Quantification of secondary structure prediction improvement using multiple alignments

The use of multiple sequence alignments for secondary structurepredictions is analysed. Seven different protein families, containingonly sequences of known structure, were considered to providea range of alignment and prediction conditions. Using alignmentsobtained by spatial superposition of main chain atoms in knowntertiary protein structures allowed a mean of 8% in secondarystructure prediction accuracy, when compared to those obtainedfrom the individual sequences. Substitution of these alignmentsby those determined directly from an automated sequence alignmentalgorithm showed variations in the prediction accuracy whichcorrelated with the quality of the multiple alignments and distanceof the primary sequence. Secondary structure predictions canbe reliably improved using alignments from an automatic alignmentprocedure with a mean increase of 6.87percnt;, giving an overallprediction accuracy of 68.5%, if there is a minimum of 25% sequenceidentity between all sequences in a family.     

Microstructure and morphology of amine-cured epoxy coatings before and after outdoor exposures—An AFM study

Atomic force microscopy (AFM) has been used to study the morphology and microstructure of an amine-cured epoxy before and after outdoor exposure. Measurements were made from samples prepared in an essentially CO₂-free, H₂O-free glove box and from samples prepared in ambient conditions. For those prepared in a CO₂-free glove box, AFM imaging was conducted on (1) an unexposed air/coating surface, (2) an unexposed coating bulk, (3) an unexposed coating/substrate interface, and (4) a field exposed air/coating surface. For samples prepared in ambient conditions, only the unexposed air/coating surface was investigated. The same regions of the exposed samples were scanned periodically by the AFM to monitor changes in the surface morphology of the coating as UV exposure progressed. Small angle neutron scattering and Fourier transform infrared spectroscopy (FTIR) studies were performed to verify the microstructure and to follow chemical changes during outdoor exposure, respectively. The results have shown that amine blushing, which occurs only under ambient conditions, had a significant effect on the surface morphology and microstructure of the epoxy. The surface morphology of the samples prepared under CO₂-free, dry conditions was generally smooth and homogeneous. However, the interface and the bulk samples clearly revealed a two-phase structure consisting of bright nodular domains and dark interstitial regions, indicating an inhomogeneous microstructure. Such heterogeneous structure of the bulk was in good agreement with results obtained by small angle neutron scattering of unexposed samples and by AFM phase imaging of the degraded sample surface. The relationship between submicrometer physical changes and molecular chemical degradation is discussed. Presented at the 82nd Annual Meeting of the Federation of Societies for Coatings Technology, October 27–29, 2004, in Chicago, IL.     

Use of laser scanning confocal microscopy for characterizing changes in film thickness and local surface morphology of UV-exposed polymer coatings

Laser scanning confocal microscopy (LSCM) has been used to characterize the changes in film thickness and local surface morphology of polymer coatings during the UV degradation process. With the noninvasive feature of LSCM, one can obtain thickness information directly and nondestructively at various exposure times without destroying the specimens or deriving the thickness values from IR measurement by assuming uniform film ablation. Two acrylic polymer coatings were chosen for the study, and the physical and chemical changes of the two systems at various exposure times were measured and analyzed. Those measurable physical changes caused by UV exposure include film ablation, formation of pits and other surface defects, and increases in surface roughness. It was found in both coatings that changes in measured film thickness by LSCM were not correlated linearly to the predicted thickness loss using the changes in the CH band obtained by the Fourier Transform Infrared (FTIR) spectroscopy measurements in the later degradation stages. This result suggested it was not a uniform film ablation process during the UV degradation. At later stages, where surface deformation became severe, surface roughness and profile information using LSCM were also proven to be useful for analyzing the surface degradation process Presented at the 81st Annual Meeting of the Federation of Societies for Coatings Technology, November 13–14, 2004 in Philadelphia, PA.     

Inhibition of lipid peroxidation in UVA‐treated skin fibroblasts by luteolin and its glucosides

Ultraviolet A (UVA) radiation causes oxidative damage to human skin cells. This damage may be reduced or prevented using plant compounds as photoprotectants. To investigate the relationship between chemical structure and UVA‐protective activity, three structurally related flavonoids, namely luteolin, luteolin‐7‐O‐glucoside (both present in artichoke) and luteolin‐4'‐O‐glucoside (present in wild carrot), were studied. Human skin fibroblasts exposed to UVA (250 and 500 kJ/m²) were treated with each flavonoid (30 µM) for 18 h prior to irradiation. The extent of lipid peroxidation in the cellular extracts was assessed as lipid peroxides and malondialdehyde (MDA). Luteolin and luteolin‐7‐O‐glucoside both prevented a significant increase in lipid peroxides at 250 kJ/m², but at 500 kJ/m² their effectiveness was clearly attenuated. Contrastingly, luteolin‐4'‐O‐glucoside was pro‐oxidant at both radiation doses. Measurements of MDA levels highlighted that luteolin was clearly more effective than the two glucosides at both 250 and 500 kJ/m². Overall, these results show clear differences between the three flavonoids and suggest that the B ring 3',4'‐dihydroxy group, lacking in luteolin‐4'‐O‐glucoside, may be particularly important. Flavonoid: transition metal ion chelation studies confirmed the influence of the 3',4'‐dihydroxy group, which is also relevant to the quenching of singlet oxygen. These features as well as the greater lipophilic nature of luteolin together explain the superior activity of this flavonoid which may be potentially useful as a supplement in photoprotective skin preparations.     

Microstructure and Microchemistry of Polymer-Derived Crystalline SiC Fibers

Stoichiometric and near-stoichiometric silicon carbide fibers, derived from the polymer polycarbosilane, have been characterized by scanning Auger and transmission electron microscope techniques. Excess carbon usually appeared in the fibers, but it could be eliminated by controlling processing conditions. The fibers consisted mainly of submicrometer-sized SiC microcrystals, with a considerably twinned and stacking-faulted β-SiC structure. Free carbon, which appeared in the form of graphite, was the only detectable intergranular phase in the nonstoichioinetric SiC fibers, while the stoichiometric SiC fibers contained no detectable second phase whatsoever.     

Ammoxidation of toluene over Y-Ba-Cu-Co-O perovskites

Ammoxidation of toluene over the perovskites YBa₂Cu₃O_6.1, YBa₂Cu₂CoO_6.7 and YBaCuCoO_4.9 was investigated at 400 °C. At low partial pressures of O₂ benzonitrile was selectively formed, while CO₂ was the main product at high pressures of O₂. Systematic differences in activity were observed for the three phases and are related to the crystal contents of Cu and Co. At low O₂ pressures, Cu-sites are active for nitrile formation, while Co-sites give CO₂. At high O₂ pressures, the activity for CO₂ of Cu-sites increases more than that of Co-sites due to filling of near-surface oxygen vacancies.     

Relationship between chemical degradation and thickness loss of an amine-cured epoxy coating exposed to different UV environments

The relationship between chemical degradation and thickness loss of an unpigmented, non UV-stabilized, crosslinked amine-cured epoxy coating exposed to three UV conditions was investigated. Spin-coated samples having a thickness of approximately 7 μm on an Si substrate were prepared from a stochiometric mixture of a bisphenol A epoxy resin and a tetra-functional amine curing agent. Samples were exposed outdoors and to two accelerated laboratory UV environments. Chemical degradation and thickness loss were measured by transmission Fourier transform infrared spectroscopy (FTIRS) and laser scanning confocal microscopy (LSCM), respectively. In addition, surface roughness and morphological changes were measured by atomic forcemicrosocopy (AFM) and LSCM. Substantial chemical degradation, thickness loss, and morpholocal changes occurred in the exposed films, and the rate of chemical degradation was greater than that due to the thickness loss. This additional chemical loss was attributed to an inhomogeneous degradation process in which nanoscale localized depressions initiate at certain sites on the surface, which then enlarge and deepen with exposure time. The results of this study provide a better understanding of the degradation mechanism and should lead to the development of scientific-based models for predicting the service life of crosslinked amine-cured epoxy coatings. Presented at the 82nd Annual Meeting of the Federation of Societies for Coatings Technology, October 27–29, 2004, in Chicago, IL     

Ceramics for Prosthetic Hip and Knee Joint Replacement

The most commonly used bearing couple in prosthetic hip or knee joint replacements consists of a cobalt–chrome (CoCr) metal alloy articulating against ultrahigh-molecular-weight polyethylene. Ceramics have been used as an alternative to metal-on-polyethylene in joint replacement surgery of arthritic hips and knees since the 1970s. In prosthetic hip and knee bearings, ceramic surfaces offer a major benefit of drastically reduced wear rates and excellent long-term biocompatibility, which can increase the longevity of prosthetic hip and knee joints. This benefit is important clinically because hip and knee replacement has become a very common surgical procedure, particularly in the United States, and because these procedures are being increasingly performed in younger patients who place greater demands on the prosthetic bearings. However, ceramics are brittle and the risk of catastrophic bearing failure in vivo , while rare, is a major concern. Improvements in material quality, manufacturing methods, and implant design have resulted in a drastic reduction of the incidence of such failures, so that modern ceramic bearings are safe and reliable if used with components of proven design and durability. Future material improvements are actively being investigated to reduce the risk of ceramic-bearing failures even further. The purpose of this article is to review the structure, properties, applications, and limitations of the ceramics that have been used in orthopedic bearings, and to describe the new ceramic composite materials and surface treatments that will be available for joint replacement surgery in the near future.     

正确表面预处理对涂料干膜杀菌剂抗微生物活性的影响

通过使用墙体杀菌清洁与非杀菌清洁后涂料干膜的性能比较，评价了杀菌清洗对提高涂料干膜性能的有效性，揭示了怎样用杀菌清洁提高杀菌系统的特性。同时，比较了传统杀菌剂和新式杀菌剂的性能差别。