Construction of a BAC library for Chinese amphioxus Branchiostoma belcheri and identification of clones containing Amphi-pax genes

Amphioxus is a crucial organism for the study of vertebrate evolution. Although a genomic BAC library of Branchiostoma floridae has been constructed, we report here another BAC library construction of its distant relative species Branchiostoma belcheri. The amphioxus BAC library established in present study consists of 45,312 clones arrayed in one hundred and eighteen 384-well plates. The average insert fragment size was 120 kb estimated by Pulsed Field Gel Electrophoresis (PFGE) analysis of 318 randomly selected clones. The representation of the library is about 12 equivalent to the genome, allowing a 99.9995% probability of recovering any specific sequence of interest. We further screened the library with 4 single copied Amphi-Pax genes and identified total of 26 positive clones with average of 6.5 clones for each gene. The result indicates this library is well suited for many applications and should also serve as a useful complemental resource for the scientific community.

Liriomyza huidobrensis in Yunnan, China: current distribution and genetic structure of a recently established population

Liriomyza huidobrensis Blanchard (Diptera: Agromyzidae) is a very serious and economically important pest around the world. Liriomyza huidobrensis in China was first reported from Kunming of Yunnan province in 1993. We report here that this pest has recen

Genetic differentiation and cryptic speciation in natural populations of Drosophila lacertosa

Drosophila lacertosa, an Oriental member of the robusta species group in the virilis-repleta radiation, has a wide distribution from northern India throughout China to the Far East. Phylogenetic analyses of mitochondrial ND2 gene sequences revealed two ge

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.

Acute behavioural stress facilitates long-term depression in temporoammonic-CAI pathway

Behavioural stress facilitates long-term depression in Schaffer collaterals-CAI pathway, but it is unknown whether it influences long-term depression in temporoammonic fibres-CAI. Here, we report that low-frequency stimulation induced long-term depression

Influence of leaf tissue structure on host feeding selection by pea leaf miner Liriomyza huidobrensis (Diptera : Agromyzidae)

Host feeding selection by the female pea leafminer, Liriomyza huidobrensis, on 47 species of plants was studied. The leaves were sectioned by microtome, and 15 characteristics of the leaf tissue structure were measured under a microscope. Correlation analysis between host feeding selection and leaf tissue structure indicated that the preference of host feeding selection was positively correlated with the percentage of moisture content of leaves and negatively with thickness of the epidermis wall, and densities of the palisade and spongy tissues of leaves. Leaf tissue structure was influential in feeding and probing behavior of female L. huidobrensis. So, thickness of epidermis wall, densities of the palisade and spongy tissues can act as a physical barrier to female oviposition. Furthermore, higher densities of palisade and spongy tissues can be considered a resistant trait which affects mining of leaf miner larvae as well. As a result, plants with lower leaf moisture content may not be suitable for the development of L. huidobrensis.

Factors affecting leaf morphology: a case study of Ranunculus natans C. A. Mey. (Ranunculaceae) in the arid zone of northwest China

In order to examine the role of environmental factors affecting foliar morphology, we performed a case study of leaf morphological variation of Ranunculus natans found in the arid zone of northwest China. We found that foliar phenotypic variation differed significantly between populations. We described substantial positive correlations between altitude and leaf area (LA) as well as leaf perimeter (LP), and also between longitude and number of teeth, along with dissection index (DI). The pH, conductivity, and salinity of the environment caused a significant decrease in both LA and LP. Ranked in terms of their impacts on leaf morphology, the six selected factors were: altitude > pH > conductivity > salinity > longitude > latitude. We found that foliar morphological variations are functional responses to water-quantity factors (e.g., altitude and longitude at regional scales) and water-availability relation factors (e.g., pH, conductivity, and salinity at local scales), rather than to temperature-relation factors (latitude). Therefore, altitude and longitude, along with pH, conductivity, and salinity, are the main factors that significantly influence foliar morphology in the arid zone of China. We found that main factors played major roles in plant phenotypic plasticity in a complex ecosystem, although different combinations and interactions of environmental and geographical factors in each local environment may obscure the general trends in trait changes along environmental gradients.

Identification and characterization of hypoxia-induced genes in Carassius auratus blastulae embryonic cells using suppression subtractive hybridization

Organisms living in water are inevitably exposed to periods of hypoxia. Environmental hypoxia has been an important stressor having manifold effects on aquatic life. Many fish species have evolved behavioral, physiological, biochemical and molecular adaptations that enable them to cope with hypoxia. However, the molecular mechanisms of hypoxia tolerance in fish, remain unknown. in this study, we used suppression subtractive hybridization to examine the differential gene expression in CAB cells (Carassius auratus blastulae embryonic cells) exposed to hypoxia for 24 h. We isolated 2100 clones and identified 211 differentially expressed genes (e-value <= 5e-3; Identity > 45%). Among the genes whose expression is modified in cells, a vast majority involved in metabolism, signal transduction, cell defense, angiogenesis, cell growth and proliferation. Twelve genes encoding for ERO1-L, p53, CPO, HO-1, MKP2, PFK-2, cystatin B, GLUT1, BTG1, TGF beta 1, PGAM1, hypothetical protein F1508, were selected and identified to be hypoxia-induced using semi-quantitive RT-PCR and real-time PCR. Among the identified genes, two open reading frames (ORFs) encoding for CaBTG1 and Cacystatin B were obtained. The deduced amino acid sequence of CaBTG1 had 94.1%, 72.8%, 72.8%, 72.8%, 68.6% identity with that of DrBTG1, HsBTG1, BtBTG1, MmBTG1 and XIBTG1. Comparison of Cacystatin B with known cystatin B, the molecules exhibited 49.5 to 76.0% identity overall. These results may provide significant information for further understanding of the adaptive mechanism by which C. auratus responds to hypoxia. (c) 2008 Elsevier Inc. All rights reserved.

Staphylococcus aureus lipoproteins trigger human corneal epithelial innate response through toll-like receptor-2

Bacterial lipoproteins (LP) are a family of cell wall components found in a wide variety of bacteria. In this study, we characterized the response of HUCL, a telomerase-immortalized human corneal epithelial cell (HCEC) line, to LP isolated from Staphylococcus (S) aureus. S. aureus LP (saLP) prepared by Triton X-114 extraction stimulated the activation of NF-kappa B, JNK, and P38 signaling pathways in HUCL cells. The extracts failed to stimulate NF-kappa B activation in HUCL cells after lipoprotein lipase treatment and in cell lines expressing TLR4 or TLR9, but not TLR2, indicating lipoprotein nature of the extracts. saLP induced the up-regulation of a variety of inflammatory cytokines and chemokines (IL-6, IL-8, ICAM-1). antimicrobial molecules (hBD-2, LL-37, and iNOS), and homeostasis genes (Mn-SOD) at both the mRNA level and protein level. Similar inflammatory response to saLP was also observed in primarily cultured HCECs using the production of IL-6 as readout. Moreover, TLR2 neutralizing antibody blocked the saLP-induced secretion of IL-6, IL-8 and hBD2 in HUCL cells. Our findings suggest that saLP activates TLR2 and triggers innate immune response in the cornea to S. aureus infection via production of proinflammatory cytokines and defense molecules. (C) 2007 Elsevier Ltd. All rights reserved.

Distribution of nitrogen and phosphorus in sediment cores and overlying water of Donghu Lake

In this study, the seasonal, vertical distribution of various phosphorus and nitrogen forms in the sediment and overlying water of Donghu Lake were investigated. The concentration of total nitrogen (TN) in overlying water was high in spring and autumn, but that of NO3--N reached its peak in autumn. From summer to autumn and from winter to spring, the concentration of phosphorus in overlying water decreased, while it increased from autumn to winter. Vertical characteristic forms of phosphorus in sediment cores are total phosphorus (TP), labile phosphorus (LP), Fe-P and Al-P, obviously enriched in the surface layer (0-10 cm), but their concentrations are observably reduced along with the depth of sediment. The research is of important theoretical and practical value to understand the status and to control the developmental trend of eutrophication in Donghu Lake.

Photoluminescence properties of tensile-strained GaAsP/GaInP single quantum wells grown by metal organic chemical vapor deposition

Tensile-strained GaAsP/GaInP single quantum well (QW) laser diode (I-D) structures have been grown by low-pressure metal organic chemical vapor deposition (LP-MOCVD) and related photoluminescence (PL) properties have been investigated in detail. The samples have the same well thickness of 16 nm but different P compositions in a GaAsP QW. Two peaks in room temperature (RT) PL spectra are observed for samples with a composition larger than 0.10. Temperature and excitation-power-dependent PL spectra have been measured for a sample with it P composition of 0.15. It is found that the two peaks have a 35 meV energy separation independent of temperature and only the low-energy peak exists below 85 K. Additionally, both peak intensities exhibit a monotonous increase as excitation power increases. Analyses indicate that the two peaks arise from the intrinsic-exciton recombination mechanisms of electron-heavy hole (e-hh) and electron-light hole (e-hh). A theoretical calculation based oil model-solid theory, taking, into account the spin-orbit splitting energy, shows good agreement with our experimental results. The temperature dependence of PL intensity ratio is well explained using the spontaneous emission theory for e-hh and e-hh transitions. front which the ratio can be characterized mainly by the energy separation between the fill and Ill states.

A photonic wire-based directional coupler based on SOI

A photonic wire-based directional coupler based on SOI was fabricated by e-beam lithography (EBL) and the inductively coupled plasma (ICP) etching method. The size of the sub-micron waveguide is 0.34 mu m x 0.34 mu m, and the length in the coupling region and the separation between the two parallel waveguides are 410 and 0.8 mu m, respectively. The measurement results are in good agreement with the results simulated by 3D finite-difference time-domain method. The transmission power from two output ports changed reciprocally with about 23 nm wavelength spacing between the coupled and direct ports. The extinction ratio of the device was between 5 and 10 dB, and the insertion loss of the device in the wavelength range 1520-1610 nm was between 22 and 24 dB, which included an about 18.4 +/- 0.4 dB coupling loss between the taper fibers and the polished sides of the device. (c) 2008 Elsevier B.V. All rights reserved.

Effect of indium-doped interlayer on the strain relief in GaN films grown on Si(111)

Crack-free GaN films have been achieved by inserting an Indoped low-temperature (LT) AlGaN interlayer grown on silicon by metalorganic chemical vapor deposition. The relationship between lattice constants c and a obtained by X-ray diffraction analysis shows that indium doping interlayer can reduce the stress in GaN layers. The stress in GaN decreases with increasing trimethylindium (TMIn) during interlayer growth. Moreover, for a smaller TMIn flow, the stress in GaN decreases dramatically when In acts as a surfactant to improve the crystallinity of the AlGaN interlayer, and for a larger TMIn flow, the stress will increase again. The decreased stress leads to smoother surfaces and fewer cracks for GaN layers by using an In-doped interlayer than by using an undoped interlayer. In doping has been found to enhance the lateral growth and reduce the growth rate of the c face. It can explain the strain relief and cracks reduction in GaN films. (C) 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Optical response of high-level bandgap in one-dimensional photonic crystal applying in-plane integration

A new broadband filter, based on the high level bandgap in 1-D photonic crystals (PCs) of the form Si vertical bar air vertical bar Si vertical bar air vertical bar Si vertical bar air vertical bar Si vertical bar air vertical bar Si vertical bar air vertical bar Si is designed by the plane wave expansion method (PWEM) and the transfer matrix method (TMM) and fabricated by lithography. The optical response of this filter to normal-incident and oblique-incident light proves that utilizing the high-level bandgaps of PCs is an efficient method to lower the difficulties of fabricating PCs, increase the etching depth of semiconductor materials, and reduce the coupling loss at the interface between optical fibers and the PC device. (c) 2007 Society of Photo-Optical Instrumentation Engineers.

Electroluminescence from Ge on Si substrate at room temperature

A Ge/Si heterojunction light emitting diode with a p(+)-Ge/i-Ge/N+-Si structure was fabricated using the ultrahigh vacuum chemical vapor deposition technology on N+-Si substrate. The device had a good I-V rectifying behavior. Under forward bias voltage ranging from 1.1 to 2.5 V, electroluminescence around 1565 nm was observed at room temperature. The mechanism of the light emission is discussed by the radiative lifetime and the scattering rate. The results indicate that germanium is a potential candidate for silicon-based light source material. (C) 2009 American Institute of Physics. [DOI 10.1063/1.3216577]