Reduction of oxidative tissue injury and endothelial dysfunction by graduated reperfusion after cardioplegic arrest in isolated rat hearts

The aim of this study was to investigate whether or not a graduated resumption of the perfusion pressure after cardioplegic ischaemic arrest will reduce the impact of oxygen free radicals on myocardium and the cardiovasculature. Langendorff-perfused rat hearts were subjected to cardioplegia and subsequent 40 min of global ischaemia at 25 degrees C. Reperfusion was carried out either abruptly (AR) or gradually (i.e., perfusion pressure stepwise increased from 40 to 75 mmHg within 30 min -GR). GR resulted in a significant improvement of percentage recovery of left ventricular systolic pressure as compared to AR. A marked increase of thiobarbituric acid reactive substances (TBARS) was detected in the effluent during AR, accompanied by an impaired release of the endothelial vasodilator NO and diminished coronary flow rates compared to the baseline values. GR resulted in a significant reduction of TBARS in the effluent and promoted a better recovery of coronary flow as well as endothelial release of NO during the later phase of reperfusion. It is concluded that graduated reperfusion is beneficial in reducing free radical mediated peroxidative tissue injury and endothelial dysfunction upon reoxygenation.     

Polynucleotide sequence divergence among strains of Salmonella sub-genus IV and closely related organisms

Polynucleotide sequence relatedness studies were carried out to determine the extent of divergence present in Salmonella sub-genus IV strains, related strains of Salmonella of other sub-genera and the Citrobacter genus. Salmonella sub-genus IV were 91-97% related. The Salmonella of sub-genus I, II and III showed lower binding (79-87%) to Salmonella sub-genus IV. The change in thermal elution midpoint closely followed the reassociation data. Relatedness of Salmonella sub-genus IV and C. freundii ranged between 44 and 57%, which confirms that these organisms belong to different genera. The taxonomic position of Salmonella sub-genus IV is discussed according to the actual classification of the family Enterobacteriaceae.     

Location of Lignin-Bonded Pectic Polysaccharides

The hypothesis that galactose and arabinose pectic substances are disributed with lignin throughout wood cell walls was tested by analyzing a high-yield loblolly pine kraft pulp that had been separated into middle-lamella-rich and secondary-wall-rich fractions. The fractions were first treated with a polysaccharidase enzyme mixture to obtain “enzyme lignins.” The structures of the galactose and arabinose oligomers remaining attached to the lignin were determined by methylation analysis. The 1→4 linked galactose structure, characteristic of pectic materials, was present in significant amounts in the middle-lamella-rich fraction, but to only a very small extent in the secondary-wall-rich fraction. In contrast, the pectic arabinan 1→5 linked structure was a significant proportion of the arabinose from both fractions. The 1→5 linked arabinose structure can arise from a linkage of arabinoxylan to lignin through the 5 position of the arabinose substituent as well as from pectic structures. After partial acid hydrolysis, approximately half the remaining arabinose in the secondary-wall-rich fraction was attached as monomeric units to lignin through the 5 position.     

Refining the macromolecular model – achieving the best agreement with the data from X-ray diffraction experiment

ABSTRACT

Refinement of macromolecular X-ray crystal structures involves using complex software with hundreds of different settings. The complexity of underlying concepts and the sheer amount of instructions may make it difficult for less experienced crystallographers to achieve optimal results in their refinements. This tutorial review offers guidelines for choosing the best settings for the reciprocal-space refinement of macromolecular models and provides practical tips for manual model correction. To help aspiring crystallographers navigate the process, some of the most practically important concepts of protein structure refinement are described. Among the topics covered are the use and purpose of R-free, geometrical restraints, restraints on atomic displacement parameters (ADPs), refinement weights, various parametrizations of ADPs (full anisotropic refinement and TLS), and omit maps. We also give practical tips for manual model correction in Coot, modelling of side-chains with poor or missing density, and ligand identification, fitting, and refinement.     

Cross-spectral Density of Partially Coherent Gaussian Beams for Arbitrary Space Distances

Abstract

A formula for partially coherent Gaussian beams is presented, for which both of the arguments of the cross-spectral density are arbitrary points. Numerical discussions show ‘internal’ diffraction inside the beam.     

In situ nanocompression testing of irradiated copper

Increasing demand for energy and reduction of carbon dioxide emissions has revived interest in nuclear energy. Designing materials for radiation environments necessitates a fundamental understanding of how radiation-induced defects alter mechanical properties. Ion beams create radiation damage efficiently without material activation, but their limited penetration depth requires small-scale testing. However, strength measurements of nanoscale irradiated specimens have not been previously performed. Here we show that yield strengths approaching macroscopic values are measured from irradiated ~400 nm-diameter copper specimens. Quantitative in situ nanocompression testing in a transmission electron microscope reveals that the strength of larger samples is controlled by dislocation-irradiation defect interactions, yielding size-independent strengths. Below ~400 nm, size-dependent strength results from dislocation source limitation. This transition length-scale should be universal, but depends on material and irradiation conditions. We conclude that for irradiated copper, and presumably related materials, nanoscale in situ testing can determine bulk-like yield strengths and simultaneously identify deformation mechanisms.     

Mechanical annealing and source-limited deformation in submicrometre-diameter Ni crystals

The fundamental processes that govern plasticity and determine strength in crystalline materials at small length scales have been studied for over fifty years. Recent studies of single-crystal metallic pillars with diameters of a few tens of micrometres or less have clearly demonstrated that the strengths of these pillars increase as their diameters decrease, leading to attempts to augment existing ideas about pronounced size effects with new models and simulations. Through in situ nanocompression experiments inside a transmission electron microscope we can directly observe the deformation of these pillar structures and correlate the measured stress values with discrete plastic events. Our experiments show that submicrometre nickel crystals microfabricated into pillar structures contain a high density of initial defects after processing but can be made dislocation free by applying purely mechanical stress. This phenomenon, termed 'mechanical annealing', leads to clear evidence of source-limited deformation where atypical hardening occurs through the progressive activation and exhaustion of dislocation sources.     

Aberrant DNA methylation at imprinted genes in testicular sperm retrieved from men with obstructive azoospermia and undergoing vasectomy reversal

Male factor infertility has been associated with abnormal DNA methylation at imprinted genes. Little information is available on the status of imprinting in the sperm of men with azoospermia, including the association between aberrant imprinting and obstructive azoospermia (OA) or non-OA (NOA). Analysis of DNA methylation at imprinted genes in the sperm of men undergoing vasectomy reversal would aid determination of whether aberrant imprinting is associated with obstruction. Testicular sperm was retrieved from testicular biopsies obtained from men with azoospermia (N=18), including OA (N=10), NOA (N=5), and unknown pathology (N=3), and from men undergoing vasectomy reversal (N=17). Sperm was also obtained from proven fertile men (N=9). DNA methylation was investigated at multiple CpG sites within the differentially methylated regions (DMRs) of three imprinted genes, H19, IG-GTL2 and MEST, using bisulphite sequencing. Unique clones representative of single cells were analyzed. We found a significant decrease in DNA methylation at the H19 DMR in testicular sperm of azoospermic men compared with proven fertile men. The decrease was also significant between OA and proven fertile men, and between men undergoing vasectomy reversal and proven fertile men, suggesting that aberrant DNA methylation may be associated with obstruction. Changes in DNA methylation at IG-GTL2 and MEST DMRs among groups were not significant. Our data suggest that imprinting abnormalities may be associated with obstruction and may occur in response to changes in testicular environment and not only spermatogenesis failure, as previously reported. Methylation at the H19 DMR was particularly prone to modification in testicular sperm.     

Multimodal Characterization of Crystal Structure and Formation in Rubrene Thin Films Reveals Erasure of Orientational Discontinuities

Multimodal multiscale characterization provide opportunities to study organic semiconducting thin films with multiple length scales, across multiple platforms, to elucidate crystallization mechanisms of the various microstructures that impact functionality. With polarized scanning transmission X-ray and 4D-scanning transmission electron microscopy, hybrid crystalline structures in rubrene thin films in which large crystalline domains surround a common nucleus and transition to a spherulite morphology at larger radii is observed. These high-resolution techniques reveal how azimuthal orientational discontinuities at smaller radii are erased as spherulite morphology takes hold. In situ crystallization in the films with optical microscopy is also captured, discovering the importance of considering the initial temperature increase of a film during thermal annealing over the crystallization timescale. This kinetic information of the radial crystallization rate and of corresponding film heating kinetics is used to estimate the temperature at which the larger crystalline regions transition into a spherulite. By combining the results obtained from the different characterization modes, it is learned that thermal conditions can sensitively affect the crystallization of rubrene and other organic thin films. The observations suggest opportunities for more complex temperature-dependent processing to maximize hybrid structures’ functionality in organic thin films and demonstrate that multimodal studies deepen the understanding of structure-function dynamics.