The search for the IFN-gamma receptor in fish: Functional and expression analysis of putative binding and signalling chains in rainbow trout Oncorhynchus mykiss

Interferons (IFNs), consisting of three major subfamilies, type I, type II (gamma) and type III (lambda) IFN, activate vertebrate antiviral defences once bound to their receptors. The three IFN subfamilies bind to different receptors, IFNAR1 and IFNAR2 for type I IFNs, IFN gamma R1 and IFN gamma R2 for type II IFN, and IL-28R1 and IL-10R2 for type III IFNs. In fish, although many types I and II IFN genes have been cloned, little is known about their receptors. In this report, two putative IFN-gamma receptor chains were identified and sequenced in rainbow trout (Oncorhynchus mykiss), and found to have many common characteristics with mammalian type II IFN receptor family members. The presented gene synteny analysis, phylogenetic tree analysis and ligand binding analysis all suggest that these molecules are the authentic IFN gamma Rs in fish. They are widely expressed in tissues, with IFN gamma R1 typically more highly expressed than IFN gamma R2. Using the trout RTG-2 cell line it was possible to show that the individual chains could be differentially modulated, with rIFN-gamma and rIL-1 beta down regulating IFN gamma R1 expression but up regulating IFN gamma R2 expression. Overexpression of the two receptor chains in RTG-2 cells revealed that the level of IFN gamma R2 transcript was crucial for responsiveness to rIFN-gamma, in terms of inducing gamma IP expression. Transfection experiments showed that the two putative receptors specifically bound to rIFN-gamma. These findings are discussed in the context of how the IFN gamma R may bind IFN-gamma in fish and the importance of the individual receptor chains to signal transduction. (c) 2009 Elsevier Ltd. All rights reserved.

Expression pattern of cellular nucleic acid-binding protein (CNBP) during embryogenesis and spermatogenesis of gibel carp

By differential screening, we cloned the CagCNBP, demonstrated its predominant expression in ovary and testis, and reported its development behavior during folliculogenesis and oogenesis by immunofluorescence localization (Liu and Gui, Gene 365:181-192, 2005), but its developmental behavior during spermatogenesis and its transcript distribution during embryogenesis are not revealed. In the present study, by in situ hybridization, we analyze CagCNBP expression pattern during gibel carp embryogenesis. The CagCNBP transcripts ubiquitously distributed in all embryonic cells in early developmental stage embryos, and peak in midbrain, hindbrain and somites of gibel carp larva during organogenesis. By antibody detection, we reveal CagCNBP protein distribution change during spermatogenesis. The cell-specific distribution of CagCNBP is revealed by immunofluorescence staining, and predominant CagCNBP expression in testis somatic cells and spermatogonia is demonstrated in this paper. For the first time, the CNBP distribution during spermatogenesis in vertebrate has been revealed.

Expression pattern and developmental behaviour of cellular nucleic acid-binding protein (CNBP) during folliculogenesis and oogenesis in fish

In vertebrates, folliculogeneis establishes an intricate system for somatic cell-oocyte interaction, and ultimately leads to the acquisition of their respective competences. Although the formation process and corresponding interactions are strikingly similar in diverse organisms, knowledge of genes and signaling pathways involved in follicle formation is very incomplete and the underlying molecular mechanisms remain enigmatic. CNBP has been identified for more than ten years, and the highest level of CNBP transcripts has been observed in adult zebrafish ovary, but little is known about its functional significance during folliculogeneis and oogenesis. In this study, we clone CNBP cDNA from gibel carp (Carassius auratus gibelio), and demonstrate its predominant expression in gibel carp ovary and testis not only by RTPCR but also by Western blot. Its full-length cDNA is 1402 bp, and has an ORF of 489 nt for encoding a peptide of 163 aa. And its complete amino acid sequence shared 68.5%-96.8% identity with CNBPs from other vertebrates. Based on the expression characterization, we further analyze its expression pattern and developmental behaviour during folliculogeneis and oogenesis. Following these studies, we reveal an unexpected discovery that the CagCNBP is associated with follicular cells and oocytes, and significant distribution changes have occurred in degenerating and regenerating follicles. More interestingly, the CagCNBP is more highly expressed in some clusters of interconnected cells within ovarian cysts, no matter whether the cell clusters are formed from the original primordial germ cells or from the newly formed cells from follicular cells that invaded into the atretic oocytes. It is the first time to reveal CNBP relevance to folliculogeneis and oogenesis. Moreover, a similar stage-specific and cell-specific expression pattern has also been observed in the gibel carp testis. Therefore, further studies on CNBP expression pattern and developmental behaviour will be of significance for understanding functional roles of CNBP during gametogenests. (c) 2005 Elsevier B.V. All rights reserved.

Molecular cloning of TRAF2 binding protein gene and its promoter region from the grass carp Ctenopharyngodon idellus

A tumor necrosis factor receptor-associated factor 2 binding protein (T2BP) gene was isolated from the grass carp (Ctenopharyngodon idellus) by utilizing suppression subtractive hybridization (SSH) and rapid amplification of cDNA ends (RACE). The grass carp T2BP (GT2BP) gene contains an open reading frame of 579 nucleotide(s) (nt), encoding 193 amino acids, with 23 nt 5'-untranslated region and a long 3'-untranslated region of 434 nt including poly (A), 1 AUUUA motif and 4 AUUUUA motifs. No signal peptide has been detected in the predicted GT2BP, but a characteristic forkhead associated domain is present. The GT2BP mRNA shares 83% identity with the zebrafish DNA sequence, and they both have no introns in the genomic DNA. The putative transcription factor binding sites of GT2BP include two C/EBP alpha binding sites, and one c-Jun binding, one AP-1 binding, and one nuclear factor kappa B (NF kappa B) binding sites. Southern blot analysis revealed that the GT2BP was a single-copy gene. Individual difference was observed in GT2BP expression in examined organs of healthy grass carp. However, the expression of GT2BP in all examined organs in a fish with the highest copepod infection level and the significantly higher expression level in spleen and liver in infected fish may indicate its up-regulation with the parasite infection. (c) 2005 Elsevier B.V. All rights reserved.

Donor-donor binding in In2O3: Engineering shallow donor levels

Using first-principles band structure methods, we investigate the interactions between different donors in In2O3. Through the formation energy and transition energy level calculations, we find that an oxygen-vacancy creates a deep donor level, while an indium-interstitial or a tin-dopant induces a shallow donor level. The coupling between these donor levels gives rise to even shallower donor levels and leads to a significant reduction in their formation energies. Based on the analysis of the PBE0-corrected band structure and the molecular-orbital bonding diagram, we demonstrate these effects of donor-donor binding. In addition, total energy calculations show that these defect pairs tend to be more stable with respect to the isolated defects due to their negative binding energies. Thus, we may design shallow donor levels to enhance the electrical conductivity via the donor donor binding.

Size dependence of biexciton binding energy in single InAs/GaAs quantum dots

This paper studies the size dependence of biexciton binding energy in single quantum dots (QDs) by using atomic force microscopy and micro-photoluminescence measurements. It finds that the biexciton binding energies in the QDs show "binding" and "antibinding" properties which correspond to the large and small sizes of QDs, respectively. The experimental results can be well interpreted by the biexciton potential curve, calculated from the exciton molecular model and the Heitler-London method.

A full spd tight-binding treatment for electronic bands of graphitic tubes

A tight-binding (TB) treatment with the inclusion of d orbitals is applied to the electronic structures of graphitic tubes. The results show that the high angular moment bases in TB scheme are necessary to account the severe curvature effect in ultra-thin single wall carbon nanotubes, especially for properly reproducing the band edge overlap behavior in (5, 0) tube, predicted by the existing ab initio calculations. In the large diameter limit, the participation of two synnmetry-allowed d bases provides a natural replication to the recent measured electronic dispersions of valence band of graphene when the strong anisotropy due to the two-dimensional planar hexagonal sheet structure is dealt with properly. In addition, the detailed relation between the two sets of quantum numbers of screw symmetry and that of zone folding is formulated in appendix. (C) 2008 Elsevier Ltd. All rights reserved.

Binding Energy and Spin-Orbit Splitting of a Hydrogenic Donor Impurity in AlGaN/GaN Triangle-Shaped Potential Quantum Well

In the framework of effective-mass envelope function theory, including the effect of Rashba spin-orbit coupling, the binding energy E-b and spin-orbit split energy Gamma of the ground state of a hydrogenic donor impurity in AlGaN/GaN triangle-shaped potential heterointerface are calculated. We find that with the electric field of the heterojunction increasing, (1) the effective width of quantum well (W) over bar decreases and (2) the binding energy increases monotonously, and in the mean time, (3) the spin-orbit split energy Gamma decreases drastically. (4) The maximum of Gamma is 1.22 meV when the electric field of heterointerface is 1 MV/cm.

Binding energy of a hydrogenic donor impurity in a rectangular parallelepiped-shaped quantum dot: Quantum confinement and Stark effects

We calculate the binding energy of a hydrogenic donor impurity in a rectangular parallelepiped-shaped quantum dot (QD) in the framework of effective-mass envelope-function theory using the plane wave basis. The variation of the binding energy with edge length, position of the impurity, and external electric field is studied in detail. A finite potential model is adopted in our calculations. Compared with the infinite potential model [C. I. Mendoza , Phys. Rev. B 71, 075330 (2005)], the following results are found: (1) if the impurity is located in the interior of the QD, our results give a smaller binding energy than the infinite potential model; (2) the binding energies are more sensitively dependent on the applied electric field in the finite potential model; (3) the infinite potential model cannot give correct results for a small QD edge length for any location of the impurity in the QD; (4) some degeneracy is lifted when the dot is no longer cubic. (C) 2007 American Institute of Physics.

Electronic structure and binding energy of a hydrogenic impurity in a hierarchically self-assembled GaAs/AlxGa1-xAs quantum dot

We calculate the electronic structures and binding energy of a hydrogenic impurity in a hierarchically self-assembled GaAs/AlxGa1-xAs quantum dot (QD) in the framework of effective-mass envelope-function theory. The variation of the electronic structures and binding energy with the QD structure parameters and the position of the impurity are studied in detail. We find that (1) acceptor impurity energy levels depend more sensitively on the size of the QD than those of a donor impurity; (2) all impurity energy levels strongly depend on the GaAs quantum well (QW) width; (3) a donor impurity in the QD has only one binding energy level except when the GaAs QW is large; (4) an acceptor impurity in the QD has two binding energy levels, which correspond to heavy- and light-hole quantum states; (5) the binding energy has a maximum value when the impurity is located below the symmetry axis along the growth direction; and (6) the binding energy has a minimum value when the impurity is located at the top corner of the QD. (c) 2006 American Institute of Physics.

Binding energy of positively and negatively charged excitons in GaAs/AlxGa1-xAs quantum wells

Using a simple two-parameter wavefunction, we calculate variationally the binding energy of positively and negatively charged excitons in GaAs/AlxGa1-xAs quantum wells for well widths from 10 to 300Angstrom. We consider the effect of effective mass, dielectric constant mismatch in the two materials, and the whole correlation among the particles. The results are discussed and compared in detail with previous experimental and theoretical results, which show fair agreement with them.

Energy band and acceptor binding energy of GaN and AlxGa1-xN

The hole effective-mass Hamiltonian for the semiconductors of wurtzite structure is established, and the effective-mass parameters of GaN and AlxGa1-xN are given. Besides the asymmetry in the z and x, y directions, the linear term of the momentum operator in the Hamiltonian is essential in determining the valence band structure, which is different from that of the zinc-blende structure. The binding energies of acceptor states are calculated by solving strictly the effective-mass equations. The binding energies of donor and acceptor for wurtzite GaN are 20 and 131, 97 meV, respectively, which are inconsistent with the recent experimental results. It is proposed that there are two kinds of acceptors in wurtzite GaN. One kind is the general acceptor such as C, substituting N, which satisfies the effective-mass theory, and the other includes Mg, Zn, Cd etc., the binding energy of which deviates from that given by the effective-mass theory. Experimentally, wurtzite GaN was grown by the MBE method, and the PL spectra were measured. Three main peaks are assigned to the DA transitions from the two kinds of acceptor. Some of the transitions were identified as coming from the cubic phase of GaN, which appears randomly within the predominantly hexagonal material. The binding energy of acceptor in ALN is about 239, 158 meV, that in AlxGa1-xN alloys (x approximate to 0.2) is 147, 111 meV, close to that in GaN. (C) 2000 Published by Elsevier Science S.A. All rights reserved.

Binding energy of ionized-donor-bound excitons in the GaAs-AlxGa1-xAs quantum wells

The binding energy of an exciton bound to an ionized donor impurity (D+,X) located st the center or the edge in GaAs-AlxGa1-xAs quantum wells is calculated variationally for the well width from 10 to 300 Angstrom by using a two-parameter wave function, The theoretical results are discussed and compared with the previous experimental results.

Binding energy of excitons bound to neutral donors in two-dimensional semiconductors

The binding energies of excitons bound to neutral donors in two-dimensional (2D) semiconductors within the spherical-effective-mass approximation, which are nondegenerate energy bands, have been calculated by a variational method for a relevant range of the effective electron-to-hole mass ratio sigma. The ratio of the binding energy of a 2D exciton bound to a neutral donor to that of a 2D neutral donor is found to be from 0.58 to 0.10. In the limit of vanishing sigma and large sigma, the results agree fairly well with previous experimental results. The results of this approach are compared with those of earlier theories.

Energy bands and acceptor binding energies of GaN

The energy bands of zinc-blende and wurtzite GaN are calculated with the empirical pseudopotential method, and the pseudopotential parameters for Ga and N atoms are-given. The calculated energy bands are in agreement with those obtained by the ab initio method. The effective-mass theory for the semiconductors of wurtzite structure is established, and the effective-mass parameters of GaN for both structures are given The binding energies of acceptor states are calculated by solving strictly the effective-mass equations. The binding energies of donor and acceptor are 24 and 142 meV for the zinc-blende structure, 20 and 131, and 97 meV for the wurtzite structure, respectively, which are consistent with recent experimental results. It is proposed that there are two kinds of acceptor in wurtzite GaN. One kind is the general acceptor such as C, which substitutes N, which satisfies the effective-mass theory. The other kind of acceptor includes Mg, Zn, Cd, etc., the binding energy of these accepters is deviated from that given by the effective mass theory. In this report, wurtzite GaN is grown by the molecular-beam epitaxy method, and the photoluminescence spectra were measured. Three main peaks are assigned to the donor-acceptor transitions from two kinds of accepters. Some of the transitions were identified as coming from the cubic phase of GaN, which appears randomly within the predominantly hexagonal material. [S0163-1829(99)15915-0].