The identification and quantification of highly stable 'common hairpin' in the dynamic process of co-transcriptional mRNA folding

In our studies, 88 human mRNA samples were collected from the Integrated Sequence-Structure database and then the dynamic process in co-transcriptional mRNA folding was simulated using the RNAstructure version 4.1 program. Through statistical analyses of the frequencies of occurrence of hairpins, a group of special folding structures-the 'common hairpins'-were identified. These 'common hairpins' have lower energies and occur in all the subsequent folding units that formed in the dynamic folding process. By applying the formulas (1)-(4) of the 'common hairpins' statistical model, 163 'common hairpins' were found, to make up about 7% of the total of 2286 hairpins. Classified studies further show that the 'common hairpins' that were studied may oscillate in the dynamic folding process. However, the hairpin loops of the 'common hairpins' and stems proximal to those 'common hairpins' loops maintain topologically stable structures, while other loops and stems distal to the 'common hairpins' loops are shown to be alterable structures. Strikingly, further studies indicate that the stable structures of these 'common hairpins' may have unbeknown effects on controlling the formation of protein structures in the translation process (unpublished results). (c) 2005 Elsevier B.V. All rights reserved.

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.

Optimizing the GaAs capping layer growth of 1.3 mu m InAs/GaAs quantum dots by a combined two-temperature and annealing process at low temperatures

We report on optimizing the GaAs capping layer growth of 1.3 mu m InAs quantum dots (QDs) by a combined two-temperature and annealing process at low temperatures using metalorganic chemical vapor deposition. The initial part (tnm) of the capping layer is deposited at a low temperature of 500 degrees C, which is the same for the growth of both the QDs and a 5-nm-thick In0.15Ga0.85As strain-reducing capping layer on the QDs, while the remaining part is grown at a higher temperature of 560 degrees C after a rapid temperature rise and subsequent annealing period at this temperature. The capping layer is deposited at the low temperatures (<= 560 degrees C) to avoid postgrowth annealing effect that can blueshift the emission wavelength of the QDs. We demonstrate the existence of an optimum t (=5 nm) and a critical annealing time (>= 450s) during the capping, resulting in significantly enhanced photoluminescence from the QDs. This significant enhancement in photoluminescence is attributed to a dramatic reduction of defects due to the optimized capping growth. The technique reported here has important implications for realizing stacked 1.3 mu m InAs/GaAs QD lasers. (C) 2008 Elsevier B.V. All rights reserved.

Fabrication process and power and lifetime characteristics of very-small-aperture laser

High output power very-small-aperture laser has been created on 650 nm edge emitting laser diodes. The far-field output power is 0.4 mW at the 25 mA driving current, and the highest output power exceeds 1 mW. The special fabrication process is described and the failure mechanism leading to the short lifetime of the devices is discussed.

Creation and suppression of point defects through a kick-out substitution process of Fe in InP

Indium antisite defect In-P-related photoluminescence has been observed in Fe-diffused semi-insulating (SI) InP. Compared to annealed undoped or Fe-predoped SI InP, there are fewer defects in SI InP obtained by long-duration, high-temperature Fe diffusion. The suppression of the formation of point defects in Fe-diffused SI InP can be explained in terms of the complete occupation by Fe at indium vacancy. The In-P defect is enhanced by the indium interstitial that is caused by the kick out of In and the substitution at the indium site of Fe in the diffusion process. Through these Fe-diffusion results, the nature of the defects in annealed undoped SI InP is better understood. (C) 2002 American Institute of Physics.

Influences of initial nitridation process on the optical and structural characterization of GaN layer grown on sapphire (0001) by metalorganic chemical vapor deposition

In this paper. we investigate the influences of the initial nitridation of sapphire substrates on the optical and structural characterizations in GaN films. Two GaN samples with and without 3 min nitridation process were investigated by photoluminescence (PL) spectroscopy in the temperature range of 12-300 K and double-crystal X-ray diffraction (XRD). In the 12 K PL spectra of the GaN sample without nitridation, four dominant peaks at 3.476, 3.409 3.362 and 3.308 eV were observed, which were assigned to donor bound exciton, excitons bound to stacking faults and extended structural defects. In the sample with nitridation, three peaks at 3.453, 3.365. and 3.308 eV were observed at 12 K, no peak related to stacking faults. XRD results at different reflections showed that there are more stacking faults in the samples without nitridation.

Influence of 5A-Type Zeolite Powder on Tetrahydrofuran Hydrate Formation and Dissociation Process

Visual observations of tetrahydrofuran (THF) hydrate formation and dissociation processes with 5A-type zeolite powder were made at normal atmospheric conditions and below zero temperature by microscope. Results indicate that 5A-type zeolite powder can promote THF hydrate growth. At the same time, in the presence of 5A-type zeolite, agglomerated crystals and vein-like crystals of THF hydrate were also formed. SA-type zeolite powder increases the crystallization temperature and decreases the dissociation temperature. The particle size distribution of 5A-type zeolite powder influences THF hydrate formation and its dissociation characteristics significantly.

THEORETICAL INVESTIGATION OF THE DYNAMIC PROCESS OF THE ILLUMINATION OF GAAS

The dynamic process of light illumination of GaAs is studied numerically in this paper to understand the photoquenching characteristics of the material. This peculiar behavior of GaAs is usally ascribed to the existence of EL2 states and their photodriven metastable states. To understand the conductivity quenching, we have introduced nonlinear terms describing the recombination of the nonequilibrium free electrons and holes into the calculation. Though some photoquenching such as photocapacitance, infrared absorption, and electron-paramagnetic-resonance quenching can be explained qualitatively by only considering the internal transfer between the EL2 state and its metastability, it is essential to take the recombination into consideration for a clear understanding of the photoquenching process. The numerical results and approximate analytical approach are presented in this paper for the first time to our knowledge. The calculation gives quite a reasonable explanation for n-type semiconducting GaAs to have infrared absorption quenching while lacking photoconductance quenching. Also, the calculation results have allowed us to interpret the enhanced photoconductance phenomenon following the conductance quenching in typical semi-insulating GaAs and have shown the expected thermal recovery temperature of about 120 K. The numerical results are in agreement with the reported experiments and have diminished some ambiguities in previous works.

PROCESS OF PHOTOLUMINESCENCE AND PHOTOSTIMULATED LUMINESCENCE IN BAFBR-EU PHOSPHORS

The photoluminescence (PL) and photostimulated luminescence (PSL) of BaFBr: Eu phosphors are reported. In the photoluminescence of BaFBr:Eu, the emission of Eu2+, e-h recombination and Eu3+ have been observed, while in the photostimulated luminescence only the emission of Eu2+ was observed. This phenomenon may be explained well by the suggestion of a two-hand model for the host emission in which the host emission energy may transfer to Eu2+ difference of excitation in those two processes results in different transfer rates which makes the PL and PSL emission different.

Influences of initial nitridation process on the optical and structural characterization of GaN layer grown on sapphire (0001) by metalorganic chemical vapor deposition

In this paper. we investigate the influences of the initial nitridation of sapphire substrates on the optical and structural characterizations in GaN films. Two GaN samples with and without 3 min nitridation process were investigated by photoluminescence (PL) spectroscopy in the temperature range of 12-300 K and double-crystal X-ray diffraction (XRD). In the 12 K PL spectra of the GaN sample without nitridation, four dominant peaks at 3.476, 3.409 3.362 and 3.308 eV were observed, which were assigned to donor bound exciton, excitons bound to stacking faults and extended structural defects. In the sample with nitridation, three peaks at 3.453, 3.365. and 3.308 eV were observed at 12 K, no peak related to stacking faults. XRD results at different reflections showed that there are more stacking faults in the samples without nitridation.