The three dimensional structure and biological domains of the p53 C-terminus.

It was expected that there are a coil (289 similar to 325) and two a helix (alpha(1)368 similar to 373, alpha(2)381 similar to 388) structures in p53 protein C-terminal region based on its mRNA secondary structure template and Chou-Fasman's protein secondary structure principle of prediction. The result was conformed by the other four methods of protein secondary structure prediction that are based on the multiple sequence alignment (accuracy = 73.20%). Combine with the 31 amino acids crystal structure of the oligomerization, the three dimensional conformation of p53 C-terminal 108 residues was built using the SGI INDIGO(2) computer. This structure further expounds the relationship among those biological function domains of p53 C- terminus at three-dimensional level.

Exploring consensus mRNA secondary (folding) structure units by stochastic sampling and folding simulation

It is extremely difficult to explore mRNA folding structure by biological experiments. In this report, we use stochastic sampling and folding simulation to test the existence of the stable secondary structural units of-mRNA, look for the folding units, and explore the probabilistic stabilization of the units. Using this method, We made simulations for all possible local optimum secondary structures of a single strand mRNA within a certain range, and searched for the common parts of the secondary structures. The consensus secondary structure units (CSSUs) extracted from the above method are mainly hairpins, with a few single strands. These CSSUs suggest that the mRNA folding units could be relatively stable and could perform specific biological function. The significance of these observations for the mRNA folding problem in general is also discussed. (c) 2004 Elsevier B.V. All rights reserved.

Cardioviral RNA structure logo analysis: entropy, correlations, and prediction

In recent years, there has been an increased number of sequenced RNAs leading to the development of new RNA databases. Thus, predicting RNA structure from multiple alignments is an important issue to understand its function. Since RNA secondary structures are often conserved in evolution, developing methods to identify covariate sites in an alignment can be essential for discovering structural elements. Structure Logo is a technique established on the basis of entropy and mutual information measured to analyze RNA sequences from an alignment. We proposed an efficient Structure Logo approach to analyze conservations and correlations in a set of Cardioviral RNA sequences. The entropy and mutual information content were measured to examine the conservations and correlations, respectively. The conserved secondary structure motifs were predicted on the basis of the conservation and correlation analyses. Our predictive motifs were similar to the ones observed in the viral RNA structure database, and the correlations between bases also corresponded to the secondary structure in the database.

Structure, organization and expression of common carp (Cyprinus carpio L.) NKEF-B gene

Natural killer (NK) cell enhancing factor (NKEF) belongs to the newly defined peroxiredoxin (Prx) family. Its functions are to enhance NK cell cytotoxicity and to protect DNA and proteins from oxidative damage. In this study, a partial cDNA sequence of carp NKEF-B was isolated from thymus cDNA library. Subsequently, the full-length cDNA of carp NKEF-B was obtained by means of 3' and 5' RACE, respectively. The full-length cDNA of carp NKEF-B was 1022 bp, consisting of a 73 bp 5'-terminal untranslated region (UTR), a 355 bp T-terminal UTR, and a 594 bp open reading frame coding for a protein of 197 amino acids. Carp NKEF-B contained two consensus Val-Cys-Pro (VCP) motifs and three consensus cysteine (Cys-51, Cys-70 and Cys-172) residues. Sequence comparison showed that the deduced amino acid sequence of carp NKEF-B had an overall similarity of 74-96% to that of other species homologues. Phylogenetic analysis revealed that carp NKEF-B forms a cluster with other known teleost NKEF-Bs. Then, by PCR we obtained a 5.1 -k long genomic DNA of carp NKEF-B containing six exons and five introns. Realtime RT-PCR results showed that carp NKEF-B gene was predominantly detected in kidney and head kidney under un-infected conditions. Whereas under SVCV-infection condition, the expression of NKEF-B gene was significantly increased in blood cells, gill, intestine and spleen, but maintained in liver, and decreased significantly in kidney and head kidney. Finally, the rNKEF-B was constructed and expressed in Escherichia coli. By using an antibody against carp rNKEF-B, immunohistochemical study further indicated that NKEF-B positive cells are mainly some RBCs and a few epithelial cells in gill and intestine, and that under SVCV-infection condition, these positive cells or positive products in their cytoplasm were mainly increased in gill and spleen sections of carp. The results obtained in the present study will help to understand the function of NKEF-B in teleost innate immunity. (C) 2008 Elsevier Ltd. All rights reserved.

Structure, organization and expression of common carp (Cyprinus carpio L.) SLP-76 gene

SLP-76 is an important member of the SLP-76 family of adapters, and it plays a key role in TCR signaling and T cell function. Partial cDNA sequence of SLP-76 of common carp (Cyprinus carpio L.) was isolated from thymus cDNA Library by the method of suppression subtractive hybridization (SSH). Subsequently, the full length cDNA of carp SLP-76 was obtained by means of 3' RACE and 5' RACE, respectively. The full Length cDNA of carp SLP-76 was 2007 bp, consisting of a T-terminal untranslated region (UTR) of 285 bp, a T-terminal. UTR of 240 bp, and an open reading frame of 1482 bp. Sequence comparison showed that the deduced amino acid sequence of carp SLP-76 had an overall similarity of 34-73% to that of other species homotogues, and it was composed of an NH2-terminal domain, a central proline-rich domain, and a C-terminal SH2 domain. Amino acid sequence analysis indicated the existence of a Gads binding site R-X-X-K, a 10-aa-long sequence which binds to the SH3 domain of LCK in vitro, and three conserved tyrosine-containing sequence in the NH2-terminal domain. Then we used PCR to obtain a genomic DNA which covers the entire coding region of carp SLP-76. In the 9.2 k-long genomic sequence, twenty one exons and twenty introns were identified. RT-PCR results showed that carp SLP-76 was expressed predominantly in hematopoietic tissues, and was upregulated in thymus tissue of four-month carp compared to one-year old carp. RT-PCR and virtual northern hybridization results showed that carp SLP-76 was also upregulated in thymus tissue of GH transgenic carp at the age of four-months. These results suggest that the expression level of SLP-76 gene may be related to thymocyte development in teleosts. (c) 2007 Published by Elsevier Ltd.

Electronic energy levels in an asymmetric quantum-dots-in-a-well structure for infrared photodetectors

Theoretical calculation of electronic energy levels of an asymmetric InAs/InGaAS/GaAS quantum-dots-in-a-well (DWELL) structure for infrared photodetectors is performed in the framework of effective-mass envelope-function theory. Our calculated results show that the electronic energy levels in quantum dots (QDs) increase when the asymmetry increases and the ground state energy increases faster than the excited state energies. Furthermore, the results also show that the electronic energy levels in QDs decrease as the size of QDs and the width of quantum well (QW) in the asymmetric DWELL structure increase. Additionally, the effects of asymmetry, the size of QDs and the width of QW on the response peak of asymmetry DWELL photodetectors are also discussed.

Peculiarity of constant photocurrent method for silicon films with mixed amorphous-nanocrystalline structure

The results of conductivity, photoconductivity and constant photocurrent method absorption measurements by DC and AC methods in hydrogenated silicon films with mixed amorphous-nanocrystalline structure are presented. A series of diphasic silicon films was deposited by very high frequency plasma enhanced chemical vapor deposition technique, using different hydrogen dilution ratios of silane. The increase of hydrogen dilution ratio results in five orders of magnitude increase of conductivity and a sharp increase of grain volume fraction. The comparison of the absorption spectra obtained by DC and AC methods showed that they are similar for silicon films with the predominantly amorphous structure and films with high grain volume fraction. However we found a dramatic discrepancy between the absorption spectra obtained by DC and AC constant photocurrent methods in silicon films deposited in the regime of the structure transition from amorphous to nanocrystalline state. AC constant photocurrent method gives higher absorption coefficient than DC constant photocurrent method in the photon energy range of 1.2-1.7 eV. This result indicates the possibility of crystalline grains contribution to absorption spectra measured by AC constant photocurrent method in silicon films with intermediate crystalline grain volume fraction. (c) 2008 Published by Elsevier B.V.

Electronic structure and optical gain of wurtzite ZnO nanowires

The electronic structure and optical gain of wurtzite ZnO nanowires are investigated in the framework of effective-mass envelope-function theory. We found that as the elliptical aspect ratio e increases to be larger than a critical value, the hole ground states may change from optically dark to optically bright. The optical gain of ZnO nanowires increases as the hole density increases. For elliptical wire with large e, the y-polarized mode gain can be several thousand cm(-1), while the x-poiarized mode gain may be 26 times smaller than the former, so they can be used as ultraviolet linearly polarized lasers. (C) 2008 American Institute of Physics.

Electronic structure of a hydrogenic acceptor impurity in semiconductor nano-structures

The electronic structure and binding energy of a hydrogenic acceptor impurity in 2, 1, and 0-dimensional semiconductor nano-structures (i.e. quantum well (QW), quantum well wire (QWW), and quantum dot (QD)) are studied in the framework of effective-mass envelope-function theory. The results show that (1) the energy levels monotonically decrease as the quantum confinement sizes increase; (2) the impurity energy levels decrease more slowly for QWWs and QDs as their sizes increase than for QWs; (3) the changes of the acceptor binding energies are very complex as the quantum confinement size increases; (4) the binding energies monotonically decrease as the acceptor moves away from the nano-structures' center; (5) as the symmetry decreases, the degeneracy is lifted, and the first binding energy level in the QD splits into two branches. Our calculated results are useful for the application of semiconductor nano-structures in electronic and photoelectric devices.

Structure, magnetization, and low-temperature spin dynamic behavior of zincblende Mn-rich Mn(Ga)As nanoclusters embedded in GaAs

We have fabricated a set of samples of zincblende Mn-rich Mn(Ga)As clusters embedded in GaAs matrices by annealing (Ga,Mn)As films with different nominal Mn content at 650 degrees C. For the samples with Mn content no more than 4.5%, the Curie temperature reaches nearly 360 K. However, when Mn content is higher than 5.4%, the samples exhibit a spin-glass-like behavior. We suggest that these different magnetic properties are caused by the competing result of dipolar and Ruderman-Kittel-Kasuya-Yosida interaction among clusters. The low-temperature spin dynamic behavior, especially the relaxation effect, shows the extreme creeping effect which is reflected by the time constant tau of similar to 10(11) s at 10 K. We explain this phenomenon by the hierarchical model based on the mean-field approach. We also explain the memory effect by the relationship between the correlation function and the susceptibility.

Electronic structure of self-assembled InAs quantum disks in an axial magnetic field and two-electron quantum-disk qubit

We have studied the single-electron and two-electron vertically assembled quantum disks in an axial magnetic field using the effective mass approximation. The electron interaction is treated accurately by the direct diagonalization of the Hamiltonian matrix. We calculate the six energy levels of the single-electron quantum disks and the two lowest energy levels of the two-electron quantum disks in an axial magnetic field. The change of the magnetic field strongly modifies the electronic structures as an effective potential, leading to the splitting of the levels and the crossings between the levels. The effect of the vertical alignment on the electronic structures is discussed. It is demonstrated that the switching of the ground-state spin exists between S=0 and S=1. The energy difference DeltaE between the lowest S=0 and S=1 states is shown as a function of the axial magnetic field. It is also found that the variation of the energy difference between the lowest S=0 and S=1 states in the strong-B S=0 state is fairly linear. Our results provide a possible realization for a qubit to be fabricated by current growth techniques. (C) 2004 American Institute of Physics.

Role of interactions in electronic structure of a two-electron quantum dot molecule

We have studied a two-electron quantum dot molecule in a magnetic field. The electron interaction is treated accurately by the direct diagonalization of the Hamiltonian matrix. We calculate two lowest energy levels of the two-electron quantum dot molecule in a magnetic field. Our results show that the electron interactions are significant, as they can change the total spin of the two-electron ground state of the system by adjusting the magnetic field between S = 0 and S = 1. The energy difference DeltaE between the lowest S = 0 and S = 1 states is shown as a function of the axial magnetic field. We found that the energy difference between the lowest S = 0 and S = 1 states in the strong-B S = 0 state varies linearly. Our results provide a possible realization for a qubit to be fabricated by current growth techniques.

Effect of interaction between periodic delta-doping in both well and barrier layers on modulation of superlattice band structure

The modulation of superlattice band structure via periodic delta-doping in both well and barrier layers have been theoretically investigated, and the importance of interaction between the delta-function potentials in the well layers and those in the barrier layers on SL band structure have been revealed. It is pointed out that the energy dispersion relation Eq. (3) given in [G. Ihm, S.K. Noh, J.I. Lee, J.-S. Hwang, T.W. Kim, Phys. Rev. B 44 (1991) 6266] is an incomplete one, as the interaction between periodic delta-doping in both well and barrier layers had been overlooked. Finally, we have shown numerically that the electron states of a GaAs/Ga0.7Al0.3As superlattice can be altered more efficiently by intelligent tuning the two delta-doping's positions and heights. (c) 2007 Elsevier B.V. All rights reserved.

Effects of the wave function localization in AlInGaN quaternary alloys

Using the first-principles band-structure method and the special quasirandom structures approach, the authors have investigated the band structure of random AlxInyGa1-x-yN quaternary alloys. They show that the wave functions of the band edge states are more localized on the InN sites. Consequently, the photoluminescence transition intensity in the alloy is higher than that in GaN. The valence band maximum state of the quaternary alloy is also higher than GaN with the same band gap, indicating that the alloy can be doped more easily as p-type. (c) 2007 American Institute of Physics.

Electronic structure of ZnO wurtzite quantum wires

The electronic structure and optical properties of ZnO wurtzite quantum wires with radius R >= 3 nm are studied in the framework of six-band effective-mass envelope function theory. The hole effective-mass parameters of ZnO wurtzite material are calculated by the empirical pseudopotential method. It is found that the electron states are either two-fold or four-fold degenerate. There is a dark exciton effect when the radius R of the ZnO quantum wires is in the range of [3,19.1] nm (dark range in our model). The dark ranges of other wurtzite semiconductor quantum wires are calculated for comparison. The dark range becomes smaller when the |Delta(so)| is larger, which also happens in the quantum-dot systems. The linear polarization factor of ZnO quantum wires is larger when the temperature is higher.