Molecular phylogeography of endangered sharp-snouted pitviper (Deinagkistrodon acutus; Reptilia, Viperidae) in Mainland China

Using phylogenetic and population genetic approaches, the present study reports the phylogeographic structure of the sharp-snouted pitviper (Deinagkistrodon acutus), a threatened snake species with commercial and medicinal importance in China. The entire mitochondrial ND2 gene (NADH dehydrogenase subunit 2) sequences of 86 individuals of D. acutus from 14 localities across its range in China were determined. Based on the results of phylogenetic analyses, distribution of diagnostic sites, haplotype network, and AMOVA hierarchical analysis, an cast-west division of the whole D. acutus population could be observed. Geographically, a line formed by a lake, river, and mountain chain (the Poyang Lake, Gan River to the southern end of the Wuyi Mountains), results in vicariance and approximately vertically splits the range into two and the whole population into two main lineages (western and eastern). The bifurcating tree suggested generally west to east dispersal trend. The data fit the isolation by distance (IBD) model well. Star-like clusters in haplotype network, significantly negative values of Fs statistics, and unimodal mismatch distributions all suggest recent demographic expansions in four areas. The results show that isolation, dispersal, bottleneck, and expansion jointly constitute the history of D. acutus. In a haplotype network, the excessive predominance of central haplotypes, few medium-frequency haplotypes, predominance (73.1 %) of the singletons among the derived haplotypes, most of which are connected to the central haplotype by only one mutational step, unsymmetrical campanulate unimodal curve of mismatch distributions and leftwards shift of the peaks, all suggest that the whole D. acutus population is a young population with low genetic diversity. Based on the data, the first priority for conservation action should be given to the Huangshan unit. (c) 2007 Elsevier Inc. All rights reserved.

The complete mitochondrial genome of the Chinese hook snout carp Opsariichthys bidens (Actinopterygii : Cyprinifonnes) and an altemative pattem of mitogenomic evolution in vertebrate

The complete mitochondrial genome sequence of the Chinese hook snout carp, Opsariichthys bidens, was newly determined using the long and accurate polymerase chain reaction method. The 16,611-nucleotide mitogenome contains 13 protein-coding genes, two rRNA genes (12S, 16S) 22 tRNA genes, and a noncoding control region. We use these data and homologous sequence data from multiple other ostariophysan fishes in a phylogenetic evaluation to test hypothesis pertaining to codon usage pattern of O. bidens mitochondrial protein genes as well as to re-examine the ostariophysan phylogeny. The mitochondrial genome of O. bidens reveals an alternative pattern of vertebrate mitochondrial evolution. For the mitochondrial protein genes of O. bidens, the most frequently used codon generally ends with either A or C, with C preferred over A for most fourfold degenerate codon families; the relative synonymous codon usage of G-ending codons is greatly elevated in all categories. The codon usage pattern of O. bidens mitochondrial protein genes is remarkably different from the general pattern found previously in the relatively closely 9 related zebrafish and most other vertebrate mitochondria. Nucleotide bias at third codon positions is the main cause of codon bias in the mitochondrial protein genes of O. bidens, as it is biased particularly in favor of C over A. Bayesian analysis of 12 concatenated mitochondrial protein sequences for O. bidens and 46 other teleostean taxa supports the monophyly of Cypriniformes and Otophysi and results in a robust estimate of the otophysan phylogeny. (C) 2007 Published by Elsevier B.V.

Characterization of cDNA encoding immunoglobulin light chain of the Mandarin fish (Siniperca chuatsi)

Immunoglobulin light chain cDNA sequences of a perciform fish, the mandarin fish Siniperca chuatsi were amplified from head kidney mRNA by reverse transcription (RT)-PCR and RACE methods using degenerated primer and gene specific ones. In cDNA sequences of the VL region, nucleotide exchanges were present mainly within CDRs, although a lesser degree of variability was also found in FRs. Moreover, the length of CDRI and CDR3 in the mandarin fish is shorter than in most other fish species. In the middle of S. chuatsi CL region, a microsatellite sequence (AGC)(6-8) was found, which is also present in another perciform species, the spotted wolffish (Anarhichas minor). The comparison of amino acid sequence of the mandarin fish CL domain with those of other vertebrates showed the highest degree of similarity of 94.5% to the spotted wolffish, while the similarity with rainbow trout (Oncorhynchus mykiss) Ig L1 (62.7%) and channel catfish (Ictalurus punctatus) Ig LG (55.9%) isotypes is also higher. However, there is only 50% identity in the VL regions between the mandarin fish and the wolffish. The sequence similarity of the mandarin fish CL domain with those of higher vertebrate did not readily allow it to be classified as kappa or lambda isotype. The phylogenetic analyses also demonstrated that the CL genes of the mandarin fish and most other teleost fish cluster as a separate branch out of the mammal kappa and lambda branches. (C) 2003 Elsevier B.V. All rights reserved.

Construction and characterization of a novel recombinant single-chain variable fragment antibody against White Spot Syndrome Virus from shrimp

An antibody phage display library against White Spot Syndrome Virus (WSSV) was constructed. After four rounds of panning against WSSV, 192 out of 480 clones displayed WSSV binding activity. One of the positive clones, designated A1, had relatively higher activity specifically binding to WSSV A1-soluble, single-chain fragment variable (scFv) antibody has an affinity constant (K-aff) of 2.02 +/- 0.42 x 10(9) M-1. Dot blot assays showed that A1-soluble scFv could detect WSSV directly from shrimp hemolymph after 24-h feeding infection by WSSV. A1 scFv has potential for the development of a cheap, simple and sensitive diagnostic kit for WSSV in the field. (C) 2003 Elsevier Science B.V. All rights reserved.

Isolation by phage display and characterization of a single-chain antibody specific for O-6-methyldeoxyguanosine

New approaches of making single chain Fv antibodies against O-6-methyl-2'-deoxyguanosine (O(6)MdG) have been demonstrated by using the phage antibody display system. Using O(6)MdG as an antigen, 21 positive clones were identified by ELISA from this library, one of which, designated H3, specifically binds to O(6)MdG with high affinity. The H3 scFv antibody has an affinity constant (K-aff) of 5.94 x 10(11)(mol/L)(-1). H3 scFv has been successfully used to detect O-6 MdG in DNA hydrolyses from yeast or E. coli cells treated with a DNA methylating agent. To our knowledge, this is the first report of the selection of a specific scFv against DNA adducts. The results demonstrate the potential applications of the phage display technology for the detection of DNA lesions caused by mutagens and carcinogens.

A detection method for grass carp hemorrhagic virus (GCHV) based on a reverse transcription polymerase chain reaction

A rapid, sensitive and highly specific detection method for grass carp hemorrhagic virus (GCHV) based on a reverse transcription-polymerase chain reaction (RT-PCR) has been developed. Two pairs of PCR primers were synthesized according to the cloned cDNA sequences of the GCHV-861 strain. For each primer combination, only one specific major product was obtained when amplification was performed by using the genomic dsRNA of GCHV-861 strain. The lengths of their expected products were 320 and 223 bp, respectively. No products were obtained when nucleic acids other than GCHV-861 genomic RNA were used as RT-PCR templates. To assess the sensitivity of the method, dilutions of purified GCHV-861 dsRNA total genome (0.01 pg up to 1000 pg) were amplified and quantities of as little as 0.1 pg of purified dsRNA were detectable when the amplification product was analyzed by 1.5% agarose gel electrophoresis. This technique could detect GCHV-861 not only in infected cell culture fluids, but also in infected grass carp Ctenopharyngodon idellus and rare minnow Gobiocypris rarus with or without hemorrhagic symptoms. The results show that the RT-PCR amplification method is useful for the direct detection of GCHV.

Quantum phase transitions in the S=1/2 distorted diamond chain

By means of the second derivative of the ground-state and first-excited energy, the quantum phase transitions (QPTs) for the distorted diamond chain (DDC) with ferromagnetic and antiferromagnetic frustrated interactions and the trimerized case are investigated, respectively. Our results show the plentiful quantum phases owing to the spin interaction competitions in the model. Meanwhile, by using the transfer-matrix renormalization-group technique, we study the two-site thermal entanglement of the DDC model in the thermodynamic limit for a further understanding of the QPTs.

Quantum teleportation via a two-qubit Heisenberg XXZ chain - effects of anisotropy and magnetic field

We study quantum teleportation via a two-qubit Heisenberg XXZ, chain under an inhomogeneous magnetic field. We first consider entanglement teleportation, and then focus on the teleportation fidelity under different conditions. The effects of anisotropy and the magnetic field, both uniform and inhomogeneous, are discussed. We also find that, though entanglement teleportation does require an entangled quantum channel, a nonzero critical value of minimum entanglement is not always necessary.

Recent progresses of Si-based photonics in chinese main land

Si-based photonic materials and devices, including SiGe/Si quantum structures, SOI and InGaAs bonded on Si, PL of Si nanocrystals, SOI photonic crystal filter, Si based RCE (Resonant Cavity Enhanced) photodiodes, SOI TO (thermai-optical) switch matrix were investigated in Institute of Serniconductors, Chinese Academy of Sciences. The main results in recent years are presented in the paper. The mechanism of PL from Si NCs embedded in SiO2 matrix was studied, a greater contribution of the interface state recombination (PL peak in 850 similar to 900 nm) is associated with larger Si NCs and higher interface state density. Ge dots with density of order of 10(11) cm(-2) were obtained by UHV/CVD growth and 193 nm excimer laser annealing. SOI photonic crystal filter with resonant wavelength of 1598 nm and Q factor of 1140 was designed and made. Si based hybrid InGaAs RCE PD with eta of 34.4% and FWHM of 27 nut were achieved by MOCVD growth and bonding technology between InGaAs epitaxial and Si wafers. A 16x16 SOI optical switch matrix were designed and made. A new current driving circuit was used to improve the response speed of a 4x4 SOI rearrangeable nonblocking TO switch matrix, rising and failing time is 970 and 750 ns, respectively.

Disentanglement of two qubits coupled to an XY spin chain: Role of quantum phase transition

We study the disentanglement evolution of two spin qubits which interact with a general XY spin-chain environment. The dynamical process of the disentanglement is numerically and analytically investigated in the vicinity of a quantum phase transition (QPT) of the spin chain in both weak and strong coupling cases. We find that the disentanglement of the two spin qubits may be greatly enhanced by the quantum critical behavior of the environmental spin chain. We give a detailed analysis to facilitate the understanding of the QPT-enhanced decaying behavior of the coherence factor. Furthermore, the scaling behavior in the disentanglement dynamics is also revealed and analyzed.

Optimal teleportation via thermal entangled states of a two-qubit Heisenberg chain

We study the optimal teleportation based on Bell measurements via the thermal states of a two-qubit Heisenberg XXX chain in the presence of the Dzyaloshinsky-Moriya (DM) anisotropic antisymmetric interaction and obtain an optimal unitary transformation. The explicit expressions of the output state and the teleportation fidelity are presented and compared with those of the standard protocol. It is shown that in this protocol the teleportation fidelity is always larger and the unit fidelity is achieved at zero temperature. The DM interaction can enhance the teleportation fidelity at finite temperatures, as opposed to the effect of the interaction in the standard protocol. Cases with other types of anisotropies are also discussed. Copyright (C) EPLA, 2009

Entanglement evolution of a spin-chain bath coupled to a quantum spin

For an electron spin in coupling with an interacting spin chain via hyperfine-type interaction, we investigate the dynamical evolutions of the pairwise entanglement of the spin chain, and a correlation function joined the electron spin with a pair of chain spins in correspondence to the electron-spin coherence evolution. Both quantities manifest a periodic and a decaying evolution. The entanglement of the spin bath is significant in distinguishing the zero-coherence status exhibited in periodic and decoherence evolutions of the electron spin. The periodical concurrence evolution of the spin bath characterizes the whole system in a coherence-preserving phase, particularly for the case that the associated periodic coherence evolution is predominated by zero value in the infinite chain-length limit, which was often regarded as the realization of decoherence.

Quantum critical phenomena in the XY spin chain with the Dzyaloshinski-Moriya interaction (Retracted article. See vol 80, artn 019903, 2009)

We study the effects of the Dzyaloshinski-Moriya (DM) anisotropic interaction on the ground-state properties of the Heisenberg XY spin chain by means of the fidelity susceptibility, order parameter, and entanglement entropy. Our results show that the DM interaction could influence the distribution of the regions of quantum phase transitions and cause different critical regions in the XY spin model. Meanwhile, the DM interaction has effective influence on the degree of entanglement of the system and could be used to increase the entanglement of the spin system.

Thermal entanglement in a two-qubit Heisenberg XXZ spin chain under an inhomogeneous magnetic field

The thermal entanglement in a two-qubit Heisenberg XXZ spin chain is investigated under an inhomogeneous magnetic field b. We show that the ground-state entanglement is independent of the interaction of z-component J(z). The thermal entanglement at the fixed temperature can be enhanced when J(z) increases. We strictly show that for any temperature T and J(z), the entanglement is symmetric with respect to zero inhomogeneous magnetic field, and the critical inhomogeneous magnetic field b(c) is independent of J(z). The critical magnetic field B-c increases with the increasing parallel to b parallel to but the maximum entanglement value that the system can arrive at becomes smaller.