7,156 research outputs found
Checking nucleic acid crystal structures
No full textThe program SFCHECK [Vaguine et al. (1999), Acta Cryst. D55, 191-205] is used to survey the quality of the structure-factor data and the agreement of those data with the atomic coordinates in 105 nucleic acid crystal structures for which structure-factor amplitudes have been deposited in the Nucleic Acid Database [NDB; Berman et al. (1992), Biophys. J. 63, 751-759]. Nucleic acid structures present a particular challenge for structure-quality evaluations. The majority of these structures, and DNA molecules in particular, have been solved by molecular replacement of the double-helical motif, whose high degree of symmetry can lead to problems in positioning the molecule in the unit cell. In this paper, the overall quality of each structure was evaluated using parameters such as the R factor, the correlation coefficient and various atomic error estimates. In addition, each structure is characterized by the average values of several local quality indicators, which include the atomic displacement, the density correlation, the B factor and the density index. The latter parameter measures the relative electron-density level at the atomic position. In order to assess the quality of the model in specific regions, the same local quality indicators are also surveyed for individual groups of atoms in each structure. Several of the global quality indicators are found to vary linearly with resolution and less than a dozen structures are found to exhibit values significantly different from the mean for these indicators, showing that the quality of the nucleic acid structures tends to be rather uniform. Analysis of the mutual dependence of the values of different local quality indicators, computed for individual residues and atom groups, reveals that these indicators essentially complement each other and are not redundant with the B factor. Using several of these indicators, it was found that the atomic coordinates of the nucleic acid bases tend to be better defined than those of the backbone. One of the local indicators, the density index, is particularly useful in spotting regions of the model that fit poorly in the electron density. Using this parameter, the quality of crystallographic water positions in the analyzed structures was surveyed and it was found that a sizable fraction of these positions have poorly defined electron density and may therefore not be reliable. The possibility that cases of poorly positioned water molecules are symptomatic of more widespread problems with the structure as a whole is also raised
Composite PEOn:NaTFSI polymer electrolyte: Preparation, thermal and electrochemical characterization
No full textMembranes of sodium bis(trifluoromethanesulfonate) imide (NaTFSI) complexed with poly(ethylene oxide) (PEO) salt have been prepared by a solvent-free hot-pressing technique with different EO:Na molar ratio. All membranes show good ionic conductivities in the range of 10(-3) S cm(-1) above 70 degrees C. However, the more NaTFSI-concentrated samples are sticky gums due to the plasticizing nature of the anion. The PEO20:NaTFSI sample exhibits the compromise of conductivity, thermal and mechanical properties. The addition of nanometric SiO2 to the PEO20:NaTFSI membranes further enhances their mechanical properties. Moreover, the PEO20:NaTFSI + 5 wt.% SiO2 membranes show similar ionic conductivity and similar anodic electrochemical stability in comparison to the ceramic free PEO20:NaTFSI sample. In a Na-(s)/polymer electrolyte/Na-(s) symmetrical cell followed up to 30 days, the presence of the ceramic filler slightly increased the interface resistance in comparison to the ceramic-free membrane. Nuclear magnetic resonance determinations of anion diffusion coefficients and Na+ mobility suggest that presence of filler may have a positive affect on the cation transference number that is in accordance with the t(Na)(+) transference number measurement. (C) 2013 Elsevier B.V. All rights reserved
Analysis of heat transfer in Berman flow of nanofluids with Navier slip, viscous dissipation, and convective cooling
No full textPlease cite as follows: Makinde, O. D., Khamis, S., Tshehla, M. S. & Franks, O. 2014. Analysis of heat transfer in Berman flow of nanofluids with Navier slip, viscous dissipation, and convective cooling. Advances in Mathematical Physics, 2014:1-13 (Article ID 809367), doi:10.1155/2014/809367.The original publication is available at http://www.hindawi.com/journals/ampHeat transfer characteristics of a Berman flow of water based nanofluids containing copper (Cu) and alumina (Al2O3) as nanoparticles in a porous channel with Navier slip, viscous dissipation, and convective cooling are investigated. It is assumed that the exchange of heat with the ambient surrounding takes place at the channel walls following Newton’s law of cooling. The governing partial differential equations and boundary conditions are converted into a set of nonlinear ordinary differential equations using appropriate similarity transformations. These equations are solved analytically by regular perturbation methods with series improvement technique and numerically using an efficient Runge-Kutta Fehlberg integration technique coupled with shooting scheme.The effects of the governing parameters on the dimensionless velocity, temperature, skin friction, pressure drop, and Nusselt numbers are presented graphically and discussed quantitatively.http://www.hindawi.com/journals/amp/2014/809367/Publisher's versio
Dopamine D2/D3 receptor availability in genetically leptin-deficient patients after long-term leptin replacement
No full textAbstract not availableK Ishibashi, S M Berman, G Paz-Filho, B Lee, C Robertson, M A Mandelkern, M-L Wong, J Licinio, E D Londo
Protein-RNA interactions: a structural analysis
No full textA detailed computational analysis of 32 protein-RNA complexes is presented. A number of physical and chemical properties of the intermolecular interfaces are calculated and compared with those observed in protein-double-stranded DNA and protein-single-stranded DNA complexes. The interface properties of the protein-RNA complexes reveal the diverse nature of the binding sites. van der Waals contacts played a more prevalent role than hydrogen bond contacts, and preferential binding to guanine and uracil was observed. The positively charged residue, arginine, and the single aromatic residues, phenylalanine and tyrosine, all played key roles in the RNA binding sites. A comparison between protein-RNA and protein-DNA complexes showed that whilst base and backbone contacts (both hydrogen bonding and van der Waals) were observed with equal frequency in the protein-RNA complexes, backbone contacts were more dominant in the protein-DNA complexes. Although similar modes of secondary structure interactions have been observed in RNA and DNA binding proteins, the current analysis emphasises the differences that exist between the two types of nucleic acid binding protein at the atomic contact level
Supplemental Material, Figure_1S - Steroid-Free Immune Suppression Impairs Glycemic Control in a Healthy Cynomolgus Monkey
No full textSupplemental Material, Figure_1S for Steroid-Free Immune Suppression Impairs Glycemic Control in a Healthy Cynomolgus Monkey by Dora M. Berman, Phillip Ruiz, Manuel Blandino-Rosano, Ernesto Bernal-Mizrachi, and Norma S. Kenyon in Cell Transplantation</p
Crella (Crella) hennequinae Goodwin & Berman & Hendry 2019, sp. nov.
No full textCrella (Crella) hennequinae sp. nov. (Figure 7, Table 5) lsid:zoobank.org:act: 81218B8F-1C10-4711-A2E2-D51FD220A60 Type material: Holotype: BELUM. Mc 2015.725 Port Charcot, Booth Island (65°03.853’S, 64° 01.868’W), depth 6–16 m; collected by C. Goodwin and E. Priestley, 23/02/2015. Paratypes: BELUM. Mc 2015.693 Vieugue Island (65°38.758’S, 65° 12.540’W), depth 10–22 m; collected by C. Goodwin and E. Priestley, 23/02/2015. BELUM. Mc 2015.640 Rocks near San Martin Islands (65°41.297’S, 65° 20.091’W), depth 6–21 m; collected by C. Goodwin and E. Priestley, 17/02/2015. Other specimen: BELUM. Mc 2015.736 Port Charcot, Booth Island (65°03.853’S, 64° 01.868’W), depth 6–16 m; collected by C. Goodwin and E. Priestley, 23/02/2015. Diagnosis. Southern Ocean Crella (Crella) with one category of lightly and evenly spined basal acanthostyles. Etymology. Named after Juliette Hennequin, first mate of the expedition vessel the Hans Hansson, in recognition of her support. External morphology. In situ appearance (Figure 7A): Bright orange crust with prominent pore sieves. Growing over bedrock. Some patches were very large (> 50 cm in diameter). Preserved appearance. Fairly firm pale yellow crust with smooth, detachable, surface on which pore sieves are clearly visible. Storage ethanol has turned orange. Skeleton (Figure 7B): Plumose. Strongly hispid ascending columns of acanthostyles and tornotes. Dense ectosomal layer of acanthoxea. Spicules: Measurements given here are from the holotype BELUM.Mc2015.725. See Table 5 for dimensions of paratypes. Acanthostyles (Figure 7C,D): 454(465)477 by 16(20) 26 µm. Slightly curved with small spines very sparsely scattered along their length, in some spicules these are so sparse that they initially appear smooth. The heads are not tylote. There is no secondary class of echinating acanthostyles. Ectosomal anisotornotes (Figure 7E): 294(325)353 by 7(11) 15 µm. Slightly fusiform tornotes with asymmetrical ends, one end usually smoothly tapered and one more abruptly pointed. Ectosomal acanthoxeas (Figure 7F): 53(62)74 by 4(7) 10 µm. Often slightly curved. Entirely spined with large spines. Remarks. These specimens are assigned to Crella as they possess an ectosomal crust of acanthoxeas and do not have chelae. As basal acanthostyles echinating the substrate are present they are assigned to Crella (Crella) (Van Soest 2002a). There are currently only five valid species of Crella (Crella) two of which, Crella (Crella) aurantiaca Bertolino, Calcinai & Pansini, 2009 and Crella (Crella) tubifex (Hentschel, 1914), have been recorded from the Antarctic. C. aurantiaca differs from our specimen in having two categories of basal acanthostyles. The form of both the categories of acanthostyles also differs in that they have very dense clumps of large recurved spines on their heads, whereas our specimen has very small spines evenly spread along the length of the shaft. Crella (Crella) tubifex possesses amphistrongyles rather than tornotes, and ectosomal acanthostrongyles rather than acanthoxeas.Published as part of Goodwin, Claire E., Berman, Jade & Hendry, Katharine R., 2019, Demosponges from the sublittoral and shallow-circalittoral (<24 m depth) Antarctic Peninsula with a description of four new species and notes on in situ identification characteristics, pp. 461-508 in Zootaxa 4658 (3) on pages 477-478, DOI: 10.11646/zootaxa.4658.3.3, http://zenodo.org/record/337602
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