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  • American Institute of Physics (AIP)  (7)
  • Oxford University Press  (6)
  • Wiley-Blackwell  (3)
  • 2010-2014  (7)
  • 1995-1999  (7)
  • 1960-1964  (2)
  • 1
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    Erratum: “A method to determine fault vectors in 4H-SiC from stacking sequences observed on high resolution transmission electron microscopy images” [J. Appl. Phys. 116, 104905 (2014)] (2014)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2014-10-23
    Print ISSN: 0021-8979
    Electronic ISSN: 1089-7550
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 2
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    A method to determine fault vectors in 4H-SiC from stacking sequences observed on high resolution transmission electron microscopy images (2014)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2014-09-12
    Description: A new method has been developed to determine the fault vectors associated with stacking faults in 4H-SiC from their stacking sequences observed on high resolution TEM images. This method, analogous to the Burgers circuit technique for determination of dislocation Burgers vector, involves determination of the vectors required in the projection of the perfect lattice to correct the deviated path constructed in the faulted material. Results for several different stacking faults were compared with fault vectors determined from X-ray topographic contrast analysis and were found to be consistent. This technique is expected to applicable to all structures comprising corner shared tetrahedra.
    Print ISSN: 0021-8979
    Electronic ISSN: 1089-7550
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 3
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    The Genome Database for Rosaceae (GDR): year 10 update (2013)
    Oxford University Press
    Details
    Publication Date: 2013-12-29
    Description: The Genome Database for Rosaceae (GDR, http:/www.rosaceae.org ), the long-standing central repository and data mining resource for Rosaceae research, has been enhanced with new genomic, genetic and breeding data, and improved functionality. Whole genome sequences of apple, peach and strawberry are available to browse or download with a range of annotations, including gene model predictions, aligned transcripts, repetitive elements, polymorphisms, mapped genetic markers, mapped NCBI Rosaceae genes, gene homologs and association of InterPro protein domains, GO terms and Kyoto Encyclopedia of Genes and Genomes pathway terms. Annotated sequences can be queried using search interfaces and visualized using GBrowse. New expressed sequence tag unigene sets are available for major genera, and Pathway data are available through FragariaCyc, AppleCyc and PeachCyc databases. Synteny among the three sequenced genomes can be viewed using GBrowse_Syn. New markers, genetic maps and extensively curated qualitative/Mendelian and quantitative trait loci are available. Phenotype and genotype data from breeding projects and genetic diversity projects are also included. Improved search pages are available for marker, trait locus, genetic diversity and publication data. New search tools for breeders enable selection comparison and assistance with breeding decision making.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    Metal-induced DNA translocation leads to DNA polymerase conformational activation (2012)
    Oxford University Press
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    Publication Date: 2012-04-15
    Description: Binding of the catalytic divalent ion to the ternary DNA polymerase β/gapped DNA/dNTP complex is thought to represent the final step in the assembly of the catalytic complex and is consequently a critical determinant of replicative fidelity. We have analyzed the effects of Mg 2+ and Zn 2+ on the conformational activation process based on NMR measurements of [methyl- 13 C]methionine DNA polymerase β. Unexpectedly, both divalent metals were able to produce a template base-dependent conformational activation of the polymerase/1-nt gapped DNA complex in the absence of a complementary incoming nucleotide, albeit with different temperature thresholds. This conformational activation is abolished by substituting Glu295 with lysine, thereby interrupting key hydrogen bonds necessary to stabilize the closed conformation. These and other results indicate that metal-binding can promote: translocation of the primer terminus base pair into the active site; expulsion of an unpaired pyrimidine, but not purine, base from the template-binding pocket; and motions of polymerase subdomains that close the active site. We also have performed pyrophosphorolysis studies that are consistent with predictions based on these results. These findings provide new insight into the relationships between conformational activation, enzyme activity and polymerase fidelity.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    Genomic, RNAseq, and Molecular Modeling Evidence Suggests That the Major Allergen Domain in Insects Evolved from a Homodimeric Origin (2013)
    Oxford University Press
    Details
    Publication Date: 2013-12-12
    Description: The major allergen domain (MA) is widely distributed in insects. The crystal structure of a single Bla g 1 MA revealed a novel protein fold in which the fundamental structure was a duplex of two subsequences (monomers), which had diverged over time. This suggested that the evolutionary origin of the MA structure may have been a homodimer of this smaller subsequence. Using publicly available genomic data, the distribution of the basic unit of this class of proteins was determined to better understand its evolutionary history. The duplication and divergence is examined at three distinct levels of resolution: 1) within the orders Diptera and Hymenoptera, 2) within one genus Drosophila , and 3) within one species Aedes aegypti . Within the family Culicidae, we have found two separate occurrences of monomers as independent genes. The organization of the gene family in A. aegypti shows a common evolutionary origin for its monomer and several closely related MAs. Molecular modeling of the A. aegypti monomer with the unique Bla g 1 fold confirms the distant evolutionary relationship and supports the feasibility of homodimer formation from a single monomer. RNAseq data for A. aegypti confirms that the monomer is expressed in the mosquito similar to other A. aegypti MAs after a blood meal. Together, these data support the contention that the detected monomer shares similar functional characteristics to related MAs in other insects. An extensive search for this domain outside of Insecta confirms that the MAs are restricted to insects.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    Selective unfolding of one Ribonuclease H domain of HIV reverse transcriptase is linked to homodimer formation (2014)
    Oxford University Press
    Details
    Publication Date: 2014-05-01
    Description: HIV-1 reverse transcriptase (RT), a critical enzyme of the HIV life cycle and an important drug target, undergoes complex and largely uncharacterized conformational rearrangements that underlie its asymmetric folding, dimerization and subunit-selective ribonuclease H domain (RH) proteolysis. In the present article we have used a combination of NMR spectroscopy, small angle X-ray scattering and X-ray crystallography to characterize the p51 and p66 monomers and the conformational maturation of the p66/p66' homodimer. The p66 monomer exists as a loosely structured molecule in which the fingers/palm/connection, thumb and RH substructures are connected by flexible (disordered) linking segments. The initially observed homodimer is asymmetric and includes two fully folded RH domains, while exhibiting other conformational features similar to that of the RT heterodimer. The RH' domain of the p66' subunit undergoes selective unfolding with time constant ~6.5 h, consistent with destabilization due to residue transfer to the polymerase' domain on the p66' subunit. A simultaneous increase in the intensity of resonances near the random coil positions is characterized by a similar time constant. Consistent with the residue transfer hypothesis, a construct of the isolated RH domain lacking the two N-terminal residues is shown to exhibit reduced stability. These results demonstrate that RH' unfolding is coupled to homodimer formation.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    Metal and ligand binding to the HIV-RNase H active site are remotely monitored by Ile556 (2012)
    Oxford University Press
    Details
    Publication Date: 2012-11-04
    Description: HIV-1 reverse transcriptase (RT) contains a C-terminal ribonuclease H (RH) domain on its p66 subunit that can be expressed as a stable, although inactive protein. Recent studies of several RH enzymes demonstrate that substrate binding plays a major role in the creation of the active site. In the absence of substrate, the C-terminal helix E of the RT RNase H domain is dynamic, characterized by severe exchange broadening of its backbone amide resonances, so that the solution characterization of this region of the protein has been limited. Nuclear magnetic resonance studies of 13 C-labeled RH as a function of experimental conditions reveal that the 1 methyl resonance of Ile556, located in a short, random coil segment following helix E, experiences a large 13 C shift corresponding to a conformational change of Ile556 that results from packing of helix E against the central β-sheet. This shift provides a useful basis for monitoring the effects of various ligands on active site formation. Additionally, we report that the RNase H complexes formed with one or both divalent ions can be individually observed and characterized using diamagnetic Zn 2+ as a substitute for Mg 2+ . Ordering of helix E results specifically from the interaction with the lower affinity binding to the A divalent ion site.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    Ray tracing in random media (1996)
    Oxford University Press
    Details
    Publication Date: 1996-01-01
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
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  • 9
    Electronic Resource
    Electronic Resource
    Traps in undoped semi-insulating InP obtained by high temperature annealing (1996)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 79 (1996), S. 6947-6950 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The presence and evolution of traps in undoped semi-insulating (SI) InP obtained by high temperature annealing (900 °C for 90 h) in poor or rich phosphorus atmosphere has been studied by means of photoinduced current transient spectroscopy. Six traps named A1 to A6 having activation energies ranging from 0.2 to 0.6 eV have been detected in three samples submitted to the same annealing process. The samples differ in the Fe concentration of the starting material and the applied phosphorus pressure in the annealing process. A comparison of the corresponding photoinduced current transient spectroscopy spectra shows that among the observed traps, the 0.2 eV one can be related to a phosphorus deficiency, and the 0.3 eV and 0.4 eV traps could be due to an excess of phosphorus during annealing. Moreover, the trap corresponding to iron (0.6 eV) has been observed in all the studied samples. © 1996 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.361432
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  • 10
    Electronic Resource
    Electronic Resource
    Effect of the Onsager coefficient and internal relaxation modes on spinodal decomposition in the high molecular isotopic blend polystyrene/deutero-polystyrene studied with small angle neutron scattering (1996)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 104 (1996), S. 5326-5337 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The early state of spinodal decomposition was studied by small angle neutron scattering in the critical mixture of the isotopic blend deutero-polystyrene/polystyrene (d-PS/PS) of equal molecular volume of 1.42×106 cm3/mol in a temperature range 12 K≤||Tc−T||≤82 K. This process can be described by the relaxation between two static structure factors, S(Q) representing the equilibrium values of the system in the mixed state and at the temperature where phase separation occurs. The time evolution of the relaxation process is described by the dynamical structure factor, L(Q,t) which depends on the dynamic properties of the mixture. It will be shown that the static structure factor of a mixed system can also be determined in the unstable two-phase region during the early state of spinodal decomposition. Consistent values for the Flory–Huggins parameter were found in comparison with a lower molecular d-PS/PS sample and, therefore, a lower critical temperature which was even smaller than the phase separation temperatures of the present system.The observed time evolution of the fluctuation modes is nonexponential. Therefore, it was originally supposed that internal modes of the coil come into play. The analysis of the data with an ansatz by Akcasu, which takes internal modes into account showed, however, that the phase separation in the experimental range of wave number and time is dominated by the centre of mass diffusion as in the C–H–C case and the nonexponential behavior was attributed to a time dependent increase of the "range'' of the Onsager coefficient. A range of the Onsager coefficient larger than the radius of gyration of a single coil is predicted in case of entangled polymers. However, no time dependence was predicted so far. The evaluated diffusion constants follow an Arrhenius behavior and are consistent with earlier studies. They show a D0∝N−2 scaling consistent with reptation. A further result is the observation of a second order peak in the structure factor already in the early times of spinodal decomposition. So far, this was only attributed to the late state of spinodal decomposition. © 1996 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.471262
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