Molecular identification and expression analysis of tumor necrosis factor receptor-associated factor 2 in grass carp Ctenopharyngodon idella

Tumor necrosis factor receptor-associated factor 2 (TRAF2) is a crucial component of almost the entire tumor necrosis factor receptor superfamily signaling pathway. In the present study, a TRAF2 gene has been cloned from grass carp (Ctenopharyngodon idella) by reverse transcription-polymerase chain reaction and rapid amplification of cDNA ends. The full-length cDNA is 3162 bp, including a 60 bp 5' untranslated region (UTR), a 1611 bp open reading frame, and a 1491 bp 3' UTR. The polyadenylation signal (AATAAA) and the mRNA instability motifs (ATTTTA, ATTTA) were followed by a poly(A) tail in the 3' UTR. No signal peptide or transmembrane region has been found in the putative amino acids of grass carp TRAF2 (gcTRAF2). Phylogenetic tree analysis clearly showed that gcTRAF2 is nearest to the TRAF2 gene of goldfish. The identity of gcTRAF2 with its homologs in other vertebrates ranges from 56% to 97%. It is characterized by one RING-type signature at the N-terminus, one zinc finger in the middle part, and one conserved TRAF domain consisting of a C-proximal (TRAF-C) subdomain and a N-proximal (TRAF-N) subdomain. The identity of TRAF-C among all TRAF2 homologs in vertebrates varies from 78% to 97%, whereas the identity of TRAF-N ranges from 56% to 100%. The recombinant gcTRAF2 has been expressed in Escherichia coli using pET-32a expression vector. The rabbit anti-gcTRAF2 polyclonal antibody was obtained. The expression of gcTRAF2 in different organs was examined by real-time quantitative polymerase chain reaction and Western blot analysis. It was widely distributed in heart, head kidney, thymus, brain, gill, liver, spleen, and trunk kidney. This is the first report of a TRAF2 homolog molecule in fish.

Phylogeny of diplozoids in five genera of the subfamily diplozoinae palombi, 1949 as inferred from ITS-2 rDNA sequences

The phylogenetic relationship of 5 genera, i.e. Diplozoon Nordmann, 1832, Paradiplozoon Achmerov, 1974, Inustiatus Khotenovsky, 1978, Sindiplozoon Khotenovsky, 1981, and Eudiplozoon Khotenovsky, 1985 in the subfamily Diplozoinae Palombi, 1949 (Monogenea, Polyopisthocotylea) was inferred from rDNA ITS-2 region using neighbour-joining (NJ), maximum likelihood (ML) and Bayesian methods. The phylogenetic trees produced by using NJ, ML and Bayesian methods exhibit essentially the same topology. Surprisingly, freshwater species of Paradiplozoon from Europe clustered together with species of Diplozoon, but separated from Chinese Paradiplozoon species. The results of molecular phylogeny and lower level of divergence (4(.)1-15(.)7%) in ITS-2 rDNA among Paradiplozoon from Europe and Diplozoon and, on the other hand, high level of divergence (45(.)3-53(.)7%) among Paradiplozoon species from Europe and China might indicate the non-monophyletic origin of the genus Paradiplozoon. Also, the generic status of European Paradiplozoon needs to be revised. The species of Paradiplozoon in China is a basal group in Diplozoinae as revealed by NJ and Bayesian methods, and Sindiplozoon appears to be closely related to European Paradiplozoon and Diplozoon. with their relationship to Eudiplozoon and Inustiatus being unresolved.

Shrinkage of Gobiocypris rarus, Procypris rabaudi, and Sinilabeo rendahli preserved in formalin

Length measurements of preserved fishes are necessary in many types of fish surveys because logistics often do not allow for fish measurement immediately after catch. If the fixative causes significant shrinkage, then the preserved lengths cannot be directly used to indicate accurate live lengths. The objective of this study was to determine how preservation in formalin affects standard length of Gobiocypris rarus larvae (24-day-old and newly hatched), larval Procypris rabaudi (4-day-old), and larval Sinilabeo rendahli (12-day-old). Fishes were measured (to nearest 0.01 mm) and individually fixed in the appropriate formalin solution (2.5% or 5.0% formalin), then re-measured at 0.5, 1, 3, 7, 14, 30, 45 and 75 days after preservation to follow the time course of shrinkage. Most of the shrinkage occurred within the first half day after preservation. The 5.0% formalin caused a higher relative shrinkage rate than did the 2.5% solution; however, the difference was not statistically significant. In G. rarus, initial shrinkage of newly hatched larvae was higher than that of 24-day-old larvae.

Isolation and characterization of Scophthalmus maximus rhabdovirus

A rhabdovirus associated with a lethal hemorrhagic disease in cultured turbot Scophthalm us maximus Linnaeus was isolated. The virus induced typical cytopathogenic effects (CPE) in 9 of 15 fish cell lines examined and was then propagated and isolated from infected carp leucocyte cells (CLC). Electron microscopy observations revealed that the negatively stained virions had a typical bullet-shaped morphology with one rounded end and one flat base end. The bullet-shaped morphology was more obvious and clear in ultrathin sections of infected cells. Experimental infections also indicated that the S. maximus rhabdovirus (SMRV) was not only a viral pathogen for cultured turbot, but also had the ability to infect other fish species, such as freshwater grass carp. A partial nucleotide sequence of the SMRV polymerase gene was determined by RT-PCR using 2 pairs of degenerate primers designed according to the conserved sequences of rhabdovirus polymerase genes. Homology analysis, amino acid sequence alignment, and phylogenetic relationship analysis of the partial SMRV polymerase sequence indicated that SMRV was genetically distinct from other rhabdoviruses. Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) analysis of the purified SMRV revealed 5 major structural proteins, and their molecular masses were estimated to be about 250, 58, 47, 42, and 28 kDa. Significant serological reactivity differences were also observed between SMRV and its nearest neighbor, spring viremia of carp virus (SVCV). The data suggest that SMRV is likely a novel fish rhabdovirus, although it is closely related to rhabdoviruses in the genus Vesiculovirus.

The Yangtze River dolphin or baiji (Lipotes vexillifer): population status and conservation issues in the Yangtze River, China

1. Baiji were sighted 17 times during three recent simultaneous multi-vessel surveys in the Yangtze River, China (November 4-10, 1997; December 4-9, 1998; October 31-November 5, 1999). There were 11 sightings in 1997 (consisting of 17 animals), five in 1998 (seven animals), and two in 1999 (four animals). It was concluded that 13 individuals Could be considered as a minimum number of the baiji currently in the Yangtze River. 2. An annual rate of population decrease was roughly estimated as 10%. From the body sizes observed, the proportions of old, adult and immature individuals were approximately estimated at 57, 26, and 17% respectively. 3. Baiji showed a significant attraction to confluences and sand bars with large eddies. The present distribution range of the baiji is less than 1400 km in length in the Yangtze main river. Distances between the two nearest groups of baiji appear to be increasing. 4. Two typical sightings are described, in which surfacing and movements of baiji were recorded. Baiji were often found swimming together with finless porpoise. In the surveys they occurred in the same group in 63% of occurrences. Interactions between baiji and finless porpoise are described and discussed. 5. Human activities are the main threats to the baiji. Illegal electrical fishing accounted for 40% of known mortalities during the 1990s. Engineering explosions for maintaining navigation channels have become another main cause of baiji deaths. The last hope of saving the species may be to translocate the remaining baiji into a semi-captive reserve. known as the 'Baiji Semi-natural Reserve'. Copyright (C) 2003 John Wiley Sons, Ltd.

Sixfold symmetry of excitonic transition energies in c-plane for wurtzite GaN

The optical properties of the strained wurtzite GaN are investigated theoretically within the nearest neighbor tight-binding method. The piezoelectric effect is also taken into account. The empirical rule has been used in the strained band-structure calculation. The results show that the excitonic transition energies are anisotropic in the c-plane in a high electronic concentration system and have a 60 degrees periodicity, which is in agreement with experiment. (C) 2008 American Institute of Physics. [DOI: 10.1063/1.3001937]

First-principles study of transition metal impurities in Si

By using ab initio electronic structure calculations within density functional theory, we study the structural, electronic, and magnetic properties of Si doped with a transition metal impurity. We consider the transition metals of the 3d series V, Cr, Mn, Fe, Co, and Ni. To get insight into the level filling mechanism and the magnetization saturation, we first investigate the transition metal-Si alloys in the zinc-blende structure. Next, we investigate the doping of bulk Si with a transition metal atom, in which it occupies the substitutional site, the interstitial site with tetrahedral symmetry, and the interstitial site with hexagonal symmetry. It is found that all of these transition metal impurities prefer an interstitial position in Si. Furthermore, we show that it is possible to interpret the electronic and magnetic properties by using a simple level filling picture and a comparison is made to Ge doped with the same transition metal atoms. In order to get insight into the effect of a strained environment, we calculate the formation energy as a function of an applied homogeneous pressure and we show that an applied pressure can stabilize the substitutional position of transition metal impurities in Si. Finally, the energies of the ferromagnetic states are compared to those of the antiferromagnetic states. It is shown that the interstitial site of the Mn dopant helps us to stabilize the nearest neighbor substitutional site to realize the ferromagnetic state. For doping of Si with Cr, a ferrimagnetic behavior is predicted.

Magnetic coupling properties of mn-doped ZnO nanowires: First-principles calculations

Based on the density functional theory, we study the magnetic coupling properties of Mn-doped ZnO nanowires. For the nanowires with passivated surfaces, the antiferromagnetic state is found and the Mn atoms have a clustering tendency. When the distance between two Mn atoms is large, the system energetically favors the paramagnetic or spin-glass state. For the nanowires with unpassivated surfaces, the ferromagnetic (FM) coupling states appear between the two nearest Mn atoms, and the zinc vacancies can further stabilize the FM states between them. The electrons with enough concentration possibly mediate the FM coupling due to the negative exchange splitting of conduction band minimum induced by the s-d coupling, which could be useful in nanomaterial design for spintronics. (C) 2008 American Institute of Physics.

Magnetic coupling properties of rare-earth metals (Gd, Nd) doped ZnO: First-principles calculations

The electronic structure and magnetic coupling properties of rare-earth metals (Gd, Nd) doped ZnO have been investigated using first-principles methods. We show that the magnetic coupling between Gd or Nd ions in the nearest neighbor sites is ferromagnetic. The stability of the ferromagnetic coupling between Gd ions can be enhanced by appropriate electron doping into ZnO Gd system and the room-temperature ferromagnetism can be achieved. However, for ZnO Nd system, the ferromagnetism between Nd ions can be enhanced by appropriate holes doping into the sample. The room-temperature ferromagnetism can also be achieved in the n-conducting ZnO Nd sample. Our calculated results are in good agreement with the conclusions of the recent experiments. The effect of native defects (V-Zn, V-O) on the ferromagnetism is also discussed. (C) 2009 American Institute of Physics. [DOI 10.1063/1.3176490]

Band-gap bowing and p-type doping of (Zn, Mg, Be)O wide-gap semiconductor alloys: a first-principles study

Using a first-principles band-structure method and a special quasirandom structure (SQS) approach, we systematically calculate the band gap bowing parameters and p-type doping properties of (Zn, Mg, Be)O related random ternary and quaternary alloys. We show that the bowing parameters for ZnBeO and MgBeO alloys are large and dependent on composition. This is due to the size difference and chemical mismatch between Be and Zn(Mg) atoms. We also demonstrate that adding a small amount of Be into MgO reduces the band gap indicating that the bowing parameter is larger than the band-gap difference. We select an ideal N atom with lower p atomic energy level as dopant to perform p-type doping of ZnBeO and ZnMgBeO alloys. For N doped in ZnBeO alloy, we show that the acceptor transition energies become shallower as the number of the nearest neighbor Be atoms increases. This is thought to be because of the reduction of p-d repulsion. The N-O acceptor transition energies are deep in the ZnMgBeO quaternary alloy lattice-matched to GaN substrate due to the lower valence band maximum. These decrease slightly as there are more nearest neighbor Mg atoms surrounding the N dopant. The important natural valence band alignment between ZnO, MgO, BeO, ZnBeO, and ZnMgBeO quaternary alloy is also investigated.

Nitrogen defects and ferromagnetism in Cr-doped dilute magnetic semiconductor AlN from first principles

High Curie temperature of 900 K has been reported in Cr-doped AlN diluted magnetic semiconductors prepared by various methods, which is exciting for spintronic applications. It is believed that N defects play important roles in achieving the high-temperature ferromagnetism in good samples. Motivated by these experimental advances, we use a full-potential density-functional-theory method and supercell approach to investigate N defects and their effects on ferromagnetism of (Al,Cr)N with N vacancies (V-N). We investigate the structural and electronic properties of V-N, single Cr atom, Cr-Cr atom pairs, Cr-V-N pairs, and so on. In each case, the most stable structure is obtained by comparing different atomic configurations optimized in terms of the total energy and the force on every atom, and then it is used to calculate the defect formation energy and study the electronic structures. Our total-energy calculations show that the nearest substitutional Cr-Cr pair with the two spins in parallel is the most favorable and the nearest Cr-V-N pair makes a stable complex. Our formation energies indicate that V-N regions can be formed spontaneously under N-poor condition because the minimal V-N formation energy equals -0.23 eV or Cr-doped regions with high enough concentrations can be formed under N-rich condition because the Cr formation energy equals 0.04 eV, and hence real Cr-doped AlN samples are formed by forming some Cr-doped regions and separated V-N regions and through subsequent atomic relaxation during annealing. Both of the single Cr atom and the N vacancy create filled electronic states in the semiconductor gap of AlN. N vacancies enhance the ferromagnetism by adding mu(B) to the Cr moment each but reduce the ferromagnetic exchange constants between the spins in the nearest Cr-Cr pairs. These calculated results are in agreement with experimental observations and facts of real Cr-doped AlN samples and their synthesis. Our first-principles results are useful to elucidate the mechanism for the ferromagnetism and to explore high-performance Cr-doped AlN diluted magnetic semiconductors.

Mutual passivation of donors and isovalent nitrogen in GaAs

We study the mutual passivation of shallow donor and isovalent N in GaAs. We find that all the donor impurities, Si-Ga, Ge-Ga, S-As, and Se-As, bind to N in GaAsN, which has a large N-induced band-gap reduction relative to GaAs. For a group-IV impurity such as Si, the formation of the nearest-neighbor Si-Ga-N-As defect complex creates a deep donor level below the conduction band minimum (CBM). The coupling between this defect level with the CBM pushes the CBM upwards, thus restoring the GaAs band gap; the lowering of the defect level relative to the isolated Si-Ga shallow donor level is responsible for the increased electrical resistivity. Therefore, Si and N mutually passivate each other's electrical and optical activities in GaAs. For a group-VI shallow donor such as S, the binding between S-As and N-As does not form a direct bond; therefore, no mutual passivation exists in the GaAs(S+N) system.

Correlation effects for semiconducting single-wall carbon nanotubes: A density matrix renormalization group study

In this paper we report the applicability of the density matrix renormalization group (DMRG) approach to the cylindrical single wall carbon nanotube (SWCN) for the purpose of its correlation effect. By applying the DMRG approach to the t+U+V model, with t and V being the hopping and Coulomb energies between the nearest neighboring sites, respectively, and U the on-site Coulomb energy, we calculate the phase diagram for the SWCN with chiral numbers (n(1)=3, n(2)=2), which reflects the competition between the correlation energy U and V. Within reasonable parameter ranges, we investigate possible correlated ground states, the lowest excitations, and the corresponding correlation functions in which the connection with the excitonic insulator is particularly addressed.

Analog computation using quantum-dot cell network

A novel analog-computation system using a quantum-dot cell network is proposed to solve complex problems. Analog computation is a promising method for solving a mathematical problem by using a physical system analogous to the problem. We designed a novel quantum-dot cell consisting of three-stacked. quantum dots and constructed a cell network utilizing the nearest-neighbor interactions between the cells. We then mapped a graph 3-colorability problem onto the network so that the single-electron configuration of the network in the ground state corresponded to one of the solutions. We calculated the ground state of the cell network and found solutions to the problems. The results demonstrate that analog computation is a promising approach for solving complex problems.

Influence of Fe3+ on perovskite oxides: La2/3Ca1/3Mn1-xFexO3

The structure and magnetoresistance properties in sintered samples of La-2/3 Ca-1/3 Mn1-x FexO3 (0 less than or equal to x less than or equal to 0.84) are studied by using Mossbauer spectroscopy, XRD and magnetic measurement. There are antiferromagnetic interactions between Fe and its nearest neighbors (Fe, Mn) when 0 less than or equal to x less than or equal to 0.67, which are important factors influencing the double-exchange between Mn3+ and Mn4+, Curie temperature, magnetic moment and GMR. It is suggested that the Mn3+(Fe3+)/Mn4+ system also consists of magnetic clusters with different sizes.