18 research outputs found
[Photograph 2012.201.B0248.0276]
No full textPhotograph used for a story in the Oklahoma Times newspaper. Caption: "Hair stylist author and educator Peter Hantz explains the technique of French lacing at a recent Oklahoma City seminar.
Structure and Dynamics of Phosphate Linkages and Sugars in an Abasic Hexaloop RNA Hairpin
No full textAbstractHairpins containing hexaloops are well represented among the diverse conformations adopted by the RNA molecules. To investigate the intrinsic properties of a backbone submitted to a hexaloop fold, we present here a molecular dynamics study of an abasic hexaloop closed by an A-form 6 basepair stem. The analysis of the 23ns trajectory made in explicit solvent shows that both the sugars and the torsion angles in the loop undergo numerous conformational transitions. The south sugars, although not in a majority, are the major actors of the loop stretching. The five torsion angles, ɛ, ζ, α, β, and γ, are unequally variable, and only ζ and α exhibit trimodal distributions. The analysis of the phosphate linkages in terms of ɛ-ζ˜-α˜-β˜-γ-combinations allows us to define five conformational families, each one composed of one major substate in equilibrium with several less populated ones. The transitions between the substates within a family follow specific pathways involving the angles ɛ, ζ, and α. Thus, this work reveals that the backbone conformational space is both reduced and ordered even in a hexaloop devoid of bases
Current Awareness
No full textInternational audienceIn order to keep subscribers up-to-date with the latest developments in their field, John Wiley & Sons are providing a current awareness service in each issue of the journal. The bibliography contains newly published material in the field of NMR in biomedicine. Each bibliography is divided into 9 sections: 1 Books, Reviews ' Symposia; 2 General; 3 Technology; 4 Brain and Nerves; 5 Neuropathology; 6 Cancer; 7 Cardiac, Vascular and Respiratory Systems; 8 Liver, Kidney and Other Organs; 9 Muscle and Orthopaedic. Within each section, articles are listed in alphabetical order with respect to author. If, in the preceding period, no publications are located relevant to any one of these headings, that section will be omitted
Solution structure of a non-palindromic 16 base-pair DNA related to the HIV-1 kappa B site: evidence for BI-BII equilibrium inducing a global dynamic curvature of the duplex.
No full textInternational audience1H and 31P NMR spectroscopy have been used together with molecular modelling to determine the fine structure of a non-palindromic 16 bp DNA containing the NF-kappa B binding site. Much emphasis has been placed upon NMR optimization of both two-dimensional 31P NMR techniques to extract structural information defining the phosphodiester backbone conformation and selective homonuclear 2D COSY experiments to determine sugar conformations. NMR data show evidence for a dynamic behaviour of steps flanking the ten base-pairs of the NF-kappa B binding site. A BI-BII equilibrium at these steps is demonstrated and two models for each extreme conformation are proposed in agreement with NMR data. In the refined BII structures, the NF-kappa B binding site exhibits an intrinsic curvature towards the major groove that is magnified by the four flanking steps in the BII conformation. Furthermore, the base-pairs are translated into the major groove. Thus, we present a novel mode of dynamic intrinsic curvature compatible with the DNA curvature observed in the X-ray structure of the p50-DNA complex
Solution conformation of an RNA–DNA hybrid duplex containing a pyrimidine RNA strand and a purine DNA strand
No full textInternational audienceRNA–DNA hybrid duplexes are involved in transcription, replication and reverse transcription of nucleic acids. Informationon such duplexes may shed some light on the mechanism of these processes. For this purpose, the influence of base compositionon the structure of a polypyrimidine–polypurine RNA–DNA duplex r(cucuccuucucuu). d(GAGAGGAAGAGAA) has beenstudied using 1H, 31P and 13C NMR experiments, molecular modeling (JUMNA program) and NOE back-calculation methods.The resulting structure of the 13-mer hybrid duplex shows that the RNA strand is in the expected A-type conformation while theDNA strand is in a very flexible conformation. In the DNA strand, the desoxyribose sugars retain the C2%-endo B-typeconformation. The duplex helical parameters (such as inclination, twist and displacement of the bases) are close to the A-typeconformation. No bending was observed for the global axis curvature. The major groove width is close to the B-form value andthe minor groove width is intermediate between standard values for A and B-forms. These results are in favour of theindependence of minor groove size (where RNase H interacts) and the base composition of the hybrid duplexes. © 2001 ElsevierScience B.V. All rights reserved
Additional file 1 of Nuclear magnetic resonance-based serum metabolomic analysis reveals different disease evolution profiles between septic shock survivors and non-survivors
Get PDFTable S1. Assignment of spectra recorded with one exemplar serum sample from a septic shock patient. Figure S1. Assignment of spectra recorded with an example of a representative 1H-NMR spectrum. The assigned peaks corresponding with the key metabolite discriminants have been marked in the figure. Figure S2. A PCA calculated with H0 samples from 11 nonsurvivors who died during the first 24 h (red dots) and those from the other non-survivors who died from the second day to the seventh day after the first sampling (blue dots). Figure S3. PCA model separating survivors from non-survivors with H0 samples before the exclusion of outlier. One sample of a non-survivor was observed as an outlier for the PCA. This outlier has been removed before statistical analyses. Blue dots: survivors, yellow dots: non-survivors. Figure S4 (respectively S5). Cross-validation by 200 times permutation between X and Y for the OPLS-DA model with H0 samples (respectively H24). The green dots stand for the obtained R2 value and the blue dots stand for the obtained Q2 value within the 200 permutations. The Y-axis represents R2 and Q2 calculated for every model while the X-axis represents the correlation coefficient between original and permuted response data. Figure S6. Loading plots for paired OPLS-DA models showing important discriminatory metabolites that contribute to the separation between H0 and H24 samples. The paired models for the survivors and non-survivors are shown separately. The peaks are assigned to corresponding discriminatory metabolites. The correlations between the assigned metabolites and the model have been shown with the colors. a: loading plot for the separation between H0 and H24 for the survivors; b: loading plot for the separation between H0 and H24 for the non-survivors. (DOCX 829 kb
Aminoglycoside and glycopeptide renal toxicity in intensive care patients studied by proton magnetic resonance spectroscopy of urine
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Magnetic resonance spectroscopy of cellular lipid extracts from sensitive, resistant and reverting K562 cells and flow cytometry for investigating the P-glycoprotein function in resistance reversion
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