Bioinformatics approaches for disulfide connectivity prediction

Protein structure prediction with computational methods has gained much attention in the research fields of protein engineering and protein folding studies. Due to the vastness of conformational space, one of the major tasks is to restrain the flexibility of protein structure and reduce the search space. Many studies have revealed that, with the information of disulfide connectivity available, the search in conformational space can be dramatically reduced and lead to significant improvements in the prediction accuracy. As a result, predicting disulfide connectivity using bioinformatics approaches is of great interest nowadays. In this mini-review, the prediction of disulfide connectivity in proteins will be discussed in four aspects: (1) how the problem formulated and the computational techniques used in the literatures; (2) the effects of the features adopted to encode the information and the biological meanings implied; (3) the problems encountered and limitations of disulfide connectivity prediction; and (4) the practical usages of predicted disulfide bond information in molecular simulation and the prospects in the future.     

A New Benzoquinone from Antrodia camphorata

Chemistry of Natural Compounds - A new benzoquinone, 2-hydroxy-3-methoxy-5-methyl-p-benzoquinone (1), along with 11 known compounds including three benzoquinones, 2-methoxy-6-methyl-p-benzoquinone...     

A New Benzenoid from Liriodendron chinense

Chemistry of Natural Compounds - A new benzenoid, liriodenchic acid (1), along with nine known compounds that include two aporphine alkaloids, liriodenine (2) and (–)-anonaine (3); two...     

Hyperbaric oxygen upregulates cochlear constitutive nitric oxide synthase

Background  

Hyperbaric oxygen therapy (HBOT) is a known adjuvant for treating ischemia-related inner ear diseases. Controversies still exist in the role of HBOT in cochlear diseases. Few studies to date have investigated the cellular changes that occur in inner ears after HBOT. Nitric oxide, which is synthesized by nitric oxide synthase (NOS), is an important signaling molecule in cochlear physiology and pathology. Here we investigated the effects of hyperbaric oxygen on eardrum morphology, cochlear function and expression of NOS isoforms in cochlear substructures after repetitive HBOT in guinea pigs.     

Efficiency decomposition for general multi-stage systems in data envelopment analysis

Conventional data envelopment analysis (DEA) models only consider the inputs supplied to the system and the outputs produced from the system in measuring efficiency, ignoring the operations of the internal processes. The results thus obtained sometimes are misleading. This paper discusses the efficiency measurement and decomposition of general multi-stage systems, where each stage consumes exogenous inputs and intermediate products (produced from the preceding stage) to produce exogenous outputs and intermediate products (for the succeeding stage to use). A relational model is developed to measure the system and stage efficiencies at the same time. By transforming the system into a series of parallel structures, the system efficiency is decomposed into the product of a modification of the stage efficiencies. Efficiency decomposition enables decision makers to identify the stages that cause the inefficiency of the system, and to effectively improve the performance of the system. An example of an electricity service system is used to explain the idea of efficiency decomposition.     

Impurity induced interactions in diluted La2CuO4

A non-magnetic impurity, such as Zn, doped into a non-frustrated antiferromagnet can induce substantial frustrating interactions among the spins surrounding it and result in an enhanced suppression of the antiferromagnetic order. In addition, the strength of the intra-plane exchange couplings surrounding impurities is reduced by the lattice distortions. Using quantum Monte Carlo, we calculate the initial suppression rate of the staggered magnetization in a two-dimensional diluted Heisenberg antiferromagnet with both frustrating interaction and lattice distortion induced by the impurity. We find that the lattice distortion alone cannot explain the experimental results, while the dominant effect of enhanced order suppression is due to the frustrating interaction.     

XANES Spectroscopic Studies of the Phase Transition in Gd2Zr2O7

The structural phase transition from fluorite to pyrochlore and the strength of the coordination bond of Zr–O in Gd₂Zr₂O₇ were investigated by XANES spectra of both O and Zr K‐edge. The energy difference of the O K‐edge absorption spectra at 532 and 536 eV was assigned to the crystal field splitting energy of the 4d orbital (ΔE_4d, t_2g and e_g) of the Zr ion. Also, in the samples prepared at higher temperatures, the 536 eV peak moves slightly to higher energy, whereas the absorption energy of 532 eV peak does not shift. A correlation between ΔE_4d and the strength of interaction between Zr (4d) and O (2p) orbitals has been found. Furthermore, two Zr K‐edge absorptions at 18020 and 18030 eV of Gd₂Zr₂O₇ have been observed; the splitting energy (ΔE), peak intensity ratio (I₁₈₀₃₀/I₁₈₀₂₀), and FWHM of the first derivative of the absorption curve depend on the preparation temperatures. The effect of crystal symmetry and Zr‐O bonding character on the XANES spectral profile was discussed.     

Collapsed (kippah) hollow silica nanoparticles

Novel collapsed kippah-like mesoporous silica nanoparticles were synthesized using an O/W microemulsion system. The oil (hexadecane) can escape from the core while water could not enter through the surfactant filled nanopores of the soft shell during synthesis.