Functional domains and the antiviral effect of the double-stranded RNA-dependent protein kinase PKR from Paralichthys olivaceus

The double-stranded RNA (dsRNA)-dependent protein kinase PKR is thought to mediate a conserved antiviral pathway by inhibiting viral protein synthesis via the phosphorylation of the alpha subunit of eukaryotic initiation factor 2 (eIF2 alpha). However, little is known about the data related to the lower vertebrates, including fish. Recently, the identification of PKR-like, or PKZ, has addressed the question of whether there is an orthologous PKR in fish. Here, we identify the first fish PKR gene from the Japanese flounder Paralichthys olivaceus (PoPKR). PoPKR encodes a protein that shows a conserved structure that is characteristic of mammalian PKRs, having both the N-terminal region for dsRNA binding and the C-terminal region for the inhibition of protein translation. The catalytic activity of PoPKR is further evidence that it is required for protein translation inhibition in vitro. PoPKR is constitutively transcribed at low levels and is highly induced after virus infection. Strikingly, PoPKR overexpression increases eIF2 alpha phosphorylation and inhibits the replication of Scophthalmus maximus rhabdovirus (SMRV) in flounder embryonic cells, whereas phosphorylation and antiviral effects are impaired in transfected cells expressing the catalytically inactive PKR-K421R variant, indicating that PoPKR inhibits virus replication by phosphorylating substrate eIF2 alpha. The interaction between PoPKR and eIF2 alpha is demonstrated by coimmunoprecipitation assays, and the transfection of PoPKR-specific short interfering RNA further reveals that the enhanced eIF2 alpha phosphorylation is catalyzed by PoPKR during SMRV infection. The current data provide significant evidence for the existence of a PKR-mediated antiviral pathway in fish and reveal considerable conservation in the functional domains and the antiviral effect of PKR proteins between fish and mammals.

The functional divergence of two glgP homologues in Synechocystis sp PCC 6803

Glycogen phosphorylase (GlgP, EC 2.4.1.1) catalyzes the cleavage of glycogen into glucose-1-phosphate (Glc-1-P), the first step in glycogen catabolism. Two glgP homologues are found in the genome of Synechocystis sp. PCC 6803, a unicellular cyanobacterium: sll1356 and slr1367. We report on the different functions of these glgP homologues. sll1356, rather than slr1367, is essential for growth at high temperatures. On the other hand, when CO2-fixation and the supply of glucose are both limited, slr1367 is the key factor in glycogen metabolism. In cells growing autotrophically, sll1356 plays a more important role in glycogen digestion than slr1367. This functional divergence is also supported by a phylogenetic analysis of glgP homologues in cyanobacteria.

Gene cloning and functional analysis of glycosaminoglycan-degrading enzyme chondroitin AC lyase from Flavobacterium columnare G(4)

The chondroitin AC lyase gene, cslA, was cloned for the first time from the fish bacterial pathogen F. columnare G(4). From the first transcription initiation site, the cslA extends 2620 nucleotides to the end of the 3' region. The open reading frame of cslA transcript has 2286 nucleotides encoding 762 amino acids with a 16 residues long signal peptide at the N-terminus. The gene, cslA was then successfully expressed in Escherichia coli and recombinant chondroitin AC lyase, rChonAC was purified, with its lytic activity analyzed. Zymography analysis copolymerized with chondroitin sulphate revealed the lytic activity of rChonAC and also the crude native ChonAC isolated from periplamic space of cultured F. columnare G(4). The low level of lytic activity observed in crude native ChonAC may be due possibly to the low level of expression of this gene in the cultured condition. The expression and the role of this virulence factor is of interest for further research on the pathogenesis of F. columnare.

Functional analysis of FP25K of Helicoverpa armigera single nucleocapsid nucleopolyhedrovirus

The fp25k gene of Helicoverpa armigera single nucleocapsid nucleopolyhedrovirus (HearNPV) was studied. HearNPV fp25k gene transcription was found starting from about 18 h post-infection, and protein could be detected from the same time with antiserum against FP25K. To study the function of HearNPV fp25k, a recombinant HearNPV (HaBacWD11) with an enhanced green fluorescent protein (GFP) gene replacing the fp25k was constructed using HaBacHZ8, a bacmid of HearNPV that lacks the polyhedrin gene. Growth curve analysis showed that HaBacWD11 produced higher titres of budded viruses (BVs) than its wild-type counterpart HaBacHZ8-GFP. Electron microscopic analysis indicated that at the late stage of infection, the number of intranuclear enveloped nucleocapsids in HaBacWD11-infected cells was much less than that of HaBacHZ8-GFP. A rescue recombinant virus HaBacWD14 was constructed by reintroducing fp25k gene into HaBacWD11. The growth curve and electron microscopic analysis of the rescued recombinant confirmed that the increase of BV yield and the decrease of the virion production in infected cells were the result of fp25k deletion. The expression of membrane fusion protein (Ha133) and ODV-E66 were studied using the FP25K mutants HaBacWD11 and HaBacHZ8-GFP. Unlike FP25K mutants in Autographa californica multicapsid NPV (AcMNPV), which caused an increase in the expression of membrane fusion protein GP64 and a decrease of ODV-E66, no obvious changes at the expression level of Ha133 and ODV-E66 were observed in HearNPV FP25K mutant.

Use of PFU protozoan community structural and functional characteristics in assessment of water quality in a large, highly polluted freshwater lake in China

Structural and functional parameters of protozoan communities colonizing on PFU (polyurethane foam unit) artificial substrate were assessed as indicators of water quality in the Chaohu Lake, a large, shallow and highly polluted freshwater lake in China. Protozoan communities were sampled 1, 3, 6, 9 and 14 days after exposure of PFU artificial substrate in the lake during October 2003. Four study stations with the different water quality gradient changes along the lake were distinguishable in terms of differences in the community's structural (species richness, individual abundance, etc.) and functional parameters (protozoan colonization rates on PFU). The concentrations of TP, TN, COD and BOD as the main chemical indicators of pollution at the four sampling sites were also obtained each year during 2002-2003 for comparison with biological parameters. The results showed that the species richness and PFU colonization rate decreased as pollution intensity increased and that the Margalef diversity index values calculated at four sampling sites also related to water quality. The three functional parameters based on the PFU colonization process, that is, S-eq, G and T-90%, were strongly related to the pollution status of the water. The number of protozoan species colonizing on PFU after exposure of 1 to 3 days was found to give a clear comparative indication of the water quality at the four sampling stations. The research provides further evidence that the protozoan community may be utilized effectively in the assessment of water quality and that the PFU method furnishes rapid, cost-effective and reliable information that may be useful for measuring responses to pollution stress in aquatic ecosystems.

Origin of antiferromagnetism in CoO: A density functional theory study

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Correcting the systematic error of the density functional theory calculation: the alternate combination approach of genetic algorithm and neural network

The alternate combinational approach of genetic algorithm and neural network (AGANN) has been presented to correct the systematic error of the density functional theory (DFT) calculation. It treats the DFT as a black box and models the error through external statistical information. As a demonstration, the AGANN method has been applied in the correction of the lattice energies from the DFT calculation for 72 metal halides and hydrides. Through the AGANN correction, the mean absolute value of the relative errors of the calculated lattice energies to the experimental values decreases from 4.93% to 1.20% in the testing set. For comparison, the neural network approach reduces the mean value to 2.56%. And for the common combinational approach of genetic algorithm and neural network, the value drops to 2.15%. The multiple linear regression method almost has no correction effect here.

Design of shallow acceptors in ZnO through compensated donor-acceptor complexes: A density functional calculation

The intrinsic large electronegativity of O 2p character of the valence-band maximum (VBM) of ZnO renders it extremely difficult to be doped p type. We show from density functional calculation that such VBM characteristic can be altered by compensated donor-acceptor pairs, thus improve the p-type dopability. By incorporating (Ti+C) or (Zr+C) into ZnO simultaneously, a fully occupied impurity band that has the C 2p character is created above the VBM of host ZnO. Subsequent doping by N in ZnO: (Ti+C) and ZnO: (Zr+C) lead to the acceptor ionization energies of 0.18 and 0.13 eV, respectively, which is about 200 meV lower than it is in pure ZnO.

A density-functional study of Al-doped Ti clusters: TinAl (n=1-13)

Equilibrium geometries, stabilities, and electronic properties of TinAl (n=1-13) clusters have been studied by using density-functional theory with local spin density approximation and generalized gradient approximation. The ground-state structures of TinAl clusters have been obtained. The resulting geometries show that the aluminum atom remains on the surface of clusters for n<9, but is slowly getting trapped beyond n=9, meanwhile, the Al atom exhibits a valent transition from monovalent to trivalent. The geometric effects and electronic effects clearly demonstrate the Ti4Al cluster to be endowed with special stability. The studies on the bonds indicate the change from ionic to metalliclike. (C) 2004 American Institute of Physics.

Quantum master equation scheme of time-dependent density functional theory to time-dependent transport in nanoelectronic devices

In this work a practical scheme is developed for the first-principles study of time-dependent quantum transport. The basic idea is to combine the transport master equation with the well-known time-dependent density functional theory. The key ingredients of this paper include (i) the partitioning-free initial condition and the consideration of the time-dependent bias voltages which base our treatment on the Runge-Gross existence theorem; (ii) the non-Markovian master equation for the reduced (many-body) central system (i.e., the device); and (iii) the construction of Kohn-Sham master equations for the reduced single-particle density matrix, where a number of auxiliary functions are introduced and their equations of motion (EOMs) are established based on the technique of spectral decomposition. As a result, starting with a well-defined initial state, the time-dependent transport current can be calculated simultaneously along with the propagation of the Kohn-Sham master equation and the EOMs of the auxiliary functions.

Exploration on enhancing innovation capability of functional information materials in China

The present status and future prospects of functional information materials, mainly focusing on semiconductor microstructural materials, are introduced first in this paper. Then a brief discussion how to enhance the academic level and innovation capability of research and development of functional information materials in China are made. Finally the main problems concerning the studies of materials science and technology are analyzed, and possible measures for promoting its development are proposed.

Deep centers investigations of P-HEMT functional materials of ultra-high-speed microstructures grown by MBE

The deep centers of high electron mobility transistor (HEMT) and pseudomorphic-HEMT (P-HEMT) functional materials of ultra-high-speed microstructures grown by MBE are investigated using deep level transient spectroscopy (DLTS) technique. DLTS spectra demonstrate that midgap states, having larger concentrations and capture cross sections, are measured in n-AlGaAs layers of HEMT and P-HEMT structures. These states may correlate strongly with oxygen content of n-AlGaAs layer. At the same time, one can observe that the movement of DX center is related to silicon impurity that is induced by the strain in AlGaAs layer of the mismatched AlGaAs/InGaAs/GaAs system of P-HEMT structure. The experimental results also show that DLTS technique may be a tool of optimization design of the practical devices.

A density-functional study of small titanium clusters

The atomic structures and electronic properties of small Ti-N (N=2-10) clusters have been studied by using the density-functional theory with a local spin density approximation. We find that the inner-shells (3s3p) of the titanium atom plays an important role in the formation of the small clusters. We have obtained the ground state of titanium clusters, Ti-7 is found to be a magic cluster, which is in good agreement with the experimental results. Starting with Ti-8 cluster some features of the electronic structure of the titanium bulk have been developed. The ionization potentials and magnetic moments for these small titanium clusters are also presented. (C) 2000 American Institute of Physics. [S0021- 9606(00)30544-X].

Assembly of side-functional monomers with inorganic nanometer particles

Monomers of methacrylate with various pi -conjugated pendants were designed and prepared in our laboratory, The monomer with suitable end-group was successfully assembled with nano-scale inorganic particles to form an orderly-aligned structure that showed special optical properties, both absorption and emission band were much red-shifted compared with the monomer, A new type of organic/inorganic hybrid materials was obtained by in situ polymerization of the assembly, The hybrid materials could also show special optical properties as the assembly, This might open a new route to tune the emission color.

Application of the compatibility relationship(1) in seeking a functional relationship among species' equilibrium quantities in complex systems

A new algorithm, representing an important advance in determination of the functional relationship, is first reported here. The algorithm is very useful and convenient for analyzing the incorporation of impurities. To show how the algorithm works, two early and well-known vapor phase epitaxy (VPE) experiments-Ashen's (Ashen, D. J.; Dean, P. J.; Hurle, D. T. J.; Mullin, J. B.; Royle, A.; White, A. M. Gallium Arsenide and Related Compounds, Institute of Physics Conference Series 24, 1974; Institute of Physics: London, 1975; p 229.), involving the doping of silicon and DiLorenzo's (DiLorenzo, J. V. J. Cryst. Growth 1972, 17, 189.), involving the mole fraction effect-are calculated to find the functional relationship between the Si contamination and the partial pressure of HCl. The calculated curves agree with the experimental results. A conclusion that the calculated values are greater than the true values has been drawn.