Cultured gill epithelial cells from tilapia (Oreochromis niloticus): a new in vitro assay for toxicants

A culture gill epithelium from seawater-adapted tilapia (Oreochromis niloticus) was developed for testing PAHs and dioxin-like contaminants in seawater. The epithelia consists two to three layers of epithelial cells incorporating both pavement cells and mitochondria-rich cells (MRCs). Polarity and a stable transepithelial resistance (TER) were maintained. and closely resembled those in fish gills in vivo. The tightness (integrity) of the epithelia remained unchanged upon exposure to benzo[a]pyrene (B[a]P). 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and 3,3',4,4',5-pentachlorobiphenyl (PCB#126), while a concentration-dependent response of EROD activity in the epithelia was induced within 18-24 h when the apical side was exposed to these toxicants. The 24 h EC50 of EROD activity was 2.77 x 10(-7) M for PCB#126, 1.85 x 10(-7) M for B[a]P and 7.38 x 10(-10) M for TCDD. showing: that the preparation was not only sensitive to PAHs and dioxin-like compounds, but also able to produce inductive potency of AhR agonists that generally agreed with those derived from other established in vitro and in vivo systems. The results suggest, that the cultured gill epithelia from seawater-adapted tilapia may serve as a simple. rapid and cost-effective tool for assessing exposure and potential effects of toxicants in marine waters. (C) 2004 Elsevier B.V. All rights reserved.

Multiplex detection of mutations in clinical isolates of rifampin-resistant Mycobacterium tuberculosis by short oligonucleotide Ligation assay on DNA chips

A new approach, short-oligonucleotide-ligation assay on DNA chip (SOLAC), is developed to detect mutations in rifampin-resistant Mycobacterium tuberculosis. The method needs only four common probes to detect 15 mutational variants of the rpoB gene within 12 h. Fifty-five rifampin-resistant M. tuberculosis isolates were analyzed, resulting in 87.3% accuracy and 83.6% concordance relative to DNA sequencing.

Linear dimensionality reduction: Survey, insights, and generalizations

© 2015 John P. Cunningham and Zoubin Ghahramani. Linear dimensionality reduction methods are a cornerstone of analyzing high dimensional data, due to their simple geometric interpretations and typically attractive computational properties. These methods capture many data features of interest, such as covariance, dynamical structure, correlation between data sets, input-output relationships, and margin between data classes. Methods have been developed with a variety of names and motivations in many fields, and perhaps as a result the connections between all these methods have not been highlighted. Here we survey methods from this disparate literature as optimization programs over matrix manifolds. We discuss principal component analysis, factor analysis, linear multidimensional scaling, Fisher's linear discriminant analysis, canonical correlations analysis, maximum autocorrelation factors, slow feature analysis, sufficient dimensionality reduction, undercomplete independent component analysis, linear regression, distance metric learning, and more. This optimization framework gives insight to some rarely discussed shortcomings of well-known methods, such as the suboptimality of certain eigenvector solutions. Modern techniques for optimization over matrix manifolds enable a generic linear dimensionality reduction solver, which accepts as input data and an objective to be optimized, and returns, as output, an optimal low-dimensional projection of the data. This simple optimization framework further allows straightforward generalizations and novel variants of classical methods, which we demonstrate here by creating an orthogonal-projection canonical correlations analysis. More broadly, this survey and generic solver suggest that linear dimensionality reduction can move toward becoming a blackbox, objective-agnostic numerical technology.

Development of a rapid, sensitive and specific diagnostic assay for fish Aquareovirus based on RT-PCR

A rapid, sensitive and highly specific detection method for Aquareovirus based on reverse-transcription polymerase chain reaction (RT-PCR) was developed. Based on multiple sequence alignment of the cloned sequences of a local isolates, the Threadfin reovirus (TFV) and Guppy reovirus (GPV) with Grass carp reovirus (GCRV), a pair of degenerate primers was selected carefully and synthesized. Using this primer combination, only one specific product, approximately 450 bp in length was obtained when RT-PCR was carried out using the genomic double-stranded RNA (dsRNA) of TFV, GPV and GCRV. Similar results were also obtained when Chum salmon reovirus (CSRV) and Striped bass reovirus (SBRV) dsRNA were used as templates. No products were observed when nucleic acids other than the dsRNA of the aquareoviruses described above were used as RT-PCR templates. This technique could detect not only TFV but also GPV and GCRV in low titer virus-infected cell cultured cells. Furthermore, this method has also been shown to be able to diagnose GPV-infected guppy (Poecilia reticulata) that exhibit clinical symptoms as well as GPV-carrier guppy. Collectively, these results showed that the RT-PCR amplification method using specific degenerate primers described below is very useful for rapid and accurate detection of a variety of aquareovirus strains isolated from different host species and origin. (C) 2004 Elsevier B.V. All rights reserved.

Oligonucleotide ligation assay-based DNA chip for multiplex detection of single nucleotide polymorphism

An oligonucleotide ligation assay-based DNA chip has been developed to detect single nucleotide polymorphism. Synthesized nonamers, complementary to the flanking sequences of the mutation sites in target DNA, were immobilized onto glass slides through disulfide bonds on their 5' terminus. Allele-specific pentamers annealed adjacent to the nonamers on the complementary target DNA, containing 5'-phosphate groups and biotin labeled 3'-ends, were mixed with the target DNA in tube. Ligation reactions between nonamers and pentamers were carried out on chips in the presence of T4 DNA ligase. Ligation products were directly visualized on chips through enzyme-linked assay. The effect of G:T mismatch at different positions of pentamers on the ligation were evaluated. The results showed that any mismatch between pentamer and the target DNA could lead to the decrease of ligation, which can be detected easily. The established approach was further used for multiplex detection of mutations in rpoB gene of rifampin-resistant Mycobacterium tuberculosis clinical isolates. (C) 2003 Elsevier B.V. All rights reserved.

A new enzyme immunoassay for PCDD/F TEQ screening in environmental samples: Comparison to micro-EROD assay and to chemical analysis

A new Enzyme ImmunoAssay (EIA) for PCDD/F TEQ measurement in extracts of environmental samples was described. The bioassay TEQ which derived from EIA and EROD were compared with each other and with results from chemical analysis. For all environmental samples, the EROD-TEQ is higher than the value from chemical analysis. However, the EIA-TEQ is much more identical with the value from chemical analysis. Our results indicate that the EIA assay is a complementary method to the EROD assay and should be useful as a rapid and sensitive screening tool for environmental samples in many situations. (C) 1999 Elsevier Science Ltd. All rights reserved

Does an enhanced yellow luminescence imply a reduction of electron mobility in n-type GaN?

It is studied whether there is any regular relationship between the yellow luminescence band and electron mobility of n-type GaN. For a series of GaN samples grown with the same Si doping, it is found that the electron mobility decreases with an increase of relative intensity of yellow luminescence, accompanied by an increase of edge dislocation density. Further research indicates that it is acceptors introduced by edge dislocations which lead to the concomitant changes of yellow luminescence and electron mobility. Similar changes are induced by Si doping in the n-type GaN samples with relatively low edge dislocation density. However, the relationship between the yellow luminescence and electron mobility of n-type GaN is not a simple one. A light Si doping may simultaneously increase yellow luminescence and electron mobility when Si doping plays a dominant role in reducing the carrier scattering. This means that even the intensity of yellow luminescence is often used as an indicator of material quality for GaN, it does not have any monotonous correlation with the electron mobility of GaN. (c) 2007 American Institute of Physics.

Reduction of tensile stress in GaN grown on Si(111) by inserting a low-temperature AlN interlayer

This study describes the growth of a low-temperature AlN interlayer for crack-free GaN growth on Si(111). It is demonstrated that, in addition to the lower growth temperature, growth of the AlN interlayer under Al-rich conditions is a critical factor for crack-free GaN growth on Si(111) substrates. The effect of the AlN interlayer thickness and NH3/TMA1 ratios on the lattice constants of subsequently grown high temperature GaN was investigated by X-ray triple crystal diffraction. The results show that the elimination of micro-cracks is related to the reduction of the tensile stress in the GaN epitaxial layers. This was also coincident with a greater number of pits formed in the AlN interlayer grown under Al rich conditions. It is proposed that these pits act as centers for the generation of misfit dislocations, which in turn leads to the reduction of tensile stress. (C) 2004 Elsevier B.V. All rights reserved.

Research on improved methods of reduction of bend loss of silicon-on-insulator waveguides

Improved methods of reduction of bend loss of silicon-on-insulator waveguides were simulated and analyzed by means of effective index method (EIM) and two dimensional beam propagation method (2D-BPM). The simulation results indicate that two different methods, one of which are introducing an offset at the junction of two waveguides and the other is etching groove at the outside of bend waveguide, can decrease bend loss. And the later one is more effective. Meanwhile, experiments validate them. By etching groove, the insertion loss of bend waveguide of R = 16mm, transverse displacement 70mum was decreased 5dB. And its bend loss was almost eliminated.

Stress reduction in GaN films on (111) silicon-on-insulator substrate grown by metal-organic chemical vapor deposition

The GaN film was grown on the (111) silicon-on-insulator (SOI) substrate by metal-organic chemical vapor deposition and then annealed in the deposition chamber. A multiple beam optical stress sensor was used for the in-situ stress measurement, and X-ray diffraction (XRD) and Raman spectroscopy were used for the characterization of GaN film. Comparing the characterization results of the GaN films on the bulk silicon and SOI substrates, we can see that the Raman spectra show the 3.0 cm(-1) frequency shift of E-2(TO), and the full width at half maximum of XRD rocking curves for GaN (0002) decrease from 954 arc see to 472 are sec. The results show that the SOI substrates can reduce the tensile stress in the GaN film and improve the crystalline quality. The annealing process is helpful for the stress reduction of the GaN film. The SOI substrate with the thin top silicon film is more effective than the thick top silicon film SOI substrate for the stress reduction. (C) 2007 Elsevier B.V. All rights reserved.

Reduction of dislocations in GaN epilayer grown on Si (111) substrates using a GaN intermedial layer

GaN intermedial layers grown under different pressures are inserted between GaN epilayers and AlN/Si(111) substrates. In situ optical reflectivity measurements show that a transition from the three-dimensional (3D) mode to the 2D one occurs during the GaN epilayer growth when a higher growth pressure is used during the preceding GaN intermedial layer growth, and an improvement of the crystalline quality of GaN epilayer will be made. Combining the in situ reflectivity and transmission electron microscopy (TEM) measurements, it is suggested that the lateral growth at the transition of growth mode is favourable for bending of dislocation lines, thus reducing the density of threading dislocations in the epilayer.

Study on the oxygen concentration reduction in heavily Sb-doped silicon

It was determined that oxygen concentration in heavily Sb-doped silicon was about 40% lower than that in the lightly doped Czochralski grown silicon and decreased with increasing content of Sb by means of coincident elastic recoil detection analysis. Through thermodynamic calculation, the oxygen loss by evaporation from the free surface of melt is only due to the formation of SiO, and Sb2O3 evaporation can be neglected. The basic reason for oxygen concentration reduction in heavily Sb-doped CZSi was that oxygen solubility decreased when element Sb with larger radius doped degenerately into silicon crystal. (C) 1999 Elsevier Science B.V. All rights reserved.