The evolution of YidC/Oxa/Alb3 family in the three domains of life: a phylogenomic analysis

Background: YidC/Oxa/Alb3 family includes a group of conserved translocases that are essential for protein insertion into inner membranes of bacteria and mitochondria, and thylakoid membranes of chloroplasts. Because mitochondria and chloroplasts are of b

The three dimensional structure and biological domains of the p53 C-terminus.

It was expected that there are a coil (289 similar to 325) and two a helix (alpha(1)368 similar to 373, alpha(2)381 similar to 388) structures in p53 protein C-terminal region based on its mRNA secondary structure template and Chou-Fasman's protein secondary structure principle of prediction. The result was conformed by the other four methods of protein secondary structure prediction that are based on the multiple sequence alignment (accuracy = 73.20%). Combine with the 31 amino acids crystal structure of the oligomerization, the three dimensional conformation of p53 C-terminal 108 residues was built using the SGI INDIGO(2) computer. This structure further expounds the relationship among those biological function domains of p53 C- terminus at three-dimensional level.

Expression, purification and characterization of recombinant Jerdonitin, a P-II class snake venom metalloproteinase comprising metalloproteinase and disintegrin domains

Jerdonitin is a P-II class snake venom metalloproteinase comprising metalloproteinase and disintegrin domains. In this study, we established a high-level expression system in Pichia pastoris and developed a purification strategy for the recombinant Jerdonitin. This recombinant Jerdonitin degraded fibrinogen at a level of activity comparable with its wild type. The effects of recombinant Jerdonitin on inhibiting ADP-induced human platelet aggregation were in a dose-dependent manner with an IC50 of 248 nM. In addition, we reported here that Jerdonitin can significantly inhibit the growth of several cell lines, including human liver cancer cells (Bel7402), human leukemia cells (K562) and human gastric carcinoma cells (BGC823). This study offers recombinant Jerdonitin that will be valuable for further functional and structural studies of Jerdonitin. (C) 2009 Elsevier Ltd. All rights reserved.

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.

Construction of cytoplasmic molecular markers distinguishing Danio rerio from Gobiocypris rarus at high identity domains based on MP-PCR strategy and Sybr Green I detection

To distinguish the cytoplasm of Danio rerio from that of Gobiocypris rarus, we cloned G. rarus COXI and constructed cytoplasmic molecular markers at the high identity domains of COXI by mutated primer PCR (MP-PCR for short). Then Sybr Green I was used to detect the single amplicon. As a result, we succeeded in getting the cytoplasmic molecular markers, G.M COXI and Z.M COXI, by MP-PCR strategy. They were used to detect the sperm-derived mtDNA in the sexual hybrid embryos (D. rerio female x G. rarus male) before the sphere stage. In the present study, all results demonstrate that MP-PCR approach and Sybr Green I detection are feasible to construct the molecular markers to identify genes that shared high identity.

Differential expression and characterization analysis of a new gene with WD domains in fish oogenesis

A new gene with WD domains is cloned and characterized according to its differential transcription and expression between previtellogenic oocytes (phase I oocytes) and fully-grown oocytes (phase V oocytes) from natural gynogenetic silver crucian carp (Carassius auratus gibelio) by using the combinative methods of suppressive subtraction hybridization, SMART cDNA synthesis and RACE-PCR. The full-length cDNA is 1870 bp. Its 5 ' untranslated region is 210 bp, followed by an open reading frame of 990 bp, which has the typical vertebrate initiator codon of ANNATG. The open reading frame encodes a protein with 329 amino acids. It has 670 bp of 3 ' untranslated region and an AATAAA polyadenylation signal. Because it has 92% homology to STRAP (serine-threonine kinase receptor-associated protein), a recently reported gene, we named it FSTRAP (fish STRAP). Virtual Northern blotting indicated that the FSTRAP was transcribed in fully-grown oocytes (phase V oocytes), but not in previtellogenic oocytes (phase I oocytes). RT-PCR analysis showed that FSTRAP was transcribed in brain, heart, kidney, muscle, ovary, spleen and testis, but not in liver. And its mRNA could be detected in the oocytes from phase II to phase V. Western blotting also showed that FSTRAP protein could be detected in brain, heart, kidney, muscle, ovary, spleen and testis except liver. Results of Western blotting on various oocytes were also similar to the RT-PCR data. FSTRAP protein was not expressed in the previtellogenic oocytes. Its expression initiated from phase II oocytes after vitellogenesis, and was consistent with the mRNA transcription.

Abnormal ferroelectric response and enhancement of piezoelectricity of PbTiO3 under uniaxial compression

The ferroelectricity of rhombohedral PbTiO3 under uniaxial compression is investigated from first-principles study. Upon compression, the ferroelectricity decreases until a critical stress of -29 GPa and then increases with a further increase of the magnitude of the uniaxial compressive stress. We also find that uniaxial compression could enhance piezoelectricity and that the maximum piezoelectric coefficient d(33) occurs at sigma(33)=-49 GPa, which supports the experimentally observed piezoelectric behavior in rhombohedral Pb(Mg1/3Nb2/3O3)-0.32PbTiO(3) [Q. Wan, C. Chen, and Y. P. Shen, J. Appl. Phys. 98, 024103 (2005)]. Our calculated results show that the Pb, Ti, and O atoms have different contributions to the total polarization with increasing the magnitude of uniaxial compressive stress, and that when -sigma(33)>55 GPa, the Ti atoms no longer have contributions to the polarization, which leads to the changes of ferroelectricity and piezoelectricity. (C) 2008 American Institute of Physics.

Effect of incorporating nonlanthanoidal indium on optical properties of ferroelectric Bi4Ti3O12 thin films

Bi4Ti3O12 (BTO) and Bi3.25In0.75Ti3O12 (BTO:In) thin films were prepared on fused quartz and LaNiO3/Si (LNO) substrates by chemical solution deposition (CSD). Their microstructures, ferroelectric and optical properties were investigated by X-ray diffraction, scanning electron microscope, ferroelectric tester and UV-visible-NIR spectrophotometer, respectively. The optical band-gaps of the films were found to be 3.64 and 3.45 eV for the BTO and BTO:In films, respectively. Optical constants (refractive indexes and extinction coefficients) were determined from the optical transmittance spectra using the envelope method. Following the single electronic oscillator model, the single oscillator energy E-0, the dispersion energy E-d, the average interband oscillator wavelength lambda(0), the average oscillator strength S-0, the refractive index dispersion parameter (E-0/S-0), the chemical bonding quantity beta, and the long wavelength refractive index n(infinity) were obtained and analyzed. Both the refractive index and extinction coefficient of the BTO:In films are smaller than those of the BTO films. Furthermore, the refractive index dispersion parameter (E-0/S-0) increases and the chemical bonding quantity beta decreases in the BTO and BTO:In films compared with those of bulk. (C) 2007 Published by Elsevier B.V.

Role of amorphous silicon domains on Er3+ emission in the Er-doped hydrogenated amorphous silicon suboxide film

An investigation on the correlation between amorphous Si (a-Si) domains and Er3+ emission in the Er-doped hydrogenated amorphous silicon suboxide (a-Si:O:H) film is presented. On one hand, a-Si domains provide sufficient carriers for Er3+ carrier-mediated excitation which has been proved to be the highest excitation path for Er3+ ion; on the other hand, hydrogen diffusion from a-Si domains to amorphous silicon oxide (a-SiOx) matrix during annealing has been found and this possibly decreases the number of nonradiative centres around Er3+ ions. This study provides a better understanding of the role of a-Si domains on Er3+ emission in a-Si:O:H films.

Investigation on the origin of wurtzite domains in thick cubic GaN using reactive ion etching

We measured the depth profiling of photoluminescence (PL) in cubic GaN films. The depth-resolved PL of normal grown GaN layers showed that the near-band-edge luminescence intensities of both cubic and wurtzite domains remained constant only until an etching depth of up to 2.7 mu m, but their ratio remained unchanged at all etching depths. Moreover, when a thin In0.1Ga0.9N layer was sandwiched between two GaN layers, the content of the wurtzite domains increased, and its distribution showed a dependence on thickness. As the reactive ion etching depth increased, the PL intensity ratio of cubic GaN to wurtzite domains increased. Based on the distribution, the strain relaxation, instead of the instability of cubic GaN at high temperature, was attributed to the origin of wurtzite domains. (C) 2000 Elsevier Science S.A. All rights reserved.

Formation mechanism of electric field domains

Hydrostatic pressure measurements are used to investigate the formation mechanism of electric field domains in doped weakly-coupled GaAs/AlAs superlattices. For the first plateau-like region in the I-V curve, two kinds of sequential resonant tunnelling are observed. For P<2 kbar the high-field domain is formed by the Gamma-Gamma process, while for P>2 kbar the high-field domain is formed by the T-X process. For the second plateau-libe region, the high-field domain is attributed to Gamma-X sequential resonant tunnelling. (C) 1998 Elsevier Science B.V. All rights reserved.

Current oscillations and stable electric field domains in doped GaAs/AlAs superlattices

The crossover between two regimes has been observed in the vertical electric transport of weakly coupled GaAs/AlAs superlattices (SLs). At fixed d.c. bias, the SLs can be triggered by illumination to switch from a regime of temporal current oscillation to the formation of a stable electric field domain. The conversion can be reversed by raising the sample temperature to about 200 K. An effective carrier injection model is proposed to explain the conversion processes, taking into account the contact resistance originating from DX centres in the n(+)-Al0.5Ga0.5As contact layers which is sensitive to light illumination and temperature. In addition, quasiperiodic oscillations have been observed at a particular d.c. bias voltage.

An investigation of the formation mechanisms of electric field domains in GaAs/AlAs superlattices

We have studied the vertical transport and formation mechanisms of electric field domains in doped weakly-coupled GaAs/AlAs superlattices. Under hydrostatic pressure two kinds of sequential resonant tunneling are observed within the pressure range from 0 to 4.5 kbar. A transition from Gamma-Gamma to Gamma-X sequential resonant tunneling occurs at P-t approximate to 1.6 kbar. For P < P-t, the high electric field domain is formed by the Gamma-Gamma process, while for P > P-t it is preferentially formed by the Gamma-X process.