; the cytosolic hCA I and II, the membrane-bound hCA IV, the mitochondrial hCA V, and the tumor-associated, transmembrane hCA IX, with anions isosteric and isoelectronic with sulfate, nitrate, and carbonate; such as chlorate, perchlorate, bromate, iodate, periodate, silicate, bismuthate, vanadate, molybdate, and wolframate is reported. Apparently, the geometry of the inhibitor (tetrahedral or trigonal) does not influence its binding to the Zn(II) ion of the enzyme active site, but the nature of the central element is the most important factor influencing potency. Isozymes hCA I and II are best inhibited by chlorate, perchlorate, and silicate, together with the anions structurally related to sulfate, sulfamate, and sulfamidate, but sulfate itself is a weak inhibitor (inhibition constant of 74 mM against hCA I and 183 mM against hCA II). Molybdate is a very weak hCA I inhibitor (K(I) of 914 mM) but it interacts with hCA II (K(I) of 27.5mM). Isozyme IV is well inhibited by sulfate (K(I) of 9 mM), sulfamate, and sulfamidate (in the low micromolar range), but not by perchlorate (K(I) of 767 mM). The mitochondrial isozyme V has the lowest affinity for sulfate (K(I) of 680 mM) and carbonate (K(I) of 95 mM) among all the investigated isozymes, suggesting on one hand its possible participation in metabolon(s) with sulfate anion exchanger(s), and on the other hand an evolutionary adaptation to working at higher pH values (around 8.5 in mitochondria) where rather high amounts of carbonate in equilibrium with bicarbonate may be present. Metasilicate, isosteric to carbonate, is also about a 10 times weaker inhibitor of this isozyme as compared to other CAs investigated here (K(I) of 28.2 mM). Surprisingly, the tumor-associated isozyme IX is resistant to sulfate inhibition (K(I) of 154 mM) but has affinity in the low micromolar range for carbonate, sulfamate, and sulfamidate (K(I) in the range of 8

  7. 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.

  8. Isoelectronic caesium compounds: the triphosphenide Cs[tBu3SiPPPSitBu3] and the enolate Cs[OCH=CH2].

    PubMed

    Lerner, Hans-Wolfram; Sänger, Inge; Schödel, Frauke; Lorbach, Andreas; Bolte, Michael; Wagner, Matthias

    2008-02-14

    The caesium triphosphenide Cs[tBu3SiPPPSitBu3] was accessible from the reaction of CsF with the sodium triphosphenide Na[tBu3SiPPPSitBu3] in tetrahydrofuran at room temperature. In contrast to the preparation of tetrahydrofuran-solvated silanides M[SitBu3] (M = Li, Na, K), our efforts to synthesize the caesium silanide Cs[SitBu3] as a tetrahydrofuran complex failed. When tBu3SiBr was treated with an excess of caesium metal in tetrahydrofuran at room temperature, the caesium enolate Cs[OCH=CH2] and the supersilane tBu3SiH formed rather than the silanide Cs[SitBu3]. X-Ray quality crystals of the enolate Cs[OCH=CH2] (orthorhombic, Pnma) were obtained from tetrahydrofuran at ambient temperature. In contrast to the structures of its homologues M[tBu3SiPPPSitBu3] (M = Na, K), the caesium triphosphenide Cs[tBu3SiPPPSitBu3] features a polymer in the solid state (orthorhombic, Cmcm).

  9. Genome Sequencing.

    PubMed

    Verma, Mansi; Kulshrestha, Samarth; Puri, Ayush

    2017-01-01

    Genome sequencing is an important step toward correlating genotypes with phenotypic characters. Sequencing technologies are important in many fields in the life sciences, including functional genomics, transcriptomics, oncology, evolutionary biology, forensic sciences, and many more. The era of sequencing has been divided into three generations. First generation sequencing involved sequencing by synthesis (Sanger sequencing) and sequencing by cleavage (Maxam-Gilbert sequencing). Sanger sequencing led to the completion of various genome sequences (including human) and provided the foundation for development of other sequencing technologies. Since then, various techniques have been developed which can overcome some of the limitations of Sanger sequencing. These techniques are collectively known as "Next-generation sequencing" (NGS), and are further classified into second and third generation technologies. Although NGS methods have many advantages in terms of speed, cost, and parallelism, the accuracy and read length of Sanger sequencing is still superior and has confined the use of NGS mainly to resequencing genomes. Consequently, there is a continuing need to develop improved real time sequencing techniques. This chapter reviews some of the options currently available and provides a generic workflow for sequencing a genome.

  10. Stability and instability of the isoelectronic UO2(2+) and PaO2+ actinyl oxo-cations in aqueous solution from density functional theory based molecular dynamics.

    PubMed

    Spezia, Riccardo; Siboulet, Bertrand; Abadie, Sacha; Vuilleumier, Rodolphe; Vitorge, Pierre

    2011-04-07

    In this work, Pa(V) monocations have been studied in liquid water by means of density functional theory (DFT) based molecular dynamic simulations (CPMD) and compared with their U(VI) isoelectronic counterparts to understand the peculiar chemical behavior of Pa(V) in aqueous solution. Four different Pa(V) monocationic isomers appear to be stable in liquid water from our simulations: [PaO(2)(H(2)O)(5)](+)(aq), [Pa(OH)(4)(H(2)O)(2)](+)(aq), [PaO(OH)(2)(H(2)O)(4)](+)(aq), and [Pa(OH)(4)(H(2)O)(3)](+)(aq). On the other hand, in the case of U(VI) only the uranyl, [UO(2)(H(2)O)(5)](2)(+)(aq), is stable. The other species containing hydroxyl groups replacing one or two oxo bonds are readily converted to uranyl. The Pa-OH bond is stable, while it is suddenly broken in U-OH. This makes possible the formation of a broad variety of Pa(V) species in water and participates to its unique chemical behavior in aqueous solution. Further, the two actinyl oxocations in water are different in the ability of the oxygen atoms to form stable and extended H-bond networks for Pa(V) contrary to U(VI). In particular, protactinyl is found to have between 2 and 3 hydrogen bonds per oxygen atom while uranyl has between zero and one.

  11. Violation of the weak noncrossing rule between totally symmetric closed-shell states in the valence-isoelectronic series O{sub 3}, S{sub 3}, SO{sub 2}, and S{sub 2}O

    SciTech Connect

    Ivanic, J.; Atchity, G.J.; Ruedenberg, K.

    1997-09-01

    The ground and next excited {sup 1}A{sub 1} potential energy surfaces of the valence-isoelectronic molecules O{sub 3}, S{sub 3}, SO{sub 2}, and S{sub 2}O have been studied using full-valence-space-multiconfiguration self-consistent-field calculations. An open and a ring minimum were found for all species. In each case, interconversion between the C{sub 2v} open and closed isomers proceeds via a C{sub 2v} transition state which lies on a very sharp ridge separating the basins surrounding the minima. In the immediate vicinity of these transition states, the upper state for each species is found to have a minimum, also in C{sub 2v}. Furthermore, not far away on the C{sub 2v} ridges, the 1{sup 1}A{sub 1} and 2{sup 1}A{sub 1} surfaces intersect conically for all molecules. {copyright} {ital 1997 American Institute of Physics.}

  12. Transitions of the type 2s-2p in highly ionized Cu, Zn, Ga, and Ge

    NASA Technical Reports Server (NTRS)

    Behring, W. E.; Cohen, L.; Seely, J. F.; Feldman, U.; Goldsmith, S.; Richardson, M.

    1985-01-01

    Transitions of the type 2s-2p in the F I, O I, N I, and C I isoelectronic sequences of copper, zinc, gallium, and germanium have been identified in the spectra from plasmas produced by the Omega laser system at the University of Rochester. The wavelengths are in the range 50 to 112 A and are measured using silicon and oxygen lines as wavelength standards for gallium and using several lines from the F I, O I, and Na I isoelectronic sequences as wavelength standards for copper, zinc, and germanium. The energy levels that are determined from the measured wavelengths are also presented. Based on these measurements, the wavelengths for a number of magnetic-dipole transitions within the ground configurations of the F I, O I, and N I isoelectronic sequences are predicted.

  13. Sequence landscapes.

    PubMed Central

    Clift, B; Haussler, D; McConnell, R; Schneider, T D; Stormo, G D

    1986-01-01

    We describe a method for representing the structure of repeating sequences in nucleic-acids, proteins and other texts. A portion of the sequence is presented at the bottom of a CRT screen. Above the sequence is its landscape, which looks like a mountain range. Each mountain corresponds to a subsequence of the sequence. At the peak of every mountain is written the number of times that the subsequence appears. A data structure called a DAWG, which can be built in time proportional to the length of the sequence, is used to construct the landscape. For the 40 thousand bases of bacteriophage T7, the DAWG can be built in 30 seconds. The time to display any portion of the landscape is less than a second. Using sequence landscapes, one can quickly locate significant repeats. PMID:3753762

  14. Structure and magnetic properties of an unprecedented syn-anti μ-nitrito-1κO:2κO' bridged Mn(III)-salen complex and its isoelectronic and isostructural formate analogue.

    PubMed

    Kar, Paramita; Biswas, Rituparna; Drew, Michael G B; Ida, Yumi; Ishida, Takayuki; Ghosh, Ashutosh

    2011-04-07

    The preparation, crystal structures and magnetic properties of two new isoelectronic and isomorphous formate- and nitrite-bridged 1D chains of Mn(III)-salen complexes, [Mn(salen)(HCOO)](n) (1) and [Mn(salen)(NO(2))](n) (2), where salen is the dianion of N,N'-bis(salicylidene)-1,2-diaminoethane, are presented. The structures show that the salen ligand coordinates to the four equatorial sites of the metal ion and the formate or nitrite ions coordinate to the axial positions to bridge the Mn(III)-salen units through a syn-antiμ-1κO:2κO' coordination mode. Such a bridging mode is unprecedented in Mn(III) for formate and in any transition metal ion for nitrite. Variable-temperature magnetic susceptibility measurements of complexes 1 and 2 indicate the presence of ferromagnetic exchange interactions with J values of 0.0607 cm(-1) (for 1) and 0.0883 cm(-1) (for 2). The ac measurements indicate negligible frequency dependence for 1 whereas compound 2 exhibits a decrease of χ(ac)' and a concomitant increase of χ(ac)'' on elevating frequency around 2 K. This finding is an indication of slow magnetization reversal characteristic of single-chain magnets or spin-glasses. The μ-nitrito-1κO:2κO' bridge seems to be a potentially superior magnetic coupler to the formate bridge for the construction of single-molecule/-chain magnets as its coupling constant is greater and the χ(ac)' and χ(ac)'' show frequency dependence. © The Royal Society of Chemistry 2011

  15. Sequencing technologies and genome sequencing.

    PubMed

    Pareek, Chandra Shekhar; Smoczynski, Rafal; Tretyn, Andrzej

    2011-11-01

    The high-throughput - next generation sequencing (HT-NGS) technologies are currently the hottest topic in the field of human and animals genomics researches, which can produce over 100 times more data compared to the most sophisticated capillary sequencers based on the Sanger method. With the ongoing developments of high throughput sequencing machines and advancement of modern bioinformatics tools at unprecedented pace, the target goal of sequencing individual genomes of living organism at a cost of $1,000 each is seemed to be realistically feasible in the near future. In the relatively short time frame since 2005, the HT-NGS technologies are revolutionizing the human and animal genome researches by analysis of chromatin immunoprecipitation coupled to DNA microarray (ChIP-chip) or sequencing (ChIP-seq), RNA sequencing (RNA-seq), whole genome genotyping, genome wide structural variation, de novo assembling and re-assembling of genome, mutation detection and carrier screening, detection of inherited disorders and complex human diseases, DNA library preparation, paired ends and genomic captures, sequencing of mitochondrial genome and personal genomics. In this review, we addressed the important features of HT-NGS like, first generation DNA sequencers, birth of HT-NGS, second generation HT-NGS platforms, third generation HT-NGS platforms: including single molecule Heliscope™, SMRT™ and RNAP sequencers, Nanopore, Archon Genomics X PRIZE foundation, comparison of second and third HT-NGS platforms, applications, advances and future perspectives of sequencing technologies on human and animal genome research.

  16. Computational interpretation of 23Na MQMAS NMR spectra: A comprehensive investigation of the Na environment in silicate glasses

    NASA Astrophysics Data System (ADS)

    Gambuzzi, Elisa; Charpentier, Thibault; Menziani, Maria Cristina; Pedone, Alfonso

    2014-09-01

    Molecular dynamics, density functional theory calculations and 23Na NMR experiments have been used to inspect the chemical and structural characteristics of the Na environment in soda-lime silicate (CSN) and aluminosilicate (CASN) glasses. The use of an improved 3QMAS pulse sequence has allowed a clear identification of different Na sites. Average coordination numbers have been extracted by fitting the 23Na 3QMAS spectra with the computed NMR parameters. The results show that the 23Na δiso values correlate with the average <Na-O> distances only when the different coordination numbers are explicitly taken into account.

  17. Sample sequencing

    SciTech Connect

    Prange, C.

    1994-04-01

    The goal of the Human Genome Project is to sequence all 3 billion basepairs of human DNA. At Lawrence Livermore Lab, attention is focused on Chromosome 19, which has been estimated to contain approximately 2000 genes. So far, only 200 have been mapped to specific areas on the chromosome. For this reason, a simple method is needed to predict the most likely locations of the coding regions in the DNA. In addition, there is also a need for unique market sites (STS`s) along the chromosome. Sample sequencing uses standard cloning techniques to prepare DNA for sequencing. Once sequence is obtained, it is analyzed using databases to predict the regions most likely to contain genes. All sequences may also be used to generate STS`s. So far, 21 fragments from five different clones have been completely sequenced, with fragments from eight more clones in progress. Constant improvement of methods to increase efficiency and accuracy combined with utilization of the most current databases available make sample sequencing a useful tool for reaching the goals of the Human Genome Project.

  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. 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.

  20. 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

  1. 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

  2. Arbitrarily accurate narrowband composite pulse sequences

    SciTech Connect

    Vitanov, Nikolay V.

    2011-12-15

    Narrowband composite pulse sequences containing an arbitrary number N of identical pulses are presented. The composite phases are given by a very simple analytic formula and the transition probability is merely sin{sup 2N}(A/2), where A is the pulse area. These narrowband sequences can be made accurate to any order with respect to variations in A for sufficiently many constituent pulses, i.e., excitation can be suppressed below any desired value for any pulse area but {pi}.

  3. Route, mechanism, and implications of proton import during Na+/K+ exchange by native Na+/K+-ATPase pumps.

    PubMed

    Vedovato, Natascia; Gadsby, David C

    2014-04-01

    A single Na(+)/K(+)-ATPase pumps three Na(+) outwards and two K(+) inwards by alternately exposing ion-binding sites to opposite sides of the membrane in a conformational sequence coupled to pump autophosphorylation from ATP and auto-dephosphorylation. The larger flow of Na(+) than K(+) generates outward current across the cell membrane. Less well understood is the ability of Na(+)/K(+) pumps to generate an inward current of protons. Originally noted in pumps deprived of external K(+) and Na(+) ions, as inward current at negative membrane potentials that becomes amplified when external pH is lowered, this proton current is generally viewed as an artifact of those unnatural conditions. We demonstrate here that this inward current also flows at physiological K(+) and Na(+) concentrations. We show that protons exploit ready reversibility of conformational changes associated with extracellular Na(+) release from phosphorylated Na(+)/K(+) pumps. Reversal of a subset of these transitions allows an extracellular proton to bind an acidic side chain and to be subsequently released to the cytoplasm. This back-step of phosphorylated Na(+)/K(+) pumps that enables proton import is not required for completion of the 3 Na(+)/2 K(+) transport cycle. However, the back-step occurs readily during Na(+)/K(+) transport when external K(+) ion binding and occlusion are delayed, and it occurs more frequently when lowered extracellular pH raises the probability of protonation of the externally accessible carboxylate side chain. The proton route passes through the Na(+)-selective binding site III and is distinct from the principal pathway traversed by the majority of transported Na(+) and K(+) ions that passes through binding site II. The inferred occurrence of Na(+)/K(+) exchange and H(+) import during the same conformational cycle of a single molecule identifies the Na(+)/K(+) pump as a hybrid transporter. Whether Na(+)/K(+) pump-mediated proton inflow may have any physiological or

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

    PubMed

    Heather, James M; Chain, Benjamin

    2016-01-01

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

  5. Preserving sequence annotations across reference sequences.

    PubMed

    Tatum, Zuotian; Roos, Marco; Gibson, Andrew P; Taschner, Peter Em; Thompson, Mark; Schultes, Erik A; Laros, Jeroen Fj

    2014-01-01

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

  6. Preserving sequence annotations across reference sequences

    PubMed Central

    2014-01-01

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

  7. Testing Na+ in blood

    PubMed Central

    Lava, Sebastiano A.G.; Bianchetti, Mario G.; Milani, Gregorio P.

    2017-01-01

    Abstract Both direct potentiometry and indirect potentiometry are currently used for Na+ testing in blood. These measurement techniques show good agreement as long as protein and lipid concentrations in blood remain normal. In severely ill patients, indirect potentiometry commonly leads to relevant errors in Na+ estimation: 25% of specimens show a disagreement between direct and indirect potentiometry, which is ≥4 mmol/L (mostly spuriously elevated Na+ level due to low circulating albumin concentration). There is a need for increased awareness of the poor performance of indirect potentiometry in some clinical settings.

  8. Contrasting Sequence Groups by Emerging Sequences

    NASA Astrophysics Data System (ADS)

    Deng, Kang; Zaïane, Osmar R.

    Group comparison per se is a fundamental task in many scientific endeavours but is also the basis of any classifier. Contrast sets and emerging patterns contrast between groups of categorical data. Comparing groups of sequence data is a relevant task in many applications. We define Emerging Sequences (ESs) as subsequences that are frequent in sequences of one group and less frequent in the sequences of another, and thus distinguishing or contrasting sequences of different classes. There are two challenges to distinguish sequence classes: the extraction of ESs is not trivially efficient and only exact matches of sequences are considered. In our work we address those problems by a suffix tree-based framework and a similar matching mechanism. We propose a classifier based on Emerging Sequences. Evaluating against two learning algorithms based on frequent subsequences and exact matching subsequences, the experiments on two datasets show that our model outperforms the baseline approaches by up to 20% in prediction accuracy.

  9. 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.

  10. 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

  11. Conduction of Na+ and K+ through the NaK Channel: Molecular and Brownian Dynamics Studies

    PubMed Central

    Vora, Taira; Bisset, David; Chung, Shin-Ho

    2008-01-01

    Conduction of ions through the NaK channel, with M0 helix removed, was studied using both Brownian dynamics and molecular dynamics. Brownian dynamics simulations predict that the truncated NaK has approximately a third of the conductance of the related KcsA K+ channel, is outwardly rectifying, and has a Michaelis-Menten current-concentration relationship. Current magnitude increases when the glutamine residue located near the intracellular gate is replaced with a glutamate residue. The channel is blocked by extracellular Ca2+. Molecular dynamics simulations show that, under the influence of a strong applied potential, both Na+ and K+ move across the selectivity filter, although conduction rates for Na+ ions are somewhat lower. The mechanism of conduction of Na+ differs significantly from that of K+ in that Na+ is preferentially coordinated by single planes of pore-lining carbonyl oxygens, instead of two planes as in the usual K+ binding sites. The water-containing filter pocket resulting from a single change in the selectivity filter sequence (compared to potassium channels) disrupts several of the planes of carbonyl oxygens, and thus reduces the filter's ability to discriminate against sodium. PMID:18456826

  12. Conduction of Na+ and K+ through the NaK channel: molecular and Brownian dynamics studies.

    PubMed

    Vora, Taira; Bisset, David; Chung, Shin-Ho

    2008-08-01

    Conduction of ions through the NaK channel, with M0 helix removed, was studied using both Brownian dynamics and molecular dynamics. Brownian dynamics simulations predict that the truncated NaK has approximately a third of the conductance of the related KcsA K+ channel, is outwardly rectifying, and has a Michaelis-Menten current-concentration relationship. Current magnitude increases when the glutamine residue located near the intracellular gate is replaced with a glutamate residue. The channel is blocked by extracellular Ca2+. Molecular dynamics simulations show that, under the influence of a strong applied potential, both Na+ and K+ move across the selectivity filter, although conduction rates for Na+ ions are somewhat lower. The mechanism of conduction of Na+ differs significantly from that of K+ in that Na+ is preferentially coordinated by single planes of pore-lining carbonyl oxygens, instead of two planes as in the usual K+ binding sites. The water-containing filter pocket resulting from a single change in the selectivity filter sequence (compared to potassium channels) disrupts several of the planes of carbonyl oxygens, and thus reduces the filter's ability to discriminate against sodium.

  13. Multimodal sequence learning.

    PubMed

    Kemény, Ferenc; Meier, Beat

    2016-02-01

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

  14. 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 ...

  15. Synthesis of NaYF4, NaLuF4 and NaGdF4-based upconversion nanocrystals with hydro (solvo) thermal methods.

    PubMed

    Yin, Dongguang; Song, Kailin; Ou, Yangjuan; Wang, Chengcheng; Liu, Bing; Wu, Minghong

    2013-06-01

    Serials of NaYF4, NaLuF4 and NaGdF4-based nanocrystals have been synthesized successfully by solvothermal and hydrothermal, respectively. The properties of the products were characterized and compared. The nanocrystals prepared by hydrothermal method exhibited uniform hexagonal phase and large size, while the nanocrystals prepared by solvothermal method displayed high upconversion luminescence (UCL) and small size. The UCL intensities of the nanocrystals prepared by solvothermal method were higher than that of nanocrystals from hydrothermal method. Whether using solvothermal or hydrothermal method, the UCL intensities of the nanocrystals were in the sequence (from strong to weak) of NaLuF4:Gd/Yb/Tm, NaLuF4:Yb/Tm, NaGdF4:Yb/Tm, NaYF4:Gd/Yb/Tm and NaYF4:Yb/Tm, respectively. This is the first time to systematically compare three kinds of host-based nanocrystals, which are prepared by two different approaches with various lanthanide ions doped. This work could provide new insight into fabrication of upconversion nanocrystals with intense UCL and controllable morphology and size via using suitable doping ions, host materials and efficient approaches.

  16. 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.

  17. 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.

  18. Expression of diverse Na+ channel messenger RNAs in rat myocardium. Evidence for a cardiac-specific Na+ channel.

    PubMed Central

    Sills, M N; Xu, Y C; Baracchini, E; Goodman, R H; Cooperman, S S; Mandel, G; Chien, K R

    1989-01-01

    This study examined the diversity of Na+ channel gene expression in intact cardiac tissue and purified myocardial cells. The screening of neonatal rat myocardial cell cDNA libraries with a conserved rat brain Na+ channel cDNA probe, resulted in the isolation and characterization of a putative rat cardiac Na+ channel cDNA probe (pCSC-1). The deduced amino acid sequence of pCSC-1 displayed a striking degree of homology with the eel, rat brain-1, and rat brain-2 Na+ channel, thereby identifying pCSC-1 as a related member of the family of Na+ channel genes. Northern blot analysis revealed the expression of a 7-kb CSC-1 transcript in rat cardiac tissue and purified myocardial cells, but little or no detectable expression of CSC-1 in rat brain, skeletal muscle, denervated skeletal muscle, or liver. Using RNase protection and Northern blot hybridization with specific rat brain Na+ channel gene probes, expression of the rat brain-1 Na+ channel was observed in rat myocardium, but no detectable expression of the rat brain-2 gene was found. This study provides evidence for the expression of diverse Na+ channel mRNAs in rat myocardium and presents the initial characterization of a new, related member of the family of Na+ channel genes, which appears to be expressed in a cardiac-specific manner. Images PMID:2544627

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

    SciTech Connect

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

    1994-09-01

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

  20. MRO Sequence Checking Tool

    NASA Technical Reports Server (NTRS)

    Fisher, Forest; Gladden, Roy; Khanampornpan, Teerapat

    2008-01-01

    The MRO Sequence Checking Tool program, mro_check, automates significant portions of the MRO (Mars Reconnaissance Orbiter) sequence checking procedure. Though MRO has similar checks to the ODY s (Mars Odyssey) Mega Check tool, the checks needed for MRO are unique to the MRO spacecraft. The MRO sequence checking tool automates the majority of the sequence validation procedure and check lists that are used to validate the sequences generated by MRO MPST (mission planning and sequencing team). The tool performs more than 50 different checks on the sequence. The automation varies from summarizing data about the sequence needed for visual verification of the sequence, to performing automated checks on the sequence and providing a report for each step. To allow for the addition of new checks as needed, this tool is built in a modular fashion.

  1. Two Completely Different Mechanisms for Highly Specific Na(+) Recognition by DNAzymes.

    PubMed

    Zhou, Wenhu; Saran, Runjhun; Ding, Jinsong; Liu, Juewen

    2017-09-19

    Our view of the interaction between Na(+) and nucleic acids was changed by a few recently discovered Na(+) -specific RNA-cleaving DNAzymes. In addition to nonspecific electrostatic interactions, highly specific recognition is also possible. Herein, two such DNAzymes, named EtNa and Ce13d, are compared to elucidate their mechanisms of Na(+) binding. Mutation studies indicate that they have different sequence requirements. Phosphorothioate (PS) substitution at the scissile phosphate drops the activity of EtNa 140-fold, and it cannot be rescued by thiophilic Cd(2+) or Mn(2+) , whereas the activity of PS-modified Ce13d can be rescued. Na(+) -dependent activity assays indicate that two Na(+) ions bind cooperatively in EtNa, and each Na(+) likely interacts with a nonbridging oxygen atom in the scissile phosphate, whereas Ce13d binds only one Na(+) ion in a well-defined Na(+) aptamer, and this Na(+) ion does not directly interact with the scissile phosphate. Both DNAzymes display a normal pH-rate profile, with a single deprotonation reaction required for catalysis. For EtNa, Na(+) fails to protect the conserved nucleotides from dimethyl sulfate attack, and no specific Na(+) binding is detected by 2-aminopurine fluorescence, both of which are different from those observed for Ce13d. This work suggests that EtNa binds Na(+) mainly through its scissile phosphate without significant involvement of the nucleotides in the enzyme strand, whereas Ce13d has a well-defined aptamer for Na(+) binding. Therefore, DNA has at least two distinct ways to achieve highly selective Na(+) binding. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. The Connell Sum Sequence

    NASA Astrophysics Data System (ADS)

    Bullington, Grady D.

    2007-01-01

    The Connell sum sequence refers to the partial sums of the Connell sequence. In this paper, the Connell sequence, Connell sum sequence and generalizations from Iannucci and Mills-Taylor are interpreted as sums of elements of triangles, relating them to polygonal number-stuttered arithmetic progressions. The n-th element of the Connell sum sequence is established as a sharp upper bound for the value of a gamma-labeling of a graph of size n. The limiting behavior and a explicit formula for the Connell (m,r)-sum sequence are also given.

  3. 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.

  4. 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.

  5. Sequence information signal processor

    NASA Technical Reports Server (NTRS)

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

    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.

  6. 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.

  7. 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.

  8. Nonparametric Combinatorial Sequence Models

    NASA Astrophysics Data System (ADS)

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

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

  9. Cellulases and coding sequences

    SciTech Connect

    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.

  10. 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.

  11. 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.

  12. Schur monotone decreasing sequences

    NASA Astrophysics Data System (ADS)

    Ganikhodjaev, Rasul; Saburov, Mansoor; Saburov, Khikmat

    2013-09-01

    In this paper, we introduce Schur monotone decreasing sequences in an n-dimensional space by considering a majorization pre-order. By means of down arrow mappings, we study omega limiting points of bounded Schur monotone decreasing sequences. We provide convergence criteria for such kinds of sequences. We prove that a Cesaro mean (or an arithmetic mean) of any bounded Schur monotone decreasing sequences converges to a unique limiting point.

  13. Enhanced virome sequencing using targeted sequence capture.

    PubMed

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

    2015-12-01

    Metagenomic shotgun sequencing (MSS) is an important tool for characterizing viral populations. It is culture independent, requires no a priori knowledge of the viruses in the sample, and may provide useful genomic information. However, MSS can lack sensitivity and may yield insufficient data for detailed analysis. We have created a targeted sequence capture panel, ViroCap, designed to enrich nucleic acid from DNA and RNA viruses from 34 families that infect vertebrate hosts. A computational approach condensed ∼1 billion bp of viral reference sequence into <200 million bp of unique, representative sequence suitable for targeted sequence capture. We compared the effectiveness of detecting viruses in standard MSS versus MSS following targeted sequence capture. First, we analyzed two sets of samples, one derived from samples submitted to a diagnostic virology laboratory and one derived from samples collected in a study of fever in children. We detected 14 and 18 viruses in the two sets, comprising 19 genera from 10 families, with dramatic enhancement of genome representation following capture enrichment. The median fold-increases in percentage viral reads post-capture were 674 and 296. Median breadth of coverage increased from 2.1% to 83.2% post-capture in the first set and from 2.0% to 75.6% in the second set. Next, we analyzed samples containing a set of diverse anellovirus sequences and demonstrated that ViroCap could be used to detect viral sequences with up to 58% variation from the references used to select capture probes. ViroCap substantially enhances MSS for a comprehensive set of viruses and has utility for research and clinical applications. © 2015 Wylie et al.; Published by Cold Spring Harbor Laboratory Press.

  14. 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

  15. Single Na+ channels activated by veratridine and batrachotoxin

    PubMed Central

    1987-01-01

    Voltage-sensitive Na+ channels from rat skeletal muscle plasma membrane vesicles were inserted into planar lipid bilayers in the presence of either of the alkaloid toxins veratridine (VT) or batrachotoxin (BTX). Both of these toxins are known to cause persistent activation of Na+ channels. With BTX as the channel activator, single channels remain open nearly all the time. Channels activated with VT open and close on a time scale of 1-10 s. Increasing the VT concentration enhances the probability of channel opening, primarily by increasing the rate constant of opening. The kinetics and voltage dependence of channel block by 21-sulfo-11-alpha-hydroxysaxitoxin are identical for VT and BTX, as is the ionic selectivity sequence determined by bi-ionic reversal potential (Na+ approximately Li+ greater than K+ greater than Rb+ greater than Cs+). However, there are striking quantitative differences in open channel conduction for channels in the presence of the two activators. Under symmetrical solution conditions, the single channel conductance for Na+ is about twice as high with BTX as with VT. Furthermore, the symmetrical solution single channel conductances show a different selectivity for BTX (Na+ greater than Li+ greater than K+) than for VT (Na+ greater than K+ greater than Li+). Open channel current-voltage curves in symmetrical Na+ and Li+ are roughly linear, while those in symmetrical K+ are inwardly rectifying. Na+ currents are blocked asymmetrically by K+ with both BTX and VT, but the voltage dependence of K+ block is stronger with BTX than with VT. The results show that the alkaloid neurotoxins not only alter the gating process of the Na+ channel, but also affect the structure of the open channel. We further conclude that the rate-determining step for conduction by Na+ does not occur at the channel's "selectivity filter," where poorly permeating ions like K+ are excluded. PMID:2435846

  16. 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)…

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

    PubMed

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

    2016-09-13

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

  18. 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.)

  19. [Sequencing - classical method].

    PubMed

    Sedivcová, Monika; Martínek, Petr; Stehlík, Jan; Grossmann, Petr; Kašpírková, Jana; Vaneček, Tomáš

    2013-06-01

    In this article the basic methods of reading nucleotide sequences in DNA molecules are summarized. Sanger sequencing is described most thoroughly as it is the most frequent routine method currently being utilized. The article describes in detail the principle of sequence determination through the production of fragments with a known end base using chain termination synthesis of DNA and ways of separation and detection of the fragments. Some alternative methods of sequencing are mentioned in short. Basic approaches of analyzing sequence data are explained as well as different outcomes, obstacles and challenges.

  20. 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.

  1. HIV Sequence Databases

    PubMed Central

    Kuiken, Carla; Korber, Bette; Shafer, Robert W.

    2008-01-01

    Two important databases are often used in HIV genetic research, the HIV Sequence Database in Los Alamos, which collects all sequences and focuses on annotation and data analysis, and the HIV RT/Protease Sequence Database in Stanford, which collects sequences associated with the development of viral resistance against anti-retroviral drugs and focuses on analysis of those sequences. The types of data and services these two databases offer, the tools they provide, and the way they are set up and operated are described in detail. PMID:12875108

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

    PubMed Central

    Shamraj, O I; Lingrel, J B

    1994-01-01

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

  3. Light-driven Na+ pump from Gillisia limnaea: A high-affinity Na+ binding site is formed transiently in the photocycle

    DOE PAGES

    Balashov, Sergei P.; Imasheva, Eleonora S.; Dioumaev, Andrei K.; ...

    2014-11-06

    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 decaymore » 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. Furthermore, 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.« less

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

    PubMed

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

    2014-12-09

    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.

  5. Multiple Sequence Alignment.

    PubMed

    Bawono, Punto; Dijkstra, Maurits; Pirovano, Walter; Feenstra, Anton; Abeln, Sanne; Heringa, Jaap

    2017-01-01

    The increasing importance of Next Generation Sequencing (NGS) techniques has highlighted the key role of multiple sequence alignment (MSA) in comparative structure and function analysis of biological sequences. MSA often leads to fundamental biological insight into sequence-structure-function relationships of nucleotide or protein sequence families. Significant advances have been achieved in this field, and many useful tools have been developed for constructing alignments, although many biological and methodological issues are still open. This chapter first provides some background information and considerations associated with MSA techniques, concentrating on the alignment of protein sequences. Then, a practical overview of currently available methods and a description of their specific advantages and limitations are given, to serve as a helpful guide or starting point for researchers who aim to construct a reliable MSA.

  6. Computer assisted multiplex sequencing

    SciTech Connect

    Church, G.M.

    1992-08-01

    The objectives of this project are automation and optimization of multiplex sequencing. This year we have integrated direct transfer electrophoresis, automated multiplex hybridizations and automated film reading and applied this toward sequencing of three contiguous E. coli cosmids. Primers for the directed dideoxy sequence walking and sequence confirmation steps were synthesized with a 15 base tag complimentary to an alkaline phosphatase conjugate. A higher throughput synthesis device is well along in testing as are new automated hybridization devices. We have developed software for automatically annotating ORFs and databases of precise termini of proteis and RNA.

  7. 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:

  8. 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

  9. 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.

  10. Na+ coordination at the Na2 site of the Na+/I− symporter

    PubMed Central

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

    2016-01-01

    The sodium/iodide symporter (NIS) mediates active I− transport in the thyroid—the first step in thyroid hormone biosynthesis—with a 2 Na+: 1 I− stoichiometry. The two Na+ binding sites (Na1 and Na2) and the I− binding site interact allosterically: when Na+ binds to a Na+ site, the affinity of NIS for the other Na+ and for I− increases significantly. In all Na+-dependent transporters with the same fold as NIS, the side chains of two residues, S353 and T354 (NIS numbering), were identified as the Na+ ligands at Na2. To understand the cooperativity between the substrates, we investigated the coordination at the Na2 site. We determined that four other residues—S66, D191, Q194, and Q263—are also involved in Na+ coordination at this site. Experiments in whole cells demonstrated that these four residues participate in transport by NIS: mutations at these positions result in proteins that, although expressed at the plasma membrane, transport little or no I−. These residues are conserved throughout the entire SLC5 family, to which NIS belongs, suggesting that they serve a similar function in the other transporters. Our findings also suggest that the increase in affinity that each site displays when an ion binds to another site may result from changes in the dynamics of the transporter. These mechanistic insights deepen our understanding not only of NIS but also of other transporters, including many that, like NIS, are of great medical relevance. PMID:27562170

  11. 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…

  12. 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…

  13. 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;…

  14. Sequences, Series, and Mathematica.

    ERIC Educational Resources Information Center

    Mathews, John H.

    1992-01-01

    Describes how the computer algebra system Mathematica can be used to enhance the teaching of the topics of sequences and series. Examines its capabilities to find exact, approximate, and graphically generated approximate solutions to problems from these topics and to understand proofs about sequences. (MDH)

  15. Lichenase and coding sequences

    SciTech Connect

    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.

  16. 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…

  17. Can sequence determine function?

    PubMed Central

    Gerlt, John A; Babbitt, Patricia C

    2000-01-01

    The functional annotation of proteins identified in genome sequencing projects is based on similarities to homologs in the databases. As a result of the possible strategies for divergent evolution, homologous enzymes frequently do not catalyze the same reaction, and we conclude that assignment of function from sequence information alone should be viewed with some skepticism. PMID:11178260

  18. Biotools: Patenting DNA sequences

    SciTech Connect

    Yablonsky, M.D.; Hone, W.J.

    1995-07-01

    The decision, known as In re Deuel{sup 2}, rejects the PTO`s interpretation of a previous decision of the Federal Circuit and makes it more possible that a {open_quotes}nucleic acid of a particular sequence{close_quotes} - commonly known as a gene sequence - may be patentable. 15 refs.

  19. 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;…

  20. 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.

  1. Sequencing the maize genome.

    PubMed

    Martienssen, Robert A; Rabinowicz, Pablo D; O'Shaughnessy, Andrew; McCombie, W Richard

    2004-04-01

    Sequencing of complex genomes can be accomplished by enriching shotgun libraries for genes. In maize, gene-enrichment by copy-number normalization (high C(0)t) and methylation filtration (MF) have been used to generate up to two-fold coverage of the gene-space with less than 1 million sequencing reads. Simulations using sequenced bacterial artificial chromosome (BAC) clones predict that 5x coverage of gene-rich regions, accompanied by less than 1x coverage of subclones from BAC contigs, will generate high-quality mapped sequence that meets the needs of geneticists while accommodating unusually high levels of structural polymorphism. By sequencing several inbred strains, we propose a strategy for capturing this polymorphism to investigate hybrid vigor or heterosis.

  2. Effect of sequence and metal ions on UVB-induced anti cyclobutane pyrimidine dimer formation in human telomeric DNA sequences.

    PubMed

    Smith, Jillian E; Lu, Chen; Taylor, John-Stephen

    2014-04-01

    Irradiation of G-quadruplex forming human telomeric DNA with ultraviolet B (UVB) light results in the formation of anti cyclobutane pyrimidine dimers (CPDs) between loop 1 and loop 3 in the presence of potassium ions but not sodium ions. This was unexpected because the sequences involved favor the nonphotoreactive hybrid conformations in K(+) solution, whereas a potentially photoreactive basket conformation is favored in Na(+) solution. To account for these contradictory results, it was proposed that the loops are too far apart in the basket conformation in Na(+) solution but close enough in a two G-tetrad basket-like form 3 conformation that can form in K(+) solution. In the current study, Na(+) was still found to inhibit anti CPD formation in sequences designed to stabilize the form 3 conformation. Furthermore, anti CPD formation in K(+) solution was slower for the sequence previously shown to exist primarily in the proposed photoreactive form 3 conformation than the sequence shown to exist primarily in a nonphotoreactive hybrid conformation. These results suggest that the form 3 conformation is not the principal photoreactive conformation, and that G-quadruplexes in K(+) solution are dynamic and able to access photoreactive conformations more easily than in Na(+) solution.

  3. Laser ablation of NaN3 and CsN3

    NASA Astrophysics Data System (ADS)

    Belau, Leonid; Gorodetsky, Jonathan; Haas, Yehuda

    2005-06-01

    Solid sodium azide and cesium azide crystals were irradiated by high power laser pulses; the ablation products were rapidly cooled by a supersonic expansion of helium and detected by a time of flight mass spectrometer. Neutral and positively charged species were separately recorded and analyzed using N15 isotopomers to help in their assignment. Cluster series of the sequences Na(NaN3)n [or Cs(CsN3)n] were observed, as well as clusters containing NaOH and NaCN; the origin of the C, H, and O atoms appears to be water and CO2 occluded in the salt. Addition of D2O increased the intensity of large clusters and added deuterated ones, whereas addition of chloroform leads to formation of clusters of a Na atom with (NaCl)n clusters. Possible mechanisms for the formation of these clusters are discussed.

  4. Laser ablation of NaN{sub 3} and CsN{sub 3}

    SciTech Connect

    Belau, Leonid; Gorodetsky, Jonathan; Haas, Yehuda

    2005-06-08

    Solid sodium azide and cesium azide crystals were irradiated by high power laser pulses; the ablation products were rapidly cooled by a supersonic expansion of helium and detected by a time of flight mass spectrometer. Neutral and positively charged species were separately recorded and analyzed using {sup 15}N isotopomers to help in their assignment. Cluster series of the sequences Na(NaN{sub 3}){sub n} [or Cs(CsN{sub 3}){sub n}] were observed, as well as clusters containing NaOH and NaCN; the origin of the C, H, and O atoms appears to be water and CO{sub 2} occluded in the salt. Addition of D{sub 2}O increased the intensity of large clusters and added deuterated ones, whereas addition of chloroform leads to formation of clusters of a Na atom with (NaCl){sub n} clusters. Possible mechanisms for the formation of these clusters are discussed.

  5. Next-Generation Sequencing.

    PubMed

    Le Gallo, Matthieu; Lozy, Fred; Bell, Daphne W

    2017-01-01

    Endometrial cancers are the most frequently diagnosed gynecological malignancy and were expected to be the seventh leading cause of cancer death among American women in 2015. The majority of endometrial cancers are of serous or endometrioid histology. Most human tumors, including endometrial tumors, are driven by the acquisition of pathogenic mutations in cancer genes. Thus, the identification of somatic mutations within tumor genomes is an entry point toward cancer gene discovery. However, efforts to pinpoint somatic mutations in human cancers have, until recently, relied on high-throughput sequencing of single genes or gene families using Sanger sequencing. Although this approach has been fruitful, the cost and throughput of Sanger sequencing generally prohibits systematic sequencing of the ~22,000 genes that make up the exome. The recent development of next-generation sequencing technologies changed this paradigm by providing the capability to rapidly sequence exomes, transcriptomes, and genomes at relatively low cost. Remarkably, the application of this technology to catalog the mutational landscapes of endometrial tumor exomes, transcriptomes, and genomes has revealed, for the first time, that serous and endometrioid endometrial cancers can be classified into four distinct molecular subgroups. In this chapter, we overview the characteristic genomic features of each subgroup and discuss the known and putative cancer genes that have emerged from next-generation sequencing of endometrial carcinomas.

  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. Personalized Course Sequence Recommendations

    NASA Astrophysics Data System (ADS)

    Xu, Jie; Xing, Tianwei; van der Schaar, Mihaela

    2016-10-01

    Given the variability in student learning it is becoming increasingly important to tailor courses as well as course sequences to student needs. This paper presents a systematic methodology for offering personalized course sequence recommendations to students. First, a forward-search backward-induction algorithm is developed that can optimally select course sequences to decrease the time required for a student to graduate. The algorithm accounts for prerequisite requirements (typically present in higher level education) and course availability. Second, using the tools of multi-armed bandits, an algorithm is developed that can optimally recommend a course sequence that both reduces the time to graduate while also increasing the overall GPA of the student. The algorithm dynamically learns how students with different contextual backgrounds perform for given course sequences and then recommends an optimal course sequence for new students. Using real-world student data from the UCLA Mechanical and Aerospace Engineering department, we illustrate how the proposed algorithms outperform other methods that do not include student contextual information when making course sequence recommendations.

  8. Solidification of NaCl-NaF eutectic in space

    NASA Technical Reports Server (NTRS)

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

    1974-01-01

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

  9. Phylogenetic Trees From Sequences

    NASA Astrophysics Data System (ADS)

    Ryvkin, Paul; Wang, Li-San

    In this chapter, we review important concepts and approaches for phylogeny reconstruction from sequence data.We first cover some basic definitions and properties of phylogenetics, and briefly explain how scientists model sequence evolution and measure sequence divergence. We then discuss three major approaches for phylogenetic reconstruction: distance-based phylogenetic reconstruction, maximum parsimony, and maximum likelihood. In the third part of the chapter, we review how multiple phylogenies are compared by consensus methods and how to assess confidence using bootstrapping. At the end of the chapter are two sections that list popular software packages and additional reading.

  10. 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

  11. Toward nanoscale genome sequencing.

    PubMed

    Ryan, Declan; Rahimi, Maryam; Lund, John; Mehta, Ranjana; Parviz, Babak A

    2007-09-01

    This article reports on the state-of-the-art technologies that sequence DNA using miniaturized devices. The article considers the miniaturization of existing technologies for sequencing DNA and the opportunities for cost reduction that 'on-chip' devices can deliver. The ability to construct nano-scale structures and perform measurements using novel nano-scale effects has provided new opportunities to identify nucleotides directly using physical, and not chemical, methods. The challenges that these technologies need to overcome to provide a US$1000-genome sequencing technology are also presented.

  12. DNA sequences encoding osteoinductive products

    SciTech Connect

    Wang, E.A.; Wozney, J.M.; Rosen, V.

    1991-05-07

    This patent describes an isolated DNA sequence encoding an osteoinductive protein the DNA sequence comprising a coding sequence. It comprises: nucleotide No.1 through nucleotide No.387, nucleotide No.356 through nucleotide No.1543, nucleotide $402 through nucleotide No.1626, naturally occurring allelic sequences and equivalent degenerative codon sequences and sequences which hybridize to any of sequences under stringent hybridization conditions; and encode a protein characterized by the ability to induce the formation of bone and/or cartilage.

  13. Advances in sequence analysis.

    PubMed

    Califano, A

    2001-06-01

    In its early days, the entire field of computational biology revolved almost entirely around biological sequence analysis. Over the past few years, however, a number of new non-sequence-based areas of investigation have become mainstream, from the analysis of gene expression data from microarrays, to whole-genome association discovery, and to the reverse engineering of gene regulatory pathways. Nonetheless, with the completion of private and public efforts to map the human genome, as well as those of other organisms, sequence data continue to be a veritable mother lode of valuable biological information that can be mined in a variety of contexts. Furthermore, the integration of sequence data with a variety of alternative information is providing valuable and fundamentally new insight into biological processes, as well as an array of new computational methodologies for the analysis of biological data.

  14. 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.

  15. Pierre Robin sequence

    MedlinePlus

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

  16. Genomic Sequencing in Cancer

    PubMed Central

    Tuna, Musaffe; Amos, Christopher I.

    2013-01-01

    Genomic sequencing has provided critical insights into the etiology of both simple and complex diseases. The enormous reductions in cost for whole genome sequencing have allowed this technology to gain increasing use. Whole genome analysis has impacted research of complex diseases including cancer by allowing the systematic analysis of entire genomes in a single experiment, thereby facilitating the discovery of somatic and germline mutations, and identification of the function and impact of the insertions, deletions, and structural rearrangements, including translocations and inversions, in novel disease genes. Whole-genome sequencing can be used to provide the most comprehensive characterization of the cancer genome, the complexity of which we are only beginning to understand. Hence in this review, we focus on whole-genome sequencing in cancer. PMID:23178448

  17. 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

  18. 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

  19. Event-sequence detector

    NASA Technical Reports Server (NTRS)

    Hanna, M. F.

    1973-01-01

    Detector consists of matrix of storage elements which are activated by coincidence of failure-voltage pulses and clock pulses. Clock frequency used for event sequence detector can be selected to provide time resolution demanded by test at hand.

  20. 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.

  1. Sequences in drug discovery.

    PubMed

    Khurdayan, V; Davies, S

    2005-04-01

    Sequences in Drug Discovery is a new series of distinct brief reports on breaking topics in the field of drug R&D. This month's Sequences in Drug Discovery contains the following reports: Spotlight on West Nile virus vaccines. p38alpha MAPK--a dynamic target in rheumatoid arthritis. The need for new contraceptives: targeting PDE3. Vasopeptidase inhibition with a triple mode of action. Current advances in the development of 5-HT(6) receptor antagonists.

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

    USDA-ARS?s Scientific Manuscript database

    Information on the effects of long-term tillage and cropping sequence on dryland soil nutrients and chemical properties is scanty. We examined the effect of 30 yr of tillage frequency and cropping sequence combination on dryland soil Olsen-P, exchangeable K, Ca, Mg, Na, SO4-S, and Zn contents, pH, e...

  3. 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).

  4. 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.

  5. n/a

    NASA Image and Video Library

    1975-10-10

    This diagram illustrates the Space Shuttle mission sequence. The Space Shuttle was approved as a national program in 1972 and developed through the 1970s. Part spacecraft and part aircraft, the Space Shuttle orbiter, the brain and the heart of the Space Transportation System (STS), required several technological advances, including thousands of insulating tiles able to stand the heat of reentry over the course of many missions, as well as sophisticated engines that could be used again and again without being thrown away. The airplane-like orbiter has three main engines, that burn liquid hydrogen and oxygen stored in the large external tank, the single largest structure in the Shuttle. Attached to the tank are two solid rocket boosters that provide the vehecile with most of the thrust needed for liftoff. Two minutes into the flight, the spent solids drop into the ocean to be recovered and refurbished for reuse, while the orbiter engines continue burning until approximately 8 minutes into the flight. After the mission is completed, the orbiter lands on a runway like an airplane.

  6. Nanopore sequencing in microgravity

    PubMed Central

    McIntyre, Alexa B R; Rizzardi, Lindsay; Yu, Angela M; Alexander, Noah; Rosen, Gail L; Botkin, Douglas J; Stahl, Sarah E; John, Kristen K; Castro-Wallace, Sarah L; McGrath, Ken; Burton, Aaron S; Feinberg, Andrew P; Mason, Christopher E

    2016-01-01

    Rapid DNA sequencing and analysis has been a long-sought goal in remote research and point-of-care medicine. In microgravity, DNA sequencing can facilitate novel astrobiological research and close monitoring of crew health, but spaceflight places stringent restrictions on the mass and volume of instruments, crew operation time, and instrument functionality. The recent emergence of portable, nanopore-based tools with streamlined sample preparation protocols finally enables DNA sequencing on missions in microgravity. As a first step toward sequencing in space and aboard the International Space Station (ISS), we tested the Oxford Nanopore Technologies MinION during a parabolic flight to understand the effects of variable gravity on the instrument and data. In a successful proof-of-principle experiment, we found that the instrument generated DNA reads over the course of the flight, including the first ever sequenced in microgravity, and additional reads measured after the flight concluded its parabolas. Here we detail modifications to the sample-loading procedures to facilitate nanopore sequencing aboard the ISS and in other microgravity environments. We also evaluate existing analysis methods and outline two new approaches, the first based on a wave-fingerprint method and the second on entropy signal mapping. Computationally light analysis methods offer the potential for in situ species identification, but are limited by the error profiles (stays, skips, and mismatches) of older nanopore data. Higher accuracies attainable with modified sample processing methods and the latest version of flow cells will further enable the use of nanopore sequencers for diagnostics and research in space. PMID:28725742

  7. Nanopore sequencing in microgravity.

    PubMed

    McIntyre, Alexa B R; Rizzardi, Lindsay; Yu, Angela M; Alexander, Noah; Rosen, Gail L; Botkin, Douglas J; Stahl, Sarah E; John, Kristen K; Castro-Wallace, Sarah L; McGrath, Ken; Burton, Aaron S; Feinberg, Andrew P; Mason, Christopher E

    2016-01-01

    Rapid DNA sequencing and analysis has been a long-sought goal in remote research and point-of-care medicine. In microgravity, DNA sequencing can facilitate novel astrobiological research and close monitoring of crew health, but spaceflight places stringent restrictions on the mass and volume of instruments, crew operation time, and instrument functionality. The recent emergence of portable, nanopore-based tools with streamlined sample preparation protocols finally enables DNA sequencing on missions in microgravity. As a first step toward sequencing in space and aboard the International Space Station (ISS), we tested the Oxford Nanopore Technologies MinION during a parabolic flight to understand the effects of variable gravity on the instrument and data. In a successful proof-of-principle experiment, we found that the instrument generated DNA reads over the course of the flight, including the first ever sequenced in microgravity, and additional reads measured after the flight concluded its parabolas. Here we detail modifications to the sample-loading procedures to facilitate nanopore sequencing aboard the ISS and in other microgravity environments. We also evaluate existing analysis methods and outline two new approaches, the first based on a wave-fingerprint method and the second on entropy signal mapping. Computationally light analysis methods offer the potential for in situ species identification, but are limited by the error profiles (stays, skips, and mismatches) of older nanopore data. Higher accuracies attainable with modified sample processing methods and the latest version of flow cells will further enable the use of nanopore sequencers for diagnostics and research in space.

  8. Na+ recirculation and isosmotic transport.

    PubMed

    Larsen, E H; Møbjerg, N

    2006-01-01

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

  9. Identification of the Intracellular Na+ Sensor in Slo2.1 Potassium Channels.

    PubMed

    Thomson, Steven J; Hansen, Angela; Sanguinetti, Michael C

    2015-06-05

    Slo2 potassium channels have a very low open probability under normal physiological conditions, but are readily activated in response to an elevated [Na(+)]i (e.g. during ischemia). An intracellular Na(+) coordination motif (DX(R/K)XXH) was previously identified in Kir3.2, Kir3.4, Kir5.1, and Slo2.2 channel subunits. Based loosely on this sequence, we identified five potential Na(+) coordination motifs in the C terminus of the Slo2.1 subunit. The Asp residue in each sequence was substituted with Arg, and single mutant channels were heterologously expressed in Xenopus oocytes. The Na(+) sensitivity of each of the mutant channels was assessed by voltage clamp of oocytes using micropipettes filled with 2 M NaCl. Wild-type channels and four of the mutant Slo2.1 channels were rapidly activated by leakage of NaCl solution into the cytoplasm. D757R Slo2.1 channels were not activated by NaCl, but were activated by the fenamate niflumic acid, confirming their functional expression. In whole cell voltage clamp recordings of HEK293 cells, wild-type but not D757R Slo2.1 channels were activated by a [NaCl]i of 70 mM. Thus, a single Asp residue can account for the sensitivity of Slo2.1 channels to intracellular Na(+). In excised inside-out macropatches of HEK293 cells, activation of wild-type Slo2.1 currents by 3 mM niflumic acid was 14-fold greater than activation achieved by increasing [NaCl]i from 3 to 100 mM. Thus, relative to fenamates, intracellular Na(+) is a poor activator of Slo2.1.

  10. Identification of the Intracellular Na+ Sensor in Slo2.1 Potassium Channels*

    PubMed Central

    Thomson, Steven J.; Hansen, Angela; Sanguinetti, Michael C.

    2015-01-01

    Slo2 potassium channels have a very low open probability under normal physiological conditions, but are readily activated in response to an elevated [Na+]i (e.g. during ischemia). An intracellular Na+ coordination motif (DX(R/K)XXH) was previously identified in Kir3.2, Kir3.4, Kir5.1, and Slo2.2 channel subunits. Based loosely on this sequence, we identified five potential Na+ coordination motifs in the C terminus of the Slo2.1 subunit. The Asp residue in each sequence was substituted with Arg, and single mutant channels were heterologously expressed in Xenopus oocytes. The Na+ sensitivity of each of the mutant channels was assessed by voltage clamp of oocytes using micropipettes filled with 2 m NaCl. Wild-type channels and four of the mutant Slo2.1 channels were rapidly activated by leakage of NaCl solution into the cytoplasm. D757R Slo2.1 channels were not activated by NaCl, but were activated by the fenamate niflumic acid, confirming their functional expression. In whole cell voltage clamp recordings of HEK293 cells, wild-type but not D757R Slo2.1 channels were activated by a [NaCl]i of 70 mm. Thus, a single Asp residue can account for the sensitivity of Slo2.1 channels to intracellular Na+. In excised inside-out macropatches of HEK293 cells, activation of wild-type Slo2.1 currents by 3 mm niflumic acid was 14-fold greater than activation achieved by increasing [NaCl]i from 3 to 100 mm. Thus, relative to fenamates, intracellular Na+ is a poor activator of Slo2.1. PMID:25903137

  11. 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.

  12. 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.

  13. 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.

  14. Sequence-controlled polymers.

    PubMed

    Lutz, Jean-François; Ouchi, Makoto; Liu, David R; Sawamoto, Mitsuo

    2013-08-09

    Sequence-controlled polymers are macromolecules in which monomer units of different chemical nature are arranged in an ordered fashion. The most prominent examples are biological and have been studied and used primarily by molecular biologists and biochemists. However, recent progress in protein- and DNA-based nanotechnologies has shown the relevance of sequence-controlled polymers to nonbiological applications, including data storage, nanoelectronics, and catalysis. In addition, synthetic polymer chemistry has provided interesting routes for preparing nonnatural sequence-controlled polymers. Although these synthetic macromolecules do not yet compare in functional scope with their natural counterparts, they open up opportunities for controlling the structure, self-assembly, and macroscopic properties of polymer materials.

  15. 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

  16. A highly specific sodium aptamer probed by 2-aminopurine for robust Na+ sensing.

    PubMed

    Zhou, Wenhu; Ding, Jinsong; Liu, Juewen

    2016-12-01

    Sodium is one of the most abundant metals in the environment and in biology, playing critical ecological and physiological roles. Na(+) is also the most common buffer salt for nucleic acids research, while its specific interaction with DNA has yet to be fully studied. Herein, we probe a highly selective and robust Na(+) aptamer using 2-aminopurine (2AP), a fluorescent adenine analog. This aptamer has two DNA strands derived from the Ce13d DNAzyme. By introducing a 2AP at the cleavage site of the substrate strand, Na(+) induces ∼40% fluorescence increase. The signaling is improved by a series of rational mutations, reaching >600% with the C10A20 double mutant. This fluorescence enhancement suggests relaxed base stacking near the 2AP label upon Na(+) binding. By replacing a non-conserved adenine in the enzyme strand by 2AP, Na(+)-dependent fluorescence quenching is observed, suggesting that the enzyme loop folds into a more compact structure upon Na(+) binding. The fluorescence changes allow for Na(+) detection. With an optimized sequence, a detection limit of 0.4 mM Na(+) is achieved, reaching saturated signal in less than 10 s. The sensor response is insensitive to ionic strength, which is critical for Na(+) detection.

  17. A highly specific sodium aptamer probed by 2-aminopurine for robust Na+ sensing

    PubMed Central

    Zhou, Wenhu; Ding, Jinsong; Liu, Juewen

    2016-01-01

    Sodium is one of the most abundant metals in the environment and in biology, playing critical ecological and physiological roles. Na+ is also the most common buffer salt for nucleic acids research, while its specific interaction with DNA has yet to be fully studied. Herein, we probe a highly selective and robust Na+ aptamer using 2-aminopurine (2AP), a fluorescent adenine analog. This aptamer has two DNA strands derived from the Ce13d DNAzyme. By introducing a 2AP at the cleavage site of the substrate strand, Na+ induces ∼40% fluorescence increase. The signaling is improved by a series of rational mutations, reaching >600% with the C10A20 double mutant. This fluorescence enhancement suggests relaxed base stacking near the 2AP label upon Na+ binding. By replacing a non-conserved adenine in the enzyme strand by 2AP, Na+-dependent fluorescence quenching is observed, suggesting that the enzyme loop folds into a more compact structure upon Na+ binding. The fluorescence changes allow for Na+ detection. With an optimized sequence, a detection limit of 0.4 mM Na+ is achieved, reaching saturated signal in less than 10 s. The sensor response is insensitive to ionic strength, which is critical for Na+ detection. PMID:27655630

  18. 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.

  19. 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…

  20. Lining up Arithmetic Sequences

    ERIC Educational Resources Information Center

    Bell, Carol J.

    2011-01-01

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

  1. Prenatal Whole Genome Sequencing

    PubMed Central

    Donley, Greer; Hull, Sara Chandros; Berkman, Benjamin E.

    2014-01-01

    With whole genome sequencing set to become the preferred method of prenatal screening, we need to pay more attention to the massive amount of information it will deliver to parents—and the fact that we don't yet understand what most of it means. PMID:22777977

  2. Na Deposition on MnO(100)

    NASA Astrophysics Data System (ADS)

    Feng, Xu; Cox, David F.

    2016-03-01

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

  3. MARS: improving multiple circular sequence alignment using refined sequences.

    PubMed

    Ayad, Lorraine A K; Pissis, Solon P

    2017-01-14

    A fundamental assumption of all widely-used multiple sequence alignment techniques is that the left- and right-most positions of the input sequences are relevant to the alignment. However, the position where a sequence starts or ends can be totally arbitrary due to a number of reasons: arbitrariness in the linearisation (sequencing) of a circular molecular structure; or inconsistencies introduced into sequence databases due to different linearisation standards. These scenarios are relevant, for instance, in the process of multiple sequence alignment of mitochondrial DNA, viroid, viral or other genomes, which have a circular molecular structure. A solution for these inconsistencies would be to identify a suitable rotation (cyclic shift) for each sequence; these refined sequences may in turn lead to improved multiple sequence alignments using the preferred multiple sequence alignment program. We present MARS, a new heuristic method for improving Multiple circular sequence Alignment using Refined Sequences. MARS was implemented in the C++ programming language as a program to compute the rotations (cyclic shifts) required to best align a set of input sequences. Experimental results, using real and synthetic data, show that MARS improves the alignments, with respect to standard genetic measures and the inferred maximum-likelihood-based phylogenies, and outperforms state-of-the-art methods both in terms of accuracy and efficiency. Our results show, among others, that the average pairwise distance in the multiple sequence alignment of a dataset of widely-studied mitochondrial DNA sequences is reduced by around 5% when MARS is applied before a multiple sequence alignment is performed. Analysing multiple sequences simultaneously is fundamental in biological research and multiple sequence alignment has been found to be a popular method for this task. Conventional alignment techniques cannot be used effectively when the position where sequences start is arbitrary. We present

  4. Multiplexed fragaria chloroplast genome sequencing

    Treesearch

    W. Njuguna; A. Liston; R. Cronn; N.V. Bassil

    2010-01-01

    A method to sequence multiple chloroplast genomes using ultra high throughput sequencing technologies was recently described. Complete chloroplast genome sequences can resolve phylogenetic relationships at low taxonomic levels and identify informative point mutations and indels. The objective of this research was to sequence multiple Fragaria...

  5. Targeted sequencing of plant genomes

    Treesearch

    Mark D. Huynh

    2014-01-01

    Next-generation sequencing (NGS) has revolutionized the field of genetics by providing a means for fast and relatively affordable sequencing. With the advancement of NGS, wholegenome sequencing (WGS) has become more commonplace. However, sequencing an entire genome is still not cost effective or even beneficial in all cases. In studies that do not require a whole-...

  6. Compression of Multiple DNA Sequences Using Intra-Sequence and Inter-Sequence Similarities.

    PubMed

    Cheng, Kin-On; Wu, Paula; Law, Ngai-Fong; Siu, Wan-Chi

    2015-01-01

    Traditionally, intra-sequence similarity is exploited for compressing a single DNA sequence. Recently, remarkable compression performance of individual DNA sequence from the same population is achieved by encoding its difference with a nearly identical reference sequence. Nevertheless, there is lack of general algorithms that also allow less similar reference sequences. In this work, we extend the intra-sequence to the inter-sequence similarity in that approximate matches of subsequences are found between the DNA sequence and a set of reference sequences. Hence, a set of nearly identical DNA sequences from the same population or a set of partially similar DNA sequences like chromosome sequences and DNA sequences of related species can be compressed together. For practical compressors, the compressed size is usually influenced by the compression order of sequences. Fast search algorithms for the optimal compression order are thus developed for multiple sequences compression. Experimental results on artificial and real datasets demonstrate that our proposed multiple sequences compression methods with fast compression order search are able to achieve good compression performance under different levels of similarity in the multiple DNA sequences.

  7. Calmodulin limits pathogenic Na+ channel persistent current

    PubMed Central

    Yan, Haidun; Wang, Chaojian; Marx, Steven O.

    2017-01-01

    Increased “persistent” current, caused by delayed inactivation, through voltage-gated Na+ (NaV) channels leads to cardiac arrhythmias or epilepsy. The underlying molecular contributors to these inactivation defects are poorly understood. Here, we show that calmodulin (CaM) binding to multiple sites within NaV channel intracellular C-terminal domains (CTDs) limits persistent Na+ current and accelerates inactivation across the NaV family. Arrhythmia or epilepsy mutations located in NaV1.5 or NaV1.2 channel CTDs, respectively, reduce CaM binding either directly or by interfering with CTD–CTD interchannel interactions. Boosting the availability of CaM, thus shifting its binding equilibrium, restores wild-type (WT)–like inactivation in mutant NaV1.5 and NaV1.2 channels and likewise diminishes the comparatively large persistent Na+ current through WT NaV1.6, whose CTD displays relatively low CaM affinity. In cerebellar Purkinje neurons, in which NaV1.6 promotes a large physiological persistent Na+ current, increased CaM diminishes the persistent Na+ current, suggesting that the endogenous, comparatively weak affinity of NaV1.6 for apoCaM is important for physiological persistent current. PMID:28087622

  8. High Throughput Sequencing: An Overview of Sequencing Chemistry.

    PubMed

    Ambardar, Sheetal; Gupta, Rikita; Trakroo, Deepika; Lal, Rup; Vakhlu, Jyoti

    2016-12-01

    In the present century sequencing is to the DNA science, what gel electrophoresis was to it in the last century. From 1977 to 2016 three generation of the sequencing technologies of various types have been developed. Second and third generation sequencing technologies referred commonly to as next generation sequencing technology, has evolved significantly with increase in sequencing speed, decrease in sequencing cost, since its inception in 2004. GS FLX by 454 Life Sciences/Roche diagnostics, Genome Analyzer, HiSeq, MiSeq and NextSeq by Illumina, Inc., SOLiD by ABI, Ion Torrent by Life Technologies are various type of the sequencing platforms available for second generation sequencing. The platforms available for the third generation sequencing are Helicos™ Genetic Analysis System by SeqLL, LLC, SMRT Sequencing by Pacific Biosciences, Nanopore sequencing by Oxford Nanopore's, Complete Genomics by Beijing Genomics Institute and GnuBIO by BioRad, to name few. The present article is an overview of the principle and the sequencing chemistry of these high throughput sequencing technologies along with brief comparison of various types of sequencing platforms available.

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

    PubMed Central

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

    2009-01-01

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

  10. Sequencing of aromatase inhibitors

    PubMed Central

    Bertelli, G

    2005-01-01

    Since the development of the third-generation aromatase inhibitors (AIs), anastrozole, letrozole and exemestane, these agents have been the subject of intensive research to determine their optimal use in advanced breast cancer. Not only have they replaced progestins in second-line therapy and challenged the role of tamoxifen in first-line, but there is also evidence for a lack of cross-resistance between the steroidal and nonsteroidal AIs, meaning that they may be used in sequence to obtain prolonged clinical benefit. Many questions remain, however, as to the best sequence of the two types of AIs and of the other available agents, including tamoxifen and fulvestrant, in different patient groups. PMID:16100523

  11. 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.

  12. 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

  13. 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.

  14. The Fermi blazar sequence

    NASA Astrophysics Data System (ADS)

    Ghisellini, G.; Righi, C.; Costamante, L.; Tavecchio, F.

    2017-07-01

    We revisit the blazar sequence exploiting the complete, flux-limited sample of blazars with known redshift detected by the Fermi satellite after 4 yr of operations (the 3LAC sample). We divide the sources into γ-ray luminosity bins, collect all the archival data for all blazars, and construct their spectral energy distribution (SED). We describe the average SED of blazars in the same luminosity bin through a simple phenomenological function consisting of two broken power laws connecting with a power law describing the radio emission. We do that separately for BL Lacs and for flat spectrum radio quasars (FSRQs) and also for all blazars together. The main results are: (i) FSRQs display approximately the same SED as the luminosity increases, but the relative importance of the high-energy peak increases; (ii) as a consequence, the X-ray spectra of FSRQs become harder for larger luminosities; (iii) BL Lacs indeed form a sequence: they become redder (i.e. smaller peak frequencies) with increasing luminosities, with a softer γ-ray slope and a larger dominance of the high-energy peak; (iv) for all blazars (BL Lacs+FSRQs), these properties become more prominent, as the highest luminosity bin is populated mostly by FSRQs and the lowest luminosity bin mostly by BL Lacs. This agrees with the original blazar sequence, although BL Lacs never have an average γ-ray slope as hard as found in the original sequence. (v) At high luminosities, a large fraction of FSRQs show signs of thermal emission from the accretion disc, contributing to the optical-UV (ultraviolet).

  15. Sequencing BPS spectra

    DOE PAGES

    Gukov, Sergei; Nawata, Satoshi; Saberi, Ingmar; ...

    2016-03-02

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

  16. Sequencing BPS spectra

    SciTech Connect

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

    2016-03-02

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

  17. 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.

  18. The Galaxy End Sequence

    NASA Astrophysics Data System (ADS)

    Eales, Stephen; de Vis, Pieter; Smith, Matthew W. L.; Appah, Kiran; Ciesla, Laure; Duffield, Chris; Schofield, Simon

    2017-03-01

    A common assumption is that galaxies fall in two distinct regions of a plot of specific star formation rate (SSFR) versus galaxy stellar mass: a star-forming galaxy main sequence (GMS) and a separate region of 'passive' or 'red and dead galaxies'. Starting from a volume-limited sample of nearby galaxies designed to contain most of the stellar mass in this volume, and thus representing the end-point of ≃12 billion years of galaxy evolution, we investigate the distribution of galaxies in this diagram today. We show that galaxies follow a strongly curved extended GMS with a steep negative slope at high galaxy stellar masses. There is a gradual change in the morphologies of the galaxies along this distribution, but there is no clear break between early-type and late-type galaxies. Examining the other evidence that there are two distinct populations, we argue that the 'red sequence' is the result of the colours of galaxies changing very little below a critical value of the SSFR, rather than implying a distinct population of galaxies. Herschel observations, which show at least half of early-type galaxies contain a cool interstellar medium, also imply continuity between early-type and late-type galaxies. This picture of a unitary population of galaxies requires more gradual evolutionary processes than the rapid quenching process needed to explain two distinct populations. We challenge theorists to predict quantitatively the properties of this 'Galaxy End Sequence'.

  19. A simplified Sanger sequencing method for full genome sequencing of multiple subtypes of human influenza A viruses.

    PubMed

    Deng, Yi-Mo; Spirason, Natalie; Iannello, Pina; Jelley, Lauren; Lau, Hilda; Barr, Ian G

    2015-07-01

    Full genome sequencing of influenza A viruses (IAV), including those that arise from annual influenza epidemics, is undertaken to determine if reassorting has occurred or if other pathogenic traits are present. Traditionally IAV sequencing has been biased toward the major surface glycoproteins haemagglutinin and neuraminidase, while the internal genes are often ignored. Despite the development of next generation sequencing (NGS), many laboratories are still reliant on conventional Sanger sequencing to sequence IAV. To develop a minimal and robust set of primers for Sanger sequencing of the full genome of IAV currently circulating in humans. A set of 13 primer pairs was designed that enabled amplification of the six internal genes of multiple human IAV subtypes including the recent avian influenza A(H7N9) virus from China. Specific primers were designed to amplify the HA and NA genes of each IAV subtype of interest. Each of the primers also incorporated a binding site at its 5'-end for either a forward or reverse M13 primer, such that only two M13 primers were required for all subsequent sequencing reactions. This minimal set of primers was suitable for sequencing the six internal genes of all currently circulating human seasonal influenza A subtypes as well as the avian A(H7N9) viruses that have infected humans in China. This streamlined Sanger sequencing protocol could be used to generate full genome sequence data more rapidly and easily than existing influenza genome sequencing protocols. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

  20. Astrocytes generate Na+-mediated metabolic waves.

    PubMed

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

    2004-10-12

    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.

  1. 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

  2. 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

  3. 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.

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

    DOE PAGES

    You, Ya; Yu, Xi -Qian; Yin, Ya -Xia; ...

    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

  5. Dynamic Sequence Assignment.

    DTIC Science & Technology

    1983-12-01

    represented by a proba- bility of existence anymore; it either exists or doesn’t. Thus, S=(NA1, NAq, IDl’ .T, Tn (3-9) here 1 - if object X exists SX 0...a a a a CDP CNI.I- 5 c.4. too -A9 - . - i DphFrtDnmcPormn lo~h .-. -II S.S. INTRODUCTION In this Appendix, we present a new dynamic programming...max J f (x ix;yjs Si sx . + y - R 1- J-k (P) XitYjCI+ - 10,1,2.... SCi l ... ,sl Ju 4where f has the following properties: :(a) f (O;Yjtics) 0 for all yE

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

    PubMed

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

    2015-12-15

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

  7. Sequence Polishing Library (SPL) v10.0

    SciTech Connect

    Oberortner, Ernst

    2016-06-03

    The Sequence Polishing Library (SPL) is a suite of software tools in order to automate "Design for Synthesis and Assembly" workflows. Specifically: The SPL "Converter" tool converts files among the following sequence data exchange formats: CSV, FASTA, GenBank, and Synthetic Biology Open Language (SBOL); The SPL "Juggler" tool optimizes the codon usages of DNA coding sequences according to an optimization strategy, a user-specific codon usage table and genetic code. In addition, the SPL "Juggler" can translate amino acid sequences into DNA sequences.:The SPL "Polisher" verifies NA sequences against DNA synthesis constraints, such as GC content, repeating k-mers, and restriction sites. In case of violations, the "Polisher" reports the violations in a comprehensive manner. The "Polisher" tool can also modify the violating regions according to an optimization strategy, a user-specific codon usage table and genetic code;The SPL "Partitioner" decomposes large DNA sequences into smaller building blocks with partial overlaps that enable an efficient assembly. The "Partitioner" enables the user to configure the characteristics of the overlaps, which are mostly determined by the utilized assembly protocol, such as length, GC content, or melting temperature.

  8. 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

  9. Plant DNA sequencing for phylogenetic analyses: from plants to sequences.

    PubMed

    Neves, Susana S; Forrest, Laura L

    2011-01-01

    DNA sequences are important sources of data for phylogenetic analysis. Nowadays, DNA sequencing is a routine technique in molecular biology laboratories. However, there are specific questions associated with project design and sequencing of plant samples for phylogenetic analysis, which may not be familiar to researchers starting in the field. This chapter gives an overview of methods and protocols involved in the sequencing of plant samples, including general recommendations on the selection of species/taxa and DNA regions to be sequenced, and field collection of plant samples. Protocols of plant sample preparation, DNA extraction, PCR and cloning, which are critical to the success of molecular phylogenetic projects, are described in detail. Common problems of sequencing (using the Sanger method) are also addressed. Possible applications of second-generation sequencing techniques in plant phylogenetics are briefly discussed. Finally, orientation on the preparation of sequence data for phylogenetic analyses and submission to public databases is also given.

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

    SciTech Connect

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

    1987-01-01

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

  11. 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

  12. A vision for ubiquitous sequencing.

    PubMed

    Erlich, Yaniv

    2015-10-01

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

  13. 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

  14. 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

  15. 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.

  16. 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.

  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. Na+ Tolerance and Na+ Transport in Higher Plants

    PubMed Central

    TESTER, MARK; DAVENPORT, ROMOLA

    2003-01-01

    Tolerance to high soil [Na+] involves processes in many different parts of the plant, and is manifested in a wide range of specializations at disparate levels of organization, such as gross morphology, membrane transport, biochemistry and gene transcription. Multiple adaptations to high [Na+] operate concurrently within a particular plant, and mechanisms of tolerance show large taxonomic variation. These mechanisms can occur in all cells within the plant, or can occur in specific cell types, reflecting adaptations at two major levels of organization: those that confer tolerance to individual cells, and those that contribute to tolerance not of cells per se, but of the whole plant. Salt‐tolerant cells can contribute to salt tolerance of plants; but we suggest that equally important in a wide range of conditions are processes involving the management of Na+ movements within the plant. These require specific cell types in specific locations within the plant catalysing transport in a coordinated manner. For further understanding of whole plant tolerance, we require more knowledge of cell‐specific transport processes and the consequences of manipulation of transporters and signalling elements in specific cell types. PMID:12646496

  19. 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.

  20. 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

  1. Spaces of Ideal Convergent Sequences

    PubMed Central

    Mursaleen, M.; Sharma, Sunil K.

    2014-01-01

    In the present paper, we introduce some sequence spaces using ideal convergence and Musielak-Orlicz function ℳ = (Mk). We also examine some topological properties of the resulting sequence spaces. PMID:24592143

  2. 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.

  3. 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

  4. 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.

  5. Molecular phylogenetics before sequences

    PubMed Central

    Ragan, Mark A; Bernard, Guillaume; Chan, Cheong Xin

    2014-01-01

    From 1971 to 1985, Carl Woese and colleagues generated oligonucleotide catalogs of 16S/18S rRNAs from more than 400 organisms. Using these incomplete and imperfect data, Carl and his colleagues developed unprecedented insights into the structure, function, and evolution of the large RNA components of the translational apparatus. They recognized a third domain of life, revealed the phylogenetic backbone of bacteria (and its limitations), delineated taxa, and explored the tempo and mode of microbial evolution. For these discoveries to have stood the test of time, oligonucleotide catalogs must carry significant phylogenetic signal; they thus bear re-examination in view of the current interest in alignment-free phylogenetics based on k-mers. Here we consider the aims, successes, and limitations of this early phase of molecular phylogenetics. We computationally generate oligonucleotide sets (e-catalogs) from 16S/18S rRNA sequences, calculate pairwise distances between them based on D2 statistics, compute distance trees, and compare their performance against alignment-based and k-mer trees. Although the catalogs themselves were superseded by full-length sequences, this stage in the development of computational molecular biology remains instructive for us today. PMID:24572375

  6. Towards Sequencing Cotton (Gossypium) Genomes

    USDA-ARS?s Scientific Manuscript database

    Despite rapidly decreasing costs and innovative technologies, sequencing of angiosperm genomes is not yet undertaken lightly. Generating larger amounts of sequence data more quickly does not address the difficulties of sequencing and assembling complex genomes de novo. The cotton genomes represent a...

  7. 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…

  8. 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).

  9. 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.

  10. 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

  11. Stepping stones in DNA sequencing

    PubMed Central

    Stranneheim, Henrik; Lundeberg, Joakim

    2012-01-01

    In recent years there have been tremendous advances in our ability to rapidly and cost-effectively sequence DNA. This has revolutionized the fields of genetics and biology, leading to a deeper understanding of the molecular events in life processes. The rapid technological advances have enormously expanded sequencing opportunities and applications, but also imposed strains and challenges on steps prior to sequencing and in the downstream process of handling and analysis of these massive amounts of sequence data. Traditionally, sequencing has been limited to small DNA fragments of approximately one thousand bases (derived from the organism's genome) due to issues in maintaining a high sequence quality and accuracy for longer read lengths. Although many technological breakthroughs have been made, currently the commercially available massively parallel sequencing methods have not been able to resolve this issue. However, recent announcements in nanopore sequencing hold the promise of removing this read-length limitation, enabling sequencing of larger intact DNA fragments. The ability to sequence longer intact DNA with high accuracy is a major stepping stone towards greatly simplifying the downstream analysis and increasing the power of sequencing compared to today. This review covers some of the technical advances in sequencing that have opened up new frontiers in genomics. PMID:22887891

  12. 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.

  13. Structure and Function of Na+-Symporters with Inverted Repeats

    PubMed Central

    Abramson, Jeff; Wright, Ernest M.

    2009-01-01

    Summary Symporters are membrane proteins that couple energy stored in electrochemical potential gradients to drive the cotransport of molecules and ions into cells. Traditionally, proteins are classified into gene families based on sequence homology and functional properties, e.g. the sodium glucose (SLC5 or Sodium Solute Symporter Family, SSS or SSF) and GABA (SLC6 or Neurotransmitter Sodium Symporter Family, NSS or SNF) symporter families [1-4]. Recently, it has been established that four Na+-symporter proteins with unrelated sequences have a common structural core containing an inverted repeat of 5 transmembrane (TM) helices [5-8]. Analysis of these four structures reveals that they reside in different conformations along the transport cycle providing atomic insight into the mechanism of sodium solute cotransport. PMID:19631523

  14. In vivo sodium (23Na) imaging of the human kidneys at 7 T: preliminary results.

    PubMed

    Haneder, Stefan; Juras, Vladimir; Michaely, Henrik J; Deligianni, Xeni; Bieri, Oliver; Schoenberg, Stefan O; Trattnig, Siegfried; Zbýň, Štefan

    2014-02-01

    To evaluate the feasibility of in vivo (23)Na imaging of the corticomedullary (23)Na gradient and to measure (23)Na transverse relaxation times (T2*) in human kidneys. In this prospective, IRB-approved study, eight healthy volunteers (4 female, 4 male; mean age 29.4 ± 3.6 years) were examined on a 7-T whole-body MR system using a (23)Na-only spine-array coil. For morphological (23)Na-MRI, a 3D gradient echo (GRE) sequence with a variable echo time scheme (vTE) was used. T2* times were calculated using a multiecho 3D vTE-GRE approach. (23)Na signal-to-noise ratios (SNR) were given on a pixel-by-pixel basis for a 20-mm section from the cortex in the direction of the medulla. T2* maps were calculated by fitting the (23)Na signal decay monoexponentially on a pixel-by-pixel basis, using least squares fit. Mean corticomedullary (23)Na-SNR increased from the cortex (32.2 ± 5.6) towards the medulla (85.7 ± 16.0). The SNR increase ranged interindividually from 57.2% to 66.3%. Mean (23)Na-T2* relaxation times differed statistically significantly (P < 0.001) between the cortex (17.9 ± 0.8 ms) and medulla (20.6 ± 1.0 ms). The aim of this study was to evaluate the feasibility of in vivo (23)Na MRI of the corticomedullary (23)Na gradient and to measure the (23)Na T2* relaxation times of human kidneys at 7 T. • High field MR offers new insights into renal anatomy and physiology. • (23) Na MRI of healthy human kidneys is feasible at ultra-high field. • Renal (23) Na concentration increases from the cortex in the medullary pyramid direction. • In vivo measurements of renal (23) Na-T2* times are demonstrated at 7.0 T.

  15. RIKEN integrated sequence analysis (RISA) system--384-format sequencing pipeline with 384 multicapillary sequencer.

    PubMed

    Shibata, K; Itoh, M; Aizawa, K; Nagaoka, S; Sasaki, N; Carninci, P; Konno, H; Akiyama, J; Nishi, K; Kitsunai, T; Tashiro, H; Itoh, M; Sumi, N; Ishii, Y; Nakamura, S; Hazama, M; Nishine, T; Harada, A; Yamamoto, R; Matsumoto, H; Sakaguchi, S; Ikegami, T; Kashiwagi, K; Fujiwake, S; Inoue, K; Togawa, Y

    2000-11-01

    The RIKEN high-throughput 384-format sequencing pipeline (RISA system) including a 384-multicapillary sequencer (the so-called RISA sequencer) was developed for the RIKEN mouse encyclopedia project. The RISA system consists of colony picking, template preparation, sequencing reaction, and the sequencing process. A novel high-throughput 384-format capillary sequencer system (RISA sequencer system) was developed for the sequencing process. This system consists of a 384-multicapillary auto sequencer (RISA sequencer), a 384-multicapillary array assembler (CAS), and a 384-multicapillary casting device. The RISA sequencer can simultaneously analyze 384 independent sequencing products. The optical system is a scanning system chosen after careful comparison with an image detection system for the simultaneous detection of the 384-capillary array. This scanning system can be used with any fluorescent-labeled sequencing reaction (chain termination reaction), including transcriptional sequencing based on RNA polymerase, which was originally developed by us, and cycle sequencing based on thermostable DNA polymerase. For long-read sequencing, 380 out of 384 sequences (99.2%) were successfully analyzed and the average read length, with more than 99% accuracy, was 654.4 bp. A single RISA sequencer can analyze 216 kb with >99% accuracy in 2.7 h (90 kb/h). For short-read sequencing to cluster the 3' end and 5' end sequencing by reading 350 bp, 384 samples can be analyzed in 1.5 h. We have also developed a RISA inoculator, RISA filtrator and densitometer, RISA plasmid preparator which can handle throughput of 40,000 samples in 17.5 h, and a high-throughput RISA thermal cycler which has four 384-well sites. The combination of these technologies allowed us to construct the RISA system consisting of 16 RISA sequencers, which can process 50,000 DNA samples per day. One haploid genome shotgun sequence of a higher organism, such as human, mouse, rat, domestic animals, and plants, can be

  16. RIKEN Integrated Sequence Analysis (RISA) System—384-Format Sequencing Pipeline with 384 Multicapillary Sequencer

    PubMed Central

    Shibata, Kazuhiro; Itoh, Masayoshi; Aizawa, Katsunori; Nagaoka, Sumiharu; Sasaki, Nobuya; Carninci, Piero; Konno, Hideaki; Akiyama, Junichi; Nishi, Katsuo; Kitsunai, Tokuji; Tashiro, Hideo; Itoh, Mari; Sumi, Noriko; Ishii, Yoshiyuki; Nakamura, Shin; Hazama, Makoto; Nishine, Tsutomu; Harada, Akira; Yamamoto, Rintaro; Matsumoto, Hiroyuki; Sakaguchi, Sumito; Ikegami, Takashi; Kashiwagi, Katsuya; Fujiwake, Syuji; Inoue, Kouji; Togawa, Yoshiyuki; Izawa, Masaki; Ohara, Eiji; Watahiki, Masanori; Yoneda, Yuko; Ishikawa, Tomokazu; Ozawa, Kaori; Tanaka, Takumi; Matsuura, Shuji; Kawai, Jun; Okazaki, Yasushi; Muramatsu, Masami; Inoue, Yorinao; Kira, Akira; Hayashizaki, Yoshihide

    2000-01-01

    The RIKEN high-throughput 384-format sequencing pipeline (RISA system) including a 384-multicapillary sequencer (the so-called RISA sequencer) was developed for the RIKEN mouse encyclopedia project. The RISA system consists of colony picking, template preparation, sequencing reaction, and the sequencing process. A novel high-throughput 384-format capillary sequencer system (RISA sequencer system) was developed for the sequencing process. This system consists of a 384-multicapillary auto sequencer (RISA sequencer), a 384-multicapillary array assembler (CAS), and a 384-multicapillary casting device. The RISA sequencer can simultaneously analyze 384 independent sequencing products. The optical system is a scanning system chosen after careful comparison with an image detection system for the simultaneous detection of the 384-capillary array. This scanning system can be used with any fluorescent-labeled sequencing reaction (chain termination reaction), including transcriptional sequencing based on RNA polymerase, which was originally developed by us, and cycle sequencing based on thermostable DNA polymerase. For long-read sequencing, 380 out of 384 sequences (99.2%) were successfully analyzed and the average read length, with more than 99% accuracy, was 654.4 bp. A single RISA sequencer can analyze 216 kb with >99% accuracy in 2.7 h (90 kb/h). For short-read sequencing to cluster the 3′ end and 5′ end sequencing by reading 350 bp, 384 samples can be analyzed in 1.5 h. We have also developed a RISA inoculator, RISA filtrator and densitometer, RISA plasmid preparator which can handle throughput of 40,000 samples in 17.5 h, and a high-throughput RISA thermal cycler which has four 384-well sites. The combination of these technologies allowed us to construct the RISA system consisting of 16 RISA sequencers, which can process 50,000 DNA samples per day. One haploid genome shotgun sequence of a higher organism, such as human, mouse, rat, domestic animals, and plants, can

  17. Sequence dependent conformations of glycidyl methacrylate/butyl methacrylate copolymers in the gas phase

    NASA Astrophysics Data System (ADS)

    Baker, Erin Shammel; Gidden, Jennifer; Simonsick, William J.; Grady, Michael C.; Bowers, Michael T.

    2004-11-01

    Sequence dependent conformations of a series of glycidyl methacrylate/butyl methacrylate (GMA/BMA) copolymers cationized by sodium were analyzed in the gas phase using ion mobility methods. GMA and BMA have the same nominal mass but vary in exact mass by 0.036 Da (CH4 versus O). Matrix assisted laser desorption/ionization (MALDI) was used to form Na+(GMA/BMA) copolymer ions and their collision cross-sections were measured in helium using ion mobility methods. The copolymer sequences from Na+(GMA/BMA)3 to Na+(GMA/BMA)5 (i.e. for the trimer to the pentamer) were studied. Analysis by molecular mechanics/dynamics indicates that each copolymer (regardless of sequence) forms a ring around the sodium ions due to Na+/oxygen electrostatic interactions. However, the structures vary in size, since the epoxy oxygen atoms in the glycidyl groups are attracted to the sodium ions while the carbon-composed butyl groups are not. This allows copolymers with more GMA segments to fold tighter (more spherically) around the sodium ion and have smaller cross-sections than copolymers with a larger amount of BMA segments in the sequence. Due to this cross-sectional difference, the GMA/BMA sequence compositions of the trimer and tetramer could be quantified.

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

    PubMed Central

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

    2012-01-01

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

  19. Event sequence detector

    NASA Technical Reports Server (NTRS)

    Hanna, M. F. (Inventor)

    1973-01-01

    An event sequence detector is described with input units, each associated with a row of bistable elements arranged in an array of rows and columns. The detector also includes a shift register which is responsive to clock pulses from any of the units to sequentially provide signals on its output lines each of which is connected to the bistable elements in a corresponding column. When the event-indicating signal is received by an input unit it provides a clock pulse to the shift register to provide the signal on one of its output lines. The input unit also enables all its bistable elements so that the particular element in the column supplied with the signal from the register is driven to an event-indicating state.

  20. 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.

  1. 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.

  2. 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.

  3. Recent Advances in Sequencing Technology

    NASA Astrophysics Data System (ADS)

    Thompson, John F.; Ozsolak, Fatih; Milos, Patrice M.

    As we celebrate the tenth anniversary of the sequencing of the first human genome, we recognize the remarkable technological innovation that now provides the ability to resequence thousands of human genomes a year. While the current methods of choice utilize amplification-based methods and the corresponding challenges of sample preparation that accompany these methods, new technologies that do not require amplification have emerged. Single-molecule sequencing methods have the potential to dramatically shape the next 10 years of technological progress driven by the continuing interest of driving the cost of whole genome sequencing below the 1000 cost threshold. Yet while whole genome sequencing remains of interest, sequencing technologies also enable new approaches for genome exploration and experimentation including direct RNA sequencing, complete transcript sequencing and real time methods for both nucleic acid and enzyme kinetics.

  4. The evolution of nanopore sequencing

    PubMed Central

    Wang, Yue; Yang, Qiuping; Wang, Zhimin

    2014-01-01

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

  5. 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

  6. 3T renal (23)Na-MRI: effects of desmopressin in patients with central diabetes insipidus.

    PubMed

    Haneder, Stefan; Michaely, Henrik J; Konstandin, Simon; Schad, Lothar R; Morelli, John N; Krämer, Bernhard K; Schoenberg, Stefan O; Lammert, Alexander

    2014-02-01

    The purpose of this prospective study was to assess physiologic changes in the renal corticomedullary (23)Na-concentration ([(23)Na]) gradient with (23)Na-MRI at 3.0T in patients with central diabetes insipidus (CDI) before and after intranasal administration of 20 μg desmopressin (DDAVP). Four patients with CDI (all male, mean age 60.2 years) were included in this IRB-approved study. For (23)Na-imaging, a 3D density adapted, radial GRE-sequence (TE = 0.55 ms; TR = 120 ms; projections = 8,000; spatial resolution = 5 × 5 × 5 mm(3)) was used in combination with a dedicated (23)Na-coil and reference phantoms. The corticomedullary [(23)Na] gradient (in mmol/L/mm) was calculated pixel-by-pixel along a linear region-of-interest (ROI) spanning from the renal cortex in the direction of the medulla. Mean ± SDs of [(23)Na] were calculated for each patient as well as for the entire group. Mean [(23)Na] increased along the corticomedullary gradient from the cortex (pre-DDAVP 38.0 ± 6.3 mmol/L vs. post-DDAVP 30.7 ± 3.5 mmol/L) to the medulla (pre-DDAVP 71.6 ± 14.8 mmol/L vs. post-DDAVP 59.7 ± 10.8 mmol/L). The overall mean decrease of [(23)Na] after DDAVP administration was 17.1 ± 1.1 %. (23)Na-MRI with state-of-the-art techniques at 3T depicts the physiologic renal response to the administration of desmopressin in patients with central diabetes insipidus.

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

    PubMed Central

    2013-01-01

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

  8. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  10. Conversion and Distribution of Lead and Tin in NaOH-NaNO3 Fusion Process

    NASA Astrophysics Data System (ADS)

    Liu, Jingxin; Guo, Xueyi

    2016-12-01

    Oxidizing alkali fusion process has been studied to extract amphoteric metals. Transformation and distribution behaviors of typical amphoteric metals Pb and Sn in the NaOH-NaNO3 fusion process are systemically studied by theoretical analysis and experimental verification done in this work. Functions of NaOH and NaNO3 in the fusion process were also investigated. The results show the fused products, Na2PbO3 and Na2SnO3, are captured in the flux, and Na2PbO4 is speculated to reduce to Pb(II) in the following leaching process. By measuring solubility data of NaOH-Na2SnO3-PbO-H2O system, a strategy of crystallization is proposed to separate Sn with Pb in concentrated alkaline solution, and slice Na2Sn(OH)6 is obtained as a product.

  11. Conversion and Distribution of Lead and Tin in NaOH-NaNO3 Fusion Process

    NASA Astrophysics Data System (ADS)

    Liu, Jingxin; Guo, Xueyi

    2017-04-01

    Oxidizing alkali fusion process has been studied to extract amphoteric metals. Transformation and distribution behaviors of typical amphoteric metals Pb and Sn in the NaOH-NaNO3 fusion process are systemically studied by theoretical analysis and experimental verification done in this work. Functions of NaOH and NaNO3 in the fusion process were also investigated. The results show the fused products, Na2PbO3 and Na2SnO3, are captured in the flux, and Na2PbO4 is speculated to reduce to Pb(II) in the following leaching process. By measuring solubility data of NaOH-Na2SnO3-PbO-H2O system, a strategy of crystallization is proposed to separate Sn with Pb in concentrated alkaline solution, and slice Na2Sn(OH)6 is obtained as a product.

  12. Molecular cloning of rat brain Na,K-ATPase alpha-subunit cDNA.

    PubMed Central

    Schneider, J W; Mercer, R W; Caplan, M; Emanuel, J R; Sweadner, K J; Benz, E J; Levenson, R

    1985-01-01

    We have isolated a cDNA clone for the rat brain Na,K-ATPase alpha subunit. A lambda gt11 cDNA expression library constructed from mRNA of 1- and 2-week-old rat brains was screened with an antibody reactive with rat brain Na,K-ATPase. A positive phage clone, lambda rb5, containing a 1200-base-pair cDNA insert expressed a beta-galactosidase-cDNA fusion protein that was reactive by immunoblotting with the Na,K-ATPase antibody. This fusion protein was also reactive in ELISA with a monoclonal antibody directed against the alpha subunit of the Na,K-ATPase. A 27S mRNA species exhibiting sequence hybridization to the cDNA insert of lambda rb5 was identified in rat brain, kidney, and liver, as well as in dog kidney. This 27S mRNA exhibited a tissue-specific pattern of abundance consistent with the relative abundance of Na,K-ATPase polypeptides in vivo: kidney greater than brain greater than liver. In a ouabain-resistant HeLa cell line, C+, which contains minute chromosomes and at least a 10-fold greater number of sodium pumps than parental HeLa cells, DNA sequences complementary to lambda rb5 cDNA were amplified approximately 40-fold. Analysis of the lambda rb5 cDNA sequence demonstrated a perfect nucleotide sequence match between a portion of the cDNA and the amino acid sequence of the Na,K-ATPase alpha-subunit fluorescein isothiocyanate binding site. Taken together, the data presented here demonstrate that the lambda rb5 cDNA clone is a portion of the gene coding for the rat brain Na,K-ATPase alpha subunit. The ATPase gene appears to be present in one or very few copies in the rat and human genomes and to be transcriptionally regulated in different rat tissues. In a ouabain-resistant human cell line, on the other hand, ouabain resistance appears to involve an increase in the number of gene copies coding for the Na,K-ATPase. Images PMID:2994074

  13. 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.

  14. A long-life Na-air battery based on a soluble NaI catalyst.

    PubMed

    Yin, Wen-Wen; Shadike, Zulipiya; Yang, Yin; Ding, Fei; Sang, Lin; Li, Hong; Fu, Zheng-Wen

    2015-02-11

    A Na-air battery with NaI dissolved in a typical organic electrolyte could run up to 150 cycles with a capacity limit of 1000 mA h g(-1). The low charge voltage plateau of 3.2 V vs. Na(+)/Na in a Na-air battery should mainly be attributed to the oxidation reaction of active iodine anions.

  15. Silicene for Na-ion battery applications

    NASA Astrophysics Data System (ADS)

    Zhu, Jiajie; Schwingenschlögl, Udo

    2016-09-01

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

  16. 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

  17. Large-Scale Sequence Comparison.

    PubMed

    Lal, Devi; Verma, Mansi

    2017-01-01

    There are millions of sequences deposited in genomic databases, and it is an important task to categorize them according to their structural and functional roles. Sequence comparison is a prerequisite for proper categorization of both DNA and protein sequences, and helps in assigning a putative or hypothetical structure and function to a given sequence. There are various methods available for comparing sequences, alignment being first and foremost for sequences with a small number of base pairs as well as for large-scale genome comparison. Various tools are available for performing pairwise large sequence comparison. The best known tools either perform global alignment or generate local alignments between the two sequences. In this chapter we first provide basic information regarding sequence comparison. This is followed by the description of the PAM and BLOSUM matrices that form the basis of sequence comparison. We also give a practical overview of currently available methods such as BLAST and FASTA, followed by a description and overview of tools available for genome comparison including LAGAN, MumMER, BLASTZ, and AVID.

  18. Explanatory chapter: next generation sequencing.

    PubMed

    Yegnasubramanian, Srinivasan

    2013-01-01

    Technological breakthroughs in sequencing technologies have driven the advancement of molecular biology and molecular genetics research. The advent of high-throughput Sanger sequencing (for information on the method, see Sanger Dideoxy Sequencing of DNA) in the mid- to late-1990s made possible the accelerated completion of the human genome project, which has since revolutionized the pace of discovery in biomedical research. Similarly, the advent of next generation sequencing is poised to revolutionize biomedical research and usher a new era of individualized, rational medicine. The term next generation sequencing refers to technologies that have enabled the massively parallel analysis of DNA sequence facilitated through the convergence of advancements in molecular biology, nucleic acid chemistry and biochemistry, computational biology, and electrical and mechanical engineering. The current next generation sequencing technologies are capable of sequencing tens to hundreds of millions of DNA templates simultaneously and generate >4 gigabases of sequence in a single day. These technologies have largely started to replace high-throughput Sanger sequencing for large-scale genomic projects, and have created significant enthusiasm for the advent of a new era of individualized medicine. Copyright © 2013 Elsevier Inc. All rights reserved.

  19. Kinetic Analysis of H(+)-Na(+) Selectivity in a Light-Driven Na(+)-Pumping Rhodopsin.

    PubMed

    Kato, Yoshitaka; Inoue, Keiichi; Kandori, Hideki

    2015-12-17

    Krokinobacter eikastus rhodopsin 2 (KR2) is a recently identified light-driven Na(+) pump from a marine bacterium. KR2 pumps Na(+) in NaCl solution but pumps H(+) in the absence of Na(+) and Li(+). The Na(+) transport mechanism in KR2 has been extensively studied, whereas understanding of the H(+) transport mechanism is very limited. Here we studied ion uptake mechanisms and H(+)-Na(+) selectivity using flash photolysis. The results show that decay of the blue-shifted M intermediate is dependent on both [Na(+)] and [H(+)], indicating that KR2 competitively uptakes Na(+) or H(+) upon M decay. Comprehensive concentration dependence of Na(+) and H(+) revealed that the rate constant of H(+) uptake (kH) was much larger than that of Na(+) uptake (kNa) with a ratio (kH/kNa) of >10(3). Therefore, KR2 pumps only H(+) when Na(+) and H(+) concentrations are similar. On the contrary, KR2 pumps Na(+) exclusively under physiological conditions in which [Na(+)] is much greater than [H(+)].

  20. 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.

  1. Solid phase sequencing of biopolymers

    SciTech Connect

    Cantor, Charles R.; Hubert, Koster

    2014-06-24

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

  2. Towards single molecule DNA sequencing

    NASA Astrophysics Data System (ADS)

    Liu, Hao

    Single molecule DNA Sequencing technology has been a hot research topic in the recent decades because it holds the promise to sequence a human genome in a fast and affordable way, which will eventually make personalized medicine possible. Single molecule differentiation and DNA translocation control are the two main challenges in all single molecule DNA sequencing methods. In this thesis, I will first introduce DNA sequencing technology development and its application, and then explain the performance and limitation of prior art in detail. Following that, I will show a single molecule DNA base differentiation result obtained in recognition tunneling experiments. Furthermore, I will explain the assembly of a nanofluidic platform for single strand DNA translocation, which holds the promised to be integrated into a single molecule DNA sequencing instrument for DNA translocation control. Taken together, my dissertation research demonstrated the potential of using recognition tunneling techniques to serve as a general readout system for single molecule DNA sequencing application.

  3. Nuclear RNA Isolation and Sequencing.

    PubMed

    Dhaliwal, Navroop K; Mitchell, Jennifer A

    2016-01-01

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

  4. 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.

  5. 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?

  6. Structural effects of 34Na in the 33Na(n ,γ )34Na radiative capture reaction

    NASA Astrophysics Data System (ADS)

    Singh, G.; Shubhchintak, Chatterjee, R.

    2017-06-01

    Background: The path towards the production of r -process seed nuclei follows a course where the neutron rich light and medium mass nuclei play a crucial role. The neutron capture rates for these exotic nuclei could dominate over their α -capture rates, thereby enhancing their abundances at or near the drip line. Sodium isotopes especially should have a strong neutron capture flow to gain abundance at the drip line. In this context, study of 33Na(n ,γ )34Na and 33Na(α ,n )36Al reactions becomes indispensable. Purpose: In this paper, we calculate the radiative neutron capture cross section for the 33Na(n ,γ )34Na reaction involving deformation effects. Subsequently, the rate for this reaction is found and compared with that of the α -capture for the 33Na(α ,n )36Al reaction to determine the possible path flow for the abundances of sodium isotopes. Method: We use the entirely quantum mechanical theory of finite-range distorted-wave Born approximation upgraded to incorporate deformation effects, and calculate the Coulomb dissociation of 34Na as it undergoes elastic breakup on 208Pb when directed at a beam energy of 100 MeV/u. Using the principle of detailed balance to study the reverse photodisintegration reaction, we find the radiative neutron capture cross section with variation in one-neutron binding energy and quadrupole deformation of 34Na. The rate of this 33Na(n ,γ )34Na reaction is then compared with that of the α -capture by 33Na deduced from the Hauser-Feshbach theory. Results: The nonresonant one-neutron radiative capture cross section for 33Na(n ,γ )34Na is calculated and is found to increase with increasing deformation of 34Na. An analytic scrutiny of the capture cross section with neutron separation energy as a parameter is also done at different energy ranges. The calculated reaction rate is compared with the rate of the 33Na(α ,n )36Al reaction, and is found to be significantly higher below a temperature of T9=2 . Conclusion: At the

  7. 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

  8. A reference human genome dataset of the BGISEQ-500 sequencer.

    PubMed

    Huang, Jie; Liang, Xinming; Xuan, Yuankai; Geng, Chunyu; Li, Yuxiang; Lu, Haorong; Qu, Shoufang; Mei, Xianglin; Chen, Hongbo; Yu, Ting; Sun, Nan; Rao, Junhua; Wang, Jiahao; Zhang, Wenwei; Chen, Ying; Liao, Sha; Jiang, Hui; Liu, Xin; Yang, Zhaopeng; Mu, Feng; Gao, Shangxian

    2017-05-01

    BGISEQ-500 is a new desktop sequencer developed by BGI. Using DNA nanoball and combinational probe anchor synthesis developed from Complete Genomics™ sequencing technologies, it generates short reads at a large scale. Here, we present the first human whole-genome sequencing dataset of BGISEQ-500. The dataset was generated by sequencing the widely used cell line HG001 (NA12878) in two sequencing runs of paired-end 50 bp (PE50) and two sequencing runs of paired-end 100 bp (PE100). We also include examples of the raw images from the sequencer for reference. Finally, we identified variations using this dataset, estimated the accuracy of the variations, and compared to that of the variations identified from similar amounts of publicly available HiSeq2500 data. We found similar single nucleotide polymorphism (SNP) detection accuracy for the BGISEQ-500 PE100 data (false positive rate [FPR] = 0.00020%, sensitivity = 96.20%) compared to the PE150 HiSeq2500 data (FPR = 0.00017%, sensitivity = 96.60%) better SNP detection accuracy than the PE50 data (FPR = 0.0006%, sensitivity = 94.15%). But for insertions and deletions (indels), we found lower accuracy for BGISEQ-500 data (FPR = 0.00069% and 0.00067% for PE100 and PE50 respectively, sensitivity = 88.52% and 70.93%) than the HiSeq2500 data (FPR = 0.00032%, sensitivity = 96.28%). Our dataset can serve as the reference dataset, providing basic information not just for future development, but also for all research and applications based on the new sequencing platform.

  9. Nonlinear analysis of biological sequences

    SciTech Connect

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

    1998-11-01

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

  10. 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.

  11. 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.

  12. Direct-Sequence Communication Systems

    DTIC Science & Technology

    2004-03-01

    modulation; CMF = chip-matched filter; SSG = spreading sequence generator. Delay = 0 for QPSK; delay = Tc/2 for OQPSK and MSK...balanced quaternary modulation (de- lay = 0 for QPSK and delay = Tc/2 for OQPSK and MSK); CMF = chip- matched filter; SSG = spreading sequence...with dual quaternary modulation; CMF = chip-matched filter; SSG = spreading sequence generator. Delay = 0 for QPSK; delay = Tc/2 for OQPSK and MSK. 33 N

  13. 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.

  14. Orbital-Maneuver-Sequence Optimization

    DTIC Science & Technology

    1985-12-01

    optimization computer program and applied it to the generation of optimal cog-brbital attack4ianeuver sequences * and to the generation of optimal evasions...maneuver-sequence- optimization computer programs can be improved by a general restructuring and streamlining and the addition of various features. It is...believed that with further development and systematic testing the programs have potential for real-time generation of optimal maneuver sequences in an

  15. Fungal Genome Sequencing and Bioenergy

    SciTech Connect

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

    2008-09-30

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

  16. Intracellular Na and K distribution in Debaryomyces hansenii. Cloning and expression in Saccharomyces cerevisiae of DhNHX1.

    PubMed

    Montiel, Vera; Ramos, José

    2007-01-01

    Debaryomyces hansenii is a salt-tolerant yeast that contains high amounts of internal Na(+). Debaryomyces hansenii kept more sodium than Saccharomyces cerevisiae in both the cytoplasm and vacuole when grown under a variety of NaCl concentrations. These results indicate a higher tolerance of Debaryomyces to high internal Na(+), and, in addition, suggest the existence of a transporter driving Na(+) into the vacuole. Moreover, a gene encoding a Na(+) (K(+))/H(+) antiporter from D. hansenii was cloned and sequenced. The gene, designated DhNHX1, exhibited significant homology with genes of the NHE/NHX family. DhNHX1 expression was induced neither at low pH nor by extracellular NaCl. A mutant of S. cerevisiae lacking its own Na(+) transporters (ena1-4Delta nha1 Delta nhx1 Delta), when transformed with DhNHX1, partially recovered cation tolerance as well as the ability to accumulate Na(+) and K(+) into the vacuole. Our analysis provides evidence that DhNhx1p transports Na(+) (and K(+)) into the vacuole and that it can play an important role in ion homeostasis and salt tolerance.

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

    PubMed Central

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

    2011-01-01

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

  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. 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.

  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. 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.

  2. 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.

  3. 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.

  4. Preferential Amplification of Pathogenic Sequences.

    PubMed

    Ge, Fang; Parker, Jayme; Chul Choi, Sang; Layer, Mark; Ross, Katherine; Jilly, Bernard; Chen, Jack

    2015-06-11

    The application of next generation sequencing (NGS) technology in the diagnosis of human pathogens is hindered by the fact that pathogenic sequences, especially viral, are often scarce in human clinical specimens. This known disproportion leads to the requirement of subsequent deep sequencing and extensive bioinformatics analysis. Here we report a method we called "Preferential Amplification of Pathogenic Sequences (PATHseq)" that can be used to greatly enrich pathogenic sequences. Using a computer program, we developed 8-, 9-, and 10-mer oligonucleotides called "non-human primers" that do not match the most abundant human transcripts, but instead selectively match transcripts of human pathogens. Instead of using random primers in the construction of cDNA libraries, the PATHseq method recruits these short non-human primers, which in turn, preferentially amplifies non-human, presumably pathogenic sequences. Using this method, we were able to enrich pathogenic sequences up to 200-fold in the final sequencing library. This method does not require prior knowledge of the pathogen or assumption of the infection; therefore, it provides a fast and sequence-independent approach for detection and identification of human viruses and other pathogens. The PATHseq method, coupled with NGS technology, can be broadly used in identification of known human pathogens and discovery of new pathogens.

  5. Revisiting the hydration structure of aqueous Na+

    NASA Astrophysics Data System (ADS)

    Galib, M.; Baer, M. D.; Skinner, L. B.; Mundy, C. J.; Huthwelker, T.; Schenter, G. K.; Benmore, C. J.; Govind, N.; Fulton, J. L.

    2017-02-01

    A combination of theory, X-ray diffraction (XRD) and extended x-ray absorption fine structure (EXAFS) are used to probe the hydration structure of aqueous Na+. The high spatial resolution of the XRD measurements corresponds to Qmax = 24 Å-1 while the first-reported Na K-edge EXAFS measurements have a spatial resolution corresponding to 2k = Qmax = 16 Å-1. Both provide an accurate measure of the shape and position of the first peak in the Na-O pair distribution function, gNaO(r). The measured Na-O distances of 2.384 ± 0.003 Å (XRD) and 2.37 ± 0.024 Å (EXAFS) are in excellent agreement. These measurements show a much shorter Na-O distance than generally reported in the experimental literature (Na-Oavg ˜ 2.44 Å) although the current measurements are in agreement with recent neutron diffraction measurements. The measured Na-O coordination number from XRD is 5.5 ± 0.3. The measured structure is compared with both classical and first-principles density functional theory (DFT) simulations. Both of the DFT-based methods, revPBE and BLYP, predict a Na-O distance that is too long by about 0.05 Å with respect to the experimental data (EXAFS and XRD). The inclusion of dispersion interactions (-D3 and -D2) significantly worsens the agreement with experiment by further increasing the Na-O distance by 0.07 Å. In contrast, the use of a classical Na-O Lennard-Jones potential with SPC/E water accurately predicts the Na-O distance as 2.39 Å although the Na-O peak is over-structured with respect to experiment.

  6. Revisiting the hydration structure of aqueous Na().

    PubMed

    Galib, M; Baer, M D; Skinner, L B; Mundy, C J; Huthwelker, T; Schenter, G K; Benmore, C J; Govind, N; Fulton, J L

    2017-02-28

    A combination of theory, X-ray diffraction (XRD) and extended x-ray absorption fine structure (EXAFS) are used to probe the hydration structure of aqueous Na(+). The high spatial resolution of the XRD measurements corresponds to Qmax = 24 Å(-1) while the first-reported Na K-edge EXAFS measurements have a spatial resolution corresponding to 2k = Qmax = 16 Å(-1). Both provide an accurate measure of the shape and position of the first peak in the Na-O pair distribution function, gNaO(r). The measured Na-O distances of 2.384 ± 0.003 Å (XRD) and 2.37 ± 0.024 Å (EXAFS) are in excellent agreement. These measurements show a much shorter Na-O distance than generally reported in the experimental literature (Na-Oavg ∼ 2.44 Å) although the current measurements are in agreement with recent neutron diffraction measurements. The measured Na-O coordination number from XRD is 5.5 ± 0.3. The measured structure is compared with both classical and first-principles density functional theory (DFT) simulations. Both of the DFT-based methods, revPBE and BLYP, predict a Na-O distance that is too long by about 0.05 Å with respect to the experimental data (EXAFS and XRD). The inclusion of dispersion interactions (-D3 and -D2) significantly worsens the agreement with experiment by further increasing the Na-O distance by 0.07 Å. In contrast, the use of a classical Na-O Lennard-Jones potential with SPC/E water accurately predicts the Na-O distance as 2.39 Å although the Na-O peak is over-structured with respect to experiment.

  7. [Detection of an NA gene molecular marker in H7N9 subtype avian influenza viruses by pyrosequencing].

    PubMed

    Zhao, Yong-Gang; Liu, Hua-Lei; Wang, Jing-Jing; Zheng, Dong-Xia; Zhao, Yun-Ling; Ge, Sheng-Qiang; Wang, Zhi-Liang

    2014-07-01

    This study aimed to establish a method for the detection and identification of H7N9 avian influenza viruses based on the NA gene by pyrosequencing. According to the published NA gene sequences of the avian influenza A (H7N9) virus, a 15-nt deletion was found in the NA gene of H7N9 avian influenza viruses. The 15-nt deletion of the NA gene was targeted as the molecular marker for the rapid detection and identification of H7N9 avian influenza viruses by pyrosequencing. Three H7N9 avian influenza virus isolates underwent pyrosequencing using the same assay, and were proven to have the same 15-nt deletion. Pyrosequencing technology based on the NA gene molecular marker can be used to identify H7N9 avian influenza viruses.

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

    NASA Technical Reports Server (NTRS)

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

    1993-01-01

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

  9. Extracellular Na+ inhibits Na+/H+ exchange: cell shrinkage reduces the inhibition.

    PubMed

    Dunham, Philip B; Kelley, Scott J; Logue, Paul J

    2004-08-01

    Na+/H+ exchangers (NHE) are ubiquitous transporters participating in regulation of cell volume and pH. Cell shrinkage, acidification, and growth factors activate NHE by increasing its sensitivity to intracellular H+ concentration. In this study, the kinetics were studied in dog red blood cells of Na+ influx through NHE as a function of external Na+ concentration ([Na+](o)). In cells in isotonic media, [Na+](o) inhibited Na+ influx >40 mM. Osmotic shrinkage activated NHE by reducing this inhibition. In cells in isotonic media + 120 mM sucrose, there was no inhibition, and influx was a hyperbolic function of [Na+](o). The kinetics of Na+-inhibited Na+ influx were analyzed at various extents of osmotic shrinkage. The curves for inhibited Na+ fluxes were sigmoid, indicating more than one Na+ inhibitory site associated with each transporter. Shrinkage significantly increased the Na+ concentration at half-maximal velocity of Na+-inhibited Na+ influx, the mechanism by which shrinkage activates NHE.

  10. Mechanism of epithelial lithium transport. Evidence for basolateral Na:Na and Na:Li exchange

    PubMed Central

    1983-01-01

    Measurement of transmural sodium fluxes across isolated, ouabain- inhibited turtle colon in the presence of a serosal-to-mucosal sodium gradient shows that in the absence of active transport the amiloride- sensitive cellular path contains at least two routes for the transmural movement of sodium and lithium, one a conductive path and the other a nonconductive, cation-exchange mechanism. The latter transport element can exchange lithium for sodium, and the countertransport of these two cations provides a mechanistic basis for the ability of tight epithelia to actively absorb lithium despite the low affinity of the basolateral Na/K-ATPase for this cation. PMID:6644269

  11. 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

  12. 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.

  13. 13C and 23Na NMR studies of Na2C60 and Na6C60 fullerides

    NASA Astrophysics Data System (ADS)

    Rachdi, F.; Hajji, L.; Galtier, M.; Yildirim, T.; Fischer, J. E.; Goze, C.; Mehring, M.

    1997-10-01

    We report on 13C and 23Na NMR measurements on Na2C60 and Na6C60 compounds. The room-temperature 13C NMR spectra of Na2C60 and Na6C60 samples present a narrow isotropic line at 172 and 176 ppm, respectively. The Na6C60 resonance is shifted 20 ppm more down field than the resonances of A6C60 compounds with heavier alkalis, indicating a partial charge transfer to the threefold degenerate t1u level which is totally filled in the latter compounds. The 23Na NMR spectrum of A2C60 shows one line at 73 ppm and the one of A6C60 presents two lines at 73 and 147 ppm. The intensity ratio of the latter lines is about 2:1. According to previously reported x-ray data we attribute the line at 147 ppm to the Na tetramers in the octahedral sites and the line at 73 ppm to the Na cations in the tetrahedral ones which are singly occupied.

  14. Characteristics of NaNO3-Promoted CdO as a Midtemperature CO2 Absorbent.

    PubMed

    Kim, Kang-Yeong; Kwak, Jin-Su; An, Young-In; Oh, Kyung-Ryul; Kwon, Young-Uk

    2017-06-28

    In this study, we explored the reaction system CdO(s) + CO2(g) ⇄ CdCO3(s) as a model system for CO2 capture agent in the intermediate temperature range of 300-400 °C. While pure CdO does not react with CO2 at all up to 500 °C, CdO mixed with an appropriate amount of NaNO3 (optimal molar ratio NaNO3/CdO = 0.14) greatly enhances the conversion of CdO into CdCO3 up to ∼80% (5.68 mmol/g). These NaNO3-promoted CdO absorbents can undergo many cycles of absorption and desorption by temperature swing between 300 and 370 °C under a 100% CO2 condition. Details of how NaNO3 promotes the CO2 absorption of CdO have been delineated through various techniques using thermogravimetry, coupled with X-ray diffraction and electron microscopy. On the basis of the observed data, we propose a mechanism of CO2 absorption and desorption of NaNO3-promoted CdO. The absorption proceeds through a sequence of events of CO2 adsorption on the CdO surface covered by NaNO3, dissolution of so-formed CdCO3, and precipitation of CdCO3 particles in the NaNO3 medium. The desorption occurs through the decomposition of CdCO3 in the dissolved state in the NaNO3 medium where CdO nanoparticles are formed dispersed in the NaNO3 medium. The CdO nanoparticles are aggregated into micrometer-large particles with smooth surfaces and regular shapes.

  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.

  17. 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

  18. Real-Time PCR Assay for a Unique Chromosomal Sequence of Bacillus anthracis

    DTIC Science & Technology

    2004-12-01

    33672 Bacillus megaterium ................................................................ NA...Assay for a Unique Chromosomal Sequence of Bacillus anthracis Elizabeth Bode,1 William Hurtle,2† and David Norwood1* United States Army Medical...modification 4 June 2004/Accepted 9 August 2004 Real-time PCR has become an important method for the rapid identification of Bacillus anthracis since the

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

    USDA-ARS?s Scientific Manuscript database

    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...

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

    PubMed

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

    2016-01-01

    The Na(+)/K(+) ATPase is a ubiquitous pump coordinating the transport of Na(+) and K(+) across the membrane of cells and its role is fundamental to cellular functions. It is heteromer in eukaryotes including two or three subunits (α, β and γ which is specific to the vertebrates). The catalytic functions of the enzyme have been attributed to the α subunit. Several complete α protein sequences are available, but only few gene structures were characterized. We identified the genomic sequences coding the α-subunit of the Na(+)/K(+) ATPase, from the whole-genome shotgun contigs (WGS), NCBI Genomes (chromosome), Genomic Survey Sequences (GSS) and High Throughput Genomic Sequences (HTGS) databases across distinct phyla. One copy of the α subunit gene was found in Annelida, Arthropoda, Cnidaria, Echinodermata, Hemichordata, Mollusca, Placozoa, Porifera, Platyhelminthes, Urochordata, but the nematodes seem to possess 2 to 4 copies. The number of introns varied from 0 (Platyhelminthes) to 26 (Porifera); and their localization and length are also highly variable. Molecular phylogenies (Maximum Likelihood and Maximum Parsimony methods) showed some clusters constituted by (Chordata/(Echinodermata/Hemichordata)) or (Plathelminthes/(Annelida/Mollusca)) and a basal position for Porifera. These structural analyses increase our knowledge about the evolutionary events of the α subunit genes in the invertebrates. Copyright © 2016 Elsevier Inc. All rights reserved.

  1. Quantifying population genetic differentiation from next-generation sequencing data.

    PubMed

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

    2013-11-01

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

  2. A general sequence processing and analysis program for protein engineering.

    PubMed

    Stafford, Ryan L; Zimmerman, Erik S; Hallam, Trevor J; Sato, Aaron K

    2014-10-27

    Protein engineering projects often amass numerous raw DNA sequences, but no readily available software combines sequence processing and activity correlation required for efficient lead identification. XLibraryDisplay is an open source program integrated into Microsoft Excel for Windows that automates batch sequence processing via a simple step-by-step, menu-driven graphical user interface. XLibraryDisplay accepts any DNA template which is used as a basis for trimming, filtering, translating, and aligning hundreds to thousands of sequences (raw, FASTA, or Phred PHD file formats). Key steps for library characterization through lead discovery are available including library composition analysis, filtering by experimental data, graphing and correlating to experimental data, alignment to structural data extracted from PDB files, and generation of PyMOL visualization scripts. Though larger data sets can be handled, the program is best suited for analyzing approximately 10 000 or fewer leads or naïve clones which have been characterized using Sanger sequencing and other experimental approaches. XLibraryDisplay can be downloaded for free from sourceforge.net/projects/xlibrarydisplay/ .

  3. 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

  4. 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

  5. Sequence-specific nucleic acid detection from binary pore conductance measurement

    PubMed Central

    Esfandiari, Leyla; Monbouquette, Harold G.; Schmidt, Jacob J.

    2012-01-01

    We describe a platform for sequence-specific nucleic acid (NA) detection utilizing a micropipette tapered to a 2 μm diameter pore and 3 μm diameter polystyrene beads to which uncharged peptide nucleic acid (PNA) probe molecules have been conjugated. As the target NAs hybridize to the complementary PNA-beads, the beads acquire negative charge and become electrophoretically mobile. An applied electric field guides these NA-PNA-beads toward the pipette tip, which they obstruct, leading to an indefinite, electrically detectable, partial blockade of the pore. In the presence of non-complementary NA, even to the level of single base mismatch, permanent pore blockade is not seen. We show application of this platform to detection of the anthrax lethal factor sequence. PMID:22931376

  6. 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.

  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. 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;…

  9. DNA Sequencing Sensors: An Overview

    PubMed Central

    Garrido-Cardenas, Jose Antonio; Garcia-Maroto, Federico; Alvarez-Bermejo, Jose Antonio; Manzano-Agugliaro, Francisco

    2017-01-01

    The first sequencing of a complete genome was published forty years ago by the double Nobel Prize in Chemistry winner Frederick Sanger. That corresponded to the small sized genome of a bacteriophage, but since then there have been many complex organisms whose DNA have been sequenced. This was possible thanks to continuous advances in the fields of biochemistry and molecular genetics, but also in other areas such as nanotechnology and computing. Nowadays, sequencing sensors based on genetic material have little to do with those used by Sanger. The emergence of mass sequencing sensors, or new generation sequencing (NGS) meant a quantitative leap both in the volume of genetic material that was able to be sequenced in each trial, as well as in the time per run and its cost. One can envisage that incoming technologies, already known as fourth generation sequencing, will continue to cheapen the trials by increasing DNA reading lengths in each run. All of this would be impossible without sensors and detection systems becoming smaller and more precise. This article provides a comprehensive overview on sensors for DNA sequencing developed within the last 40 years. PMID:28335417

  10. The EMBL Nucleotide Sequence Database.

    PubMed

    Stoesser, Guenter; Baker, Wendy; van den Broek, Alexandra; Camon, Evelyn; Garcia-Pastor, Maria; Kanz, Carola; Kulikova, Tamara; Leinonen, Rasko; Lin, Quan; Lombard, Vincent; Lopez, Rodrigo; Redaschi, Nicole; Stoehr, Peter; Tuli, Mary Ann; Tzouvara, Katerina; Vaughan, Robert

    2002-01-01

    The EMBL Nucleotide Sequence Database (aka EMBL-Bank; http://www.ebi.ac.uk/embl/) incorporates, organises and distributes nucleotide sequences from all available public sources. EMBL-Bank is located and maintained at the European Bioinformatics Institute (EBI) near Cambridge, UK. In an international collaboration with DDBJ (Japan) and GenBank (USA), data are exchanged amongst the collaborating databases on a daily basis. Major contributors to the EMBL database are individual scientists and genome project groups. Webin is the preferred web-based submission system for individual submitters, whilst automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO). Database releases are produced quarterly. Network services allow free access to the most up-to-date data collection via FTP, email and World Wide Web interfaces. EBI's Sequence Retrieval System (SRS), a network browser for databanks in molecular biology, integrates and links the main nucleotide and protein databases plus many other specialized databases. For sequence similarity searching, a variety of tools (e.g. Blitz, Fasta, BLAST) are available which allow external users to compare their own sequences against the latest data in the EMBL Nucleotide Sequence Database and SWISS-PROT. All resources can be accessed via the EBI home page at http://www.ebi.ac.uk.

  11. 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

  12. 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…

  13. Chameleon sequences in neurodegenerative diseases.

    PubMed

    Bahramali, Golnaz; Goliaei, Bahram; Minuchehr, Zarrin; Salari, Ali

    2016-03-25

    Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to "helix to strand (HE)", "helix to coil (HC)" and "strand to coil (CE)" alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases.

  14. Chameleon sequences in neurodegenerative diseases

    SciTech Connect

    Bahramali, Golnaz; Goliaei, Bahram; Minuchehr, Zarrin; Salari, Ali

    2016-03-25

    Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to “helix to strand (HE)”, “helix to coil (HC)” and “strand to coil (CE)” alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases.

  15. 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…

  16. 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…

  17. 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…

  18. 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.

  19. 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…

  20. 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...

  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. Commercial Art: Scope and Sequence.

    ERIC Educational Resources Information Center

    Nashville - Davidson County Metropolitan Public Schools, TN.

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

  3. Venturia carpophila draft genome sequence

    USDA-ARS?s Scientific Manuscript database

    Venturia carpophila causes peach scab, a disease that renders peach fruit unmarketable. We report a high-quality draft genome sequence (36.9 Mb) of V. carpophila from an isolate collected from a peach tree in central Georgia in the United States. The genome sequence described will be a useful resour...

  4. 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;…

  5. VOE Clerical: 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 clerical skills. The guide consists of a course description; general course…

  6. 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…

  7. 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…

  8. 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…

  9. 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...

  10. 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…

  11. 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

  12. Simulation study of Na-majorite

    NASA Astrophysics Data System (ADS)

    Dymshits, A.; Vinograd, V.; Paulsen, N.; Winkler, B.; Perchuk, L.; Bobrov, A.

    2009-04-01

    Garnets, which are found as inclusions in diamonds, often have the excess of Na2O and SiO2 [Stachel, 2001]. Experimental studies suggest that Na is incorporated in pyrope-rich garnet via the coupled substitution Mg+Al=Na+Si [Bobrov et al., 2008]. This study is concerned with the determination of the structure and the thermodynamic properties of NaGrt (Na2MgSi5O12), which is assumed to be the end-member of pyrope-rich garnets with the excess of Na2O and SiO2. Static lattice energy calculations were performed with the program GULP [Gale & Rohl, 2003] using the force-field model [Vinograd et al., 2007] for 200 structures of Na2MgSi5O12 composition. These structures were prepared from Ia3-d pyrope Mg3Al2Si3O12 by replacing all octahedral Al atoms with Si and 2/3 of Mg atoms with Na. The distribution of Mg and Na was varied randomly. The static energies of these structures were cluster expanded using 8 pairwise effective cluster interactions (ECI). The ECIs were used to constrain Monte Carlo simulations within a 4×4×4 supercell (NNN exchangeable sites). The annealing experiments have shown that the lowest energy structure has the space group I4

  13. Painful Na-channelopathies: an expanding universe.

    PubMed

    Waxman, Stephen G

    2013-07-01

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

  14. 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.

  15. 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.

  16. Recent advances in nanopore sequencing

    PubMed Central

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

    2013-01-01

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

  17. Confirmation of mutant alpha 1 Na,K-ATPase gene and transcript in Dahl salt-sensitive/JR rats.

    PubMed

    Ruiz-Opazo, N; Barany, F; Hirayama, K; Herrera, V L

    1994-09-01

    As the sole renal Na,K-ATPase isozyme, the alpha 1 Na,K-ATPase accounts for all active transport of Na+ throughout the nephron. This role in renal Na+ reabsorption and the primacy of the kidney in hypertension pathogenesis make it a logical candidate gene for salt-sensitive genetic hypertension. An adenine (A)1079-->thymine (T) transversion, resulting in the substitution of glutamine276 with leucine and associated with decreased net 86Rb+ (K+) influx, was identified in Dahl salt-sensitive/JR rat kidney alpha 1 Na,K-ATPase cDNA. However, because a Taq polymerase chain reaction amplification-based reanalysis did not detect the mutant T1079 but rather only the wild-type A1079 alpha 1 Na,K-ATPase allele in Dahl salt-sensitive rat genomic DNA, we reexamined alpha 1 Na,K-ATPase sequences using Taq polymerase error-independent amplification-based analyses of genomic DNA (by polymerase allele-specific amplification and ligase chain reaction analysis) and kidney RNA (by mRNA-specific thermostable reverse transcriptase-polymerase chain reaction analysis). We also performed modified 3' mismatched correction analysis of genomic DNA using an exonuclease-positive thermostable DNA polymerase. All the confirmatory test results were concordant, confirming the A1079-->T transversion in the Dahl salt-sensitive alpha 1 Na,K-ATPase allele and its transcript, as well as the wild-type A1079 sequence in the Dahl salt-resistant alpha 1 Na,K-ATPase allele and its transcript. Documentation of a consistent Taq polymerase error that selectively substituted A at T1079 (sense strand) was obtained from Taq polymerase chain reaction amplification and subsequent cycle sequencing of reconfirmed known Dahl salt-sensitive/JR rat mutant T1079 alpha 1 cDNA M13 subclones. This Taq polymerase error results in the reversion of mutant sequence back to the wild-type alpha 1 Na,K-ATPase sequence. This identifies a site- and nucleotide-specific Taq polymerase misincorporation, suggesting that a structural

  18. Pathogenetic mechanisms of fetal akinesia deformation sequence and oligohydramnios sequence.

    PubMed

    Rodríguez, J I; Palacios, J

    1991-09-01

    This article briefly reviews the participation of fetal compression, muscular weakness, and fetal akinesia in the genesis of the anomalies found in fetal akinesia deformation sequence (FADS) and oligohydramnios sequence (OS). Both sequences share phenotypic manifestations, such as arthrogryposis, short umbilical cord, and lung hypoplasia, in relation to decreased intrauterine fetal motility. Other characteristic manifestations found in OS, such as Potter face, and redundant skin, are produced by fetal compression. On the other hand, growth retardation, craniofacial anomalies, micrognathia, long bone hypoplasia, and polyhydramnios found in FADS could be related to intrauterine muscular weakness.

  19. Double-quantum-filtered 23Na NMR study of intracellular sodium in the perfused liver.

    PubMed Central

    Lyon, R C; McLaughlin, A C

    1994-01-01

    We acquired double-quantum-filtered 23Na NMR spectra from perfused liver, using a range of tau values from 0.2 to 24 ms, where tau is the separation between the first and second pi/2 pulses in the radio-frequency pulse sequence. For each tau value we compared the amplitude of the double-quantum-filtered 23Na NMR signal acquired from intracellular sodium ions when the liver was perfused with buffer containing the "shift reagent" Dy(PPP)2 to the amplitude of the total double-quantum-filtered 23Na NMR signal acquired when the liver was perfused with buffer containing no Dy(PPP)2. For tau < or = 4 ms, the average ratio of the two amplitudes was 0.98 +/- 0.03 (mean +/- SEM). For tau > or = 8 ms, the average ratio was significantly less than 1. These results demonstrate that double-quantum-filtered 23Na NMR signals acquired from perfused liver using short tau values arise almost exclusively from intracellular sodium ions, but double-quantum-filtered 23Na NMR signals acquired from perfused liver using long tau values contain contributions from both intracellular and extracellular sodium ions. This conclusion suggests that multiple-quantum-filtered 23Na NMR spectroscopy will be useful in studying intracellular sodium levels in the perfused liver, and possibly in the intact liver in vivo. PMID:7919009

  20. First mesopause Na retrievals from satellite Na D-line nightglow observations

    NASA Astrophysics Data System (ADS)

    Savigny, C.; Langowski, M. P.; Zilker, B.; Burrows, J. P.; Fussen, D.; Sofieva, V. F.

    2016-12-01

    We report the retrieval of Na concentration profiles in the mesopause region from satellite observations of the Na D-line nightglow emission near 589 nm made by the Scanning Imaging Absorption Spectrometer for Atmospheric Chartography (SCIAMACHY) on the Envisat spacecraft. The retrieval assumes the Na D-line excitation mechanism originally proposed by Chapman in 1939. The retrieval approach, including treatment of self-absorption by Na, a retrieval uncertainty budget, and first retrieval results, is presented. The retrieved Na profiles are compared to independent satellite measurements. Good agreement in terms of peak altitude, peak concentration, and vertical column density is found. The retrievals constitute the first Na profile retrievals from satellite observations of the Na D-line nightglow emission profile. They enable our understanding of the Na nightglow excitation mechanism to be tested.

  1. 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

  2. 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.

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

    PubMed

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

    2005-01-01

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

  4. Exploration of NaVOPO4 as a cathode for a Na-ion battery.

    PubMed

    Song, Jie; Xu, Maowen; Wang, Long; Goodenough, John B

    2013-06-11

    Monoclinic NaVOPO4 is explored as a cathode material for a sodium ion battery. It exhibits electrochemical activity operating at an average potential of 3.6 V (vs. Na(+)/Na) and delivers a reversible capacity of 90 mA h g(-1) at 1/15 C.

  5. 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.

  6. Compilation of small RNA sequences.

    PubMed

    Shumyatsky, G; Reddy, R

    1992-05-11

    This is an update containing small RNA sequences published during 1991. Approximately two hundred small RNA sequences are available in this and earlier compilations. The hard copy print out of this set will be available directly from us (inquiries should be addressed to R. Reddy). These files are also available on GenBank computer. Sequences from various sources covered in earlier compilations (see Reddy, R. Nucl. Acids Res. 16:r71; Reddy, R. and Gupta, S. Nucl Acids Res. 1990 Supplement, 18:2231 and 1991 Supplement, 19:2073) are not included in this update but are listed below.

  7. Inferring phylogenies of evolving sequences without multiple sequence alignment.

    PubMed

    Chan, Cheong Xin; Bernard, Guillaume; Poirion, Olivier; Hogan, James M; Ragan, Mark A

    2014-09-30

    Alignment-free methods, in which shared properties of sub-sequences (e.g. identity or match length) are extracted and used to compute a distance matrix, have recently been explored for phylogenetic inference. However, the scalability and robustness of these methods to key evolutionary processes remain to be investigated. Here, using simulated sequence sets of various sizes in both nucleotides and amino acids, we systematically assess the accuracy of phylogenetic inference using an alignment-free approach, based on D2 statistics, under different evolutionary scenarios. We find that compared to a multiple sequence alignment approach, D2 methods are more robust against among-site rate heterogeneity, compositional biases, genetic rearrangements and insertions/deletions, but are more sensitive to recent sequence divergence and sequence truncation. Across diverse empirical datasets, the alignment-free methods perform well for sequences sharing low divergence, at greater computation speed. Our findings provide strong evidence for the scalability and the potential use of alignment-free methods in large-scale phylogenomics.

  8. Multiple sequence alignment based on profile alignment of intermediate sequences.

    PubMed

    Lu, Yue; Sze, Sing-Hoi

    2008-09-01

    Despite considerable efforts, it remains difficult to obtain accurate multiple sequence alignments. By using additional hits from database search of the input sequences, a few strategies have been proposed to significantly improve alignment accuracy, including the construction of profiles from the hits while performing profile alignment, the inclusion of high scoring hits into the input sequences, the use of intermediate sequence search to link distant homologs, and the use of secondary structure information. We develop an algorithm that integrates these strategies to further improve alignment accuracy by modifying the pair-Hidden Markov Model (HMM) approach in ProbCons to incorporate profiles of intermediate sequences from database search and utilize secondary structure predictions as in SPEM. We test our algorithm on a few sets of benchmark multiple alignments, including BAliBASE, HOMSTRAD, PREFAB, and SABmark, and show that it significantly outperforms MAFFT and ProbCons, which are among the best multiple alignment algorithms that do not utilize additional information, and SPEM, which is among the best multiple alignment algorithms that utilize additional hits from database search. The improvement in accuracy over SPEM can be as much as 5-10% when aligning divergent sequences. A software program that implements this approach (ISPAlign) is available at http://faculty.cs.tamu.edu/shsze/ispalign.

  9. Inferring phylogenies of evolving sequences without multiple sequence alignment

    PubMed Central

    Chan, Cheong Xin; Bernard, Guillaume; Poirion, Olivier; Hogan, James M.; Ragan, Mark A.

    2014-01-01

    Alignment-free methods, in which shared properties of sub-sequences (e.g. identity or match length) are extracted and used to compute a distance matrix, have recently been explored for phylogenetic inference. However, the scalability and robustness of these methods to key evolutionary processes remain to be investigated. Here, using simulated sequence sets of various sizes in both nucleotides and amino acids, we systematically assess the accuracy of phylogenetic inference using an alignment-free approach, based on D2 statistics, under different evolutionary scenarios. We find that compared to a multiple sequence alignment approach, D2 methods are more robust against among-site rate heterogeneity, compositional biases, genetic rearrangements and insertions/deletions, but are more sensitive to recent sequence divergence and sequence truncation. Across diverse empirical datasets, the alignment-free methods perform well for sequences sharing low divergence, at greater computation speed. Our findings provide strong evidence for the scalability and the potential use of alignment-free methods in large-scale phylogenomics. PMID:25266120

  10. Evaluation of the Abbott HBV RUO sequencing assay combined with laboratory-modified interpretive software.

    PubMed

    Germer, Jeffrey J; Abraham, Priya; Mandrekar, Jayawant N; Yao, Joseph D C

    2013-01-01

    The Abbott HBV RUO Sequencing assay (Abbott Molecular Inc., Des Plaines, IL), which combines automated sample processing, real-time PCR, and bidirectional DNA sequencing, was evaluated for detection of nucleos(t)ide analogue (NA) resistance-associated mutations located in the hepatitis B virus (HBV) polymerase (Pol) gene. Interpretive software from the assay manufacturer was modified to allow interrogation of the overlapping HBV surface (S) gene sequence for HBV genotype determination and detection of immune escape mutations. Analytical sensitivity (detection and sequencing) of the assay was determined to be 103.9 IU/ml (95% confidence interval [CI], 80.0 to 173.3) for HBV genotype A. Testing of commercially available HBV genotype panels consisting of 23 individual members yielded complete agreement between expected results and results obtained from the laboratory-developed HBV genotype library. Excellent specificity was observed among clinical specimens with serologic or molecular markers for various unrelated blood-borne viruses (n = 6) and sera obtained from healthy, HBV-negative blood donors (n = 20). Retrospectively selected clinical specimens tested by a commercial reference laboratory HBV sequencing assay (n = 54) or the Trugene HBV Genotyping kit (n = 7) and the Abbott HBV RUO Sequencing assay showed minor differences in detection and reporting of NA resistance-associated mutations in 7 of 61 (11.5%) specimens but complete agreement of genotype results. The Abbott HBV RUO Sequencing assay provided a convenient and efficient assay workflow suitable for routine clinical laboratory use, with the flexibility to be modified for customized detection of NA resistance-associated mutations, HBV genotype determination, and detection of immune escape mutations from a single contiguous HBV sequence.

  11. Tetramerization of an RNA oligonucleotide containing a GGGG sequence.

    PubMed

    Kim, J; Cheong, C; Moore, P B

    1991-05-23

    Poly rG can form four-stranded helices. The Hoogsteen-paired quartets of G residues on which such structures depend are so stable that they will form in 5'-GMP solutions, provided that Na+ or K+ are present (see for example, refs 2-4). Telomeric DNA sequences, which are G-rich, adopt four-stranded antiparallel G-quartet conformations in vitro, and parallel tetramerization of G-rich sequences may be involved in meiosis. Here we show that RNAs containing short runs of Gs can also tetramerize. A 19-base oligonucleotide derived from the 5S RNA of Escherichia coli (strand III), 5'GCCGAUGGUAGUGUGGGGU3', forms a K(+)-stabilized tetrameric aggregate that depends on the G residues at its 3' end. This complex is so stable that it would be surprising if similar structures do not occur in nature.

  12. Kinetin Reversal of NaCl Effects

    PubMed Central

    Katz, Adriana; Dehan, Klara; Itai, Chanan

    1978-01-01

    Leaf discs of Nicotiana rustica L. were floated on NaCl in the presence of kinetin or abscisic acid. On the 5th day 14CO2 fixation, [3H]leucine incorporation, stomatal conductance, and chlorophyll content were determined. Kinetin either partially or completely reversed the inhibitory effects of NaCl while ABA had no effect. PMID:16660618

  13. Deduced amino acid sequence of a putative sodium channel from the scyphozoan jellyfish Cyanea capillata.

    PubMed Central

    Anderson, P A; Holman, M A; Greenberg, R M

    1993-01-01

    Members of the phylum Cnidaria are the lowest extant organisms to possess a nervous system and are the first that are known to contain cells that produce action potentials carried exclusively by Na+ ions. They thus occupy an important position in the evolution of Na+ channels. A cDNA encoding a 198-kDa protein with high sequence identity to known Na+ channels was isolated from the scyphozoan jellyfish Cyanea capillata. The similarity between this and other Na+ channels is greatest in the transmembrane segments and the putative pore region and less so in the cytoplasmic loops that link the four domains of the protein. Phylogenetic analysis of the deduced protein reveals that it is closely related to known Na+ channels, particularly those of squid and Drosophila, and more distantly separated from Ca2+ channels. Scrutiny of the Cyanea channel in regions corresponding to those purported to form the tetrodotoxin receptor and selectivity filter of Na+ channels in higher animals reveals several anomalies that suggest that current models of the location of the tetrodotoxin binding site and Na+ channel selectivity filter are incomplete. Images Fig. 1 Fig. 2 Fig. 3 PMID:8394021

  14. Deduced amino acid sequence of a putative sodium channel from the scyphozoan jellyfish Cyanea capillata.

    PubMed

    Anderson, P A; Holman, M A; Greenberg, R M

    1993-08-01

    Members of the phylum Cnidaria are the lowest extant organisms to possess a nervous system and are the first that are known to contain cells that produce action potentials carried exclusively by Na+ ions. They thus occupy an important position in the evolution of Na+ channels. A cDNA encoding a 198-kDa protein with high sequence identity to known Na+ channels was isolated from the scyphozoan jellyfish Cyanea capillata. The similarity between this and other Na+ channels is greatest in the transmembrane segments and the putative pore region and less so in the cytoplasmic loops that link the four domains of the protein. Phylogenetic analysis of the deduced protein reveals that it is closely related to known Na+ channels, particularly those of squid and Drosophila, and more distantly separated from Ca2+ channels. Scrutiny of the Cyanea channel in regions corresponding to those purported to form the tetrodotoxin receptor and selectivity filter of Na+ channels in higher animals reveals several anomalies that suggest that current models of the location of the tetrodotoxin binding site and Na+ channel selectivity filter are incomplete.

  15. Na+ and Ca2+ cooperatively down regulate the A-type potassium currents in Helix neurons.

    PubMed

    Erdélyi, L

    1995-01-01

    Modulatory actions of Na+, Tris+, Li+ and Ca2+ on A-type potassium currents were investigated in identified neurons of the snail, Helix pomatia L. A-currents were isolated under spike threshold voltages by use of the double pulse method in combination with computer techniques. To estimate the action of Na+ on A-type potassium currents the normal physiological solution was changed to Na-free (mannitol) medium which increased the amplitude of the A-currents at -30 mV membrane potential by 20.5% without significant modulation of the time-dependent inactivation. When Tris-HCl or LiCl substituted for NaCl, the amplitude of the A-currents decreased by 27.5 or 32.5%, respectively. Li+ did not modify the time constant of decay of the A-currents, but Tris+ decreased it by 15.8%. There was an increase of the amplitude of the A-currents in the Na-, Ca-free (Tris) medium relative to the Na-free (Tris) solution by 27.7% and a decrease of the time constant of decay by 25.3%. It is concluded that A-currents are down regulated by Na+ and Ca2+ under physiological circumstances, but the modulatory action of Ca2+ is more complex and influences the amplitude, time-dependent inactivation and potential-dependent inactivation characteristics of IA. Among monovalent cations, the A-current attenuation increases in the sequence of Na+ < Tris+ < Li+. All identified neurons react in a similar way but with different sensitivities.

  16. DNA double-strand breaks induced by high NaCl occur predominantly in gene deserts

    PubMed Central

    Dmitrieva, Natalia I.; Cui, Kairong; Kitchaev, Daniil A.; Zhao, Keji; Burg, Maurice B.

    2011-01-01

    High concentration of NaCl increases DNA breaks both in cell culture and in vivo. The breaks remain elevated as long as NaCl concentration remains high and are rapidly repaired when the concentration is lowered. The exact nature of the breaks, and their location, has not been entirely clear, and it has not been evident how cells survive, replicate, and maintain genome integrity in environments like the renal inner medulla in which cells are constantly exposed to high NaCl concentration. Repair of the breaks after NaCl is reduced is accompanied by formation of foci containing phosphorylated H2AX (γH2AX), which occurs around DNA double-strand breaks and contributes to their repair. Here, we confirm by specific comet assay and pulsed-field electrophoresis that cells adapted to high NaCl have increased levels of double-strand breaks. Importantly, γH2AX foci that occur during repair of the breaks are nonrandomly distributed in the mouse genome. By chromatin immunoprecipitation using anti-γH2AX antibody, followed by massive parallel sequencing (ChIP-Seq), we find that during repair of double-strand breaks induced by high NaCl, γH2AX is predominantly localized to regions of the genome devoid of genes (“gene deserts”), indicating that the high NaCl-induced double-strand breaks are located there. Localization to gene deserts helps explain why the DNA breaks are less harmful than are the random breaks induced by genotoxic agents such as UV radiation, ionizing radiation, and oxidants. We propose that the universal presence of NaCl around animal cells has directly influenced the evolution of the structure of their genomes. PMID:22106305

  17. 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.

  18. Negative electrodes for Na-ion batteries.

    PubMed

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

    2014-08-07

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

  19. Na+ binding to the Na(+)-glucose cotransporter is potential dependent.

    PubMed

    Bennett, E; Kimmich, G A

    1992-02-01

    Activity of the Na(+)-glucose cotransporter in LLC-PK1 epithelial cells was assayed by measuring sugar-induced currents (IAMG) using whole cell recording techniques. IAMG was compared among cells by standardizing the measured currents to cell size using cell capacitance measurements. IAMG at a given membrane potential was measured as a function of alpha-methylglucoside (AMG) concentration and can be fit to Michaelis-Menten kinetics. IAMG at varying Na+ concentrations can be described by the Hill equation with a Hill coefficient of 1.6 at all tested potentials. At high external Na+ levels (155 mM), Na+ is at least 90% saturating at all tested potentials. Maximal currents at a given membrane potential (Im) are calculated from the Michaelis-Menten equation fit to data measuring IAMG vs. AMG concentration at a constant Na+ concentration. Im showed potential dependence under all conditions. Potential-dependent Na+ binding rate(s) cannot alone explain the observed potential dependence of Im under saturating Na+ conditions. Therefore, because Im is potential dependent, at least one step of the transport cycle other than external Na+ binding must be potential dependent. Im was also calculated from data taken at 40 mM external Na+. At all potentials studied, Im at 155 mM Na+ is greater than Im calculated at 40 mM Na+. This implies that the rate of external Na+ binding to the transporter at 40 mM also affects the maximal transport rate. Furthermore, Im at 40 mM external Na+ increases with hyperpolarization faster than Im at 155 mM Na+. Together, these facts indicate that the rate at which Na+ binds to the transporter is also potential dependent.(ABSTRACT TRUNCATED AT 250 WORDS)

  20. Sequencing as an Item Type.

    ERIC Educational Resources Information Center

    Alderson, J. Charles; Percsich, Richard; Szabo, Gabor

    2000-01-01

    Reports on the potential problems in scoring responses to sequencing tests, the development of a computer program to overcome these difficulties, and an exploration of the value of scoring procedures. (Author/VWL)

  1. 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)

  2. 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.)

  3. 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)

  4. Molecular beacon sequence design algorithm.

    PubMed

    Monroe, W Todd; Haselton, Frederick R

    2003-01-01

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

  5. 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)

  6. Archiving next generation sequencing data.

    PubMed

    Shumway, Martin; Cochrane, Guy; Sugawara, Hideaki

    2010-01-01

    Next generation sequencing platforms are producing biological sequencing data in unprecedented amounts. The partners of the International Nucleotide Sequencing Database Collaboration, which includes the National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EBI), and the DNA Data Bank of Japan (DDBJ), have established the Sequence Read Archive (SRA) to provide the scientific community with an archival destination for next generation data sets. The SRA is now accessible at http://www.ncbi.nlm.nih.gov/Traces/sra from NCBI, at http://www.ebi.ac.uk/ena from EBI and at http://www.ddbj.nig.ac.jp/sub/trace_sra-e.html from DDBJ. Users of these resources can obtain data sets deposited in any of the three SRA instances. Links and submission instructions are provided.

  7. Na-doped optical Germanium bulk crystals

    NASA Astrophysics Data System (ADS)

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

    2012-09-01

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

  8. Pharmacological modulation of human cardiac Na+ channels.

    PubMed

    Krafte, D S; Davison, K; Dugrenier, N; Estep, K; Josef, K; Barchi, R L; Kallen, R G; Silver, P J; Ezrin, A M

    1994-02-15

    Pharmacological modulation of human sodium current was examined in Xenopus oocytes expressing human heart Na+ channels. Na+ currents activated near -50 mV with maximum current amplitudes observed at -20 mV. Steady-state inactivation was characterized by a V1/2 value of -57 +/- 0.5 mV and a slope factor (k) of 7.3 +/- 0.3 mV. Sodium currents were blocked by tetrodotoxin with an IC50 value of 1.8 microM. These properties are consistent with those of Na+ channels expressed in mammalian myocardial cells. We have investigated the effects of several pharmacological agents which, with the exception of lidocaine, have not been characterized against cRNA-derived Na+ channels expressed in Xenopus oocytes. Lidocaine, quinidine and flecainide blocked resting Na+ channels with IC50 values of 521 microM, 198 microM, and 41 microM, respectively. Use-dependent block was also observed for all three agents, but concentrations necessary to induce block were higher than expected for quinidine and flecainide. This may reflect differences arising due to expression in the Xenopus oocyte system or could be a true difference in the interaction between human cardiac Na+ channels and these drugs compared to other mammalian Na+ channels. Importantly, however, this result would not have been predicted based upon previous studies of mammalian cardiac Na+ channels. The effects of DPI 201-106, RWJ 24517, and BDF 9148 were also tested and all three agents slowed and/or removed Na+ current inactivation, reduced peak current amplitudes, and induced use-dependent block. These data suggest that the alpha-subunit is the site of interaction between cardiac Na+ channels and Class I antiarrhythmic drugs as well as inactivation modifiers such as DPI 201-106.

  9. Evaluation of whole exome sequencing by targeted gene sequencing and Sanger sequencing.

    PubMed

    Chang, Ya-Sian; Huang, Hsien-Da; Yeh, Kun-Tu; Chang, Jan-Gowth

    2017-08-01

    Targeted gene sequencing (TGS) and whole exome sequencing (WES) are being used in clinical testing in laboratories. We compared the performances of TGS and WES using the same DNA samples. DNA was extracted from 10 endometrial tumor tissue specimens. Sequencing were performed with an Illumina HiSeq 2000. We randomly selected variants to confirm through Sanger sequencing or mutant-enriched PCR with Sanger sequencing. We found that the variants identified in both TGS and WES were true positives (47/47), regardless of the sequencing depth. Most variants found in TGS only were true positives (34/40), and most of the variants found by WES only were false positives (8/18). From these results, we suggest that the sequencing depth may not play important role in the accuracy of NGS-based methods. After analysis, we found that WES had a sensitivity of 72.70%, specificity of 96.27%, precision of 99.44%, and accuracy of 75.03%. The results of NGS-based methods must currently be validated, especially for important reported variants regardless of the methods used, and for the use of WES in cancers a higher false negative rate must be considered. More sensitive methods should be used to confirm the NGS results in uneven cancer tissues. Copyright © 2017 Elsevier B.V. All rights reserved.

  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. 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

  12. Long range intermolecular interactions between the alkali diatomics Na2, K2, and NaK

    NASA Astrophysics Data System (ADS)

    Zemke, Warren T.; Byrd, Jason N.; Michels, H. Harvey; Montgomery, John A.; Stwalley, William C.

    2010-06-01

    Long range interactions between the ground state alkali diatomics Na2-Na2, K2-K2, Na2-K2, and NaK-NaK are examined. Interaction energies are first determined from ab initio calculations at the coupled-cluster with singles, doubles, and perturbative triples [CCSD(T)] level of theory, including counterpoise corrections. Long range energies calculated from diatomic molecular properties (polarizabilities and dipole and quadrupole moments) are then compared with the ab initio energies. A simple asymptotic model potential ELR=Eelec+Edisp+Eind is shown to accurately represent the intermolecular interactions for these systems at long range.

  13. Long range intermolecular interactions between the alkali diatomics Na(2), K(2), and NaK.

    PubMed

    Zemke, Warren T; Byrd, Jason N; Michels, H Harvey; Montgomery, John A; Stwalley, William C

    2010-06-28

    Long range interactions between the ground state alkali diatomics Na(2)-Na(2), K(2)-K(2), Na(2)-K(2), and NaK-NaK are examined. Interaction energies are first determined from ab initio calculations at the coupled-cluster with singles, doubles, and perturbative triples [CCSD(T)] level of theory, including counterpoise corrections. Long range energies calculated from diatomic molecular properties (polarizabilities and dipole and quadrupole moments) are then compared with the ab initio energies. A simple asymptotic model potential E(LR)=E(elec)+E(disp)+E(ind) is shown to accurately represent the intermolecular interactions for these systems at long range.

  14. 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.

  15. 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

  16. Overview of Sequence Data Formats.

    PubMed

    Zhang, Hongen

    2016-01-01

    Next-generation sequencing experiment can generate billions of short reads for each sample and processing of the raw reads will add more information. Various file formats have been introduced/developed in order to store and manipulate this information. This chapter presents an overview of the file formats including FASTQ, FASTA, SAM/BAM, GFF/GTF, BED, and VCF that are commonly used in analysis of next-generation sequencing data.

  17. Mycobacterium abscessus multispacer sequence typing

    PubMed Central

    2013-01-01

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

  18. Nanogrid rolling circle DNA sequencing

    DOEpatents

    Church, George M.; Porreca, Gregory J.; Shendure, Jay; Rosenbaum, Abraham Meir

    2017-04-18

    The present invention relates to methods for sequencing a polynucleotide immobilized on an array having a plurality of specific regions each having a defined diameter size, including synthesizing a concatemer of a polynucleotide by rolling circle amplification, wherein the concatemer has a cross-sectional diameter greater than the diameter of a specific region, immobilizing the concatemer to the specific region to make an immobilized concatemer, and sequencing the immobilized concatemer.

  19. 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

    2015-05-14

    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).

  20. Complete Genome Sequences of Caldicellulosiruptor sp. Strain Rt8.B8, Caldicellulosiruptor sp. Strain Wai35.B1, and “Thermoanaerobacter cellulolyticus”

    PubMed Central

    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

    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

  1. 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

  2. Graphene Nanopores for Protein Sequencing

    PubMed Central

    Wilson, James; Sloman, Leila; He, Zhiren

    2016-01-01

    An inexpensive, reliable method for protein sequencing is essential to unraveling the biological mechanisms governing cellular behavior and disease. Current protein sequencing methods suffer from limitations associated with the size of proteins that can be sequenced, the time, and the cost of the sequencing procedures. Here, we report the results of all-atom molecular dynamics simulations that investigated the feasibility of using graphene nanopores for protein sequencing. We focus our study on the biologically significant phenylalanine-glycine repeat peptides (FG-nups)—parts of the nuclear pore transport machinery. Surprisingly, we found FG-nups to behave similarly to single stranded DNA: the peptides adhere to graphene and exhibit step-wise translocation when subject to a transmembrane bias or a hydrostatic pressure gradient. Reducing the peptide’s charge density or increasing the peptide’s hydrophobicity was found to decrease the translocation speed. Yet, unidirectional and stepwise translocation driven by a transmembrane bias was observed even when the ratio of charged to hydrophobic amino acids was as low as 1:8. The nanopore transport of the peptides was found to produce stepwise modulations of the nanopore ionic current correlated with the type of amino acids present in the nanopore, suggesting that protein sequencing by measuring ionic current blockades may be possible. PMID:27746710

  3. Cytosolic Na+ controls and epithelial Na+ channel via the Go guanine nucleotide-binding regulatory protein.

    PubMed Central

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

    1996-01-01

    In tight Na+-absorbing epithelial cells, the fate 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-beta-S, pertussis toxin, and antibodies against the alpha-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-. Images Fig. 4 PMID:8755611

  4. 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-.

  5. Anomalously high Na(+) and low Li(+) mobility in intercalated Na2Ti6O13.

    PubMed

    Ling, Chen; Zhang, Ruigang

    2017-04-12

    We report an anomalous diffusion behavior in intercalated Na2Ti6O13. Using first-principles calculations, the direct migration of inserted Na(+) along the tunnel direction is predicted to have a barrier of 0.24-0.44 eV, while the migration of inserted Li(+) along the tunnel direction has a barrier of 0.86-1.15 eV. Although Li(+) can also diffuse along a zig-zag path in the tunnel, the barrier of 0.86-0.99 eV is still much higher than that for Na(+). Our results surprisingly lead to the conclusion that the diffusion of larger Na(+) is 4-8 orders of magnitude faster than Li(+) in the same host lattice, and explain the experimentally observed exceptional rate capability of Na2Ti6O13 as the Na-ion battery anode. The anomalous diffusion behavior is attributed to the geometric features of Na2Ti6O13. For migration of Li(+) it is necessary to weaken Li-O bonds and to overcome the repulsion between Li and host Na ions simultaneously, while for Na(+) diffusion the improved Na-O bonding at the transition state partially compensates for the energy penalty from the repulsion of host Na ions.

  6. Ordering and spin waves in NaNi O2 : A stacked quantum ferromagnet

    NASA Astrophysics Data System (ADS)

    Lewis, M. J.; Gaulin, B. D.; Filion, L.; Kallin, C.; Berlinsky, A. J.; Dabkowska, H. A.; Qiu, Y.; Copley, J. R. D.

    2005-07-01

    Neutron scattering measurements on powder NaNiO2 reveal magnetic Bragg peaks and spin waves characteristic of strongly correlated s=1/2 magnetic moments arranged in ferromagnetic layers which are stacked antiferromagnetically. This structure lends itself to stacking sequence frustration in the presence of mixing between nickel and alkali metal sites, possibly providing a natural explanation for the enigmatic spin glass state of the isostructural compound, LiNiO2 .

  7. 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

  8. 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

  9. 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

  10. Long-range barcode labeling-sequencing

    DOEpatents

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

    2016-10-18

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

  11. Conservation of sequence in recombination signal sequence spacers.

    PubMed Central

    Ramsden, D A; Baetz, K; Wu, G E

    1994-01-01

    The variable domains of immunoglobulins and T cell receptors are assembled through the somatic, site specific recombination of multiple germline segments (V, D, and J segments) or V(D)J rearrangement. The recombination signal sequence (RSS) is necessary and sufficient for cell type specific targeting of the V(D)J rearrangement machinery to these germline segments. Previously, the RSS has been described as possessing both a conserved heptamer and a conserved nonamer motif. The heptamer and nonamer motifs are separated by a 'spacer' that was not thought to possess significant sequence conservation, however the length of the spacer could be either 12 +/- 1 bp or 23 +/- 1 bp long. In this report we have assembled and analyzed an extensive data base of published RSS. We have derived, through extensive consensus comparison, a more detailed description of the RSS than has previously been reported. Our analysis indicates that RSS spacers possess significant conservation of sequence, and that the conserved sequence in 12 bp spacers is similar to the conserved sequence in the first half of 23 bp spacers. PMID:8208601

  12. 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.

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

    PubMed Central

    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

  14. An investigation of Hebbian phase sequences as assembly graphs

    PubMed Central

    Almeida-Filho, Daniel G.; Lopes-dos-Santos, Vitor; Vasconcelos, Nivaldo A. P.; Miranda, José G. V.; Tort, Adriano B. L.; Ribeiro, Sidarta

    2014-01-01

    Hebb proposed that synapses between neurons that fire synchronously are strengthened, forming cell assemblies and phase sequences. The former, on a shorter scale, are ensembles of synchronized cells that function transiently as a closed processing system; the latter, on a larger scale, correspond to the sequential activation of cell assemblies able to represent percepts and behaviors. Nowadays, the recording of large neuronal populations allows for the detection of multiple cell assemblies. Within Hebb's theory, the next logical step is the analysis of phase sequences. Here we detected phase sequences as consecutive assembly activation patterns, and then analyzed their graph attributes in relation to behavior. We investigated action potentials recorded from the adult rat hippocampus and neocortex before, during and after novel object exploration (experimental periods). Within assembly graphs, each assembly corresponded to a node, and each edge corresponded to the temporal sequence of consecutive node activations. The sum of all assembly activations was proportional to firing rates, but the activity of individual assemblies was not. Assembly repertoire was stable across experimental periods, suggesting that novel experience does not create new assemblies in the adult rat. Assembly graph attributes, on the other hand, varied significantly across behavioral states and experimental periods, and were separable enough to correctly classify experimental periods (Naïve Bayes classifier; maximum AUROCs ranging from 0.55 to 0.99) and behavioral states (waking, slow wave sleep, and rapid eye movement sleep; maximum AUROCs ranging from 0.64 to 0.98). Our findings agree with Hebb's view that assemblies correspond to primitive building blocks of representation, nearly unchanged in the adult, while phase sequences are labile across behavioral states and change after novel experience. The results are compatible with a role for phase sequences in behavior and cognition. PMID

  15. An investigation of Hebbian phase sequences as assembly graphs.

    PubMed

    Almeida-Filho, Daniel G; Lopes-dos-Santos, Vitor; Vasconcelos, Nivaldo A P; Miranda, José G V; Tort, Adriano B L; Ribeiro, Sidarta

    2014-01-01

    Hebb proposed that synapses between neurons that fire synchronously are strengthened, forming cell assemblies and phase sequences. The former, on a shorter scale, are ensembles of synchronized cells that function transiently as a closed processing system; the latter, on a larger scale, correspond to the sequential activation of cell assemblies able to represent percepts and behaviors. Nowadays, the recording of large neuronal populations allows for the detection of multiple cell assemblies. Within Hebb's theory, the next logical step is the analysis of phase sequences. Here we detected phase sequences as consecutive assembly activation patterns, and then analyzed their graph attributes in relation to behavior. We investigated action potentials recorded from the adult rat hippocampus and neocortex before, during and after novel object exploration (experimental periods). Within assembly graphs, each assembly corresponded to a node, and each edge corresponded to the temporal sequence of consecutive node activations. The sum of all assembly activations was proportional to firing rates, but the activity of individual assemblies was not. Assembly repertoire was stable across experimental periods, suggesting that novel experience does not create new assemblies in the adult rat. Assembly graph attributes, on the other hand, varied significantly across behavioral states and experimental periods, and were separable enough to correctly classify experimental periods (Naïve Bayes classifier; maximum AUROCs ranging from 0.55 to 0.99) and behavioral states (waking, slow wave sleep, and rapid eye movement sleep; maximum AUROCs ranging from 0.64 to 0.98). Our findings agree with Hebb's view that assemblies correspond to primitive building blocks of representation, nearly unchanged in the adult, while phase sequences are labile across behavioral states and change after novel experience. The results are compatible with a role for phase sequences in behavior and cognition.

  16. Laser-induced ionization of Na vapor

    SciTech Connect

    Wu, R.C.Y.; Judge, D.L.; Roussel, F.; Carre, B.; Breger, P.; Spiess, G.

    1982-01-01

    The production of Na/sub 2//sup +/ ions by off-resonant laser excitation in the 5800-6200A region mainly results from two-photon absorption by the Na/sub 2/ molecule to highly excited gerade states followed by (a) direct ionization by absorbing a third photon or (b) coupling to the molecular Na/sub 2/ D/sup 1/PI..mu.. Rydberg state which is subsequently ionized by absorbing a third photon. This mechanism, i.e., a two-photon resonance three photon ionization process, explains a recent experimental observation of Roussel et al. It is suggested that the very same mechanism is also responsible for a similar observation reported by Polak-Dingels et al in their work using two crossed Na beams. In the latter two studies the laser-induced associative ionization processes were reported to be responsible for producing the Na/sub 2//sup +/ ion. From the ratio of molecular to atomic concentration in the crossed beam experiment of Polak-Dingels et al we estimate that the cross section for producing Na/sub 2//sup +/ through laser-induced associative ionization is at least four orders of magnitude smaller than ionization through the two-photon resonance three photon ionization process in Na/sub 2/ molecules.

  17. Laser-induced ionization of Na vapor

    NASA Astrophysics Data System (ADS)

    Wu, C. Y. Robert; Judge, D. L.; Roussel, F.; Carré, B.; Breger, P.; Spiess, G.

    1982-09-01

    The production of Na2+ ions by off-resonant laser excitation in the 5800-6200Å region mainly results from two-photon absorption by the Na2 molecule to highly excited gerade states followed by (a) direct ionization by absorbing a third photon or (b) coupling to the molecular Na2 D1Πu Rydberg state which is subsequently ionized by absorbing a third photon. This mechanism, i.e., a two-photon resonance three photon ionization process, explains a recent experimental observation of Roussel et al. It is suggested that the very same mechanism is also responsible for a similar observation reported by Polak-Dingels et al in their work using two crossed Na beams. In the latter two studies the laser-induced associative ionization processes were reported to be responsible for producing the Na2+ ion. From the ratio of molecular to atomic concentration in the crossed beam experiment of Polak-Dingels et al. we estimate that the cross section for producing Na2+ through laser-induced associative ionization is at least four orders of magnitude smaller than ionization through the two-photon resonance three photon ionization process in Na2 molecules.

  18. Ossification sequence heterochrony among amphibians.

    PubMed

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

    2013-01-01

    Heterochrony is an important mechanism in the evolution of amphibians. Although studies have centered on the relationship between size and shape and the rates of development, ossification sequence heterochrony also may have been important. Rigorous, phylogenetic methods for assessing sequence heterochrony are relatively new, and a comprehensive study of the relative timing of ossification of skeletal elements has not been used to identify instances of sequence heterochrony across Amphibia. In this study, a new version of the program Parsimov-based genetic inference (PGi) was used to identify shifts in ossification sequences across all extant orders of amphibians, for all major structural units of the skeleton. PGi identified a number of heterochronic sequence shifts in all analyses, the most interesting of which seem to be tied to differences in metamorphic patterns among major clades. Early ossification of the vomer, premaxilla, and dentary is retained by Apateon caducus and members of Gymnophiona and Urodela, which lack the strongly biphasic development seen in anurans. In contrast, bones associated with the jaws and face were identified as shifting late in the ancestor of Anura. The bones that do not shift late, and thereby occupy the earliest positions in the anuran cranial sequence, are those in regions of the skull that undergo the least restructuring throughout anuran metamorphosis. Additionally, within Anura, bones of the hind limb and pelvic girdle were also identified as shifting early in the sequence of ossification, which may be a result of functional constraints imposed by the drastic metamorphosis of most anurans. © 2013 Wiley Periodicals, Inc.

  19. 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

  20. Additives and solvents-induced phase and morphology modification of NaYF{sub 4} for improving up-conversion emission

    SciTech Connect

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

    2016-01-15

    Both cubic and hexagonal NaYF{sub 4} were synthesized in different reaction systems via hydro/solvo-thermal route. The effects of reaction temperature, solvents, and additives on the synthesis of NaYF{sub 4} have been studied in detail. It has been shown that phase transformation from cubic NaYF{sub 4} to hexagonal NaYF{sub 4} always occurred. The sequence of the ability for inducing the phase transformation was ethanol>H{sub 2}O>acetic acid. It is found that ethanol can not only facilitate the formation of hexagonal NaYF{sub 4} but also control the growth of the crystal. This is quite unusual for the growth of H-NaYF{sub 4}. The up-conversion emission properties of Yb/Er co-doped NaYF{sub 4} have also been investigated and the results demonstrated some general principles for improving up-conversion emission. - Graphical abstract: Additives and solvents can induce the phase transformation of NaYF{sub 4}, typically the use of organic sodium salt and ethanol. - Highlights: • The effect of additives and solvents on the synthesis of NaYF{sub 4} was studied in detail. • Ethanol can facilitate the formation of H-NaYF{sub 4} while acetic acid restrain it. • Three general principles for improving up-conversion emission were summarized.

  1. 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.

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

    SciTech Connect

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

    2009-01-01

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

  3. 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%.

  4. Myocardial Na,K-ATPase: Clinical aspects

    PubMed Central

    Kjeldsen, Keld

    2003-01-01

    The specific binding of digitalis glycosides to Na,K-ATPase is used as a tool for Na,K-ATPase quantification with high accuracy and precision. In myocardial biopsies from patients with heart failure, total Na,K-ATPase concentration is decreased by around 40%; a correlation exists between a decrease in heart function and a decrease in Na,K-ATPase concentration. During digitalization, around 30% of remaining pumps are occupied by digoxin. Myocardial Na,K-ATPase is also influenced by other drugs used for the treatment of heart failure. Thus, potassium loss during diuretic therapy has been found to reduce myocardial Na,K-ATPase, whereas angiotensin-converting enzyme inhibitors may stimulate Na,K pump activity. Furthermore, hyperaldosteronism induced by heart failure has been found to decrease Na,K-ATPase activity. Accordingly, treatment with the aldosterone antagonist, spironolactone, may also influence Na,K-ATPase activity. The importance of Na,K pump modulation with heart disease, inhibition in digitalization and other effects of medication should be considered in the context of sodium, potassium and calcium regulation. It is recommended that digoxin be administered to heart failure patients who, after institution of mortality-reducing therapy, still have heart failure symptoms, and that the therapy be continued if symptoms are revealed or reduced. Digitalis glycosides are the only safe inotropic drugs for oral use that improve hemodynamics in heart failure. An important aspect of myocardial Na,K pump affection in heart disease is its influence on extracellular potassium (Ke) homeostasis. Two important aspects should be considered: potassium handling among myocytes, and effects of potassium entering the extracellular space of the heart via the bloodstream. It should be noted that both of these aspects of Ke homeostasis are affected by regulatory aspects, eg, regulation of the Na,K pump by physiological and pathophysiological conditions, as well as by medical

  5. Comparing K-mer based methods for improved classification of 16S sequences.

    PubMed

    Vinje, Hilde; Liland, Kristian Hovde; Almøy, Trygve; Snipen, Lars

    2015-07-01

    The need for precise and stable taxonomic classification is highly relevant in modern microbiology. Parallel to the explosion in the amount of sequence data accessible, there has also been a shift in focus for classification methods. Previously, alignment-based methods were the most applicable tools. Now, methods based on counting K-mers by sliding windows are the most interesting classification approach with respect to both speed and accuracy. Here, we present a systematic comparison on five different K-mer based classification methods for the 16S rRNA gene. The methods differ from each other both in data usage and modelling strategies. We have based our study on the commonly known and well-used naïve Bayes classifier from the RDP project, and four other methods were implemented and tested on two different data sets, on full-length sequences as well as fragments of typical read-length. The difference in classification error obtained by the methods seemed to be small, but they were stable and for both data sets tested. The Preprocessed nearest-neighbour (PLSNN) method performed best for full-length 16S rRNA sequences, significantly better than the naïve Bayes RDP method. On fragmented sequences the naïve Bayes Multinomial method performed best, significantly better than all other methods. For both data sets explored, and on both full-length and fragmented sequences, all the five methods reached an error-plateau. We conclude that no K-mer based method is universally best for classifying both full-length sequences and fragments (reads). All methods approach an error plateau indicating improved training data is needed to improve classification from here. Classification errors occur most frequent for genera with few sequences present. For improving the taxonomy and testing new classification methods, the need for a better and more universal and robust training data set is crucial.

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

    PubMed

    Tan, M K

    1991-08-01

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

  7. Genetics Home Reference: isolated Pierre Robin sequence

    MedlinePlus

    ... Health Conditions isolated Pierre Robin sequence isolated Pierre Robin sequence Enable Javascript to view the expand/collapse ... Download PDF Open All Close All Description Pierre Robin sequence is a set of abnormalities affecting the ...

  8. A Demonstration of Automated DNA Sequencing.

    ERIC Educational Resources Information Center

    Latourelle, Sandra; Seidel-Rogol, Bonnie

    1998-01-01

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

  9. 22Ne and 23Na ejecta from intermediate-mass stars: the impact of the new LUNA rate for 22Ne(p, γ)23Na

    NASA Astrophysics Data System (ADS)

    Slemer, A.; Marigo, P.; Piatti, D.; Aliotta, M.; Bemmerer, D.; Best, A.; Boeltzig, A.; Bressan, A.; Broggini, C.; Bruno, C. G.; Caciolli, A.; Cavanna, F.; Ciani, G. F.; Corvisiero, P.; Davinson, T.; Depalo, R.; Di Leva, A.; Elekes, Z.; Ferraro, F.; Formicola, A.; Fülöp, Zs.; Gervino, G.; Guglielmetti, A.; Gustavino, C.; Gyürky, G.; Imbriani, G.; Junker, M.; Menegazzo, R.; Mossa, V.; Pantaleo, F. R.; Prati, P.; Straniero, O.; Szücs, T.; Takács, M. P.; Trezzi, D.

    2017-03-01

    We investigate the impact of the new LUNA rate for the nuclear reaction 22Ne(p, γ)23Na on the chemical ejecta of intermediate-mass stars, with particular focus on the thermally pulsing asymptotic giant branch (TP-AGB) stars that experience hot-bottom burning. To this aim, we use the PARSEC and COLIBRI codes to compute the complete evolution, from the pre-main sequence up to the termination of the TP-AGB phase, of a set of stellar models with initial masses in the range 3.0-6.0 M⊙ and metallicities Zi = 0.0005, 0.006 and 0.014. We find that the new LUNA measures have much reduced the nuclear uncertainties of the 22Ne and 23Na AGB ejecta that drop from factors of ≃10 to only a factor of few for the lowest metallicity models. Relying on the most recent estimations for the destruction rate of 23Na, the uncertainties that still affect the 22Ne and 23Na AGB ejecta are mainly dominated by the evolutionary aspects (efficiency of mass-loss, third dredge-up, convection). Finally, we discuss how the LUNA results impact on the hypothesis that invokes massive AGB stars as the main agents of the observed O-Na anticorrelation in Galactic globular clusters. We derive quantitative indications on the efficiencies of key physical processes (mass-loss, third dredge-up, sodium destruction) in order to simultaneously reproduce both the Na-rich, O-poor extreme of the anticorrelation and the observational constraints on the CNO abundance. Results for the corresponding chemical ejecta are made publicly available.

  10. 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.

  11. 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.

  12. Sequence-dependent nucleosome positioning.

    PubMed

    Chung, Ho-Ryun; Vingron, Martin

    2009-03-13

    Eukaryotic DNA is organized into a macromolecular structure called chromatin. The basic repeating unit of chromatin is the nucleosome, which consists of two copies of each of the four core histones and DNA. The nucleosomal organization and the positions of nucleosomes have profound effects on all DNA-dependent processes. Understanding the factors that influence nucleosome positioning is therefore of general interest. Among the many determinants of nucleosome positioning, the DNA sequence has been proposed to have a major role. Here, we analyzed more than 860,000 nucleosomal DNA sequences to identify sequence features that guide the formation of nucleosomes in vivo. We found that both a periodic enrichment of AT base pairs and an out-of-phase oscillating enrichment of GC base pairs as well as the overall preference for GC base pairs are determinants of nucleosome positioning. The preference for GC pairs can be related to a lower energetic cost required for deformation of the DNA to wrap around the histones. In line with this idea, we found that only incorporation of both signal components into a sequence model for nucleosome formation results in maximal predictive performance on a genome-wide scale. In this manner, one achieves greater predictive power than published approaches. Our results confirm the hypothesis that the DNA sequence has a major role in nucleosome positioning in vivo.

  13. 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.

  14. Thermoelectric method for sequencing DNA.

    PubMed

    Nestorova, Gergana G; Guilbeau, Eric J

    2011-05-21

    This study describes a novel, thermoelectric method for DNA sequencing in a microfluidic device. The method measures the heat released when DNA polymerase inserts a deoxyribonucleoside triphosphate into a primed DNA template. The study describes the principle of operation of a laminar flow microfluidic chip with a reaction zone that contains DNA template/primer complex immobilized to the inner surface of the device's lower channel wall. A thin-film thermopile attached to the external surface of the lower channel wall measures the dynamic change in temperature that results when Klenow polymerase inserts a deoxyribonucleoside triphosphate into the DNA template. The intrinsic rejection of common-mode thermal signals by the thermopile in combination with hydrodynamic focused flow allows for the measurement of temperature changes on the order of 10(-4) K without control of ambient temperature. To demonstrate the method, we report the sequencing of a model oligonucleotide containing 12 bases. Results demonstrate that it is feasible to sequence DNA by measuring the heat released during nucleotide incorporation. This thermoelectric method for sequencing DNA may offer a novel new method of DNA sequencing for personalized medicine applications. © The Royal Society of Chemistry 2011

  15. Characteristics and pharmacological regulation of epithelial Na+ channel (ENaC) and epithelial Na+ transport.

    PubMed

    Marunaka, Yoshinori

    2014-01-01

    Epithelial Na(+) transport participates in control of various body functions and conditions: e.g., homeostasis of body fluid content influencing blood pressure, control of amounts of fluids covering the apical surface of alveolar epithelial cells at appropriate levels for normal gas exchange, and prevention of bacterial/viral infection. Epithelial Na(+) transport via the transcellular pathway is mediated by the entry step of Na(+) across the apical membrane via Epithelial Na(+) Channel (ENaC) located at the apical membrane, and the extrusion step of Na(+) across the basolateral membrane via the Na(+),K(+)-ATPase located at the basolateral membrane. The rate-limiting step of the epithelial Na(+) transport via the transcellular pathway is generally recognized to be the entry step of Na(+) across the apical membrane via ENaC. Thus, up-/down-regulation of ENaC essentially participates in regulatory systems of blood pressure and normal gas exchange. Amount of ENaC-mediated Na(+) transport is determined by the number of ENaCs located at the apical membrane, activity (open probability) of individual ENaC located at the apical membrane, single channel conductance of ENaC located at the apical membrane, and driving force for the Na(+) entry via ENaCs across the apical membrane. In the present review article, I discuss the characteristics of ENaC and how these factors are regulated.

  16. Computational and Experimental Investigations of Na-Ion Conduction in Cubic Na3PSe4

    DOE PAGES

    Bo, Shou -Hang; Wang, Yan; Kim, Jae Chul; ...

    2015-11-17

    All-solid-state Na-ion batteries that operate at or close to room temperature are a promising next-generation battery technology with enhanced safety and reduced manufacturing cost. An indispensable component of this technology is the solid-state electrolyte that allows rapid shuttling of the mobile cation (i.e., Na+) between the cathode and anode. However, there are very few fast Na-ion conductors with ionic conductivity approaching that of the liquid counterparts (i.e., 1 mS cm–1). In this work, we present the synthesis and characterization of a fast Na-ion conductor, cubic Na3PSe4. This material possesses a room-temperature ionic conductivity exceeding 0.1 mS cm–1 and does notmore » require high-temperature sintering to minimize grain boundary resistance, making it a promising solid-state electrolyte candidate for all-solid-state Na-ion battery applications. On the basis of density functional theory, nudged elastic band, and molecular dynamics investigations, we demonstrate that the framework of cubic Na3PSe4 only permits rapid Na+ diffusion with the presence of defects, and that the formation of the Na vacancy (charge-balanced by slight Se2– oxidation) is more energetically favorable among the various defects considered. This finding provides important guidelines to further improve Na-ion conductivity in this class of materials.« less

  17. 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

    2016-03-08

    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

  18. Catalysis of Na+ permeation in the bacterial sodium channel NaVAb

    PubMed Central

    Chakrabarti, Nilmadhab; Ing, Christopher; Payandeh, Jian; Zheng, Ning; Catterall, William A.; Pomès, Régis

    2013-01-01

    Determination of a high-resolution 3D structure of voltage-gated sodium channel NaVAb opens the way to elucidating the mechanism of ion conductance and selectivity. To examine permeation of Na+ through the selectivity filter of the channel, we performed large-scale molecular dynamics simulations of NaVAb in an explicit, hydrated lipid bilayer at 0 mV in 150 mM NaCl, for a total simulation time of 21.6 μs. Although the cytoplasmic end of the pore is closed, reversible influx and efflux of Na+ through the selectivity filter occurred spontaneously during simulations, leading to equilibrium movement of Na+ between the extracellular medium and the central cavity of the channel. Analysis of Na+ dynamics reveals a knock-on mechanism of ion permeation characterized by alternating occupancy of the channel by 2 and 3 Na+ ions, with a computed rate of translocation of (6 ± 1) × 106 ions⋅s−1 that is consistent with expectations from electrophysiological studies. The binding of Na+ is intimately coupled to conformational isomerization of the four E177 side chains lining the extracellular end of the selectivity filter. The reciprocal coordination of variable numbers of Na+ ions and carboxylate groups leads to their condensation into ionic clusters of variable charge and spatial arrangement. Structural fluctuations of these ionic clusters result in a myriad of ion binding modes and foster a highly degenerate, liquid-like energy landscape propitious to Na+ diffusion. By stabilizing multiple ionic occupancy states while helping Na+ ions diffuse within the selectivity filter, the conformational flexibility of E177 side chains underpins the knock-on mechanism of Na+ permeation. PMID:23803856

  19. Interaction between Na+ and H+ ions on Na-H exchange in sheep cardiac Purkinje fibers.

    PubMed

    Wu, M L; Vaughan-Jones, R D

    1997-04-01

    The interaction between Na+ and H+ ions upon Na-H exchange (NHE) was examined in sheep cardiac Purkinje fibers. Acid equivalent fluxes through NHE were examined using recordings of intracellular pH and Na+ in isolated preparations measured with ion selective microelectrodes. The extent of acid-extrusion by NHE was estimated from pH(i) recovery-rate, multiplied by beta(i) (intracellular buffering power) in response to an internal acid load induced by 20 mm NH4Cl removal (nominally HCO3- free media). A mixed inhibitory effect was found of extracellular H+ on external Na+-activation of NHE (i.e. an increase, at low pH(o), in the apparent Michaelis constant for external Na+ ions [K(Nao)(0.5)] and a decrease in the maximum transport rate [V(Nao)(max)]). In addition, we confirmed that the stoichiometry of Na(o) binding is unaffected by the pH(o) (between 7.5 and 6.5), showing a Hill coefficient close to one. The interaction between Na+ and H+ ions at the internal face of the cardiac NHE was also studied. Our evidence suggests that an increase in the intracellular Na+ ion concentration ([Na+]i) inhibits acid efflux and that this inhibition can be approximated by the decrease in thermodynamic driving force caused by reducing the transmembrane Na+ gradient. It appears, however, that small variations in [Na+]i from the normal resting level (intracellular sodium activity, a(i)Na = 7 to 13 mm) have little or no effect on acid efflux, suggesting that variation of a(i)Na is not a physiologically important controller of NHE activity in heart.

  20. Glutathionylation-Dependence of Na+-K+-Pump Currents Can Mimic Reduced Subsarcolemmal Na+ Diffusion

    PubMed Central

    Garcia, Alvaro; Liu, Chia-Chi; Cornelius, Flemming; Clarke, Ronald J.; Rasmussen, Helge H.

    2016-01-01

    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 of conformation-dependent β1 pump subunit