Cloning and analysis of 16 Rab genes from macronuclear DNA of Euplotes octocarinatus

Rab proteins belong to the largest family of the Ras superfamily of small GTPase that play an important role in intracellular vesicular traffic. So far, almost 60 members of Rab family have been identified in mammalian cells. To further study the diversity and function of Rab protein in evolution, unicellular protozoa ciliates, Euplotes octocarinatus, were used in this study, Rab genes were screened by PCR method from macronuclear DNA of E. octocarinatus. Sixteen Rab genes were obtained. They share 87.6 - 99.5% identities. Highly conserved GTP-binding domains were found. There are some hot regions that diverse sharply in these genes as well.

Analysis of mode characteristics for deformed square resonators by FDTD technique

The mode frequencies and quality factors (Q-factors) in two-dimensional (2-D) deformed square resonators are analyzed by finite-difference time-domain (FDTD) technique. The results show that the deformed square cavities with circular and cut corners have larger Q-factors than the perfect ones at certain conditions. For a square cavity with side length of 2 mu m and refractive index of 3.2, the mode Q-factor can increase 13 times as the perfect corners are replaced by a quarter of circle with radius of 0.3 pm. Furthermore the blue shift with the increasing deformations is found as a result of the reduction in effective resonator area. In square cavities with periodic roughness at sidewalls which maintains the symmetry of the square, the Q-factors of the whisperin gallery (WG)-like modes are still one order of magnitude larger that those of non-WG-like modes. However, the Q-tactors of these two types of modes are of the same order in the square cavity with random roughness. We also find that the rectangular and rhombic deformation largely reduce the Q-factors with the increasing offset and cause the splitting of the doubly degenerate modes due to the breaking of certain symmetry properties.

The PL "violet shift" of cerium dioxide on silicon

CeO2 thin film was fabricated by dual ion beam epitaxial technique. The phenomenon of PL violet shift at room temperature was observed, and the distance of shift was about 65 nm. After the analysis of crystal structure and valence in the compound were carried out by XRD and XPS technique, it was concluded that the PL shift was related with valence of cerium ion in the oxides. When the valence of cerium ion varied front tetravalence to trivalence, the PL peak position would move from blue region to violet region and the phenomenon of "violet shift" was observed.

Principle and analysis of the moving-optical-wedge interferometer

A new type of interferometer, the moving-optical-wedge interferometer, is presented, and its principle and properties are studied. The novel interferometer consists of one beam splitter, two flat fixed mirrors, two fixed compensating plates, one fixed optical wedge, and one moving optical wedge. The optical path difference (OPD) as a function of the displacement of the moving optical wedge from the zero path difference position is accomplished by the straight reciprocating motion of the moving optical wedge. A large physical shift of the moving optical wedge corresponds to a very short OPD value of the new interferometer if the values of the wedge angle and the refractive index of the two optical wedges are given properly. The new interferometer is not so sensitive to the velocity variation of the moving optical wedge and the mechanical disturbances compared with the Michelson interferometer, and it is very applicable to low-spectral-resolution application for any wavenumber region from the far infrared down to the ultraviolet. (C) 2008 Optical Society of America.

Stress analysis of silica-based arrayed waveguide grating by a finite element method

The stress distribution in silica optical waveguides on silicon is calculated by using finite element method (FEM). The waveguides are mainly subjected to compressive stress along the x direction and the z direction, and it is accumulated near the interfaces between the core and cladding layers. The shift of central wavelength of silica arrayed waveguide grating (AWG) on silicon-substrate with the designed wavelength and the polarization dependence are caused by the stress in the silica waveguides.

A New Method for Analysis of Disulfide-Containing Proteins by Matrix-Assisted Laser Desorption Ionization (MALDI) Mass Spectrometry

A simple and high-throughput method for the identification of disulfide-containing peptides utilizing peptide-matrix adducts is described. Some commonly used matrices in MALDI mass spectrometry were found to specifically react with sulfhydryl groups within peptide, thus allowing the observation of the peptide-matrix adduct ion [M + n + n' matrix + H](+) or [M + n + n' matrix + Na](+) (n = the number of cysteine residues, n' = 1, 2, ..., n) in MALDI mass spectra after chemical reduction of disulfide-linked peptides. Among several matrices tested, alpha-cyano-4-hydroxycinnamic acid (CHCA, molecular mass 189 Da) and alpha-cyano-3-hydroxycinnamic acid (3-HCCA) were found to be more effective for MALDI analysis of disulfide-containing peptides/proteins. Two reduced cysteines involved in a disulfide bridge resulted in a mass shift of 189 Da per cysteine, so the number of disulfide bonds could then be determined, while for the other matrices (sinapinic acid, ferulic acid, and caffeic acid), a similar addition reaction could not occur unless the reaction was carried out under alkaline conditions. The underlying mechanism of the reaction of the matrix addition at sulfhydryl groups is proposed, and several factors that might affect the formation of the peptide-matrix adducts were investigated.

In situ analysis of electropolymerization of aniline by combined electrochemistry and surface plasmon resonance

The combination of electrochemistry with surface plasmon resonance (SPR) has been used to characterize the growth of polyaniline (PAn) on a gold electrode surface during potential cycling. Potential-modulated SPR characteristics of the PAn film were also revealed. The potential switch between the oxidized and reduced states of PAn can lead to a large change of SPR response due to the variation in the imaginary part of the dielectric constant of PAn film resulting from the transition of the film in conductivity. The redox transition of the PAn film during potential cycling is very profitable to the SPR measurements. Two modes of SPR measurement, SPR angular scan (R-theta) and the time evolution of the reflectivity change at a fixed angle (R-t), were displayed to study the growth process of the PAn film. The angle shift of the resonance minimum recorded at each cathodic limit of cyclic potential scanning allows for the unambiguous measurement of the film growth. During cyclic potential scanning, the R-t curve was repeatedly modulated with the direction of the potential ramp as a result of the redox switch of the PAn film, and the amplitude of potential-modulated reflectivity change was well correlated with the cyclic number. The time differential of the R-t curve permits continuous monitoring of the film growth process. These results illustrate that the combined technique is suitable for studying the electropolymerization process of a conducting polymer.

Factor analysis used to peak position optimization and spectral interference correction in inductively coupled plasma atomic emission spectrometry

Target transformation factor analysis was used to correct spectral interference in inductively coupled plasma atomic emission spectrometry (ICP-BES) for the determination of rare earth impurities in high purity thulium oxide. Data matrix was constructed with pure and mixture vectors and background vector. A method based on an error evaluation function was proposed to optimize the peak position, so the influence of the peak position shift in spectral scans on the determination was eliminated or reduced. Satisfactory results were obtained using factor analysis and the proposed peak position optimization method.

Structural analysis of SNARE motifs from sea perch, Lateolabrax japonicus by computerized approaches

Three cDNA sequences encoding four SNARE (N-ethylmaleimide-sensitive fusion protein attachment protein receptors) motifs were cloned from sea perch, and the deduced peptide sequences were analyzed for structural prediction by using 14 different web servers and softwares. The "ionic layer" structure, the three dimensional extension and conformational characters of the SNARE 7S core complex by using bioinformatics approaches were compared respectively with those from mammalian X-ray crystallographic investigations. The result suggested that the formation and stabilization of fish SNARE core complex might be driven by hydrophobic association, hydrogen bond among R group of core amino acids and electrostatic attraction at molecular level. This revealed that the SNARE proteins interaction of the fish may share the same molecular mechanism with that of mammal, indicating the universality and solidity of SNARE core complex theory. This work is also an attempt to get the protein 3D structural information which appears to be similar to that obtained through X-ray crystallography, only by using computerized approaches. (C) 2007 Elsevier Ltd. All rights reserved.

Molecular cloning, characterization and expression analysis of a putative C-type lectin (Fclectin) gene in Chinese shrimp Fenneropenaeus chinensis

Lectin is regarded as a potential molecule involved in immune recognition and phagocytosis through opsonization in crustacean. Knowledge on lectin at molecular level would help us to understand its regulation mechanism in crustacean immune system. A novel C-type lectin gene (Fclectin) was cloned from hemocytes of Chinese shrimp Fenneropenaeus chinensis by 3' and 5' rapid amplification of cDNA ends (RACE) PCR. The full-length cDNA consists of 1482 bp with an 861 bp open reading frame, encoding 287 amino acids. The deduced amino acid sequence contains a putative signal peptide of 19 amino acids. It also contains two carbohydrate recognition domains/C-type lectin-like domains (CRD1 and CRD2), which share 78% identity with each other. CRD1 and CRD2 showed 34% and 30% identity with that of mannose-binding lectin from Japanese lamprey (Lethenteron japonicum), respectively. Both CRD1 and CRD2 of Fclectin have I I amino acids residues, which are relatively invariant in animals' C-type lectin CRDs. Five residues at Ca2+ binding site I are conserved in Fclectin. The potential Ca2+/carbohydrate-binding (site 2) motif QPD, E, NP (Gln-Pro-Asp, Glu, Asn-Pro) presented in the two CRDs of Fclectin may support its ability to bind galactose-type sugars. It could be deduced that Fclectin is a member of C-type lectin superfamily. Transcripts of Fclectin were found only in hemocytes by Northern blotting and RNA in situ hybridization. The variation of mRNA transcription level in hemocytes during artificial infection with bacteria and white spot syndrome virus (WSSV) was quantitated by capillary electrophoresis after RT-PCR. An exploration of mRNA expression variation after LPS stimulation was carried out in primarily cultured hemocytes in vitro. Expression profiles of Fclectin gene were greatly modified after bacteria, LPS or WSSV challenge. The above-stated data can provide us clues to understand the probable role of C-type lectin in innate immunity of shrimp and would be helpful to shrimp disease control. (c) 2006 Elsevier Ltd. All rights reserved.