Identification of Differentially Expressed Genes Between Cloned and Zygote-Developing Zebrafish (Danio rerio) Embryos at the Dome Stage Using Suppression Subtractive Hybridization

Comparative analyses of differentially expressed genes between somatic cell nuclear transfer (SCNT) embryos and zygote-developing (ZD) embryos are important for understanding the molecular mechanism underlying the reprogramming processes. Herein, we used the suppression subtractive hybridization approach and from more than 2900 clones identified 96 differentially expressed genes between the SCNT and ZD embryos at the dome stage in zebrafish. We report the first database of differentially expressed genes in zebrafish SCNT embryos. Collectively, our findings demonstrate that zebrafish SCNT embryos undergo significant reprogramming processes during the dome stage. However, most differentially expressed genes are down-regulated in SCNT embryos, indicating failure of reprogramming. Based on Ensembl description and Gene Ontology Consortium annotation, the problems of reprogramming at the dome stage may occur during nuclear remodeling, translation initiation, and regulation of the cell cycle. The importance of regulation from recipient oocytes in cloning should not be underestimated in zebrafish.

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.

RNAi suppression of zebrafish peptidoglycan recognition protein 6 (zfPGRP6) mediated differentially expressed genes involved in Toll-like receptor signaling pathway and caused increased susceptibility to Flavobacterium columnare

In Drosophila, Toll signaling cascade, which resembles the mammalian Toll-like receptor (TLR)/IL-1R signaling pathways and regulates the expression of anti-microbial peptide genes, mainly relies on peptidoglycan recognition proteins (PGRPs) for the detection of bacterial pathogens. To explore the effect of zebrafish peptidoglycan recognition protein 6 (zfPGRP6) on Toll-like receptor signaling pathway, RNA interference (siRNA) and real time quantitative PCR (RQ-PCR) methods were used to identify differentially expressed genes regulated by zfPGRP6. The target genes included TLR2, TLR3, TLR5, TLR7, TLR8, IL1R, Sterile-alpha and Armadillo motif containing protein (SARM), myeloid differentiation factor 88 (MyD88) and nuclear factor (NF)-kappa B2 (p100/p52). The results of RQ-PCR showed that RNAi-mediated Suppression of zfPGRP6 significantly down-regulated the expression of TLR2, TLR5, IL1R, SARM, MyD88 and p100/p52. The expression of beta-defensin-1 was also down-regulated in those embryos silenced by zfPGRP6. In challenge experiments to determine the anti-bacterial response to Gram-negative bacteria, RNAi knock-down of zfPGRP6 markedly increased susceptibility to Flavobacterium columnare. (C) 2008 Elsevier B.V. All rights reserved.

GPU-accelerated optimization of fuel treatments for mitigating wildfire hazard

Fuel treatment is considered a suitable way to mitigate the hazard related to potential wildfires on a landscape. However, designing an optimal spatial layout of treatment units represents a difficult optimization problem. In fact, budget constraints, the probabilistic nature of fire spread and interactions among the different area units composing the whole treatment, give rise to challenging search spaces on typical landscapes. In this paper we formulate such optimization problem with the objective of minimizing the extension of land characterized by high fire hazard. Then, we propose a computational approach that leads to a spatially-optimized treatment layout exploiting Tabu Search and General-Purpose computing on Graphics Processing Units (GPGPU). Using an application example, we also show that the proposed methodology can provide high-quality design solutions in low computing time. © 2013 The Authors. Published by Elsevier B.V.

Difterentially expressed genes of Tetrahymena thermophila in response to tributyltin (TBT) identified by suppression subtractive hybridization and real time quantitative PCR

Tributyltin (TBT) is widely used as antifouling paints, agriculture biocides, and plastic stabilizers around the world, resulting in great pollution problem in aquatic environments. However, it has been short of the biomonitor to detect TBT in freshwater. We constructed the suppression subtractive hybridization library of Tetrahymena thermophila exposed to TBT, and screened out 101 Expressed Sequence Tags whose expressions were significantly up- or down-regulated with TBT treatment. From this, a series of genes related to the TBT toxicity were discovered, such as glutathione-S-transferase gene (down-regulated), plasma membrane Ca2+ ATPase isoforms 3 gene (up-regulated) and NgoA (up-regulated). Furthermore, their expressions under different concentrations of TBT treatment (0.5-40 ppb) were detected by real time fluorescent quantitative PCR. The differentially expressed genes of T thermophila in response to TBT were identified, which provide the basic to make Tetrahymena as a sensitive, rapid and convenient TBT biomonitor in freshwater based on rDNA inducible expression system. (c) 2006 Elsevier B.V. All rights reserved.

Identification of differentially expressed genes in Tetrahmena thermophila in response to dichlorodiphenyltrichloroethane (DDT) by suppression subtractive hybridization

The insecticide dichlorodiphenyltrichloroethane (DDT) is persistent in the environment, and continues to cause health problems. Tetrahymena has potential as a model organism for assaying low levels of DDT and for analysing the mechanisms of its toxicity. We constructed the suppression subtractive hybridization library of T thermophila exposed to DDT, and screened out 90 Expressed Sequence Tags whose expressions were significantly up- or downregulated with DDT treatment. From this, a series of important genes related to the DDT metabolism and detoxification were discovered, such as P450 gene, glutathione S-transferase gene and sterol carrier protein 2 gene. Furthermore, their expressions under different concentrations of DDT treatment were detected by real-time fluorescent quantitative PCR. The results show that Tetrahymena is a relevant and useful model organism for detecting DDT in the environment and for discovering biomarkers that can be used to develop specific bio-reporters at the molecular and genomic levels.

Noise suppression in a novel monolithically integrated michelson interferometer

A novel monolithically integrated Michelson Interferometer using intersecting twincontact semiconductor optical amplifiers is proposed whereby the two arms are gain imbalanced to give noise suppression. Experimental OSNR improvements of 6.2dB for 8ps pulses is demonstrated. © 2005 Optical Society of America.

Noise suppression in a novel monolithically integrated michelson interferometer

A novel monolithically integrated Michelson Interferometer using intersecting twincontact semiconductor optical amplifiers is proposed whereby the two arms are gain imbalanced to give noise suppression. Experimental OSNR improvements of 6.2dB for 8ps pulses is demonstrated. © 2005 Optical Society of America.

Mechanism on Effect of Surface Plasmons Coupling with InGaN/GaN Quantum Wells: Enhancement and Suppression of Photoluminescence Intensity

The photoluminescence (PL) intensity enhancement and suppression mechanism on surface plasmons (SPs) coupling with InGaN/GaN quantum wells (QWs) have been systematically studied. The SP-QW coupling behaviors in the areas of GaN cap layer coated with silver thin film were compared at different temperatures and excitation powers. It is found that the internal quantum efficiency (IQE) of the light emitting diodes (LEDs) varies with temperature and excitation power, which in turn results in anomalous emission enhancement and suppression tendency related to SP-QW coupling. The observation is explained by the balance between the extraction efficiency of SPs and the IQE of LEDs

Suppression of indium droplet formation by adding CCl4 during metalorganic chemical vapor deposition growth of InN films

In this work, the influences of CCl4 on the metalorganic chemical vapor deposition (MOCVD) growth of InN were studied for the first time. It was found that the addition of CCl4 can effectively suppress the formation of metal indium (In) droplets during InN growth, which was ascribed to the etching effect of Cl to In. However, with increasing of CCl4 flow, the InN growth rate decreased but the lateral growth of InN islands was enhanced. This provides a possibility of promoting islands coalescence toward a smooth surface of the InN film by MOCVD. The influence of addition of CCl4 on the electrical properties was also investigated.

Phase-separation suppression in GaN-rich side of GaNP alloys grown by metal-organic chemical vapor deposition

The GaN-rich side of GaNP ternary alloys has been successfully synthesized by light-radiation heating and low-pressure metal-organic chemical vapor deposition. X-ray diffraction (XRD) rocking curves show that the ( 0002) peak of GaNP shifts to a smaller angle with increasing P content. From the GaNP photoluminescence (PL) spectra, the red shifts from the band-edge emission of GaN are determined to be 73, 78 and 100 meV, respectively, in the GaNP alloys with the P contents of 1.5%, 5.5% and 7.5%. No PL peak or XRD peak related to GaP is observed, indicating that phase separation induced by the short-range distribution of GaP-rich regions in the GaNP layer has been effectively suppressed. The phase-separation suppression in the GaNP layer is associated with the high growth rate and the quick cooling rate under the given growth conditions, which can efficiently restrain the accumulation of P atoms in the GaNP layer.

Suppression of exciton recombination in symmetric GaAs0.7Sb0.3/GaAs/GaAs0.7P0.3 coupled quantum wells induced by an in-plane magnetic field

Suppression of the exciton recombination in GaAs0.7Sb0.3/GaAs/GaAs0.7P0.3 coupled quantum well (CQW) induced by an external magnetic field is investigated theoretically. Unlike the usual electro-Stark effect, the exciton energy dispersion of an exciton is modified by an external in-plane magnetic field, the ground state of the magnetoexciton shifts from a zero in-plane center of mass (CM) momentum to a finite CM momentum, and the Lorentz force induces the spatial separation of electron and hole. Consequently, this effect renders the ground state of magnetoexciton stable against radiative recombination due to momentum conservation. This effect depends sensitively on the thickness and height of GaAs0.7Sb0.3 layer, therefore it could provide us useful infometion about the band alignment of CQW. (C) 2004 American Institute of Physics.

Prediction and suppression of strong dispersive coupling in microracetrack channel drop filters

For a four-port microracetrack channel drop filter, unexpected transmission characteristics due to strong dispersive coupling are demonstrated by the light tunneling between the input-output waveguides and the resonator, where a large dropping transmission at off-resonance wavelengths is observed by finite-difference time-domain simulation. It causes a severe decline of the extinction ratio and finesse. An appropriate decrease of the coupling strength is found to suppress the dispersive coupling and greately increase the extinction ratio and finesse, a decreased coupling strength can be realized by the application of an asymmetrical coupling waveguide structure. In addition, the profile of the coupling dispersion in the transmission spectra can be predicted based on a coupled mode theory analysis of an equivalent system consisting of two coupling straight waveguides. The effects of structure parameters on the transmission spectra obtained by this method agree well with the numerical results. It is useful to avoid the strong dispersive coupling region in the filter design. (c) 2007 Optical Society of America.

Generation and suppression of deep level defects in InP

Deep level defects in as-grown and annealed n-type and semi-insulating InP have been studied. After annealing in phosphorus ambient, a large quantity of deep level defects were generated in both n-type and semi-insulating InP materials. In contrast, few deep level defects exist in InP after annealing in iron phosphide ambient. The generation of deep level defects has direct relation with in-diffusion of iron and phosphorus in the annealing process. The in-diffused phosphorus and iron atoms occupy indium sites in the lattice, resulting in the formation of P anti-site defects and iron deep acceptors, respectively. T e results indicate that iron atoms fully occupy indium sites and suppress the formation of indium vacancy and P anti-site, etc., whereas indium vacancies and P anti-site defects. are formed after annealing in phosphor-us ambient. The nature of the deep level defects in InP has been studied based on the results.

Growth of high quality semi-insulating InP single crystal by suppression of compensation defects

Deep level defects in as-grown and annealed SI-InP samples were investigated by thermally stimulated current spectroscopy. Correlations between electrical property, compensation ratio, thermal stability and deep defect concentration in SI-InP were revealed. An optimized crystal growth condition for high quality SI-InP was demonstrated based on the experimental results.