The Genomes of Oryza sativa: A history of duplications

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped superscaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000 - 40,000. Only 2% - 3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism ( SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family.

芒果果肉象(\sl Sternochetus frigidus Fabricius)生物学及其综合防治的研究

芒果果肉象幼虫蛀害芒果果肉, 在果肉内形成纵横交错的蛀道或洞穴, 粪便污染果肉, 失去食用价值。该虫在云南景谷一年发生一代, 以成虫在树干翘皮裂缝, 树洞或表土层中越冬。

A new species of sisorid catfish genus Glyptothorax (Teleostei: Sisoridae) from Salween drainage of Yunnan, China

A new species of the genus Glyptothorax, Glyptothorax obliquimaculatus sp. nov. is described from the Xiaohei River, a tributary of the Nanting River, Salween drainage, in southwestern Yunnan province, China. This new species can be distinguished from its congeners by the following combination of characteristics: unculiferous ridges of the thoracic adhesive apparatus extending anteriorly onto the gular region; body with irregular dark blotches scattered along lateral surface (blotches mostly oblique); skin smooth on head and body; dorsal spine smooth without serrations on its posterior margin; lips smooth; posterior margin of pectoral spine with 7-8 serrations; dorsal-fin base 11.0-13.2% SL; pectoral-fin length 15.6-19.6% SL; depth of caudal peduncle 8.6-9.8% SL; head width 19.1-24.0% SL; nasal barbel length 23.3-33.3% HL.

The reproductive strategies of an endemic Tibetan fish, Gymnocypris selincuoensis

The reproductive traits of Gymnocypris selincuoensis from Selincuo Lake and its tributaries were investigated in 1997 and 1998. The youngest mature male was age 7 with a standard length (SL) of 172.0 mm, and the youngest mature female was age 8 with a SL of 194.0 mm. The L(50)s Of SL and age at first maturity were respectively 250.32 mm and age 9 for males and 224.71 mm and age 8 for females. The gonadosomatic index (GSI) significantly changed with seasons for mature individuals but not for immature individuals. GSIs of mature females at stages IV and V of ovary development increased with SL and reached a maximum value at the SL range from 370 mm to 390 mm; the GSIs of mature males were negatively correlated with SL. The breeding season lasted from early April to early August. Egg size did not significantly change with SL but increased with the delay of spawning. The individual absolute fecundity varied from 1,341 to 28,002 eggs (mean 12,607+/-7,349), and the individual relative fecundity varied from 6.4 to 42.0 eggs.g(-1) (mean 25.5+/-9.7). The individual fecundity increased with total body weight; it also increased with SL for those of SL less than 370 mm. There was a rest of spawning for mature individuals.

The reproductive strategies of an endemic Tibetan fish, Gymnocypris selincuoensis

The reproductive traits of Gymnocypris selincuoensis from Selincuo Lake and its tributaries were investigated in 1997 and 1998. The youngest mature male was age 7 with a standard length (SL) of 172.0 mm, and the youngest mature female was age 8 with a SL of 194.0 mm. The L(50)s Of SL and age at first maturity were respectively 250.32 mm and age 9 for males and 224.71 mm and age 8 for females. The gonadosomatic index (GSI) significantly changed with seasons for mature individuals but not for immature individuals. GSIs of mature females at stages IV and V of ovary development increased with SL and reached a maximum value at the SL range from 370 mm to 390 mm; the GSIs of mature males were negatively correlated with SL. The breeding season lasted from early April to early August. Egg size did not significantly change with SL but increased with the delay of spawning. The individual absolute fecundity varied from 1,341 to 28,002 eggs (mean 12,607+/-7,349), and the individual relative fecundity varied from 6.4 to 42.0 eggs.g(-1) (mean 25.5+/-9.7). The individual fecundity increased with total body weight; it also increased with SL for those of SL less than 370 mm. There was a rest of spawning for mature individuals.

Effective recombination velocity of textured surfaces

Surface texturization is an effective way to enhance the absorption of light for optoelectronic devices but it also aggravates the surface recombination by enlarging the surface area. In order to evaluate the influence of texture structures on the surface recombination, an effective surface recombination velocity is defined which is assumed to have an equivalent recombination effect on a flat surface. Based on numerical and analytical calculation, the dependences of effective surface recombination on the pattern geometry, the surface recombination velocity, and the diffusion length are analyzed.

Violet electroluminescence of AlInGaN-InGaN multiquantum-well light-emitting diodes: Quantum-confined stark effect and heating effect

Electroluminescence (EL) from AlInGaN-InGaN multiquantum-well violet light-emitting diodes is investigated as a function of forward bias. Two distinct regimes have been identified: 1) quantum-confined Stark effect at low and moderately high forward biases; 2) heating effect at high biases. In the different regimes, the low-temperature EL spectra exhibit different spectral features which are discussed in detail.

Spatial interference effect of two-photon in femtosecond-pulse pumped spontaneous parametric down-conversion

We have used the transverse correlated properties of the entangled photon pairs generated in the process of spontaneous parametric down-conversion, which is pumped by a femtosecond pulse laser, to perform Young's interference experiment. Unlike the case of a continuous wave laser pump, a broadband pulse laser pump can submerge an interference pattern. In order to obtain a high visibility interference pattern, we used a lens with a tunable focal length and two interference filters to eliminate the effects of the broadband pump laser. It is proven that the process of two-photon direct interference is a post-selection process.

Modification of emission wavelength of self-assembled In(Ga)As/GaAs quantum dots covered by InxGa1-xAs(0 <= x <= 0.3) layer

Red shifts of emission wavelength of self-organized In(Cla)As/GaAs quantum dots (QDs) covered by 3 nm thick InxGa1-xAs layer with three different In mole fractions (x = 0.1, 0.2 and 0.3, respectively) have been observed. Transmission electron microscopy images demonstrate that the stress along growth direction in the InAs dots was reduced due to introducing the InxGa1-xAs (x = 0.1, 0.2 and 0.3) covering layer instead of GaAs layer. Atomic force microscopy pictures show a smoother surface of InAs islands covered by an In0.2Ga0.8As layer. It is explained by the calculations that the redshifts of the photoluminescence (PL) spectra from the QDs covered by the InxGa1-xAs (x greater than or equal to 0.1) layers were mainly due to the reducing of the strain other than the InAs/GaAs intermixing in the InAs QDs. The temperature dependent PL spectra further confirm that the InGaAs covering layer can effectively suppress the temperature sensitivity of PL emissions. 1.3 mum emission wavelength with a very narrow linewidth of 19.2 mcV at room temperature has been obtained successfully from In,In0.5Ga0.5As/GaAs self-assembled QDs covered by a 3-nm In0.2Ga0.2As strain reducing layer. (C) 2001 Elsevier Science B.V. All rights reserved.

Photoluminescence properties of self-organized InGaAs/GaAs quantum dot structures

Optical properties of InGaAs/GaAs self-organized quantum dots (QDs) structures covered by InxGa1-x As capping layers with different In contents chi ranging from 0. 0 (i.e., GaAs) to 0. 3 were investigated systematically by photoluminescence (PL) measurements. Red-shift of the PL peak energies of the InAs QDs covered by InxGa1-xAs layers with narrower linewidth and less shifts of the PL emissions via variations of the measurement temperatures were observed compared with that covered by GaAs layers. Calculation and structural measurements confirm that the red-shift of the PL peaks are mainly due to strain reduction and suppression of the In/Ga intermixing due to the InxGa1-xAs cover layer, leading to better size uniformity and thus narrowing the PL linewidth of the QDs. 1. 3 mum wavelength emission with very narrow linewidth of only 19. 2 meV at room temperature was successfully obtained from the In0.5Ga0.5As/GaAs QDs covered by the In0.2Ga0.8As layer.

1.35 mu m photoluminescence from In0.5Ga0.5As/GaAs islands grown by molecular beam epitaxy via cycled (InAs)(1)/(GaAs)(1) monolayer deposition

1.35 mum photoluminescence (PL) with a narrow linewidth of only 19.2 meV at room temperature has been achieved in In0.5Ga0.5As islands structure grown on GaAs (1 0 0) substrate by solid-source molecular beam epitaxy. Atomic force microscopy (AFM) measurement reveals that the 16-ML-thick In0.5Ga0.5As islands show quite uniform InGaAs mounds morphology along the [ 1(1) over bar 0] direction with a periodicity of about 90 nm in the [1 1 0] direction. Compared with the In0.5Ga0.5As alloy quantum well (QW) of the same width, the In0.5Ga0.5As islands structure always shows a lower PL peak energy and narrower full-width at half-maximum (FWHM), also a stronger PL intensity at low excitation power and more efficient confinement of the carriers. Our results provide important information for optimizing the epitaxial structures of 1.3 mum wavelength quantum dots devices. (C) 2000 Elsevier Science B.V. All rights reserved.

The influence of growth interruption on quantum dot laser

Growth interruption was introduced during the growth of GaAs capping layer of self-organized quantum dots. The comparison of two QD lasers with and without growth interruption in their active regions shows that growth interruption leads to lower threshold current, higher characteristic temperature, and weaker temperature dependence of lasing energy.

Study of self-assembled InAs quantum dots grown on low temperature GaAs epi-layer

InAs self-organized quantum dots (QDs) grown on annealed low temperature GaAs (LT-GaAs) epi-layer were investigated by transmission electron microscopy (TEM) and photoluminescence (PL) measurement. TEM showed that QDs formed on annealed LT-GaAs epi-layer have a smaller size and a higher density than QDs formed on normal GaAs buffer layer. In addition, the PL spectra analysis showed that the LT-GaAs epi-layer resulted in a blue shift in peak energy, and a narrower linewidth in the PL peak. The differences were attributed to the point defects and As precipitates in annealed LT-GaAs epi-layer for the point defects and As precipitates change the strain field of the surface. The results provide a method to improve the uniformity and change the energy band structure of the QDs by controlling the defects in the LT-GaAs epi-layer.

The improvement characteristics of homoepitaxial GaAs grown by atomic hydrogen-assisted molecular beam epitaxy

The electrical activity of defects in GaAs grown on GaAs substrates doped with Si and Be by both conventional molecular beam epitaxy (MBE) and atomic hydrogen-assisted MBE (H-MBE) were characterized by deep level transient spectroscopy. The trap densities are significantly reduced in the homoepitaxial GaAs grown by H-MBE compared to that grown by MBE. The reduction of trap densities is attributed to in situ passivation of these defects by atomic H during the growth. The improvement characteristics of GaAs materials will be significance for fabrication of semiconductor devices.