Class III peroxidases (PRXs) are plant-specific enzymes that play key roles in the responses to biotic and abiotic stress during plant growth and development. In this study, we identified 119 nonredundant PRX genes (d...
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Class III peroxidases (PRXs) are plant-specific enzymes that play key roles in the responses to biotic and abiotic stress during plant growth and development. In this study, we identified 119 nonredundant PRX genes (designated ZmPRXs). These PRX genes were divided into 18 groups based on their phylogenetic relationships. We performed systematic bioinformatics analysis of the PRX genes, including analysis of gene structures, conserved motifs, phylogenetic relationships and gene expression profiles. The ZmPRXs are unevenly distributed on the 10 maize chromosomes. In addition, these genes have undergone 16 segmental duplication and 12 tandem duplication events, indicating that both segmental and tandem duplication were the main contributors to the expansion of the maize PRX family. Ka/Ks analysis suggested that most duplicated ZmPRXs experienced purifying selection, with limited functional divergence during the duplication events, and comparative analysis among maize, sorghum and rice revealed that there were independent duplication events besides the whole-genome duplication of the maize genome. Furthermore, microarray analysis indicated that most highly expressed genes might play significant roles in root. We examined the expression of five candidate ZmPRXs under H2O2, SA, NaCl and PEG stress conditions using quantitative real-time PCR (qRT-PCR), revealing differential expression patterns. This study provides useful information for further functional analysis of the PRX gene family in maize. (C) 2015 Elsevier B.V. All rights reserved.
The stereospecificity of D-glucarate dehydratase (GlucD) is explored by QM/MM calculations. Both the substrate binding and the chemical steps of GlucD contribute to substrate specificity. Although the identification o...
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The stereospecificity of D-glucarate dehydratase (GlucD) is explored by QM/MM calculations. Both the substrate binding and the chemical steps of GlucD contribute to substrate specificity. Although the identification of transition states remains computationally intensive, we suggest that QM/MM computations on ground states or intermediates can capture aspects of specificity that cannot be obtained using docking or molecular mechanics methods.
The water quality of Erhai Lake is good as a whole, but its decreasing trend is not optimistic;the water ecosystem of Erhai Lake has changed dramatically, showing an obvious degenerating trend. The main reasons for th...
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The water quality of Erhai Lake is good as a whole, but its decreasing trend is not optimistic;the water ecosystem of Erhai Lake has changed dramatically, showing an obvious degenerating trend. The main reasons for the ecosystem degeneration are as follows: inflow pollution load exceeding the water environmental capacity, not favorable water habitat for the propagation of submerged plants, and the weak management for the lake basin. To prevent the degeneration of Erhai ecosystem, two key problems should be solved: one is to reduce the inflow pollution load to prevent the increase of nitrogen and phosphorus concentrations in the overlying water;and the other is to implement the ecosystem regulation, namely improve the stability and biodiversity of Erhai ecosystem by habitat improvement, ecological restoration and ecological regulation. In terms of the preventive measures against the Erhai ecosystem degeneration, the pollution source control in combination with ecosystem regulation should be taken as the focus. Pollution source control, habitat improvement, ecological restoration, ecological regulation and watershed management should be emphasized simultaneously. To be specific, the key tasks for preventing Erhai ecosystem degeneration include five points namely, the reduction of pollution loading into lake, adjustment of ecological fishery, restoration of submerged vegetation, watershed integrated management, and emergency treatment of water blooms.
Robust homology modeling to atomic-level accuracy requires in the general case successful prediction of protein loops containing small segments of secondary structure. Further, as loop prediction advances to success w...
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Robust homology modeling to atomic-level accuracy requires in the general case successful prediction of protein loops containing small segments of secondary structure. Further, as loop prediction advances to success with larger loops, the exclusion of loops containing secondary structure becomes awkward. Here, we extend the applicability of the Protein Local Optimization Program (PLOP) to loops up to 17 residues in length that contain either helical or hairpin segments. In general, PLOP hierarchically samples conformational space and ranks candidate loops with a high-quality molecular mechanics force field. For loops identified to possess alpha-helical segments, we employ an alternative dihedral library composed of (phi, psi) angles commonly found in helices. The alternative library is searched over a user-specified range of residues that defines the helical bounds. The source of these helical bounds can be from popular secondary structure prediction software or from analysis of past loop predictions where a propensity to form a helix is observed. Due to the maturity of our energy model, the lowest energy loop across all experiments can be selected with an accuracy of sub-Angstrom RMSD in 80% of the cases, 1.0 to 1.5 angstrom RMSD in 14% of the cases, and poorer than 1.5 angstrom RMSD in 6% of the cases. The effectiveness of our current methods in predicting hairpin containing loops is explored with hairpins up to 13 residues in length and again reaching an accuracy of sub Angstrom RMSD in 83% of the cases, 1.0 to 1.5 angstrom RMSD in 10% of the cases, and poorer than 1.5 angstrom RMSD in 7% of the cases. Finally, we explore the effect of an imprecise surrounding environment, in which side chains, but not the backbone, are initially in perturbed geometries. In these cases, loops perturbed to 3 angstrom RMSD from the native environment were restored to their native conformation with sub-Angstrom RMSD.
Long and thin In2O3/ZnO heterostructured microbelts were synthesized by sol-gel combined with electrospinning process. The as-prepared microbelts show the well defined one-dimensional belt structures with 1-5 mu m in ...
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Long and thin In2O3/ZnO heterostructured microbelts were synthesized by sol-gel combined with electrospinning process. The as-prepared microbelts show the well defined one-dimensional belt structures with 1-5 mu m in width and tens of millimeters in length. The polycrystalline microbelts calcined at 973 K for 1 h are still continuous and have the uniform rectangular cross sections and the thickness to width ratio is around 1:10. The crystalline phases of samples are investigated by X-ray diffraction and the morphology is examined using transmission electron microscope and scanning electron microscope. In2O3/ZnO heterostructured microbelts exhibit the excellent visible photocatalytic property in the photodegradation of methyl orange (MO), and over 94 % of MO was degraded within 3 h.
In2O3/ZnO heterostructured nanotubes with cubic In2O3 and hexagonal ZnO were successfully synthesized via the combination of electrospinning and calcination process. The as-prepared materials are investigated by using...
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In2O3/ZnO heterostructured nanotubes with cubic In2O3 and hexagonal ZnO were successfully synthesized via the combination of electrospinning and calcination process. The as-prepared materials are investigated by using thermogravimetric and differential scanning calorimetry, fourier transform infrared spectroscope, X-ray diffraction, scanning electron microscope and high-resolution transmission electron microscope techniques. The formation mechanism of In2O3/ZnO heterostructured nanotubes based on the kinetics of phase separation which results from the decomposition of polyvinyl pyrrolidone during the calcination process is also discussed in detail. The photocatalytic degradation tests reveal that In2O3/ZnO heterostructured nanotubes exhibit the highly improved photocatalytic properties compared with the single-component ZnO and In2O3 materials.
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