Characterization of complete genome sequence of the spring viremia of carp virus isolated from common carp (Cyprinus carpio) in China

The complete genome of spring viraemia of carp virus (SVCV) strain A-1 isolated from cultured common carp (Cyprinus carpio) in China was sequenced and characterized. Reverse transcription-polymerase chain reaction (RT-PCR) derived clones were constructed and the DNA was sequenced. It showed that the entire genome of SVCV A-1 consists of 11,100 nucleotide base pairs, the predicted size of the viral RNA of rhabdoviruses. However, the additional insertions in bp 4633-4676 and bp 4684-4724 of SVCV A-1 were different from the other two published SVCV complete genomes. Five open reading frames (ORFs) of SVCV A-1 were identified and further confirmed by RT-PCR and DNA sequencing of their respective RT-PCR products. The 5 structural proteins encoded by the viral RNA were ordered 3'-N-P-M-G-L-5'. This is the first report of a complete genome sequence of SVCV isolated from cultured carp in China. Phylogenetic analysis indicates that SVCV A-1 is closely related to the members of the genus Vesiculovirus, family Rhabdoviridae.

Phylogenetic relationships of the Chinese cyprinid genus Rhinogobio Bleeker (Teleostei : Cyprinidae) based on sequences of the mitochondrial DNA control region, with comments on character adaptations

Rhinogobio is a cyprinid genus restricted to the river drainages of China. Sequences of the mitochondrial DNA control region were determined for four Rhinogohio species and one outgroup species, Coreius heterodon, to investigate the phylogenetic relationships within the genus. The control region of the Rhinogobio species ranges from 922 to 930 base pairs and comprises 930 base pairs in Coreius. Our phylogenetic analysis indicates two distinct lineages in the genus Rhinogobio. The first includes only R. ventralis. In the second lineage there are three species, two closely related species R. cylindricus and R. hunanensis, and their sister species R. typus. An analysis of character adaptations suggests an evolutionary trend in this genus towards a relatively lower body and caudal peduncle depth, a shorter dorsal fin, and a more anterior anus. In addition, there is a trend towards shorter barbels and relatively larger eyes. Some or all of these traits may be associated with a habitat shift from fast-flowing turbid rivers to slower-flowing clear river habitats.

Testing the relationships of Chinese freshwater Unionidae (bivalvia) based on analysis of partial mitochondrial 16s rRNA sequences

This study presents partial mitochondrial 16S rRNA sequences of 13 unionid bivalve species from China and analyses their relationships in combination with known data of 21 American mussels. According to our results, Chinese unionids, formerly regarded as two subfamilies, should be divided into three subfamilies: Ambleminae, Anodontinae and Unioninae. The genera Hyriopsis, Solenaia, Lamprotula and Ptychorhynchus, hitherto placed in Unioninae or Anodontinae, should be moved to the subfamily Ambleminae, demonstrated for the first time from China. The other genera recorded from China are suggested to belong to Anodontinae and Unioninae, which is in agreement with traditional classifications, except for the genus Lepidodesma.

Complete nucleotide sequence of the S10 genome segment of grass carp reovirus (GCRV)

Hemorrhagic disease, caused by the grass carp reovirus (GCRV), is one of the major diseases of grass carp in China. Little is known about the structure and function of the gene segments of this reovirus. The S10 genome segment of GCRV was cloned and the complete nucleotide sequence is reported here. The S10 is 909 nucleotides long and contains a large open reading frame (ORF) encoding a protein of 276 amino acids with a deduced molecular weight of approximately 29.7 kDa. Comparisons of the deduced amino acid sequence of GCRV S10 with those of other reoviruses revealed no significant homologies. However, GCRV S10 shared a putative zinc-finger sequence and a similar distribution of hydrophilic motifs with the outer capsid proteins encoded by Coho salmon aquareovirus (SCSV) S10, striped bass reovirus (SBRV) S10, and mammalian reovirus (MRV) S4. It was predicted that this segment gene encodes an outer capsid protein.

Sequence of genome segments 1, 2, and 3 of the grass carp reovirus (Genus Aquareovirus, family Reoviridae)

The genome segments 1, 2, and 3 of the grass carp reovirus (GCRV), a tentative species assigned to genus Aquareouirus, family Reouiridae, were sequenced. The respective segments 1, 2, and 3 were 3949, 3877, and 3702 nucleotides long. Conserved moths 5' (GUUAUUU) and 3' (UUCAUC) were found at the ends of each segment. Each segment contains a single ORF and the negative strand does not permit identification of consistent ORFs. Sequence analysis revealed that VP2 is the viral polymerase, while VPI might represent the viral guanyly/methyl transferase (involved in the capping process of RNA transcripts) and VP3 the NTPase/helicase (involved in the transcription and capping of viral RNAs), The highest amino acid identities (26-41%) were found with orthoreovirus proteins. Further genomic characterization should provide insight about the genetic relationships between GCRV, aquareoviruses, and orthoreoviruses, It should also permit to precise the taxonomic status of these different viruses. (C) 2000 Academic Press.

Numerical analysis for four-wave mixing based wavelength conversion of differential phase-shift keying signals

We numerically investigate the main constrains for high efficiency wavelength conversion of differential phase-shift keying (DPSK) signals based on four-wave mixing (FWM) in highly nonlinear fiber (HNLF). Using multi-tone pump phase modulation techniques, high efficiency wavelength conversion of DPSK signals is achieved with the stimulated Brillouin scattering (SBS) effects effectively suppressed. Our analysis shows that there is a compromise between conversion efficiency and converted idler degradation. By optimizing the pump phase modulation configuration, the converted DPSK idler's degradation can be dramatically decreased through balancing SBS suppression and pump phase modulation degradation. Our simulation results also show that these multi-tone pump phase modulation techniques are more appropriate for the future high bit rate systems.

Rate-equation-based circuit model of high-speed semiconductor lasers

Based oil rare equations of semiconductor laser, a symbolically-defined model for optical transmission system performance evaluation and network characterization in both time- and frequency domains is presented. The steady-state and small-signal characteristics, such as current-photon density curve, current-voltage curve, and input impedance, call be predicted from this model. Two important dynamic characteristics, second-order harmonic distortion and two-tone third-order intermodulation products, are evaluated under different driving conditions. Experiments show that the simulated results agree well with the published data. (c) 2007 Wiley Periodicals, Inc.

Monolithic optical gates based on integration of evanescently-coupled uni-traveling-carrier photodiodes and electroabsorption modulators

We report on chip-scale optical gates based on the integration of evanescent waveguide unitraveling-carrier photodiodes (EC-UTC-PDs) and intra-step quantum well electroabsorption modulators (IQW-EAMs) on n-InP substrates. These devices exhibit simultaneously 2.1 GHz and -16.2 dB RF-gain at 21 GHz with a 450 Omega thin-film resistor and a bypass capacitor integrated on a chip.

Phase reconstruction from three interferograms based on integral of phase gradient

A novel algorithm of phase reconstruction based on the integral of phase gradient is presented. The algorithm directly derives two real-valued partial derivatives from three phase-shifted interferograms. Through integrating the phase derivatives, the desired phase is reconstructed. During the phase reconstruction process, there is no need for an extra rewrapping manipulation to ensure values of the phase derivatives lie in the interval [-pi, pi] as before, thus this algorithm can prevent error or distortion brought about by the phase unwrapping operation. Additionally, this algorithm is fast and easy to implement, and insensitive to the nonuniformity of the intensity distribution of the interferogram. The feasibility of the algorithm is demonstrated by both computer simulation and experiment.

Global transposable characteristics in the complete DNA sequence of the yeast

Global transposable characteristics in the complete DNA sequence of the Saccharomyces cevevisiae yeast is determined by using the metric representation and recurrence plot methods. On the basis of the correlation distance of nucleotide strings, 16 chromosome sequences of the yeast, which are divided into 5 groups, display 4 kinds of the fundamental transposable characteristics: a short increasing period, a long increasing quasi-period, a long major value and hardly relevant.

Reduction-Based Model Updating of a Scaled Offshore Platform Structure

This paper attempts to develop a reduction-based model updating technique for jacket offshore platform structure. A reduced model is used instead of the direct finite-element model of the real structure in order to circumvent such difficulties as huge degrees of freedom and incomplete experimental data that are usually civil engineers' trouble during the model updating. The whole process consists of three steps: reduction of FE model, the first model updating to minimize the reduction error, and the second model updating to minimize the modeling error of the reduced model and the real structure. According to the performance of jacket platforms, a local-rigidity assumption is employed to obtain the reduced model. The technique is applied in a downscale model of a four-legged offshore platform where its effectiveness is well proven. Furthermore, a comparison between the real structure and its numerical models in the following model validation shows that the updated models have good approximation to the real structure. Besides, some difficulties in the field of model updating are also discussed.